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VHL Synthetic Lethality Signatures Uncovered by Genotype-Specific CRISPR-Cas9 Screens

Ning Sun1, Sakina Petiwala1, Charles Lu1

  • 1AbbVie Inc., North Chicago, Illinois.

The CRISPR Journal
|August 23, 2019
PubMed

Insights

Researchers used CRISPR screening to find synthetic lethal partners for the VHL gene in clear cell renal cell carcinoma. This identified new targets like DNA damage response and selenocysteine pathways for cancer therapy.

Area of Science:

  • Oncology
  • Genetics
  • Molecular Biology

Background:

  • The von Hippel-Lindau (VHL) tumor suppressor gene is frequently inactivated in clear cell renal cell carcinoma (ccRCC).
  • Identifying synthetic lethal (SL) genes that are essential only in VHL-deficient cancer cells offers therapeutic opportunities.
  • Genome-wide CRISPR-Cas9 screening is a powerful tool for discovering genetic vulnerabilities.

Purpose of the Study:

  • To identify novel synthetic lethal (SL) partners of the VHL gene in clear cell renal cell carcinoma (ccRCC).
  • To explore potential drug targets for VHL-mutated cancers using a CRISPR-based screening strategy.

Main Methods:

  • Performed parallel genome-wide CRISPR-Cas9 essentiality screens in isogenic ccRCC cell lines differing in VHL status.
  • Utilized comparative analysis of screening data to identify genes synthetically lethal with VHL inactivation.
  • Conducted follow-up studies to provide cellular and mechanistic insights into identified SL interactions.

Main Results:

  • Confirmed the role of mTOR signaling and identified DNA damage response and selenocysteine biosynthesis pathways as novel SL targets in VHL-inactivated ccRCC cells.
  • Provided cellular and mechanistic validation for the identified SL interactions.
  • Generated valuable CRISPR and RNA-seq datasets for VHL tumor suppressor research.

Conclusions:

  • CRISPR-based synthetic lethality screening is efficient in human isogenic cell pairs for identifying cancer targets.
  • Novel SL targets in DNA damage response and selenocysteine biosynthesis pathways were discovered for VHL-deficient ccRCC.
  • This strategy can be applied to discover SL partners for other oncogenic drivers in cancer therapy development.

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