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Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

Kotliar, Dylan, Veres, Adrian, Nagy, M Aurel, Tabrizi, Shervin, Hodis, Eran, Melton, Douglas A, Sabeti, Pardis C·2019·eLife
DOI 10.7554/elife.43803PMC PMC6639075

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Abstract

Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although single-cell RNA-Seq (scRNA-Seq) can quantify transcripts in individual cells, each cell’s expression profile may be a mixture of both types of programs, making them difficult to disentangle. Here, we benchmark and enhance the use of matrix factorization to solve this problem. We show with simulations that a method we call consensus non-negative matrix factorization (cNMF) accurately infers identity and activity programs, including their relative contributions in each cell. To illustrate the insights this approach enables, we apply it to published brain organoid and visual cortex scRNA-Seq datasets; cNMF refines cell types and identifies both expected (e.g. cell cycle and hypoxia) and novel activity programs, including programs that may underlie a neurosecretory phenotype and synaptogenesis.

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  • These genes were in a single inhibitory program (Inh-22, from NMF) that included the SCENIC-predicted subtype regulators FOXP2 and LEF1.

    “These genes were in a single inhibitory program (Inh-22, from NMF) that included the SCENIC-predicted subtype regulators FOXP2 and LEF134,36”

    From Single-cell multiregion dissection of Alzheimer’s disease (2024) · cites this paper as [34]

  • Excitatory neurons in the thalamus were predominantly composed (74%) of a subtype (NXPH1+RNF220+) not observed in the neocortex and predicted to be regulated by LHX9, SOX2, SHOX2 and TCF7L2.

    “Excitatory neurons in the TH were predominantly composed (74%) of a subtype (NXPH1+RNF220+) that was not observed in the neocortex and is predicted to be regulated by LHX9, SOX2, SHOX2 and TCF7L234,36”

    From Single-cell multiregion dissection of Alzheimer’s disease (2024) · cites this paper as [34]

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Authors
Kotliar, D., Veres, A., Nagy, M. A., Tabrizi, S., Hodis, E., Melton, D. A., & Sabeti, P. C.
Affiliations
  • Department of Systems Biology, Harvard Medical School, Boston, United States
  • Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, United States
  • Broad Institute of MIT and Harvard, Cambridge, United States
  • Harvard Stem Cell Institute, Harvard University, Cambridge, United States
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2019-07-08
Volume
8
ISSN
2050-084X
DOI
10.7554/elife.43803
PMC
PMC6639075
Cited by
638
References
15
Language
en
Licence
Funders
  • National Institute of General Medical Sciences (T32GM007753)
  • National Institute of Allergy and Infectious Diseases (R01AI099210)
  • U.S. Food and Drug Administration (HHSF223201810172C)

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