CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing

PLoS Genet. 2019 Oct 21;15(10):e1008464. doi: 10.1371/journal.pgen.1008464. eCollection 2019 Oct.

Abstract

SF3B1 is the most frequently mutated splicing factor in cancer. Mutations in SF3B1 likely confer clonal advantages to cancer cells but they may also confer vulnerabilities that can be therapeutically targeted. SF3B1 cancer mutations can be maintained in homozygosis in C. elegans, allowing synthetic lethal screens with a homogeneous population of animals. These mutations cause alternative splicing (AS) defects in C. elegans, as it occurs in SF3B1-mutated human cells. In a screen, we identified RNAi of U2 snRNP components that cause synthetic lethality with sftb-1/SF3B1 mutations. We also detected synthetic interactions between sftb-1 mutants and cancer-related mutations in uaf-2/U2AF1 or rsp-4/SRSF2, demonstrating that this model can identify interactions between mutations that are mutually exclusive in human tumors. Finally, we have edited an SFTB-1 domain to sensitize C. elegans to the splicing modulators pladienolide B and herboxidiene. Thus, we have established a multicellular model for SF3B1 mutations amenable for high-throughput genetic and chemical screens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / drug effects
  • Alternative Splicing / genetics
  • Animals
  • Antineoplastic Agents / pharmacology
  • Antineoplastic Agents / therapeutic use
  • CRISPR-Cas Systems
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans Proteins / genetics*
  • Disease Models, Animal
  • High-Throughput Screening Assays / methods
  • Homozygote
  • Humans
  • Mutation, Missense
  • Neoplasms / drug therapy
  • Neoplasms / genetics*
  • Protein Domains / genetics
  • RNA Interference
  • RNA Splicing Factors / genetics*
  • Ribonucleoprotein, U2 Small Nuclear / genetics*
  • Spliceosomes / drug effects
  • Synthetic Lethal Mutations

Substances

  • Antineoplastic Agents
  • Caenorhabditis elegans Proteins
  • RNA Splicing Factors
  • Ribonucleoprotein, U2 Small Nuclear

Grant support

This work has been supported by a grant from the Instituto de Salud Carlos III (ISCIII), http://www.isciii.es/, to JC (PI15-00895), co-funded by FEDER funds/European Regional Development Fund (ERDF) — a way to build Europe, https://ec.europa.eu/regional_policy/en/funding/erdf/. AEC is funded by ISCIII, http://www.isciii.es/, of the MINECO (reference PT17/0009/0019) and co-financed by FEDER, https://ec.europa.eu/regional_policy/en/funding/erdf/. EC is supported by a Pasteur-Roux postdoctoral fellowship program, https://research.pasteur.fr/en/call/call-for-application-pasteur-roux-and-pasteurcantarini- postdoctoral-fellowships-2019-spring-session/. XS has an FPU PhD fellowship from MINECO, http://www.educacionyfp.gob.es/servicios-al-ciudadano-mecd/becas-ayudas.html. DK has an FI AGAUR fellowship from Generalitat de Catalunya, http://agaur.gencat.cat/en/inici/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.