Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers

Justin Ashworth, Brady Bernard, Sheila Reynolds, Christopher Plaisier, Ilya Shmulevich, Nitin S. Baliga

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Thousands of unique mutations in transcription factors (TFs) arise in cancers, and the functional and biological roles of relatively few of these have been characterized. Here, we used structure-based methods developed specifically for DNA-binding proteins to systematically predict the consequences of mutations in several TFs that are frequently mutated in cancers. The explicit consideration of protein-DNA interactions was crucial to explain the roles and prevalence of mutations in TP53 and RUNX1 in cancers, and resulted in a higher specificity of detection for known p53-regulated genes among genetic associations between TP53 genotypes and genome-wide expression in The Cancer Genome Atlas, compared to existing methods of mutation assessment. Biophysical predictions also indicated that the relative prevalence of TP53 missense mutations in cancer is proportional to their thermodynamic impacts on protein stability and DNA binding, which is consistent with the selection for the loss of p53 transcriptional function in cancers. Structure and thermodynamics-based predictions of the impacts of missense mutations that focus on specific molecular functions may be increasingly useful for the precise and large-scale inference of aberrant molecular phenotypes in cancer and other complex diseases.

Original languageEnglish (US)
Pages (from-to)12973-12983
Number of pages11
JournalNucleic Acids Research
Volume42
Issue number21
DOIs
StatePublished - Dec 1 2014
Externally publishedYes

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Transcription Factors
Gene Expression
Mutation
Neoplasms
Missense Mutation
Thermodynamics
Genome
Protein Stability
Atlases
DNA
p53 Genes
DNA-Binding Proteins
Genotype
Phenotype
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers. / Ashworth, Justin; Bernard, Brady; Reynolds, Sheila; Plaisier, Christopher; Shmulevich, Ilya; Baliga, Nitin S.

In: Nucleic Acids Research, Vol. 42, No. 21, 01.12.2014, p. 12973-12983.

Research output: Contribution to journalArticle

Ashworth, Justin ; Bernard, Brady ; Reynolds, Sheila ; Plaisier, Christopher ; Shmulevich, Ilya ; Baliga, Nitin S. / Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers. In: Nucleic Acids Research. 2014 ; Vol. 42, No. 21. pp. 12973-12983.
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