Biology subjects

Cnop, M.

Publications and source records attributed to Cnop, M..

9 recordsLinked to original sources

bioRxiv2026

TRMT10A deficiency and tRNA fragmentation disrupt human pancreatic β-cell identity and insulin maturation

Mutations in the tRNA-modifying enzyme TRMT10A cause a rare monogenic syndrome characterized by early-onset diabetes and neurodevelopmental defects, yet the molecular mechanisms underlying TRMT10A diabetes remain unclear. Using human TRMT10A-deficient (knockout and mutant) induced pluripotent stem cells (iPSCs) differentiated into islet-like aggregates and TRMT10A-silenced EndoC-{beta}H1 human {beta}-cells, we show that TRMT10A deficiency impairs {beta}-cell differentiation, insulin content and glucose-stimulated insulin secretion while inducing widespread transcriptional alterations. These defects are accompanied by oxidative stress, diminished antioxidant capacity, and defective proinsulin processing driven by reduced PCSK1 expression. Mechanistically, the loss of TRMT10A promotes tRNA fragmentation and the generation of fragments derived from the 5 end of tRNAGln-CTG (tDRGln-CTG) that interact with hnRNPM. Our data support the existence of a previously unrecognized hnRNPM-PTBP1 interaction in human {beta}-cells and suggest that this complex may contribute to the regulation of PCSK1 mRNA stability and/or translation. Furthermore, through its interaction with hnRNPM, tDRGln-CTG may alter the function of the complex thereby contributing to reduced PCSK1 expression, defective proinsulin processing, and impaired insulin content. Our findings link tRNA fragmentation, RNA-binding protein networks and insulin maturation, positioning TRMT10A as a critical regulator of {beta}-cell identity and function and uncovering a novel mechanism of {beta}-cell failure in the pathogenesis of diabetes.

molecular biology↗

bioRxiv2024

ER stress relief drives beta cell proliferation

Regenerating endogenous pancreatic {beta}-cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote {beta}-cell regeneration. We aimed to investigate whether recovery from experimental hypovascularization of the endocrine pancreas, achieved by modulating the transgenic production of a VEGF-A blocker in {beta}-cells, could trigger mouse {beta}-cell proliferation. Serendipitously, we found that transgene overexpression in {beta}-cells induces endoplasmic reticulum (ER) stress and that subsequent relief from this stress stimulates {beta}-cell proliferation independent of vessel recovery. Transient GFP overexpression in vivo and chemical induction of ER stress in vitro replicated this {beta}-cell cycling response. Our findings highlight the potential side effects of ER stress due to transgene overexpression in {beta}-cells and assert that ER stress relief serves as a potent regenerative stimulus.

molecular biology↗

bioRxiv2022

The type 1 diabetes-associated lncRNA ARGI participates in virus-induced pancreatic beta cell inflammation.

Type 1 diabetes-associated single nucleotide polymorphisms are mainly located in non-coding regions of the human genome. Single nucleotide polymorphisms located in long non-coding RNAs may result in the disruption of their secondary structure, affecting their function. Here, we functionally characterized the virus-induced type 1 diabetes-associated lncRNA ARGI (Antiviral Response Gene Inducer). ARGI upregulation in pancreatic {beta} cells leads to the transcriptional activation of antiviral and pro-inflammatory genes. Upon a viral insult, ARGI is upregulated in the nuclei of pancreatic {beta} cells and binds to CTCF to interact with the regulatory regions of IFN{beta} and interferon-stimulated genes, promoting their transcriptional activation in an allele-specific manner. The presence of the risk allele for type 1 diabetes in ARGI induces an hyperactivation of type I IFN response in {beta} cells, an expression signature that is present in the pancreas of diabetic patients. These data shed light on the molecular mechanisms by which type 1 diabetes-related single nucleotide polymorphisms in long non-coding RNAs influence pathogenesis at the pancreatic {beta} cell level.

genetics↗

bioRxiv2022

RedRibbon: A new rank-rank hypergeometric overlap pipeline to compare gene and transcript expression signatures

MotivationHigh throughput omics technologies have generated a wealth of large protein, gene and transcript datasets that have exacerbated the need for new methods to analyse and compare big datasets. Rank-rank hypergeometric overlap is an important threshold-free method to combine and visualize two ranked lists of P-values or fold-changes, usually from differential gene expression analyses. Here, we introduce a new rank-rank hypergeometric overlap-based method aimed at both gene level and alternative splicing analyses at transcript or exon level, hitherto unreachable as transcript numbers are an order of magnitude larger than gene numbers. ResultsWe tested the tool on synthetic and real datasets at gene and transcript levels to detect correlation and anti-correlation patterns and found it to be fast and accurate, even on very large datasets thanks to an evolutionary algorithm based minimal P-value search. The tool comes with a ready-to-use permutation scheme allowing the computation of adjusted P-values at low time cost. Additionally, the package is a drop-in replacement to previous packages as a compatibility mode is included, allowing to re-run older studies with close to no change to existing pipelines. RedRibbon holds the promise to accurately extricate detailed information from large analyses. AvailabilityRNA-sequencing datasets are available through the Gene Expression Omnibus (GEO) portal with accession numbers GSE159984, GSE133218, GSE137136, GSE98485, GSE148058 and GSE108413. The C libraries and R package code are open to the community with a permissive licence (GPL3) and available for download from GitHub https://github.com/antpiron/ale, https://github.com/antpiron/cRedRibbon and https://github.com/antpiron/RedRibbon. Contactanthony.piron@ulb.be

bioinformatics↗

bioRxiv2021

TIGER: The gene expression regulatory variation landscape of human pancreatic islets

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

bioinformatics↗

bioRxiv2021

A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis

Exposure of human pancreatic beta cells to pro-inflammatory cytokines or metabolic stressors is used to model events related to type 1 and type 2 diabetes, respectively. Quantitative real-time PCR is commonly used to quantify changes in gene expression. The selection of the most adequate reference gene(s) for gene expression normalization is an important pre-requisite to obtain accurate and reliable results. There are no universally applicable reference genes, and the human beta cell expression of commonly used reference genes can be altered by different stressors. Here we aimed to identify the most stably expressed genes in human beta cells to normalize quantitative real-time PCR gene expression. We used comprehensive RNA-sequencing data from the human pancreatic beta cell line EndoC-{beta}H1, human islets exposed to cytokines or the free fatty acid palmitate in order to identify the most stably expressed genes. Genes were filtered based on their level of significance (adjusted P-value >0.05), fold-change (|fold-change| <1.5) and a coefficient of variation <10%. Candidate reference genes were validated by quantitative real-time PCR in independent samples. We identified a total of 264 genes stably expressed in EndoC-{beta}H1 cells and human islets following cytokine- or palmitate-induced stress, displaying a low coefficient of variation. Validation by quantitative real-time PCR of the top five genes ARF1, CWC15, RAB7A, SIAH1 and VAPA corroborated their expression stability under most of the tested conditions. Further validation in independent samples indicated that the geometric mean of ACTB and VAPA expression can be used as a reliable normalizing factor in human beta cells.

systems biology↗

bioRxiv2020

The position of single-base deletions in the VNTR sequence of the carboxyl ester lipase (CEL) gene determines pathogenicity

Variable number of tandem repeat (VNTR) sequences present in the genome can have functional consequences that contribute to human disease. This is the case for the CEL gene, which encodes the digestive enzyme carboxyl ester lipase. CEL has a VNTR located in exon 11, and rare single-base deletions (DELs) within this region cause MODY8, an inherited disorder characterized by exocrine pancreatic dysfunction and diabetes. Here, we have studied how the position of single-base deletions within the CEL VNTR affects the proteins pathogenic properties. We investigated four naturally occurring CEL variants with single-base deletions in different VNTR segments (DEL1, DEL4, DEL9, DEL13), of which only DEL1 and DEL4 have been observed in MODY8 patients. When expressed in a cellular model system, only DEL1 and DEL4 exhibited significantly reduced secretion and increased intracellular aggregation compared to normal CEL. We found that all DEL variants had slightly decreased enzymatic activity and that their level of O-glycosylation was affected. Moreover, only DEL1 and DEL4 significantly increased endoplasmic reticulum (ER) stress. In conclusion, CEL single-base deletion variants have the highest pathogenic potential when the mutational event has taken place in the proximal VNTR part, resulting in the longest aberrant protein tails. Thus, DEL1 and DEL4 are pathogenic CEL variants, whereas we consider DEL13 as benign and DEL9 as likely benign. These findings have implications for our understanding of how CEL mutations cause pancreatic disease through protein misfolding and proteotoxicity, leading to ER stress and activation of the unfolded protein response.

cell biology↗

bioRxiv2020

Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas

Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. Both BHLHE41 and JUND depletion seemed to increase the number of sc-enterochromaffin cells in hiPSC-derived islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity in the human adult pancreas. Furthermore, given that transcription factors are major regulators of embryo development and are often perturbed in diseases, a comprehensive understanding of how transcription factors work will be relevant in development and disease. HIGHLIGHTSO_LIReconstruction of gene regulatory networks for human adult pancreatic cell types C_LIO_LIAn interactive resource to explore and visualize gene expression and regulatory states C_LIO_LIPrediction of putative transcription factors that drive pancreatic cell identity C_LIO_LIBHLHE41 depletion in primary islets induces apoptosis C_LI

bioinformatics↗

bioRxiv2017

Heterozygous RFX6 protein truncating variants cause Maturity-Onset Diabetes of the Young (MODY) with reduced penetrance

Finding new genetic causes of monogenic diabetes can help to understand development and function of the human pancreas. We aimed to find novel protein-truncating variants causing Maturity-Onset Diabetes of the Young (MODY), a subtype of monogenic diabetes. We used a combination of next-generation sequencing of MODY cases with unknown aetiology along with comparisons to the ExAC database to identify new MODY genes. In the discovery cohort of 36 European patients, we identified two probands with novel RFX6 heterozygous nonsense variants. RFX6 protein truncating variants were enriched in the MODY discovery cohort compared to the European control population within ExAC (odds ratio, OR=131, P=lxl0-4). We found similar results in non-Finnish European (n=348, OR=43, P=5xl0-5) and Finnish (n=80, OR=22, P=1xl0-6) replication cohorts. The overall meta-analysis OR was 34 (P=lxl0-16). RFX6 heterozygotes had reduced penetrance of diabetes compared to common HNF1A and HNF4A-MODY mutations (27%, 70% and 55% at 25 years of age, respectively). The hyperglycaemia resulted from beta-cell dysfunction and was associated with lower fasting and stimulated gastric inhibitory polypeptide (GIP) levels. Our study demonstrates that heterozygous RFX6 protein truncating variants are associated with MODY with reduced penetrance.

genetics↗