Cancer Histone Mutations Impact Binding and DNA Repair Processes, Leading to Increased Mutagenesis

Abstract

Histones are key epigenetic factors for regulating the accessibility and compaction of eukaryotic genomes, affecting the replication, repair, and expression of DNA. Recent studies have demonstrated that histone missense mutations can perturb normal histone function, promoting the development of phenotypically distinguishable cancers. However, most histone mutations observed in cancer patients remain enigmatic in their potential to promote cancer development. To assess the oncogenic potential of histone missense mutations, we have gathered whole-exome sequencing data for the tumors of over 12,000 patients. Overall, histone mutations occurred in about 16% of cancer patients, although specific cancer types showed substantially higher rates. Using a combination of genomic, structural, and biophysical analyses, we found several predominant modes of action, where cancer missense mutations in histones affected acidic patches and protein binding interfaces in a cancer-specific manner and targeted interaction sites with specific DNA repair proteins. Consistent with this finding, we observed a high tumour mutational burden in patients with histone mutations affecting interactions of DNA repair proteins. We also identified potential cancer driver mutations in several histone genes, including histone H4-a highly conserved histone without previously documented driver mutations.