Integrated Genome Sequencing Reveals Frequent Loss of Function Alterations of ARID1A and Other Epigenetic Modifiers in Sezary Syndrome

Introduction

Sezary Syndrome (SS) is an aggressive mature T-cell neoplasm characterized by erythroderma, generalized lymphadenopathy and circulating T-cells. SS cells are characterized by complex karyotypes with numerous structural alterations and copy-number variants. Previous studies have implicated disruption and/or haploinsufficiency of TP53, CDKN2A, RB1 and PTEN in SS. Nevertheless, the comprehensive genetic alterations underlying the pathogenesis of SS are unknown. In this study, we used an integrated genomic sequencing approach to characterize the genetic basis of SS.

Methods

SS cases that fulfilled established diagnostic criteria including characteristic cytologic, immunophenotypic and karyotypic features were analyzed. We performed genomic analysis on 84 primary SS cases using whole genome sequencing (WGS; n = 6), high-resolution array comparative genome hybridization (aCGH using NimbleGen 270K Feature Array; n = 80) and whole exome sequencing (WES) using Illumina TruSeq Exome Capture (n = 66). We filtered this combined dataset to identify 463 genes within regions of recurrent copy-number variations that were also impacted by protein coding mutations. We focused on 16 of these genes and confirmed 75 mutations in these genes by Sanger sequencing. For 35 of these mutations, normal tissue was available to confirm somatic acquisition.

Results

WGS revealed a complex structural genome with numerous regions of chromothrypsis and aneuploidy with over 1,000 inter- and intra-chromosomal translocations in the 6 SS genomes but did not reveal recurrent structural alterations. Array CGH identified many aneuploidies reported previously including 8+, 10-, 17p-/iso17 and 19q-. These results were corroborated by aCGH analysis which also revealed recurrent genomic losses at 9p21.3 (CDKN2A), 10p11.22 (PTEN) and 13q14.2 (RB1). Importantly, exome sequencing further identified several novel somatic, deleterious mutations in these three genes. Strikingly, in addition to confirming loss of function alterations of genes previously implicated in SS pathogenesis, we identified genetic alterations in genes involved in epigenetic modification including chromatin/histone modification (including ARID1A, ARID5B, MLL, MLL2, MLL4, SETD1A, SETD1B, SETD6) and DNA methylation (including NCOR1, TET1, TET2, DNMT3A, DNMT3B) not previously implicated in SS pathogenesis.

Among the most frequent and most restricted regions of recurrent deletion was the 1p36.11 region. Of the 18 genes within this region, ARID1A showed the highest frequency of disruption (27/80 showing deletion; 7/66 showing novel mutations including a frameshift mutation at residue 1449 within the GR binding domain of ARID1A). Of the SS genomes for which both WES and aCGH analysis were performed, 25/62 (40.3%) showed disruption of ARID1A either by deletion or mutation or both. Moreover ARID5B was also targeted by deletions of region 10q21.2 in 23/80 genomes and 3/66 SS genomes showed mutations. We also identified a narrow region of recurrent aneuploidy affecting the SWI/SNF family-member of SMARC genes known to interact with ARID-family SMARCC1at 3p21.31. This gene was recurrently targeted by a deletion in 17/80 (21.3%) SS genomes by highly restricted deletional events (<4Mb).

Altogether, deletions and/or mutations in ARID1A, ARID5B or SMARCC1 were identified in 38 of 62 (61.3%) of SS genomes. Further analysis revealed that other members of the ARID- and SMARC-families, ARID1B, ARID2 and ARID4A, were mutated. Moreover, ARID3A and SMARCA4 (both located on 19p) were targeted by recurrent deletions in 29/80 and 18/80 SS genomes, respectively. Altogether, deletions and/or mutations in at least one of the ARID- or SMARC-family genes were identified in 91.9% of SS.

Conclusion

This study is the first to comprehensively profile the genomic landscape in SS. Integration of high-resolution aCGH with mutational analysis reveals alterations in epigenetic regulators through loss-of-function lesions in ARID- and SMARC-family genes in over 90% of SS. The results of our study offer further insights into the pathogenesis of SS and provide support for use of drugs targeting deregulated chromatin remodeling pathways in the treatment of SS patients.