Systematic morphological profiling of human gene and allele function via Cell Painting

  1. Mohammad Hossein Rohban
  2. Shantanu Singh
  3. Xiaoyun Wu
  4. Julia B Berthet
  5. Mark-Anthony Bray
  6. Yashaswi Shrestha
  7. Xaralabos Varelas
  8. Jesse S Boehm
  9. Anne E Carpenter  Is a corresponding author
  1. Broad Institute, United States
  2. Boston University School of Medicine, United States
  3. Novartis Institutes for BioMedical Research, United States

Abstract

We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation-based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/c-REL negative regulation of YAP1/WWTR1-responsive pathways. We confirmed this discovery of functional connectivity between the NF-κB pathway and Hippo pathway effectors at the transcriptional level, thereby expanding knowledge of these two signaling pathways that critically regulate tumor initiation and progression. We make the images and raw data publicly available, providing an initial morphological map of major biological pathways for future study.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Mohammad Hossein Rohban

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6589-850X
  2. Shantanu Singh

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Xiaoyun Wu

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Julia B Berthet

    Department of Biochemistry, Boston University School of Medicine, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Mark-Anthony Bray

    Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Yashaswi Shrestha

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Xaralabos Varelas

    Department of Biochemistry, Boston University School of Medicine, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2882-4541
  8. Jesse S Boehm

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Anne E Carpenter

    Broad Institute, Cambridge, United States
    For correspondence
    anne@broadinstitute.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1555-8261

Funding

National Science Foundation (NSF CAREER DBI 1148823)

  • Anne E Carpenter

Broad Institute

  • Anne E Carpenter

Carlos Slim Foundation

  • Anne E Carpenter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jeffrey Settleman, Calico Life Sciences, United States

Publication history

  1. Received: December 7, 2016
  2. Accepted: March 14, 2017
  3. Accepted Manuscript published: March 18, 2017 (version 1)
  4. Version of Record published: April 10, 2017 (version 2)

Copyright

© 2017, Rohban et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Mohammad Hossein Rohban
  2. Shantanu Singh
  3. Xiaoyun Wu
  4. Julia B Berthet
  5. Mark-Anthony Bray
  6. Yashaswi Shrestha
  7. Xaralabos Varelas
  8. Jesse S Boehm
  9. Anne E Carpenter
(2017)
Systematic morphological profiling of human gene and allele function via Cell Painting
eLife 6:e24060.
https://doi.org/10.7554/eLife.24060
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