For many of these patients, care has long meant pain and disfigurement alongside other severe side effects, rather than receiving treatment that addresses the disease itself. This new ARPA-H award marks a potential turning point.

Lead researcher Susan Napier Thomas, Woodruff Professor in the George W. Woodruff School of Mechanical Engineering and the Parker H. Petit Institute of Bioengineering and Bioscience (IBB), has collaborated with her colleague J. Brandon Dixon, Woodruff Professor in the Woodruff School and IBB, for more than a decade on this project. The research partners are driven by the lack of meaningful treatment options available to patients.

“Funding support at this level is unprecedented,” Thomas said. “It finally gives us a chance to move beyond symptom management and toward real treatment. We’re addressing an underserved population with a huge unmet need.” 

A Gap in Care

The lymphatic system helps keep fluid moving through the body and plays a key role in immune health. When it does not function properly, fluid can build up in tissues, causing chronic pain and other long-term complications. Thomas noted that despite its toll on patients, lymphatic disease has lagged decades behind cardiovascular care in both treatment and research investment. 

“We are excited about this groundbreaking project in lymphatic engineering,” said Andrés García, IBB executive director. “By uniting interdisciplinary expertise, this work addresses long-standing challenges in lymphatic disease and moves meaningful solutions closer to the patients who need them most.”

What Comes Next

In the coming years, Thomas, Dixon, and their research partners will work toward an initial human trial, with an early focus on rare lymphatic conditions in children, as well as chronic disease in adults.

“This award reflects Georgia Tech’s growing leadership in using engineering to solve some of healthcare’s biggest challenges,” said Carolyn Seepersad, Eugene C. Gwaltney Jr. School Chair and professor in the Woodruff School. “It reinforces the Institute’s role in advancing innovations that improve patient care and strengthen Georgia’s position as a hub for health technology and biomedical innovation.”

The award was made through ARPA-H’s Groundbreaking Lymphatic Interventions and Drug Exploration (GLIDE) program led by Dr. Kimberley Steele.

This research was funded, in part, by the Advanced Research Projects Agency for Health (ARPA-H) under Agreement No. 1AY2AX000137-01. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the U.S. government.

“Georgia Tech and UGA's collective commitment to advancing science and technology exceeds the intensity of our athletic rivalry,” Fedorov said. “Together, we’re advancing cell and therapy biomanufacturing to develop lifesaving treatments for the most devastating diseases.”
 
Georgia Tech’s Francisco Robles and UGA’s Lohitash Karumbaiah are using manufactured T cells to target cancer. Robles, who leads the Optical Imaging and Spectroscopy Lab in the Wallace H. Coulter Department of Biomedical Engineering, developed quantitative Oblique Back-illumination Microscopy (qOBM) to monitor tumor growth in real time. The method allows scientists to visualize patient-derived glioblastoma cell clusters generated in the Karumbaiah Lab, tracking tumor structure and behavior at various stages.

“Assessing therapeutic potency is often complex, costly, and ineffective for solid tumors,” Karumbaiah said. “qOBM simplifies the process by providing real-time, label-free monitoring of therapeutic efficacy against 3D solid tumors.”   

The work could help doctors personalize cancer treatments by providing early, detailed signs of whether a therapy is working.

“This technique is more compact and affordable and lets us watch T cells attack cell cultures in real time,” Robles said. “This breakthrough could transform how we study disease and screen new treatments.”

A Playbook for Local Healthcare
Created in 2007 by the National Institutes of Health, Georgia CTSA is one of several NIH-funded national partnerships advancing new health therapeutics and practices. Since 2017, it has comprised UGA, Georgia Tech, Emory, and the Morehouse School of Medicine. The alliance’s reach extends far beyond campus borders, bringing together researchers, clinicians, professional societies, and community and industry partners to identify local health challenges and translate research into practical solutions.

And out of this alliance have come many collaborative studies among CTSA’s members.

One, the Georgia Health Landscape Dashboard, is a tool to identify local health gaps and connect regional health professionals or policymakers with the researchers who can best address their community’s challenges. UGA College of Family and Consumer Sciences Associate Professors Alison Berg and Dee Warmath, along with community health engagement coordinator Courtney Still Brown, are working with Georgia Tech’s Jon Duke, director of the Center for Health Analytics and Informatics at the Georgia Tech Research Institute and a principal research scientist in the School of Interactive Computing.

The dashboard has already helped match researchers with communities by combining epidemiological data with “community voice” insights through surveys of residents and local leaders.

For example, when examining diabetes data, the dashboard indicates Randolph County has the state’s highest prevalence, despite declining by about 8% between 2021-24. Meanwhile, Treutlen County’s rate increased 29.2% during the same period. Perhaps Treutlen’s need for diabetic care is a growing concern, while Randolph’s is being addressed. And perhaps Hancock County, which ranks diabetes its top priority in the community voice category, is in search of immediate solutions.

“The Landscape Dashboard is a fantastic example of how the unique expertise found at Georgia Tech and UGA can be brought together to create something truly valuable for all Georgia,” Duke said. “By bringing together a range of data sources and health analytics approaches, this collaboration has created a tool that delivers novel insights into health, community, and policy across the state.”

Supported by UGA Cooperative Extension and the Biomedical and Translational Sciences Institute, the project leverages a network of agents in every county across the state. Warmath said the project’s strength lies in its ability to connect research with real-world needs.

“To build a community-responsive ecosystem for biomedical research, scientists must recognize local needs, share progress with communities to foster trust and acceptance, recruit clinicians and industry partners, and strengthen the relationships between patient and caregiver,” Warmath said.

Teaming Up for Maternal Health
Warmath and a team of researchers at UGA, Georgia Tech, and Emory are also collaborating on an NIH-funded project uniting experts in maternal health, biostatistics, and consumer science to explore how wearable technologies could improve delivery-room care.

During childbirth, clinicians monitor countless maternal and fetal vitals — contractions, heart rates, oxygen levels, kidney function, and more. What new insights, the researchers asked, could advanced wearable technologies offer in the delivery room, and what barriers might prevent their use?

Using nationwide surveys and focus groups, the team gathered information from a representative sample of pregnant, postpartum, and reproductive-age women, as well as healthcare professionals, to examine acceptance of wearable health technologies during labor and delivery. In their analysis of this rich data source, the team is identifying key variables that reveal gaps in technology acceptance and the unique needs of diverse maternal populations.

Each partner institution brings unique expertise. At Emory, principal investigator Suchitra Chandrasekaran contributes clinical insights from direct patient care. At UGA, Warmath applies her knowledge in consumer science to analyze end-user motivation, attitudes, and behaviors. At Georgia Tech, experts like Sarah Farmer in the Center for Advanced Communications Policy’s Home Lab facilitate large-scale data collection.

With data collection now complete, the team is analyzing results to inform future design and deployment of wearable technologies.
“Each school has a different perspective,” Farmer said. “It’s not as simple as one school does this but doesn’t do that. Each has their expertise, but they offer different perspectives and different resources that, when pooled, can make our research that much more effective.”

Whether advancing maternal health, mapping Georgia’s health needs, or engineering next-generation therapies, UGA and Georgia Tech continue to prove that collaboration is Georgia’s strongest tradition. Further, the undergraduate and graduate students who work in these labs and others represent the state’s highly skilled workforce of tomorrow.

“When our institutions work together, Georgia wins,” Warmath said.

— By David Mitchell

But a busy travel schedule is nothing new for Rogers. Diagnosed with hepatoblastoma at the age of 3, he spent over a decade traveling between Augusta, Philadelphia, and Atlanta, with lengthy hospital stays in between, undergoing treatment for the rare childhood liver cancer.  

Given a prognosis with a "one-in-a-million" chance of survival, Rogers had two liver transplants before the cancer spread to his lungs and brain. In total, he endured 50 surgeries before his 13th birthday, and it was during the countless trips to Atlanta that he dreamed of two things — attending Georgia Tech and making a difference for kids facing similar struggles.  

Unlike chemotherapy or other procedures, Rogers found radiation therapy to be a painless experience, in part thanks to the radiation therapists administering the treatment.  

"They may not have thought much of it at the time, but in those moments, by playing with me, making me laugh, making me a Spiderman radiation mask, they helped me forget — even for a second — that I had cancer and helped me enjoy life. I think about that every day. I hope to one day change a child's life like my therapists did for me,” he said.  

Now 18 years cancer-free, Rogers earned a bachelor's degree in radiation therapy from Augusta University. A program director told him about Georgia Tech's medical physics program, and, since arriving at the Institute in 2021, he has sought hands-on experience in the field. Completing the clinical portion of the program through a partnership with the Medical College of Georgia in Augusta, Rogers learned each role within the rotation.  

"From booting up machines and checking on patients to everything else, I just started wanting to come in every day. I'd go in for free just because I love what I'm doing," he said.  

Rogers wasn't immune to the stresses of everyday college life, but he approached them with a positive perspective.  

"My parents told me that there's always a light at the end of every tunnel, and it's always going to be worth it in the end. So, I will keep telling myself and everybody else that when they're going through a hard time, keep pushing,” he said. “Things may be painful and stressful now, but think about what you will achieve in the future and the people you will help get through battles of their own. That will always keep me motivated." 

Rogers isn't done with medical appointments, but with each yearly checkup, he never tires of hearing the words he hopes to deliver in his career: "All clear." 

John McDonald, professor emeritus in the School of Biological Sciences, founding director of the ICRC, and the study’s corresponding author, explains that the new test’s accuracy is better in detecting ovarian cancer than existing tests for women clinically classified as normal, with a particular improvement in detecting early-stage ovarian disease in that cohort.

The team’s results and methodologies are detailed in a new paper, “A Personalized Probabilistic Approach to Ovarian Cancer Diagnostics,” published in the March 2024 online issue of the medical journal Gynecologic Oncology. Based on their computer models, the researchers have developed what they believe will be a more clinically useful approach to ovarian cancer diagnosis — whereby a patient’s individual metabolic profile can be used to assign a more accurate probability of the presence or absence of the disease.

“This personalized, probabilistic approach to cancer diagnostics is more clinically informative and accurate than traditional binary (yes/no) tests,” McDonald says. “It represents a promising new direction in the early detection of ovarian cancer, and perhaps other cancers as well.”

The study co-authors also include Dongjo Ban, a Bioinformatics Ph.D. student in McDonald’s lab; Research Scientists Stephen N. Housley, Lilya V. Matyunina, and L.DeEtte (Walker) McDonald; Regents’ Professor Jeffrey Skolnick, who also serves as Mary and Maisie Gibson Chair in the School of Biological Sciences and Georgia Research Alliance Eminent Scholar in Computational Systems Biology; and two collaborating physicians: University of North Carolina Professor Victoria L. Bae-Jump and Ovarian Cancer Institute of Atlanta Founder and Chief Executive Officer Benedict B. Benigno. Members of the research team are forming a startup to transfer and commercialize the technology, and plan to seek requisite trials and FDA approval for the test.

Silent killer

Ovarian cancer is often referred to as the silent killer because the disease is typically asymptomatic when it first arises — and is usually not detected until later stages of development, when it is difficult to treat.

McDonald explains that while the average five-year survival rate for late-stage ovarian cancer patients, even after treatment, is around 31 percent — but that if ovarian cancer is detected and treated early, the average five-year survival rate is more than 90 percent.

“Clearly, there is a tremendous need for an accurate early diagnostic test for this insidious disease,” McDonald says.

And although development of an early detection test for ovarian cancer has been vigorously pursued for more than three decades, the development of early, accurate diagnostic tests has proven elusive. Because cancer begins on the molecular level, McDonald explains, there are multiple possible pathways capable of leading to even the same cancer type.

“Because of this high-level molecular heterogeneity among patients, the identification of a single universal diagnostic biomarker of ovarian cancer has not been possible,” McDonald says. “For this reason, we opted to use a branch of artificial intelligence — machine learning — to develop an alternative probabilistic approach to the challenge of ovarian cancer diagnostics.”

Metabolic profiles

Georgia Tech co-author Dongjo Ban, whose thesis research contributed to the study, explains that “because end-point changes on the metabolic level are known to be reflective of underlying changes operating collectively on multiple molecular levels, we chose metabolic profiles as the backbone of our analysis.”

“The set of human metabolites is a collective measure of the health of cells,” adds coauthor Jeffrey Skolnick, “and by not arbitrarily choosing any subset in advance, one lets the artificial intelligence figure out which are the key players for a given individual.”

Mass spectrometry can identify the presence of metabolites in the blood by detecting their mass and charge signatures. However, Ban says, the precise chemical makeup of a metabolite requires much more extensive characterization.

Ban explains that because the precise chemical composition of less than seven percent of the metabolites circulating in human blood have, thus far, been chemically characterized, it is currently impossible to accurately pinpoint the specific molecular processes contributing to an individual's metabolic profile.

However, the research team recognized that, even without knowing the precise chemical make-up of each individual metabolite, the mere presence of different metabolites in the blood of different individuals, as detected by mass spectrometry, can be incorporated as features in the building of accurate machine learning-based predictive models (similar to the use of individual facial features in the building of facial pattern recognition algorithms).

“Thousands of metabolites are known to be circulating in the human bloodstream, and they can be readily and accurately detected by mass spectrometry and combined with machine learning to establish an accurate ovarian cancer diagnostic,” Ban says.

A new probabilistic approach

The researchers developed their integrative approach by combining metabolomic profiles and machine learning-based classifiers to establish a diagnostic test with 93 percent accuracy when tested on 564 women from Georgia, North Carolina, Philadelphia and Western Canada. 431 of the study participants were active ovarian cancer patients, and while the remaining 133 women in the study did not have ovarian cancer.

Further studies have been initiated to study the possibility that the test is able to detect very early-stage disease in women displaying no clinical symptoms, McDonald says.

McDonald anticipates a clinical future where a person with a metabolic profile that falls within a score range that makes cancer highly unlikely would only require yearly monitoring. But someone with a metabolic score that lies in a range where a majority (say, 90%) have previously been diagnosed with ovarian cancer would likely be monitored more frequently — or perhaps immediately referred for advanced screening.

Citation: https://doi.org/10.1016/j.ygyno.2023.12.030

Funding

This research was funded by the Ovarian Cancer Institute (Atlanta), the Laura Crandall Brown Foundation, the Deborah Nash Endowment Fund, Northside Hospital (Atlanta), and the Mark Light Integrated Cancer Research Student Fellowship.

Disclosure

Study co-authors John McDonald, Stephen N. Housley, Jeffrey Skolnick, and Benedict B. Benigno are the co-founders of MyOncoDx, Inc., formed to support further research, technology transfer, and commercialization for the team’s new clinical tool for the diagnosis of ovarian cancer.

It’s the kind of massive undertaking that would result in vastly improved precision therapies for patients. And it’s the kind of journey that starts with a single cell. Coskun and team are off to a fast start with the introduction of a new integrative technique for profiling human tissue that enables researchers to capture the geography, structure, movement, and function of molecules in a 3D picture. 

The researchers described their new approach, the Single Cell Spatially resolved Metabolic (scSpaMet) framework, in the journal Nature Communications on Dec. 13. The study builds on a technique Coskun’s team developed and described in a 2021 article, “3D Spatially resolved Metabolomic profiling Framework,” published in Science Advances. In that work, the team introduced a technique that measures the activity of metabolites and proteins as part of a comprehensive profile of human tissue samples. 

“Earlier we couldn’t achieve single-cell resolution, but with this new approach, we can,” said Coskun, Bernie Marcus Early Career Professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “With this new approach, we can get spatial details of proteins and metabolites in single cells– no one else has yet reached this level of high subcellular resolution.”

He added, “We’re pioneering a new field of research with this work, single cell spatial metabolomics.”

A Bigger, Better Molecular Picture

Human tissue is spatially crowded with all kinds of stuff, so investigators need tools that can see clearly into, through, and around that multilayered biological traffic – everything, all at once, in high-definition 3D. With scSpaMet, Coskun’s team can capture single cell details such as the naturally occurring lipids, proteins, as well as metabolites (with their multiple functions, including energy conversion and cell signaling). And other details, like those provided by researchers: Intracellular and surface markers are used to label and track cell activity and behavior. 

The team broadened the scope of this study, extending its investigation beyond human tonsil tissue. 

“We showed the crucial role of immune cells in lung cancer for the study of lung cancer for the study of immunometabolism of T cells and macrophages as they interact with tumors,” Coskun said. “Then we created dynamic immune metabolic changes in tonsils as they go through germinal center reactions to give rise to the antibody-producing cells. Finally, we demonstrated the role of immune cells in the endometrium, a membrane in the uterus that might lead to conditions impacting a woman’s health.”

The wide-angled study required plenty of cross-country collaboration with other institutions, although Coskun’s lab guided the wide-angled study, integrating its expertise in bioimaging, chemistry, tissue biology, and artificial intelligence. 

Cold Spring Harbor Laboratory (New York) provided access to its endometrium tissue bank. Oak Ridge National Laboratory (Tennessee) provided data from its complex metabolic imaging instrumentation, to further demonstrate how single cell spatial metabolomics imaging can generate rich data. 

The University of California-Davis provided kidney biospecimens as both fixed tissue and frozen embedded tissue, in two halves of the same sample, “so we could demonstrate the effect of tissue preparation on the sensitivity of our single cell spatial metabolomics pipeline,” Coskun said.

The team also included Thomas Hu and Mayar Allam, graduate researchers in Coskun’s lab, who guided the research as lead authors, and Walter Henderson, a research scientist who manages the IEN/IMat Materials Characterization Facility at Georgia Tech.

Considering the Whole Person's Biochemistry

The ability to generate single cell spatial metabolic profiling of individual patients can reveal a world of possibility and potential for clinicians who need to fully understand a patient’s biophysical makeup to contrive the best treatment options.

“For example, it can provide mechanisms of how immune responses can be boosted by adding dietary molecules along with immunotherapies,” Coskun said. “It can also help adjust the dose of cell-based treatments, based on the body mass index of individual patients, whether they are obese or not.”

Coskun believes this new arena of single cell metabolomics research his lab is developing will complement the field of single cell genomics, which has led to genomic medicine. His team’s comprehensive exploration and imaging of the geography of normal and unhealthy human tissues – of every single cell – can further explain cellular regulation in ways that were previously overlooked, due to the lack of technology.

He envisions a future in which a patient’s BMI, dietary habits, and exercise commitments, along with their single cell spatial metabolomic atlas of disease progression, will be analyzed all together to find optimum therapies that can work with biologics and metabolic boosting regimens, potentially increasing the survival of cancers, women’s diseases, and metabolic disorders.

“We will have opportunities to talk about spatial single cell metabolomic medicine, to stratify patients and design next-generation combination therapies with an integrated view of genes and chemical activity roadmaps, for more efficient management of cancer and other diseases,” Coskun said.

In creating their scSpaMet framework, the researchers must integrate expensive machines that live in the worlds of nanotechnology and chemistry right now. The system will require clinical-friendly optimizations to be able to run single cell metabolic imaging measurements in healthcare settings. Coskun expects the cost and user-friendliness will be improved in the near future to reach the bedside.

“When researchers achieved single cell sequencing, it was a revolutionary moment in medicine,” Coskun said. “Now, we believe single cell spatial metabolic profiling will push the medical practice into new heights.” 

This research was supported by the Burroughs Wellcome Fund, and the Bernie Marcus Early Career Professorship, as well as the National Science Foundation (Grant ECCS-1542174), (Grant ECCS-2-25462), American Cancer Society, and National Institutes of Health grants (R21AG081715, R21AI173900, and R35GM151028)

Citation: Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson, Brian Yueh, Aybuke Garipcan, Anton V. Ievlev, Maryam Afkarian, Semir Beyaz, and Ahmet F. Coskun. “Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology,” Nature Communications (Dec. 13, 2023)

A new study by Georgia Tech researchers in the lab of Timothy C. Cope has found a novel pathway for understanding why these debilitating conditions happen for cancer patients and why scientists should focus on all of the possible neural processes that deliver sensory or motor problems to a patient’s brain — including the central nervous system — and not just the “peripheral degeneration of sensory neurons” that occurs away from the center of the body.

The new findings “Neural circuit mechanisms of sensorimotor disability in cancer treatment” are published in the Proceedings of the National Academy of Sciences (PNAS) and could impact development of effective treatments that are not yet available for restoring a patient’s normal abilities to receive and process sensory input as part of post cancer treatment, in particular.

Stephen N. (Nick) Housley, a postdoctoral researcher in the School of Biological Sciences, the Integrated Cancer Research Center, and the Parker H. Petit Institute for Bioengineering and Bioscience at Georgia Tech, is the study’s lead author. Co-authors include Paul Nardelli, research scientist and Travis Rotterman, postdoctoral fellow (both of the School of Biological Sciences), along with Timothy Cope, who serves as a professor with joint appointments in the School of Biological Sciences at Georgia Tech and in the Coulter Department of Biomedical Engineering at Emory University and Georgia Tech.

Neurologic consequences

“Chemotherapy undoubtedly negatively influences the peripheral nervous system, which is often viewed as the main culprit of neurologic disorders during cancer treatment,” shares Housley. However, he says, for the nervous system to operate normally, both the peripheral and central nervous system must cooperate.

“This occurs through synaptic communication between neurons. Through an elegant series of studies, we show that those hubs of communication in the central nervous system are also vulnerable to cancer treatment’s adverse effects,” Housley shares, adding that the findings force “recognition of the numerous places throughout the nervous system that we have to treat if we ever want to fix the neurological consequences of cancer treatment — because correcting any one may not be enough to improve human function and quality of life.”

“These disabilities remain clinically unmitigated and empirically unexplained as research concentrates on peripheral degeneration of sensory neurons,” the research team explains in the study, “while understating the possible involvement of neural processes within the central nervous system. The present findings demonstrate functional defects in the fundamental properties of information processing localized within the central nervous system,” concluding that “long-lasting sensorimotor and possibly other disabilities induced by cancer treatment result from independent neural defects compounded across both peripheral and central nervous systems.”

Sensorimotor disabilities and ‘cOIN’

The research team notes that cancer survivors “rank sensorimotor disability among the most distressing, long-term consequences of chemotherapy. Disorders in gait, balance, and skilled movements are commonly assigned to chemotoxic damage of peripheral sensory neurons without consideration of the deterministic role played by the neural circuits that translate sensory information into movement,” adding that this oversight “precludes sufficient, mechanistic understanding and contributes to the absence of effective treatment for reversing chemotherapy-induced disability.”

Cope says the team resolved this omission “through the use of a combination of electrophysiology, behavior, and modeling to study the operation of a spinal sensorimotor circuit in vivo” in a rodent model of “chronic, oxaliplatin (chemotherapy)–induced neuropathy: cOIN.”

Key sequential events were studied in the encoding of “propriosensory” information (think kinesthesia: the body's ability to sense its location, movements, and actions) and its circuit translation into the synaptic potentials produced in motoneurons.

In the “cOIN” rats, the team noted multiple classes of propriosensory neurons expressed defective firing that reduced accurate sensory representation of muscle mechanical responses to stretch, adding that accuracy “degraded further in the translation of propriosensory signals into synaptic potentials as a result of defective mechanisms residing inside the spinal cord.”

Joint expression, independent defects

“These sequential, peripheral, and central defects compounded to drive the sensorimotor circuit into a functional collapse that was consequential in predicting the significant errors in propriosensory-guided movement behaviors demonstrated here in our rat model and reported for people with cOIN,” Cope and Housley report. “We conclude that sensorimotor disability induced by cancer treatment emerges from the joint expression of independent defects occurring in both peripheral and central elements of sensorimotor circuits.”

“These findings have broad impact on the scientific field and on clinical management of neurologic consequences of cancer treatment,” Housley says. “As both a clinician and scientist, I can envision the urgent need to jointly develop quantitative clinical tests that have the capacity to identify which parts of a patient nervous system are impacted by their cancer treatment.”

Housley also says that having the capacity to monitor neural function across various sites during the course of treatment “will provide a biomarker on which we can optimize treatment — e.g. maximize anti-neoplastic effects while minimizing the adverse effects,” adding that, as we move into the next generation cancer treatments, “clinical tests that can objectively monitor specific aspects of the nervous system will be exceptionally important to test for the presence off-target effect.”

***

FUNDING: This work is supported by NIH Grants R01CA221363 and R01HD090642 and the Northside Hospital Foundation, Inc.

DOI: doi.org/10.1073/pnas.2100428118

ACKNOWLEDGMENTS: The researchers thank Marc Binder (Department of Physiology & Biophysics at University of Washington) and Todd Streelman (School of Biological Sciences at Georgia Tech) for providing useful discussions and comments on a preliminary version of the manuscript. Lead author Housley also serves as chief scientific officer for Motus Nova, a healthcare robotics and technology company.

***

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 44,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

This more personalized approach to chemotherapy became possible when genomic profiling of individual patient tumors led researchers to identify specific "cancer driver genes" that, when mutated or abnormally expressed, led to the onset and development of cancer.

Different types of cancer — like lung cancer versus breast cancer — and, to some extent, different patients diagnosed with the same cancer type — show variations in the cancer driver genes believed to be responsible for disease onset and progression. “For example, the therapeutic drug Herceptin is commonly used to treat breast cancer patients when its target gene, HER-2, is found to be over-expressed,” says John F. McDonald, professor in the School of Biological Sciences.

McDonald explains that, currently, the identification of potential targets for gene therapy relies almost exclusively on genomic analyses of tumors that identify cancer driver genes that are significantly over-expressed.

But in their latest study, McDonald and Bioinformatics Ph.D. student Zainab Arshad have found that another important class of genetic changes may be happening in places where scientists don’t normally look: the network of gene-gene interactions associated with cancer onset and progression.

“Genes and the proteins they encode do not operate in isolation from one another,” McDonald says. “Rather, they communicate with one another in a highly integrated network of interactions.”

“What I think is most remarkable about our findings is that the vast majority of changes — more than 90% — in the network of interactions accompanying cancer are not associated with genes displaying changes in their expression,” adds Arshad, co-author of the paper. “What this means is that genes playing a central role in bringing about changes in network structure associated with cancer — the ‘hub genes’ — may be important new targets for gene therapy that can go undetected by gene expression analyses.”

Their research paper “Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression” is published in the journal iScience.

Mutations, expression — and changes in network structure

In the study, Arshad and McDonald worked with samples of brain, thyroid, breast, lung adenocarcinoma, lung squamous cell carcinoma, skin, kidney, ovarian, and acute myeloid leukemia cancers — and they noticed differences in cell network structure for each of these cancers as they progressed from early to later stages.

When early-stage cancers develop, and stayed confined to their body tissue of origin, they noted a reduction in network complexity relative to normal pre-cursor cells. Normal, healthy cells are highly differentiated, but as they transition to cancer, “[T]hey go through a process of de-differentiation to a more primitive or stem cell-like state. It’s known from developmental biology that as cells transition from early embryonic stem cells to highly specialized fully differentiated cells, network complexity increases. What we see in the transition from normal to early-stage cancers is a reversal of this process,” McDonald explains.

McDonald says as the cancers progress to advanced stages, when they can spread or metastasize to other parts of the body, “[W]e observe re-establishment of high levels of network complexity, but the genes comprising the complex networks associated with advanced cancers are quite different from those comprising the complex networks associated with the precursor normal tissues.”

“As cancers evolve in function, they are typically associated with changes in DNA structure, and/or with changes in the RNA expression of cancer driver genes. Our results indicate that there’s an important third class of changes going on — changes in gene interactions — and many of these changes are not detectable if all you’re looking for are changes in gene expression.”

DOI: https://doi.org/10.1016/j.isci.2021.103522

Acknowledgments: This research was supported by the Mark Light Integrated Cancer Research Center Student Fellowship , the Deborah Nash Endowment Fund , and the Ovarian Cancer Institute (Atlanta), where John F. McDonald serves as chief research officer. The results shown here are based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/.

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

“In medicine, we need to be able to make predictions,” said John F. McDonald, professor in the School of Biological Sciences and director of the Integrated Cancer Research Center in the Petit Institute for Bioengineering and Bioscience at the Georgia Institute of Technology. One way is through understanding cause and reflect relationships, like a cancer patient’s response to drugs, he explained. The other way is through correlation. 

“In analyzing complex datasets in cancer biology, we can use machine learning, which is simply a sophisticated way to look for correlations. The advantage is that computers can look for these correlations in extremely large and complex data sets.”

Now, McDonald’s team and the Ovarian Cancer Institute are using ensemble-based machine learning algorithms to predict how patients will respond to cancer-fighting drugs with high accuracy rates. The results of their most recent work have been published in the Journal of Oncology Research .  

For the study, McDonald and his colleagues developed predictive machine learning-based models for 15 distinct cancer types, using data from 499 independent cell lines provided by the National Cancer Institute. Those models were then validated against a clinical dataset containing seven chemotherapeutic drugs, administered either singularly or in combination, to 23 ovarian cancer patients. The researchers found an overall predictive accuracy of 91%.

“While additional validation will need to be carried out using larger numbers of patients with multiple types of cancer,” McDonald noted, “our preliminary finding of 90% accuracy in the prediction of drug responses in ovarian cancer patients is extremely promising and gives me hope that the days of being able to accurately predict optimal cancer drug therapies for individual patients is in sight."

The study was conducted in collaboration with the Ovarian Cancer Institute (OCI) in Atlanta, where McDonald serves as chief research officer. Other authors are Benedict Benigno, MD (OCI founder and chief executive officer, as well as an obstetrician-gynecologist, surgeon, and oncologist); Nick Housley, a postdoctoral researcher in McDonald’s Georgia Tech lab; and the paper’s lead author, Jai Lanka, an intern with OCI. 

The challenges in predicting cancer treatments

The complex nature of cancer makes it a challenging problem when it comes to predicting drug responses, McDonald said. Patients with the same type of cancer will often respond differently to the same therapeutic treatment. 

“Part of the problem is that the cancer cell is a highly integrated network of pathways and patient tumors that display the same characteristics clinically may be quite different on the molecular level,” he explained. 

A major goal of personalized cancer medicine is to accurately predict likely responses to drug treatments based upon genomic profiles of individual patient tumors. 

“In our approach, we utilize an ensemble of machine learning methods to build predictive algorithms — based on correlations between gene expression profiles of cancer cell lines or patient tumors with previously observed responses — to a variety of cancer drugs. The future goal is that gene expression profiles of tumor biopsies can be fed into the algorithms, and likely patient responses to different drug therapies can be predicted with high accuracy,” said McDonald.   

Machine learning is already being applied to the data coming from the genomic profiles of tumor biopsies, but prior to the researchers’ work, these methods have typically involved a single algorithmic approach. 

McDonald and his team decided to combine several algorithm approaches that use multiple ways to analyze complex data; one even uses a three-dimensional approach. They found using this ensemble-based approach significantly boosted predictive accuracy.

The algorithms the team used have names like Support Vector Machines (SVM), Random Forest classifier (RF), K-Nearest Neighbor classifier (KNN), and Logistic Regression classifier (LR). 

“They’re all fairly technical, and they’re all different computational mathematical approaches, and all of them are looking for correlations,” said McDonald. “It’s just a question of which one to use, and for different data sets, we find that one model might work better than another.”

However, more patient datasets that combine genomic profiles with responses to cancer drugs are needed to advance the research.  

“If we want to have a clinical impact, we must validate our models using data from a large number of patients,” said McDonald, who added that many datasets are held by pharmaceutical companies who use them in drug development. That data is typically considered proprietary, private information. And although a significant amount of genomic data of cancer patients is generally available, it’s not typically correlated with patient responses to drugs.

McDonald is currently talking with medical insurance companies about access to relevant datasets, as well. “It costs insurance companies a significant amount of money to pay for drug treatments that don’t work,” he noted. Time, medical fees, and ultimately, many lives could be saved by providing researchers with these types of information. 

“Right now, a percentage of patients will not respond to a drug, but we don’t know that until after six weeks of chemotherapy,” said McDonald. “What we hope is that we will soon have tools that can accurately predict the probability of a patient responding to first line therapies — and if they don’t respond, to be able to make accurate predictions as to the next drug to be tried.”

Citation: Lanka J, Housley SN, Benigno BB, McDonald JF. “ELAFT: An Ensemble-based Machine-learning Algorithm that Predicts Anti-cancer Drug Responses with High Accuracy.” Journal of Oncology Research. ISSN: 2637-6148.

Funding for this research provided by the Ovarian Cancer Institute, Atlanta, Georgia; Northside Hospital (Atlanta); and The Deborah Nash Endowment Fund. John F. McDonald serves as chief research officer of the Ovarian Cancer Institute (OCI) in Atlanta.

About Georgia Tech

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students, representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

CAR T-Cell therapy involves engineering a patient’s T-cells, a type of white blood cell, in a lab. Then a chimeric antigen receptor (CAR) is added, and these customized immune cells are returned to the patient’s body, where they seek and destroy cancer cells. That’s how it works, when it works.

It’s a new, evolving, and booming area of immunotherapy, with more than 500 clinical trials analyzing CAR T-cells for cancer treatment going on right now around the world.

“These therapies have proven to be remarkably effective for patients with liquid tumors – so, tumors that are circulating in the blood, such as leukemia,” said Gabe Kwong, associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory. “Unfortunately, for solid tumors – sarcomas, carcinomas – they don’t work well. There are many different reasons why. One huge problem is that the CAR T-cells are immunosuppressed by the tumor microenvironment.”

Kwong and his collaborators are changing the environment and making some cell modifications of their own to enhance the way CAR T-cells fight cancer. They’ve added a genetic on-off switch to the cells and a developed a remote-control system that sends the modified T-cells on a precision invasion of the tumor microenvironment, where they kill the tumor and prevent a relapse. And they explain it all in a study published recently in the journal Nature Biomedical Engineering.

The latest study builds on the lab’s body of work exploring remotely controlled cell therapies, in which the researchers can precisely target tumors, wherever they are in the body, with a local deposition of heat. “And this heat basically activates the CAR T-cells inside the tumors, overcoming the problems of immunosuppression,” said Kwong.

In the earlier study, the researchers did not clinically treat tumors, but they are doing that now with the new work. To generate heat in a mouse’s tumor, they shone laser pulses from outside the animal’s body, onto the spot where a tumor is located. Gold nanorods delivered to the tumor turn the light waves into localized, mild heat, raising the temperature to 40-42 Celsius (104-107.6 F), just enough to activate the T-Cells’ on-switch, but not so hot that it would damage healthy tissue, or the T-cells. Once turned on, the cells go to work, increasing the expression of cancer-fighting proteins.

The real novelty, Kwong said, was in genetically engineering clinical-grade CAR T-Cells, something the team worked on for the past three years. Now, in addition to a switch that responds to heat, the researchers have added a few upgrades to the T-cells, rewiring them to produce molecules to stimulate the immune system.

Localized production of these potent, engineered proteins (cytokines and Bispecific T-cell Engagers) has to be controlled precisely.

“These cancer-fighting proteins are really good at stimulating CAR T-cells, but they are too toxic to be used outside of tumors,” said Kwong. “They are too toxic to be delivered systemically. But with our approach we can localize these proteins safely. We get all the benefits without the drawbacks.”

The latest study shows the system cured cancer in mice, and the team’s approach not only shrunk tumors but prevented relapse – critical for long-term survival. Further studies will delve into additional tailoring of T-cells, as well as how heat will be deposited at the tumor site. A gentle laser was used to heat the tumor site. That won’t be the case when the technology moves on to human studies.

“We’ll use focused ultrasound, which is completely non-invasive and can target any site in the body,” Kwong said. “One of the limitations with laser is that it doesn’t penetrate very far in the body. So, if you have a deep-seated malignant tumor, that would be a problem. We want to eliminate problems.”

The research was funded by the NIH Director’s New Innovator Award (DP2HD091793), the National Center for Advancing Translational Sciences (UL1TR000454), and the Shurl and Kay Curci Foundation.

CITATION: Ian C. Miller, Ali Zamat, Lee-Kai Sun, Hathaichanok Phuengkham, Adrian M. Harris, Lena Gamboa1, Jason Yang7, John P. Murad7, Saul J. Priceman, Gabriel A. Kwong. “Enhanced intratumoural activity of CAR T cells engineered to produce immunomodulators under photothermal control.” (Nature Biomedical Engineering, August 2021)

About Georgia Tech

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 40,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

For instance, RNA-sequencing (RNA-seq) is an NGS technology that examines the presence and quantity of RNA in biological samples, and it requires bioinformatics analysis to make sense of it all. However, there are hundreds of bioinformatics tools with different data analysis pipelines that result in various results for the same dataset. This can significantly hinder the ability to reliably reproduce RNA-seq related research and applications, especially for the regulatory approval process by the U.S. Food and Drug Administration (FDA). 

Choosing the right analysis model and tool to do the proper job for high throughput data analysis remains a great challenge. So the FDA invited a team of researchers at the Georgia Institute of Technology to conduct a comprehensive investigation of RNA-seq data analysis pipelines for gene expression estimation to recommend best practices. 

“No common standard for selecting high throughput RNA-seq data analysis tools has been established yet. This has been a huge challenge for studying hundreds of tools that form tens of thousands of analysis pipelines,” noted May Dongmei Wang, a professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University who led the investigation.

Wang and her colleagues presented their results in the journal Nature Scientific Reports. In their study, the researchers developed three metrics – accuracy, precision, and reliability – and systematically evaluated 278 representative NGS RNA-seq pipelines. 

“We demonstrate that those RNA-seq pipelines performing well in gene expression estimation will lead to the improved downstream prediction of disease outcome. This is an important discovery,” said Wang, corresponding author of the paper, “Impact of RNA-seq Data Analysis Algorithms on Gene Expression Estimation and Downstream Prediction.”

She added, “Because the FDA is a regulatory agency for approving novel medical devices for NGS-genomics to be utilized in daily clinical practices for personalized and precision medicine and health, it is critical to see whether gene expression generated from RNA-seq acquisition and analysis pipeline are reproducible and reliable.”

The team’s comprehensive investigation revealed that the high throughput RNA-seq data quantification modules – mapping, quantification, and normalization – jointly impacted the accuracy, precision, and reliability of gene expression estimation, which in turn affected the downstream clinical outcome prediction (as shown in two cancer case studies of neuroblastoma and lung adenocarcinoma).

“Clinicians and biomedical researchers can use our findings to select RNA-seq pipelines for their clinical practice or research,” Wang said. “And bioinformaticians can use these benchmark datasets, results, and metrics to develop and evaluate new RNA-seq tools and pipelines.”

But one size does not fit every need, as in any machine learning paradigm, Wang noted. 

“The machine learning and algorithms are heavily dependent on goals,” she said. “Thus, based on our extensive experience in biomedical big data analytics and AI for almost two decades, we suggested that the FDA identify top goals for clinical genomics applications first. Based on different needs, different RNA-seq pipelines will be selected to achieve the optimal performance.”

In addition to Wang, the research team included lead author Li Tong, Po-Yen Wu, John H. Phan, Hamid R. Hassazadeh, Weida Tong, and members of the FDA’s Sequencing Quality Control project (Wendell D. Jones, Leming Shi, Matthias Fischer, Christopher E. Mason, Sheng Li, Joshua Xu, Wei Shi, Jian Wang, Jean Thierry-Mieg, Danielle Thierry-Mieg, Falk Hertwig, Frank Berthold, Barbara Hero, Yang Liao, Gordon K. Smyth, David Kreil, Pawel P. Tabaj, Dalila Megherbi, Gary Schroth, and Hong Fang).

This work was supported by grants from the National Institutes of Health (U54CA119338, R01CA163256, and UL1TR000454), the National Science Foundation (EAGER Award NSF1651360), Children's Healthcare of Atlanta and Georgia Tech Partnership Grant, Giglio Breast Cancer Research Fund, the Centers for Disease Control and Prevention (CDC), and the Carol Ann and David D. Flanagan Faculty Fellow Research Fund.

CITATION: Li Tong, et al., “Impact of RNA-seq Data Analysis Algorithms on Gene Expression Estimation and Downstream Prediction.” (Nature Scientific Reports 2020)

Writer: Jerry Grillo

By learning from a groundbreaking cancer treatment strategy based on a recent Nobel Prize-winning discovery, researchers at the Georgia Institute of Technology and University of Missouri developed a new microgel drug delivery method that could extend the effectiveness of pancreatic islet transplantations — from several years to possibly the entire lifespan of a recipient. 

Working across multidisciplinary teams using an animal model, the labs of Professors Andrés García at Georgia Tech and Haval Shirwan at the University of Missouri have developed a new biomaterial microgel that could deliver safer, smaller, and more cost-effective dosages of an immune-suppressing protein that could lead to better long-term acceptance of islet transplantations within the body. 

The study was published August 28, 2020, in the journal Science Advances. The research was led by Maria Coronel, a postdoctoral fellow in the lab of García, the Parker H. Petit Chair and executive director of the Petit Institute for Bioengineering and Bioscience. García is also a Regents Professor in the George W. Woodruff School of Mechanical Engineering.

In 2018, the Nobel Prize for medicine was awarded for discovering how cancer cells send molecular signals to suppress immune response, thus hiding and protecting those cancer cells from the body’s immune system. Researchers soon developed pioneering treatment methods to signal and “turn on” the immune system (such as T cells) so the invading cancer would once again be recognized, allowing a patient’s own immune system to more effectively eliminate their cancer cells. 

“The work we are doing is taking a page from that discovery and using immunotherapy in the opposite sense used by cancer treatments to control and ‘turn off’ an immune response to transplant a graft,” Coronel said. “When you get a transplant, like an islet transplant or organ transplant, even if it’s matched, you will have an immune response to that graft, and your immune system will recognize it as non-self and will try to reject and attack the site of the graft.”

After islet transplant surgery, traditional postoperative treatments use immune-suppressing systemic drugs that affect the entire body, and can be toxic — creating numerous, unwelcome side effects, whose severity often limits the number of candidates for islet and other organ transplants. 

“A unique aspect of our method is that we have greatly reduced the dosage needed, which will significantly reduce or eliminate side effects currently caused by today’s systemic drug treatments,” said Coronel. 

The research team developed a new “immune-acceptance” method, which inserts an engineered biomaterial — in this case a microgel — with the islets at the time of the transplantation. The microgels, which resemble clusters of micro-sized fish eggs, held and delivered a protein (SA-PD-L1) to a specific transplant area that successfully signaled the immune system to hold back an immune response, protecting a transplanted islet graft from being rejected. This locally delivered molecular signal, using SA-PD-L1, was designed to quietly suppress any immune response and was effective for up to 100 days with no additional systemic immune-suppressing drug intervention.  

“We wanted to use PD-L1 for the prevention of allogeneic islet graft rejection by simulating the way tumor cells use this molecule to evade the immune system, but without resorting to gene therapy,” said Shirwan, professor of child health and molecular microbiology and immunology at the University of Missouri School of Medicine. 

To achieve this goal, Shirwan worked with Esma Yolcu, professor of child health, also at the University of Missouri School of Medicine. Both were previously at the University of Louisville, where they generated the SA-PD-L1, a novel form of the molecule that can be positionally displayed on the surface of islet grafts or microgels for delivery to the graft site. 

“Microgels presenting SA-PD-L1 represent an important technological development that has potential not only for the treatment of type 1 diabetes, but also other autoimmune diseases and various transplant types,” Shirwan said. 

In addition to engineering this specific biomaterial microgel, the team tested its lifespan durability and dosage release possibilities. They also looked at its longer-term effects on both the graft and the immune response and function of the recipient — evaluating its long-term biocompatibility potential.  

“One of the major goals in the diabetes field over the past two decades has been to allow the immune-acceptance of grafts and avoid the toxic drugs used to induce immune suppression, which affect the entire body,” García said. 

“Generally speaking, organ transplantation is very successful at dealing with a variety of chronic conditions. These are very exciting results as proof of principle that demonstrate this engineered biomaterial and procedure may provide a platform technology that is applicable to other transplantation settings and may enlarge the pool of candidates who can safely receive transplants.”

These researchers also coauthored the study: Karen E. Martin, Michael D. Hunckler, Graham Barber, Eric B. O’Neill, Juan D. Medina, Claire A. McClain, Jessica D. Weaver, Hong S. Lim, Peng Qiu, and Edward A. Botchwey from the Georgia Institute of Technology; Enrico Opri from Emory University; and Lalit Batra from the University of Louisville. 

The research was funded by the National Institutes of Health (R21EB020107, R01AI121281, U01AI132817, and S10OD016264), the National Institute of General Medical Sciences (NIGMS) Biotechnology Training Program on Cell and Tissue Engineering (T32GM008433), the Juvenile Diabetes Research Foundation Postdoctoral Fellowships, and a National Science Foundation Graduate Fellowship. Any findings, conclusions, and recommendations are those of the authors and not necessarily of the funding agencies.

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Writer: Walter Rich

The lymphedema monitoring technology originated through research at the Georgia Institute of Technology and was further developed for market by the company LymphaTech, which also emerged from Georgia Tech. Now, a new study has benchmarked the technology, finding that it effectively detects early arm swelling associated with lymphedema in breast cancer patients.

The detection technology is intended to improve not only patients’ physical health but also their peace of mind and finances.

Severe depression

“The most immediate awful consequence of lymphedema is seen in mental health. Severe depression is very high,” said Brandon Dixon, who co-led the study and is an associate professor in Georgia Tech’s George W. Woodruff School of Mechanical Engineering. “If you detect it early, managing it could cost as little as $2,500 in a patient’s lifetime. If you catch it too late, the costs can rise as high as $200,000.”

“Lymphedema is under-researched, so we don’t know directly how it may lead to deadly health conditions, but there are more cases than AIDS, Parkinson’s disease, and Alzheimer’s disease combined, and it diminishes patients’ health,” Dixon said.

The researchers published the detector’s test results in the journal Physical Therapy in February 2019. Dixon and Georgia Tech graduates founded LymphaTech through the initiative TI:GER, Technology Innovation: Generating Economic Results at Georgia Tech’s Scheller College of Business. The startup received early funding from the Georgia Research Alliance. 

No cure

Lymphedema can strike breast cancer survivors if surgery includes the removal of a lymph node, slowing the flow of lymph. The liquid waste can congest the arm, at first subtly but later so drastically that patients may no longer fit into their clothing.

“It makes the stigma of cancer stick out,” Dixon said. “And it is a very underappreciated disorder in medical treatment, so patients can feel stuck with it with no way out.”

A German device called a perometer accurately detects arm swelling caused by lymphedema, but perometers are seldom available in the U.S. The research team could find only one in metropolitan Atlanta to benchmark the LymphaTech system against. It was located at TurningPoint Breast Cancer Rehabilitation, a non-profit center that co-led the new study in collaboration with Dixon.

The advantages of the new technology over perometers are cost and convenience. Perimeters are bulky, costly machines, while the LymphaTech system runs on iPhone or iPad and requires only a $400 camera attachment and a paid smartphone app. Both perometers and the app technology simply determine total volume of the arm for swelling diagnosis.

The new app system performed comparably in its accuracy to the perometer in the study.

^{[Ready for graduate school? Here's how to apply to Georgia Tech.]} 

Awareness barriers

Developing LymphaTech has faced a more challenging component – spreading lymphedema awareness – and a less challenging component – arriving at the technology to make the app measurements work.

“In the past 20 years, depth-sensor cameras have become significantly cheaper and better. Video games, self-driving cars, robotics – they have all required better depth sensors, and we took advantage of that by using a commercially available lens attachment,” Dixon said.

The camera attachment creates point clouds, 3D representations of objects, in this case of human arms, which the app uses to calculate the total arm volume. Usually, only one arm is afflicted with lymphedema, allowing clinicians to compare it with the unaffected arm for easier gauging of disease severity.

As with perometers, the LymphaTech technology avoids human error that creeps in when recording arm volume with a tape measure, a currently common method to assess lymphedema.

“The real battle has been to convince a medical market that has not much cared about lymphedema in the past or sought solutions to care,” Dixon said. “Hopefully, the high accessibility of our solution will make it easier to care.”

In a separate study involving the LymphaTech system, a research team traveled to Sri Lanka to measure lymphedema in legs, Dixon said. And in Germany, the technology is catching on with medical garment manufacturers to help them custom-fit compression sleeves to treat lymphedema.

Also read: Experimental flickering light device to treat Alzheimer's triggers special brain chemistry

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These researchers and clinicians co-authored the study: Jill Binkley and Lauren Bober from TurningPoint Breast Cancer Rehabilitation, and LymphaTech’s Michael Weiler and Nathan Frank, both of whom graduated from Georgia Tech. Paul Stratford from McMaster University also co-authored the study. Disclosures: B. Dixon owns equity in LymphaTech and may benefit financially from the technology. J.B. Dixon is affiliated with LymphaTech Inc and serves as a scientific advisor. Georgia Institute of Technology has licensed to LymphaTech technology that is related to this study and that is covered by patent applications for which J.B. Dixon is an inventor. In addition, J.B. Dixon is eligible to receive royalties under the license agreement for LymphaTech.

This content is a public domain news release and may also be republished without charge.

Writer & Media Representative: Ben Brumfield (404-272-2780), email: ben.brumfield@comm.gatech.edu

Georgia Institute of Technology

“There was some distress caused by cancer alone and some distress from chemo alone, but when you put the two things together, it was off the charts, seven times the trauma to neurons of the two things added together,” said Nick Housley, first author of the study performed in rats at the Georgia Institute of Technology. “It turned out to be the first-ever evidence that there is this exacerbation going on.”

Every year in the U.S., there are 1.8 million new cancer diagnoses, and about half of patients receive platinum-based drugs, which are very effective. About 40 percent of patients receiving platinum chemotherapy come down with neuropathy, suffering strange sensations, pain, fatigue, or loss of muscle coordination that impedes day-to-day life. Neuropathy can persist for years after chemotherapy ends.

Hope for treatment

The new study also challenges established medical explanations that neuropathy is caused by structural damage to nerves alone and that it is untreatable.

“The idea of damage has been the standard explanation – that these neurons are dying back and that they are retracting. And we have found time and time again zero evidence of this in the neurons we studied here,” Housley said. 

“The evidence does not support physical damage as the basis for the disabilities we observe. We find functional problems that might be fixable,” said Tim Cope, one of two principal investigators of the study. Functional problems usually refer to neurons not firing properly versus actual tears or shrinkage in neurons.

Cope is a professor in Georgia Tech’s School of Biological Sciences and in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. Housley is a postdoctoral researcher in his lab.

The researchers published their results in the journal Cancer Research on April 28, 2020. The research was funded by the National Institutes of Health’s National Cancer Institute. John McDonald, the other principal investigator, is a professor in Georgia Tech’s School of Biological Sciences and the director of Georgia Tech’s Integrative Cancer Research Center.

Gene expression surprises

To explore neuropathy’s causes, the researchers cast a broad net. They examined gene expression in neurons, protein expression, and neuron signaling, and they measured body movements, which became markedly uncoordinated.

Gene dysregulation went into overdrive in reaction to chemo and cancer, including boosting inflammatory responses while suppressing some of neurons’ protective mechanisms. But despite the plethora of gene regulation red flags, there were also surprising signs of intact neuron health. 

“Many things the neuron relies on to live and function were unscathed on the gene expression level. That’s potentially good news for patients and for fixing neuropathy because it means there may be just one thing or a few things to fix to restore normal functioning,” Cope said. “The downregulation of just a few genes may be responsible for the problems we’ve seen.”

Ion channel mystery

Clues from one downregulated gene took a twist that led to a new scientific discovery in neuronal biology before arriving at what appeared to be a pathology.

The downregulated gene is responsible for creating protein structures called ion channels that appear in a neuron’s cell wall and enable the neuron to fire electrical impulses, i.e. action potentials. Ion channels abruptly shuttle potassium ions (K+) and sodium ions (Na+) in and out of cells, flipping the net negative and net positive charges on either side of cell walls, which creates the action potentials.

This particular downregulated gene was for a potassium ion channel called Kv3.3, which was not previously known to exist in muscle spindles – neural receptors embedded in muscles to sense when they are contracting or stretching. The researchers found the channel to be prolific there.

“That was a discovery in its own right in basic neuroscience. Finding its involvement in this sensory-motor problem was also profound,” Housley said.

Most Kv3.3 expression disappeared under the combination of chemo and cancer. More research is needed to establish whether the lack of Kv3.3 is indeed an important contributor to neuropathy, but in this study, it strongly correlated with observed neural pathology.

“Despite the neurons still having the ability to fire action potentials, the process of neurons encoding information was really corrupted,” Housley said.

Also read: App Detects Harsh Side Effect of Breast Cancer Treatment

The following researchers from Georgia Tech coauthored the study: Paul Nardelli, Dario Carrasco, Travis Rotterman, Emily Pfahl, and Lilya Matyunina. The research was funded by the National Institutes of Health’s National Cancer Institute (grants R01CA221363 and R01HD090642). Any findings, conclusions, and recommendations are those of the authors and not necessarily of the NCI.

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Writer & media inquiries: Ben Brumfield (404-272-2780), ben.brumfield@comm.gatech.edu or John Toon (404-894-6986), jtoon@gatech.edu.

Georgia Institute of Technology

In a study published on March 9, 2020, in the journal Nature Medicine, Prausnitz and his team of researchers report on research using a skin cream infused with microscopic particles, named STAR particles. To the naked eye, STAR particles look like a powder, but closer inspection reveals tiny microneedle projections sticking out from the particles like a microscopic star. A particle-containing cream could potentially facilitate better treatment of skin diseases including psoriasis, warts, and certain types of skin cancer.

Following the successful study of his microneedle patches for vaccination, Prausnitz and postdoctoral scholar Andrew Tadros have advanced the technology with the objective of treating skin conditions by simply rubbing STAR particles on the skin. In a study in mice, skin cancer tumors were treated with 5-fluorouracil, a cancer therapy drug that works by limiting replication of abnormal cells. Tumor growth was inhibited only when the drug was rubbed on the skin above the tumor in combination with STAR particles, whereas the drug without STAR particles was much less effective.

“Andrew [Tadros] and I teamed up to adapt the microneedle technology and make it useful, especially in dermatology,” said Prausnitz, Regents Professor and J. Erskine Love Jr. Chair in the Georgia Tech School of Chemical and Biomolecular Engineering. “Microneedle patches are good at administering drugs or vaccines to a small area of skin, but many dermatological conditions are spread over larger areas. Rather than trying to make really big patches, which would be difficult to use, we ultimately arrived at STAR particles that can be rubbed on the skin – just like any skin lotion – and poke tiny holes in the skin to better deliver drugs.” 

STAR particles are mixed into a therapeutic cream or gel and applied to the skin, painlessly creating micropores in the skin’s surface that dramatically – but temporarily – increase skin permeability to drugs. 

The problem is that most drugs are not absorbed well into skin, so often a drug needs to be given to the whole body by pill or injection just to treat the skin. Exposing the whole body to dermatological drugs often leads to unwanted side effects such as nausea or organ damage. Fortunately, the barrier layer of skin – called the stratum corneum – is thinner than the width of a human hair. While STAR particles are tiny, they are large enough to poke through this barrier layer when rubbed on the skin and let drugs enter the body through the micropores without pain.

More effectively delivering medicine directly to where it’s needed could improve treatments for patients dealing with many kinds of skin diseases. Oral methotrexate is a common course of treatment for psoriasis –  a dermatological condition in which skin cells build up and form scales and itchy, dry patches – but because the therapy is systemic, it exposes the whole body to a drug that can cause serious side effects like diarrhea, hair loss, and liver problems. 

Prausnitz said doctors must weigh the costs of exposing the whole body to a drug versus treating psoriasis topically, which may be less effective. That’s where STAR particles could provide value. 

“Based on our studies, you could feasibly combine methotrexate with STAR particles into a cream and localize the therapy where it is needed,” Tadros said. “The STAR particles in the cream would enable drugs to get into skin and treat diseases locally, right where it needs to be treated, and without exposing the whole body to the drug.”

Skin creams that deliver drug therapies could widen the range of compounds administered topically, Prausnitz and Tadros suggested. Non-medicinal creams infused with STAR particles have been tested on humans, who generally reported experiencing a mild and comfortable tingling sensation, but no pain or skin irritation. 

Each STAR particle is no larger than a millimeter, with sharp and strong microneedle structures protruding from the surface that are 100 to 300 microns long. While the particles are barely perceptible to the human eye, the microneedles on them are not.

Moreover, when mixed in with a cream, the STAR particles disappear from sight. The research team uses a laser to make the particles from ceramic materials like titanium dioxide, a common ingredient in sunscreens and other cosmetic products. 

“Titanium dioxide is a common material that we have adapted to make STAR particles,” said Prausnitz. “The material is well established, but it’s the star-shaped geometry of the particle that’s new.” 

Prausnitz said he hopes to scale the STAR particles for commercial use not only in dermatology, but for cosmetic purposes as well, where they could potentially deliver anti-aging treatments without injections or other harsh procedures. 

“Our research philosophy is to develop an understanding of biomedical science and engineering technology, and then bring them together to create something that is practical and can benefit patients,” Prausnitz said. 

Prausnitz and Tadros have started a new company called Microstar Biotech that’s working to commercialize the STAR particle technology. 

“Georgia Tech has been instrumental in enabling us to bring this research to the forefront of the medical field, but universities can only do so much,” said Prausnitz. “Commercialization by a company is the mechanism to bring this novel research to the public for their benefit, and I’m hopeful for the future of STAR particles.” 

Results of the study are published in the March issue of the medical journal Nature Medicine. This work was supported financially by the Georgia Research Alliance and as a joint project of the CDC Foundation and UNICEF. 

Prausnitz and Tadros are inventors of the STAR particle technology used in this study and have ownership interest in Microstar Biotech LLC, which is developing technology related to this study. They are entitled to royalties derived from Microstar Biotech’s future sales of products related to the research. These potential conflicts of interest have been disclosed and are overseen by the Georgia Institute of Technology. 

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Writer: Georgia Parmelee

The bandits are cathepsins, enzymes that normally dispose of unneeded protein in our cells. But in unhealthy scenarios, cathepsins can promote illnesses like cancer, atherosclerosis, and sickle cell disease. Many experimental drugs that inhibit them, while effective, have failed due to side effects that could not be well explained, so researchers at the Georgia Institute of Technology abandoned the common focus on single cathepsins to model three key cathepsins as a system.

The researchers found that the cathepsins, denoted by the letters K, L, and S, not only degrade extracellular structures – proteins outside of cells that support cells – but also cannibalize, distract, and deactivate each other. Cathepsins are proteases, enzymes that degrade proteins, and since the cathepsins are themselves proteins, they can degrade each other, too.

Cathepsin Three Stooges

“Auto-digestion is my personal favorite. Think about it: You take a group of cathepsin Ks, and they eat each other. Why? Because they’re just closer to each other than to what they would otherwise eat,” said the study’s principal investigator Manu Platt, an associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

In disease, cathepsins appear to be like The Three Stooges in a porcelain shop, tearing the shop down while they torment each other. As a result, early on, when the Georgia Tech researchers tried to influence a single cathepsin in the group, outcomes were puzzling, and the researchers felt they might be onto something relevant to past mysterious drug failures.

Through lab experiments and mathematical calculations, they arrived at a computational model that showed how single influences ripple through the system. They published the model as a tool online that other researchers can use to jigger the three cathepsins in group settings, their levels of available targets, and inhibitor chemicals. The tool contrasts cathepsin bungling with cathepsin effectiveness.

The researchers publish their research results in the journal the Proceedings of the National Academy of Sciences in the week of January 20, 2020. The research, which took a systems biology approach, was funded by the National Science Foundation and the National Institutes of Health.

Q&A 

How do cathepsins go wrong?

The three cathepsins in this study are best known for their activity in cell organelles called lysosomes under healthy conditions, where they work like molecular woodchippers to cut protein down to amino acids.

“They also serve functions in specific cell types, such as cathepsin S helping the immune system to recognize what to attack and what not to,” Platt said.

“Problems happen when cathepsins get overexpressed and end up in the wrong places. They’re crazy powerful and degrade the structural proteins elastin and collagen that make up arteries, tendons, the endometrium, and many tissue structures.”

“In healthy settings, cathepsin K breaks down old bone to recycle calcium. But when breast cancer comes, those cancerous cells make cathepsin K to destroy collagen around the tumor. And that allows the cells to escape and metastasize to the bone,” Platt said.

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How is this research relevant to drug development?

“I study cathepsins in illnesses like tendinopathy, endometriosis, atherosclerosis, cancer, and sickle cell disease,” Platt said. “So, having a drug on the market to handle cathepsins would be a big deal.”

“Many cathepsin inhibitor drugs that have failed clinical trials were very finely targeted but caused big side effects, and some of those cathepsin inhibitor drugs did not even cross-react with other cathepsins they were not targeting – which is usually a good thing – so the cause of the side effects was a mystery,” Platt said. “By modeling a system of cathepsins, we think we have a good start toward uncovering that mystery.”

“If we don’t know how these cathepsins are working with and against each other in complex systems, similar to how they exist in our bodies, then we are going to have a hard time getting anything into the medicine cabinet to inhibit them.”

The study floats ideas on new approaches to drug research. For example, cathepsin S could be strategically boosted in situations where it is not the culprit to break down cathepsins K and L.

What can other researchers expect from the online model?

“They can set up their own experiments and make predictions, including what inhibitors will do, so they can test inhibitors at varying strengths in this system,” Platt said. “They can ask questions that they can’t answer yet experimentally then test the model’s predictions in the lab.”

The model processes varying inputs into resulting changes in cathepsin levels and outcomes of degradation and indicates whether they have been deactivated or demolished. Scenarios can be exported as a report and a data spreadsheet. 

Also read: Chemical Octopus Catches Sneaky Cancer Clues, Trace Glycoproteins

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These researchers coauthored the study: Meghan Ferrall-Fairbanks, a former graduate research assistant in Platt’s lab; and Chris Kieslich, a former research engineer in Platt’s lab. The research was funded by the National Science Foundation through the Science and Technology Center Emergent Behaviors of Integrated Cellular Systems (EBICS) (Grant CBET-576 0939511) and New Innovator Grant (1DP2OD007433-01) from the Office the Director, National Institutes of Health. Any findings, conclusions, or recommendations are those of the authors and not necessarily of the sponsors.

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Plans for the device, known as the ElectroPen, are being made available, along with the files necessary for creating a 3D-printed casing. 

“Our goal with the ElectroPen was to make it possible for high schools, budget-conscious laboratories, and even those working in remote locations without access to electricity to perform experiments or processes involving electroporation,” said M. Saad Bhamla, an assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering. “This is another example of looking for ways to bypass economic limitations to advance scientific research by putting this capability into the hands of many more scientists and aspiring scientists.”

In a study reported January 10 in the journal PLOS Biology and sponsored by the National Science Foundation and the National Institutes of Health, the researchers detail the method for constructing the ElectroPen, which is capable of generating short bursts of more than 2,000 volts needed for a wide range of laboratory tasks.

One of the primary jobs of a cell membrane is to serve as a protective border, sheltering the inner workings of a living cell from the outside environment.

But all it takes is a brief jolt of electricity for that membrane to temporarily open and allow foreign molecules to flow in — a process called electroporation, which has been used for decades in molecular biology labs for tasks ranging from bacterial detection to genetic engineering. 

Despite how commonplace the practice has become, the high cost of electroporators and their reliance on a source of electricity have kept the technique mostly within the confines of academic or professional labs. Bhamla and undergraduate student Gaurav Byagathvalli set out to change that, with help from collaborators Soham Sinha, Yan Zhang, Assistant Professor Mark Styczynski, and Lambert High School teacher Janet Standeven.

"Once we decided to tackle this issue, we began to explore the inner workings of electroporators to understand why they are so bulky and expensive,” said Byagathvalli. “Since their conception in the early 1980s, electroporators have not had significant changes in design, sparking the question of whether we could achieve the same output at a fraction of the cost. When we identified a lighter that could produce these high voltages through piezoelectricity, we were excited to uncover new mysteries behind this common tool."

In addition to the piezoelectric lighter crystal – which generates current when pressure is applied to it – the other parts in the device include copper-plated wire, heat-shrinking wire insulator, and aluminum tape. To hold it all together, the researchers designed a 3D-printed casing that also serves as its activator. With all the parts on hand, the device can be assembled in 15 minutes, the researchers reported.

While the ElectroPen is not designed to replace a lab-grade electroporator, which costs thousands of dollars and is capable of processing a broad range of cell mixtures, the device is still highly capable of performing tasks when high volumes are not required.

The researchers tested several different lighter crystals to find ones that produced a consistent voltage using a spring-based mechanism. To understand more about how the lighters function, the team used a high-speed camera at 1,057 frames per second to view device mechanics in slow motion.

“One of the fundamental reasons this device works is that the piezoelectric crystal produces a consistently high voltage, independent of the amount of force applied by the user,” Bhamla said. “Our experiments showed that the hammer in these lighters is able to achieve acceleration of 3,000 G’s, which explains why it is capable of generating such a high burst of voltage.”

To test its capabilities, the researchers used the device on samples of E. coli to add a chemical that makes the bacterial cells fluorescent under special lights, illuminating the cell parts and making them easier to identify. Similar techniques could be used in a lab or in remote field operations to detect the presence of bacteria or other cells.

The team also evaluated whether the device was easy to use, shipping the assembled ElectroPens to students at other universities and high schools. 

“The research teams were able to successfully obtain the same fluorescence expression, which I think validates how easily these devices can be disseminated and adopted by students across the globe,” Bhamla said.

To that end, the researchers have made available the plans for how to build the device, along with digital files to be used by a 3D printer to fabricate the casing and actuator. Next steps of the research include testing a broader range of lighters looking for consistent voltages across a wider range, with the goal of creating ElectroPens of varying voltages. 

This research was supported by the National Science Foundation (NSF) under grant No. 1817334, the Mindlin Foundation under grant No. MF19-1T1P03, and the National Institutes of Health (NIH) under grant No. R01-EB022592. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring organizations.

CITATION: Gaurav Byagathvalli, Soham Sinha, Yan Zhang, Mark P. Styczynski, Janet Standeven, and M. Saad Bhamla, “ElectroPen: An ultralow-cost electricity-free, portable electroporator.” (PLOS Biology, January 2020) https://doi.org/10.1371/journal.pbio.3000589

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The research team devised a way to create silica-based hollow spheres around 200 nanometers in size, each with one small hole in the surface that could enable the spheres to encapsulate a wide range of payloads to be released later at certain temperatures only.

In the study, which was published on June 4 in the journal Angewandte Chemie International Edition, the researchers describe packing the spheres with a mixture of fatty acids, a near-infrared dye, and an anticancer drug. The fatty acids remain solid at human body temperature but melt a few degrees above. When an infrared laser is absorbed by the dye, the fatty acids will be quickly melted to release the therapeutic drug.

“This new method could allow infusion therapies to target specific parts of the body and potentially negating certain side effects because the medicine is released only where there’s an elevated temperature,” said Younan Xia, professor and Brock Family Chair in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “The rest of the drug remains encapsulated by the solid fatty acids inside the bottles, which are biocompatible and biodegradable.”

The researchers also showed that the size of the hole could be changed, enabling nanocapsules that release their payloads at different rates.

“This approach holds great promise for medical applications that require drugs to be released in a controlled fashion and has advantages over other methods of controlled drug release,” Xia said.

An earlier method for achieving controlled drug release involves loading the temperature-sensitive material into low-density lipoproteins, which is often referred to as “bad cholesterol.” Another method involves loading the mixture into gold nanocages. Both have disadvantages in how the material used to encapsulate the drugs interact with the body, according to the study.

To make the silica-based bottles, the research team started by fabricating spheres out of polystyrene with a small gold nanoparticle embedded in its surface. The spheres are then coated with a silica-based material everywhere except where the gold nanoparticle is embedded. Once the gold and polystyrene are removed, only a hollow silica sphere with a small opening remains. To adjust the size of the opening, the researchers simply changed the size of the gold nanoparticle.

The process to load the bottles with their payload involves soaking the spheres in a solution containing the mixture, removing the trapped air, then washing away the excess material and payload with water. The resulting nanocapsules contain an even mixture of the temperature-sensitive material, the therapeutic drug, and the dye.

To test the release mechanism, the researchers then put the nanocapsules in water and used a near-infrared laser to heat the dye while tracking the concentration of the released therapeutic. The test confirmed that without the use of the laser, the medicine remains encapsulated. After several minutes of heating, concentrations of the therapeutic rose in the water.

“This controlled release system enables us to deal with the adverse impacts associated with most chemotherapeutics by only releasing the drug at a dosage above the toxic level inside the diseased site,” said Jichuan Qiu, a postdoctoral fellow in the Xia group.

This research was supported by the National Science Foundation under grant No. ECCS-1542174 through the National Nanotechnology Coordinated Infrastructure. The work was also supported by the China Scholarship Council through a graduate student fellowship. The content is the responsibility of the authors and does not necessarily represent the official views of the sponsoring agencies.

CITATION:  Jichuan Qiu, Da Huo, Jiajia Xue, Guanghui Zhu, Hong Lui, and Younan Xia, “Encapsulation of a Phase-Change Material in Nanocapsules with a Well-Defined Hole in the Wall for the Controlled Release of Drugs,” (Angewandte Chemie International Edition, July 2019). http://dx.doi.org/10.1002/anie.201904549

Trapping the white blood cells – which are about the size of cancer cells – and filtering out smaller red blood cells leaves behind the tumor cells, which could then be used to diagnose the disease, potentially provide early warning of recurrence and enable research into the cancer metastasis process. The work, led by researchers at the Georgia Institute of Technology, could advance the goal of personalized cancer treatment by allowing rapid and low-cost separation of tumor cells circulating in the bloodstream.

“Isolating circulating tumor cells from whole blood samples has been a challenge because we are looking for a handful of cancer cells mixed with billions of normal red and white blood cells,” said A. Fatih Sarioglu, an assistant professor in Georgia Tech’s School of Electrical and Computer Engineering (ECE). “With this device, we can process a clinically-relevant volume of blood by capturing nearly all of the white blood cells and then filtering out the red blood cells by size. That leaves us with undamaged tumor cells that can be sequenced to determine the specific cancer type and the unique characteristics of each patient’s tumor.”

The research was reported September 20 in the journal Lab on a Chip, and was supported by a seed grant from the Integrated Cancer Research Center at Georgia Tech.

Other attempts to capture circulating tumor cells have attempted to extract them from the blood using microfluidic technology that recognizes specific surface markers on the cancer cells. But because the cancer can change over time, the malignant cells can’t be recognized with certainty. And even if they can be captured, the tumor cells must be removed from circuitous channels in the device and separated from the antigen without causing damage.

Sarioglu and collaborators, including ECE graduate student and first author Chia-Heng Chu, decided to take a different approach, building 3D-printed traps lined with antigens to capture the white blood cells in a sample. The 3D printed traps allowed the researchers to greatly expand the surface area for capturing the white blood cells as they pass by in blood samples. Zig-zagging fluid channels, some as much as half a meter long, increase the likelihood that every white blood cell would come into contact with a channel wall.

“Usual microfluidic devices have just a single layer with channel heights of 50 to 100 microns,” Sarioglu said. “They are thick, but most of it just empty plastic. Using 3D printing liberates us from the single channel and allows us to create many channels in three dimensions that better utilize the space.”

While the 3D printing allowed an increase in channel density, that came with a significant challenge. Earlier microfluidic devices could be designed with etched channels to carry the blood. But with 3D printing processes that are fabricated layer-by-layer, channels had to be filled with wax to allow more channels to be built atop them. The torturous channel structure, designed to maximize cell-wall interaction, made it virtually impossible to get the wax out after fabrication.

The solution was to design cell traps that fit into standard centrifuges designed to spin samples for separation. The traps were heated in the centrifuge and then spun to allow the melted wax to escape. After removing the liquid wax, the channels received the antigen coating.

After the white blood cells are removed, the smaller red blood cells pass through a simple commercial filter that traps the cancer cells and any remaining white blood cells. The tumor cells can then be removed from the filter, which is integrated into the 3D printed device.

Minimal processing of blood samples is a goal for the project to make the process available to clinics and hospitals without requiring specialized technician skills. Less processing also reduces the risk of damage to the tumor cells and minimizes other cellular changes that could skew the evaluation.

As part of the proof of principle testing, the researchers coated the white blood cells with biotin to accelerate testing. Future cell traps will use antigens designed to attract the cells to the channel walls without the biotin processing step.

The researchers tested their approach by adding cancer cells to blood taken from healthy people. Because they knew how many cells were added, they could tell how many they should extract, and the experiment showed the trap could capture around 90 percent of the tumor cells. Later testing of blood samples from prostate cancer patients isolated tumor cells from a 10-milliliter whole blood sample.

Testing included cells from prostate, breast and ovarian cancer, but Sarioglu believes that the device will capture circulating tumor cells from any type of cancer because the removal mechanism targets blood cells rather than cancer cells.

Next steps will be to narrow the channels in the device, test white blood cell removal without the use of biotin, boost the percentage of white cell extraction and connect cell traps to increase trapping capacity.

“We expect that this will really be an enabling tool for clinicians,” Sarioglu said. “In our lab, the mindset is always toward translating our research by making the device simple enough to be used in hospitals, clinics and other facilities that will help diagnose disease in patients.”

Other co-authors of the paper include Ruxiu Liu, Tevhide Ozkaya-Ahmadov, Mert Boya, Brandi E. Swain, Jacob M. Owens, Enerelt Burentugs, and John F. McDonald, all from Georgia Tech, and Mehmet Asim Bilen from Emory University.

CITATION: Chia-Heng Chu, et al, “Hybrid Negative Enrichment of Circulating Tumor Cells from Whole Blood in a 3D-Printed Monolithic Device.” (Lab on a Chip, 2019) http://dx.doi.org/10.1039/C9LC00575G

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The injectable hydrogel, which is a network of cross-linked polymer chains, contains the enzyme lysostaphin and the bone-regenerating protein BMP-2. In a new study using a small animal model, researchers at the Georgia Institute of Technology showed significant reduction in an infection caused by Staphylococcus aureus – a common infection in orthopedic surgery – along with regeneration within large bone defects.

“Treatment for bone infections now often requires two surgeries to both eliminate the infection and heal the injured bone,” said Andrés J. García, executive director of the Parker H. Petit Institute for Bioengineering & Bioscience at the Georgia Institute of Technology. “Our idea was to develop a bifunctional material that does both things in a single step. That would be better for the patient, cost less and reduce hospitalization time. We have shown that we can engineer the hydrogel to control the delivery and release of both the antimicrobial enzyme and the regenerative protein.”

The hydrogel-based therapy could be used to treat established bone infections, and as a prophylactic during surgery to prevent infection. The study, funded by the National Institutes of Health, was reported May 17 in the journal Science Advances.

Bone infections today are often treated with systemic antibiotics and surgery to clean the injury. If the infection occurs with implants, they often must be removed. Once the infection is gone, additional surgery may be required to implant proteins that stimulate bone regrowth and restore the implant. And the dead bacteria can prompt a harmful inflammatory reaction.

García and his collaborators – including first author Christopher Johnson – chose lysostaphin, an enzyme that kills the bacteria by cleaving cell walls without generating inflammation. The enzyme keeps working within the hydrogel after it polymerizes.

“With this strategy, we can get rid of the bacteria in such a way that the body re-establishes a normal inflammatory environment that allows the bone to heal,” García said. “Use of lysostaphin has been limited by poor stability inside the body, but in the gel, it can maintain stability for at least two weeks. That allows for controlled release over a longer period of time, which is sufficient for what we are trying to do.”

Beyond treating infections, the new technique might be used to prevent infection during surgery. For instance, if a screw was being inserted to repair an injury, the hydrogel might be applied to the screw threads. The soft gel would not affect the repair.

The next step in the research would be to repeat the study in large animals, after which clinical trials could be considered if the material proves promising.

“The mechanisms used to fight off infection depends on the species,” Garcia noted. “That’s why it’s so important to repeat the studies in a large animal after testing in mice or rats. Showing efficacy in a large animal model would be a key step toward human trials.”

The hydrogel material has been used in the human body before, and is designed to quickly leave the treatment site. “The hydrogel breaks down into small building blocks that are excreted in the urine,” Garcia said. “After several weeks, there is no synthetic material left in the body and it is replaced by normal healing tissue.”

In addition to those already named, co-authors on the paper included Mary Caitlin P. Sok, Karen E. Martin, Pranav P. Kalelkar, Jeremy D. Caplin, and Edward A. Botchwey.

This research was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the NIH under award numbers R01AR062920 and F30AR069472. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

CITATION: “Lysostaphin and BMP-2 co-delivery reduces S. aureus infection and regenerates critical-sized segmental bone defects,” (Science Advances 2019). http://dx.doi.org/10.1126/sciadv.aaw1228

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The device, a portable centrifuge for preparing scientific samples including DNA, is reported May 21 in the journal PLOS Biology. The co-first author of the paper is Gaurav Byagathvalli, a senior at Lambert High School in Georgia. His colleagues are M. Saad Bhamla, an assistant professor at the Georgia Institute of Technology; Soham Sinha, a Georgia Tech undergraduate; Janet Standeven, Byagathvalli’s biology teacher at Lambert; and Aaron F. Pomerantz, a graduate student at the University of California, Berkeley.

“I am exceptionally proud of this paper and will remember it 10, 20, 30 years from now because of the uniquely diverse team we put together,” said Bhamla, who is an assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering.

From a Rainforest to a High School

Together the team demonstrated the device, dubbed the 3D-Fuge because it is created through 3D printing, in two separate applications. In a rainforest in Peru the 3D-Fuge was an integral part of a “lab in a backpack” used to identify four previously-unknown plants and insects by sequencing their DNA. Back in the United States, a slightly different design enabled a new approach to creating living bacterial sensors for the potential detection of disease. That work was conducted at Lambert High School for a synthetic biology competition.

Thanks to social media and a preprint of the PLOS Biology paper on BioRxiv, the 3D-Fuge has already generated interest from around the world, including emails from high-school teachers in Zambia and Kenya. “It’s awesome to see research not just remain isolated to one location but see it spread,” said Byagathvalli. “Through this, we’ve realized how much of an impact simple yet effective tools can have, and hope this technology motivates others to continue along the same path and innovate new solutions to global issues.”

To better share the work, the team has posted the 3D-Fuge designs, videos, and photos online available to anyone.

Frugal Science

One focus of Bhamla’s lab at Georgia Tech is the development of tools for frugal science, or real research that just about anyone can afford. The tools behind state-of-the-art science often cost thousands of dollars that make them inaccessible to those without serious resources.

Centrifuges are a good example.  A small benchtop unit costs between $3,000 and $5,000; larger units cost many times that. Yet the devices are necessary to produce concentrated amounts of, say, genomic materials like DNA. By rapidly spinning samples, they separate materials of interest from biological debris.

The Bhamla team found that the 3D-Fuge works as well as its more expensive cousins, but costs less than $1.

An Ancient Toy

The 3D-Fuge is based on earlier work by Bhamla and colleagues at Stanford University on a simple centrifuge made of paper. The “paperfuge,” in turn, was inspired by a toy composed of string and a button that Bhamla played with as a child. He later discovered that these toys, known as whirligigs, have existed for some 5,000 years.

They consist of a disk – like a button – with two holes, through which is threaded a length of flexible cord whose ends are knotted to create a single loop with the disk in the middle. That simple contraption is then swung with two hands until the button is spinning and whirring at very fast speeds.

The earlier paperfuge uses a disk of paper. To that disk Bhamla glued small plastic tubes filled with a sample. He and colleagues reported that the device did indeed create high-quality samples. 

In late 2017 Bhamla was separately approached by the Lambert High team and Pomerantz to see if the paperfuge could be adapted for the larger samples they needed (the paperfuge is limited to small samples of ~1 microliter—or one drop of blood). 

Together they came up with the 3D-Fuge, which includes cavities for tubes that can hold some 100 times more of a sample than the paperfuge. The team developed two equally effective designs: one for field biology (led by Pomerantz) and the other for the high-school’s synthetic biology project (led by Byagathvalli).

Bhamla notes that the 3D-Fuge has some limitations. For example, it can only process a few samples at a time (some applications require thousands of samples). Further, because it’s 10 times heavier than the paperfuge, it can’t reach the same speeds or produce the same forces of that device. That said, it still weighs only 20 grams, slightly less than a AA battery.

“But it works,” said Bhamla. “All you need is an [appropriate] application and some creativity.”

This work was funded by the National Science Foundation (award no.181733), the Mindlin Foundation, and the Jacobs Institute Innovation Catalyst Award.

CITATION: Gaurav Byagathvalli, Aaron F. Pomerantz, Soham Sinha, Janet Standeven, and M. Saad Bhamla, “A 3D-printed hand-powered centrifuge for molecular biology,” (PLOS Biology, 2019) https://doi.org/10.1371/journal.pbio.3000251

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The National Institutes of Health has granted $1.8 million to a research project at the Georgia Institute of Technology, where the lab of Gabe Kwong has already established a platform to detect complex disease and immune activity. Kwong will use the new funding from the NIH’s National Cancer Institute to advance the platform to evaluate immunotherapy progress.

The platform uses an intravenous injection of “activity sensors,” nanoparticles that detect early enzyme activity of immune cells attacking cancer. The sensor confirms the attack with a fluorescent signal in the urine.

Shifty resistance

Cancer’s defenses are crafty and can thwart treatment from the start or disrupt initially successful treatment later on, so progress must be continually monitored, which Kwong’s lab is engineering the particle to do. Early resistance to therapy looks very different from later resistance.

“We need to be able to classify different forms of resistance, so we can combat them better,” said Kwong, an assistant professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

He plans to adapt the sensing technology to profile those subtleties. It is already engineered to have advantages over other tests that have recently entered the market, which look for signals that come later, such as dead cancer cells shedding their DNA into the bloodstream.

“These tests can be quite effective, but some issues limit them, particularly in early detection: You have five liters of blood. Whatever the cells shed gets diluted significantly in your bloodstream,” Kwong said.

That makes these signals harder to detect in blood tests.

Enriched signals

“Our sensors’ signals get concentrated in the urine, so, not only are they not diluted in the blood, but we usually see a hundred- to thousandfold signal enrichment.”

Kwong’s lab has already developed the sensors, which are biocompatible nanoparticles, refined them as a reliable platform, and engineered variations that experimentally sense blood clots, liver fibrosis, organ transplant rejection, and cancer. Kwong has published multiple papers on activity sensor urine test successes.

Kwong’s endgame ambitions: “In five to ten years, we want to expand the platform to detect most all major complex diseases and progress in treating them.”

Q & A

What is the activity sensor and how does the urine test work?

The sensors are nanoscale balls with bristles made of short amino acid strands that have fluorescent “reporter” molecules attached to their tips. The sensors tend to accumulate in compromised tissue like cancer.

When immunotherapy -- which can be engineered T cells or the body’s own T cells aided by medication -- attack cancer cells, the T cells secrete an enzyme called granzyme that severs target amino acid strands in the cancer cells, triggering their death. The activity sensor’s bristles mimic those strands, so granzymes cut the bristles at the same time.

“That releases the reporter molecules, which are so small that they easily make it through the kidney’s filtration and go into the urine,” said Kwong who directs the Laboratory for Synthetic Immunity in the Coulter Department.

Then the urine turns a fluorescent color that can be analyzed to determine the intensity of the immunotherapy’s attack on cancer.

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Is there a need for this kind of test?

“Many patients, especially those with solid tumors, are not responding to this treatment,” Kwong said. “The non-responders need to be detected very quickly.”

There are also diagnostic pitfalls the experimental sensor is devised to overcome: For example, a current measure of treatment success is tumor shrinkage, but when T cells initially cram into a tumor, it can swell. That sometimes leads doctors to believe that a therapy that is actually very effective is not working, and they may discontinue it.

“This test does not measure size; it measures activity,” Kwong. “If those swelling tumors are very high in granzyme activity, that’s a great sign, and we will be able to pick that up.”

How is the dream of detecting most known complex diseases even feasible?

Quite conveniently, the human genome produces “only” 550 proteases, a particular type of enzyme relevant to detecting and combating disease. Kwong believes researchers can adapt this platform to detect any of them and that there’s a need for that.

“Granzymes are also activated by other things like an infection, so detecting granzyme alone risks getting interference when you’re looking at cancer treatment effectiveness. We’re developing a panel of sensors that gives us the specificity of T cell activity in tumors over the possible activity of T cells fighting, say, a cold,” Kwong said.

“We want to build 550 different protease-detecting probes, and depending on what disease you have, they would expose a profile of the proteases in varying ratios.”

The probes could be combined into a cocktail to detect budding cancer, immunotherapy effectiveness or infections, and machine learning would analyze their respective fingerprints in the urine signals.

Also READ: Mending a Broken Heart - 6 cardiac solutions currently in testing

The grant was provided by the National Cancer Institute at the National Institutes of Health. The grant number is 1 R01 CA237210-01. The content is the sole responsibility of the authors and does not necessarily represent official views of the National Institutes of Health.

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If validated, the general technique for the work could also have a variety of other applications. “In my dream world, a single blood test could be used to screen for multiple diseases,” said John McDonald, the leader of the research and a professor in the School of Biological Sciences at the Georgia Institute of Technology.

Ovarian cancer is especially dangerous because women often don’t show symptoms until the disease is in an advanced stage and difficult to treat. In contrast, when caught early “about 94 percent of patients live longer than five years after diagnosis,” according to the American Cancer Society. 

The problem is that there is no good test for detecting the disease at an early stage. 

About seven years ago McDonald and colleagues decided to see if they could change that by merging the disparate disciplines of biology, analytical chemistry and computer science. “Bringing the computer into it was novel at the time,” said McDonald, who is also director of Georgia Tech’s Integrated Cancer Research Center.

His Georgia Tech collaborators on the initial work were Professor Facundo Fernández, the Vasser Woolley Foundation Chair in Bioanalytical Chemistry, and Alex Gray, an assistant professor of computer science (Gray has since left Georgia Tech to become VP for Artificial Intelligence Science at IBM). They were joined by clinical consultant Dr. Benedict Benigno, a gynecological oncologist and CEO of the Ovarian Cancer Institute in Atlanta.

Promising Results

The researchers initially analyzed blood samples from 49 healthy women and 46 with early-stage ovarian cancer. They specifically focused on metabolites in those samples. Metabolites are molecules like fatty acids that our cells produce through enzymatic reactions.  

In the molecular equivalent of finding needles in a haystack, they proceeded to analyze some 40,000 metabolites to see if there were any associated with the cancer patients that differed from those in samples from the healthy women. These could be biomarkers for the disease; molecules to screen for in an annual test.

Through a variety of techniques, the team first pared down the original thousands of metabolites to a collection of 255 candidate biomarkers. They then applied machine learning to that set, asking the computer to find any metabolites that were over- or under-expressed in the cancer samples. 

“That’s what machine learning is all about,” McDonald said. “The computer is simply looking for correlations in very large data sets, then it comes back to you with what it has found.”

In 2015 the team reported in the journal Scientific Reports the discovery of 16 metabolites that could distinguish women with ovarian cancer from those without the disease with 100 percent accuracy. “Basically we modeled the face of cancer at the metabolic level,” McDonald said. 

Moving Forward

With the new $100,000 grant, the researchers hope to validate their earlier work with samples from some 1,000 women, as compared to the roughly 100 they originally studied. The new study will also include samples from a much more diverse set of women (the original samples were from Caucasian women).

They also aim to expand the work to look for biomarkers associated with different types of ovarian cancer. “We want to be able to distinguish between a Type II cancer with high malignant potential – one that’s highly likely to spread outside the ovary – and a Type I with low malignant potential. A cancer with high malignant potential you’d want to treat right away, while a cancer with low malignant potential might not require immediate surgery,” McDonald said.

In conclusion, McDonald said, “it’s exciting because the initial results look like [our approach] might work.”

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The app, called MyPath, adapts to each stage in a patient’s cancer journey. So the information available on the app – which runs on a tablet computer – regularly changes based on each patient’s progress. Are you scheduled for surgery? MyPath will tell you what you need to know the day before.

“Patients have told us, ‘It just seemed to magically know what I needed,’” said Elizabeth Mynatt, principal investigator for the work and Distinguished Professor in the School of Interactive Computing at Georgia Tech.

Mynatt, who is also Executive Director of the Institute for People and Technology, believes that MyPath is the first healthcare app capable of personalization (through its application of AI) for holistic cancer care. In addition to incorporating a patient’s medical data, the app also addresses a variety of other relevant issues such as social and emotional needs. 

She presented the work February 15 at the 2019 meeting of the American Association for the Advancement of Science. The research has been sponsored by the National Cancer Institute.

National Recognition

In January MyPath was recognized by iSchools, a consortium of some 100 institutions worldwide (including Georgia Tech) dedicated to advancing the information field. Maia Jacobs, who recently received her Ph.D. from Georgia Tech for her work on MyPath, was named winner of the 2019 iSchools Doctoral Dissertation Award.

According to iSchools, “the Award Committee felt [that Jacobs’ work] was timely and important, and lauded its impact in how patients manage their health.” Jacobs, now a postdoctoral fellow at Harvard, is currently exploring how to expand MyPath to other diseases.

The work was also honored in 2016 when it was featured in a report to President Barack Obama by the President’s Cancer Panel. The report, Improving Cancer-Related Outcomes with Connected Health, aimed to “help patients manage their health information and participate in their own care,” according to a Georgia Tech story at the time.

The Beginning

Six years ago Mynatt’s team began working with the Harbin Clinic in Rome, Georgia. “They have a tremendous program in holistic cancer care where they recognize that their patients, who are from a large rural area, face a variety of challenges to be able to successfully navigate the cancer journey,” Mynatt said.

But the Harbin doctors and cancer navigators – people who help patients through the cancer journey – wanted a better way to stay connected to patients on a regular basis. The navigators, in particular, found that they tended to interact with patients a great deal at diagnosis, but less frequently over time. And that meant that although there are many recommendations for, say, lowering anxiety, they weren’t necessarily being communicated. 

Said Mynatt, “We wondered how technology could amplify what these great people are doing.”

How it Works

MyPath begins with a mobile library of resources compiled from the American Cancer Society and other reputable organizations. Then, it is personalized with each patient’s diagnosis and treatment plan, including the dates for specific procedures. Patients also complete regular surveys that help inform the system – and caregivers – of their changing needs and symptoms.

The result is a system that provides each patient with resources and suggestions specific to their personal situation. Because MyPath knows, for example, that you have stage 2 breast cancer and will be undergoing a lumpectomy on a specific date, when you click on the category “Preparing for Surgery” it will suggest relevant articles to prepare you for what’s ahead. Have you reported nausea in the system’s survey? MyPath will bring your attention to resources that can help combat the side effect. The system also provides quick access to contact information for specific caregivers.

Other apps – and the Internet – aren’t personalized. That means slogging through a great deal of often technical information that’s not relevant to your situation. In contrast, “Every day MyPath puts the right resources at your fingertips to help you through your cancer journey,” Mynatt said.

More than Medical

Some of MyPath’s most popular features have nothing to do directly with cancer. Buttons for “Emotional Support” and “Day to Day Matters” are regularly consulted by patients. “When we asked them about how they used the tablet for healthcare, many patients would talk to us about playing Angry Birds, which they would download to distract them during chemo sessions,” Mynatt said. 

MyPath is the second generation of the app. Patient feedback from its predecessor, My Journey Compass, led to changes including the personalization. Development continues. For example, Mynatt’s team is hoping to expand the app for use by cancer survivors, who often face additional challenges like hormone replacement therapy. The team is also working on a version that individual patients could download, which would make the app available to many more users.

This work is sponsored by the National Cancer Institute, part of the National Institutes of Health, under award RO1 CA195653. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Although the mechanisms are intertwined with biochemical processes, they also work mechanically, grasping, tugging and clamping, say researchers at the Georgia Institute of Technology, who, for a new study in the journal Nature Immunology, measured responses to physical force acting upon these elimination mechanisms.

The mechanisms’ purpose is to make dangerously aggressive developing immune cells called thymocytes destroy themselves to keep them from attacking the body, while sparing healthy thymocytes as they mature into T cells. Understanding these selection mechanisms, which ensure T cells aggressively pursue hordes of infectors and cancers but not damage healthy human tissue, could someday lead to new immune-regulating therapies.

Two-handed handshake

Usually, researchers pursue such mechanisms using chemistry experiments, but Georgia Tech’s Cheng Zhu, who led the study, makes atypical discoveries via physical experiments to observe effects of forces between key proteins in living cells.

“Experiments where the proteins are isolated and used in chemical reactions in vitro miss this force dynamic,” said Zhu, a Regents Professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “Before our work, force was not considered as a factor in thymocyte selection and now it is.”

In this study, they discovered a loop of physical signals resembling a double-handed handshake that encourages cell apoptosis. It is described in more detail below.

The medical significance of this field of research was highlighted by the 2018 Nobel Prize in medicine, which was awarded to other researchers at other institutions, James Allison of MD Anderson Cancer Center and Tasuku Honjo of Kyoto University. Allison and Honjo received the prize for their cancer therapies exploiting T cell regulating mechanisms intertwined with those that the Georgia Tech researchers study.

Georgia Tech's Zhu and first authors Jinsung Hong and Chenghao Ge published their new research paper on November 12, 2018. The research was funded by the National Cancer Institute, the National Institute of Allergy and Infectious Diseases, and the National Institute of Neurological Disorders and Stroke. The agencies are part of the National Institutes of Health.

Thymocyte selection gauntlet

Like blood cells, human thymocytes are born in bone marrow, but they travel to the thymus, a small organ just below the neck, where they run a gauntlet of selection tests. Failing any one selection means cell self-destruction; passing all selections promotes thymocytes to T cells that depart the thymus to battle our bodies’ foes.

One selection checks T cell receptors (TCR), which are on the thymocyte’s membrane, to ensure they are properly formed then to see if they recognize self-antigens, i.e. molecules that identify the body’s own cells. Then another selection, called negative selection, tests TCRs to make sure they don’t react too aggressively to self-antigens.

Cells that pass these checks then have TCRs that tolerate self- yet react to enemy antigens.

“You don’t want the cells with strongly grabbing receptor sites to turn against the body itself,” said Zhu, whose study focused on negative selection.

Self-antigen grip

In negative selection, other cells extend self-antigens on their membrane to interact with the thymocytes’ T cell receptors. Those interactions seal the thymocytes’ fate: advance or die.

Studying forces in those interactions revealed a new signaling loop with mechanical properties analogous to a two-handed grip and tug by the thymocyte.

The first hand would be the T cell receptor itself, and the other cell presenting the self-antigen would be like someone else’s hand holding a special ball out to the T cell’s first hand. The handshake begins as the self-antigen gives a signal to the T cell receptor.

If the TCR reacts too strongly to the self-antigen, the thymocyte adds the second, assisting hand, which comes in from the side to make a two-handed handshake. The additional hand is a lever called CD8 (cluster of differentiation 8), which connects to key mechanisms inside the thymocyte and is considered part of the TCR site.

Demolition handshakes

For about two weeks in the thymus, multiple T cell receptor sites engage in one- or two-handed handshakes, which send signals into the thymocyte that make it either mature into a T cell or begin the process of programmed cell death.

The researchers found that the two-handedness markedly resisted the force applied to break the grip between the T cell receptor and the self-antigen, thus prolonging the duration of the handshake. A long grip sent signals for the thymocyte to die.

“That’s the study’s elegant finding,” Zhu said. “That the force is significant for the selection to work.”

New signaling loop

The researchers also made the novel discovery that CD8’s handshake participation constitutes a signal coming from inside the thymocyte back out to the self-antigen in answer to its initial signal.

“The inside-out return signal had not yet been reported for this T cell receptor,” Zhu said.

Together, the outside-in and inside-out signals create a feedback loop that perpetuates the handshake:

1. Self-antigen touches receptor.
2. Receptor fires signal into cell and interacts with self-antigen too aggressively.
3. Inside cell membrane, signal pulls CD8 closer.
4. Outside cell membrane, CD8 strengthens handshake.
5. When the self-antigen slips a bit, the double-handed grip can coax it back into the receptor, kicking off another signal, restarting the signaling cycle again and again.
6. Many feedback loops increase likelihood of programmed cell death.

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Coauthors on the study were: Prithiviraj Jothikumar, Zhou Yuan, Baoyu Liu, Ke Bai, Kaitao Li, William Rittase, all of Georgia Tech at the time of the research; Miho Shinzawa and Alfred Singer of the National Cancer Institute at the National Institutes of Health; Brian Evavold, Khalid Salaita and Yun Zhang of Emory University; Amy Palin and Paul Love of the NIH Eunice Kennedy Shriver National Institute of Child Health and Development; and Xinhua Yu of University of Memphis. The research was funded by the National Cancer Institute (NCI) (grant CA214354), the National Institute of Allergy and Infectious Diseases (NIAID) (grants AI124680, AI096879), the National Institute of Neurological Disorders and Stroke (NINDS) (grant NS071518). The funders belong to the National Institutes of Health. Hong and Bai now research at NIAID; Liu and Evavold now research at the University of Utah. Zhu is also in Georgia Tech’s George W. Woodruff School of Mechanical Engineering and in Georgia Tech’s Petit Institute for Bioengineering and Bioscience. Any findings, opinions or recommendations are those of the authors and not necessarily of the funding agencies

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That’s where Georgia Institute of Technology researchers believe their new open source decision support tool could come in. Using machine learning to analyze RNA expression tied to information about patient outcomes with specific drugs, the open source tool could help clinicians chose the chemotherapy drug most likely to attack the disease in individual patients.

In a study using RNA analysis data from 152 patient records, the system predicted the chemotherapy drug that had provided the best outcome 80 percent of the time. The researchers believe the system’s accuracy could further improve with inclusion of additional patient records along with information such as family history and demographics.

“By looking at RNA expression in tumors, we believe we can predict with high accuracy which patients are likely to respond to a particular drug,” said John McDonald, a professor in the Georgia Tech School of Biological Sciences and director of its Integrated Cancer Research Center. “This information could be used, along with other factors, to support the decisions clinicians must make regarding chemotherapy treatment.”

The research, which could add another component to precision medicine for cancer treatment, was reported November 6 in the journal Scientific Reports. The work was supported in part by the Atlanta-based Ovarian Cancer Institute, the Georgia Research Alliance, and a National Institutes of Health fellowship.

As with other machine learning decision support tools, the researchers first “trained” their system using one part of a data set, then tested its operation on the remaining records. In developing the system, the researchers obtained records of RNA from tumors, along with with the outcome of treatment with specific drugs. With only about 152 such records available, they first used data from 114 records to train the system. They then used the remaining 38 records to test the system’s ability to predict, based on the RNA sequence, which chemotherapy drugs would have been the most likely to be useful in shrinking tumors.

The research began with ovarian cancer, but to expand the data set, the research team decided to include data from other cancer types – lung, breast, liver and pancreatic cancers – that use the same chemotherapy drugs and for which the RNA data was available. “Our model is predicting based on the drug and looking across all the patients who were treated with that drug regardless of cancer type,” McDonald said.

The system produces a chart comparing the likelihood that each drug will have an effect on a patient’s specific cancer. If the system were to be used in a clinical setting, McDonald believes doctors would use the predictions along with other critical patient information.

Because it measures the expression levels for genes, analysis of RNA could have an advantage over sequencing of DNA, though both types of information could be useful in choosing a drug therapy, he said. The cost of RNA analysis is declining and could soon cost less than a mammogram, McDonald said.

The system will be made available as open source software, and McDonald’s team hopes hospitals and cancer centers will try it out. Ultimately, the tool’s accuracy should improve as more patient data is analyzed by the algorithm. He and his collaborators believe the open source approach offers the best path to moving the algorithm into clinical use.

“To really get this into clinical practice, we think we’ve got to open it up so that other people can try it, modify if they want to, and demonstrate its value in real-world situations,” McDonald said. “We are trying to create a different paradigm for cancer therapy using the kind of open source strategy used in internet technology.”

Open source coding allows many experts across multiple fields to review the software, identify faults and recommend improvements, said Fredrik Vannberg, an assistant professor in the Georgia Tech School of Biological Sciences. “Most importantly, that means the software is no longer a black box where you can’t see inside. The code is openly shared for anybody to improve and check for potential issues.”

Vannberg envisions using the decision-support tool to create “virtual tumor boards” that would bring together broad expertise to examine RNA data from patients worldwide. 

“The hope would be to provide this kind of analysis for any new cancer patient who has this kind of RNA analysis done,” he added. “We could have a consensus of dozens of the smartest people in oncology and make them available for each patient’s unique situation.”

The tool is available on the open source Github repository for download and use. Hospitals and cancer clinics may install the software and use it without sharing their results, but the researchers hope organizations using the software will help the system improve.

“The accuracy of machine learning will improve not only as the amount of training data increases, but also as the diversity within that data increases,” said Evan Clayton, a Ph.D. student in the Georgia Tech School of Biological Sciences. “There's potential for improvement by including DNA data, demographic information and patient histories. The model will incorporate any information if it helps predict the success of specific drugs."

In addition to those already mentioned, the research team included Cai Huang, Lilya Matyunina, and DeEtte McDonald from the Georgia Tech School of Biological Sciences, and Benedict Benigno from the Georgia Tech Integrated Cancer Research Center and the Ovarian Cancer Institute.

Support for the project came from the Ovarian Cancer Institute, and equipment used was provided by the Georgia Research Alliance. In addition, the National Institutes of Health supported a graduate fellowship.

CITATION: Cai Huang, et al., “Machine learning predicts individual cancer patient responses to therapeutic drugs with high accuracy,” (Scientific Reports 2018). http://dx.doi.org/10.1038/s41598-018-34753-5

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“The blood-brain barrier is a challenge in the treatment of brain malignancies,” said Costas Arvanitis, an assistant professor at the Georgia Institute of Technology in the George W. Woodruff School of Mechanical Engineering. “Even when a drug reaches the brain’s circulation, abnormal blood vessels in and around tumors lead to non-uniform drug delivery with low concentrations in some areas of the tumor.”

If a drug does make it through the distorted blood vessels, then dense tumorous tissue often blocks the drug’s path to the malignant cells. Arvanitis co-led the new study with Dr. Vasileios Askoxylakis at Massachusetts General Hospital to explore the effectiveness of ultrasound that is focused on affected brain areas to buzz the drugs through these barriers and into the cancer.

Already, the method had proven effective enough in fighting tumors to make it to phase I clinical trials, but until now, it was not well observed how it actually worked. 

Beaming tumors

Arvanitis, also an assistant professor in the Wallace E. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, and his collaborators sought to determine tissue-level mechanisms behind the new ultrasound treatment’s improved drug delivery throughout brain tumors. The findings will help researchers and clinicians fine-tune this potential treatment against cancers in the brain.

The team, which included researchers from the University of Edinburgh, and Brigham and Women’s Hospital, published its findings in the journal Proceedings of the National Academy of Sciences on August 27, 2018. The research was funded by the National Institutes of Health, the German Research Foundation, the Solidar-Immun Foundation, the Harvard Ludwig Cancer Center, and the National Foundation for Cancer Research. 

The therapy is minimally invasive, focusing multiple beams of ultrasound energy onto a cancerous spot, where microbubbles, tiny lipid bubbles in the bloodstream that vibrate in response to ultrasound signals, can temporarily breach the blood-brain barrier at the target site. That creates an opening for drugs to get through. The microbubbles are injected intravenously before ultrasound is applied.

Observing success

The team studied the new method on mice with metastasized breast cancer cells in the brain. In lab experiments, the researchers observed improved delivery of two cancer therapies, the common chemotherapy drug doxorubicin, and the targeted drug T-DM1.

“We established that we were able to get more of both drugs across blood vessel walls,” said Yutong Guo, a graduate student in Arvanitis’s lab and coauthor of the study. “The doxorubicin molecule is small, and it got the bigger boost, but altogether, the therapy distributed more of both drugs to more tumor tissue.”

Also, the fluid that surrounds cells, interstitial fluid, which can serve as a conduit for drugs, was seen flowing more freely between cells of a tumor in high-resolution images taken following ultrasound treatment. The drugs appeared to make it through significant barriers to reach tumors.

“Evidence of increased cellular transmembrane transport and uptake of doxorubicin by focused ultrasound was largely unknown until now,” Askoxylakis said.

The improved delivery dissipated five days after treatment, suggesting that the higher T-DM1 accumulation indeed had resulted from the ultrasound method better permeating blood vessels and tumor tissue.

Optimizing treatment

The researchers quantified the changes in tissues and in cellular drug transport properties using mathematical modeling and used this to devise parameters for optimal drug delivery, which may prove useful in the design of new rounds of clinical trials.

“By explaining and underscoring the potential of combining focused ultrasound with different drugs for the treatment of brain metastases, our findings provide important scientific principles for the optimal clinical use of the technology,” said Rakesh Jain, who collaborated on the study and is a professor of radiation oncology at Harvard Medical School.

The study may also stimulate a broader discussion on how some cancer drugs should be administered, perhaps in some cases as a slow infusion rather than a quicker injection. The researchers would like to explore tuning the new method to optimize delivery of varying drugs or engineered immune cells to fight an array of tumors occurring in the brain.

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Also READ: Punching Cancer with RNA Knuckles

These researchers co-authored the study: Meenal Datta, Jonas Kloepper, Gino Ferraro, and Dai Fukumura of Steele Labs, Mass Gen Radiation Oncology; Miguel Bernabeu of the University of Edinburgh; and Nathan McDannold of Brigham and Women’s Hospital. The research was funded by the National Institutes of Health’s National Institute of Biomedical Imaging and Bioengineering (grant R00 EB016971) and the National Heart, Blood, and Lung Institute (F31 HL126449), the German Research Foundation (grant AS 422-2/1) and grants from the Solidar-Immun Foundation, the Harvard Ludwig Cancer Center, and the National Foundation for Cancer Research. Findings, opinions, and conclusions are those of the authors and not necessarily of the funding agencies. 

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The iconic research magazine applauded Dahlman because, as it stated in its headline, “His method makes it possible to test 300 drugs at once.” The “35” roster is noted for having anticipated the successes of Zuckerberg and Page, as well as that of Helen Greiner, co-founder of iRobot, Jonathan Ive, chief designer at Apple, and other consummate go-getters in industry, technology, and research.

Dahlman felt honored to join the list, which was published on June 27, but also humbled.

“I wouldn’t put myself in the same category as those people, but research colleagues who have made this list have gone on to make very significant contributions to science,” said Dahlman, an assistant professor at the Georgia Institute of Technology.

“It’s hard to get on that list, so I was thrilled, and a little surprised,” he said. “It also comes with certain expectations to live up to.”

DNA-barcoding

What Dahlman scrutinizes with his methods are, more precisely, nanoparticles designed to deliver a drug or gene therapy.

He calls his invention “DNA-barcoding," because it tracks hundreds of different nanoparticles at once to see how well they hit targeted tumor cells by loading up each one of the particles with its own custom-coded piece of DNA. Researchers can inject the particles all at once into a live mouse then later excise the tumor and sequence the DNA strands to see which nanoparticles best delivered their payloads to tumor cells.

The top nanoparticles could be loaded up with an effective therapy for targeted delivery.

“DNA makes for a fantastic tracker,” Dahlman said. “There are thousands to millions to billions of code combinations. It’s nature’s way of storing information, so we can exploit that.”

DNA barcoding has upended other methods of tracking nanoparticles. It has flatly nullified the results of tracking via lab samples, in vitro. And barcoding has left traditional tracking in vivo, in live mice, which can only follow one or a few particles at a time, in the dust.

Parkinson’s and heart disease

The Review cited specifically DNA barcoding’s potential for honing nanoparticles’ aim at cancer cells, but there are many possible uses.

“It can be for any cell type. We’re also using it for heart disease and for Parkinson’s,” Dahlman said.

Dahlman gives the real credit for the “35” kudos to the graduate students and postdoctoral researchers in his Lab for Precision Therapies in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

“They have done a lot of the actual work,” Dahlman said. “If you don’t get good students, you won’t be able to do anything, and the school here should get a lot of credit for recruiting them.”

The graduate students were jazzed to see their principal investigator on a pedestal.

“We were all super excited and all huddled around the computer looking at James’s profile and at the other people on that list to see what they accomplished to get on that list,” said Ph.D. student Cory Sago, who chose Georgia Tech largely because of Dahlman.

Past Georgia Tech honorees

Past Georgia Tech researchers named in the “35” list include microneedle patch co-inventor Mark Prausnitz, and microfluidics engineer and genotype-phenotype researcher Hang Lu. More Georgia Tech graduates, mainly from master’s programs, have appeared on the MIT Technology Review roster for making notable entrepreneurial waves.

Dahlman’s inclusion in the 2018 edition of “35 Innovators Under 35” follows a string of prior acknowledgments and fellowships awarded Dahlman by the National Science Foundation, the Defense Advanced Research Projects Agency, the National Institutes of Health and private foundations.

The MIT Technology Review was founded at the Massachusetts Institute of Technology in 1899, and later became independent but maintains its affiliation with MIT. Dahlman received his Ph.D. jointly from MIT and Harvard Medical School in 2014 and was a postdoctoral researcher at their shared Broad Institute, which is dedicated to improving human health through genomics.

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The new Good Manufacturing Practice (GMP) like ISO 8 and ISO 7 compliant facility is part of the existing Marcus Center for Therapeutic Cell Characterization and Manufacturing (MC3M). The center was established in 2016 and made possible by a $15.75 million gift from philanthropist Bernie Marcus, with a $7.25 million investment from Georgia Tech and another $1 million from the Georgia Research Alliance. 

MC3M is already helping researchers from Georgia Tech and partner organizations develop ways to provide therapeutic living cells of consistent quality in quantities large enough to meet the growing demands for the cutting-edge treatments. The center and this new facility also provide the infrastructural foundation for the Georgia Tech-led National Science Foundation Engineering Research Center for Cell Manufacturing Technologies (CMaT), which was announced in September 2017.

The Marcus Foundation’s gift along with the NSF’s expected funding over ten years in CMaT, together with potential private-sector contributions and the state of Georgia’s investment in infrastructure related bio manufacturing, could result in a combined statewide investment of more than $70 million in cell manufacturing. Beyond developing technologies to help make these life-saving cell therapies broadly available and affordable, the initiative will also help train the specialized workforce needed to manufacture these therapies at large scale. 

“This initiative has the potential to change the way we think about medical treatments, to change the way we think about medicine, and the way we approach cures for different diseases,” said Georgia Tech President G.P. “Bud” Peterson, who opened the dedication event. “Here, we will develop the tools and technologies to produce these cells at lower cost, more rapidly and for more people.”

MC3M is already supporting 23 research projects aimed at all components of the challenge, from understanding cell quality and developing scalable processes, to chip-based disease models for safety and efficacy testing and new models for supply-chain optimization and logistics. The center collaborates with several other institutions, supporting the work of 29 faculty members, and helping train 27 students and fellows for the emerging cell manufacturing industry.

The new facility dedicated on June 6 is a unique “sandbox” for collaboration among engineers, clinicians, and industry to develop and validate new scalable manufacturing processes for cell therapies under GMP conditions necessary to eventually obtain regulatory approvals. It will serve as the translational arm of the Marcus Center and CMaT to help researchers throughout the state of Georgia translate emerging cell therapies to clinical practice. This facility – designed to enable real time quality monitoring and control of cell products during manufacturing – is a one-of-a-kind space that will be instrumental in bringing affordable cell therapies to patients faster. 

The new cell-based therapies being approved for use in humans can have dramatic impact. But the therapies are costly, as much as a $500,000 per patient. The MC3M will help develop new technologies and processes to make these treatments consistent in quality and available to the average person.

“The center is about providing access for patients and enabling patients to benefit from these incredible therapies that could change their lives,” said Krishnendu Roy, who directs both MC3M and CMaT. “We need to scale these therapies up to treat hundreds of thousands of patients. This is the vision of Mr. Marcus – to make this available to everyone regardless of their socio-economic status.”

Marcus, who recalled working as a pharmacist before co-founding home improvement retailer The Home Depot, noted that common drugs such as aspirin are chemically consistent around the world, regardless of where they are sold. The consistency of living cell therapies can’t be similarly counted on because their properties may depend on the specific skills and facilities of the research center producing them. 

“Patients receiving these cells need to know that they are getting the right things,” Marcus said. “This is a very practical question for which we have no answer now.” Beyond consistency, the cells also need to be affordable, he said.  

The new cell manufacturing facility will connect cell-based therapies being developed in research facilities with the appropriate tools and technologies that ensure consistency in manufacturing and product quality while enabling scalability. “There is a gap right now between what we do in the research lab and what we need to do to get these therapies to a hundred thousand or even millions of patients,” Roy noted. 

Beyond developing quality control and analytical techniques to ensure consistency, the center will also develop novel feedback-controlled automation systems to lower the cost, Roy said. 

Peterson noted the potential economic impact of building a cell manufacturing industry in Georgia. “Working with our partner universities, the Technical College System of Georgia and the private sector, we will be able to attract new industries, create new jobs and help build the economy of the state of Georgia.”

The initiative began, he noted, with the development of a national cell manufacturing roadmap, an effort supported by the National Institute of Standards and Technology (NIST). The Marcus gift built on that foundation, and in turn, made it possible for Georgia Tech to lead a team including the University of Wisconsin, University of Georgia, University of Puerto Rico-Mayaguez, and other partners, to win the NSF Engineering Research Center award last fall.

Other collaborators in Georgia include Emory University and Children’s Healthcare of Atlanta.

The NSF ERC could provide up to $40 million over ten years, and attract private and local investment that could boost that amount much higher.

“We have incredible momentum,” Roy said. “We are bonded together by a single goal: getting these therapies to many patients at a lower cost to really help them.”

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Researchers at the Georgia Institute of Technology have engineered a chemical trap that exhaustively catches what are called glycoproteins, including minuscule traces that have previously escaped detection.

Glycoproteins are protein molecules bonded with sugar molecules, and they’re very common in all living things. Glycoproteins come in myriad varieties and sizes and make up important cell structures like cell receptors. They also wander around our bodies in secretions like mucus or hormones.

But some glycoproteins are very, very rare and can serve as an early signal, or biomarker, indicating there’s something wrong in the body – like cancer. Existing methods to reel in glycoproteins for laboratory examination are relatively new and have had big holes in their nets, so many of these molecules, especially those very rare ones produced by cancer, have tended to slip by.

Cancerous traces

“These tiny traces are critically important for early disease detection,” said principal investigator Ronghu Wu, a professor in Georgia Tech’s School of Chemistry and Biochemistry. “When cancer is just getting started, aberrant glycoproteins are produced and secreted into body fluids such as blood and urine. Often their abundances are extremely low, but catching them is urgent.”

This new chemical trap, which took Georgia Tech chemists several years to develop and is based on a boronic acid, has proven extremely effective in lab tests including on cultured human cells and mouse tissue samples.

“This method is very universal,” said first author Haopeng Xiao, a graduate research assistant. “We get over 1,000 glycoproteins in a really small lab sample.”

In comparison tests with existing methods, the chemical trap, a complex molecular construction reminiscent of an octopus, captured exponentially more glycoproteins, especially more of those trace glycoproteins.

Wu, Xiao and Weixuan Chen, a former Georgia Tech postdoctoral researcher, who was also first author of the study alongside Xiao, published their results in the journal Nature Communications. The research was funded by the National Science Foundation and the National Institutes of Health.

Boronic bungles

For chemistry whizzes, here’s a short summary of how the researchers made the octopus. They took a good thing and doubled then tripled down on it.

Those who recall high school chemistry class may still know what boric acid is, as do people who use it to kill roaches. Its chemical structure is an atom of boron bonded with three hydroxyl groups (H₃BO₃).

Boronic acids are a family of organic compounds that build on boric acid. There are many members of the boronic acid family, and they tend to bond well with glycoproteins, but their bonds can be less reliable than needed.

“Most boronic acids let too many low-abundance glycoproteins get away,” Wu said. “They can catch glycoproteins that are in high abundance but not those in low abundance, the ones that tell us more valuable things about cell development or about human disease.”

Benzoboroxole octopus

But the Georgia Tech chemists were able to leverage the strengths of boronic acids to develop a glycoprotein capturing method that works exceptionally well.

First, they tested several boronic acid derivatives and found that one called benzoboroxole strongly bound with each sugar component on the glycopeptide. (“Peptide” refers to the basic chemical composition of a protein.)  

Then they stitched many benzoboroxole molecules together with other components to form a "dendrimer," which refers to the resulting branch- or tentacle-like structure. The finished large molecule resembled an octopus ready to go after those sugar components.

In its middle, similarly positioned to an octopus's head, was a magnetic bead, which acted as a kind of handle. Once the dendrimer caught a glycoprotein, the researchers used a magnet to grab the bead and pull out their chemical octopus along with its ensnared glycopeptides (e.g. glycoproteins).

“Then we washed the dendrimer off with a low pH solution, and we had the glycoproteins analyzed with things like mass spectrometry,” Wu said.

Cancer treatments?

The researchers have some ideas about how medical laboratory researchers could make practical use of the new Georgia Tech method to detect odd biomolecules emitted by cancer, such as antigens. For example, the chemical octopus could improve detection of prostate-specific antigens (PSA) in prostate cancer screenings.

“PSA is a glycoprotein. Right now, if the level is very high, we know that the patient may have cancer, and if it’s very low, we know cancer is not likely,” Wu said. “But there is a gray area in between, and this method could lead to much more detailed information in that gray area.”

The researchers also believe that developers could leverage the chemical invention to produce targeted cancer treatments. Immune cells could be trained to recognize the aberrant glycoproteins, track down their source cancer cells in the body and kill them.

The research’s potential for science goes far beyond its possible future medical applications.

The fields of genomics and proteomics have made great strides. Following in their footsteps, this new molecular trap could advance the study of the rising field of glycoscience.

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ALSO read: Cancer-killing T-cells switched on via remote control

Georgia Tech’s Johanna Smeekens coauthored the research paper. The research was funded by the National Science Foundation (CAREER award CHE-1454501), and the National Institutes of Health (R01GM118803). Findings and any opinions are those of the authors’ and not necessarily of the funding agencies.

Light of specific wavelengths causes the nanoparticles to assemble and disassemble on demand, allowing the dynamic organization of the nanoparticles for smart in vitro drug release. By including chemotherapy molecules in the nanoparticle structures when they are assembled, the molecules could be drawn into tumors – and then released with the application of a light at a shorter wavelength that triggers disassembly through photo-cleavage. 

In addition to such a dynamic self-assembly and disassembly, the encapsulation and release of chemotherapy molecules could also be achieved by reversible covalent bonding of anticancer drugs to the polymeric “hairs” situated on the surface of nanoparticles. And by absorbing the same light that triggers the drug release, the gold nanoparticles could also heat the cancer cells, providing a double punch.

In a broad range of other applications, the nanoparticle self-assembly process could also be triggered by environmental factors including temperature, pH or solvent polarity by rationally designing the polymeric hairs. In this study, gold nanoparticles were used, but the process could also make self-assembled nanoparticles from a variety of metals and metal oxides. By tailoring the surface of nanoparticles with water-absorbing polymers containing near-infrared responsive components, the drug release could be performed in vivo. 

The spherical gold nanoparticles can be replaced with more complex shaped nanomaterials – such as hollow nanoparticles, nanorods, or nanotubes – to render a better absorption of near-infrared light to penetrate biological tissues. No testing of these nanoparticles has been done so far in living cells or organisms.

The research was supported by the Air Force Office of Scientific Research and the National Science Foundation, and was reported January 31 in the early edition of the journal Proceedings of the National Academy of Sciences. Materials scientists from the Georgia Institute of Technology and South China University of Technology co-authored the paper.

“We envision that these photo-responsive polymer-capped gold nanoparticles could one day serve as nano-carriers for drug delivery into the body using our robust and reversible process for assembly and disassembly,” said Zhiqun Lin, a professor in the Georgia Tech School of Materials Science and Engineering. “Used in cancer therapy, this process could increase the impact of a treatment by heating the cancer cells while introducing the drug compound into the tumor.”

Under light, the assemblies of photo-sensitive nanoparticles separate over a period of hours at a rate that can be controlled by the intensity and wavelength of the light. “Because the disassembly can be turned on and off at will, we could provide a timed release of the drug by controlling the short-wavelength light exposure,” Lin added.

The hairy nanoparticles are fabricated around a tiny core of beta-cyclodextrin from which polymer chains of poly(acrylicacid)-block-poly(7-methylacryloyloxy-4-methylcoumarin) (PAA-b-PMAMC) are grown. That material attracts water-soluble metal precursors, which use the space within the polymer hairs as nano-reactors to form gold nanoparticles. 

To these inner structures – which are hydrophilic PAA polymers – the researchers add hairs made from the hydrophobic monomer MAMC. These materials are sensitive to light, and cause the nanoparticles to self-assemble through a photo-dimerization process – crosslinking – when subjected to light at a wavelength of 365 nanometers.

The assembly process can be reliably reversed on demand using a shorter wavelength at 254 nanometers.

“Once the polymer chains from adjacent gold nanoparticles begin to photo-crosslink, they bring nanoparticles together via a self-assembly process to generate large assemblies of nanoparticles,” said Lin. “This process is completely reversible and can be repeated in many cycles.”

The research team incorporated dye molecules into the self-assembled nanoparticles to simulate what might be done to incorporate and then release chemotherapy agents. A magnetic oxide material incorporated into the nanoparticles could allow the assemblies to be directed to a tumor site by an external magnet, and could also support diagnostic imaging. 

Beyond the activity of the drugs, the plasmonic effects of the gold nanoparticles could heat the nanoparticles when they are subjected to light, attacking the cancer cells through a second route.

In addition to the potential medical uses, the self-assembly technique could have applications in optics, optoelectronics, magnetic technologies, sensing materials and devices, catalysis and nanotechnology. The technique could also lead to new basic research in crystallization kinetics, using the self-assembly process to create “artificial crystals” held together by polymer chains.

Lin’s lab has worked on the amphiphilic star-shaped block polymers for several years, adding new features and exploring new capabilities for the nanoparticle systems.

“Our work provides a design strategy that allows the manipulation of both the outer block and the inner block of a star-shaped block co-polymer,” he said. “Our fundamental contribution in this work is to judiciously prepare a star-shaped block co-polymer in which the inner block has the capability to coordinate with metal precursors while the outer block allows photo-responsive materials to interact, which in turn renders the crafting of photo-responsive gold nanoparticles for light-enabled reversible and reliable self-assembly.”

The research team included Yihuang Chen, associated with both Georgia Tech and the South China University of Technology; Zewei Wang, Yanjie He, Young Jun Yoon, and Jaehan Jung, associated with Georgia Tech, and Guangzhao Zhang from South China University of Technology.

This work is supported by the Air Force Office of Scientific Research (Grant FA9550-16-1-0187) and the National Science Foundation (Civil, Mechanical, and Manufacturing Innovation Grants 1562075 and 1727313; Division of Materials Research Grant 1709420). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsors.

CITATION: Yihuang Chen, et al., “Light-enabled reversible self-assembly and tunable optical properties of stable hairy nanoparticles,” (Proceedings of the National Academy of Sciences, 2018). http://www.pnas.org/content/early/2018/01/30/1714748115.

The researchers who built the program at the Georgia Institute of Technology would like cancer fighters to take it for free, or even just swipe parts of their programming code, so they’ve made it open source. They hope to attract a crowd of researchers who will also share their own cancer and computer expertise and data to improve upon the program and save more lives together.

The researchers’ invitation to take their code is also a gauntlet.

They’re challenging others to come beat them at their own game and help hone a formidable software tool for the greater good. Not only the labor but also the fruits will remain openly accessible to benefit the treatment of patients as best possible.

“We don’t want to hold the code or data for ourselves or make profits with this,” said John McDonald, the director of Georgia Tech’s Integrated Cancer Research Center.  “We want to keep this wide open so it will spread.”

The goods

Researchers wanting to participate can follow this link to a new study published on October 26, 2017, in the journal PLOS One. There they will find links to download the software from GitHub and to access the code.

They’ll start out with a current program that has been about 85% accurate in assessing treatment effectiveness of nine drugs across the genetic data of 273 cancer patients. The study by McDonald and collaborator Fredrik Vannberg details how and why.

“Nine drugs are in the published study, but we’ve actually run about 120 drugs through the program all total,” said Vannberg, an assistant professor in Georgia Tech’s School of Biological Sciences.

The program uses proven machine learning mechanisms and also normalizes data. The latter allows the machine learning to work with data from varying sources by making them compatible.

The bias

And the researchers have reduced human bias about which data are important for predicting outcomes.

“It’s much more effective to put in loads of raw data and let the algorithm sort it out,” McDonald said. “It’s looking for correlations, not causes, so it’s not good to preselect data for what you suspect are most relevant.”

One big bias the researchers tossed out was a concentration only on gene expression data pertaining to the specific type of cancer they were aiming to treat.

“It turns out that it’s better to give the program data from a broad diversity of cancers, and that will actually later give a better prediction of drug effectiveness for a specific cancer like breast cancer,” Vannberg said.

“On a molecular level, some breast cancers, for example, are going to be more similar to some ovarian cancers than to other breast cancers,” McDonald said. “We just let the algorithm work with about everything we had, and we got high accuracy.”

The winners

The researchers also want the project to pool large amounts of anonymous patient treatment success and failure data, which will help the program optimize predictions for everyone’s benefit. But that doesn’t mean some companies can’t benefit, too.

“If a company comes along and makes profits while using the program to help patients, that’s fine, and there’s no obligation to give back to the project,” said McDonald, who is also a professor in Georgia Tech’s School of Biological Sciences. “Others may just take if they so please.”

But hopefully, most players will catch the spirit of kindness.

“With our project, we’re advertising that sharing should be what everybody does,” Vannberg said. “This can be a win for everybody, but really it’s a win for the cancer patients.”

Also READ: Basic premise in targeted cancer treatments wrong 60% of the time

Georgia Tech researchers Cai Huang and Roman Mezencev coauthored the study. The research was funded by the Rising Tide Foundation.

Since the new degree program was approved by the Board of Regents on Valentine’s Day 2017, nearly 200 students clamored to sign on.

This enthusiastic response was surprising — but then again, not, says Tim Cope, chair of the Undergraduate Neuroscience Curriculum Committee and professor in the School of Biological Sciences and the Wallace H. Coulter Department of Biomedical Engineering.

“Hardly a day goes by that there’s not something in the news — a health concern or a recent breakthrough or societal challenge — that doesn’t involve neuroscience,” he says. “It’s a growing field with so many opportunities, and it’s inspired a lot of interest from our students.”

One of them is Yeseul Heo.

“I got really excited when I learned about the new major,” the rising second-year student says. “I think I was one of the first to turn in my paper to switch.”

Heo’s original major was psychology — and she is keeping that as a minor, along with a double major in international affairs — but she sees neuroscience as a way to put her studies on a more quantitative footing.

“Along with psychology, I wanted to focus more on hard research, specifically on brain activity, and working with quantitative data,” she says.

Heo has gotten a taste of neuroscience already as a student assistant in the lab of Associate Professor of Psychology Eric Schumacher, whose research uses functional magnetic resonance imaging (fMRI) and other experimental techniques to investigate the neural mechanisms for vision, attention, memory, learning, and cognitive control.

A Research Community

Schumacher is one of more than 50 faculty members from disciplines across Georgia Tech who are involved in neuroscience research — and have been for years. But however collaborative, widespread, and even world-renowned these neuroscience efforts have been, what they have lacked, Cope suggests, is “community.”

He and many others anticipate this new undergraduate degree will build that necessary component, for both faculty and students. “It’s a very important, symbolic event in the development of neuroscience on this campus,” he says.

Neuroscience is “the perfect incarnation of an interdisciplinary subject,” says College of Sciences Dean and Sutherland Chair Paul M. Goldbart. 

“It’s also a subject of deep intellectual interest. Who couldn't be curious about how the brain and nervous systems work at the most basic level?”

Goldbart “couldn’t be more excited” about the new degree, because “It opens up a marvelous new channel to a wide variety of career paths and will make Georgia Tech even more appealing to prospective undergraduates in the sciences.”

“I am grateful to everyone who worked so hard to create a program that defines 21^st-century neuroscience education for a 21^st-century technological research university.” 

NeuroX Factor

Getting from neuroscience activity to neuroscience community at Georgia Tech has been something of a journey, starting with the formation of a “NeuroX” committee back in 2014 and ending with Board of Regents approval for the new undergraduate degree in February 2017.

To reach this place, certain boxes had to be checked. It was not enough that faculty were engaged in neuroscience and students wanted it, although that was clearly the case.

Every time the Institute offered a neuroscience course, it maxed out, and professors were constantly asked if there would be more courses, or if they could open up another section.

Still, Cope points out, “It’s a legitimate thing for the administration to think about these things exceedingly carefully. No university can be everything — there’s a limit to resources and we have to be strategic with our planning.”

Basically, the key questions were: Is there a demand for this major from employers? Is there a demand for this degree from students? How would a neuroscience degree program advance Georgia Tech’s strategic plan? And would the program be redundant within the University System of Georgia?

This last question sent Cope over to Georgia State University — the only other USG school with an undergraduate neuroscience degree — to meet with the leadership of their Neuroscience Institute.

“I said, ‘Here’s what we’re planning to do,’” Cope recalls.

“They said, ‘Oh, this is fantastic, with Georgia Tech’s traditions and resources, you bring something unique to the table,’ and they wrote a letter for me right on the spot — they endorsed our plan 100 percent.”

'Kind of Pulsing'

While every neuroscience program has its “multiplication tables,” as Cope terms them — certain facts every neuroscientist has to know — the bigger challenge is, where do students take it from there?

Heo eventually wants to take her neuroscience focus into the study of first impressions. “You develop this first impression within two seconds in your brain, and you don’t control that, ever,” she says.

“So, I want to figure what’s the reason behind it, and if we learn the reason, is there a way to, not eliminate it, but maybe try to understand each other better, avoid racism and discrimination, and bring about more peace.”

As a neuroscience undergraduate, Heo will learn what Cope calls “the three flavors of neuroscience” — cell and molecular, behavioral, and systems.

Beyond these basics, Heo can branch out into one of 10 different specializations — biochemistry, biology, chemistry, computer science, engineering, health and medical, physics, physiology, or psychology.

In her case, completing the psychology specialization will qualify her for a minor in that field.

Students are coming into the program from disciplines all over campus, and all these areas can and do intersect with neuroscience, notes Cope. “To have a degree in neuroscience means you have to be conversant in wide-ranging concepts,” he says.

“In my mind’s eye, I have the sense of neuroscience kind of pulsing — it borrows concepts and technologies from all the fields, but it doesn’t only take, it gives back.”

The undergraduate neuroscience degree will — as with all Georgia Tech disciplines — culminate in a senior research or capstone project.

“We want to leave our students with an experience that really gets their creative juices going and gives them a tantalizing view of what they might do next,” Cope says.

The program website lists 50 occupations for which neuroscience can serve as preparation or grad school foundation, and then, of course, there’s entrepreneurship.

Among the many other student startup and business incubators in and around Georgia Tech, there’s even one called NeuroLaunch, which introduces itself as “the world’s first neuroscience startup accelerator.”

Proving It

Georgia Tech’s Bachelor of Science in Neuroscience launched this fall.

As the community builds and the degree program gains visibility, Cope expects Georgia Tech to carve its niche among neuroscience programs as only Georgia Tech can.

“We’re especially mindful of active learning here, of inquiry-based education, where the students are led to discovery, not just have the discovery dumped in their laps,” he says.

“What we’d like to bring to neuroscience is the strong analytical, deep understanding of concepts and methods that Tech brings to its curriculum in all fields.”

Down the road, Cope sees the undergraduate degree program leading to more and bigger grants for neuroscience research at Tech, and ultimately a Ph.D. program.

In the meantime, he says, there’s much to learn and do, quoting a fortune cookie slip he’s kept in his wallet for more than 25 years now: “It says, ‘You are respectable, you are intelligent, you are creative — prove it.’

I think that applies here. We’ve got a lot of what we need to do some really great things in neuroscience. Now we’ve got to prove it.”

Neuroscience Research in the College of Sciences

Neuroscience is “the perfect incarnation of an interdisciplinary subject,” says College of Sciences Dean and Sutherland Chair Paul M. Goldbart. “It’s also a subject of deep intellectual interest. Who couldn’t be curious about how the brain and nervous systems work at the most basic level?”

Neuroscience majors interested in research have a broad array of options. Researchers at Tech seek to understand the mechanics of brain function and the emergence of normal, aberrant, or developmental behavior from the components of the nervous system at multiple scales of complexity.

The details of every faculty member’s research are diverse, but they all aim to address one or more of the following overarching questions:

1. How does the brain perceive the world, learn new information, express emotions, and produce behaviors?
2. How does the nervous system cooperate with the body it lives in?
3. How does the brain compute responses and commands?
4. How do behaviors emerge from molecules, cells, and systems?
5. How can genetic and environmental factors impact neural functions?

Here are examples of research led by College of Sciences faculty members.

The Reorganization Problem of Neurons: Addressing the neurotoxicity of chemotherapy

By A. Maureen Rouhi

Even as a child, Tim Cope was fascinated by how physically disabled people move. Why can’t they move normally? That fascination led to scientific curiosity about why it can be so difficult to recover normal movement after disease or damage.

One path of inquiry Cope has pursued is the organization of sensory signals to the spinal cord. Over more than two decades of research, he and others have shown that sensory signals can be restored to normal when damaged sensory nerves regenerate and reconnect with muscle; however, their connections in the central nervous system reorganize.  

Central reorganization changes the flow of sensory information, so some neurons completely lose sensory signals, while others receive twice as much input. Thus, regeneration is not synonymous to recovery, says Cope, a professor in the School of Biological Sciences and in the Wallace H. Coulter Department of Biomedical Engineering and member of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB).

Another condition that may cause peripheral nerve damage, and subsequent reorganization is chemotherapy. “We have peripheral nerve regeneration after chemo, but we don’t regain normal function,” Cope says. “Maybe it’s this reorganization problem again.”

To explore this possibility, researchers in Cope’s lab recorded sensory signals of rats after chemotherapy. In this case, the sensory signal itself showed long-lasting abnormality. However, they also found that even when nerves are not structurally damaged by chemotherapy, the sensory signal remains atypical.

These puzzling findings led to the discovery that chemotherapy affects cellular mechanisms responsible for translating mechanical stimuli — for example, muscle stretch — into sensory signals. As with peripheral nerve trauma, sensory information changes, but for a very different reason. 

Cope relishes this unexpected turn of the research. “Our chemo studies led us to a way of restoring the signals to normal, and I think our findings may have some translation to humans,” he says. “We believe if we can fix the signal, then we can improve the daily movement activity in patients who otherwise might experience disability long after chemotherapy is discontinued.”

Fixing the signal means restoring the damaged proteins, or just bypassing them. Cope’s team has identified a drug to do the latter. “But a better solution is to find out exactly what protein is damaged and restore it through genetic therapy or other molecular techniques.”

Next, Cope hopes to do genetic screening to try to get a comprehensive list of the proteins damaged by chemotherapeutic neurotoxicity, particularly those involved in generating sensory signals. This work would be in collaboration with John McDonald, a cancer expert, professor in the School of Biological Sciences and member of IBB.

Meanwhile, other work goes on in the Cope lab. “If you’re interested in how we generate movement and how sensory information is required to generate that movement, and what goes wrong in various disease and damage situations, then whether you’re a chemist, an engineer, or interested in behavioral science, there is an entry level for you in my lab to study those things,” he says.

Memory, Emotion, and Aging: Exploring “memory clutter” and the neuroscience of human cognition

By Renay San Miguel

Forget where you parked your car? Misplaced your keys? Can’t remember what a restaurant dinner companion just said to you? All signs of early-onset dementia, right?

Not quite, says Audrey Duarte, associate professor in the School of Psychology and principal investigator in Georgia Tech’s Memory and Aging Lab. “There are memory changes we think of as being associated with dementia, and that’s very concerning, but that’s not really what we’re talking about,” Duarte says. “Just by getting older, we experience more memory impairment.”

Take that restaurant dinner, for example. When you’re younger, people coming in and out of the dining room, nearby conversations, and any other distractions are easier to tune out. “As we get older and we have that impaired ability to ignore distracting information, it gets incorporated into our memories,” Duarte says. “That information is there even at the subconscious level, and that creates what we call memory clutter.”

That clutter gums up the brain and forces older adults to work harder than before to recreate that restaurant experience in their minds in the hopes of remembering information.

Duarte’s 2016 study on memory clutter is the latest example of her focus on human cognition. How does the brain process new information, and how is that tied to emotions and behaviors?

“I’m a memory person, so I always think memory is the most important thing,” she says. The information we take into our brains has to be processed by our sensory systems — what we see, hear, etc. — and then filtered through our past experiences. “Those memories have emotional associations with them, some positive, some negative. If it comes down to why a particular emotion is stronger than others, we don’t really understand why the brain is organized that way.”

Duarte’s research involves exploring which areas of the brain are necessary for emotional processing. She and her team in the Memory and Aging Lab use electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) to determine which parts of the brain make those connections between memory and emotion.

It’s known that the amygdala, located within the brain’s medial temporal lobes, is associated with processing emotions. Duarte says her research shows that “if you see something that’s negative, the amygdala is sensitive to that.” But she emphasizes that other brain regions also seem to process stimuli associated with bad emotions such as disgust, sadness, anger, etc.

Duarte is determined to discover how disease, injury and aging effect all aspects of human cognition. She believes the future of her field will bring an interdisciplinary focus, folding in computational modeling, biology, genetics and biomedical engineering.

The research tools she’s using now are noninvasive. “We’re not implanting electrodes in people.” But to get a complete picture of neural communications — how that supports human cognition and what happens when that communication breaks down — “we’re going to have to drill down to the neuron level itself.”

Protective Responses: Neurons linked to itch and bronchoconstriction

By A. Maureen Rouhi

Itch. Just seeing the word makes you feel itchy. The sensation that makes you want to scratch your skin does the same to other mammals, amphibians, reptiles and birds. “Itch sensation is an evolutionarily conserved way used by many animals to sense environmental irritations and respond accordingly,” says Liang Han, an assistant professor in the School of Biological Sciences. 

Han’s laboratory strives to understand how the nervous system receives, transmits, and interprets stimuli to induce responses. In particular, she is interested in the mechanisms of nocifensive — or protective — responses. She wants to know how alterations in neural pathways that mediate these responses lead to chronic disease. For now, she’s focusing on two protective responses: itch and constriction of the lungs’ airways, or bronchoconstriction.

“Everyone experiences itchy feelings — when they get a mosquito bite or are wearing a prickly wool sweater.” Han says. In these cases, the itch is relieved by scratching. But imagine if the itchiness goes on and on!

“Chronic itch accompanying disease can be devastating,” Han says. More than 40 percent of patients receiving dialysis for end-stage renal disease suffer from severe itching, as do 60 to 70 percent of patients with advanced liver disease, according to Han. Persistent itching can lead to sleep deprivation and depression. Despite the clinical importance of itch sensation, Han says, the mechanisms governing it are largely unknown.

A long-standing question is whether itch-sensing neurons are itch specific or also signal other sensations such as pain. In earlier work using molecular genetic approaches, Han discovered a subpopulation of sensory neurons specifically linked to itch sensation. When those neurons are removed from experimental mice, the animals do not sense itch from multiple stimuli, but they continue to sense pain or pressure. Conversely, when these neurons are activated by painful stimuli, they elicit itch, not pain. “The data demonstrate the existence of the dedicated itch-sensing neurons,” Han says, “and advances our understanding of the cellular mechanisms of itch sensation.”

Now at Georgia Tech, Han aims to discover the mechanisms of chronic itch and find therapeutic targets for treatment, while also advancing understanding of bronchoconstriction.

The lungs’ sensory nerves help regulate the respiratory system, for example, by controlling breathing patterns and evoking airway-protective behavior such as coughing, airway constriction, and mucus secretion. Han’s lab recently discovered a subpopulation of sensory neurons that, when stimulated, induce bronchoconstriction and airway hyperresponsiveness, both of which are hallmarks of asthma.

“Current investigations of the pathogenesis of asthma have largely focused on immune responses,” Han says. “However, anti-inflammatory treatment only partially controls asthma symptoms. We need to understand the involvement of non-immune systems in the disease.”

Recent studies, including Han’s, indicate an important role for the nervous system in the pathogenesis of asthma. “We are currently using molecular genetic tools to investigate whether blocking those neurons can inhibit asthma in a mouse model,” she says. “We hope to obtain insights into the neural mechanisms of asthma and identify neuronal targets for management of asthma symptoms.”

Muscle-Neuron Connections: Maintaining contact as aging occurs

By A. Maureen Rouhi

Young C. Jang aspires to understand the aging process, particularly as it relates to muscle loss. An assistant professor in the School of Biological Sciences and the Wallace H. Coulter Department of Biomedical Engineering, and member of the Parker H. Petit Institute for Bioengineering and Bioscience, Jang hopes that therapeutic interventions could be developed to treat muscle loss, whether from aging or disease.

In considering scientific questions, Jang’s approach is to look at the forest. “You can be interested in muscle,” he says, “but you can’t just work on muscle to understand the whole biological process.”

Motor neurons connect muscles to the nervous system; however, the muscle-neuron connection can be severed by injury or disease. When the muscle is restored to function, the junction can be reconnected.

With age, the reconnection between muscle and neuron becomes increasingly difficult. When contact disappears, Jang explains, “muscles cannot communicate with the spinal cord and brain, and they start to degenerate.” Jang studies how to keep these connections going in hopes of developing ways to prevent or treat muscle loss. 

Aging and disease have some common pathways, Jang says. One is oxidative stress. When the body has an excess of reactive, oxidizable species, aging occurs faster than usual.

Jang’s work has shown that oxidative stress contributes to disconnection of the muscle-neuron junction. Oxidative stress is a well-accepted theory of aging, Jang says. It posits that when the body’s balance of antioxidant enzyme and oxidizing free radicals tilts in favor of free radicals, aging accelerates.

Jang’s early work showed that, in mice, removing the antioxidant enzyme — which increases reactive oxygen species — promotes severance of the muscle-neuron junction. In humans, Jang notes, genetic mutation of the same enzyme leads to amyotrophic lateral sclerosis (ALS) or Lou Gehrig’s disease, a motor neuron disease.

“We’ve found one mechanism that promotes detachment,” Jang says. “Can we reverse the process or slow it down?” Looking for ways to halt or reverse muscle-neuron detachment has taken Jang to multiple paths of inquiry, including caloric restriction, parabiosis, and organs-on-a-chip.

Jang’s caloric restriction research showed that mice receiving only 60 percent of the normal caloric requirement form fewer reactive oxygen species, and the treatment promotes muscle-neuron attachment. Furthermore, caloric restriction rejuvenates muscle stem cells, which help restore the function of muscles degenerated by aging or disease. With aging, these stem cells’ number and viability diminish, thus making muscle more prone to damage, a trend that slows with caloric restriction. 

In physiological research, parabiosis is the physical joining of two individuals. Jang turned to this approach because blood is a way for cells, tissues, and organs to communicate. When Jang joined a young mouse to an old one so that they share the same circulating blood, he found that the muscle-neuron junction in the old animal is rejuvenated. However, “if you put two old animals together, that junction detaches,” Jang says. “Something in young blood is helping preserve the muscle-neuron junction.”

Indeed, Jang has reported a circulating protein in the blood that seems to be an important factor in connecting the muscle-neuron junction. However, this protein “is not the only one,” Jang says. “We need more research.”

Meanwhile, how could parabiosis be applied to humans? “Obviously, we can’t put two humans together,” Jang says. But it is possible to faithfully mimic parabiosis of organs on microfluidic chips. Jang is collaborating with YongTae (Tony) Kim, an assistant professor in the George W. Woodruff School of Mechanical Engineering, to design organ-on-a-chip systems for parabiosis of human organs.

Sensory Input, Neural Networks, and Locomotion: Creating a new rehabilitation paradigm

By A. Maureen Rouhi

So you think walking across a room is easy, peasy? Think again.

“Walking across the room is one of the most complicated things we do,” says T. Richard Nichols, a professor in the School of Biological Sciences and the Wallace H. Coulter Department of Biomedical Engineering and a member of the Parker H. Petit Institute for Bioengineering and Bioscience. Locomotion is complex, he says, the result of networks of nerve cells communicating, processing information, and integrating myriad sensory signals.

In studying how sensory information from muscles helps regulate movement, Nichols has focused on the Golgi tendon organs (GTOs). These sensory receptors in the muscle tell the central nervous system — which consists of the brain and the spinal cord — the amount of force generated by muscles. The spinal cord then distributes the information to different muscles in the limb. The feedback of muscular forces is thought to help determine how the body responds to obstacles or unexpected circumstances.

So far, what we know about GTOs comes from research on animal subjects. Injury to the spinal cord disrupts communication between the central nervous system and the muscles and causes malfunctioning of the spinal cord’s neural circuits, Nichols says. “Muscle weakness or paralysis can result, as well as loss of balance and stability.”

Working with Dena Howland at the University of Louisville, Nichols has discovered a link between the disruption of the force-regulating system and motor disorders from partial spinal cord injury in animal models. They recently started two projects based on the GTO research.

One project, funded by the National Institutes of Health (NIH), aims to discover how the brain stem controls the GTO-generated neural circuits in the spinal cord to meet the needs of different movement tasks. The other project, funded by the Department of Veterans Affairs, will help define the extent to which malfunction in the force-regulating system contributes to motor dysfunction in partial spinal cord injury. It will also test the efficacy of a potential new treatment for spinal cord injury in humans that would not require special equipment.

The potential new treatment is based on the force-regulating neural networks of cats walking up — or down — hill. Researchers in the Nichols lab have shown that these networks are organized for propulsion when cats walk uphill and for suspension and braking when cats walk downhill.

“It turns out that in spinal cord injury, the downhill pathway becomes extreme” Nichols says. “Animals with spinal cord injury tend to crouch; it’s like an exaggeration of walking downhill.”

Suppose animals with spinal cord injury are rehabilitated by exercising under downhill-walking conditions? The idea is counterintuitive but, Nichols thought, “maybe the central nervous system has some internal wisdom that will say, okay, now we need to repair this injury.” Could training in this particular way promote recovery from partial spinal cord injury?

Nichols and Howland proposed this rehabilitation treatment to Veterans Affairs and received funding. “At the same time, because of our work at Tech, we can find whether the same exercise causes a change in the neural networks of the spinal cord,” Nichols says. Through the NIH grant funding, Howland and Nichols aim to mechanistically connect the recovery with restoration of normal function in the spinal network.

Biomechanics of Locomotion: Toward next-generation artificial limbs

By A. Maureen Rouhi

Research in the lab of Boris I. Prilutsky aims to understand the biomechanics and control of locomotion, which comprises the movements that take two- and four-footed animals from place to place.

During locomotion, sensations from the limbs (called sensory feedback) inform the nervous system about the state of the movement. Prilutsky studies how this sensory feedback affects locomotion. In particular, he investigates feedback from foot pressure and limb motion.

Disrupting the feedback, through injury for example, can lead to instability and falls during locomotion. “We modify sensory pathways in experimental animals and in computational models and observe the effects on locomotion,” says Prilutsky, a professor in the School of Biological Sciences and a member of the Parker H. Petit Institute for Bioengineering and Bioscience.

A key research tool is a neuromechanical model the Prilutsky group developed in collaboration with the group of Ilya A. Rybak, at Drexel University. This model accurately reproduces the walking mechanics and muscle activity of cats. Computational experiments have pinpointed the sensory feedback pathways that produce mild and severe locomotion defects when interrupted. These predictions have been experimentally tested.

In a recent study, for example, Prilutsky’s team injected local anesthetic to the paw pads on one side of a cat to block the sense of touch. Under this condition, the animal loses the symmetry of its gait and becomes less stable. The effect can be reversed, however, by electrically stimulating the nerves that convey the sense of touch to the central nervous system. When that happens, the cat’s walk becomes symmetric and stable again.  

In other experiments, they removed muscle stretch feedback – or stretch reflex – from selected muscles and investigated the effects. “We found that this feedback is task- and muscle-dependent,” Prilutsky says. For example, loss of feedback from certain muscles of the ankle causes problems only in downslope walking. More recently, they found that removing the stretch reflex from hip flexors causes profound changes in locomotion, as predicted and explained by their computational model.

“From our experimental and computational studies, we gain insight into how spinal circuits cooperate with the moving body segments during locomotion,” Prilutsky says.

Those insights are now propelling Prilutsky and others toward prosthetic devices that behave like natural limbs. For example, Prilutsky is applying discoveries about sensory pathways, feedback loops, and natural control signals from the nervous system in the field of osseointegrated — or bone-anchored — limb prostheses. In this approach to attaching prosthetic devices, the artificial limb is directly anchored to the bone through a titanium rod, similar to a dental implant. Potentially this implant can be used as a neural interface between the prosthesis and nerves in the stump.

Although used in Europe, bone-anchored limb prostheses are not approved in the U.S. because of the high rate of skin infections, which develop when skin fails to form a close connection with the bone implant. However, Prilutsky and others have shown that, in rats, use of porous titanium allows skin to grow into the implant, thereby reducing infections. Recently they experimented with cats to test this implant in natural walking conditions to see whether it forms a tight bond with skin and bone and whether and how the animals use a bone-anchored prosthesis for walking. “It works,” Prilutsky says.

Now the stage is set for the next phase: using the implant as a neural interface between the prosthetic device and the nerves in the residual limb so that the nerves and prosthesis talk to each other, and the prosthesis is controlled naturally without the person’s attention. If the promise of this approach is fulfilled, it could revolutionize prosthetics.

Moving in a Complex World: How do insects do it?

By A. Maureen Rouhi

How do animals navigate their environments? That question motivates the research of Simon Sponberg. An assistant professor in the School of Physics with a joint appointment in the School of Biological Sciences, Sponberg studies animals to discover how they move around in a complex world.

“Perceiving and then navigating the irregular terrain of Earth requires sophisticated processing by the brain,” says Sponberg, who received a National Science Foundation Early-Career Award in 2016 in recognition of his promise as a teacher-scholar and is a member of the Parker H. Petit Institute for Bioengineering and Bioscience. “It also demands that the brain work in conjunction with an animal’s body and the environment surrounding it.”

Animals have evolved to negotiate almost every environment on this planet. To do this, Sponberg says, their nervous systems acquire, process, and act upon information. “Yet their brains must operate through the mechanics of the body’s sensors and actuators to both perceive and act upon the environment,” he adds.

In Sponberg’s lab, researchers are studying how muscles operate as soft, living matter. They’re trying to understand the physics of moving animal bodies and the computational principles implemented in the sensors — such as eyes or antennae — of animals in motion.

“Our research investigates how physics and physiology enable animals in motion to achieve the remarkable stability and maneuverability we see in biological systems,” Sponberg says. “We explore how animals fly and run stably even in the face of repeated perturbations, how the multifunctionality of muscles arises from their physiological properties, and how the tiny brains of insects organize and execute movement. We study how the grace and agility of animal movement arises from the synthesis of its parts. Among these is the brain — a crucial part, but not the only one.”

The hawkmoth is a frequent subject of Sponberg’s investigations. The swift-flying insect typically imbibes nectar while hovering over a flower. Feeding usually takes place at dusk, when light is limited. It’s hard enough to see in dim light and even more when it gets dimmer with time. Yet hawkmoths also hover in air while following a flower that’s swaying with the wind. How do they do it?

Sponberg’s group has shown that hawkmoths slow their brain down to improve vision in dim light, much like increasing the exposure on a camera.  However, this adjustment can cause their motion to blur, so they only slow down to the point where they can still track the wind-blown motions of the flowers they prefer in nature. The behavior demonstrates that their neural circuits adapt exquisitely to the environment.

More recent work on three hawkmoth species tracking the group’s “roboflowers” suggests that simple models of neuronal processing can account for interspecies differences in adapting to different light intensities, and the moths actually use touch sensors on their proboscis to help feel the flower’s movements.

“Behavior, especially movement, arises from the context in which the brain acts,” Sponberg says. “We start by asking questions like, “If we know something about the biophysics of how muscles works, how might the brain activate and control muscle to enable an animal to be most agile and versatile?

“What we are finding is that how brains process sensory input and program motor output is intimately coupled to the physics of the surrounding systems and the features of the environment the animal most cares about. Figuring out these coupling principles is a huge task but one that we are confident will help us better understand how we think and act.”

Intent and Action: Unpacking a little-understood aspect of skilled movement

By A. Maureen Rouhi

Lewis A. Wheaton wishes to play golf like a pro. He could raise his game by watching videos of star players like Rory McIlroy. But Wheaton knows from experience — and his research — that observation alone doesn’t always help motor learning.

Research in Wheaton’s lab is explaining why observing people who are highly skilled at motor tasks may not be helpful to those who are far less proficient. Wheaton is interested in unpacking how the brain integrates information to effect motor behavior, particularly highly skilled tasks that involve hands and tools. His findings underscore the importance of intent.

Consider an array of objects on a table: pens, paper, mug, stapler. “You need intent to use things together,” Wheaton says. “If you decide to write a note, you’ll focus attention on the pen and paper.”

That’s obvious, yet some people with certain neurological injuries have trouble understanding what they need to do to write a note. “It’s not automatic that you can string the information together,” Wheaton says. “Part of our work is understanding the relationship between intent and action and how that falls apart in case of neurological injury.”

Using brain-imaging techniques, Wheaton identifies neural signals that capture intent.

Recently he conducted an experiment with people with sound limbs wearing artificial limbs. The participants were asked to learn how to use the prosthetic limbs by watching a video of another prosthetic-device user.

“The norm in prosthetic limb rehabilitation is to let people figure it out themselves, with help from physical therapists,” Wheaton says. “But most physical therapists have two hands. They don’t know what it’s like to be an amputee.”

The study showed that people who watched other prosthetic-device users became more efficient than those who watched people with sound limbs. 

Another tool is eye-tracking, based on the well-known correlation of eye and arm movements. “Particularly in tasks that involve reaching, the eyes precede the hand,” Wheaton says. Can we see intent from what the eyes are doing?

New research suggests that a key to rehabilitation gains might be rooted in visual strategies that capture specific action intent. The eyes see differently when observing different people do the same task, like bringing an object from one side of a barrier to the other side. When watching a person with sound limbs, the prosthetic-device user’s eyes look only at the task itself: The object starts on one side and ends on the other, Wheaton says.

When watching another prosthetic-device user, the subject’s eyes go over the barrier and are paying attention to the shoulders, which power the prosthetic limb. “They are paying attention to the motor intent instead of just the task,” Wheaton says. “Instead of training execution, which we do a lot in rehabilitation, perhaps we should be training intent.”

Back to golf, Wheaton suggests, “Its’ hard to understand the intent of a professional when you are an amateur, until you develop more skill. Instead of watching Rory, take a different approach. You may be more like Joe, who will help you progress to the next step. Then you’ll meet Mary, who’s a bit better than Joe. She’ll take you farther.”

When to Make a Decision: Accumulating and evaluating evidence

By A. Maureen Rouhi

What was your dinner last night? How about the previous night? How about the week before?

Mark E. Wheeler is interested in memories and what happens in the brain that allows us to remember. Part of what he studies is how we make decisions about the accuracy of what we retrieve. “You can’t remember immediately what you had for dinner a week before because you lack information,” he says. “If you think about it a bit more, you may remember. How can you evaluate the accuracy of your memory? What is happening in the brain when we decide whether our memories are accurate or not?”

Memory is difficult to study, however. “People are often not good at describing how they remember,” says Wheeler, a professor in the School of Psychology. “Some retrieved information may not be easy to communicate, people may ignore some memories, or they may be unaware of other memories.”

To get at memory, Wheeler studies perception, which is easier to manipulate and measure. The hope is that understanding how we evaluate evidence in making decisions based on perception can help us understand what happens when retrieving memories.

When viewed from the brain’s perspective, even simple tasks — such as deciding whether an object is green or yellow — consist of a sequence of processing stages, Wheeler says. These stages can be represented by different patterns of brain activity. “If we understand the process as a system,” Wheeler says, “then we can ask: What parts of this system are involved when things break down or don’t function well?” 

Central to Wheeler’s work is the concept of an accumulation-to-boundary mechanism. “In the midst of gathering evidence, you reach some threshold of evidence: Okay, now I’m going to decide,” Wheeler explains. “The idea is that brain activity that is thought to reflect evidence builds up, and when it crosses that threshold, that is the signal that you have enough information to commit to a decision. We don’t understand precisely how that works, which is why we’re studying it, but there’s a lot of data that this happens at the neural level.”

Instead of asking experimental subjects to remember what they had for dinner, Wheeler asks them to lie still while being scanned by a functional MRI (fMRI) machine at the Georgia State University/Georgia Tech Center for Advanced Brain Imaging. Amid the constant beeping of the scanner, participants receive visual stimuli and make decisions about what they see.

Brain activity data reveal how much evidence participants accumulate before they decide. The basis for this approach was developed a decade ago, when Wheeler and others showed that fMRI allows identification of distinct neural processes that work together when people make decisions based on perception.

Currently Wheeler is interested in how aging affects the way decision-making evidence accumulates and how that manifests in brain activity. His recent work, funded by the National Science Foundation and Georgia Tech, examines how noise — anything that degrades information — affects the accumulation of evidence and decision-making as we get older.

“Perception and decision-making,” Wheeler says, “can involve a series of stages, where you take in sensory information, analyze the information, and accumulate evidence, until you can make a decision. Suppose that aging affects the first stage most significantly, but the latter two are fine. You could target interventions more precisely, if you know where the problem lies.”

The experimental approach, Wheeler notes, can apply to other conditions, such as drug addiction or alcoholism. If one can deconstruct how the brain of an alcoholic takes in and processes information, it may be possible to develop better ways to train alcoholics to avoid that first drink.

Led by the Georgia Institute of Technology, the NSF Engineering Research Center for Cell Manufacturing Technologies (CMaT) could help revolutionize the treatment of cancer, heart disease, autoimmune diseases and other disorders by enabling broad use of potentially curative therapies that utilize living cells – such as immune cells and stem cells – as “drugs.” Examples of these highly promising therapies include T cell-based immunotherapies for blood cancers, such as the one developed at the University of Pennsylvania and approved in August by the U.S. Food & Drug Administration, and a gene-modified stem cell therapy recently approved in Europe for a form of the so-called “bubble boy” syndrome.

To facilitate the widespread application of these cutting-edge emerging treatments, CMaT will develop robust and scalable technologies, innovative analytical tools, and engineering systems that will enable industry and clinical facilities to reproducibly manufacture efficient, safe and affordable cell-therapy products. The center, one of four ERCs announced September 12 by the NSF, will also develop improved models for a robust supply chain, storage and distribution system for these therapeutic cell products.

“For over 30 years, NSF Engineering Research Centers have promoted innovation, helped to maintain our competitive edge, and added billions of dollars to the U.S. economy,” said NSF Director France Córdova. “They bring together talented innovators and entrepreneurs with resources from academia, industry and government to produce engineers and engineering systems that solve real-world problems.  I am confident that these new ERCs will strengthen U.S. competitiveness for the next generation and continue our legacy of improving the quality of life for all Americans.”

In addition to the consistent manufacture of  cell-based therapies, the public-private CMaT initiative will also help develop a skilled, diverse and inclusive bio-manufacturing workforce through extensive education and training activities at the K-12, technical college, undergraduate, graduate and postdoctoral levels.

Living cells become “drugs”

“Unlike pharmaceuticals and other products now used in medical treatments, cells are living entities whose properties can significantly change depending on nuances in the way they are grown, stored or otherwise manipulated,” said Krishnendu Roy, director of CMaT and the Robert A. Milton chair professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “The center will develop new engineering tools and scalable methods to better characterize, expand, differentiate, separate, transport and store high-quality cells so they provide consistent therapeutic effects, allowing them to be used in standardized therapies by clinicians to serve large numbers of patients worldwide.”

Beyond Georgia Tech, the center will include major partners – the University of Georgia, the University of Wisconsin-Madison and the University of Puerto Rico, Mayaguez Campus – as well as affiliate partners such as the University of Pennsylvania, Emory University, the Gladstone Institutes and Michigan Technological University. Additional international academic partners, as well as industry and the U.S. national laboratories, will also be critical collaborators in the effort.

Moving discoveries into application

“Georgia Tech has a long history of building collaborative partnerships with industry, the national labs and other research universities. With the support of the NSF and this new ERC, we will be able to capitalize on expertise in multiple areas, taking transformative research from the laboratory to practice much more quickly,” said Georgia Tech President G. P. “Bud” Peterson. “The Center for Cell Manufacturing Technologies will also help us educate, train and prepare the workforce in a new industry, thereby continuing to strengthen the U.S. economy.”

Clinical trials have already established the effectiveness of several cell-based therapies and many other trials are underway. But for these exciting therapies to advance into broad healthcare use, the cells will have to be produced in much larger quantities and with more consistent quality than is now available. There are also very few, if any, established industry standards for analytics and processes in cell manufacturing, which hinders consistent production of safe and efficacious cells. Another key limitation identified by industry is the need for a highly-trained workforce.

CMaT would address these barriers through transformative innovations that build upon a series of earlier efforts, including the National Cell Manufacturing Consortium (NCMC) roadmap, infrastructure established at Georgia Tech with support from the Marcus Foundation, quality and other standards programs from the National Institute of Standards and Technology (NIST) and independent industry-led bodies, and translational activities by industry, entrepreneurs and other partners.

The NSF’s multidisciplinary engineering research centers address unique, complex engineering challenges by stimulating knowledge and tech transfer between different sectors, from electronics to energy to infrastructure. Each center takes on a specific engineering research challenge.

“The overall goal of the NSF Engineering Research Centers program is nothing less than to revolutionize engineering research and education in the United States,” said Dawn Tilbury, NSF assistant director for engineering. “We look forward to the exciting advances and outcomes in these important areas.”

Accelerating clinical trials

Beyond established cell-based therapies, the work of CMaT should accelerate the development of new therapies and the testing needed to bring them into the clinic, said Steven Stice, director of the University of Georgia’s Regenerative Bioscience Center (RBC). Regenerative medicine applications could offer new ways of treating diseases for which there are now essentially no treatments, including Parkinson's, Alzheimer’s, heart disease and stroke.

“There are a significant number of cell therapy clinical trials and investments in the field,” Stice said. “But there is little or no investment in a set of consistent standardization methods to optimize how these therapies should work. For instance, we know that cell therapies will improve human health, but right now it’s difficult to guarantee that each dose produced will be as potent as the next. The work done by CMaT researchers will help solve some of these problems.”

The University of Pennsylvania develops cellular therapies and has conducted more than 40 clinical trials of cell-based therapies, including those for engineered T cell therapies and chimeric antigen receptor (CAR) T cells. An example is recently-approved treatment for relapsed and refractory acute lymphoblastic leukemia in pediatric and young adult patients.

“The cell and gene therapy fields are on the cusp of multiple regulatory approvals in the near term,” said Bruce Levine, Barbara and Edward Netter Professor in Cancer Gene Therapy in the Perelman School of Medicine at the University of Pennsylvania. “The challenges ahead lie in developing manufacturing and testing processes incorporating automation that can bring costs down and allow access to more patients.”

Developing broad-based innovations

Critical innovations often occur at the boundaries of disciplines, and CMaT will bring together relevant specialties for both research and workforce development, noted Madeline Torres-Lugo, a professor in the Department of Chemical Engineering at the University of Puerto Rico, Mayaguez Campus.

“Due to the complexity of cells as living organisms, a team with a strong background in biology, chemistry, physics, materials science, and engineering is required for this initiative,” Torres-Lugo said. “Our participation and contribution to CMaT will ensure that Puerto Rico not only remains at the forefront of pharma manufacturing, but also supports cell manufacturing technologies here and around the world by educating highly talented engineering students.”

CMaT testbeds have been selected to address several cell types that are in early stages of clinical adoption or moving toward clinical applications, but it isn't yet clear what cell types will have the greatest therapeutic impacts, noted Sean Palecek, the Milton J. and A. Maude Shoemaker Professor in chemical and biological engineering at the University of Wisconsin-Madison. Therefore, one of the center’s challenges will be to ensure that fundamental discoveries, and tool and technology development efforts, will apply to multiple cell types.

“Our work will provide safer and more potent cell products that will allow clinical studies to establish the effectiveness of these cells as therapeutics,” Palecek said. “In addition, our work on scaling cell production will enable manufacturing of sufficient numbers of cells to replace damaged organs, such as the loss of heart muscle after a heart attack, at a cost that makes these therapies accessible to broad segments of society. We will also train the future leaders of the emerging therapeutic cell manufacturing industry. These students and their work establishing this industry will be the most significant impact of CMaT.”

New centers among 19 ERCs

Since the program’s inception in 1985, NSF has funded a total of 74 ERCs and will support 19 in this fiscal year, including four new centers. Each center receives NSF funding for up to 10 years. During this time, centers build partnerships with industry, universities and other government agencies that will sustain them for years to come.

In May, the National Academies published a report, “A new vision for center-based engineering research,” which was the result of an NSF-funded study to examine the future of the NSF ERC program.

The report identifies and recommends strategies to enable NSF multidisciplinary engineering research centers to continue addressing key research, education and innovation needs of the United States in a changing global context.

“ERCs are widely known as outstanding examples of successful partnerships between universities, private industry and government that have made significant contributions to address national challenges,” said Don Millard, acting division director for the NSF Division of Engineering Education and Centers. “We are continually working with the scientific and engineering communities, as well as private industry and government partners, to ensure NSF-funded centers and grantees are best-equipped to match societal needs with research abilities.”

Research News

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Writer: John Toon

Headlines, of late, have touted the successes of targeted gene-based cancer therapies, such as immunotherapies, but, unfortunately, also their failures.

Broad inadequacies in a widespread biological concept that affects cancer research could be significantly deflecting the aim of such targeted drugs, according to a new study. A team exploring genetic mechanisms in cancer at the Georgia Institute of Technology has found evidence that a prevailing concept about how cells produce protein molecules, particularly when applied to cancer, could be erroneous as much as two-thirds of the time.

Prior studies by other researchers have also critiqued this concept about the pathway leading from genetic code to proteins, but this new study, led by cancer researcher John McDonald, has employed rare analytical technology to explore it in unparalleled detail. The study also turned up novel evidence for regulating mechanisms that could account for the prevailing concept’s apparent shortcomings.

RNA concept incomplete

The concept stems from common knowledge about the assembly line inside cells that produces protein molecules. It starts with code in DNA, which is transcribed to messenger RNA, then translated into protein molecules, the cell’s building blocks.

That model seems to have left the impression that cellular protein production works analogously to an old-style factory production line: That the amount of a messenger RNA encoded by DNA on the front end translates directly into the amount of a corresponding protein produced on the back end. That idea is at the core of how gene-based cancer drug developers choose their targets.

To put that assumed congruence between RNA production and protein production to the test, the researchers examined -- in ovarian cancer cells donated by a patient -- 4,436 genes, their subsequently transcribed messenger RNA, and the resulting proteins. The assumption, that proverbial factory orders passed down the DNA-RNA line determine in a straightforward manner the amount of a protein being produced, proved incorrect 62 percent of the time.

RNA skews drug cues

“The messenger RNA-protein connection is important because proteins are usually the targets of gene-based cancer therapies,” McDonald said. “And drug developers typically measure messenger RNA levels thinking they will tell them what the protein levels are.” But the significant variations in ratios of messenger RNA to protein that the researchers found make the common method of targeting proteins via RNA seem much less than optimal.

McDonald, Mengnan Zhang and Ronghu Wu published their results on August 15, 2017 in the journal Scientific Reports. The work was funded by the Ovarian Cancer Institute, The Deborah Nash Endowment, Atlanta’s Northside Hospital and the National Science Foundation. The spectrophotometric technology needed to closely identify a high number of proteins is not widespread and is quite costly but is available in Wu’s lab at Georgia Tech.

Whereas many studies look at normal tissue versus cancerous tissue, this new study focused on cancer progression, or metastasis, which is what usually makes cancer deadly. The researchers looked at primary tumor tissue and also metastatic tissue.

Hiding drug targets

“The idea that any change in RNA level in cancerous development flows all the way up to the protein level could be leading to drug targeting errors,” said McDonald, who heads Georgia Tech’s Integrated Cancer Research Center. Drug developers often look for oddly high messenger RNA levels in a cancer then go after what they believe must be the resulting oddly high levels of a corresponding protein.

Taking messenger RNA as a protein level indicator could actually work some of the time. In the McDonald team’s latest experiment, in 38 percent of the cases, the rise of RNA levels in cancerous cells did indeed reflect a comparable rise of protein levels. But in the rest of cases, they did not.

“So, there are going to be many instances where if you’re predicting what to give therapeutically to a patient based on RNA, your prescription could easily be incorrect,” McDonald said. “Drug developers could be aiming at targets that aren’t there and also not shooting for targets that are there.”

RNA muted or magnified

The analogy of a factory producing building materials can help illustrate what goes wrong in a cancerous cell, and also help describe the study’s new insights into protein production. To complete the metaphor: The materials produced are used in the construction of the factory’s own building, that is, the cell’s own structures.

In cancer cells, a mutation makes protein production go awry usually not by deforming proteins but by overproducing them. “A lot of mutations in cancer are mutations in production levels. The proteins are being overexpressed,” said McDonald, who is also a professor in Georgia Tech’s School of Biological Sciences.

A bad factory order can lead to the production of too much of a good material and then force it into the structures of the cell, distorting it. The question is: Where in the production line do bad factory orders appear?

According to the new study, the answer is less straightforward than previously thought.

Micro RNA managing

The orders don’t all appear on the front end of the assembly line with DNA over-transcribing messenger RNA. Additionally, some mutations that do over-transcribe messenger RNA on the front end are tamped down or canceled by regulating mechanisms further down the line, and may never end up boosting protein levels on the back end.

Regulating mechanisms also appear to be making other messenger RNA, transcribed in normal amounts, unexpectedly crank out inordinate levels of proteins.

At the heart of those regulating systems, another RNA called micro RNA may be micromanaging how much, or little, of a protein is actually produced in the end.

“We have evidence that micro RNAs may be responsible for the non-correlation between the proteins and the RNA, and that’s completely novel,” McDonald said. “It’s an emerging area of research.”

Micro RNA, or miRNA, is an extremely short strand of RNA.

No one at fault

McDonald would like to see tissues from more cancer patients undergo similar testing. “Right now, with just one patient, the data is limited, but I also really think it shows that the phenomenon is real,” McDonald said.

“Many past studies have looked at one particular protein and a particular gene, or a particular handful. We looked at more than 4,000,” McDonald said. “What that brings up is that the phenomenon is probably not isolated but instead genome-wide.”

The study’s authors would also like to see currently less accessible, advanced protein detecting technology become more widely available to biomolecular researchers, especially in the field of cancer drug development. “Targeted gene therapy is a good idea, but you need the full knowledge of whether it’s affecting the protein level,” McDonald said.

He pointed out that no one is at fault for the possible incompleteness of commonly held concepts about protein production.

As science progresses, it naturally illuminates new details, and formerly useful ideas need updating. With the existence of new technologies, it may be time to flesh out this particular concept for the sake of cancer research progress.

Also READ: Punching Cancer With RNA Knuckles – with John McDonald

The research was supported by grants from the Ovarian Cancer Institute, The Deborah Nash Endowment Fund, Northside Hospital (Atlanta), and the National Science Foundation (CHE-452 1454501). Cancer tissues from ovary and omental sites were collected from a cancer patient at Northside Hospital with informed consent under Georgia Institute of Technology Institutional Review Board protocols (H14337). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of those agencies.

Cancer cells kill most often by crawling away from their original tumors to later re-root in vital parts of the body in a process called metastasis. Now, a research team led by the Georgia Institute of Technology has developed a new treatment to thwart cancer's spread through the body by, in a sense, breaking cancer cells’ legs.

Cancer cells often cover themselves with bristly leg-like protrusions that enable them to creep. The researchers have used minuscule gold rods heated gently by a laser to mangle the protrusions, according to a new study. The treatment prevented cell migration, a key mechanism in metastasis, in experiments on common laboratory cultures (in vitro) of cancerous human cells.

The method could potentially, in the future, offer clinicians going after individual tumors a weapon to combat cancer’s deadly spread at the same time. The medical field is currently less than well-equipped to stop metastasis.

“If cancer stays in a tumor in one place, you can get to it, and it’s not so likely to kill the patient, but when it spreads around the body, that’s what really makes it deadly,” said lead researcher Mostafa El-Sayed, Julius Brown Chair and Regents Professor at Georgia Tech’s School of Chemistry and Biochemistry.

The treatment can also easily kill cancer cells, but in this experiment, it was vital to specifically show that it greatly slowed cell migration. The method is not scheduled for human testing.

Halting cancer softly

The experimental treatment also spared healthy cells, in these and in prior experiments, making the method potentially much less taxing on patients than commonly used chemotherapy. In past tests in animal models, the researchers have uncovered no toxic side effects from the gold used in the treatment, and have found no observable damage to healthy tissue from the low-energy laser.

And they did not see recurrence of the treated cancer.

“The method appears to be very effective as a locally administered treatment that also protects the body from cancer’s spread away from the treated tumors, and it is also very mild, so it can be applied many times over if needed,” El-Sayed said.

El-Sayed, co-lead author Ronghu Wu, and first authors Yue Wu and Moustafa Ali published the results of their current in vitro experiments, a new development in photothermal gold nanorod therapy, on June 26, 2017, in the Proceedings of the National Academy of Sciences. The research was funded by the National Science Foundation and the National Institutes of Health.

How it works: Icky legs

To understand how the treatment works, let’s take a close-up look at a cell and some things that happen to it in malignant cancer.

Many people think of cells as watery balloons -- fluid encased in a membrane sheath with organelles floating around inside. But that picture is incomplete. Cells have support grids called cytoskeletons that give them form and that have functions.

The cytoskeletons also form bristly protrusions called filopodia, which extend out from a weave of fibers called lamellipodia that are on the cell’s fringes. The protrusions normally help healthy cells shift their location in the tissue that they are part of.

But in malignant cancer, normally healthy cell functions often lunge into destructive overdrive. Lamellipodia and filopodia are wildly overproduced.

“All these lamellipodia and filopodia give the cancer cells legs,” said Yue Wu, a graduate student in bioanalytical chemistry. “The metastasis requires those protrusions, so the cells can travel.”

How it works: Sticky rods

The gold nanorods thwart the protrusions in two ways. The rods are comprised of a small collection of gold atoms – nano refers to something being just billionths of meters (or feet) in size.

First, El-Sayed’s nanorods are introduced locally, where they encumber the leggy protrusions on cancerous cells. The rods are coated with molecules (RGD-peptides) that make them stick specifically to a type of cell protein called integrin.

“The targeted nanorods tied up the integrin and blocked its functions, so it could not keep guiding the cytoskeleton to overproduce lamellipodia and filopodia,” said Yan Tang, a postdoctoral assistant in computational biology who worked on the study. The binding of the integrin alone slowed down the migration of malignant cells.

But healthy cells were not targeted. “There are certain, specific integrins that are overproduced in cancerous cells,” said Moustafa Ali, one of the study’s first authors. “And you don’t find them so much in healthy cells.”

How it works: Gentle laser heating

In the second phase, researchers hit the gold nanoparticles with a low-energy laser of near-infrared (NIR) light. It brought the migration of the cancer cells to an observable halt.

“The light was not absorbed by the cells, but the gold nanorods absorbed it, and as a result, they heated up and partially melted cancer cells they are connected with, mangling lamellipodia and filopodia,” Ali said. “It didn’t kill all the cells, not in this experiment. If we killed them, we would not have been able to observe whether we stopped them from migrating or not.”

If desired, the treatment can also be adjusted to kill the cells.

Early experiments in animal models in vivo with hotter lasers didn’t work as well.  “That caused inflammation, which made it possible to heat one time only,” Ali said. “As a result, that high temperature would wipe out many cancer cells, but not all of them. Some hidden ones might have survived, and also still been able to migrate.”

“This gentle laser didn’t burn the skin or damage tissue, so it could be dosed multiple times and more thoroughly stop the cancer cells from being able to travel,” said researcher Ronghu Wu.

Medical possibilities

The researchers presently envision treating head, neck, breast, and skin cancers with direct, local nanorod injections combined with the low-power near-infrared laser, which can hit the gold nanorods 2-3 centimeters (a bit under or over an inch) deep inside tissue. “But it could go as deep as 4-5 centimeters,” Ali said.

Deeper tumors could conceivably be treated with deeper injections of nanorods. “Then you’d need to go in with a fiber optic or endoscopic laser,” El-Sayed said. Injecting the nanorods directly into the bloodstream as a broad treatment would not currently be a viable option.

El-Sayed’s group has previously published in vivo experiments in mice in the Proceedings of the National Academy of Sciences together with Emory University School of Medicine. That study showed no observable toxicity from the gold in mice 15 months after treatment.

“A lot of it ended up in the liver and spleen,” El-Sayed said. “But the functions of these organs appeared intact upon examination, and treated mice were alive and healthy over a year later.”

Presidential honors

Mostafa El-Sayed is one of the world’s most highly decorated and cited living chemists, and a pioneer of nanoscience and technology. Among his many recognitions are the President’s National Medal of Science, awarded by President George W. Bush, and the Priestley Medal, the American Chemical Society’s highest honor. President Barack H. Obama appointed El-Sayed to the President’s National Medal of Science Committee. El-Sayed also participated in the nomination of chemistry Nobel Laureate Ahmed Zewail.

El-Sayed is known throughout physical chemistry for “El-Sayed’s Rule,” which handles complexities of electron spin orbits, and which has found a lasting place in photochemistry textbooks. After losing his wife to cancer in 2005, El-Sayed dedicated his knowledge and research to ending the scourge.

Also read: Cancer and Technology

Also read: Punching Cancer with RNA Knuckles

The following authors also contributed to this research: Haopeng Xiao and Tiegang Han from Georgia Tech, and Kuangcai Chen and Ning Fang from Georgia State University. This research was funded by the National Science Foundation Division of Chemistry (grants 1608801, CAREER Award CHE-1454501), and the National Institutes of Health Nanotechnology Study Section (grant 1R01GM115763). Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.

With a novel targeted therapy researchers at the Georgia Institute of Technology have purged ovarian tumors in limited, in vivo tests in mice. “The dramatic effect we see is the massive reduction or complete eradication of the tumor, when the ‘nanohydrogel’ treatment is given in combination with existing chemotherapy,” said chief researcher John McDonald.

That nanohydrogel, a type of nanoparticle, is a minute gel pellet that honed in on malignant cells with a payload of an RNA strand. The RNA entered the cell, where it knocked down a protein gone awry that is involved in many forms of cancer.

In trials on mice, it put the brakes on ovarian cancer growth and broke down resistance to chemotherapy. That allowed a common chemotherapy drug, cisplatin, to drastically reduce or eliminate large carcinomas, with very similar speed and manner. The successful results treating four mice with the combination of siRNA and cisplatin showed little variance.

Chink in the armor

The therapeutic short interfering RNA (siRNA) developed by McDonald and Georgia Tech researchers Minati Satpathy and Roman Mezencev, thwarted cancer-causing overproduction of cell structures called epidermal growth factor receptors (EGFRs), which extend out of the wall of certain cell types. EGFR overproduction is associated with aggressive cancers.

The researchers from Georgia Tech’s School of Biological Sciences published their results on Monday, November 7, 2016, in the journal Scientific Reports. Research was funded by the National Institutes of Health’s IMAT Program, the Ovarian Cancer Institute, the Deborah Nash Endowment Fund, the Curci Foundation and the Markel Foundation.

The new treatment has not been tested on humans, and research would be required by science and by law to demonstrate consistent results – efficacy – among other things, before preliminary human trials could become possible.

The current in vivo success strengthens the idea that knocking out EGFR at the RNA level may be a worthy goal to explore in the fight against carcinomas in general. The same patented nanohydrogel packed with other types of therapeutic RNA is currently being tested for the treatment of other types cancers.

Helper turned killer

EGFRs are receptors found in epithelial cells, which line organs throughout the body: Lungs, mouth, throat, intestines and others. In women, it also lines reproductive organs: Ovaries, uterus and cervix.

They are long proteins that poke through the cell membrane, connecting the cell’s interior with the outside. They look like squiggly worms with tiny mouths on the outside that take up a messenger protein.

In a healthy cell, those messenger molecules cause EGFRs to trigger long chains of biochemical reactions that lead to the activation of genes involved in a variety of cellular functions. In carcinoma cells, the number of EGFRs present typically skyrockets.

“In many cancers, EGFR is overexpressed,” said McDonald, who heads Georgia Tech's Integrated Cancer Research Center. “The problem is that because of this overexpression, many cellular functions, including cell replication and resistance to certain chemotherapy drugs, are dramatically cranked up.”

The cell goes haywire, metabolizes too much sugar, divides too much, and resists chemotherapy. The cancer grows into a tumor and can spread through the body.

An overabundance of EGFRs found in a biopsy is usually a sign that cancer patient prognosis is poor. “In 70 percent of ovarian cancer patients, EGFR is overexpressed at very high levels,” McDonald said.

Cell suicide: apoptosis

EGFR overexpression also makes cancer cells resistant to chemotherapy by thwarting a natural defense mechanism.

“The platinum-based chemotherapies used to treat ovarian cancers cause DNA damage, which switches on apoptosis,” McDonald said. Apoptosis is cell suicide. When cells can’t repair DNA damage, they’re programmed to kill themselves to keep the damaged cells from spreading.

The primary chemotherapy used to treat ovarian cancer works by coaxing cancer cells to trigger the suicide program, but having too many epidermal growth factor receptors gets in the way.

“EGFR overexpression hinders apoptosis; they won’t die. By knocking down EGFR, we make the cell hypersensitive to the drug. Apoptosis is reactivated,” McDonald said.

Existing EGFR targeted drugs called tyrosine-kinase inhibitors disrupt an EGFR function, but their success in treating ovarian cancer has been limited. “Clinicians have tried EGFR inhibitors to treat ovarian cancers for some years, and they only get about 20% of patients responding to it,” McDonald said. “Apparently, the particular EGFR function inhibited by these drugs is not critical to ovarian cancer.”

Guided brass knuckles

The short interfering (si) RNA designed by the Georgia Tech researchers attacks the cancer much closer to its root.

To make the protein for EGFR, RNA has to transfer its genetic code from DNA. The researchers’ siRNA binds to the cell’s RNA and stops it from working.

“We’re knocking down EGFR at the RNA level,” he said. “Since EGFR is multi-functional, it’s not exactly clear which malfunctions contribute to ovarian cancer growth. By completely knocking out its production in ovarian cancer cells, all EGFR functions are blocked.”

The nanohydrogel that delivers the siRNA to the cancer cells is a colloid ball of a common, compact organic molecule and about 98 percent water. Another molecule is added to the surface of the nanohydrogel as a guide. It makes the pellets adhere to the cancer cells like sticky cluster bombs.

Cancerous tissue may also be aiding the nanohydrogel in targeting it. “When you get into a tumor, there are a lot of blood vessels, and many are broken,” McDonald said. “This may help the nanoparticles get passively trapped in the neighborhood of tumorous tissues.”

In the in vivo trials, the siRNA, which contained a fluorescent tag, allowed researchers to observe nanoparticles successfully honing in on the cancer cells.

Fortuitous victory

“We originally selected to target the EGFR gene because its activity is easily measured, and we wanted to use it simply as an indicator that our nanoparticle siRNA delivery system was working,” McDonald said. “The fact that the EGFR knockdown so dramatically sensitized the cells to standard chemotherapy came as a bit of a surprise.”

At first, his team observed how the tumors responded to chemotherapy alone. Then they combined it with the nanoparticle treatment.

“When we gave the chemotherapy alone, the response was moderate, but with the addition of the nanoparticles, the tumor was either significantly reduced or completely gone,” McDonald said.

But he tempered enthusiasm with caution. “Further work will be required to see if the treatment completely destroyed every trace of cancer cells in the tumors that disappeared, or if future recurrence is possible.”

If the researchers’ continuing studies further prove to be consistent, the combination of the nanohydrogel with other therapeutic RNAs could represent a significant advancement in the treatment of a wide spectrum of cancers.

Georgia Tech’s Lijuan Wang and Dr. Benedict Benigno from Atlanta’s Northside Hospital coauthored the paper. Research was funded by the National Institutes of Health’s Program for Innovative Molecular Analysis Technologies Program (grant 1R21CA155479-01), the Ovarian Cancer Institute at Northside Hospital, the Deborah Nash Endowment Fund, the Curci Foundation, and the Markel Foundation. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsoring agencies.

Radiation and chemotherapy can cause a DNA double-strand break, one of the most harmful types of DNA damage. The process of homologous recombination — which involves the exchange of genetic information between two DNA molecules — plays an important role in DNA repair, but certain gene mutations can destabilize a genome. For example, mutations in the tumor suppressor BRCA2, which is involved in DNA repair by homologous recombination, can cause the deadliest form of breast and ovarian cancer. 

Alexander Mazin, a professor at Drexel University’s College of Medicine, and Francesca Storici, an associate professor at Georgia Tech’s School of Biological Sciences, have dedicated their research to studying mechanisms and proteins that promote DNA repair. 

In 2014, Storici and Mazin made a major breakthrough when they discovered that RNA can serve as a template for the repair of a DNA double-strand break in budding yeast, and Rad52, a member of the homologous recombination pathway, is an important player in that process. 

“We provided evidence that RNA can be used as a donor template to repair DNA and that the protein Rad52 is involved in the process,” said Mazin. “But we did not know exactly how the protein is involved.”

In their current study, the research team uncovered the unusual, important role of Rad52: It promotes “inverse strand exchange” between double-stranded DNA and RNA, meaning that the protein has a novel ability to bring together homologous DNA and RNA molecules. In this RNA-DNA hybrid, RNA can then be used as a template for accurate DNA repair. 

It appeared that this ability of Rad52 is unique in eukaryotes, as otherwise similar proteins do not possess it. 

“Strikingly, such inverse strand exchange activity of Rad52 with RNA does not require extensive processing of the broken DNA ends, suggesting that RNA-templated repair could be a relatively fast mechanism to seal breaks in DNA,” Storici said. 

As a next step, the researchers hope to explore the role of Rad52 in human cells. 

“DNA breaks play a role in many degenerative diseases of humans, including cancer,” Storici added. “We need to understand how cells keep their genomes stable. These findings help bring us closer to a detailed understanding of the complex DNA repair mechanisms.”

The research was supported by the National Institutes of Health, the National Science Foundation and the Howard Hughes Medical Institute.

These results offer a new perspective on the multifaceted relationship between RNA, DNA and genome stability. They also may help to identify new therapeutic targets for cancer treatment. It is known that active Rad52 is required for proliferation of BRCA-deficient breast cancer cells. Targeting this protein with small molecule inhibitors is a promising anticancer strategy.  However, the critical activity of Rad52 required for cancer proliferation is currently unknown.

This new Rad52 activity in DNA repair, discovered by Mazin, Storici and their team, may represent this critical protein activity that can be targeted with inhibitors to develop more specific — and less toxic — anti-cancer drugs. Understanding of the mechanisms of RNA-directed DNA repair may also lead to development of new RNA-based mechanisms of genome engineering. 

This research was supported by the National Institute of General Medical Sciences (NIGMS) of the NIH (grant GM115927), the National Science Foundation (grant 1615335), and the Howard Hughes Medical Institute Faculty Scholar Program (grant 55108574). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

Written by Drexel University.

CITATION: Olga M. Mazina, Havva Keskin, Kritika Hanamshet, Francesca Storici,
Alexander V. Mazin, “Rad52 Inverse Strand Exchange Drives RNA Templated
DNA Double-Strand Break Repair,” (Molecular Cell, 2017). http://dx.doi.org/10.1016/j.molcel.2017.05.019

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Over the past decade, new and emerging cell-based medical technologies have been developed to manage and possibly cure many conditions and diseases. In 2012 alone, these technologies treated more than 160,000 patients. Before these treatments can be more widely available, however, the cell therapeutics community will have to develop the capability for advanced, large-scale manufacturing of high-quality and consistent living cells.

To advance that goal, the Georgia Research Alliance (GRA) and the Georgia Institute of Technology (Georgia Tech) have launched the National Cell Manufacturing Consortium (NCMC), an industry-academic-government partnership that recently released the National Roadmap for Advanced Cell Manufacturing. Establishment of the consortium and development of this 10-year national roadmap was sponsored by the National Institute of Standards and Technology (NIST).

The roadmap was announced June 13 at the White House Organ Summit.

“The cell manufacturing roadmap effort is mission critical to establish the United States as the world leader in cell therapy manufacturing,” said Greg Russotti, Ph.D., vice-president of technical operations for Celgene Cellular Therapeutics. “Cell therapies offer exciting next-generation opportunities that may help patients live longer and better lives, reduce the burden on health care and benefit society. Producing sufficient quantities of high quality cell therapies so that patients have access will not be possible without significant advances in the field of cell therapy manufacturing. Industrial, academic, and government stakeholders collaborated to construct this roadmap, which delineates our path to U.S. leadership in the emerging field of cell therapy production.”

Development of the roadmap required strong support and involvement from more than 60 representatives from industry, government and nonprofit organizations.

“MilliporeSigma (formerly EMD Millipore) supports consortia, like the National Cell Manufacturing Consortium, that bring together industry, innovators, clinicians and academics to advance the field of cell therapy,” said Martha S. Rook, Ph.D., head of novel therapies for the company. “The consortium’s cell manufacturing roadmap is a valuable resource to help identify and address challenges in cell manufacturing.”

While research has demonstrated the value of cell therapies – using adult stem cells and immune system cells – improvements are needed to make these cells broadly available to the medical community.

“The aspirin you buy today from one pharmacy is essentially the same as the aspirin you buy from another pharmacy, but cell-based therapies may have different efficacy depending on the source and manufacturing processes,” said Krishnendu Roy, Robert A. Milton Chair and professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “There are established ways to quickly assess the efficacy and safety of small-molecule drugs that are acceptable around the world. We want to develop and establish similar processes for therapeutic cell manufacturing.”

Established in 2014 through a NIST Advanced Manufacturing Technology (AMTech) grant, the NCMC is an industry-driven consortium including cell manufacturing experts from industry, academic research, clinical good manufacturing practice (GMP) centers, government agencies and private foundations.

Georgia is positioning itself to be at the forefront of this new and growing market with its research institutions playing a vital role in the consortium. Researchers from Emory University, Georgia Tech, and the University of Georgia are contributing to the ongoing work of the NCMC. The Atlanta-based Marcus Foundation recently made a major gift to Georgia Tech to establish the Marcus Center for Therapeutic Cell Characterization and Manufacturing (MC3M). The new center, the first of its kind in the United States, will develop processes and techniques for ensuring the consistent, low-cost, large-scale manufacture of high-quality living cells used in cell-based therapies.

“The NIST grant kick-started our efforts to develop a national roadmap for cell manufacturing” said Michael Cassidy, president and CEO of the Georgia Research Alliance. “The cell manufacturing industry is an emerging and growing industry with annual revenues of over $1 billion. Completion of this roadmap positions Georgia at the forefront of one of the most exciting new initiatives of this century.”

For more information on the National Cell Manufacturing Consortium and to view the roadmap, visit http://cellmanufacturingusa.org.

About Georgia Research Alliance
The Georgia Research Alliance (GRA) works to expand research and commercialization capacity in Georgia’s universities to recruit world-class talent, seed new companies and transform lives. For over twenty-five years, GRA has worked to strengthen the university research enterprise in Georgia by working in partnership with the University System of Georgia and the Georgia Department of Economic Development to create the companies and jobs of Georgia’s future. Visit www.gra.org for more information.

About Georgia Institute of Technology
The Georgia Institute of Technology is widely regarded as one of the world’s top technological research universities. Ranked 7th among public universities by U.S. News & World Report, Georgia Tech has more than 25,000 undergraduate and graduate students, and conduced $726 million in research during 2014. Visit www.gatech.edu for more information.

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If the miRNA molecules can be delivered to cells in the human body – potentially with nanoparticles – the technique might one day be used to battle the chemotherapy resistance that often develops during cancer treatment. A research team at the Georgia Institute of Technology identified the miRNA used in the research with a computer algorithm that compared the ability of different miRNAs to control the more than 500 genes that were up-regulated in drug-resistant cancer cells.

The study was reported May 27 in the Nature Publishing Group journal Cancer Gene Therapy.

“We were specifically interested in what role miRNAs might play in developing drug resistance in these cancer cells,” said John McDonald, a professor in Georgia Tech’s School of Biology and director of its Integrated Cancer Research Center. “By increasing the levels of the miRNA governing the suite of genes we identified, we increased the cells’ drug sensitivity back to what the baseline had been, essentially undoing the resistance. This would suggest that for patients developing chemotherapy resistance, we might one day be able to use miRNAs to restore the sensitivity of the cancer cells to the drugs.”

MicroRNAs are small non-coding molecules that function in RNA silencing and post-transcriptional regulation of gene expression. The miRNAs operate via base-pairing with complementary sequences within messenger RNA (mRNA) molecules, silencing the mRNA molecules that control the expression of certain proteins.

Roman Mezencev, a senior research scientist in the McDonald lab, began by exposing a line of pancreatic cancer cells (BxPC3) to increasing levels of the chemotherapy drug cisplatin. After each in vitro treatment, surviving cells were allowed to proliferate before being exposed to a higher level of the drug. After approximately a year and 20 treatment cycles, the resulting cell line had a resistance to cisplatin that was 15 times greater than that of the original cancer cells.

The next step was to study the genetic changes associated with the resistance, comparing levels of more than 2,000 miRNAs in the cisplatin-resistant line to the original cell line that had not been exposed to the drug. Using a hidden Markov model (HMM) algorithm, they found 57 miRNAs that were either up-regulated or down-regulated, and identified miR-374b as the molecule most likely to be controlling the genes that govern chemotherapy resistance.

While previous work by other researchers has shown that miRNAs can provide a mechanism for the development of drug resistance, the Georgia Tech team took the findings a step farther by increasing the expression of miR-374b. When they did, they found that the cells previously resistant to the cisplatin were again sensitive to the drug – almost back to their original levels.

Techniques to control protein expression are already being used in cancer therapy, but McDonald believes there may be benefits in targeting the activity higher up in the process – at the RNA level. Studies by the Georgia Tech team and by other researchers clearly show an association between chemotherapy resistance and changes in levels of certain miRNAs.

“Molecular evolution is a highly efficient process,” McDonald said. “Our evidence suggests that many of the genes regulated by a single microRNA are involved in coordinated cellular functions – in this case, drug resistance. We believe that microRNAs might be particularly good cancer therapeutic agents because when we manipulate them, we are manipulating suites of functionally coordinated genes.”

A next step will be to study the effects of manipulating miRNA levels in animal cancer models. The McDonald research team is currently pursuing this possibility by inserting the microRNAs into tumors using nanoscale hydrogels developed by Andrew Lyon, former chair of Georgia Tech’s School of Chemistry and Biochemistry.

McDonald says the study confirms the role of miR-374b in creating resistance, though he says there could be other microRNA molecules involved, as well.

“These cells have acquired resistance to the drug, and we have found a microRNA that seems to be playing a major role,” he said. “We have shown that we can bring sensitivity to drugs back by restoring levels of miR374b, but there may be other miRNAs that will work equally as well. Just as there are multiple pathways to establish cancer and chemoresistance, there may be multiple pathways to restore chemosensitivity, as well.”

If cancer could one day be treated using miRNAs, it’s likely to be a continuing battle rather than a decisive victory, McDonald said. Cancer cells are very resourceful, and will likely find a new genetic route to resistance if one pathway is destroyed. That could require use of a different miRNA to reverse resistance.

While the miRNA research isn’t likely to provide a “magic bullet” for cancer, it does show the possible role of these tiny RNA molecules in controlling a broad class of bodily processes.

“There is growing evidence that this class of small regulatory RNAs may be involved in many processes ranging from evolution to heart disease,” he said. “MiRNAs are emerging as important players in cancer in general. Here, we are focusing on just one particular aspect of it.”

In addition to those already mentioned, the research team included R. Schreiber and L.V. Matyunina, both from Georgia Tech. In addition Schreiber is affiliated with the Faculdade de Ciências Médicas – UNICAMP in Brazil. The work was supported by funds from the Deborah Nash Endowment and the Mark Light Fellowship.

CITATION: R. Schreiber, et al., “Evidence for the role of microRNA 374b in acquired cisplatin resistance in pancreatic cancer cells,” (Cancer Gene Therapy, 2016). http://dx.doi.org/10.1038/cgt.2016.23

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Researchers at the Georgia Institute of Technology used high-throughput screening techniques to study the effects of titanium dioxide nanoparticles on the expression of 84 genes related to cellular oxidative stress. Their work found that six genes, four of them from a single gene family, were affected by a 24-hour exposure to the nanoparticles.

The effect was seen in two different kinds of cells exposed to the nanoparticles: human HeLa cancer cells commonly used in research, and a line of monkey kidney cells. Polystyrene nanoparticles similar in size and surface electrical charge to the titanium dioxide nanoparticles did not produce a similar effect on gene expression.

“This is important because every standard measure of cell health shows that cells are not affected by these titanium dioxide nanoparticles,” said Christine Payne, an associate professor in Georgia Tech’s School of Chemistry and Biochemistry. “Our results show that there is a more subtle change in oxidative stress that could be damaging to cells or lead to long-term changes. This suggests that other nanoparticles should be screened for similar low-level effects.”

The research was reported online May 6 in the Journal of Physical Chemistry C. The work was supported by the National Institutes of Health (NIH) through the HERCULES Center at Emory University, and by a Vasser Woolley Fellowship.

Titanium dioxide nanoparticles help make powdered donuts white, protect skin from the sun’s rays and reflect light in painted surfaces. In concentrations commonly used, they are considered non-toxic, though several other studies have raised concern about potential effects on gene expression that may not directly impact the short-term health of cells.

To determine whether the nanoparticles could affect genes involved in managing oxidative stress in cells, Payne and colleague Melissa Kemp – an associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University – designed a study to broadly evaluate the nanoparticle’s impact on the two cell lines.

Working with graduate students Sabiha Runa and Dipesh Khanal, they separately incubated HeLa cells and monkey kidney cells with titanium oxide at levels 100 times less than the minimum concentration known to initiate effects on cell health. After incubating the cells for 24 hours with the TiO₂, the cells were lysed and their contents analyzed using both PCR and Western Blot techniques to study the expression of 84 genes associated with the cells’ ability to address oxidative processes.

Payne and Kemp were surprised to find changes in the expression of six genes, including four from the peroxiredoxin family of enzymes that helps cells degrade hydrogen peroxide, a byproduct of cellular oxidation processes. Too much hydrogen peroxide can create oxidative stress which can damage DNA and other molecules.

The effect measured was significant – changes of about 50 percent in enzyme expression compared to cells that had not been incubated with nanoparticles. The tests were conducted in triplicate and produced similar results each time.

“One thing that was really surprising was that this whole family of proteins was affected, though some were up-regulated and some were down-regulated,” Kemp said. “These were all related proteins, so the question is why they would respond differently to the presence of the nanoparticles.”

The researchers aren’t sure how the nanoparticles bind with the cells, but they suspect it may involve the protein corona that surrounds the particles. The corona is made up of serum proteins that normally serve as food for the cells, but adsorb to the nanoparticles in the culture medium. The corona proteins have a protective effect on the cells, but may also serve as a way for the nanoparticles to bind to cell receptors.

Titanium dioxide is well known for its photo-catalytic effects under ultraviolet light, but the researchers don’t think that’s in play here because their culturing was done in ambient light – or in the dark. The individual nanoparticles had diameters of about 21 nanometers, but in cell culture formed much larger aggregates.

In future work, Payne and Kemp hope to learn more about the interaction, including where the enzyme-producing proteins are located in the cells. For that, they may use HyPer-Tau, a reporter protein they developed to track the location of hydrogen peroxide within cells.

The research suggests a re-evaluation may be necessary for other nanoparticles that could create subtle effects even though they’ve been deemed safe.

“Earlier work had suggested that nanoparticles can lead to oxidative stress, but nobody had really looked at this level and at so many different proteins at the same time,” Payne said. “Our research looked at such low concentrations that it does raise questions about what else might be affected. We looked specifically at oxidative stress, but there may be other genes that are affected, too.”

Those subtle differences may matter when they’re added to other factors.

“Oxidative stress is implicated in all kinds of inflammatory and immune responses,” Kemp noted. “While the titanium dioxide alone may just be modulating the expression levels of this family of proteins, if that is happening at the same time you have other types of oxidative stress for different reasons, then you may have a cumulative effect.”

Seed funding for the research came from the HERCULES: Exposome Research Center (NIEHS: P30 ES019776) at the Rollins School of Public Health, Emory University, NIH grant DP2OD006483-01 and a Vasser Woolley Faculty Fellowship. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

CITATION: Sabiha Runa, Dipesh Khanal, Melissa L. Kemp, Christine K. Payne, “TiO2 Nanoparticles Alter the Expression of Peroxiredoxin Anti-Oxidant Genes,” (Journal of Physical Chemistry C, 2016). http://dx.doi.org/10.1021/acs.jpcc.6b01939.

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Writer: John Toon

The technique uses a simple circuit pattern with just three electrodes to assign a unique seven-bit digital identification number to each cell passing through the channels on the microfluidic chip. The new technique also captures information about the sizes of the cells, and how fast they are moving. That identification and information could allow automated counting and analysis of the cells being sorted.

The research, reported in the journal Lab on a Chip, could provide the electronic intelligence that might one day allow inexpensive labs on a chip to conduct sophisticated medical testing outside the confines of hospitals and clinics. The technology can track cells with better than 90 percent accuracy in a four-channel chip.

“We are digitizing information about the sorting done on a microfluidic chip,” explained Fatih Sarioglu, an assistant professor in Georgia Tech’s School of Electrical and Computer Engineering. “By combining microfluidics, electronics and telecommunications principles, we believe this will help address a significant challenge on the output side of lab-on-a-chip technology.”

Microfluidic chips use the unique biophysical or biochemical properties of cells and viruses to separate them. For instance, antigens can be used to select bacteria or cancer cells and route them into separate channels. But to obtain information about the results of the sorting, those cells must now be counted using optical methods.

The new technique, dubbed microfluidic CODES, adds a grid of micron-scale electrical circuitry beneath the microfluidic chip. Current flowing through the circuitry creates an electrical field in the microfluidic channels above the grid. When a cell passes through one of the microfluidic channels, it creates an impedance change in the circuitry that signals the cell’s passage and provides information about the cell’s location, size and the speed at which it is moving through the channel.

This impedance change has been used for many years to detect the presence of cells in a fluid, and is the basis for the Coulter Counter which allowed blood counts to be done quickly and reliably. But the microfluidic CODES technique goes beyond counting.

The positive and negative charges from the intermingled electrical circuits create a unique identifying digital signal as each cell passes by, and that sequence of ones and zeroes is attached to information about the impedance change. The unique identifying signals from multiple cells can be separated and read by a computer, allowing scientists to track not only the properties of the cells, but also how many cells have passed through each channel.

“By judiciously aligning the grid pattern, we can generate the codes at the locations we choose when the cells pass by,” Sarioglu explained. “By measuring the current conduction in the whole system, we can identify when a cell passes by each location.”

Because the cells sorted into each channel of a microfluidic chip have certain characteristics in common, the technique would allow the automated detection of cancer cells, bacteria or even viruses in a fluid sample. Sarioglu and his students have demonstrated that they can track more than a thousand ovarian cancer cells with an accuracy rate of better than 90 percent.

The underlying principle for the cell identification is called code division multiple access (CDMA), and it’s essential for helping cellular networks separate the signals from each user. The microfluidic channels are fabricated from a plastic material using soft lithographic techniques. The electrical pattern is fabricated separately on a glass substrate, then aligned with the plastic chip

“We have created an electronic sensor without any active components,” Sarioglu said. “It’s just a layer of metal, cleverly patterned. The cells and the metallic layer work together to generate digital signals in the same way that cellular telephone networks keep track of each caller’s identity. We are creating the equivalent of a cellphone network on a microfluidic chip.”

The next step in the research will be to combine the electronic sensor with a microfluidic chip able to actively sort cells. Beyond cancer cells, bacteria and viruses, such a system could also sort and analyze inorganic particles.

The computing requirements of the system would be minimal, requiring no more than the processor power of smartphones that already handle decoding of CDMA signals. The proof-of-principle device contains just four channels, but Sarioglu believes the design could easily be scaled up to include many more channels.

“This is like putting a USB port on a microfluidic chip,” he explained. “Our technique could turn all of the microfluidic manipulations that are happening on the chip into quantitative data related to diagnostic measurements.

Ultimately, the researchers hope to create inexpensive chips that could be used for sophisticated diagnostic testing in physician offices or remote locations. Chips might be contained on cartridges that would automate the testing process.

“It will be very exciting to scale this up, and I think that will open up the possibility for many different assays to become accessible electronically,” Sarioglu said. “Decentralizing health care is an important trend, and our technology might one day allow many kinds of diagnostic tests to be done beyond hospitals and large medical facilities.”

Other co-authors of the paper included Ruxiu Liu, Ningquan Wang, and Farhan Kamili, all Georgia Tech graduate students.

CITATION: Ruxiu Liu, Ningquan Wang, Farhan Kamili and A. Fatih Sarioglu, “Microfluidic CODES: a scalable multiplexed electronic sensor for orthogonal detection of particles in microfluidic channels,” (Lab on a Chip, 2016). http://dx.doi.org/10.1039/c6lc00209a

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The research uses DNA strand displacement, a technology that has been widely used outside of cells for the design of molecular circuits, motors and sensors. Researchers modified the process to provide both “AND” and “OR” logic gates able to operate inside the living cells and interact with native messenger RNA (mRNA).

The tools they developed could provide a foundation for bio-computers able to sense, analyze and modulate molecular information at the cellular level. Supported by the Defense Advanced Research Projects Agency (DARPA) and the National Science Foundation (NSF), the research was reported December 21 in the journal Nature Nanotechnology.

“The whole idea is to be able to take the logic that is used in computers and port that logic into cells themselves,” said Philip Santangelo, an associate professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “These devices could sense an aberrant RNA, for instance, and then shut down cellular translation or induce cell death.”

Strand displacement reactions are the biological equivalent of the switches or gates that form the foundation for silicon-based computing. They can be programmed to turn on or off in response to an external stimuli such as a molecule. An “AND” gate, for example, would switch when both conditions were met, while an “OR” gate would switch when either condition was met.

In the switches the researchers used, a fluorophore reporter molecule and its complementary quenching molecule were placed side-by-side to create an “off” mode. Binding of RNA in one of the strands then displaced a portion of nucleic acid, separating the molecules and allowing generation of a signal that created an “on” mode. Two “on” modes on adjacent nucleic acid strands created an “AND” gate.

“Demonstrating individual logic gates is only a first step,” said Georg Seelig, assistant professor of computer science and engineering and electrical engineering at the University of Washington. “In the longer term, we want to expand this technology to create circuits with many inputs, such as those we have constructed in cell-free settings.”

The researchers used ligands designed to bind to specific portions of the nucleic acid strands, which can be created as desired and produced by commercial suppliers.

“We sensed molecules and showed that we could respond to them,” said Santangelo. “We showed that we could utilize native molecules in the cell as part of the circuit, though we haven’t been able to control a cell yet.”

Getting basic computing operations to function inside cells was no easy task, and the research required a number of years to accomplish. Among the challenges were getting the devices into the cells without triggering the switches, providing operation rapid enough to be useful, and not killing the human cell lines that researchers used in the lab.

“We had to chemically change the probes to get them to work inside the cell and to make them stable enough inside the cells,” said Santangelo. “We found that these strand displacement reactions can be slow within the cytosol, so to get them to work faster, we built scaffolding onto the messenger RNA that allowed us to amplify the effects.”

The nucleic acid computers ultimately operated as desired, and the next step is to use their switching to trigger the production of signaling chemicals that would prompt the desired reaction from the cells. Cellular activity is normally controlled by the production of proteins, so the nucleic acid switches will have to be given the ability to produce enough signaling molecules to induce a change.

“We need to generate enough of whatever final signal is needed to get the cell to react,” Santangelo explained. “There are amplification methods used in strand displacement technology, but none of them have been used so far in living cells.”

Even without that final step, the researchers feel they’ve built a foundation that can be used to attain the goal.

“We were able to design some of the basic logical constructs that could be used as building blocks for future work,” Santangelo said. “We know the concentrations of chemicals and the design requirements for individual components, so we can now start putting together a more complicated set of circuits and components.”

Cells, of course, already know how to sense toxic molecules and the development malignant tendencies, and to then take action. But those safeguards can be turned off by viruses or cancer cells that know how to circumvent natural cellular processes.

“Our mechanism would just give cells a hand at doing this,” Santangelo said. “The idea is to add to the existing machinery to give the cells enhanced capabilities.”

Applying an engineering approach to the biological world sets this example apart from other efforts to control cellular machinery.

“What makes DNA strand displacement circuits unique is that all components are fully rationally designed at the level of the DNA sequence,” said Seelig. “This really makes this technology ideal for an engineering approach. In contrast, many other approaches to controlling the cellular machinery rely on components that are borrowed from biology and are not fully understood.”

Beyond those already mentioned, the research team included Benjamin Groves, Yuan-Jyue Chen and Sergii Pochekailov from the University of Washington and Chiara Zurla and Jonathan Kirschman from Georgia Tech and Emory University.

This material is based on work supported by the Defense Advanced Research Projects Agency (DARPA) under contract W911NF-11-2-0068 and by National Science Foundation CAREER award 1253691. The content is solely the responsibility of the authors and does not necessarily represent the official views of DARPA or the NSF.

CITATION: Benjamin Groves, et al., “Computing in mammalian cells with nucleic acid strand exchange,” (Nature Nanotechnology, 2015). http://dx.doi.org/10.1038/nnano.2015.278

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Using advanced liquid chromatography and mass spectrometry techniques coupled with machine learning computer algorithms, researchers have identified 16 metabolite compounds that provided unprecedented accuracy in distinguishing 46 women with early-stage ovarian cancer from a control group of 49 women who did not have the disease. Blood samples for the study were collected from a broad geographic area – Canada, Philadelphia and Atlanta.

While the set of biomarkers reported in this study are the most accurate reported thus far for early-stage ovarian cancer, more extensive testing across a larger population will be needed to determine if the high diagnostic accuracy will be maintained across a larger group of women representing a diversity of ethnic and racial groups.

The research was reported November 17 in the journal Scientific Reports, an open access journal from the publishers of Nature.

“This work provides a proof of concept that using an integrated approach combining analytical chemistry and learning algorithms may be a way to identify optimal diagnostic features,” said John McDonald, a professor in the School of Biology at the Georgia Institute of Technology and director of its Integrated Cancer Research Center. “We think our results show great promise and we plan to further validate our findings across much larger samples.”

Ovarian cancer has been difficult to treat because it typically is not diagnosed until after it has metastasized to other areas of the body. Researchers have been seeking a routine screening test that could diagnose the disease in stage one or stage two – when the cancer is confined to the ovaries.

Working with three cancer treatment centers in the U.S. and Canada, the Georgia Tech researchers obtained blood samples from women with stage one and stage two ovarian cancer. They separated out the serum, which contains proteins and metabolites – molecules produced by enzymatic reactions in the body.

The serum samples were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS), which is two instruments joined together to better separate samples into their individual components. Heavier molecules are separated from lighter molecules, and the molecular signatures are determined with enough accuracy to identify the specific compounds. The Georgia Tech researchers decided to look only at the metabolites in their research.

“People have been looking at proteins for diagnosis of ovarian cancer for a couple of decades, and the results have not been very impressive,” said Facundo Fernández, a professor in Georgia Tech’s School of Chemistry and Biochemistry who led the analytical chemistry part of the research. “We decided to look in a different place for molecules that could potentially provide diagnostic capabilities. It’s one of the places that people had really not studied before.”

Samples from each of the 46 cancer patients were divided so they could be analyzed in duplicate. The researchers also looked at serum samples from 49 women who did not have cancer. The work required eliminating unrelated compounds such as caffeine, and molecules that were not present in all the cancer patients.

“We used really high resolution equipment and instrumentation to be able to separate most of the components of the samples,” Fernández explained. “Otherwise, detection of early-stage ovarian cancer is very difficult because you have a lot of confounding factors.”

The chemical work identified about a thousand candidate compounds. That number was reduced to about 255 through the work of research scientist David Gaul, who removed duplicates and unrelated molecules from the collection.

These 255 compounds were then analyzed by a learning algorithm which evaluated the predictive value of each one. Molecules that did not contribute to the predictive accuracy of the screening were eliminated. Ultimately, the algorithm produced a list of 16 molecules that together differentiated cancer patients with extremely high accuracy – greater than 90 percent.

“The algorithm looks at the metabolic features and correlates them with whether the samples were from cancer or control patients,” McDonald explained. “The algorithm has no idea what these compounds are. It is simply looking for the combination of molecules that provides the optimal predictive accuracy. What is encouraging is that many of the diagnostic features identified are metabolites that have been previously implicated in ovarian cancer.”

As a next step, McDonald and Fernández would like to study samples from a larger population that includes significant numbers of different ethnic and racial groups. Those individuals may have different metabolites that could serve as biomarkers for ovarian cancer.

Though sophisticated laboratory equipment was required to identify the 16 molecules, a screening test would not require the same level of sophistication, Fernández said.

“Once you know what these molecules are, the next step would be to set up a clinical assay,” he said. “Mass spectrometry is a common tool in this field. We could use a clinical mass spectrometer to look at only the molecules we are interested in. Moving this to a clinical assay would take work, but I don’t see any technical barriers to doing it.”

The Fernández and McDonald groups have used a similar approach with prostate cancer and plan to explore its utility for detecting other types of cancer.

The research was supported by grants from The Laura Crandall Brown Ovarian Cancer Foundation, The Ovarian Cancer Research Fund, The Ovarian Cancer Institute, Northside Hospital (Atlanta), The Robinson Family Fund, and the Deborah Nash Endowment Fund.

CITATION: David A. Gaul, et al., “Highly-accurate metabolomics detection of early-stage ovarian cancer,” (Scientific Reports, 2015). http://www.dx.doi.org/10.1038/srep16351

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Thanks to diagnostic tests, clinicians and patients can already know the type of breast cancer they’re up against, but one big question remains: How likely is it that the cancer will invade other parts of the body? Answering that question could help guide the choice of treatment options, from aggressive and difficult therapies to more conservative ones.

By studying chemical signals from specific cells that are involved in helping cancer invade other tissues in each woman’s body, researchers have developed a predictive model that could provide an invasiveness index for each patient.

“We want women to have more information to make a personal decision beyond the averages calculated for an entire population,” said Manu Platt, an associate professor in the Department of Biomedical Engineering at Georgia Tech and Emory University. “We are using our systems biology tools and predictive medicine approaches to look at potential markers we could use to help us understand the risk each woman has. This would provide information for a more educated discussion of treatment options.”

The research, sponsored with funds from the Georgia Research Alliance and the Giglio family donation to the Department of Biomedical Engineering, was reported September 9 in the journal Scientific Reports. Beyond breast cancer, the technique could offer similar decision-making assistance for men with prostate cancer, where treatment also requires making difficult choices about the risk of metastasis.

Platt’s research team is examining chemical signals produced by the macrophages that can help aggressive tumors invade new tissues. Macrophages normally clean up foreign particles and harmful microorganisms in the body, but aggressive tumors can enlist macrophages in helping them metastasize. Tumor associated macrophages contribute significantly to tumor invasion, with cysteine cathepsin proteases – enzymes that break down proteins in the body – important contributors.

To develop their predictive index, Platt’s research team used variability in macrophage expression of four types of cathepsin, the cathepsin inhibitor cystatin C, and kinase activation levels. The model, which has been under development for two years, was produced by studying macrophages from a population of women who didn’t have breast cancer. Platt and colleagues Keon-Young Park and Gande Li co-cultured a standard breast cancer cell line (MCF-7) with macrophages produced from monocytes donated by these cancer-free women.

Next, they measured the level of invasiveness facilitated by macrophages from each individual donor, exposing the cancer cells and macrophages to a collagen gel designed to simulate breast tissue and measuring how many cells invaded it. While the breast is composed of many other tissues, collagen makes up the largest proportion and provided a good measure of how aggressively the cells would invade, Platt said.

Platt’s team correlated the level of invasion through the gel to the chemical signals being expressed by the macrophages. The researchers were surprised at the large amount of patient-to-patient variability in macrophage activity – variability that could account for the outcome differences in the patients receiving similar cancer treatments. The signaling levels and related invasion measurements were used to train a computational model developed by Platt’s team.

The researchers next obtained blood samples containing monocytes from nine patients being treated for breast cancer at DeKalb Medical Center, a major Atlanta-area hospital. They measured signals from these macrophages and used their model – which had been trained on macrophage signaling and resulting invasiveness – to predict which of the cancer patients would be expected to have more invasive types of cancer. They compared their predications to what the clinician – Dr. John Kennedy – provided as their initial diagnosis.

“Based on the cells we got from the clinic, the ones that had been predicted to have the greatest potential for invasion were the ones that had produced the most invasive form of breast cancer in the patients,” Platt said.

While the study could not account for possible differences in the length of time the cancers had been growing, they did correlate well with observations. In future research, Platt hopes to follow the women for five years to determine if the model’s predictions are related to cancer recurrence. He also plans to expand the model with additional macrophage data, and test it against additional blood samples.

“The more information you give the model, the closer you get to the prediction,” he said. “We think this is a very big start.”

The strength of this technique, Platt believes, is that it measures what’s happening at the level where cancer is metastasizing.

“We are measuring at the level of activity of these intracellular enzymes and the ultimate activity of the proteases they produce that are not only the biomarkers of the tumor, but also help the tumor grow,” he said. “Everything about us is different. Our genetics are different and our lifestyles are different, so clinicians have to make decisions in all that variability. All of those differences can be measured and captured in this output.”

Platt believes the technique could one day lead to a simple blood test that would provide information useful in making therapy recommendations. The test might also help determine which women should be monitored more closely to detect the beginnings of a cancer.

“Together, this establishes proof-of-principle that personalized information acquired from minimally invasive blood draws may provide useful information to inform oncologists and patients of invasive/metastatic risk, helping to make decisions regard radical mastectomy or milder, conservative treatments to save patients from hardship and surgical recovery,” he wrote in the paper.

CITATION: Keon-Young Park, Gande Li and Manu O. Platt, "Monocyte-derived macrophage assisted breasat cancer cell invasion as a personalized, predictive metric to score metastatic risk," (Scientific Reports 2015). http://dx.doi.org/10.1038/srep13855

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Scientists from engineering, biology, chemistry, and computing won’t discover new vaccines and medical devices — or advance what we know about diseases — by working on their own. The next biomedical breakthroughs to provide accessible health care for billions of people worldwide will come from the collaboration between different laboratories and disciplines.

That core belief led to the creation of the Engineered Biosystems Building (EBB), the newest building at the Georgia Institute of Technology. The site opened in May and a formal dedication ceremony was held today. 

EBB houses labs for research in chemical biology, cell and developmental biology, and systems biology. The building allows Georgia Tech to consolidate its biomedical research efforts in the prevention, diagnosis, and treatment of cancer, diabetes, heart disease, infections, and other life-threatening conditions.

President G.P. “Bud” Peterson said the building symbolizes what Georgia Tech is all about — collaboration and innovation.

“The EBB will drive innovation and have an undeniable impact on biomedical science and human health,” Peterson said. “EBB brings together some of the world’s finest researchers in a collaborative environment, and these collaborations will result in incredible breakthroughs.”

The building provides nearly 219,000 square feet of multidisciplinary research space and enhances the Institute’s partnerships with Emory University Hospital and with Children’s Healthcare of Atlanta.

“Together, we are changing the lives of children,” said Donna Hyland, president and CEO of Children’s Healthcare. “The space within this building helps bring our new Pediatric Technology Center to life and gives researchers another place to combine expertise in clinical care, research, and technology to solve problems that will help make kids better today and healthier tomorrow.”

The building is located on 10th Street, at the north end of the existing biotechnology complex. Other buildings in the complex include: the Parker H. Petit Institute for Bioengineering and Bioscience, the U.A. Whitaker Biomedical Engineering Building, the Ford Environmental Science and Technology Building, and the Molecular Science and Engineering Building.

More than 140 faculty and nearly 1,000 graduate students from 10 different academic units work in the labs and facilities there.

“EBB puts Georgia Tech at the forefront of biosciences and bioengineering research,” said M.G. Finn, professor and chair of the School of Chemistry and Biochemistry.

The building’s unique design allows Georgia Tech researchers to expand their work, he said.

EBB contains “research neighborhoods” designed around a specific focus or topic. These neighborhoods bring together scientists, engineers, and researchers from different disciplines around common themes or areas of interest. They share laboratories, offices, and common spaces.

Stairs alternate on various floors, encouraging people to move within the neighborhoods and throughout the building and interact with one another. Small and informal meeting areas are located near the stairwells, to further encourage researchers to talk with one another.

“We will help, influence, and support one another and bring new insights in a way that can’t happen if a building is restricted to a particular department or discipline,” Finn said.

“Ultimately we are all working to fight disease and save lives,” he said. “EBB is designed to foster the research to do just that.”

EBB is the largest building investment in Georgia Tech history. The $113 million building was made possible because of a partnership between the Institute, the Georgia Tech Foundation, and the State of Georgia, Peterson said.

State appropriations provided $64 million for the project. Georgia Tech provided $15 million in Institute funds, and private funding raised another $34 million in commitments pledged over five years.

EBB will help drive Georgia’s economy, Peterson said.

“It will foster economic development through the formation of startup enterprises, the creation of high-skilled, high-paying jobs, and the commercialization of new devices, drugs, and technologies,” Peterson said.

The device is described in a Nature Methods paper that was published online May 18. Among the members of the research team is Fatih Sarioglu, now an assistant professor in the School of Electrical and Computer Engineering at Georgia Tech.

“Early theories of cancer metastasis were based on clumps of tumor cells traveling through the bloodstream, but given that CTC clusters are even rarer in the blood than single CTCs, they have attracted minimal attention for several decades,” explained Mehmet Toner, PhD, director of the BioMicroElectroMechanical Systems Resource Center in the MGH Center for Engineering in Medicine, the paper's senior author. “The ability to isolate intact clusters will enable is to investigate carefully their role in the metastatic process, and understanding metastasis really is the ‘holy grail’ of cancer research.”

CTCs are living solid tumor cells found in the bloodstream at extremely low levels – about one in a billion cells. Starting in 2007, MGH researchers have developed three microchip-based devices that capture CTCs in ways that preserve molecular information that can help guide clinical treatment. The first two versions used antibodies directed at specific proteins on the surface of tumor cells, which limited the ability to capture cells that may have lost those marker proteins during the process of metastasis. The third version, developed in 2013, uses antigen-independent methods of isolating CTCs, which is also the case for the Cluster-Chip.

“Cancer is an extremely heterogeneous disease, and even within the same tumor you can find cells with different surface antigens,” said Sarioglu, co-lead author of the Nature Methods paper. “Since we are capturing clusters because of their physical properties, this chip is directly applicable to all types of cancer.”

Sarioglu explained that the strategy behind the design of the chip is based on the physical properties of clusters of cells. The 3- by 1 ½-inch plastic chip through which a blood sample is passed consists of rows of triangular microposts arranged in such a way that clusters passing between two posts will become trapped on the apex of a third central post and held in place by the balanced flow of fluid on either side. Single CTCs and blood cells will pass right through without being captured. In addition, passing the sample through the device at a slow rate minimizes the possibility that clusters will be broken, distorted or escape.

Initial testing of the Cluster-Chip with blood samples to which artificially formed tumor cell clusters had been introduced helped to determine the optimal flow rate to capture the most clusters in the least time. The researchers then compared the new device to the second-generation HBCTC-Chip, which relies on known cell-surface markers and was the first to isolate CTC clusters. The Cluster-Chip proved to be 40 to 50 percent better at finding clusters of cells expressing targeted markers and 100 percent better at capturing cells without target antigens.

While initial attempts to release captured clusters from the device by simply reversing the fluid flow had limited success, the investigators found that reducing the temperature of the device itself to 4 degrees Celsius (39 F) not only released 80 percent of clusters, but also improved the purity of the captured material by reducing the undesired capture of white blood cells.

Use of the Cluster-Clip to test blood samples from 60 patients with either breast cancer, melanoma or prostate cancer successfully captured CTC clusters in from 30 to 40 percent of samples. Analysis of captured clusters revealed they consisted of cells with significant molecular differences, some actively proliferating and other relatively quiescent, and were often accompanied by immune cells, an observation that could have important implications with the increased attention to immune-system-based cancer therapies.

“Testing of patient blood samples also revealed that there were significantly more CTC clusters in the blood than was previously believed,” said Toner. “We now are looking at ways to improve further the release of captured clusters, but we are only at the beginning of our quest to understand the role and biology of CTC clusters. Eventually we could develop ways to target clusters therapeutically as well as using them as a source of diagnostic information.” Toner is the the Benedict Professor of Surgery at Harvard Medical School.

“This new isolation device will be particularly useful in isolating clusters of CTCs, which seem to be the most malignant and metastasis-prone types of cancer cells in the blood,” said Daniel Haber, MD, director of the MGH Cancer Center and a co-author of the Nature Methods paper. “I’m particularly excited by the way in which the device was created – starting from a clinical and biological observation about the importance of these CTC clusters and then designing a specific microfluidic device to capture these cells, which will make it possible to study them in greater detail.”

Nicola Aceto, PhD, of the MGH Cancer Center is co-lead author of the Nature Methods paper. Support for the current study includes grants from the National Institutes of Health, the National Institute of Biomedical Imaging and Bioengineering, a “dream team” grant from Stand Up to Cancer, the Howard Hughes Medical Institute, the Prostate Cancer Foundation, the Charles Evans Foundation, and Johnson and Johnson. The MGH has filed a patent application for the Cluster-Chip.

The Georgia Institute of Technology is a leading research university committed to improving the human condition through advanced science and technology. Ranked as the #7 best U.S. public university, Georgia Tech provides a focused, technologically based education to more than 21,500 undergraduate and graduate students. As a leading technological university, Georgia Tech has more than 100 centers focused on interdisciplinary research that consistently contribute vital research and innovation to government, industry, and business. For more information, please visit www.gatech.edu.

Massachusetts General Hospital, founded in 1811, is the original and largest teaching hospital of Harvard Medical School. The MGH conducts the largest hospital-based research program in the United States, with an annual research budget of more than $760 million and major research centers in AIDS, cardiovascular research, cancer, computational and integrative biology, cutaneous biology, human genetics, medical imaging, neurodegenerative disorders, regenerative medicine, reproductive biology, systems biology, transplantation biology and photomedicine.

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