Ectopic expression of BEX genes in T-cell Acute Lymphoblastic Leukemia [CUT&Tag]

T-cell acute lymphoblastic leukemia (T-ALL) is a malignant proliferation of T-cell progenitors originating in the thymus. T-ALL is a heterogenous disease involving the dysregulation of various oncogenes/tumour suppressor (TS) genes. Loss of the TS gene PTEN, is a recurrent alteration, which is often associated to mature T-ALL sub-group expressing a T-cell receptor (TCR). Herein, we used single-cell RNA sequencing approach to investigate the impact of the absence of PTEN on pathological development of mouse thymocytes. First, our differential gene expression analysis of tumour cells versus physiologic cells uncovers an ectopic expression, in leukemic cells, of the gene encoding Bex1. Then, to determine the relevance of our observation in Human, we queried public RNAseq database from the TARGET-TCGA project. We show that BEX1, BEX2 and BEX5 genes are ectopically expressed in T-ALL samples and we further found that ectopic BEX expression is mainly restricted to the T-ALL subgroup over-expressing TAL1 oncogene. Proximity ligation assays demonstrated the nuclear colocalization of BEX1/2 proteins with TAL1 in T-ALL cells. To investigate their functional role, we generated Jurkat cells with a triple knockout of BEX1, BEX2, and BEX5 using CRISPR-Cas9. This genetic inactivation led to reduced cell proliferation, a loss of H3K4me1 marks notably at genomic regions enriched for E-box motifs, and dysregulation of several TAL1 target genes. Collectively, our findings suggest that BEX1 and BEX2 may contribute to human T-ALL oncogenesis by acting as cofactors within the TAL1 complex. Overall design: CUT&Tag on Jurkat cells and edited Jurkat cells (triple KO of BEX1, BEX2 and BEX5).