Detection of an activated JAK3 variant and a Xq26.3 microdeletion causing loss of PHF6 and miR-424 expression in myelodysplastic syndromes by combined targeted next generation sequencing and SNP array analysis

Pathol Res Pract. 2014 Jun;210(6):369-76. doi: 10.1016/j.prp.2014.02.006. Epub 2014 Feb 23.

Abstract

Myelodysplastic syndromes (MDS) are hematopoietic disorders characterized by ineffective hematopoiesis and progression to acute leukemia. In patients ineligible for hematopoietic stem cell transplantation, azacitidine is the only treatment shown to prolong survival. However, with the availability of a growing compendium of cancer biomarkers and related drugs, analysis of relevant genetic alterations for individual MDS patients might become part of routine evaluation. Therefore and in order to cover the entire bone marrow microenvironment involved in the pathogenesis of MDS, SNP array analysis and targeted next generation sequencing (tNGS) for the mostly therapy relevant 46 onco- and tumor-suppressor genes were performed on bone marrow biopsies from 29 MDS patients. In addition to the detection of mutations known to be associated with MDS in NRAS, KRAS, MPL, NPM1, IDH1, PTPN11, APC and MET, single nucleotide variants so far unrelated to MDS in STK11 (n=1), KDR (n=3), ATM (n=1) and JAK3 (n=2) were identified. Moreover, a recurrent microdeletion was detected in Xq26.3 (n=2), causing loss of PHF6 expression, a potential tumor suppressor gene, and the miR-424, which is involved in the development of acute myeloid leukemia. Finally, combined genetic aberrations affecting the VEGF/VEGFR pathway were found in the majority of cases demonstrating the diversity of mutations affecting different nodes of a particular signaling network as an intrinsic feature in MDS patients. We conclude that combined SNP array analyses and tNGS can identify established and novel therapy relevant genomic aberrations in MDS patients and track them in a clinical setting for individual therapy selection.

Keywords: MDS; SNP array; Targeted next generation sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bone Marrow / enzymology
  • Bone Marrow / pathology
  • Carrier Proteins / genetics*
  • Case-Control Studies
  • Chromosome Deletion*
  • Chromosomes, Human, X*
  • Female
  • Genetic Markers
  • Genetic Predisposition to Disease
  • Genetic Testing / methods*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Immunohistochemistry
  • Janus Kinase 3 / genetics*
  • Male
  • MicroRNAs / genetics*
  • Myelodysplastic Syndromes / enzymology
  • Myelodysplastic Syndromes / genetics*
  • Myelodysplastic Syndromes / pathology
  • Nucleophosmin
  • Oligonucleotide Array Sequence Analysis*
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Repressor Proteins
  • Risk Factors
  • Signal Transduction / genetics

Substances

  • Carrier Proteins
  • Genetic Markers
  • MIRN424 microrna, human
  • MicroRNAs
  • NPM1 protein, human
  • PHF6 protein, human
  • Repressor Proteins
  • Nucleophosmin
  • JAK3 protein, human
  • Janus Kinase 3