DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data
Name
nihms-1789716.pdf
Description
Accepted version
Size
7 MB
Format
Adobe PDF
Checksum (MD5)
a1e4ddd858e096ab7a513c5cebc3825f
Author(s)
Jerby-Arnon, Livnat
Regev, Aviv
Date Issued
2022
Journal
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Citation
Jerby-Arnon, Livnat and Regev, Aviv. 2022. "DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data." Nature Biotechnology, 40 (10).
Version
Author's final manuscript
Abstract
Deciphering the functional interactions of cells in tissues remains a major challenge. Here we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs)-combinations of coordinated cellular programs in different cell types that form higher-order functional units at the tissue level-from either spatial data or single-cell data obtained without spatial information. Tested on spatial datasets from the mouse hypothalamus, cerebellum, visual cortex and neocortex, DIALOGUE identified MCPs associated with animal behavior and recovered spatial properties when tested on unseen data while outperforming other methods and metrics. In spatial data from human lung cancer, DIALOGUE identified MCPs marking immune activation and tissue remodeling. Applied to single-cell RNA sequencing data across individuals or regions, DIALOGUE uncovered MCPs marking Alzheimer's disease, ulcerative colitis and resistance to cancer immunotherapy. These programs were predictive of disease outcome and predisposition in independent cohorts and included risk genes from genome-wide association studies. DIALOGUE enables the analysis of multicellular regulation in health and disease.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Terms of Use
Creative Commons Attribution-Noncommercial-Share Alike
Persistent DSpace Link
DOI of Published Version
10.1038/S41587-022-01288-0
