Leveraging epigenetic and epitranscriptomic aberrations in cancer to identify molecular targets for designing therapy

PROJECT SUMMARY Myelodysplastic syndromes (MDS) are clonal, heterogeneous disorders caused due to ineffective hematopoiesis characterized by refractory anemia and erythroid dysplasia. To uncover genes responsible for dysplastic erythropoiesis in MDS, our group performed methylome analysis of blood cells from MDS patients which revealed DOCK4 (Dedicator of cytokinesis 4), a guanine exchange factor was significantly hyper- methylated and under-expressed in MDS. DOCK4 is differentially expressed at various stages of the erythroid differentiation program suggesting that it has stage-specific functions. Although DOCK4 functions in other cell types have been described, its function during blood cell development is unknown. Based on this information, I hypothesize that DOCK4 is an important signaling protein that is instrumental in regulating overall cell shape and promoting terminal maturation of hematopoietic stem/progenitor cells (HSPCs) into erythrocytes. The overall goal of my research is to uncover the functional significance of DOCK4 at various stages of differentiation and elucidating the mechanisms underlying this regulation. In our recent study, I demonstrated that deficiency of DOCK4 resulted in erythroid dysplasia by disrupting F-actin organization and re-expression of DOCK4 improved the observed erythropoietic defects. During the remainder of my Ph.D., I will identify various cellular and signaling pathways deregulated by DOCK4 using primary human CD34+ HSPC derived erythroblasts haploinsufficient for DOCK4. In addition, I will determine whether modulation DOCK4 pathway by small molecule drugs can ameliorate the erythroid dysplasia caused by reduced levels of DOCK4 ex vivo using MDS erythroblasts. Altogether, the outlined studies will conclusively establish the signaling circuits perturbed by DOCK4 during malignant erythropoiesis and likely to identify novel treatment strategies for MDS patients. In addition to epigenetic mechanisms, cells possess an extra layer of RNA regulatory mechanisms where specific bases of the RNA are reversibly and dynamically modified during various cellular processes. Proteins regulating specific RNA modifications such as N6-methyladenosine and 5-methylcytosine are deregulated commonly in breast cancer however; the roles of RNA modifications in cancer pathogenesis are unknown. Therefore, it is of utmost importance to understand how tumors rewire the regulation of RNA modification mechanisms for their advantage. I want to dedicate my post-doctoral research to elucidate the key role/s played by specific RNA modifications during cancer development and progression. My proposed post- doctoral research focuses on studying the dynamic regulation of specific RNA modifications and the signaling pathways regulating it during breast cancer initiation and progression using genetically engineered mouse models, cell lines and patient samples. Understanding how tumors disrupt the regulatory pathways and studying the molecular mechanisms underlying it will potentially lead to novel treatment strategies.