Understanding the origins of the mutational landscape in cancer - PROJECT SUMMARY Exposure to environmental genotoxins poses a considerable risk, contributing to the formation of pro-mutagenic DNA lesions. These DNA lesions, in turn, can give rise to mutations and ultimately contribute to the development of cancer. Unfortunately, our knowledge of the precise origins of subsequent mutations has been hampered by the inability to comprehensively characterize the DNA lesion landscape, comprised of both the type (DNA adductome) and genomic positions of the DNA lesions. This lack of knowledge about the DNA lesion landscape has resulted in an inability to precisely link DNA lesions to subsequent mutational outcomes. Indeed, many common mutations found in human cancers are known to be derived from error-prone endogenous processes. This may explain the low level of agent-specific mutations reported in tumors, despite strong epidemiological evidence that environmental agents play key roles in carcinogenesis. Consequently, it is currently unknown whether mutations are the result of exposure-induced DNA lesions or arise indirectly from endogenous processes. We hypothesize that the error-prone endogenous processes significantly contribute to mutagenesis and are enhanced upon exposure to environmental mutagens. The overall objective of our proposed project is to elucidate the origins of mutational landscapes by adopting a highly synergistic approach that integrates cellular DNA adductomics, Nanopore long-read sequencing, and single-molecule duplex sequencing. Each platform will generate a specific dataset that relates to, respectively, DNA lesion types/amounts, DNA lesion positions/types, and mutation types/positions, along with a probability of the mechanisms involved. These complementary datasets will be analyzed for causal relationships among key DNA lesions and mutational outcomes, whether derived directly from exogenous DNA lesions or via endogenous processes. Here, we focus on 1,2,3- Trichloropropane (TCP), bromochloroacetic acid (BCA), and furan as representative environmental mutagens known for their characteristic pro-mutagen DNA lesions and mutational signatures. First, we will generate DNA suitable for studying endogenously and exogenously derived DNA lesions and mutational landscapes and generate DNA adductomes, using stable isotope labeling and high-resolution mass spectrometry (Aim 1). Second, we will map the genomic positions of DNA lesions using Nanopore sequencing (Aim 2). Lastly, we will determine the mutational landscape and build a model for predicting the probabilities of acquiring somatic mutations from DNA lesions (Aim 3). This synergistic analysis of the DNA adductome and mutational landscape will provide unprecedented insights about the positions and frequencies of exogenous and endogenous DNA lesions and subsequent mutational outcomes. This translational ViCTER project will elucidate the origins of novel and established mutational signatures and will contribute significantly to our understanding of the dynamics of the endogenous and exogenous DNA adductomes and their role in environmentally induced mutagenesis, thereby addressing key questions in cancer biology.
