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Principal Investigator: Keith D Robertson
Organization: MAYO CLINIC ROCHESTER
Fiscal Year: 2024
Award: $226,364
Funding agency: National Cancer Institute
ABSTRACT
Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers and is the 8th leading
cause of cancer death in the United States. In addition to near ubiquitous loss of VHL, the landscape of ccRCC
is dominated by mutations in epigenetic regulators SETD2, PBRM1, and BAP1. The epigenome is profoundly
disrupted in ccRCC with defects in epigenetic marks on DNA, RNA, and histones, culminating in aberrant gene
expression. Mutations in the SETD2 histone H3 lysine 36 trimethylase occur in ~25% of primary ccRCC but
increase to >60% in ccRCC metastases. Completion of TCGA enabled identification of actionable mutations in
virtually every solid tumor and those profiles now drive treatment decisions. One major exception, however, is
RCC, where the current standard of care, checkpoint inhibitor and anti-VEGF therapy, does not account for
~50% of RCCs having mutations in chromatin regulators like SETD2. Many ccRCCs display heterogeneous
and subclonal intratumor SETD2 mutations, but we do not understand how SETD2 loss deregulates cell
growth and what pathways it works through. After first-line therapy, response rates are 20%, highlighting the
need to understand and target drivers of metastasis like SETD2. A recent novel finding linked SETD2 activity
to the targeting of N6-methyladenosine in mRNA, a key mechanism for controlling many RNA metabolic
processes, which has also been shown to be deregulated in cancer and contribute to metastatic processes.
Our preliminary data demonstrate that SETD2 loss leads to large-scale re-localization of m6A and an
enhanced sensitivity to an m6A inhibitor that is entering clinical trials. This SETD2-m6A link has not been
explored in a ccRCC context but could represent a novel SETD2 effector mechanism and drug target in
ccRCC. We explore this relationship for the first time with this pilot R21 study, making it directly relevant to
NOT-CA-23-060, RNA Modifications in Cancer Biology. Our proposal is significant because ~30% of patients
diagnosed with clinically localized RCC experience metastatic progression, and once metastatic disease
develops only ~7% survive >5 years. Our central hypothesis is that loss of SETD2 drives aggressive ccRCC in
part through deregulated m6A targeting that promotes a pro-metastatic expression program. Our proposal is
expected to develop relevant ccRCC cell line models and define the links between SETD2/H3K36me3 and
METTL3/m6A in ccRCC through the following specific aims. In aim 1, we will map H3K36me3, m6A, METTL3,
and expression patterns using RIP-/ChIP-/RNA-seq in novel SETD2 isogenic renal cell line models. In aim 2,
we will perform integrative analysis of omics data to uncover genes/pathways impacted by SETD2 loss in an
m6A-dependent manner. Finally, in aim 3 we will genetically and pharmacologically modulate m6A in SETD2
isogenic cell lines and define cancer-relevant cellular growth phenotypes. This work is expected to positively
affect human health by yielding a new understanding of the mechanistic underpinnings of SETD2 driven cell
growth deregulation and uncovering new ways to therapeutically target this mutation.
Terms: <ADP-Ribosylation Factor GTPase-Activating Protein with FG Repeats 1><AGFG1><AGFG1 gene><ARFGAP with FG Repeats 1><Aberrant DNA Methylation><Affect><Anti-VEGF><Anti-VEGF Humanized Monoclonal Antibody><Anti-VEGF RhuMAb><Body Tissues><CRISPR><CRISPR/Cas system><Cancer Biology><Cancer Cause><Cancer Etiology><Cancer cell line><Cancers><Cell Body><Cell Death><Cell Line><Cell model><CellLine><Cells><Cellular Expansion><Cellular Growth><Cellular model><Cessation of life><Checkpoint inhibitor><Chromatin><Clear cell renal cell carcinoma><Clinical><Clinical Trials><Clustered Regularly Interspaced Short Palindromic Repeats><Complex><DNA><DNA Damage Repair><DNA Repair><Data><Death><Defect><Deoxyribonucleic Acid><Deposit><Deposition><Diagnosis><Disease><Disorder><Drug Targeting><Drugs><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Epithelial Cells><Frequencies><Gene Alteration><Gene Expression><Gene Mutation><Gene Transcription><Generalized Growth><Genes><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Grawitz Tumor><Growth><HIV-1 REV-Binding Protein><HRB gene><HRB protein><Health><Histone H3><Histones><Human><Hypernephroid Carcinoma><Hypernephroma><Immune checkpoint inhibitor><Intermediary Metabolism><Invaded><Kidney><Kidney Cancer><Kidney Carcinoma><Kidney Urinary System><L-Lysine><Laboratories><Link><Lysine><Malignant Neoplasms><Malignant Pancreatic Neoplasm><Malignant Tumor><Malignant Tumor of the Lung><Malignant Tumor of the Prostate><Malignant neoplasm of lung><Malignant neoplasm of pancreas><Malignant neoplasm of prostate><Malignant prostatic tumor><Maps><Medication><Messenger RNA><Metabolic Processes><Metabolism><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Tumor><MoAb VEGF><Modeling><Modern Man><Modification><Monoclonal Antibody Anti-VEGF><Mutate><Mutation><Nature><Neoplasm Metastasis><Nephroid Carcinoma><Non-Polyadenylated RNA><Pancreas Cancer><Pancreatic Cancer><Pathway interactions><Patients><Pattern><Pharmaceutical Preparations><Phenotype><Physiologic><Physiological><Process><Proliferating><Prostate CA><Prostate Cancer><Prostate malignancy><Prostatic Cancer><Proximal Kidney Tubules><Pulmonary Cancer><Pulmonary malignant Neoplasm><RAB gene><RAB protein><REV-Interacting Protein><REV/REX Activation Domain-Binding Protein><RIP gene><RIP protein><RNA><RNA Expression><RNA Gene Products><RNA Seq><RNA Splicing><RNA methylation><RNA sequencing><RNAseq><Recombinant Humanized Anti-VEGF Monoclonal Antibody><Recombinant Humanized Monoclonal Antibody to Vascular Endothelial Growth Factor><Recurrence><Recurrent><Regulator Genes><Renal Adenocarcinoma><Renal Cancer><Renal Carcinoma><Renal Cell><Renal Cell Adenocarcinoma><Renal Cell Cancer><Renal Cell Carcinoma><Reporting><RhuMAb VEGF><Ribonucleic Acid><Role><Secondary Neoplasm><Secondary Tumor><Solid Neoplasm><Solid Tumor><Splicing><Strains Cell Lines><TCGA><Testing><The Cancer Genome Atlas><Time><Tissue Growth><Tissues><Transcription><Transcriptional Regulatory Elements><United States><Unscheduled DNA Synthesis><Work><actionable mutation><actionable variants><bevacizumab><cancer initiation><cancer metastasis><cancer progression><ccRCC><cell growth><cohort><cultured cell line><design><designing><drug/agent><epigenetically><epigenome><epithelial to mesenchymal transition><experience><genome mutation><high reward><high risk><histone methylation><immune check point inhibitor><inhibitor><kidney adenocarcinoma><kidney cell><lung cancer><mRNA><malignancy><metastatic process><migration><mutant><necrocytosis><neoplasm progression><neoplasm/cancer><neoplastic progression><novel><ontogeny><pancreatic malignancy><pathway><pharmacologic><programs><regulatory gene><renal><renal proximal tubule><response><rhuMabVEGF><senescence><senescent><social role><standard of care><therapeutic target><trans acting element><transcriptome sequencing><transcriptomic sequencing><tumor cell metastasis><tumor progression><virtual>