Characterising heterogeneity in the T-cell acute lymphoblastic leukaemia jurkat cell line in the context of the TAL1 locus

Abstract

T-cell acute lymphoblastic leukaemia (T-ALL) is the hyperproliferative transformation of T-cell lymphoid progenitor cells within the blood and bone marrow and is extremely heterogeneous. T-ALL has been linked to the overexpression of transcription factors, such as TAL1, that is specific within the late-cortical subtype of T-ALL. This project has utilised clonal cell line populations for testing phenotypic intra-tumoural heterogeneity seen within cancer cell lines, such as the Jurkat cell line, to generate clonal populations relative to the parental cell line they are derived from at passages 1, 5 and 9 as a cost-effective model. We tested the phenotype of proliferation using a carboxyfluorescein succinimidyl ester (CFSE) assay which identified Jurkat clonal populations as highly proliferative and displayed lower expression of the TAL1 gene, relative to the parental cell line using real-time PCR analysis. We also identified four differentially bound putative regulatory element sites using bioinformatics analysis of publicly available data. This analysis displayed a Jurkat-specific predicted intragenic regulatory element and intergenic enhancer regions that map to the known upstream TAL1 Jurkat super-enhancer as stated by Mansour et al. (2014). DNA methylation is known to fine-tune intragenic and intergenic enhancer-mediated transcription. Thus, we used a methylation-sensitive restriction endonuclease (MSRE) assay that provided insight of dynamic and stable DNA methylation patterns at the intragenic and intergenic sites across the TAL1 locus between Jurkat clonal populations, respectively, at passages 1 and 9. Finally, using MinION nanopore sequencing, we identified single-nucleotide variants common between Jurkat clonal populations tested at passages 1 and 9, which map to regulatory elements, SNPs in linkage disequilibrium across the TAL1 locus and sites of predicted transcription factor binding, therefore suggesting regulatory functionality of these SNVs in the context of the TAL1-mediated T-ALL.

Date of Award	2019
Original language	English