Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
John P Morris
Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
Chun-Hao Huang
Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States; Howard Hughes Medical Institute, New York, United States
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, encoded by KMT2C) histone methyltransferase occur in a range of solid tumors, and heterozygous deletions encompassing KMT2C 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 Kmt2c 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 tumor suppressors p16/Ink4a and p19/Arf. Conversely, elevated KMT2C expression increases its binding to the CDKN2A locus and co-activates gene transcription. Endogenous Kmt2c 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 KMT2C and CDKN2A were associated with similar transcriptional profiles 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.