Loss of Histone H3 Lysine 36 Trimethylation Is Associated With an Increased Risk of Renal Cell Carcinoma-specific Death

Thai H Ho; Payal Kapur; Richard W Joseph; Daniel J Serie; Jeanette E Eckel-Passow; Pan Tong; Jing Wang; Erik P Castle; Melissa L Stanton; John C Cheville; Eric Jonasch; James Brugarolas; Alexander S Parker


Mod Pathol. 2016;29(1):34-42. 

In This Article

Abstract and Introduction


Sequencing of clear cell renal cell carcinomas identified loss-of-function mutations of SETD2, a gene that encodes a nonredundant methytransferase responsible for histone H3 lysine 36 trimethylation (H3K36me3), and H3K36me3 is progressively deregulated in metastases. However, few data exist regarding the impact of loss of H3K36me3 on outcomes. We assessed the association of SETD2 DNA alterations and mRNA expression with overall survival using The Cancer Genome Atlas clear cell renal carcinoma data (N=411). Additionally, we assessed the association of H3K36 loss of methylation with renal cell carcinoma-specific survival and progression-free survival using an independent cohort at Mayo Clinic (N=1454). Overall survival, renal cell carcinoma-specific survival and progression-free survival were estimated using Kaplan–Meier method, and differences in survival across groups was compared using Cox regression models, adjusted for age and the Mayo SSIGN (stage, size, grade, and necrosis) score. In The Cancer Genome Atlas cohort, SETD2 DNA alterations or mRNA expression was not associated with overall survival (P>0.05). In the Mayo cohort, patients with H3K36me3-negative tumors were two times more likely to experience renal cell carcinoma-specific death than patients with H3K36me3-positive tumors (hazard ratio, 2.23; 95% confidence interval, 1.77–2.81); P<0.0001. After stratifying for the SSIGN score, H3K36me3-negative tumors in the low-risk SSIGN group had a worse renal cell carcinoma-specific survival (hazard ratio, 2.18; 95% confidence interval, 1.09–4.36); P=0.03. Although SETD2 DNA and mRNA alterations are not associated with overall survival, we provide evidence that deregulation of the H3K36me3 axis is associated with a higher risk of renal cell carcinoma-specific death. This association remains significant after stratifying for the SSIGN score, particularly among those patients with low-risk tumors.


The molecular pathogenesis of clear cell renal cell carcinoma is linked to chromosome arm 3p copy number loss and biallelic inactivation of the von Hippel-Lindau gene located on chromosome 3p. More recently, mutations in other tumor suppressors on chromosome 3p such as PBRM1 (~40%), BAP1 (~10%), and SETD2 (~12%) have been identified as common events in clear cell renal cell carcinoma tumors.[1] To date, however, there are no investigations that have evaluated associations between loss of SETD2 function and clear cell renal cell carcinoma outcome.

The SETD2 gene encodes a nonredundant histone 3 lysine 36 trimethyltransferase and is mutated in other cancers.[2] In Setd2-knockout mice, histone 3 lysine 36 trimethylation (H3K36me3) is absent,[3] and in humans, loss-of-function SETD2 mutations are associated with loss of H3K36me3.[4–6] Of note, sequencing of various human tumors identified recurrent molecular alterations that phenotypically converge on deregulation of the H3K36me3 axis, and H3K36me3 is progressively deregulated in clear cell renal cell carcinoma metastases.[7] Motivated by this and the aforementioned lack of data on H3K36me3 loss and clear cell renal cell carcinoma outcome, we employed our own immunohistochemistry-based assay for H3K36me3 in archival formalin-fixed, paraffin-embedded tissue sections for which negative staining correlates with a SETD2 mutant genotype.[6] We hypothesized that disruption of the histone code at H3K36me3 is associated with an increased risk of cancer-specific death. Moreover, we explore the deeper clinical relevance of this association by evaluating whether loss of H3K36me3 is associated with outcome among the specific subset of clear cell renal cell carcinoma patients already determined to have 'low-risk' disease based on the externally validated Mayo Clinic SSIGN (stage, size, grade, and necrosis) prognostic scoring system.[8,9]