Leveraging Gene Redundancy to Find New Histone Drivers in Cancer

SIMPLE SUMMARY: Histones are a group of proteins that are essential for chromatin function. Histone coding genes have been found to be mutated in a number of cancers but how these mutations arise and whether they contribute to cancer biology remains largely unknown. Answering these questions is difficult because histone proteins are encoded by large families of genes that are thought to be redundant. Here, we overcome these limitations using a large dataset of whole exome sequencing data from cancer patients representing 68 different cancer types. We find that specific cancer types exhibit disproportionate susceptibilities to accruing mutations in histone genes versus other genes. We delineate factors influencing the probability of mutations accumulation in histone genes and detect new histone gene drivers. ABSTRACT: Histones play a critical role in chromatin function but are susceptible to mutagenesis. In fact, numerous mutations have been observed in several cancer types, and a few of them have been associated with carcinogenesis. Histones are peculiar, as they are encoded by a large number of genes, and the majority of them are clustered in three regions of the human genome. In addition, their replication and expression are tightly regulated in a cell. Understanding the etiology of cancer mutations in histone genes is impeded by their functional and sequence redundancy, their unusual genomic organization, and the necessity to be rapidly produced during cell division. Here, we collected a large data set of histone gene mutations in cancer and used it to investigate their distribution over 96 human histone genes and 68 different cancer types. This analysis allowed us to delineate the factors influencing the probability of mutation accumulation in histone genes and to detect new histone gene drivers. Although no significant difference in observed mutation rates between different histone types was detected for the majority of cancer types, several cancers demonstrated an excess or depletion of mutations in histone genes. As a consequence, we identified seven new histone genes as potential cancer-specific drivers. Interestingly, mutations were found to be distributed unevenly in several histone genes encoding the same protein, pointing to different factors at play, which are specific to histone function and genomic organization. Our study also elucidated mutational processes operating in genomic regions harboring histone genes, highlighting POLE as a factor of potential interest.