A Molecular Case Series: Deep Cellular and Spatial Epigenetic Characterization of Human Colorectal Cancer - PROJECT SUMMARY/ABSTRACT Cancer has long been thought of as a disease caused by genetic mutations that enable a cell to grow out of control. However, there is growing awareness of the importance of epigenetic aberrations – disruptions in the systems that control the transcriptional potential of genes – in cancer initiation and progression. Sufficient levels of DNA methyltransferase activity, which are responsible for the deposition of DNA methylation (an important epigenetic mark), have been shown to be necessary for formation of intestinal polyps in mouse models of colorectal cancer (CRC). Furthermore, hypermethylation of many genetic loci has been noted in CRC tissue samples. These hypermethylated loci are significantly enriched in genes targeted by the polycomb repressive complex (Polycomb Target Genes or PTGs), which play important roles in development and differentiation. Thus, suppression of PTGs by aberrant DNA methylation could contribute to the development and progression of CRC. However, it is unclear when and where these PTG hypermethylation (PTGH) events arise. They may arise as a result of genetic mutations, but studies of the cancer genome have failed to find any mutation linked to PTGH. Also, PTGH events have been found in histologically normal colorectal tissue. Thus, it is possible that PTGH accumulates over time in normal colorectal tissue, with excessive levels of this mark allowing malignant transformation. If this is the case, at least some PTGH events should be found clonally (in every cell of a tumor), because they existed in the founding cell of the tumor. The experiments outlined here are designed to test this model by constructing a detailed map of DNA methylation in human colorectal tumors and adjacent mucosa. Specifically, they aim to test the hypotheses that 1) PTGH exists in tumor-adjacent colorectal mucosa in a spatial and cellular distribution consistent with accumulation over time, and that 2) PTGH events are clonally present within CRC tumors. To achieve these goals, the proposed studies use bulk and single-cell whole-genome bisulfite sequencing techniques to measure genome-wide DNA methylation at single-base resolution. These studies will greatly strengthen our understanding of the cellular and spatial distribution of PTGH in CRC, giving us a better understanding of when and where this mark arises. Ultimately, these findings could help to develop more sensitive screening tests or earlier treatments for colorectal cancer. These studies will be conducted as part of the applicant’s training in a joint MD-PhD program sponsored by Michigan State University College of Human Medicine and Van Andel Institute (VAI). VAI provides a rich environment for research training, combining ample scientific resources with opportunities to learn from world- class scientists in a focused setting. The applicant will receive mentorship from leading experts in the field of DNA methylation, single-cell analysis, and bioinformatics, as well as many opportunities for collaboration, professional development, and continued clinical activity throughout the training program.
