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Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

Cigall Kadoch1, Diana C Hargreaves, Courtney Hodges

  • 1Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

Nature Genetics
|May 7, 2013
PubMed

Insights

Mammalian SWI/SNF (mSWI/SNF) subunits act as tumor suppressors. Mutations in these chromatin-regulatory complexes are found in nearly 20% of human cancers, highlighting their critical role in cancer suppression.

Area of Science:

  • Molecular Biology
  • Genetics
  • Oncology

Background:

  • Mammalian SWI/SNF (mSWI/SNF) complexes, also known as BAF complexes, are increasingly recognized for their roles as tumor suppressors in human cancers.
  • Understanding the complete subunit composition and mutation landscape of mSWI/SNF is crucial for elucidating their full impact on tumorigenesis.

Purpose of the Study:

  • To perform a comprehensive proteomic analysis of endogenous mSWI/SNF complexes to identify novel subunits.
  • To determine the mutation frequency of mSWI/SNF subunits across a wide range of human tumors.
  • To investigate the tissue-specific roles and prevalence of compound heterozygosity in mSWI/SNF mutations.

Main Methods:

  • Proteomic analysis of endogenous mSWI/SNF complexes to identify subunit composition.
  • Analysis of exome and whole-genome sequencing data from primary human tumors to assess mutation frequency.
  • Bioinformatic analysis to correlate subunit mutations with specific cancer types and tissues.

Main Results:

  • Identification of several new stable subunits of mSWI/SNF complexes, including BCL7A, BCL7B, BCL7C, BCL11A, BCL11B, BRD9, and SS18.
  • mSWI/SNF subunits are collectively mutated in 19.6% of human tumors across 44 studies.
  • Specific subunits show protective roles in distinct tissues, and compound heterozygosity is common in certain cancers.

Conclusions:

  • mSWI/SNF is the most frequently mutated chromatin-regulatory complex (CRC) in human cancer, with a mutation pattern similar to TP53.
  • The proper function of polymorphic BAF complexes is essential for tumor suppression.
  • These findings underscore the critical role of mSWI/SNF complexes in preventing cancer development.

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