김효빈 (Cedars-Sinai Medical Center) | 한빛사논문 > 한빛사

한빛사논문

조회704

Cedars-Sinai Medical Center

Mol. Syst. Biol., Oct 10 2023 | https://www.embopress.org/doi/full/10.15252/msb.202311670 CellNeighborEX: deciphering neighbor-dependent gene expression from spatial transcriptomics data.

Hyobin Kim^1,2,†, Amit Kumar^3,4,5,†, Cecilia Lövkvist⁶, António M Palma^3,4,7, Patrick Martin^1,2, Junil Kim⁸, Praveen Bhoopathi^3,4,5, Jose Trevino^3,9, Paul Fisher^3,4,5, Esha Madan^3,4,5,9, Rajan Gogna^*,3,4,5,9 and Kyoung Jae Won^*,1,2

¹Department of Computational Biomedicine, Cedars-Sinai Medical Center, Hollywood, CA, USA

²Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark

³Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA

⁴School of Medicine, Institute of Molecular Medicine, Virginia Commonwealth University, Richmond, VA, USA

⁵Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA

⁶Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark

⁷Instituto Superior Tecnico, Universidade de Lisboa, Lisboa, Portugal

⁸School of Systems Biomedical Science, Soongsil University, Seoul, Korea

⁹Department of Surgery, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA

^†These authors contributed equally to this work.

^*Corresponding authors: Rajan Gogna, Kyoung Jae Won

Abstract

Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor-dependent gene expression suggests new potential genes involved in cell-cell interactions beyond what ligand-receptor co-expression can discover.

논문정보

형식Research article
게재일2023년 10월 (BRIC 등록일 2023-10-11)
연구진국내+국외 연구진
분야 생명과학 > 분자생물학

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