PROJECT SUMMARY
DNA methylation is an epigenetic modification that plays a key role in regulating stem cells,
development and many diseases. Abnormal DNA methylation has been observed in cancer for more
than two decades, with many investigations focusing on promoter hypermethylation, which silences
tumor suppressor genes. Additionally, DNMT3A, one of de novo DNA methyltransferases, is
frequently mutated in a spectrum of hematological malignancies. Our lab has demonstrated that
Dnmt3a loss impairs hematopoietic stem cell (HSC) differentiation, while expanding HSC numbers in
bone marrow, suggesting DNMT3A may have a role in tumorigenesis and stem cell regulation.
However, DNA methylation profiling of leukemia patient samples shows DNA methylation correlates
poorly with gene expression across the genome, highlighting our limited understanding of the specific
functions of DNA methylation. Recent studies using a murine model of the most frequent DNMT3A
mutation in hematological malignancies, DNMT3AR882, demonstrated that DNMT3AR882 cooperates
with FLT3-ITD and NPM1c mutations to contribute to leukemic transformation. Nevertheless, our
knowledge of which remaining DNMT3A mutations lead to leukemogenesis and the mechanisms by
which they contribute to cancer formation remains lacking. Therefore, the long-term goal of the
proposed research is to understand how DNMT3A affects gene regulation in cancer, and how
DNMT3A mutants predispose stem cell expansion. In Aim 1, I established a novel DNA epigenome
editing tool (dCas9-SunTag-DNMT3A system) to investigate the causal relationship between DNA
methylation and gene expression. Using pan-cancer analysis of genome-wide profiles, we have
identified DNA hypermethylation occurring in the gene-body regions of canyons (broad and
undermethylated regions) with activation of corresponding gene expression. In Aim 2, using a
Dnmt3a mutant murine model I developed, I will elucidate the role of one Dnmt3a mutant in priming
stem cell expansion. The findings from this proposed research will shed the light on abnormal DNA
methylation in cancer and molecular mechanisms of DNMT3A-associated malignancies. Little is
known about how mutations in epigenetic modifiers affect the 3D genomic structure in cancer.
Therefore, in Aim 3, I plan to use my postdoctoral studies to understand how epigenetic modifiers
shape the genomic landscape in cancer and their underlying mechanism. This training program is
tailored to give me a comprehensive education in basic science research that will be extremely useful
in achieving my long-term career goal of becoming an independent cancer researcher.