GSE208746
RNA helicase DHX15 exemplifies a unique dependency in acute leukemia
RNA-binding proteins (RBPs) have emerged as essential regulators to control gene expression and modulate multiple cancer traits. T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy derived from transformation of T-cell progenitors that normally undergo discrete steps of differentiation in the thymus. Yet implications of essential RBPs during T cell neoplastic transformation remain largely unexplored. Systematic evaluation of RBPs identifies the RNA helicase DHX15, a key subunit in the intron lariat spliceosome (ILS) complex, as a potential T-ALL dependency factor. Using cell-based functional assays and the NOTCH1-induced murine T-ALL model, we demonstrate the essential importance of DHX15 in tumor cell survival and leukemogenesis. Moreover, single-cell transcriptomics reveals that DHX15 depletion in T-cell progenitors impairs normal T-cell development and, more specifically, hinders burst proliferation during CD4-CD8-(DN)-to-CD4+CD8+(DP) transition. Mechanistically, abrogation of DHX15 induces altered RNA splicing and downregulation of SLC7A6 and SLC38A5, thereby suppressing glutamine import and mTORC1 activity. Sustained mTORC1 hyperactivation significantly rescues the DHX15-deficient phenotypes, supporting mTORC1 as a prominent downstream effector mediating the pro-proliferative role of DHX15. Moreover, we propose a DHX15 signature modulator drug ciclopirox and demonstrate the prominent anti-T-ALL efficacy. We therefore highlight DHX15 as a crucial regulator during T-cell leukemogenesis, and provide mechanistic insights that DHX15, although functioning at the end of splicing catalysis, modulates a subset of pathogenic mis-splicing events. These findings exemplify a promising therapeutic approach that splicing perturbation by targeting DHX15 may achieve robust anti-tumor efficacy. Overall design: We used human T-ALL as a model system, and performed multi-omics analysis including RNA-seq and RIP-seq to study the regulatory mechanism of RNA-helicase DHX15. Meanwhile, to further clarify the heterogeneities of thymocyte subsets and the abnormal gene expression profiles in the absence of Dhx15, we performed single-cell RNA sequencing (scRNA-seq) using 10X Genomics platform on isolated single cells from thymus with or without Dhx15 expression