Regulation of β-cell death by ADP-ribosylhydrolase ARH3 via lipid signaling in insulitis

Background: Lipids are regulators of insulitis and β-cell death in type 1 diabetes development, but the underlying mechanisms are poorly understood. Here, we investigated how the islet lipid composition and downstream signaling regulate β-cell death. Methods: We performed lipidomics using three models of insulitis: human islets and EndoC-βH1 β cells treated with the pro-inflammatory cytokines interlukine-1β and interferon-γ, and islets from pre-diabetic non-obese mice. We also performed mass spectrometry and fluorescence imaging to determine the localization of lipids and enzyme in islets. RNAi, apoptotic assay, and qPCR were performed to determine the role of a specific factor in lipid-mediated cytokine signaling. Results: Across all three models, lipidomic analyses showed a consistent increase of lysophosphatidylcholine species and phosphatidylcholines with polyunsaturated fatty acids and a reduction of triacylglycerol species. Imaging assays showed that phosphatidylcholines with polyunsaturated fatty acids and their hydrolyzing enzyme phospholipase PLA2G6 are enriched in islets. In downstream signaling, omega-3 fatty acids reduce cytokine-induced β-cell death by improving the expression of ADP-ribosylhydrolase ARH3. The mechanism involves omega-3 fatty acid-mediated reduction of the histone methylation polycomb complex PRC2 component Suz12, upregulating the expression of Arh3, which in turn decreases cell apoptosis. Conclusions: Our data provide insights into the change of lipidomics landscape in β cells during insulitis and identify a protective mechanism by omega-3 fatty acids. Video Abstract

Pancreatic microexons regulate islet function and glucose homeostasis

Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycaemia. Here we uncover a conserved programme of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural programme that are particularly sensitive to SRRM3 levels. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in human and rat beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, mice harbouring mutations in Srrm3 display defects in islet cell identity and function, leading to hyperinsulinaemic hypoglycaemia. Importantly, human genetic variants that influence SRRM3 expression and IsletMIC inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk. Taken together, our data identify a conserved microexon programme that regulates glucose homeostasis.We thank B. Banfi (University of Iowa) for kindly sharing the Srrm3 gene-trapped mouse line with us; M. Ángel Maestro for excellent technical advice on multiple protocols related to the study of Srrm3 mutant mice; J. Permanyer and C. Rodriguez for help with mouse genotyping; D. Balboa, I. Miguel-Escalada and E. Bernardo, as well as members of the M.I. and J.V. groups for constant scientific discussion; A. Gohr for assistance on bioinformatic analyses; S. Taylor (University of Manchester) for kindly sharing the HeLa Flp-In T-Rex cell line with us; and CRG Genomics and Advanced Light Microscopy Units for the RNA-seq and microscopy services. The research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC-StG-LS2-637591 and ERCCoG-LS2-101002275 to M.I., ERC-AdG-LS2-670146 to J.V., and ERC-AdG-LS4-789055 to J.F.), EU Horizon 2020 TDSystems (667191) to J.F., la Caixa Foundation (ID 100010434), under the agreement LCF/PR/HR20/52400008 to M.I., an EFSD award supported by EFSD/Lilly European Diabetes Research Programme, the Spanish Ministry of Science and Innovation (BFU-2017-89308-P to J.V., BFU-2017-89201-P to M.I. and RTI2018-095666-B-I00 to J.F.) and the ‘Centro de Excelencia Severo Ochoa’ (CEX2020-001049). G.A. was supported by the Marie Skłodowska-Curie project ZENCODE-ITN (No. 643062). S.B.-G. was supported by a Juan de la Cierva postdoctoral fellowship (MINECO; FJCI-2017-32090). J.J.-M. was supported by the Beatriu de Pinós Programme and the Ministry of Research and Universities of the Government of Catalonia, and a Marie Skłodowska-Curie Individual Fellowship from the European Union’s Horizon 2020 research and innovation programme (MSCA-IF-2019-841758; http://ec.europa.eu/)

SRp55 Regulates a Splicing Network that Controls Human Pancreatic Beta Cell Function and Survival.

Progressive failure of insulin-producing beta cells is the central event leading to diabetes, but the signalling networks controlling beta cell fate remain poorly understood. Here we show that SRp55, a splicing factor regulated by the diabetes susceptibility gene GLIS3, has a major role in maintaining function and survival of human beta cells. RNA-seq analysis revealed that SRp55 regulates the splicing of genes involved in cell survival and death, insulin secretion and JNK signalling. Specifically, SRp55-mediated splicing changes modulate the function of the pro-apoptotic proteins BIM and BAX, JNK signalling and endoplasmic reticulum stress, explaining why SRp55 depletion triggers beta cell apoptosis. Furthermore, SRp55 depletion inhibits beta cell mitochondrial function, explaining the observed decrease in insulin release. These data unveil a novel layer of regulation of human beta cell function and survival, namely alternative splicing modulated by key splicing regulators such as SRp55 that may crosstalk with candidate genes for diabetes.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells

In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.Funding information: DL Eizirik is funded by Welbio/FRFS (no WELBIO-CR-2019C-04), Belgium; by the Brussels Region (INNOVIRIS BRIDGE grant DiaType), the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement numbers 115797 (INNODIA) and 945268 (INNODIA HARVEST); these Joint Undertakings receive support from the Union’s Horizon 2020 research and innovation program and “EFPIA” (European Federation of Pharmaceutical Industries Associations), “JDRF” (Juvenile Diabetes Research Foundation), “The Leona M and Harry B Helmsley Charitable Trust”), and the Dutch Diabetes Research Foundation (project Innovate2CureType1, DDRF; no. 2018.10.002). MI Alvelos was supported by Fonds pour la Formation a la Recherche dans l’Industrie et dans l’Agriculture (FRIA) fellowship from the Fonds de la Recherche Scientifique (FNRS) (reference no. 26410496), and COST: European Cooperation in Science & Technology (COST Action BM1207—Networking towards clinical application of antisense-mediated exon skipping; COST Action CA17103—Delivery of Antisense RNA Therapeutics). K Zarnack is funded by the German Research Foundation (DFG, SFB 902 – B13

SRp55 Regulates a Splicing Network That Controls Human Pancreatic β-Cell Function and Survival

Progressive failure of insulin-producing beta cells is the central event leading to diabetes, but the signalling networks controlling beta cell fate remain poorly understood. Here we show that SRp55, a splicing factor regulated by the diabetes susceptibility gene GLIS3, has a major role in maintaining function and survival of human beta cells. RNA-seq analysis revealed that SRp55 regulates the splicing of genes involved in cell survival and death, insulin secretion and JNK signalling. Specifically, SRp55-mediated splicing changes modulate the function of the pro-apoptotic proteins BIM and BAX, JNK signalling and endoplasmic reticulum stress, explaining why SRp55 depletion triggers beta cell apoptosis. Furthermore, SRp55 depletion inhibits beta cell mitochondrial function, explaining the observed decrease in insulin release. These data unveil a novel layer of regulation of human beta cell function and survival, namely alternative splicing modulated by key splicing regulators such as SRp55 that may crosstalk with candidate genes for diabetes

Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes.

DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements

The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes

The early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells. Here we show that exposure to proinflammatory cytokines reveals a marked plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the β-cell transcriptome, proteome and three-dimensional chromatin structure. Our data indicate that the β-cell response to cytokines is mediated by the induction of new regulatory regions as well as the activation of primed regulatory elements prebound by islet-specific transcription factors. We find that T1D-associated loci are enriched with newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human β cells. Our study illustrates how β cells respond to a proinflammatory environment and implicate a role for stimulus response islet enhancers in T1D.L.Pasquali was supported by grants from the Spanish Ministry of Economy and Competitiveness (nos. BFU2014-58150-R and SAF2017-86242-R), Marató TV3 (no. 201624.10) and a young investigator award from the Spanish Society of Diabetes (Ayuda SED a Proyectos de Investigación, no. 2017-SED). L.Pasquali is a recipient of a Ramon y Cajal contract from the Spanish Ministry of Economy and Competitiveness (no. RYC-2013-12864). The Pasquali lab is further supported by Instituto de Salud Carlos III (no. PIE16/00011). M.R. is supported by an FI Agència de Gestió d’Ajuts Universitaris i de Recerca PhD fellowship (no. 2019FI_B100203). J.J. was supported by a Marie Skłodowska-Curie Actions fellowship grant from the Horizons 2020 European Union (EU) Programme (project no. 660449). M.I.A. was supported by a FRIA fellowship from the Fonds de la Recherche Scientifique (FNRS) (no. 26410496). Human islets were provided through the European Consortium for Islet Transplantation distribution program for basic research supported by JDRF (no. 31-2008-416). D.L.E. was supported by the Walloon Region through the FRFS-WELBIO Fund for Strategic Fundamental research (no. CR-2015A-06s and CR-2019C-04) and by grants from the Fonds National de la Recherche Scientifique (no. T003613F), the Horizon 2020 Programme (project T2Dsystems, no. GA667191), Brussels Capital Region Innoviris (project DiaType, no. 2017-PFS-24), Dutch Diabetes Research Fundation (project Innovate2CureType1, DDRF; no. 2018.10.002) and the Innovative Medicines Initiative 2 Joint Undertaking (project INNODIA, no. 115797). This Innovative Medicines Initiative 2 Joint Undertaking receives support from the EU’s Horizon 2020 Research and Innovation Programme and European Federation of Pharmaceutical Industries and Associations, JDRF and the Leona M. and Harry B. Helmsley Charitable Trust (project INNODIA, no. 115797). T.O.M. and D.L.E. were supported by a grant from the National Institutes of Health-National Institute of Diabetes and Digestive and Kidney Diseases-Human Islet Research Network Consortium (no. 1UC4DK104166-01). Part of the work was performed at the Environmental Molecular Sciences Laboratory, a US Department of Energy national scientific user facility located at Pacific Northwest National Laboratory. Battelle operates the Pacific Northwest National Laboratory for the Department of Energy (contract no. DE-AC05-76RLO01830)

Prognostic value of X-chromosome inactivation in symptomatic female carriers of dystrophinopathy

<p>Abstract</p> <p>Background</p> <p>Between 8% and 22% of female carriers of <it>DMD</it> mutations exhibit clinical symptoms of variable severity. Development of symptoms in <it>DMD</it> mutation carriers without chromosomal rearrangements has been attributed to skewed X-chromosome inactivation (XCI) favouring predominant expression of the <it>DMD</it> mutant allele. However the prognostic use of XCI analysis is controversial. We aimed to evaluate the correlation between X-chromosome inactivation and development of clinical symptoms in a series of symptomatic female carriers of dystrophinopathy.</p> <p>Methods</p> <p>We reviewed the clinical, pathological and genetic features of twenty-four symptomatic carriers covering a wide spectrum of clinical phenotypes. <it>DMD</it> gene analysis was performed using MLPA and whole gene sequencing in blood DNA and muscle cDNA. Blood and muscle DNA was used for X-chromosome inactivation (XCI) analysis thought the <it>AR</it> methylation assay in symptomatic carriers and their female relatives, asymptomatic carriers as well as non-carrier females.</p> <p>Results</p> <p>Symptomatic carriers exhibited 49.2% more skewed XCI profiles than asymptomatic carriers. The extent of XCI skewing in blood tended to increase in line with the severity of muscle symptoms. Skewed XCI patterns were found in at least one first-degree female relative in 78.6% of symptomatic carrier families. No mutations altering XCI in the <it>XIST</it> gene promoter were found.</p> <p>Conclusions</p> <p>Skewed XCI is in many cases familial inherited. The extent of XCI skewing is related to phenotype severity. However, the assessment of XCI by means of the <it>AR</it> methylation assay has a poor prognostic value, probably because the methylation status of the <it>AR</it> gene in muscle may not reflect in all cases the methylation status of the <it>DMD</it> gene.</p