The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

Abstract

Over 90% of chondroblastomas contain a heterozygous mutation replacing lysine 36 with methionine (K36M) in the histone H3 variant H3.3. Here, we show that H3K36 methylation is reduced globally in chondroblastomas and in chondrocytes harboring the same genetic mutation due to inhibition of at least two H3K36 methyltransferases, MMSET and SETD2, by the H3.3K36M mutant proteins. Genes with altered expression as well as H3K36 di- and trimethylation in H3.3K36M cells are enriched in cancer pathways. In addition, H3.3K36M chondrocytes exhibit several hallmarks of cancer cells including increased ability to form colonies, resistance to apoptosis and defects in differentiation. Thus, H3.3K36M proteins reprogram H3K36 methylation landscape and contribute to tumorigenesis in part through altering the expression of cancer-associated genes.

Histone Lysine-to-Methionine Mutations Reduce Histone Methylation and Cause Developmental Pleiotropy

“…To further determine the potency of the K36M as an inhibitor, we searched for the peptide signature of M36, based on its mass difference from K36, using mass spectrometry. Consistent with the low amount of K36M in tumors and cultured cells (Schwartzentruber et al, 2012;Behjati et al, 2013;Fang et al, 2016;Lu et al, 2016), we found that K36M peptides were present at an abundance of 1.4% among total detected H3.3 peptides (Supplemental Fig. S3A).…”

“…Studies of K36M mutation in cell culture models suggest that endogenous H3K36 methylation reduction occurred through the inhibition of H3K36me3-specific Lys methyltransferases (Fang et al, 2016;Lu et al, 2016). Similarly, mutations of other histone Lys (K9 and K27) to Met also cause specific reduction in corresponding methylation levels by inhibiting SET-domain-containing methyltransferases (Lewis et al, 2013;Brown et al, 2014;Jayaram et al, 2016).…”

“…Such K36M mutations were associated with 95% of chondroblastomas (Behjati et al, 2013). More recently, K36M mutation was shown to contribute to tumorigenesis by altering the expression of differentiation or cancer-related genes (Fang et al, 2016;Lu et al, 2016).…”

“…While K-to-M mutations promoting tumorigenesis have been investigated (Chan et al, 2013;Lewis et al, 2013;Fang et al, 2016;Lu et al, 2016), it is unknown whether K-to-M mutations influence organismal development. Using Arabidopsis as a model system, we report, to our knowledge, the first developmental phenotypic effects for the K36M mutation.…”

Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis

“…All mice were maintained in a specific pathogen-free facility. SETD2-floxed mice were generated by Shangreported, SETD2 loss impairs ES cell differentiation (37) and expression of H3.3 mutants that inhibit H3K36 methylation compromises the differentiations of chondrocytes and mesenchymal progenitor cells (38,39). The Wnt pathway involves various feedback loops that balance the opposing processes of cell proliferation and differentiation.…”