{"678806":{"#nid":"678806","#data":{"type":"news","title":"Keeping Tabs on RNA Inside of Cells","body":[{"value":"\u003Cp\u003E\u003Ca href=\u0022https:\/\/research.gatech.edu\/people\/saurabh-sinha-phd\u0022\u003ESaurabh Sinha\u003C\/a\u003E and a multi-institutional team of researchers have created a computational toolkit with the detection power and precision of a spy satellite. But instead of keeping tabs of human traffic on the ground, or infrastructure development in a city, they\u2019re focusing on RNA with unprecedented clarity at the subcellular level.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003ETheir intracellular spatial transcriptomic analysis toolkit, or InSTAnT, can analyze cellular data and chart RNA interactions, providing new insights into the molecular processes of life and advancing an evolving field of research.\u003C\/p\u003E\u003Cp\u003E\u201cConventional spatial transcriptomics maps RNA at the tissue level,\u201d said Sinha, professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. \u201cBut InSTAnT represents a step forward. It provides, for the first time, an analytic technique to fully exploit single-molecule resolution. This means we can explore the intricate architecture, machinery, and activity of cells in ways that were not possible before.\u201d\u003C\/p\u003E\u003Cp\u003EIn addition to Georgia Tech and Emory, the team included researchers from from the \u003Ca href=\u0022https:\/\/illinois.edu\/\u0022\u003EUniversity of Illinois Urbana-Champaign\u003C\/a\u003E. With Anurendra Kumar, a grad student in the \u003Ca href=\u0022https:\/\/sites.google.com\/view\/sinhalaboratorygatech\u0022\u003ESinha lab\u003C\/a\u003E, as lead author, they explained their innovative work recently in \u003Ca href=\u0022https:\/\/www.nature.com\/articles\/s41467-024-49457-w\u0022\u003E\u003Cem\u003ENature Communications\u003C\/em\u003E\u003C\/a\u003E.\u003C\/p\u003E\u003Ch4\u003E\u003Cstrong\u003ESubcellular GPS\u003C\/strong\u003E\u003C\/h4\u003E\u003Cp\u003ESpatial transcriptomics has enhanced the study of gene expression (how genes regulate cellular functions and behaviors), revealing molecular activity in its natural environment. The aim is to gain a deeper understanding of biology, health, and disease, with the hope of developing targeted treatments.\u003C\/p\u003E\u003Cp\u003E\u201cOne of the biggest challenges in the field was the lack of systematic tools to analyze spatial relationships at the subcellular level,\u201d Sinha said. \u201cWe saw this gap as an opportunity to innovate and solve a problem that was truly spatial in nature.\u201d\u003C\/p\u003E\u003Cp\u003EInSTAnT was designed to work in tandem with imaging-based spatial transcriptomics technologies like MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization, developed by Harvard in 2015), which can observe thousands of RNA molecules inside single cells, gathering detailed information about gene activity.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003E\u201cIt\u2019s like a GPS for tissue, looking all the way down to city street level,\u201d said Sinha. \u201cThe little dots on this GPS aren\u2019t people. They\u2019re RNA molecules called gene transcripts. But we didn\u2019t really know how to make sense of this distribution of molecules in the cytoplasm or the nucleus, or generally within the cell.\u201d\u003C\/p\u003E\u003Cp\u003EInSTAnT translates what MERFISH gathers, using advanced statistical tests and algorithms, analyzing the distribution of RNA molecules that carry genetic information needed for various cell functions.\u003C\/p\u003E\u003Ch4\u003E\u003Cstrong\u003EThe Cities in Our Cells\u003C\/strong\u003E\u003C\/h4\u003E\u003Cp\u003EIf a cell was a busy little city, think of the gene transcripts \u2014 RNA molecules, the dots in Sinha\u2019s GPS scenario \u2014 as workers moving around town, performing their important tasks.\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;InSTAnT keeps tabs on this activity, investigating where and how these workers interact, and what they might be up to. So, InSTAnT identifies RNA pairs in specific areas, observing molecular interactions that are critical for cellular functions like protein production.\u003C\/p\u003E\u003Cp\u003E\u201cOur toolkit provides a level of detail crucial for understanding complex biological processes and how they contribute to diseases,\u201d said Sinha, whose team tested the toolkit on a variety of datasets, including human and mouse cells, and across multiple cell types and brain regions.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003EHe expects InSTAnT to transform how researchers study RNA interactions and explore unknown aspects of cellular organization and function.\u003C\/p\u003E\u003Cp\u003E\u201cI think we\u2019ve opened new possibilities for studying how cells coordinate their activities and adapt to challenges,\u201d said Sinha, adding, \u201cand it was a true team effort, with two other PIs from another institution, and a talented Ph.D. student as the lead author. This is a great example of how collaboration and data-driven science can uncover new biological frontiers.\u201d\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003ECITATION:\u003C\/strong\u003E Aunrendra Kumar, Alex Schrader, Bhavay Aggarwal, Ali Ebrahimpour Boroojeny, Marisa Asadian, JuYeon Lee, You Jin Song, Sihai Dave Zhao, Hee-Sun Han, Saurabh Sinha. \u201cIntracellular spatial transcriptomic analysis toolkit (InSTAnT),\u201d \u003Cem\u003ENature Communications\u003C\/em\u003E. \u003Ca href=\u0022https:\/\/doi.org\/10.1038\/s41467-024-49457-w\u0022\u003Ehttps:\/\/doi.org\/10.1038\/s41467-024-49457-w\u003C\/a\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EFUNDING:\u003C\/strong\u003E This research was supported by the National Institutes of Health, grant Nos. R35GM131819, R35GM147420, R21HG013180, and T32- 842 GM136629; Johnson \u0026amp; Johnson (WiSTEM2D Award for Science). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of any funding agency.\u003C\/p\u003E","summary":"","format":"limited_html"}],"field_subtitle":[{"value":"Researchers develop spatial transcriptomics toolkit that provides new insights into the molecular processes of life"}],"field_summary":[{"value":"\u003Cp\u003EGeorgia Tech researchers develop spatial transcriptomics toolkit that provides new insights into the molecular processes of life. It\u0027s like a spy satellite that keeps tabs on the workings of RNA inside of cells.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Georgia Tech researchers develop spatial transcriptomics toolkit that provides new insights into the molecular processes of life."}],"uid":"28153","created_gmt":"2024-12-10 19:46:15","changed_gmt":"2024-12-10 19:49:27","author":"Jerry Grillo","boilerplate_text":"","field_publication":"","field_article_url":"","location":"Atlanta, GA","dateline":{"date":"2024-12-10T00:00:00-05:00","iso_date":"2024-12-10T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"675817":{"id":"675817","type":"image","title":"Sinha research team","body":"\u003Cp\u003ESaurabh Sinha (center) and his collaborators are advancing the field of spatial transcriptomics with development of InSTAnT. Flanking Sinha are trainees from his lab (left to right), Bhavay Aggarwal and lead author of the recently published study, Anurendra Kumar.\u0026nbsp;\u003C\/p\u003E","created":"1733857850","gmt_created":"2024-12-10 19:10:50","changed":"1733860236","gmt_changed":"2024-12-10 19:50:36","alt":"BME researcher Saraubh Sinha (in foreground) and his grad students, Bhavay Aggarwal and Anurendra Kumar","file":{"fid":"259484","name":"Sinha team.jpg","image_path":"\/sites\/default\/files\/2024\/12\/10\/Sinha%20team.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2024\/12\/10\/Sinha%20team.jpg","mime":"image\/jpeg","size":4028966,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2024\/12\/10\/Sinha%20team.jpg?itok=4CqjT5VT"}}},"media_ids":["675817"],"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":"153","name":"Computer Science\/Information Technology and Security"}],"keywords":[{"id":"187915","name":"go-researchnews"},{"id":"187423","name":"go-bio"},{"id":"20571","name":"Transcriptomics"},{"id":"194125","name":"spatial transcriptomics"}],"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","format":"limited_html"}],"email":["Jerry.grillo@ibb.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}