Related Experiment Video
Updated: Apr 10, 2026
Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry
Published on: November 21, 2025
High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma
1Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA.
Abstract:
Mutations in SETD2, a histone H3 lysine trimethyltransferase, have been identified in clear cell renal cell carcinoma (ccRCC); however it is unclear if loss of SETD2 function alters the genomic distribution of histone 3 lysine 36 trimethylation (H3K36me3) in ccRCC. Furthermore, published epigenomic profiles are not specific to H3K36me3 or metastatic tumors. To determine if progressive SETD2 and H3K36me3 dysregulation occurs in metastatic tumors, H3K36me3, SETD2 copy number (CN) or SETD2 mRNA abundance was assessed in two independent cohorts: metastatic ccRCC (n=71) and the Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma data set (n=413). Although SETD2 CN loss occurs with high frequency (>90%), H3K36me3 is not significantly impacted by monoallelic loss of SETD2. H3K36me3-positive nuclei were reduced an average of ~20% in primary ccRCC (90% positive nuclei in uninvolved vs 70% positive nuclei in ccRCC) and reduced by ~60% in metastases (90% positive in uninvolved kidney vs 30% positive in metastases) (P<0.001). To define a kidney-specific H3K36me3 profile, we generated genome-wide H3K36me3 profiles from four cytoreductive nephrectomies and SETD2 isogenic renal cell carcinoma (RCC) cell lines using chromatin immunoprecipitation coupled with high-throughput DNA sequencing and RNA sequencing. SETD2 loss of methyltransferase activity leads to regional alterations of H3K36me3 associated with aberrant RNA splicing in a SETD2 mutant RCC and SETD2 knockout cell line. These data suggest that during progression of ccRCC, a decline in H3K36me3 is observed in distant metastases, and regional H3K36me3 alterations influence alternative splicing in ccRCC.
Insights
Loss of SETD2 function in clear cell renal cell carcinoma (ccRCC) leads to reduced histone H3K36 trimethylation (H3K36me3), particularly in metastases, impacting RNA splicing.
Area of Science:
- Oncology
- Epigenetics
- Molecular Biology
Background:
- Mutations in SETD2, a histone methyltransferase, are found in clear cell renal cell carcinoma (ccRCC).
- The impact of SETD2 loss on histone 3 lysine 36 trimethylation (H3K36me3) distribution in ccRCC, especially in metastatic stages, remains unclear.
- Existing epigenomic data lack specificity for H3K36me3 and metastatic ccRCC.
Purpose of the Study:
- To investigate progressive dysregulation of SETD2 and H3K36me3 during ccRCC metastasis.
- To define kidney-specific H3K36me3 profiles.
- To explore the functional consequences of SETD2 loss on H3K36me3 and RNA splicing in ccRCC.
Main Methods:
- Analysis of H3K36me3, SETD2 copy number (CN), and mRNA abundance in two independent ccRCC cohorts (metastatic n=71, TCGA n=413).
- Generation of genome-wide H3K36me3 profiles using ChIP-seq and RNA-seq in primary ccRCC samples and isogenic RCC cell lines.
- Assessment of SETD2 methyltransferase activity and its effects on H3K36me3 and RNA splicing in SETD2 mutant and knockout cell lines.
Main Results:
- SETD2 CN loss is frequent (>90%) in ccRCC, but monoallelic loss does not significantly impact overall H3K36me3 levels.
- H3K36me3-positive nuclei significantly decrease from primary ccRCC (~20% reduction) to metastases (~60% reduction).
- SETD2 loss of function causes regional H3K36me3 alterations associated with aberrant RNA splicing in ccRCC cell lines.
Conclusions:
- H3K36me3 declines during ccRCC progression, especially in distant metastases.
- Regional H3K36me3 alterations driven by SETD2 dysfunction contribute to alternative RNA splicing in ccRCC.
- These findings highlight the role of SETD2 and H3K36me3 in ccRCC pathogenesis and progression.
More Related Videos
11:42Genome-wide Mapping of Histone Modifications and Transcription Factor Binding Sites in Neuroendocrine Small Cell Lung Cancer Cell Lines Using CUT&RUN
Published on: April 3, 2026
08:12Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue
Published on: May 5, 2022
