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A helicase-independent role of DHX15 promotes MYC stability and acute leukemia cell survival

ABSTRACT: DHX15 has been implicated in RNA splicing and ribosome biogenesis, primarily functioning as an RNA helicase. To systematically assess the cellular role of DHX15, we conducted proteomic analysis to investigate the landscape of DHX15 interactome, and identified MYC as a binding partner. DHX15 co-localizes with MYC in cells and directly interacts with MYC in vitro. Importantly, DHX15 contributes to MYC protein stability at the post-translational level and independent of its RNA binding capacity. Mechanistic investigation reveals that DHX15 interferes the interaction between MYC and FBXW7, thereby preventing MYC polyubiquitylation and proteasomal degradation. Consequently, abrogation of DHX15 drastically inhibits MYC-mediated transcriptional output. While DHX15 depletion blocks T-cell development and leukemia cell survival as we recently reported, overexpression of MYC significantly rescues the phenotypic defects. These findings shed light on the essential role of DHX15 in mammalian cells and suggest that maintaining sufficient MYC expression is a significant contributor to DHX15-mediated cellular functions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE247720 | GEO | 2023/11/19

REPOSITORIES: GEO

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Project description:DHX15 is an ATP-dependent RNA helicase involved in pre-mRNA splicing. We have recently reported that DHX15 is a downstream substrate for Akt1, which plays a significant role in vascular biology. Therefore, we aimed to explore the regulatory function of DHX15 over the vasculature, and the endothelial cell biology in different contexts: development, metabolism, ischemia and tumor growth. Methods: Deficient DHX15 mice and zebrafish were generated using transcription activator-like effector nuclease (TALEN) and Crispr/cas9 gene edition. Lymphatic functionality was evaluated by lymphangiography and magnetic resonance imaging. Mouse-induced tumor and metastasis model were generated by injection of syngeneic LLC1 tumor cells. DHX15 gene silencing in mouse liver endothelial cells (LEC) was performed by the lentiviral transduction of shRNA (Dharmacon). The changes in the transcriptome and the proteome resulting from the shRNA transduction were investigated by RNAseq and mass spectrometry, respectively. Results: Homozygous DHX15 gene deficiency was lethal in mouse and zebrafish embryos. DHX15-/- zebrafish also showed an undeveloped parachordal line, which leads to the formation of lymphatic structures in the trunk during the development. DHX15+/- mice and zebrafish were viable, although DHX15+/- gene deficiency triggered lower vascular network density and impaired lymphatic function postnatally in mice. Whole transcriptome and proteome analysis of DHX15 silenced LEC revealed differential expression of enzymes involved in the glycolysis and the gluconeogenesis pathways. The functional validation of these results demonstrated an uncoupling of the glycolysis with the oxidation of pyruvate into the mitochondria and lower activity of the Complex I in the mitochondrial membrane, resulting in lower cellular ATP production. Noteworthy, heterozygous DHX15 deficiency partially inhibited primary tumor growth and reduced lung metastasis after injection of syngeneic LLC1 tumor cells, compared to wild-type mice

Project description:RNA helicases are critical regulators of gene expression and therefore strict regulation of their activities is essential to limit promiscuity and ensure target specify. While some RNA helicases appear dedicated for particular substrates others, such as DHX15, are multifunctional, contributing to more than one gene expression process. Protein cofactors play key roles both in modulating RNA helicase activities and also directing them to appropriate substrate RNAs. The largest family of RNA helicase cofactors, with more than 20 members expressed in human cells, are the G-patch proteins, characterised by a glycine-rich domain via which they associate with specific DEAH/RHA helicases. However, the cognate RNA helicases and cellular functions of numerous human G-patch proteins still remain elusive. Here, we reveal that the G-patch protein GPATCH4 is a cofactor of DHX15 that stimulates its ATPase activity. We show that GPATCH4 interacts with DHX15 in the nucleolus via residues in its G-patch domain and co-migrates with pre-ribosomal particles, wherein loss of DHX15 reduces pre-ribosomal co-migration of GPATCH4. Using a combination of high-throughput sequencing approaches (ChIP, CRAC and small RNA-seq), we discovered that GPATCH4 crosslinks to the ribosomal DNA locus and precursor ribosomal RNAs as well as binding to small nucleolar- and small Cajal body-associated- RNAs that guide rRNA and snRNA modifications. In line with this, using RiboMeth-seq analysis to globally analyse rRNA and snRNA 2’-O-methylation revealed that knockout of GPATCH4 impairs methylation at various sites. Utilizing targeted 2’-O-methylation-sensitive RNase H-based cleavage assays, we demonstrated that the regulation of 2’-O-methylation by GPATCH4 is both dependent on, and independent of, its interaction with DHX15. Intriguingly, the ATPase activity of DHX15 is necessary for efficient methylation of DHX15-dependent sites, suggesting a function of DHX15 in regulating snoRNA-guided 2’-O-methylation of rRNA that requires activation by GPATCH4. Overall, our findings not only extend knowledge on RNA helicase regulation by G-patch proteins but also provide important new insights into how the installation of rRNA and snRNA modifications, which are essential for ribosome assembly/function and pre-mRNA splicing, is regulated.

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A helicase-independent role of DHX15 promotes MYC stability and acute leukemia cell survival

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