Oncohistones are on the rise!Corinna Lieleg
The compaction of DNA into chromatin using the four canonical histones (H3, H2B, H2A, and H4) is crucial in terms of organizing our DNA into the restricted constraints of the cell nucleus. Moreover, PTMs deposited on histones as well as the incorporation of histone variants add an additional layer of complexity and provide means of regulating transcription, replication and DNA repair. But where there is light there is shadow…. Histones have been previously linked to tumorigenesis, primarily through alterations in their PTMs or in histone modifying enzymes regulating these modifications. But did you know that mutations in histone genes themselves have been recently identified that lead to the expression of histones that exhibit oncogenic features? Those histone mutants are called “oncohistones” and they accompany certain pediatric cancers. So far, mutations have been primarily identified in genes encoding H3 and its variants H3.3 and the mutations are often found within the histones near residues that are highly modified with PTMs such as H3K27 or H3K36. It has been unclear whether oncohistones are able to cause cancer on their own, or whether they need to act in concert with additional DNA mutations. If they however act on their own, then they exert a remarkably dominant negative effect: Although histones are expressed from multiple histone genes (i.e. there are 15 histone genes encoding for H3), mutation in one single allele seems sufficient to drive cancer.
The so far best studied oncohistone is H3K27M found in pediatric brain cancer. In vitro data support the idea that H3K27M inhibits the catalytic subunit of PRC2 by strongly binding and sequestering EZH2. This prevents further spreading and methylation of other K27 residues leading to an overall reduction in H3K27 methylation level and transcriptional activation. Interestingly, ChIP-Seq data revealed that there is at the same time local increase in H3K27me3 at certain genomic regions despite the global reduction in H3K27 methylation. It is not entirely understood how some genes escape the EZH2 inhibition, but H3K27me3 at selected sites seems indeed correspond to residual EZH2 activity. The recently solved crystal structure of human PRC2 bound to H3K27M peptide supports the idea of PRC2 sequestering by the oncohistone: The substituted methionine residue was found to occupy the lysine access channel of the EZH2 catalytic SET domain leading to the formation of a nonproductive complex which cannot undergo methyl transfer and thus gets stuck on chromatin.
Structure of human PRC2 bound to H3K27M (PDB code 5HYN): PRC2 subunit EED (wheat), SUZ12 (palegreen) and EZH2 (paleblue) are shown as surface representations, H3K27M peptide (yellow) is shown as sticks. The H3K27M interaction with the catalytic SET domain of EZH2 is shown in detail in the close up, showing how the methionine side chain is trapped in the hydrophobic cleft of the EZH2 active site, pointing towards the methyl donor cofactor product SAH.
A similar mode of action has been discussed for H3K36M mutations in pediatric chondroblastoma. H3K36M likely inhibits the function of SETD2 and other H3K36 methyltransferases including NSD2 through recognition by and inhibition of the SET domain (see crystal structure of SETD2 catalytic domain bound to H3K36M). The loss of the H3K36me3 mark in gene bodies triggers spurious transcription and increased methylation of the nearby H3K27 residue at intergenic regions which causes redistribution of PRC1 and de-repression of its target genes. This leads to aberrant activation of genes blocking mesenchymal progenitor cell differentiation and locks the cells in a proliferative state. Rockefeller scientists found that the injection of H3K36M mutant cells into mice is sufficient to develop undifferentiated sarcoma in vivo which argues for oncogenicity of the lone oncohistone.
Structure of humanSETD2 bound to H3K36M (PDB code 5JJY): SETD2 is shown as surface representation (palegreen) and the H3K36M peptide is shown as grey sticks. The H3K36M peptide is buried deep within the catalytic SET domain of SETD2. The binding cleft accommodating the histone tail is shown in detail. Below, a close up displaying the hydrophobic amino acids engaging into the interaction with the histone peptide is shown. The methionine side chain of the histone H3 peptide is trapped in a hydrophobic environment pointing towards the methyl donor cofactor product SAH.
Anyway, we are just beginning to understand the mechanisms by which oncohistones contribute to tumor development. Researchers are currently on the hunt for more mutations in histones that might be driving tumors. The identification and study of more oncohistones will likely shed light on the fundamental mechanisms by which oncohistones act.
By Corinna and Gunnar