Ectopic expression of <i>BEX</i> genes in T-cell acute lymphoblastic leukemia

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/tumor-suppressor (TS) genes. Loss of the TS gene phosphatase and TENsin homolog (PTEN) is a recurrent alteration, which is often associated with a mature T-ALL subgroup expressing a T-cell receptor. Herein, we used a 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 tumor cells vs physiologic cells uncovers an ectopic expression, in leukemic cells, of the gene encoding Bex1. Then, to determine the relevance of our observation in humans, we queried a public RNA-sequencing database from the TARGET-TCGA (Therapeutically Applicable Research to Generate Effective Treatments-The Cancer Genome Atlas) 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 overexpressing TAL1 oncogene. Proximity ligation assays demonstrated the nuclear colocalization of brain-expressed X-linked 1/2 (BEX1/2) proteins with T-cell acute lymphocytic leukemia protein 1 (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-CRISPR-associated protein 9. This genetic inactivation led to reduced cell proliferation, a loss of histone H3 lysine 4 monomethylation (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.