Genome-wide hypermutation and structural instability

National Institute Of Environmental Health Sciences

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Abstract

Purpose or scope: A role for somatic mutations in carcinogenesis and genetic disease is well accepted, but the degree to which mutation rates influence cancer initiation and development is under continuous debate. Recently accumulated genomic data has revealed that thousands of tumor samples are riddled by hypermutation, broadening support that many cancers acquire a mutator phenotype. This major expansion of cancer mutation datasets has provided unprecedented statistical power for the analysis of mutation spectra, which has confirmed several classical sources of mutation in cancer, highlighted new prominent mutation sources and empowered the search for cancer drivers. In our work we combined mechanistic knowledge obtained through our experiments with yeast models to interrogate the large whole-genome datasets of cancer mutations in order to gain mechanistic insight for understanding the impact of mutations on cancer and genetic disease. Research subject: The optimal levels of genome instability needed to sustain fitness of an organism are maintained by a complex set of DNA metabolic functions and pathways. Understanding the interplay between the biological mechanisms maintaining a stable genome and the environmental factors promoting genome instability is important for improving policies pertaining to the impact of the environment on human health. My long-term interest is in understanding physiological mechanisms and environmental causes of extreme levels of genome instability that can give rise to diseases and may alter the life-span of organisms. During the reviewed period, me and my group addressed these questions by combining the following general approaches: (i) Gaining new mechanistic information through research in yeast models reporter based and whole-genome sequencing. This approach elucidates mechanisms of genome instability and defines their specific features. (ii) Using mechanistic knowledge acquired from small genome studies for designing analyses of publicly available large datasets of genome changes in human cancers. Knowledge acquired from mechanistic research in yeast allows to build stringent statistical hypotheses thereby increasing the statistical power in bioinformatic interrogation of the exponentially growing datasets of cancer genomics such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). (iii) Assessing load and signatures of somatic genome changes in humans. Analytical pipeline and information about mutation signatures generated through interrogation of cancer genomics data sets are applied to whole-genome sequencing analyses of cells isolated from healthy individuals. The combination of approaches (i) and (iii) provides additional research opportunities by way of using new knowledge generated through bioinformatic analysis of large public datasets and through sequencing genomes of human subjects for developing the next level of mechanistic hypotheses testable via small genome systems. Accomplishments: Most solid tumors harbor somatic mutations attributed to off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B). However, how APOBEC3A/B enzymes affect tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, multi-omics profiling of 309 lung cancers from smokers identifies two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations; HAS for A3A-like mutagenesis and TP53 mutations. Compared to LAS, HAS have older age at onset and high proportions of newly generated progenitor-like cells likely due to the combined tobacco smoking- and APOBEC3A-associated DNA damage and apoptosis. Consistently, HAS exhibit high expression of pulmonary healing signaling pathway, stemness markers, distal cell-of-origin, more neoantigens, slower clonal expansion, but no smoking-associated genomic/epigenomic changes. With validation in 184 lung tumor samples, these findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development. Environmental exposures significantly influence cancer risk, but their mutational impact remains unclear. We perform whole-exome sequencing of hepatocellular carcinomas (HCCs) from B6C3F1/N mice that arise spontaneously with age (2 years old) or following chronic exposure to one of ten potential human carcinogens that operate through genotoxic or non-genotoxic mechanisms. HCCs from mice exposed to drinking water disinfection byproducts, such as bromochloroacetic acid (BCA) and bromodichloroacetic acid (BDCA), show dose-dependent increases in mutational burden, distinct mutational signatures (BCA-mSBS12 and BDCAmSBS25), and enrichment of the aTn→aCn mutational motif. In contrast, HCCs from other exposures, as well as from spontaneous tumors, show comparable mutational burdens, mutational signatures, and enrichment of the nCg→nTg mutational motif. These findings suggest that many environmental carcinogens promote tumorigenesis by amplifying endogenous mutagenic processes rather than initiating distinct mutational events. Our results highlight the utility of rodent models for investigating environmental carcinogenesis and provide insights relevant to human cancer risk assessment. Highlights: --Many environmental carcinogens amplify endogenous mutational processes --Exacerbation of endogenous mutagenic processes may contribute to tumor promotion --Genotoxicity of some mutagenic agents appears to be dose dependent --Carcinogen-specific mutational signatures in mice are also noted in human cancers