Biology subjects

Piemonti, L.

Publications and source records attributed to Piemonti, L..

16 recordsLinked to original sources

bioRxiv2025

Latent plasticity of the human pancreas across development, health, and disease.

The pancreas plays a central role in major human diseases, yet our understanding of its cellular diversity and plasticity remains incomplete. Here, we present a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from 57 donors across fetal development, adult homeostasis, and type 2 diabetes (T2D). Integrating sc/snRNA-seq, snATAC-seq, VASA-seq, spatial transcriptomics (Xenium), and multiplexed proteomics (CODEX), we resolve gene expression, chromatin accessibility, and spatial organization at high resolution. We identify transcriptionally plastic centroacinar-like cells (pCACs) in adults with fetal-like features, delineate endocrine and exocrine lineage trajectories during development, and uncover HNF1A-defined beta cell epigenetic states. In T2D, we observe shifts in beta cell subtypes and altered regulatory programs. Glucose perturbation of healthy islets reveals cell-type-specific adaptation and stress responses. This atlas provides a foundational framework to understand pancreas biology and the role of cellular plasticity in regeneration and disease.

genomics↗

bioRxiv2025

Bioengineering of the implantable vascularized endocrine constructs for insulin delivery suitable for clinical upscaling

Beta cell replacement therapy for type 1 diabetes is hindered by poor graft survival and suboptimal function, largely due to inadequate vascularization and lack of supportive microenvironment. To address these challenges, we developed a clinically scalable, extracellular matrix (ECM)-mimetic hydrogel, termed Amniogel, derived from human amniotic membrane via streamlined, clinically compliant process. Co-encapsulation of pancreatic islets with blood outgrowth endothelial cells (BOECs) within Amniogel facilitated the formation of prevascularized endocrine constructs (VECs). These constructs demonstrated enhanced {beta}-cell viability and function through ECM-bound pro-survival signals, rapid self-assembly of perfusable endothelial networks enabling efficient glucose sensing, and deposition of laminin-rich basement membranes enhancing {beta}-cell coupling and insulin secretion kinetics. In preclinical diabetic mouse models, VECs rapidly integrated with the host vasculature and provided sustained glycemic control when implanted subcutaneously. This integrative approach, combining a scalable, cost-effective biological scaffold with autologous vascularization potential, represents a significant advancement toward durable and clinically translatable {beta}-cell replacement therapies for T1DM. One Sentence SummaryA clinically scalable, biological hydrogel based vascularized endocrine constructs show sustained diabetes reversal.

bioengineering↗

bioRxiv2024

Liraglutide treatment reverses unconventional cellular defects in induced pluripotent stem cell-derived β cells harboring a partially functional WFS1 variant

Aims/hypothesisWolfram Syndrome 1 (WS1) is a rare genetic disorder characterized by very heterogeneous clinical manifestations caused by variants of the WFS1 gene, which encodes for the Endoplasmic Reticulum (ER) protein Wolframin, involved in cellular stress response, Ca2+ handling and autophagy. Given the central role of Wolframin, elucidating the impact of WFS1 variants on cell functions is crucial to provide an association with clinical phenotypes. Therefore, as the understanding of patient-specific defects may also help to develop targeted therapeutic approaches, here we aimed at elucidating the impact on {beta} cell function of the c.316-1G>A mutation harboring the partially functional Wolframin that we have previously characterized, and the molecular changes following treatment with the glucagon-like peptide 1 receptor (GLP-1R) agonist liraglutide. MethodsWe previously generated patient-derived iPSCs (WFS1) and isogenic line in which the c.316-1G>A mutation was genetically corrected (WFS1wt/757A>T), thus performed molecular analysis, including single cell RNAseq (scRNAseq), and functional studies on iPSC-derived {beta} cell (iBeta). Calcium flux imaging and dynamic perifusion assays were used to test glucose responsiveness of iBeta. Treatment with liraglutide was performed to investigate effects on glucose-stimulated insulin secretion (GSIS), unfolded protein response (UPR), autophagy and apoptosis. ResultsWe found that both WFS1 and WFS1wt/757A>T iBeta efficiently differentiated in vitro into pancreatic lineage, but WFS1 showed less mature endocrine phenotype, reduced glucose responsiveness and impaired insulin secretion compared to WFS1wt/757A>T counterpart. The Ca2+ dynamics were altered in WFS1 iBeta as Ca2+ oscillations after glucose challenge were not synchronized mainly due to the CACNA1D and SNAP25 downmodulation. Reduced insulin secretion was correlated with a decrease in PC1/3 levels and overall increase of RGS4 expression in WFS1 iBeta, whereas secretory defects correlated with accelerated autophagic flux. While the functional residual Wolframin in WFS1 iBeta controlled short-term ER stress, prolonged insults or inflammation highlighted ineffective UPR that make the cells unable to escape apoptosis. Interestingly, treatment with liraglutide restored the Ca2+ fluxes and secretory impairments, increasing glucose responsiveness and insulin release of WFS1 iBeta, while protecting these cells from cellular stress and inflammation-induced apoptosis. Conclusion/interpretationOur data highlighted alterations of key cellular pathways involved in WS1 {beta} cell maturation and GSIS and how the pharmacological targeting of the GLP-1/GLP-1R axis was able to restore the physiologic phenotype. This study points out the need to understand the patient-specific molecular determinants associated with WFS1 variants, to design effective therapies to treat the disease.

cell biology↗

bioRxiv2024

Post-transcriptional regulation of insulin mRNA storage by G3BP1/2+ condensates in beta cells

Hyperglycemia upregulates insulin translation in pancreatic beta cells. Several RNA- binding proteins involved in this process have been identified, including G3BP1, a stress granule marker downregulated in islets of subjects with type 2 diabetes. We show that in mouse insulinoma MIN6-K8 cells exposed to fasting glucose levels G3BP1 and its paralog G3BP2 colocalize to cytosolic condensates with eIF3b and Ins1/2 mRNA. Upon glucose stimulation, the condensates dissolve and G3BP1/2, eIF3b, and insulin mRNAs redistribute throughout the cytosol. Intriguingly, G3BP1+ condensates in MIN6-K8 cells differ from sodium arsenate-induced stress granules in regards to eIF2 and AMPK phosphorylation. Knockout of G3BP1 or G3BP2 prevented condensate assembly, but only G3BP1 deletion decreased the levels of Ins1/2 mRNA and proinsulin and impaired polysome formation. Like glucose, other insulin secretagogues such as Exendin-4 and palmitate, but not high KCl, prompted the dissolution of G3BP1+ condensates. G3BP1+/Ins mRNA+ condensates were also present in mouse and human beta cells from normoglycemic donors. Hence, G3BP1+ condensates represent a glucose-regulated compartment for the physiological storage and protection of insulin mRNA in resting beta cells.

molecular biology↗

bioRxiv2024

Implications of noncoding regulatory functions in the development of insulinomas

Insulinomas are rare neuroendocrine tumours arising from the pancreatic {beta}-cells. While retaining the ability to produce insulin, insulinomas feature aberrant proliferation and altered hormone secretion resulting in failure to maintain glucose homeostasis. With the aim of uncovering the role of noncoding regulatory regions and their aberrations to the development of these tumors, we coupled epigenetic and gene expression profiling with whole-genome sequencing. As a result, we mapped H3K27ac sites in the tumoral tissue and unraveled overlapping somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development and epigenetic modifying genes, including key components of the polycomb complex. Chromatin remodeling is apparent as insulinoma-selective regions are mostly clustered in regulatory domains, shared across patients and containing a specific set of regulatory sequences dominated by the binding motif of the transcription factor SOX17. Moreover, a large fraction of these regions are H3K27me3-repressed in unaffected {beta}-cells, suggesting that tumoral transition is coupled with derepression of {beta}-cell polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements and transcription factors that alter {beta}-cell function and fate in their progression to pancreatic neuroendocrine tumors and a framework to identify coding and noncoding driver mutations.

genomics↗

bioRxiv2023

A WFS1 variant disrupting acceptor splice site uncovers the impact of alternative splicing on ER-stress independent β cell apoptosis in a patient with Wolfram syndrome.

Aims/hypothesisWolfram Syndrome 1 (WS1) is an inherited condition mainly manifesting in childhood-onset diabetes mellitus and progressive optic nerve atrophy. The causative gene, WFS1, encodes for Wolframin, a master regulator of several cellular responses, whose mutations associate with clinical variability. Indeed, nonsense/frameshift variants correlate with more severe symptoms than missense/in-frame ones. As achieving a genotype-phenotype correlation is crucial to deal with disease outcome, works investigating the impact of transcriptional and translational landscapes stemming from such mutations are needed. Therefore, we sought to elucidate the molecular determinants behind the pathophysiological alterations in a WS1 patient carrying compound heterozygous mutations in WFS1 gene: c.316-1G>A, affecting the acceptor splice site (ASS) upstream exon 4, and c.757A>T, introducing a premature termination codon (PTC) in exon 7. MethodsBioinformatic analysis was carried out to infer the alternative splicing events occurring after disruption of ASS, followed by RNAseq and PCR to validate the transcriptional landscape. Patient-derived induced Pluripotent Stem Cells (iPSCs) were used as an in vitro model of WS1 and to investigate the WFS1 alternative splicing isoforms into pancreatic {beta} cells. CRISPR/Cas9 technology was employed to correct ASS mutation and generate a syngeneic control for the ER-stress induction and immunotoxicity assays. ResultsWe showed that patient-derived iPSCs retained the ability to differentiate into pancreatic {beta} cells. We demonstrated that the allele carrying the ASS mutation c.316-1G>A originates two PTC-containing alternative splicing transcripts (c.316del and c.316-460del), and two ORF-conserving mRNAs (c.271-513del and c.316-456del) leading to N-terminally truncated polypeptides. By retaining the C-terminal domain, these isoforms sustained the endoplasmic reticulum (ER)-stress response in {beta} cells. Otherwise, PTC-carrying transcripts were regulated by the nonsense mediated decay (NMD) in basal conditions. Exposure to cell stress inducers and pro-inflammatory cytokines affected the NMD-related gene SMG7 expression levels (>2 fold decrease; p<0.001) without eliciting a robust unfolded protein response in WFS1 {beta} cells, thus resulting in a dramatic accumulation of the PTC-containing isoforms c.316del (>100-fold increase over basal; p<0.001) and c.316-460del (>20-fold increase over basal; p<0.001) and predisposing affected {beta} cells to undergo apoptosis. Cas9-mediated recovery of ASS retrieved the canonical transcriptional landscape, rescuing the normal phenotype in patient-derived {beta} cells. Conclusions/interpretationThis study represents a new model to study Wolframin, highlighting how each single mutation of WFS1 gene can determine dramatically different functional outcomes. Our data point to increased vulnerability of WFS1 {beta} cells to stress and inflammation, and we postulate that this is triggered by escaping NMD and accumulation of mutated transcripts and truncated proteins. These findings pave the way for further studies on the molecular basis of genotype-phenotype relationship in WS1, to uncover the key determinants that might be targeted to ameliorate the clinical outcome of patients affected by this rare disease.

genetics↗

bioRxiv2023

Proinflammatory Cytokines, but not Glucolipotoxicity, Suppress Nonsense-Mediated RNA Decay to Impair Regulated Transcript Isoform Processing in Pancreatic β-Cells

Proinflammatory cytokines are implicated in pancreatic {beta}-cell failure in type 1 and type 2 diabetes and are known to stimulate alternative RNA splicing and the expression of Nonsense-Mediated RNA Decay (NMD) components. Here, we investigate whether cytokines regulate NMD activity and identify transcript isoforms targeted in {beta}-cells. A luciferase-based NMD reporter transiently expressed in rat INS1(832/13), human-derived EndoC-{beta}H3 or dispersed human islet cells is used to examine the effect of proinflammatory cytokines (Cyt) on NMD activity. Gain- or loss-of function of two key NMD components UPF3B and UPF2 is used to reveal the effect of cytokines on cell viability and function. RNA-sequencing and siRNA-mediated silencing are deployed using standard techniques. Cyt attenuate NMD activity in insulin-producing cell lines and primary human {beta}-cells. These effects are found to involve ER stress and are associated with downregulation of UPF3B. Increases or decreases in NMD activity achieved by UPF3B overexpression (OE) or UPF2 silencing, raises or lowers Cyt-induced cell death, respectively, in EndoC-{beta}H3 cells, and are associated with decreased or increased insulin content, respectively. No effects of these manipulations are observed on glucose-stimulated insulin secretion. Transcriptomic analysis reveals that Cyt increase alternative splicing (AS)-induced exon skipping in the transcript isoforms, and this is potentiated by UPF2 silencing. Gene enrichment analysis identifies transcripts regulated by UPF2 silencing whose proteins are localized and/or functional in extracellular matrix (ECM) including the serine protease inhibitor SERPINA1/-1-antitrypsin, whose silencing sensitises {beta}-cells to Cyt cytotoxicity. Cytokines suppress NMD activity via UPR signalling, potentially serving as a protective response against Cyt-induced NMD component expression. Our findings highlight the central importance of RNA turnover in {beta}-cell responses to inflammatory stress.

cell biology↗

bioRxiv2023

Immunometabolic reprogramming by LRH-1/NR5A2 pharmacological activation resolves inflammation in immune cells of type 1 diabetes mellitus individuals and improves human islet engraftment and function

The intricate etiology of type 1 diabetes mellitus (T1D), marked by a detrimental cross-talk between the immune system and insulin-producing {beta}-cells, has impeded effective disease-modifying therapies. The discovery that pharmacological activation of the nuclear receptor LRH-1/NR5A2 can reverse hyperglycemia in mouse models of T1D by attenuating the autoimmune attack coupled to {beta}-cell survival/regeneration, prompted us to investigate whether immune tolerization could be achieved in individuals with T1D by LRH-1/NR5A2 activation as well as improving islet function/survival after xenotransplantation in mice. Pharmacological activation of LRH-1/NR5A2 induced a coordinated genetic and metabolic reprogramming of T1D macrophages and dendritic cells, shifting them from a pro-to an anti-inflammatory/tolerogenic phenotype. Regulatory T-cells were also expanded resulting in the impediment of cytotoxic T-cell proliferation. LRH-1/NR5A2 activation enhanced human islet engraftment and function in hyperglycemic immunocompetent mice. In summary our findings demonstrate the feasibility of re-establishing immune tolerance within a pro-inflammatory environment, opening a new therapeutic venue for T1D.

cell biology↗

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↗

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

Glucose-dependent miR-125b is a negative regulator of β-cell function

Impaired pancreatic {beta}-cell function and insulin secretion are hallmarks of type 2 diabetes. MicroRNAs are short non-coding RNAs that silence gene expression, vital for the development and function of {beta}-cells. We have previously shown that {beta}-cell specific deletion of the important energy sensor AMP-activated protein kinase (AMPK) results in increased miR-125b-5p levels. Nevertheless, the function of this miRNA in {beta}-cells is unclear. We hypothesized that miR-125b-5p expression is regulated by glucose and that this miRNA mediates some of the deleterious effects of hyperglycaemia in {beta}-cells. Here we show that islet miR-125b-5p expression is up-regulated by glucose in an AMPK-dependent manner and that short-term miR-125b-5p overexpression impairs glucose stimulated insulin secretion (GSIS) in the mouse insulinoma MIN6 cells and in human islets. An unbiased high-throughput screen in MIN6 cells identified multiple miR-125b-5p targets, including the transporter of lysosomal hydrolases M6pr and the mitochondrial fission regulator Mtfp1. Inactivation of miR-125b-5p in the human {beta}-cell line EndoC{beta}-H1 shortened mitochondria and enhanced GSIS, whilst mice overexpressing miR-125b-5p selectively in {beta}-cells (MIR125B-Tg) were hyperglycaemic and glucose intolerant. MIR125B-Tg {beta}-cells contained enlarged lysosomal structures and showed reduced insulin content and secretion. Collectively, we identify miR-125b as a glucose-controlled regulator of organelle dynamics that modulates insulin secretion. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗

bioRxiv2020

The long non-coding RNA Pax6os1/PAX6-AS1 modulates pancreatic β-cell identity and function.

Aim/HypothesisLong non-coding RNAs (lncRNAs) are emerging as crucial regulators of beta cell development and function. Here, we investigate roles for an antisense lncRNA expressed from the Pax6 locus (annotated as Pax6os1 in mice and PAX6-AS1 in humans) in beta cell identity and functionality. MethodsPax6os1 expression was silenced in MIN6 cells using siRNAs and changes in gene expression were determined by RNA sequencing or qRT-PCR. Mice inactivated for Pax6os1 and human PAX6-AS1-null EndoC-{beta}H1 cells, were generated using CRISPR/Cas9 technology. Human islets were infected with lentiviral vectors bearing a targeted shRNA or PAX6-AS1, which were used to silence or overexpress, respectively, the lncRNA. RNA sequencing or RT-qPCR were used to measure transcriptomic changes and RNA pulldown in mice and human cells followed by mass spectrometry/western blot were performed to explore RNA protein interactions. ResultsPax6os1/PAX6-AS1 expression was upregulated at high glucose concentrations in derived beta cell lines as well as in mouse and human islets, and in pancreatic islets isolated from mice fed a high fat diet (n=6, p=0.003) and patients with type 2 diabetes (n=11-5, p<0.01). Silencing or deletion of Pax6os1/PAX6-AS1 in MIN6 or EndoC-{beta}H1cells increased the expression of several {beta}-cell signature genes, including PDX1 and INS. Female, but not male, Pax6os1 null mice fed a high fat diet showed slightly enhanced glucose clearance. ShRNA-mediated silencing of PAX6-AS1 in human islets robustly increased INS mRNA, enhanced glucose-stimulated insulin secretion and calcium dynamics, while overexpression of the lncRNA exerted opposing effects. Pax6os1/AS-1 interacted with histones H3 and H4 in mouse and human cells, indicating a possible role for this lncRNA in histone modifications in both species. ConclusionsIncreased expression of PAX6-AS1 at high glucose levels may impair beta cell functionality and thus contribute to the development of type 2 diabetes. Thus, targeting PAX6-AS1 may provide a promising strategy to enhance insulin secretion and improve glucose homeostasis in this disease. Research in contextO_ST_ABSWhat is already known about the subject?C_ST_ABSLong non-coding RNAs (lncRNAs) are crucial components of the pancreatic islet regulome, whose misexpression may contribute to the development of diabetes. What is the key question?Is the lncRNA Pax6os1/PAX6-AS1 involved in beta cell functionality and type 2 diabetes? What are the new findings?The expression of Pax6os1/PAX6-AS1 is upregulated in mice fed a high fat diet and in pancreatic islets from type 2 diabetes donors. Overexpression of PAX6-AS1 in human pancreatic islets reduces insulin expression, glucose stimulated secretion and intracellular calcium dynamics. Silencing PAX6-AS1 in human pancreatic islets upregulates insulin expression, enhances glucose stimulated insulin secretion and increases intracellular calcium dynamics. How may this impact the clinic in the foreseeable future?Understanding the genetic factors induced by high glucose/obesity involved in beta cell dysfunction is crucial for the development of new therapies to treat T2D.

cell biology↗

bioRxiv2020

Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene

Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their endogenous genomic location. This poses major limitations to understand the true consequences of causal regulatory variants. We focused on a cis-regulatory mutation (c.-331C>G) in the INS gene promoter that is recurrently mutated in unrelated patients with recessive neonatal diabetes. We created mice in which a ~3.1 kb human INS upstream region carrying -331C or -331G alleles replaced the orthologous mouse Ins2 region. This human sequence drove cell-specific transcription in mice. It also recapitulated poised chromatin during pancreas development and active chromatin in differentiated {beta}-cells. The c.-331C>G mutation, however, blocked active chromatin formation in differentiated b-cells. We further show that another neonatal diabetes gene product, GLIS3, had a singular pioneer-like ability to activate INS chromatin in non-pancreatic cells, which was hampered by the c.-331C>G mutation. This in vivo analysis of human regulatory defects, therefore, uncovered cis and trans components of a mechanism that is essential to activate the endogenous INS gene.

genomics↗

bioRxiv2019

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

Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic {beta} cells. We show here that exposure to pro-inflammatory cytokines unmasks a marked plasticity of the {beta}-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the {beta}-cell transcriptome, proteome and 3D chromatin structure. Our data indicates that the {beta} cell response to cytokines is mediated by the induction of novel regulatory regions as well as the activation of primed regulatory elements pre-bound by islet-specific transcription factors. We found that T1D-associated loci are enriched of the newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human {beta} cells. Our study illustrates how {beta} cells respond to a pro-inflammatory environment and implicate a role for stimulus-response islet enhancers in T1D.

genomics↗

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↗