Spliceosome mutations exhibit specific associations with epigenetic modifiers and proto-oncogenes mutated in myelodysplastic syndrome

Mian, Syed A; Smith, Alexander E.; Kulasekararaj, Austin; Kizilors, Aytug; Mohamedali, Azim; Lea, Nicholas; Mitsopoulos, Konstantinos; Ford, Kevin G.; Nasser, Erick E.; Seidl, Thomas; Mufti, Ghulam J.

doi:10.3324/haematol.2012.075325

Cited by 72 publications

(96 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Gene mutation screening in del(5q) MDS has been performed in previous studies, but most of these studies focused on a limited number of genes, and mainly employed traditional sequencing methods. 9,[34][35][36][37][38][39][40] Other studies have investigated a larger number of genes [41][42][43] but did not specifically focus on MDS cases with del(5q). To our knowledge, the present work is the first attempt to screen a large number of genes using a targeted next-generation sequencing approach in both early and advanced del(5q) MDS.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Targeted re-sequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes

et al. 2013

View full text Add to dashboard Cite

Interstitial deletion of chromosome 5q is the most common chromosomal abnormality in myelodysplastic syndromes. The catalogue of genes involved in the molecular pathogenesis of myelodysplastic syndromes is rapidly expanding and next-generation sequencing technology allows detection of these mutations at great depth. Here we describe the design, validation and application of a targeted next-generation sequencing approach to simultaneously screen 25 genes mutated in myeloid malignancies. We used this method alongside single nucleotide polymorphismarray technology to characterize the mutational and cytogenetic profile of 43 cases of early or advanced del(5q) myelodysplastic syndromes. A total of 29 mutations were detected in our cohort. Overall, 45% of early and 66.7% of advanced cases had at least one mutation. Genes with the highest mutation frequency among advanced cases were TP53 and ASXL1 (25% of patients each). These showed a lower mutation frequency in cases of 5q-syndrome (4.5% and 13.6%, respectively), suggesting a role in disease progression in del(5q) myelodysplastic syndromes. Fifty-two percent of mutations identified were in genes involved in epigenetic regulation (ASXL1, TET2, DNMT3A and JAK2). Six mutations had allele frequencies <20%, likely below the detection limit of traditional sequencing methods. Genomic array data showed that cases of advanced del(5q) myelodysplastic syndrome had a complex background of cytogenetic aberrations, often encompassing genes involved in myeloid disorders. Our study is the first to investigate the molecular pathogenesis of early and advanced del(5q) myelodysplastic syndromes using next-generation sequencing technology on a large panel of genes frequently mutated in myeloid malignancies, further illuminating the molecular landscape of del(5q) myelodysplastic syndromes.

show abstract

Section: Discussionmentioning

confidence: 99%

“…These data are consistent with those of a recent study that showed that TP53 mutations were associated with disease progression in del(5q) MDS. 43 The 5q-syndrome is widely considered to be relatively …”

Section: Discussionmentioning

confidence: 99%

Targeted re-sequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Leukemic mutations in some chromatin modifiers show a modest clustering in female patients, but ASXL1, and its most frequently associated genes, SRSF2 and U2AF1, are more frequent in males. 31 The basis for the gender bias observed here in GATA2 deficiency patients is unknown. However, GATA2 plays a role in the hormone-dependent recruitment of the androgen receptor to chromatin, and in this way, GATA2 influences the expression of androgen-dependent genes, while not being directly regulated by androgen.…”

mentioning

confidence: 99%

Acquired ASXL1 mutations are common in patients with inherited GATA2 mutations and correlate with myeloid transformation

et al. 2013

View full text Add to dashboard Cite

© F e r r a t a S t o r t i F o u n d a t i o n (Online Supplementary Table S2). The PCR were done with AccuPrime Taq DNA Polymerase High Fidelity (Life Technologies, Grand Island, NY, USA) using the manufacturer's recommended conditions with 30 ng of substrate DNA and 35 amplification cycles, with the following amplification parameters: 94°C for 20 seconds; 58°C for 30 seconds, and 68°C for 60 seconds/kilobase of amplified product. The p.G646Wfs*12insG mutation was verified first by repeating the PCR using two different primer sets (Online Supplementary Table S1: primers 1/4, primers 2/3), then by repeating the reactions with different polymerase enzymes [AccuPrime Pfx (Life Technologies, Grand Island, NY, USA), DreamTaq (Thermo Scientific, Pittsburgh, PA, USA)] using the manufacturers' recommended conditions. PCR products were purified using the QIAquick PCR Purification Kit (QIAGEN Sciences, Germantown, MD, USA) and sequenced using ABI 3130XL and 3730 fluorescence-based sequencers. Sequences were analyzed with MacVector, version 12.0 (MacVector, Inc, Cary, NC, USA). Mutations were confirmed with independent PCR with separate primer sets. Statistical analyses were done with GraphPad Prism, version 5.0 (GraphPad Software, Inc., La Jolla CA, USA). The clinical protocols under which these studies were undertaken were reviewed and approved by the Institutional Review Board of the National Institutes of Health, Clinical Research Center. Patients in this study were enrolled in National Institutes of Health/National Institute of Allergy and Infectious Diseases ClinicalTrials.gov Identifier: NCT00018044, NCT00404560, NCT00001467, and National Cancer Institute ClinicalTrials.gov Identifier: NCT00923364. Results and DiscussionWe screened 48 patients with inherited GATA2 mutations to determine the incidence of somatic ASXL1 mutations. A schematic of the ASXL1 region that was sequenced, which contains ~90% of known ASXL1 mutations (COSMIC, v66 14 ), and the position of the mutations found in this study, are shown in Figure 1A. Sequence variations found in the Database of Single Nucleotide Polymorphisms (dbSNP) were not included as mutations Supplementary Table S3). Somatic ASXL1 mutations were detected in 14/48 (29%) patients with GATA2 deficiency (Table 1). All of these mutations were heterozygous and located within exon 13. The ASXL1 mutations found among GATA2 deficiency patients were similar to mutations previously reported in MDS and AML patients,15 including five independent cases of the most frequently described ASXL1 mutation (p.G646Wfs*12insG). The p.G646Wfs*12insG mutation was previously reported in two cousins with a GATA2 mutation who had developed MDS. 12 However, there has been concern over the validity of this particular mutation, with suggestions that it is a PCR artifact since it occurs immediately 3' to an eight base poly G sequence. 16 We confirmed this mutation by © F e r r a t a S t o r t i F o u n d a t i o nrepeating the PCR at least three times for each positive sample (for patie...

show abstract

“…11 Like TET2, SRSF2 mutation occurs early in disease ontogeny and has been dubbed a founder mutation. 12 As such, SRSF2 mutation is thought to pre-dispose early progenitor cells to malignant selection, perhaps via its role in the acetylation/phosphorylation network and as an important regulator of DNA stability and mRNA splicing. 13 We have now sequenced for SRSF2 mutation in our cohort of mastocytosis patients, previously characterized for both KIT and TET2 mutations, 7 and have revealed a striking association between SRSF2 mutation and advanced disease types.…”

Section: Introductionmentioning

confidence: 99%

SRSF2-p95 hotspot mutation is highly associated with advanced forms of mastocytosis and mutations in epigenetic regulator genes

et al. 2014

View full text Add to dashboard Cite

International audienceMastocytosis is a rare and chronic disease with phenotypes ranging from indolent to severe. Prognosis for this disease is variable and very few biomarkers to predict disease evolution or outcome are currently known. We have performed comprehensive screening in our large cohort of mastocytosis patients for mutations previously found in other myeloid diseases and that could serve as prognostic indicators. KIT, SRSF2-P95 and TET2 mutations were by far the most frequent, detected in 81%, 24% and 21% of patients, respectively. Where TET2 and SRSF2-P95 mutation both correlated with advanced disease phenotypes, SRSF2-P95 hotspot mutation was found almost exclusively in patients diagnosed with associated clonal hematologic non-mast cell disease. Statistically, TET2 and SRSF2-P95 mutations were highly associated, suggesting a mechanistic link between these two factors. Finally, analysis of both clonal and sorted cell populations from patients confirms the presence of these mutations in the mast cell component of the disease, suggests an ontological mutation hierarchy and provides evidence for the expansion of multiple clones. This highlights the prognostic potential of such approaches, if applied systematically, for delineating the roles of specific mutations in predisposing and/or driving distinct disease phenotypes

show abstract

Spliceosome mutations exhibit specific associations with epigenetic modifiers and proto-oncogenes mutated in myelodysplastic syndrome

Cited by 72 publications

References 99 publications

Targeted re-sequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes

Targeted re-sequencing analysis of 25 genes commonly mutated in myeloid disorders in del(5q) myelodysplastic syndromes

Acquired ASXL1 mutations are common in patients with inherited GATA2 mutations and correlate with myeloid transformation

SRSF2-p95 hotspot mutation is highly associated with advanced forms of mastocytosis and mutations in epigenetic regulator genes

Contact Info

Product

Resources

About