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Thoas Fioretos

Thoas Fioretos

Research team manager

Thoas Fioretos

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

Author

  • Minjun Yang
  • Mattias Vesterlund
  • Ioannis Siavelis
  • Larissa H. Moura-Castro
  • Anders Castor
  • Thoas Fioretos
  • Rozbeh Jafari
  • Henrik Lilljebjörn
  • Duncan T. Odom
  • Linda Olsson
  • Naveen Ravi
  • Eleanor L. Woodward
  • Louise Harewood
  • Janne Lehtiö
  • Kajsa Paulsson
Show all

Summary, in English

Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass spectrometry-based analysis of >8,000 genes and proteins as well as Hi-C of primary patient samples from hyperdiploid and ETV6/RUNX1-positive pediatric ALL. We show that CTCF and cohesin, which are master regulators of chromatin architecture, display low expression in hyperdiploid ALL. In line with this, a general genome-wide dysregulation of gene expression in relation to topologically associating domain (TAD) borders were seen in the hyperdiploid group. Furthermore, Hi-C of a limited number of hyperdiploid childhood ALL cases revealed that 2/4 cases displayed a clear loss of TAD boundary strength and 3/4 showed reduced insulation at TAD borders, with putative leukemogenic effects.

Department/s

  • Aneuploidy in cancer
  • BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation
  • Paediatrics (Lund)
  • Translational Genomic and Functional Studies of Leukemia
  • Genetic and epigenetic studies of pediatric leukemia

Publishing year

2019-04-03

Language

English

Publication/Series

Nature Communications

Volume

10

Issue

1

Document type

Journal article

Publisher

Nature Publishing Group

Topic

  • Medical Genetics
  • Cancer and Oncology
  • Pediatrics

Status

Published

Research group

  • Aneuploidy in cancer
  • Translational Genomic and Functional Studies of Leukemia
  • Genetic and epigenetic studies of pediatric leukemia

ISBN/ISSN/Other

  • ISSN: 2041-1723