MLL3 ChIP sequencing in murine and human HCC cells

Mutations in genes encoding components of chromatin modifying and
remodeling complexes are among the most frequently observed somatic events
in human cancers. For example, missense and nonsense mutations targeting
the mixed lineage leukemia family member 3 (MLL3/KMT2C) histone
methyltransferase occur in a range of solid tumors and heterozygous
deletions encompassing MLL3 occur in a subset of aggressive leukemias.
Although MLL3 loss can promote tumorigenesis in mice, the molecular
targets and biological processes by which MLL3 suppresses tumorigenesis
remain poorly characterized. Here we combined genetic, epigenomic, and
animal modeling approaches to demonstrate that one of the mechanisms by
which MLL3 links chromatin remodeling to tumor suppression is by
co-activating the Cdkn2a tumor suppressor locus. Disruption of Mll3
cooperates with Myc overexpression in the development of murine
hepatocellular carcinoma (HCC), in which MLL3 binding to the Cdkn2a locus
is blunted, resulting in reduced H3K4 methylation and low expression
levels of the locus-encoded genes, Ink4a and Arf. Conversely, elevated
MLL3 expression increases its binding to the CDKN2A locus and co-activates
gene transcription. Endogenous Mll3 restoration reverses these chromatin
and transcriptional effects and triggers Ink4a/Arf-dependent apoptosis.
Underscoring the human relevance of this epistasis, we found that genomic
alterations in MLL3 and CDKN2A display mutual exclusivity in human HCC
samples. These results collectively point to a new mechanism for
disrupting CDKN2A activity during cancer development and, in doing so,
link MLL3 to an established tumor suppressor network.