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Genes Chromosomes Cancer. 2017 May;56(5):363-372. doi: 10.1002/gcc.22439. Epub 2017 Jan 18.

Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia.

Author information

1
Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK.
2
Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, UK.
3
Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, USA.
4
Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
5
Research Department of Haemaoloty, UCL Cancer Institute, London, UK.
6
Department of Haematology, Sheffield Children's Hospital, Sheffield, UK.

Abstract

Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5-15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We aimed to determine the clinical and genetic landscape of those with IGH-CRLF2 or P2RY8-CRLF2 (CRLF2-r) using multiple genomic approaches. Clinical and demographic features of CRLF2-r patients were characteristic of B-ALL. Patients with IGH-CRLF2 were older (14 y vs. 4 y, P < .001), while the incidence of CRLF2-r among Down syndrome patients was high (50/161, 31%). CRLF2-r co-occurred with primary chromosomal rearrangements but the majority (111/161, 69%) had B-other ALL. Copy number alteration (CNA) profiles were similar to B-other ALL, although CRLF2-r patients harbored higher frequencies of IKZF1 (60/138, 43% vs. 77/1351, 24%) and BTG1 deletions (20/138, 15% vs. 3/1351, 1%). There were significant differences in CNA profiles between IGH-CRLF2 and P2RY8-CRLF2 patients: IKZF1 (25/35, 71% vs. 36/108, 33%, P < .001), BTG1 (11/35, 31% vs. 10/108, 9%, P =.004), and ADD3 deletions (9/19, 47% vs. 5/38, 13%, P =.008). A novel gene fusion, USP9X-DDX3X, was discovered in 10/54 (19%) of patients. Pathway analysis of the mutational profile revealed novel involvement for focal adhesion. Although the functional relevance of many of these abnormalities are unknown, they likely activate additional pathways, which may represent novel therapeutic targets.

PMID:
28033648
PMCID:
PMC5396319
DOI:
10.1002/gcc.22439
[Indexed for MEDLINE]
Free PMC Article

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