{"671656":{"#nid":"671656","#data":{"type":"news","title":"Coskun Lab Pioneering New Field of Research: Single Cell Spatial Metabolomics","body":[{"value":"\u003Cp\u003EAhmet Coskun and his collaborators plan to create a chemical atlas of all the immune cells in the human body, a 3D micromap to help clinicians navigate the complex role of the entire immune system in the presence of different diseases.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIt\u2019s the kind of massive undertaking that would result in vastly improved precision therapies for patients. And it\u2019s 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.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe researchers described their new approach, the Single Cell Spatially resolved Metabolic (scSpaMet) framework, in the journal\u0026nbsp;\u003Ca href=\u0022https:\/\/www.nature.com\/articles\/s41467-023-43917-5\u0022\u003E\u003Cem\u003ENature Communications\u003C\/em\u003E\u0026nbsp;on Dec. 13.\u003C\/a\u003E\u003Cem\u003E\u0026nbsp;\u003C\/em\u003EThe study builds on a technique Coskun\u2019s team developed and described in a 2021 article, \u201c3D Spatially resolved Metabolomic profiling Framework,\u201d published in\u0026nbsp;\u003Ca href=\u0022https:\/\/www.science.org\/doi\/10.1126\/sciadv.abd0957\u0022\u003E\u003Cem\u003EScience Advances\u003C\/em\u003E.\u003C\/a\u003E\u0026nbsp;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.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u201cEarlier we couldn\u2019t achieve single-cell resolution, but with this new approach, we can,\u201d said Coskun,\u0026nbsp;\u003Ca href=\u0022https:\/\/www.bme.gatech.edu\/bme\/faculty\/Ahmet-F-Coskun\u0022\u003EBernie Marcus Early Career Professor\u003C\/a\u003E\u0026nbsp;in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. \u201cWith this new approach, we can get spatial details of proteins and metabolites in single cells\u2013 no one else has yet reached this level of high subcellular resolution.\u201d\u003C\/p\u003E\r\n\r\n\u003Cp\u003EHe added, \u201cWe\u2019re pioneering a new field of research with this work, single cell spatial metabolomics.\u201d\u003C\/p\u003E\r\n\r\n\u003Ch4\u003E\u003Cstrong\u003EA Bigger, Better Molecular Picture\u003C\/strong\u003E\u003C\/h4\u003E\r\n\r\n\u003Cp\u003EHuman 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 \u2013 everything, all at once, in high-definition 3D. With scSpaMet, Coskun\u2019s 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.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe team broadened the scope of this study, extending its investigation beyond human tonsil tissue.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u201cWe 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,\u201d Coskun said. \u201cThen 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\u2019s health.\u201d\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe wide-angled study required plenty of cross-country collaboration with other institutions, although\u0026nbsp;Coskun\u2019s lab guided the wide-angled study, integrating its expertise in bioimaging, chemistry, tissue biology, and artificial intelligence.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Ca href=\u0022https:\/\/www.cshl.edu\/\u0022\u003ECold Spring Harbor Laboratory\u003C\/a\u003E\u0026nbsp;(New York) provided access to its endometrium tissue bank.\u0026nbsp;\u003Ca href=\u0022https:\/\/www.ornl.gov\/\u0022\u003EOak Ridge National Laboratory\u003C\/a\u003E\u0026nbsp;(Tennessee) provided data from its complex metabolic imaging instrumentation, to further demonstrate how single cell spatial metabolomics imaging can generate rich data.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe\u0026nbsp;\u003Ca href=\u0022https:\/\/www.ucdavis.edu\/\u0022\u003EUniversity of California-Davis\u003C\/a\u003E\u0026nbsp;provided kidney biospecimens as both fixed tissue and frozen embedded tissue, in two halves of the same sample, \u201cso we could demonstrate the effect of tissue preparation on the sensitivity of our single cell spatial metabolomics pipeline,\u201d Coskun said.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EThe team also included Thomas Hu and Mayar Allam, graduate researchers in Coskun\u2019s lab, who guided the research as lead authors, and Walter Henderson, a research scientist who manages the\u0026nbsp;\u003Ca href=\u0022https:\/\/mcf.gatech.edu\/\u0022\u003EIEN\/IMat Materials Characterization Facility\u003C\/a\u003E\u0026nbsp;at Georgia Tech.\u003C\/p\u003E\r\n\r\n\u003Ch4\u003E\u003Cstrong\u003EConsidering the Whole Person\u0027s Biochemistry\u003C\/strong\u003E\u003C\/h4\u003E\r\n\r\n\u003Cp\u003EThe 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\u2019s biophysical makeup to contrive the best treatment options.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u201cFor example, it can provide mechanisms of how immune responses can be boosted by adding dietary molecules along with immunotherapies,\u201d Coskun said. \u201cIt 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.\u201d\u003C\/p\u003E\r\n\r\n\u003Cp\u003ECoskun 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\u2019s comprehensive exploration and imaging of the geography of normal and unhealthy human tissues \u2013 of every single cell \u2013 can further explain cellular regulation in ways that were previously overlooked, due to the lack of technology.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EHe envisions a future in which a patient\u2019s 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\u2019s diseases, and metabolic disorders.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u201cWe 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,\u201d Coskun said.\u003C\/p\u003E\r\n\r\n\u003Cp\u003EIn 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.\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u201cWhen researchers achieved single cell sequencing, it was a revolutionary moment in medicine,\u201d Coskun said. \u201cNow, we believe single cell spatial metabolic profiling will push the medical practice into new heights.\u201d\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cem\u003EThis research was supported by\u0026nbsp;the Burroughs\u0026nbsp;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)\u003C\/em\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003ECitation:\u003C\/strong\u003E\u0026nbsp;Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson, Brian Yueh, Aybuke Garipcan, Anton V. Ievlev, Maryam Afkarian, Semir Beyaz, and Ahmet F. Coskun.\u0026nbsp;\u003Ca href=\u0022https:\/\/www.nature.com\/articles\/s41467-023-43917-5#Ack1\u0022\u003E\u201cSingle-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology,\u201d\u0026nbsp;\u003Cem\u003ENature Communications\u003C\/em\u003E\u0026nbsp;(Dec. 13, 2023)\u003C\/a\u003E\u003C\/p\u003E\r\n","summary":"","format":"limited_html"}],"field_subtitle":[{"value":"BME researcher\u0027s immunometabolism approach pioneers single cell spatial metabolomics"}],"field_summary":[{"value":"\u003Cp\u003ECoskun lab developed scSpaMet framework, to capture 3D images of single cell details such as the naturally occurring lipids, proteins, as well as metabolites (with their multiple functions, including energy conversion and cell signaling), in hopes of creating 3D map of all human tissues.\u0026nbsp;\u003C\/p\u003E\r\n","format":"limited_html"}],"field_summary_sentence":[{"value":"BME researcher\u0027s immunometabolism approach pioneers single cell spatial metabolomics"}],"uid":"28153","created_gmt":"2023-12-20 15:07:06","changed_gmt":"2024-01-04 14:13:26","author":"Jerry Grillo","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2023-12-20T00:00:00-05:00","iso_date":"2023-12-20T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"672621":{"id":"672621","type":"image","title":"spatial meta","body":"\u003Cp\u003EImages of time in space: The top panel image shows pseudo-time single cell metabolic trajectories across distinct biogeographical regions. The dark purple represents early metabolic changes, while the bright yellow represents later metabolic activities. The bottom panel is a spatial projection of single\u0026nbsp;cells\u2019\u0026nbsp;metabolic trajectories (denoted by arrows in the dark zone and light zone regions) in tonsil tissue. \u0026nbsp;\u003Cem\u003EPhoto provided by Coskun Lab\u003C\/em\u003E\u003C\/p\u003E\r\n","created":"1703084190","gmt_created":"2023-12-20 14:56:30","changed":"1703084235","gmt_changed":"2023-12-20 14:57:15","alt":"spatal metabololomics","file":{"fid":"255896","name":"Metabolomics.jpg","image_path":"\/sites\/default\/files\/2023\/12\/20\/Metabolomics.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2023\/12\/20\/Metabolomics.jpg","mime":"image\/jpeg","size":3649852,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2023\/12\/20\/Metabolomics.jpg?itok=-1LySKl7"}},"672622":{"id":"672622","type":"image","title":"lead authors","body":"\u003Cp\u003ELead authors Mayar Allam and Thomas Hu\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n","created":"1703084247","gmt_created":"2023-12-20 14:57:27","changed":"1703084298","gmt_changed":"2023-12-20 14:58:18","alt":"Mayam and Thomas","file":{"fid":"255897","name":"Allam and Hu.jpg","image_path":"\/sites\/default\/files\/2023\/12\/20\/Allam%20and%20Hu.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2023\/12\/20\/Allam%20and%20Hu.jpg","mime":"image\/jpeg","size":4160802,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2023\/12\/20\/Allam%20and%20Hu.jpg?itok=_E3dph37"}},"672623":{"id":"672623","type":"image","title":"Coskun photo","body":"\u003Cp\u003EAhmet Coskun\u003C\/p\u003E\r\n","created":"1703084315","gmt_created":"2023-12-20 14:58:35","changed":"1703084361","gmt_changed":"2023-12-20 14:59:21","alt":"Ahmet Coskun photo","file":{"fid":"255898","name":"New Coskun photo.jpg","image_path":"\/sites\/default\/files\/2023\/12\/20\/New%20Coskun%20photo.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2023\/12\/20\/New%20Coskun%20photo.jpg","mime":"image\/jpeg","size":4491737,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2023\/12\/20\/New%20Coskun%20photo.jpg?itok=o0qvPX3w"}}},"media_ids":["672621","672622","672623"],"groups":[{"id":"1292","name":"Parker H. Petit Institute for Bioengineering and Bioscience (IBB)"},{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"138","name":"Biotechnology, Health, Bioengineering, Genetics"},{"id":"140","name":"Cancer Research"},{"id":"141","name":"Chemistry and Chemical Engineering"},{"id":"146","name":"Life Sciences and Biology"}],"keywords":[{"id":"187423","name":"go-bio"},{"id":"187915","name":"go-researchnews"},{"id":"11538","name":"Metabolomics"},{"id":"7206","name":"metabolite"},{"id":"176713","name":"metabolites"},{"id":"181801","name":"metabolome"}],"core_research_areas":[{"id":"39441","name":"Bioengineering and Bioscience"}],"news_room_topics":[{"id":"71891","name":"Health and Medicine"},{"id":"71881","name":"Science and Technology"}],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Ca href=\u0022mailto:jerry.grillo@ibb.gatech.edu\u0022\u003EJerry Grillo\u003C\/a\u003E\u003C\/p\u003E\r\n","format":"limited_html"}],"email":["jerry.grillo@ibb.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}