Roles of the SWI/SNF Chromatin Remodelling Factors in Sustaining Oncogenic Transcription Program in T-Cell Acute Lymphoblastic Leukaemia

Introduction

T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy arising from immature thymocytes. An important hallmark of this disease includes uncontrolled expression and activation of oncogenic transcription factors, such as TAL1, NOTCH1 and MYC, establishing T-ALL-specific oncogenic transcription program. While the roles of these transcription factors in T-ALL have been extensively studied, it is still unknown how epigenetic regulators or chromatin remodellers co-operate with them to initiate and maintain the transcriptional program. In particular, the SWI/SNF complex is the key regulator of nucleosome positioning, which can slide or eject nucleosomes utilizing ATP. Recurring inactivating mutations in multiple members of the SWI/SNF complex have been reported in various cancer types, suggesting that these factors predominantly act as tumour suppressors. However, their role in T-ALL is poorly understood.

Results

Integrative analysis of ATAC-Seq and transcriptomic data on human T-ALL cells and normal T-cells revealed an increased chromatin accessibility at SMARCA4 promoter region, consistent with significant upregulation of its expression. SMARCA4 encodes an ATPase subunit of the SWI/SNF complex. Notably, SMARCA2, which encodes another ATPase subunit that forms a mutually exclusive SWI/SNF complex with SMARCA4, showed a decreased chromatin accessibility at the promoter region coupled with downregulation of its expression. Thus, T-ALL cells dominantly use the SMARCA4-containing SWI/SNF complex. Next, we utilized the PROTAC drug (ACBI-1) to rapidly and specifically deplete SMARCA2 and SMARCA4 proteins via recruitment of the VHL proteasomal complex. ATAC-Seq analysis after the depletion of SMARCA4 revealed a massive reduction of chromatin accessibility at open chromatin regions (OCRs) across the genome starting from as early as 3 hours. DNA motif analysis of these affected OCRs showed that they are enriched for DNA binding motifs of transcription factors known to drive leukemogenesis in T-ALL such as RUNX1 and ETS protein. Furthermore, we observed protein-protein interactions between SMARCA4 and RUNX1 or ETS1 using co-Immunoprecipitation (Co-IP) method. Strikingly, the degradation of SMARCA4 strongly downregulates the expression of many transcription factors involved in the oncogenic transcription program, including NOTCH1, GATA3, RUNX1 and MYC. Notably, we observed a loss of accessibility at multiple OCRs located within the known MYC super-enhancer locus accompanied with decrease in MYC promoter-enhancer interactions after treatment with ACBI-1. Furthermore, direct protein interaction was confirmed between SMARCA4 and MYC by Co-IP. These results suggest that oncogenic transcription factors possibly direct the SMARCA4-dominant SWI/SNF complex to their specific target loci to remodel chromatin and thereby sustain gene expression. Lastly, depletion of SWI/SNF complex resulted in growth inhibition followed by cell cycle arrest and apoptosis induction in both T-ALL cells and patient-derived xenograft (PDX) cells. The therapeutic effect was also confirmed in T-ALL murine xenograft model as shown by a delay in the disease progression upon drug treatment.

Conclusion

Our study is the first to provide compelling evidence on how SMARCA4-dominant SWI/SNF complexes contribute to T-ALL pathogenesis in a context-specific manner. Our results suggest that this complex coordinates with T-ALL-specific oncogenic transcription factors to remodel the chromatin and thereby efficiently provide OCRs at critical gene loci, so that leukemic cells are able to sustain malignant gene expression. Our study also demonstrates the feasibility of the SMARCA4 degrader as a therapeutic drug that can inhibit T-ALL cell growth via the downregulation of oncogenic transcription factors and downstream gene expression program.

No relevant conflicts of interest to declare.