1. Genetics and Genomics
Download icon

Comparative genetic screens in human cells reveal new regulatory mechanisms in WNT signaling

  1. Andres M Lebensohn
  2. Ramin Dubey
  3. Leif R Neitzel
  4. Ofelia Tacchelly-Benites
  5. Eungi Yang
  6. Caleb D Marceau
  7. Eric M Davis
  8. Bhaven B Patel
  9. Zahra Bahrami-Nejad
  10. Kyle J Travaglini
  11. Yashi Ahmed
  12. Ethan Lee
  13. Jan E Carette  Is a corresponding author
  14. Rajat Rohatgi  Is a corresponding author
  1. Stanford University School of Medicine, United States
  2. Vanderbilt University Medical Center, United States
  3. Geisel School of Medicine at Dartmouth College, United States
  4. University of Colorado, Boulder, United States
Research Article
  • Cited 24
  • Views 5,213
  • Annotations
Cite this article as: eLife 2016;5:e21459 doi: 10.7554/eLife.21459

Abstract

The comprehensive understanding of cellular signaling pathways remains a challenge due to multiple layers of regulation that may become evident only when the pathway is probed at different levels or critical nodes are eliminated. To discover regulatory mechanisms in canonical WNT signaling, we conducted a systematic forward genetic analysis through reporter-based screens in haploid human cells. Comparison of screens for negative, sensitizing and positive regulators of WNT signaling, mediators of R-spondin-dependent signaling and suppressors of constitutive signaling induced by loss of the tumor suppressor APC or casein kinase 1α uncovered new regulatory features at many levels of the pathway. These include a requirement for the transcription factor TFAP4, a role for the DAX domain of AXIN2 in controlling β-catenin activity, a contribution of GPI anchor biosynthetic enzymes and glypicans to R-spondin-potentiated signaling, and two different mechanisms that regulate signaling when distinct components of the β-catenin destruction complex are lost.

Article and author information

Author details

  1. Andres M Lebensohn

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Ramin Dubey

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Leif R Neitzel

    Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Ofelia Tacchelly-Benites

    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Eungi Yang

    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Caleb D Marceau

    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Eric M Davis

    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Bhaven B Patel

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Zahra Bahrami-Nejad

    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Kyle J Travaglini

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Yashi Ahmed

    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Ethan Lee

    Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Jan E Carette

    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
    For correspondence
    carette@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.
  14. Rajat Rohatgi

    Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
    For correspondence
    rrohatgi@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7609-8858

Funding

National Institutes of Health (DP2 AI104557,DP2 GM105448,R01 GM081635,R01 GM103926,RO1 CA105038)

  • Yashi Ahmed
  • Ethan Lee
  • Jan E Carette
  • Rajat Rohatgi

National Science Foundation (DBI-1039423)

  • Yashi Ahmed

David and Lucile Packard Foundation (Fellow Award)

  • Jan E Carette

Helen Hay Whitney Foundation (Novartis Fellowship)

  • Andres M Lebensohn

Stanford University School of Medicine (Josephine Q. Berry Fellowship)

  • Rajat Rohatgi

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

Reviewing Editor

  1. Utpal Banerjee, University of California, Los Angeles, United States

Publication history

  1. Received: September 13, 2016
  2. Accepted: December 7, 2016
  3. Accepted Manuscript published: December 20, 2016 (version 1)
  4. Accepted Manuscript updated: December 22, 2016 (version 2)
  5. Version of Record published: January 23, 2017 (version 3)
  6. Version of Record updated: February 1, 2017 (version 4)

Copyright

© 2016, Lebensohn 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.

Metrics

  • 5,213
    Page views
  • 1,251
    Downloads
  • 24
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Genetics and Genomics
    2. Neuroscience
    Marina Kovalenko et al.
    Research Article

    Somatic expansion of the Huntington's disease (HD) CAG repeat drives the rate of a pathogenic process ultimately resulting in neuronal cell death. Although mechanisms of toxicity are poorly delineated, transcriptional dysregulation is a likely contributor. To identify modifiers that act at the level of CAG expansion and/or downstream pathogenic processes, we tested the impact of genetic knockout, in HttQ111 mice, of Hdac2 or Hdac3 in medium-spiny striatal neurons that exhibit extensive CAG expansion and exquisite disease vulnerability. Both knockouts moderately attenuated CAG expansion, with Hdac2 knockout decreasing nuclear huntingtin pathology. Hdac2 knockout resulted in a substantial transcriptional response that included modification of transcriptional dysregulation elicited by the HttQ111 allele, likely via mechanisms unrelated to instability suppression. Our results identify novel modifiers of different aspects of HD pathogenesis in MSNs and highlight a complex relationship between the expanded Htt allele and Hdac2 with implications for targeting transcriptional dysregulation in HD.

    1. Cancer Biology
    2. Genetics and Genomics
    Annie Wai Yeeng Chai et al.
    Research Article

    New therapeutic targets for oral squamous cell carcinoma (OSCC) are urgently needed. We conducted genome-wide CRISPR-Cas9 screens in 21 OSCC cell lines, primarily derived from Asians, to identify genetic vulnerabilities that can be explored as therapeutic targets. We identify known and novel fitness genes and demonstrate that many previously identified OSCC-related cancer genes are non-essential and could have limited therapeutic value, while other fitness genes warrant further investigation for their potential as therapeutic targets. We validate a distinctive dependency on YAP1 and WWTR1 of the Hippo pathway, where the lost-of-fitness effect of one paralog can be compensated only in a subset of lines. We also discover that OSCCs with WWTR1 dependency signature are significantly associated with biomarkers of favourable response towards immunotherapy. In summary, we have delineated the genetic vulnerabilities of OSCC, enabling the prioritization of therapeutic targets for further exploration, including the targeting of YAP1 and WWTR1.