دورية أكاديمية
أعرض في EDS

Screening cell-cell communication in spatial transcriptomics via collective optimal transport.

التفاصيل البيبلوغرافية
العنوان: Screening cell-cell communication in spatial transcriptomics via collective optimal transport.
المؤلفون: Cang Z; Department of Mathematics and Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA., Zhao Y; Department of Mathematics, The George Washington University, Washington, DC, USA., Almet AA; Department of Mathematics, University of California, Irvine, Irvine, CA, USA.; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA., Stabell A; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA., Ramos R; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA., Plikus MV; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA., Atwood SX; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA., Nie Q; Department of Mathematics, University of California, Irvine, Irvine, CA, USA. qnie@uci.edu.; The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA. qnie@uci.edu.; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. qnie@uci.edu.
المصدر: Nature methods [Nat Methods] 2023 Feb; Vol. 20 (2), pp. 218-228. Date of Electronic Publication: 2023 Jan 23.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
أسماء مطبوعة: Original Publication: New York, NY : Nature Pub. Group, c2004-
مواضيع طبية MeSH: Transcriptome* , Cell Communication*/genetics, Humans ; Gene Expression Profiling ; Signal Transduction ; Computer Simulation ; Single-Cell Analysis
مستخلص: Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing datasets provide unprecedented opportunities to dissect cell-cell communication (CCC). However, incorporation of the spatial information and complex biochemical processes required in the reconstruction of CCC remains a major challenge. Here, we present COMMOT (COMMunication analysis by Optimal Transport) to infer CCC in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models. We apply COMMOT to simulation data and eight spatial datasets acquired with five different technologies to show its effectiveness and robustness in identifying spatial CCC in data with varying spatial resolutions and gene coverages. Finally, COMMOT identifies new CCCs during skin morphogenesis in a case study of human epidermal development.
(© 2023. The Author(s).)
التعليقات: Comment in: Nat Methods. 2023 Feb;20(2):185-186. (PMID: 36693905)
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معلومات مُعتمدة: R01 AR079150 United States AR NIAMS NIH HHS; R01 DE030565 United States DE NIDCR NIH HHS; T32 AR080622 United States AR NIAMS NIH HHS; U01 AR073159 United States AR NIAMS NIH HHS; P30 AR075047 United States AR NIAMS NIH HHS
سلسلة جزيئية: Dryad 10.5061/dryad.8t8s248
تواريخ الأحداث: Date Created: 20230123 Date Completed: 20230213 Latest Revision: 20231012
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC9911355
DOI: 10.1038/s41592-022-01728-4
PMID: 36690742
قاعدة البيانات: MEDLINE
الوصف
تدمد:1548-7105
DOI:10.1038/s41592-022-01728-4