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: Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600 13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts. Variations in mutation rates across the genome have been demonstrated both in model organisms and in cancers. This phenomenon is largely driven by the damage specificity of diverse mutagens and the differences in DNA repair efficiency in given genomic contexts. Here, we demonstrate that the single-strand DNA-specific cytidine deaminase APOBEC3B (A3B) damages tRNA genes at a 1000-fold higher efficiency than other non-tRNA genomic regions in budding yeast. We found that A3B-induced lesions in tRNA genes were predominantly located on the non-transcribed strand, while no transcriptional strand bias was observed in protein coding genes. Furthermore, tRNA gene mutations were exacerbated in cells where RNaseH expression was completely abolished (rnh1rnh35). These data suggest a transcription-dependent mechanism for A3B-induced tRNA gene hypermutation. Interestingly, in strains proficient in DNA repair, only 1% of the abasic sites formed upon excision of A3B-deaminated cytosines were not repaired leading to mutations in tRNA genes, while 18% of these lesions failed to be repaired in the remainder of the genome. A3B-induced mutagenesis in tRNA genes was found to be efficiently suppressed by the redundant activities of both base excision repair (BER) and the error-free DNA damage bypass pathway. On the other hand, deficiencies in BER did not have a profound effect on A3B-induced mutations in CAN1, the reporter for protein coding genes. We hypothesize that differences in the mechanisms underlying ssDNA formation at tRNA genes and other genomic loci are the key determinants of the choice of the repair pathways and consequently the efficiency of DNA damage repair in these regions.
