ARID5B Activates the TAL1-Induced Core Regulatory Circuit and the MYC Oncogene in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is a malignant disorder characterized by the clonal proliferation of T-cell precursors. The most frequent molecular abnormality in T-ALL is the dysregulation of transcription factor genes, including the overexpression of TAL1/SCL . TAL1 induces a stem cell-like transcriptional regulatory program with its regulatory partners (RUNX1, GATA3 and MYB) in T-ALL cells. However, critical factors downstream of the TAL1 complex in T-ALL cells have not been fully characterized. Here, we performed RNA-seq analysis after genetic knockdown of TAL1 and each of its regulatory partners (E2A, HEB, LMO1, GATA3, RUNX1 and MYB) in a T-ALL cell line (Jurkat). We selected genes that were significantly downregulated after the knockdown of all these factors and were also directly bound by TAL1, HEB, GATA3, RUNX1 and MYB based on chromatin immunoprecipitation sequencing (ChIP-seq) analysis. We further filtered genes that were associated with "super-enhancers" based on the enrichment of histone H3 lysine 27 acetylation (H3K27ac). One of identified genes was ARID5B, which has not been previously implicated in T-ALL. ChIP-seq analysis showed DNA binding of the TAL1 transcriptional complex at a putative enhancer upstream of the ARID5B gene. A chromatin-chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the cohesin protein demonstrated a cis-regulatory interaction between the putative enhancer and the ARID5B transcriptional start site. The ARID5B enhancer locus is associated with a super-enhancer in multiple T-ALL samples but not in normal thymus, suggesting that this gene is abnormally activated in T-ALL. The shRNA knockdown experiment showed that ARID5B is required for the survival and growth of T-ALL cells in vitro. Using ChIP-seq and RNA-seq analysis for ARID5B, we discovered that ARID5B frequently co-occupies its target genes with TAL1 and co-ordinately controls their expression. Notably, ARID5B positively regulates expression of TAL1 and its regulatory partners (GATA3, RUNX1 and MYB). Additionally, we identified that ARID5B directly binds to the MYC enhancer, which has previously been reported to be activated by NOTCH1 in T-ALL cells, and activates the expression of this oncogene. Finally, transgenic study using zebrafish model indicated that forced expression of ARID5B in immature thymocytes results in thymus retention, radio-resistance and tumor formation in zebrafish. Taken together, our results indicate that ARID5B reinforces the oncogenic transcriptional program by upregulating the core regulatory circuit, the extended circuitry and the MYC oncogene in T-ALL, thereby contributing to T-cell leukemogenesis.