Publication Date:
2015-12-03
Description:
Introduction: Genetic abnormalities are important to predict prognosis and sometimes can be therapeutic target in pediatric acute lymphoblastic leukemia (ALL). Although the cell lines with recurrent chromosomal abnormalities or leukemic fusions derived from ALL patients are useful tool for various in vitro experiments, it has not been fully investigated whether there is the difference of genetic alterations between clinical samples and cell lines.Here, we performed MLPA analysis of 86 ALL cell lines to determine copy number abnormalities (CNA) and compare with those of the patient's clinical samples. Methods: We performed MLPA analysis of 86 cell lines of ALL (14 with BCR-ABL, 11 with MLL rearrangement, 18 with TCF3-PBX1, 4 with TCF3-HLF, 4 with ETV6-RUNX1 and 35 B-other ALL cell lines) to determine CNA of IKZF1, PAX5, CDKN2A, CDKN2B, ETV6, RB1, BTG1 and EBF1. Then, CNAs were compared to those of patients' samples such as UK cohort (Schwab C, et al. Haematologica, 2013) and Japanese cohort (Asai D, et al. Cancer Med, 2013) according to each specific genetic abnormality, such as BCR-ABL, ETV6-RUNX1, TCF3-PBX1 and MLL-related fusions. In addition, we performed multiplex PCR and RNA-seq to determine fusion transcripts related to Ph-like ALL for the six Ph-negative cell lines with IKZF1 deletions. To determine the expression level of IKZF1 isoform in these cell lines, we performed real time PCR analysis of IKZF1 isoform 1 (IK1) and isoform 6 (IK6). Results: In the BCR-ABL positive cell lines, the frequencies of CDKN2A/2B and BTG1 deletion significantly higher than those in UK cohort (CDKN2A/2B: 100 vs 48%, P
Print ISSN:
0006-4971
Electronic ISSN:
1528-0020
Topics:
Biology
,
Medicine
