Identification and Clinical Validation of Key Transcription Factor Isoforms Linked to Breast and Prostate Cancer Subgroups using Epigenetic Traits PROJECT SUMMARY/ABSTRACT The clinical behavior and progression of breast and prostate cancers vary case by case, in large part due to different characteristics of tumor subtypes. Clearly, different treatment regimens should be used to treat each tumor subgroup. Therefore, a comprehensive understanding of the mechanisms and molecular features that can distinguish tumor subgroups is of great importance, both for mechanistic insight and diagnostic/prognostic utility. Regulatory elements such as promoters and enhancers contain multiple transcription factor (TF) binding sites, which can alter expression of the genes they regulate. Of note, the active state of specific subsets of regulatory elements annotated by epigenomic profiles is highly linked to cellular identity and is altered in human diseases. I hypothesize that there are specific TFs differentially active in each breast and prostate tumor subtype and that these TFs inappropriately activate a set of tumor-specific regulatory elements, leading to altered expression of genes involved in disease phenotypes. To facilitate identifying the critical TFs linked to activated regulatory elements in tumor tissue samples, I developed a method called TENET (Tracing Enhancer Networks using Epigenetic Traits) that measures relationships (intra- and inter-chromosomal) between DNA methylation levels at enhancers and expression levels of all human genes. I now propose to extend my preliminary work by expanding the functionality of TENET such that I can include analysis of individual TF isoforms linked to breast and prostate cancer subgroups. I will first begin by identifying TF isoforms and activated regulatory elements, specific to each tumor subtype using epigenomic datasets from tissue samples (Aim 1). I will then characterize the molecular function of several selected key TF isoforms linked to specific tumor subtypes, mapping their binding sites and deciphering their target gene networks (Aim 2). Lastly, I will prioritize TF isoforms related to cancer progression and outcome using tumor tissue datasets and cancer patient information, in collaboration with clinicians (Aim 3). During my K01 period, I will acquire advanced training in bioinformatics and molecular biology, and newly explore translational genomics and precision medicine under the mentorship of Dr. Farnham and the other members of my mentoring team who have expertise in DNA methylation and epigenomic analyses (Drs. Berman, Carpten) and the biology of breast and prostate cancer and clinical translation (Drs. Press, Carpten, and Goldkorn). I will also participate in career development opportunities at USC, which places a strong emphasis on leadership and professional growth, hosting grant-writing, research funding strategy, responsible conduct of research, management and ethics, and mentorship workshops. As USC is a nurturing, collaborative research environment with many talented scientists, I will be able to acquire the training, resources, and networks of collaborators necessary to become an independent researcher, with expertise in bioinformatics, molecular biology, and clinical studies. My goal is to transition from the K01 into a tenure-track assistant professor position at a top-tier academic research institution with exceptional cancer and genomics programs.
Epigenetic changes may lead to loss of cell growth control and cancer in a variety of tissues. This proposal addresses an unmet medical need by characterizing key regulatory factors linked to carcinogenesis in breast and prostate tumor subgroups using bioinformatics, molecular biology, and translational genomics. The findings generated from this project will identify new factors that can improve breast and prostate cancer outcomes with precision medicine and provide a new perspective as to how epigenetics may contribute to cancer.
|Rhie, Suhn K; Schreiner, Shannon; Witt, Heather et al. (2018) Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv 4:eaav8550|