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Alternative splicing in type 1 diabetes: The role of the splicing factor SRSF6 in pancreatic β-cell function and survival.

par De Oliveira Alvelos, Maria
Président du jury Langer, Ingrid
Promoteur Cnop, Miriam
Co-Promoteur Eizirik, Decio L.
Publication Non publié, 2020-10-30

Thèse de doctorat

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Résumé :

Type 1 diabetes (T1D) is an autoimmune disease characterized by the selective destruction of pancreatic β-cells, mediated by autoreactive T cells.The resulting inflammatory response takes place in the context of a dialogue between invading immune cells and the targeted β-cells, and it is modulated by genetic susceptibility, acting on both immune and β-cells, and by inflammatory cytokines and chemokines. Stress pathways triggered within β-cells may potentiate autoimmunity, and T1D susceptibility genes shape β-cell responses to “danger signals”, innate immunity, and activation of apoptosis. However, the molecular mechanisms linking genetic variation, environmental triggers, and the signaling events promoting β-cell dysfunction and loss remain poorly clarified. Pre-mRNA splicing is a crucial mechanism for gene expression regulation, and more than 95% of the human multi-exonic primary transcripts undergo alternative splicing. Splicing dysregulation have been increasingly recognized to play a pivotal role in multiple pathologies, including autoimmune diseases. More than 15% of the mutations described in the Human Gene Mutation Database are predicted to affect splicing. Our group has shown that exposure to pro-inflammatory cytokines induces major changes on the β-cell transcriptome, affecting the splicing of genes that are key for β-cell function and survival. Importantly, our group identified that GLIS3, a susceptibility gene for both T1D and type 2 diabetes (T2D), modulates β-cell apoptosis via regulation of the splicing factor SRSF6, linking T1D genetic susceptibility and alternative splicing. The downregulation of GLIS3, either by germline mutations associated with monogenic forms of diabetes or risk single nucleotide polymorphisms, contribute to SRSF6 splicing factor downregulation. Splicing factors are the primary regulators of splicing and orchestrate functionally related transcripts into regulatory networks, therefore, oscillations of splicing factors’ expression levels have a major impact on splicing decisions. In the present study we aimed: 1. To evaluate the functional impact of SRSF6 downregulation in human pancreatic β-cells; 2. To identify the SRSF6-regulated splicing networks and to decode the SRSF6 cis-regulatory RNA binding elements.To fulfil these aims, human insulin-producing EndoC-βH1 cells were subjected to RNA sequencing (under control conditions or following SRSF6 knock down for 48h) to identify transcriptome-wide alternative splicing events regulated by SRSF6, and to individual-nucleotide resolution UV crosslinking and immunoprecipitation followed by high-throughput sequencing (iCLIP) to determine the SRSF6 mechanistic model of splicing regulation, its associated cis-regulatory elements and directly bound transcripts in human β-cells. We observed that SRSF6 depletion has a major impact on human pancreatic β-cell function and survival, leading to β-cell apoptosis and impaired insulin secretion. SRSF6 downregulation affects the splicing of transcripts involved in central pathways for β-cell function and survival, such as insulin secretion (e.g. INSR, SNAP25), apoptotic regulators (e.g. BCL2L11 (or BIM), BAX), and the mitogen-activated protein kinases (MAPKs) signaling pathway (e.g. MAPK8, MAPK9, MAP3K7). SRSF6 silencing potentiates the generation of constitutively active isoforms of pro-apoptotic inducers – BAX-β, and BIM-Small - leading to apoptosis activation, and also of different members of the MAPK signaling pathway contributing to the hyper-phosphorylation of the pathway, leading to activation of down-stream transcription factors and consequent β-cell apoptosis. These data indicate that specific splicing networks, regulated through diabetes susceptibility genes, control key pathways and processes involved in the function and survival of β-cells. The iCLIP analysis has shown that SRSF6 recognizes more than 100,000 of RNA binding sites in protein coding sequences, and it regulates splicing by preferentially binding into exons through a purine-rich consensus motif consisting of GAA triplets. The number of triplets in direct sequence correlates with increasing binding site strength. The SRSF6 binding position affects the splicing outcome, possibly resulting from the competition between alternative exons and their flanking constitutive exons for SRSF6 tethering. We identified SRSF6 binding sites on SRSF6-regulated cassette exons of several susceptibility genes for both T1D and T2D, and as a proof-of-concept, modulated the splicing of the LMO7 susceptibility gene using antisense oligonucleotides.In conclusion, our data suggest that SRSF6 is a master splicing regulator in pancreatic β-cells, downstream of the diabetes susceptibility gene GLIS3. SRSF6 silencing potentiates the splicing of constitutively active pro-apoptotic variants (BAX-β and BIM-Small), and exacerbates the MAPK signalling pathway. SRSF6 recognizes specific purine-rich RNA binding motifs, with important implications for the interpretation of sequence variants. This work unveiled a novel regulatory layer for β-cell demise and diabetes genetic susceptibility, namely through splicing mis-regulation. These observations raise the possibility that splicing networks regulated by candidate genes for diabetes contribute to β-cell dysfunction and death in diabetes.