Norodiyah Othman*, Azli Ismail, Nursaedah Abdullah Aziz, Nor Soleha Mohd Dali, Ivyna Pau Ni Bong
1. Haematology Unit, Cancer Research Centre, Institute for Medical Research (IMR), National Institutes of Health (NIH), Block C, No.1, Jalan Setia Murni U13/52, Seksyen U13 Setia Alam, 40170 Shah Alam, Selangor, Malaysia
*Corresponding author: Norodiyah Othman.
CITATION: Othman, N., Ismail, A., Abdullah Aziz, N., Mohd Dali, N. S., & Bong, I. P. N. (2025). Unraveling the genomic landscape of CCRF-CEM: a high-resolution analysis of a key leukaemia cell line. International Medical Research Journal, 11(2). https://doi.org/https://doi.org/10.63719/imrj.2025.11.02.006
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 ligase-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.
KEYWORDS: CCRF-CEM, T-cell acute lymphoblastic leukaemia (ALL), Array comparative genomic hybridisation (array CGH), Mulplex ligation-dependent probe amplification (MLPA) and Copy number aberrations (CNAs)
