Elucidating the impact of DNA hypomethylation on genome organization and anti-tumor transcriptional programs

PROJECT SUMMARY This proposed research career development program seeks to investigate the impact of DNA hypomethylation on genome organization and the mechanisms by which it drives downstream tumor suppressive transcriptional programs. The candidate is currently a clinical and research fellow in the Department of Pathology of the Massachusetts General Hospital. The proposal

incorporates specific technical skills that will be required for the project including training in advanced microscopy methods, CRISPR techniques and repetitive element biology. The structured career development plan includes training and mentorship in laboratory management, scientific leadership, research communication, grant writing, and other critical career skills. These technical

and career skills will be acquired under the guidance of Dr. Bradley Bernstein, who will serve as primary mentor and has a history of trainees that obtain group leader positions in academia, as well as a Research Advisory Committee of world-class scientists including Drs. Kathleen Burns, Ting Wu, Keith Joung and Nir Hacohen. Through this comprehensive program the candidate will

acquire a unique set of clinical and research skills that will enable her to transition to an independent physician scientist faculty position with a lab focused on basic mechanisms and therapeutic opportunities in cancer epigenetics. DNA hypomethylation is an epigenetic alteration found in most solid tumors, but its functional

consequences are not clearly defined. DNA demethylating therapies are widely used in the clinic for treatment of myelodysplastic syndrome and a subset of leukemias, and have recently been shown to sensitize tumor cells to immunotherapy, possibly through activation of ERVs. Despite this, the functional consequences of DNA hypomethylation and ERV activation remain obscure.

This project explores the mechanistic basis of findings in the candidate’s recent study of genome organization in primary colon tumors. The results link DNA hypomethylation to striking changes in the organization of chromatin compartments that are associated with tumor suppressive transcriptional programs, including induction of ERVs. The aims of this proposal are to: (1)

Investigate if DNA hypomethylation causes chromatin reorganization, (2) test if massive ERV upregulation is a mechanistic link between hypomethylation and compartment reorganization and (3) determine impact of downstream transcriptional programs. These studies will uncover novel epigenetic mechanisms that impact tumor cell identity and lay the foundation for deploying

demethylating therapies in new clinical settings to harness tumor-suppressive consequences of DNA hypomethylation.