SETD2 and histone H3 lysine 36 methylation deficiency in advanced systemic mastocytosis

Abstract

The molecular basis of advanced systemic mastocytosis (SM) is not fully understood and despite novel therapies the prognosis remains dismal. Exome sequencing of an index-patient with mast cell leukemia (MCL) uncovered biallelic loss-of-function mutations in the SETD2 histone methyltransferase gene. Copy-neutral loss-of-heterozygosity at 3p21.3 (where SETD2 maps) was subsequently found in SM patients and prompted us to undertake an in-depth analysis of SETD2 copy number, mutation status, transcript expression and methylation levels, as well as functional studies in the HMC-1 cell line and in a validation cohort of 57 additional cases with SM, including MCL, aggressive SM and indolent SM. Reduced or no SETD2 protein expression—and consequently, H3K36 trimethylation—was found in all cases and inversely correlated with disease aggressiveness. Proteasome inhibition rescued SETD2 expression and H3K36 trimethylation and resulted in marked accumulation of ubiquitinated SETD2 in SETD2-deficient patients but not in patients with near-normal SETD2 expression. Bortezomib and, to a lesser extent, AZD1775 alone or in combination with midostaurin induced apoptosis and reduced clonogenic growth of HMC-1 cells and of neoplastic mast cells from advanced SM patients. Our findings may have implications for prognostication of SM patients and for the development of improved treatment approaches in advanced SM.

Epigenetic Changes in Neoplastic Mast Cells and Potential Impact in Mastocytosis

“…In the study by Martinelli et al, a decrease in H3K36Me3 methylation was correlated with SETD2 protein down-regulation in neoplastic MC in patients with MCL. Particularly, SETD2 loss of function may occur post-translationally, in the absence of mutations and other structural aberrations [ 26 ]. Loss of SETD2 function resulted in H3K36 trimethylation deficiency observed in human acute leukemia [ 27 ].…”

“…Inhibitors of the proteasome, such as bortezomib, can rescue (the epigenetically decreased) expression of SETD2 and H3K36 trimethylation in neoplastic MC, resulting in a marked accumulation of ubiquitinated SETD2. Bortezomib was also found to counteract viability in neoplastic MC and to cooperate with midostaurin in inducing apoptosis in HMC-1 cells and neoplastic MC from patients with advanced SM [ 26 ].…”

Roles of SETD2 in Leukemia—Transcription, DNA-Damage, and Beyond

“…Focal deletions of SETD2 were identified in 10% of patients suffering from early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) [ 19 ]. Bi-allelic loss of SETD2 was identified in mast cell leukemia (MCL) [ 20 ]. Moreover, SETD2 mutations have been frequently identified in patients suffering from enteropathy-associated T-cell lymphoma and chronic lymphoblastic leukemia [ 21 , 22 ].…”

Epigenetic synthetic lethality approaches in cancer therapy

“…Pfister et al and Martinelli et al found that SETD2-deficient tumors cells such as mast cell leukemia and kidney cancers are very sensitive to WEE1 inhibitors. They found that compared to control cells, SETD2 knockout cells are hypersensitive to the WEE1 inhibitor Adavosertib (AZD1775) [40, 46]. They further found that H3K36me3 catalyzed by SETD2 promotes RRM2 expression, and WEE1 also promotes RRM2 expression through CDK1; thus, inhibition of WEE1 leads to inhibition of RRM2 [47, 48].…”