A limited set of transcriptional programs define major cell types

Breschi, A., Muñoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martín, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigó, R. (July 2020) A limited set of transcriptional programs define major cell types. Genome Res, 30 (7). pp. 1047-1059. ISSN 1088-9051 (Print)1088-9051

DOI: 10.1101/gr.263186.120

Abstract

We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.

Item Type: Paper
Additional Information: 1549-5469 Breschi, Alessandra Muñoz-Aguirre, Manuel Wucher, Valentin Davis, Carrie A Garrido-Martín, Diego Djebali, Sarah Gillis, Jesse Pervouchine, Dmitri D Vlasova, Anna Dobin, Alexander Zaleski, Chris Drenkow, Jorg Danyko, Cassidy Scavelli, Alexandra Reverter, Ferran Snyder, Michael P Gingeras, Thomas R Guigó, Roderic R01 MH101814/MH/NIMH NIH HHS/United States U41 HG007234/HG/NHGRI NIH HHS/United States U54 HG007004/HG/NHGRI NIH HHS/United States Journal Article Genome Res. 2020 Jul;30(7):1047-1059. doi: 10.1101/gr.263186.120. Epub 2020 Jul 29.
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
Investigative techniques and equipment > cell lineage tracing
organs, tissues, organelles, cell types and functions > cell types and functions > cell types
organs, tissues, organelles, cell types and functions > cell types and functions > cell types
organs, tissues, organelles, cell types and functions > cell types and functions > cell types
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Dobin Lab
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User: Matthew Dunn
Date: July 2020
Date Deposited: 02 Oct 2020 19:25
Last Modified: 29 Oct 2020 15:30
PMCID: PMC7397875
Related URLs:
URI: https://repository.cshl.edu/id/eprint/39729

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