This proposal aims to investigate how epigenetic tumor suppressors regulate tumorigenesis and their impact on tumor-immune crosstalk. Inactivating mutations of tumor suppressor genes encoding epigenetic regulators have been frequently detected in several major types of solid tumors such as lung adenocarcinoma and clear cell renal cell carcinoma (ccRCC). Among them, SETD2 is one of the top hits, which is the third most frequently mutated gene in ccRCC (13%) and the most frequently mutated epigenetic modifier in lung adenocarcinoma (9%). SETD2 encodes a non-redundant histone H3K36 trimethyltransferase, which is responsible for co-transcriptional tri-methylation of H3K36me2 to generate H3K36me3 in actively transcribed gene bodies. My doctoral research focuses on studying the tumor suppressor functions of SETD2 in lung tumorigenesis using a recently generated Setd2 conditional knockout mouse model. The long-term goal of the proposed thesis project is to address the molecular mechanisms underlying how SETD2 loss-of-function promotes lung tumorigenesis and identify therapeutic strategies for SETD2 mutant lung cancers. The thesis work to date, as outlined in Specific Aims 1.1-1.4, has demonstrated that Setd2 loss cooperates with KrasG12D to promote lung tumorigenesis. RNA-seq and ATAC-seq conducted on dissected murine lung tumors have revealed a novel tumor suppressor mechanism of SETD2 through regulation of chromatin accessibility and intronic enhancer activity to drive oncogenic transcriptional outputs. The mechanistic studies have uncovered a therapeutic vulnerability associated with SETD2 loss. Both in vitro and in vivo data have suggested that patients with SETD2 mutant tumors may benefit from pharmacological inhibition of transcription. The remainder of my dissertation research will continue to elucidate the genome-wide correlation between increased chromatin accessibility and activated enhancers in Setd2-deficient lung tumors by performing ChIP- seq and assess the functional importance of these active enhancers as proposed in Specific Aim 1.5. Another question to be addressed is whether and how SETD2 loss promotes lung tumor metastasis as outlined in Specific Aim 1.6. The proposed postdoctoral research will investigate how epigenetic tumor suppressors affect the tumor-immune interaction by conducting single-cell RNA-seq (scRNA-seq) on dissected solid tumors in genetically engineered mouse models (GEMMs). This project will focus on several tumor suppressor genes encoding epigenetic modifiers that are frequently mutated in ccRCC (Specific Aim 2.1) and lung adenocarcinoma (Specific Aim 2.2). The ultimate goal of the postdoctoral project is to understand the mechanistic links between tumor intrinsic genetic/epigenetic/transcriptional alterations and tumor-immune crosstalk, which may help identify potential therapeutic targets for immunotherapy.
Lung cancer is the leading cause of cancer death, and around 40% of diagnosed lung cancers are lung adenocarcinoma, characterized by high mutational load and poor survival. The proposed mechanistic studies in the doctoral phase of this project will help understand the pathogenesis of SETD2-deficient lung tumors and uncover therapeutic vulnerability associated with SETD2 loss. The proposed postdoctoral project will dissect mechanistic link between epigenetic tumor suppressors and tumor-immune crosstalk, which will provide novel insight into cancer immunotherapy.