EIKCS 2022: SETD2 Loss in Kidney Cancer – Setting the Stage for Synthetic Lethality

(UroToday.com) In the ninth session of the 2022 International Kidney Cancer Symposium (IKCS): Europe meeting focusing on basic science in renal cell carcinoma, Dr. de Cubas presented an abstract examining the role of SETD2 loss in kidney cancer and the potential therapeutic implications.


He began by emphasizing that previous large-scale sequencing efforts among patients with clear cell renal cell carcinoma (ccRCC) have identified a high prevalence of mutations in chromatin-related genes. Among these genes, SETD2 is one of the most prominent. SETD2 mutations have been found in approximately 15% of ccRCC and these mutations are associated with an aggressive disease phenotype. Functionally, SETD2 acts as a methyltransferase which is responsible for trimethylating lysine 36 on histone H3 (H3K36me3). The actual underlying biology of how SETD2 loss contributes to ccRCC tumorigenesis is somewhat unclear. However, is thought that SETD2 loss may contribute to a reprogramming of the epigenetic landscape of the cell.

In this study, Dr. de Cubas and colleagues examined the effect of SETD2/H3K36me3 loss on the DNA methylome in ccRCC cells. They used the EPIC DNA methylation assay to measure DNA methylation in 786-O ccRCC cells, as well as in non-cancerous transformed proximal tubule kidney cells (HKC) with and without SETD2. Using a dose-response assay employing 5-aza-2'-deoxycytidine, they assessed cellular sensitivity to DNA hypomethylating agents. They further examined apoptosis and quantified this using Annexin-V/PI staining by flow cytometry. Additionally, they evaluated mitochondrial fitness using electron microscopy and flow cytometry. Finally, in a mouse model (NOD-Scid mice), they assessed the activity of 5-aza-2'-deoxycytidine, a DNA hypomethylating agent, both SETD2 wildtype and knockout xenografts.

The authors found that loss of SETD2 was associated with DNA hypermethylation in both HKC cells and (to a greater extent) in 786-O. The 5-aza-2'-deoxycytidine based dose-response assays demonstrated that SETD2-null ccRCC cells are sensitive to DNA hypomethylating agents. Additionally, these treatments induced greater apoptosis (with increases in necrotic cells) in SETD2-null cells using Annexin-V/PI staining, though this effect could be rescued using a Caspase inhibitor.

They further found that such DNA hypomethylating agents induced profound changes in the mitochondria of SETD2-null cells, including loss of membrane potential and size reduction. Electron microscopy showed that autophagy was impaired in SETD2-null cells, which could contribute to increased sensitivity to 5-aza-2'-deoxycytidine. The subsequent in vivo experimentation in mouse models verified that there was increased sensitivity to 5-aza-2'-deoxycytidine in SETD2-null xenografts, compared to the wildtype xenografts.

Thus, Dr. de Cubas concluded that SETD2 loss in clear cell renal cell carcinoma results in DNA hypermethylation. This creates a synthetic lethal dependency that may be actionable with DNA hypomethylating agents.

Presented by: Aguirre A. de Cubas, PhD, Assistant Professor, College of Medicine, Department, Microbiology and Immunology, Medical University of South Carolina