Genomic profiling in Down syndrome acute lymphoblastic leukemia identifies histone gene deletions associated with altered methylation profiles

M. G. Loudin, J. Wang, H. C. Eastwood Leung, S. Gurusiddappa, J. Meyer, G. Condos, D. Morrison, A. Tsimelzon, M. Devidas, N. A. Heerema, A. J. Carroll, S. E. Plon, S. P. Hunger, G. Basso, A. Pession, D. Bhojwani, W. L. Carroll, K. R. Rabin

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

Abstract

Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 68 non-DS (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression and methylation analyses. We report a novel deletion within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 11 DS (22%) and only 2 NDS cases (3.1%) (Fisher's exact P=0.002). Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters and enrichment of highly methylated genes for specific pathways and transcription factor-binding motifs. Gene expression profiling demonstrated heterogeneity of DS-ALL cases overall, with supervised analysis defining a 45-transcript signature associated with CRLF2 overexpression. Further characterization of pathways associated with histone deletions may identify opportunities for novel targeted interventions.

Original languageEnglish
Pages (from-to)1555-1563
Number of pages9
JournalLeukemia
Volume25
Issue number10
DOIs
StatePublished - Oct 2011
Externally publishedYes

Keywords

  • CRLF2
  • Down syndrome
  • JAK2
  • acute lymphoblastic leukemia
  • histone

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