BRCC3 mutations in myeloid neoplasms

Abstract

© F e r r a t a S t o r t i F o u n d a t i o nUIMC1, FAM175A, BABAM1, BRE, BARD1, BRCC3 and BRCA1 and participates in DNA double-strand break (DSB) repair. 17 DSBs are associated with genomic instability, cell death 18 and carcinogenesis. 19 To repair DSBs, cells use both homologous recombination (HR), which uses sister-chromatid alleles as templates in late S and G 2 , and non-homologous end joining (NHEJ) which can operate in all phases of the cell cycle but often leaves small deletions, possibly gene inactivating at the site of repair. 20 The BRISC complex comprises the following proteins: FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and MERIT40/NBA1.Here, we report that somatic defects of BRCC3 are acquired in various myeloid neoplasms and have consequences at the cellular, and perhaps the clinical level. Methods PatientsBone marrow aspirates or blood were collected from the patients with various myeloid neoplasms seen at the Cleveland Clinic, University of Tokyo and Münchner Leukämielabor GmbH (MLL) (Online Supplementary Table S1). Informed consent for sample collection was obtained according to protocols approved by the institutional review boards in accordance with the Declaration of Helsinki. Diagnoses were confirmed according to 2008 World Health Organization classification criteria. 21 A total of 1778 patients were enrolled in this study (Online Supplementary Table S1). Next generation sequencingWhole exome sequencing (WES) was performed as previously reported. 4,6 Briefly, tumor DNAs were extracted from patients' bone marrow cells. For germ-line controls, DNA was obtained from paired CD3 + T cells. For targeted detection of sequence alterations, confirmation of WES and assessment of variant allelic frequency (VAF), we applied deep sequencing to targeted exons, as previously described. 6,22 Briefly, each targeted exon was amplified with each pair of primers, generating 200bp fragments on average. These amplicons were subjected to massive parallel sequencing (Illumina, San Diego, CA, USA) using TruSeq custom primers (Illumina) and SureSelect (Agilent, Santa Clara, CA, USA) with paired-end reads, according to the manufacture's instruction. Some of these procedures were followed by confirmation using Sanger sequencing, as previously described. 13 Annotations by NCBI reference numbers of the genes affected by somatic mutations are summarized in Online Supplementary Table S2. Cytogenetics and single nucleotide polymorphism-array analysesTechnical details about sample processing and data analyses for single nucleotide polymorphism-array (SNP-A) have been previously described.23 Affymetrix 250K and 6.0 Kit (Affymetrix) were used. Germ-line copy number variants in our internal database or in a publicly available database (Database of Genomic Variants) (http://dgv.tcag.ca/dgv/app/home) were considered non-somatic variants and excluded. Results were analyzed with CNAG (v.3.0) 24 or Genotyping Console (Affymetrix). All other lesions were confirmed as somatic or germ-line by analysis of CD3-sorted cells. Sh...

Somatic SETBP1 mutations in myeloid neoplasms

“…1) [4]. Along with these, multiple loss-of-function mutations [5][6][7][8][9][10][11][12], and recurrent activated/gain-of-function mutations [13][14][15][16] are likely to be the promising candidates for future development of novel therapy by inhibitory compounds (Fig. 2).…”

Single-cell analysis based dissection of clonality in myelofibrosis

“…At baseline, the most frequently mutated genes detected by WES were TET2 in 33% (5/15) and ASXL1 in 27% (4/15), followed by SF3B1 and BRCC3 in 13% (2/15) of patients each. While mutations in BRCC3, a metalloprotease implicated in DNA repair, have been recurrently reported in myelodysplastic syndromes (MDS) and AML 23,24 , they have not previously been reported in MF. MPN18 MPN07 MPN17 MPN03 MPN11 MPN06 MPN10 MPN01 MPN19 MPN02 MPN16 MPN08 MPN05 MPN09 SRSF2 IKZF1 HRAS EZH2 ETV6 SF3B1 BRCC3 ASXL1 TET2 CALR JAK2 7% 7% 7% 7% 7% 13% 13% 27% 33% 33% 67% MPN03 MPN01 MPN07 MPN18 MPN10 MPN17 MPN11 MPN02 MPN09 MPN19 MPN08 MPN16 MPN06 MPN04 When comparing mutations between first and last investigated time points, the majority of baseline mutations (162/201 = 81%) could be detected also at a later disease stage (Fig.…”

Transcriptomic rationale for synthetic lethality‐targeting ERCC1 and CDKN1A in chronic myelomonocytic leukaemia

“…This dependence can be targeted to induce synthetic lethality in malignant cells (Bryant et al , ; Lee et al , ). The lack of recurrent, pathogenic somatic mutations in DNA repair mechanism components in myeloid malignancy has diverted attention away from interest in this pathway (Yoshida et al , ; Huang et al , ; Papaemmanuil et al , ). However, recent studies have revealed the need for a fine‐tuned equilibrium in stimulating DNA repair machinery that can prevent mutations, but which can also preclude the extinction of malignant blood cells by therapeutic agents (Tong et al , ).…”