Biology subjects

Pattou, F.

Publications and source records attributed to Pattou, F..

14 recordsLinked to original sources

bioRxiv2026

From bats to humans: uncovering ISG15 as a new resistance factor in type 1 diabetes

Viral infections are one of the main environmental factors triggering type 1 diabetes (T1D). Pancreatic alpha cells are more resistant than beta cells to diabetogenic viruses, partially explaining their survival in T1D. Similarly, bats have enhanced viral resistance, suggesting putative convergent evolution in antiviral mechanisms. Herein, we compared global gene expression in bat fibroblasts under basal conditions or exposed to double-stranded RNA to human alpha and beta cells and found that alpha cells exhibit greater similarity than beta cells to the antiviral responses of bat cells, as well as stronger intrinsic resistance to viral infection. Interferon-stimulated gene 15 (ISG15), a key regulator of antiviral responses in humans and bats, has higher expression in alpha compared to beta cells in five single-cell RNASeq datasets from human islet cells and in human induced pluripotent stem cell (hiPSC)-derived alpha-like cells. ISG15 knockdown in human insulin-producing EndoC-{beta}H1 cells and human islets increases apoptosis under basal conditions and after IFN exposure, exacerbates IFN responses and increases cell death and viral production after infection with the diabetogenic virus coxsackievirus B1, while its overexpression protects EndoC-{beta}H1 cells from the virus. Collectively, the present results demonstrate that alpha cells but not beta cells have similarities with the virus resistance gene program present in bats and identify ISG15 as an important factor for islet cells to cope with viral and diabetogenic stresses.

immunology↗

bioRxiv2025

Deep learning models reading clinical data and liver omics strongly distinguish NASH from steatosis and suggest new genes involved in liver disease severity

Background & AimsMetabolic dysfunction-associated steatotic liver disease (MASLD, previously NAFLD) is a frequent co-morbidity of obesity and diabetes, with prevalence increasing worldwide in all age groups and both sexes. Only early stages of the disease are fully reversible. Recognising liver disease stages and elucidating the molecular underpinning of their progression are thus medically important. We developed a deep learning model to recognise simple steatosis from steatohepatitis combining liver transcriptomics, epigenetics, and clinical data. MethodsWe used clinical data, liver gene expression and liver DNA methylation gathered from 300 patients with obesity of the ABOS cohort (80 without NAFLD, 137 with simple steatosis, 83 with steatohepatitis). We selected non-redundant clinical variables, gene expressions and CpGs methylation levels most associated with severity using unsupervised approaches. We designed a multi-module, multi-layer perceptron to predict patients liver status. We trained five model instances on independent training/test sets and combined the predictions. ResultsWe used a score based on gene expression/DNA methylation and relevant principal component analysis (PCA) loadings to select 200 genes and 260 CpG methylations. Models trained on the three modalities reached an AUC of 0.945 overall on a validation set with accuracies above 81% for simple steatosis and 88% for NASH, outperforming any other machine learning model so far. We retrieved patient clusters previously found using clinical variables in the latent space of our clinical data module, but not in the gene expression and DNA methylation modules. While all three modules are needed to reach the best prediction accuracy in all classes, the gene expression module had the most impact on the decision. Independent models weighted gene expression inputs similarly, shining light on their importance. The most impactful genes were linked to immune responses and extracellular matrix. However, many of those genes were previously unassociated with steatotic liver disease onset or progression. ConclusionsA multi-omics deep-learning model can recognise steatohepatitis from simple liver steatosis with an AUC of 0.945 and identify new genes potentially involved in NAFLD progression. Gene expressions profiles predicting disease severity are largely different from those specific of clinical variable clusters. Impact and implicationsThis study suggests that clinical variables are not sufficient to recognise the severity of steatotic liver disease with high accuracy, but model efficiency increases when used together with liver epigenetics and transcriptomics.

molecular biology↗

bioRxiv2025

The Circadian Clock Controls Hepatic Stellate Cell Activation in Liver Fibrosis via a BMAL1/CK1ϵ/REV-ERBα/Transgelin Signaling Pathway.

Liver fibrosis is a progressive and life-threatening condition with no effective targeted treatments. Growing evidence indicates a two-way relationship between circadian rhythm and fibrogenesis, although the specific molecular signaling pathways involved are still not well understood. The molecular clock, which governs circadian rhythms, regulates metabolic and cellular functions, and its pharmacological manipulation has shown potential as a therapy for organ fibrosis. Although the livers molecular clock appeared resilient to the progression of chronic liver disease in humans from steatosis to fibrosis, detectable changes in the daily amplitude of clock genes were observed in a cohort of people living with obesity. We discovered a clock-controlled signaling pathway that drives hepatic stellate cell (HSC) activation, a key event in fibrosis progression. Interfering with this pathway, either by disrupting the core regulator CLOCK:BMAL1 or activating the nuclear receptors REV-ERBs, significantly reduced HSC activation. We also identified transgelin as the downstream effector of clock-regulated HSC contractility, a characteristic of HSC activation. Transgelin is regulated indirectly by a BMAL1-CK1{varepsilon} signaling pathway and directly by REV-ERB. Our findings identify a previously unknown circadian-controlled mechanism that links the molecular clock to HSC activation and cell contractile function, which is relevant to human diseases. This pathway provides several entry points for drugs to target and disrupt fibrogenic signaling. By connecting clock biology to the cellular processes that cause fibrosis, our work also offers a mechanistic basis for chronotherapeutic strategies against chronic liver disease.

molecular biology↗

bioRxiv2023

Interferons are the key cytokines acting on pancreatic islets in type 1 diabetes

The pro-inflammatory cytokines IFN, IFN{gamma}, IL-1{beta} and TNF may contribute to innate and adaptive immune responses during islet inflammation (insulitis) in type 1 diabetes (T1D). We used deep RNA-sequencing analysis to characterize the response of human pancreatic beta cells to each cytokine individually and compared the signatures obtained with those present in islets of individuals affected by T1D. IFN and IFN{gamma} had a much greater impact on the beta cell transcriptome when compared to IL-1{beta} and TNF. The IFN-induced gene signatures have a strong correlation with those observed in beta cells from T1D patients, and the level of expression of specific IFN-stimulated genes is positively correlated with proteins present in islets of these individuals, regulating beta cell responses to "danger signals" such as viral infections. These data suggest that IFN and IFN{gamma} are the central cytokines at the islet level in T1D, contributing to the triggering and amplification of autoimmunity.

immunology↗

bioRxiv2023

Advancing multi-day ex vivo kidney perfusion using spatially resolved metabolomics

The ability to preserve metabolically active kidneys ex vivo for multiple days may permit reconditioning, repair and regeneration of deceased donor kidneys. However, the kidneys high metabolic demand limits its functional preservation. Current approaches focus on normothermic machine perfusion (NMP) at 37{degrees}C or hypothermic machine perfusion (HMP) at 4-8{degrees}C. At normothermia, kidneys are metabolically active but ex vivo preservation is limited to hours. During hypothermia kidneys can be preserved up to 24 hours but are metabolically inactive and suffer cold-induced injury. Therefore, we revisited sub normothermic perfusion (at 25{degrees}C) as an alternative approach to preserve human kidneys in a metabolically active state for extended periods of time. In a custom-made platform that includes a cell-free perfusate enriched with TCA cycle fuels, urine recirculation, and continuous hemofiltration we perfused discarded human kidneys up to 8 days. Using spatially resolved single cell resolution isotope tracing we demonstrate active metabolism in all the different renal cell types over this period. However, beyond 4 days cell composition of nephron segments assessed with spatial lipidomics changed substantially and injury markers such as NGAL and LDH increased in the perfusate. Up to 4 days, perfused human discarded donor kidneys maintained metabolic fluxes, functional parameters and allow for reperfusion using a porcine auto transplantation model. These data underpin that extended multi-day metabolic preservation of human kidneys is achievable using a sub normothermic perfusion platform.

bioengineering↗

bioRxiv2022

High-resolution glucose fate-mapping reveals LDHB-dependent lactate production by human pancreatic β cells

Using 13C6 glucose labeling coupled to GC-MS and 2D 1H-13C HSQC NMR spectroscopy, we have obtained a comparative high-resolution map of glucose fate underpinning {beta} cell function. In both mouse and human islets, the contribution of glucose to the TCA cycle is similar. Pyruvate-fueling of the TCA cycle is primarily mediated by the activity of pyruvate dehydrogenase, with lower flux through pyruvate carboxylase. While conversion of pyruvate to lactate by lactate dehydrogenase (LDH) can be detected in islets of both species, lactate accumulation is six-fold higher in human islets. Human islets express LDH, with low-moderate LDHA expression and {beta} cell-specific LDHB expression. LDHB inhibition increases glucose-dependent lactate generation in mouse and human {beta} cells, and decreases Ca2+-spiking frequency without affecting ATP/ADP levels. Thus, we show that LDHB limits glucose-stimulated lactate generation in {beta} cells. Further studies are warranted to understand how lactate impacts {beta} cell metabolism and/or function. HIGHLIGHTSO_LIHuman and rodent islets generate lactate following glucose stimulation. C_LIO_LI{beta} cells specifically express LDHB, which acts to limit lactate generation. C_LIO_LILDHB inhibition influences Ca2+ spiking frequency without affecting ATP/ADP ratio. C_LI eTOCCuozzo et al show that glucose-stimulated rodent and human islets generate lactate. Transcriptomic and imaging analyses reveal that LDHB is specifically expressed in {beta} cells and unexpectedly restrains lactate production. LDHB expression and thus regulated lactate generation might reflect a key mechanism underlying {beta} cell metabolism, function and survival.

physiology↗

bioRxiv2022

The HDAC inhibitor trichostatin A impairs pancreatic β-cell function through an epigenome-wide reprogramming

ObjectiveThe pancreatic islets of Langerhans contain distinct cell subtypes including insulin-producing {beta} cells. Although their cell-specific gene expression pattern defines their identity, the underlying molecular network driving this transcriptional specificity is not fully understood. Among the numerous transcriptional regulators, histone deacetylases (HDAC) enzymes are potent chromatin modifiers which directly regulate gene expression through deacetylation of lysine residues within specific histone proteins. The precise molecular mechanisms underlying HDAC effects on cellular plasticity and {beta}-cell identity are currently unknown. MethodsThe pharmacological inhibition of HDAC activity by trichostatin A (TSA) was studied in the mouse Min6 and human EndocBH1 cell lines, as well as primary mouse sorted {beta} cells and human pancreatic islets. The molecular and functional effects of treating these complementary {beta}-cell models with TSA was explored at the epigenomic and transcriptomic level through next-generation sequencing of chromatin immunoprecipitation (ChIP) assays (ChIP-seq) and RNA sequencing (RNA-seq) experiments, respectively. ResultsWe showed that TSA alters insulin secretion associated with {beta}-cell specific transcriptome programming in both mouse and human {beta}-cell lines, as well as on human pancreatic islets. We also demonstrated that this alternative {beta}-cell transcriptional program in response to HDAC inhibition is related to an epigenome-wide remodeling at both promoters and enhancers. ConclusionsTaken together, our data indicate that full HDAC activity is required to safeguard the epigenome, to protect against loss of {beta}-cell identity with unsuitable expression of genes associated with alternative cell fates.

genomics↗

bioRxiv2021

Genetic regulation of RNA splicing in human pancreatic islets

Genetic variants that influence transcriptional regulation in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D). For many susceptibility loci, however, the mechanisms are unknown. We examined splicing QTLs (sQTLs) in islets from 399 donors and observed that genetic variation has a widespread influence on splicing of genes with important functions in islet biology. In parallel, we profiled expression QTLs, and used transcriptome-wide association and co-localization studies to assign islet sQTLs or eQTLs to T2D susceptibility signals that lacked candidate effector genes. We found novel T2D associations, including an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effectors revealed overrepresented pathways, including regulators of G-protein-mediated cAMP production. This data exposes an underappreciated layer of genetic regulation in pancreatic islets, and nominates molecular mediators of T2D susceptibility.

genetics↗

bioRxiv2021

A crosstalk between E2F1 and GLP-1 signaling pathways modulates insulin secretion

Compromised {beta}-cell function contributes to type 2 diabetes (T2D) development. The glucagon like peptide 1 (Glp-1) has emerged as a hormone with broad pharmacological potential toward T2D treatment, notably by improving {beta}-cell functions. Recent data have shown that the transcription factor E2f1, besides its role as a cell cycle regulator, is involved in glucose homeostasis by modulating {beta}-cell mass, function and identity. Here, we demonstrate a crosstalk between the E2F1, phosphorylation of retinoblastoma protein (pRb) and Glp-1 signaling pathways. We found that {beta}-cell specific E2f1 deficient mice (E2f1{beta}-/-) presented with impaired glucose homeostasis and decreased glucose stimulated-insulin secretion mediated by exendin 4 (i.e., GLP1R agonist), which were associated with decreased expression of Glp1r encoding Glp-1 receptor (GLP1R) in E2f1{beta}-/- pancreatic islets. Decreasing E2F1 transcriptional activity with an E2F inhibitor in islets from nondiabetic humans decreased GLP1R levels and blunted the incretin effect of exendin 4 on insulin secretion. Conversely, overexpressing E2f1 in pancreatic {beta} cells increased Glp1r expression associated with enhanced insulin secretion mediated by GLP1R agonist. Interestingly, kinome analysis of mouse islets demonstrated that an acute treatment with exendin 4 increased pRb phosphorylation and subsequent E2f1 transcriptional activity. This study suggests a molecular crosstalk between the E2F1/pRb and GLP1R signaling pathways that modulates insulin secretion and glucose homeostasis.

physiology↗

bioRxiv2021

The transcriptional repressor REST is a major negative regulator of endocrine differentiation during pancreas organogenesis

Understanding genomic regulatory mechanisms of pancreas differentiation is relevant to the pathophysiology of diabetes mellitus, and to the development of replacement therapies. Numerous transcription factors promote {beta} cell differentiation, although less is known about negative regulators. Earlier epigenomic studies suggested that the transcriptional repressor REST could be a suppressor of endocrine gene programs in the embryonic pancreas. However, pancreatic Rest knock-out mice failed to show increased numbers of endocrine cells, suggesting that REST is not a major regulator of endocrine differentiation. Using a different conditional allele that enables profound REST inactivation, we now observe a marked increase in the formation of pancreatic endocrine cells. REST inhibition also promoted endocrinogenesis in zebrafish and mouse early postnatal ducts, and induced {beta}-cell specific genes in human adult duct-derived organoids. Finally, we define REST genomic programs that suppress pancreatic endocrine differentiation. These results establish a crucial role of REST as a negative regulator of pancreatic endocrine differentiation.

developmental biology↗

bioRxiv2020

Pancreatic β-cell specific loss of E2f1 impairs insulin secretion and β-cell identity through the epigenetic repression of non β-cell programs

The loss of pancreatic {beta}-cell identity emerges as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cell-autonomous role of the cell cycle regulator and transcription factor E2F1 in the maintenance of {beta}-cell identity and insulin secretion. We show that the {beta}-cell-specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, an altered -to-{beta}-cell ratio, a downregulation of many {beta}-cell genes and a concomitant increase of non-{beta}-cell markers. Mechanistically, the epigenomic profiling of non-beta cell upregulated gene promoters identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that histone deacetylase inhibitors modulate E2F1 transcriptional and epigenomic signatures associated with these {beta}-cell dysfunctions. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of {beta}-cell identity genes. Our data suggest that E2F1 is critical for maintaining {beta}-cell identity through a sustained repression of non {beta}-cell transcriptional programs.

physiology↗

bioRxiv2020

Meta-analysis of genome-wide DNA methylation and integrative OMICs in human skeletal muscle.

Knowledge of age-related DNA methylation changes in skeletal muscle is limited, yet this tissue is severely affected by aging in humans. Using a large-scale epigenome-wide association study (EWAS) meta-analysis of age in human skeletal muscle from 10 studies (total n = 908 human muscle methylomes), we identified 9,986 differentially methylated regions at a stringent false discovery rate < 0.005, spanning 8,748 unique genes, many of which related to skeletal muscle structure and development. We then integrated the DNA methylation results with known transcriptomic and proteomic age-related changes in skeletal muscle, and found that even though most differentially methylated genes are not altered at the mRNA or protein level, they are nonetheless strongly enriched for genes showing age-related differential expression. We provide here the most comprehensive picture of DNA methylation aging in human skeletal muscle, and have made our results available as an open-access, user-friendly, web-based tool called MetaMeth (https://sarah-voisin.shinyapps.io/MetaMeth/).

genetics↗

bioRxiv2018

Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer regions (enhancer clusters, stretch enhancers or super-enhancers). So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in 3D-space. Furthermore, their target genes are generally unknown. We have now created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers with their target genes, often located hundreds of kilobases away. It further revealed sets of islet enhancers, super-enhancers and active promoters that form 3D higher-order hubs, some of which show coordinated glucose-dependent activity. Hub genetic variants impact the heritability of insulin secretion, and help identify individuals in whom genetic variation of islet function is important for T2D. Human islet 3D chromatin architecture thus provides a framework for interpretation of T2D GWAS signals.

genomics↗

bioRxiv2016

Human pancreatic β cell lncRNAs control cell-specific regulatory networks

Recent studies have uncovered thousands of long non-coding RNAs (IncRNAs) in human pancreatic {beta} cells. {beta} cell lncRNAs are often cell type-specific, and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role of lncRNAs in {beta} cell gene regulation and diabetes, the function of {beta} cell lncRNAs remains largely unknown. In this study, we investigated the function of {beta} cell-specific lncRNAs and transcription factors using transcript knockdowns and co-expression network analysis. This revealed lncRNAs that function in concert with transcription factors to regulate {beta} cell-specific transcriptional networks. We further demonstrate that lncRNA PLUTO affects local three-dimensional chromatin structure and transcription of PDX1, encoding a key {beta} cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets from donors with type 2 diabetes or impaired glucose tolerance. These results implicate lncRNAs in the regulation of {beta} cell-specific transcription factor networks.

genomics↗