Unraveling the genomic landscape of CCRF-CEM: a high-resolution analysis of a key leukaemia cell line

Abstract

The CCRF-CEM cell line, a key model for T-cell acute lymphoblastic leukaemia (T-ALL), is widely used in research, but its complete genomic profile has not been fully characterised. This study used high-resolution array comparative genomic hybridisation (array CGH), validated with multiplex ligation-dependent probe amplification (MLPA), to comprehensively map copy number aberrations (CNAs) in CCRF-CEM. The Agilent Human Genome Microarray Kit 244K platform, containing ~240,000 oligonucleotide probes, was utilised. A total of 65 CNAs were identified, including 27 gains and 38 losses, spanning ~131 Mb. Chromosome 14 had the highest number of CNAs (13/65). Sixteen of the 38 losses were homozygous deletions (~37 Mb). Notable CNAs included trisomy 20, an unbalanced der(5) t(5;14)(q35;q32.2) translocation, deletions at 9p24.3- p21.1 (~28.4 Mb) and 9p21.3 (~0.2 Mb) and amplifications at 20p13-11.1 (~25.7 Mb) and Xp22.3 (~0.01 Mb), affecting key genes like JAK2, CDKN2A, CDKN2B, CRLF2, and SIRPA. MLPA confirmed these findings. Additionally, 25 CNAs < 100 kb were detected, underscoring the sensitivity of our approach, which were previously undetected by conventional methods. These results enhance the understanding of CCRF-CEM as a representative T-ALL model and aid in identifying potential therapeutic targets.