Abstract 3957: Integrated molecular characterization of mast cell leukemia reveals recurrent inactivation of the SETD2 tumor suppressor gene

Among the mutated genes detected in mast cells, SETD2 is different because two mutations inactivating both alleles of the gene were identified.

Authors: Simona Soverini et al Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. Molecular and Cellular Biology, DOI: 10.1158/1538-7445.AM2015-3957 Published August 2015.

Systemic mastocytosis (SM) includes a heterogeneous group of disorders ranging from indolent SM to the rare and aggressive mast cell leukemia (MCL). Somatic mutations in the KIT receptor kinase (most frequently, D816V) can be detected in >90% of patients and are thought to play an important pathogenetic role. Nevertheless, morphological and clinical diversity, as well as the fact that some patients are negative for KIT mutations, suggest that the underlying molecular picture is far from being fully elucidated. To shed further light on this issue, we undertook an integrated molecular genetic study of a KIT gene mutation-negative MCL case who came to our attention in 2012. After having obtained written informed consent, we extracted genomic DNA and total RNA from purified mast cells (MCs) isolated from bone marrow at diagnosis and at progression, as well as DNA from saliva, and performed whole exome sequencing (WES) and RNA-seq on an HiSeq1000 (Illumina, San Diego CA). High resolution karyotyping was also performed with Cytoscan HD arrays (Affymetrix, Santa Clara CA). Among the mutated genes detected in MCs but not in saliva by WES, SETD2 stood out among others because two loss-of-function mutations (a nonsense and a frameshift mutation) inactivating both alleles of the gene were identified. Western Blotting (WB) confirmed the expression of the truncated SETD2 isoform resulting from the nonsense mutation. The SETD2 gene encodes a histone methyltransferase responsible for trimethylation of Lysine 36 of histone H3 (H3K36Me3), a key hystone mark associated not only with active chromatin but also with transcriptional elongation, alternative splicing, DNA replication and repair. Loss of the highly conserved WW and SRI domains was predicted to impair SETD2 binding with RNA polymeraseII and hNRNP L, as confirmed by co-immunoprecipitation. Accordingly, RNA-seq showed evidence of spurious transcripts initiated from cryptic promoter-like sequences within genes as well as non-canonical splice isoforms. More importantly, WB confirmed that H3K36Me3 was completely abrogated. In line with the role of SETD2-dependent H3K36Me3 in DNA repair and genome stability, Cytoscan HD arrays and WES showed that several losses at many chromosomal loci, together with more than 70 additional point mutations, undetectable at diagnosis, were acquired at the time of progression. Absence of SETD2 protein expression and/or reduced H3K36Me3 were detected in 3/3 additional MCLs and in 6/8 aggressive SMs so far screened. Our data point to epigenetic regulation and/or DNA repair as candidate pathways deserving further investigation in SM – in an attempt to elucidate the mechanisms underlying enhanced clinical aggressiveness and to identify more effective treatment modalities. Molecular characterization of 10 additional MCLs and aggressive SMs is ongoing. Supported by FP7 NGS-PTL project and Progetto Regione-Università 2010-12 (L. Bolondi).

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