Mechanisms of autoantigen generation in Type 1 diabetes

Type 1 diabetes is a chronic autoimmune disease where the insulin producing beta cells of the pancreas are attacked by the immune system. Throughout this thesis, we challenged the classical view of T1D as a solely autoimmune disease and added to all the existing evidence indicating that beta cells by being inherently vulnerable to extracellular stress signals accumulate mistakes that may trigger an immune system with “good intentions” against a defective tissue. We studied the effect of an inflammatory environment on beta cell transcriptional, post transcriptional, translational, and antigen processing machinery, providing proofs that beta cells are not inert victims of the immune system but active players in their own destruction. This thesis clarifies the consequences of environment- and pathophysiology-induced changes on beta cells that lead to the development of autoimmunity in type 1 diabetes and provides new therapeutic targets to prevent formation or presentation of neoantigens.This work is supported by JDRF, Stichting Diabetes Onderzoek Nederland (DON), and the Diabetes Fonds (Dutch Diabetes Research Foundation) and by the Innovative Medicines Initiative 2 Joint Undertaking (IMI2-JU) under grant agreement No. 115797 (INNODIA). This Joint Undertaking receives support from the European Union’s Horizon 2020 Research and Innovation program and the European Federation of Pharmaceutical Industries and Associations, JDRF, and The Leona M. and Harry B. Helmsley Charitable Trust.LUMC / Geneeskund

Machine Learning Predicts Drug Metabolism and Bioaccumulation by Intestinal Microbiota

Over 150 drugs are currently recognised as being susceptible to metabolism or bioaccumulation (together described as depletion) by gastrointestinal microorganisms; however, the true number is likely higher. Microbial drug depletion is often variable between and within individuals, depending on their unique composition of gut microbiota. Such variability can lead to significant differences in pharmacokinetics, which may be associated with dosing difficulties and lack of medication response. In this study, literature mining and unsupervised learning were used to curate a dataset of 455 drug–microbiota interactions. From this, 11 supervised learning models were developed that could predict drugs’ susceptibility to depletion by gut microbiota. The best model, a tuned extremely randomised trees classifier, achieved performance metrics of AUROC: 75.1% ± 6.8; weighted recall: 79.2% ± 3.9; balanced accuracy: 69.0% ± 4.6; and weighted precision: 80.2% ± 3.7 when validated on 91 drugs. This machine learning model is the first of its kind and provides a rapid, reliable, and resource-friendly tool for researchers and industry professionals to screen drugs for susceptibility to depletion by gut microbiota. The recognition of drug–microbiome interactions can support successful drug development and promote better formulations and dosage regimens for patients

Export pricing at the firm level with panel data

This chapter reviews the growing empirical literature that explores the determinants of export prices at the firm level. It first presents evidence from empirical studies that link firm export pricing to destination characteristics (‘gravity-type’ models). The main implications of channels that can generate price differentiation, namely quality customization, variable markups and exchange rate pass-through, and financial frictions are then explored. A newly compiled panel dataset from Greek exporting firms is used to present evidence from regressions with export price as the dependent variable and show how the main economic hypotheses derived in theoretical models are nested in empirical specifications

DigiArt: towards a virtualization of Cultural Heritage

DigiArt is a Europe-wide project aimed at providing a new, cost efficient solution to the capture, processing and display of cultural artefacts. The project will change the ways in which the public interact with cultural objects and spaces in a dramatic way. This project is unique in its collaborative approach: cultural heritage professionals working directly with electrical, mechanical, optical and software engineers to develop a solution to current issues faced by the museum sector. The innovations created by the engineers are driven by the demand of the cultural heritage sector. The diversity of the objects and spaces of the three test museums are challenging the engineers to provide a tool useful for a broad variety of indoor and outdoor museums in the future. This goes from using Unmanned Aerial Vehicle (UAVs or drones) to fly and record large sites, to using scanners to record fine jewellery. As a case study, we present here the use-case of Scladina Cave. At the end of the project, the Scladina Cave Archaeological Centre will offer two different visitor experiences. The first uses virtual reality, which will be available anytime, anywhere, to anyone with an internet connected device. The second will use augmented reality technologies within the cave site. The augmented reality visit of the cave will enhance the tour of Scladina by offering visits that would not be possible where it not for the augmented reality, where 3D objects and animations will contribute to offer a new 3D-immersive experience

IFN(sic) but not IFNa increases recognition of insulin defective ribosomal product-derived antigen to amplify islet autoimmunity

Aims/hypothesisThe inflammatory milieu characteristic of insulitis affects translation fidelity and generates defective ribosomal products (DRiPs) that participate in autoimmune beta cell destruction in type 1 diabetes. Here, we studied the role of early innate cytokines (IFNα) and late immune adaptive events (IFNɣ) in insulin DRiP-derived peptide presentation to diabetogenic CD8+ T cells.MethodsSingle-cell transcriptomics of human pancreatic islets was used to study the composition of the (immuno)proteasome. Specific inhibition of the immunoproteasome catalytic subunits was achieved using siRNA, and antigenic peptide presentation at the cell surface of the human beta cell line EndoC-βH1 was monitored using peptide-specific CD8 T cells.ResultsWe found that IFNγ induces the expression of the PSMB10 transcript encoding the β2i catalytic subunit of the immunoproteasome in endocrine beta cells, revealing a critical role in insulin DRiP-derived peptide presentation to T cells. Moreover, we showed that PSMB10 is upregulated in a beta cell subset that is preferentially destroyed in the pancreases of individuals with type 1 diabetes.Conclusions/interpretationOur data highlight the role of the degradation machinery in beta cell immunogenicity and emphasise the need for evaluation of targeted immunoproteasome inhibitors to limit beta cell destruction in type 1 diabetes.Nephrolog

The 4C5 Cell-Impermeable Anti-HSP90 Antibody with Anti-Cancer Activity, Is Composed of a Single Light Chain Dimer

MAb 4C5 is a cell impermeable, anti-HSP90 murine monoclonal antibody, originally produced using hybridoma technology. We have previously shown that mAb 4C5 specifically recognizes both the α- and to a lesser extent the β-isoform of HSP90. Additionally, in vitro and in vivo studies revealed that by selectively inhibiting the function of cell-surface HSP90, mAb 4C5 significantly impairs cancer cell invasion and metastasis. Here we describe the reconstitution of mAb 4C5 into a mouse-human chimera. More importantly we report that mAb 4C5 and consequently its chimeric counterpart are completely devoid of heavy chain and consist only of a functional kappa light chain dimer. The chimeric antibody is shown to retain the original antibody's specificity and functional properties. Thus it is capable of inhibiting the function of surface HSP90, leading to reduced cancer cell invasion in vitro. Finally, we present in vivo evidence showing that the chimeric 4C5 significantly inhibits the metastatic deposit formation of MDA-MB-453 cells into the lungs of SCID mice. These data suggest that a chimeric kappa light chain antibody could be potentially used as an anti-cancer agent, thereby introducing a novel type of antibody fragment, with reduced possible adverse immunogenic effects, into cancer therapeutics

Long RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape

Type 1 diabetes (T1D) is an autoimmune disease characterized by autoreactive T cell-mediated destruction of the insulin-producing pancreatic beta -cells. Increasing evidence suggest that the beta -cells themselves contribute to their own destruction by generating neoantigens through the production of aberrant or modified proteins that escape central tolerance. We recently demonstrated that ribosomal infidelity amplified by stress could lead to the generation of neoantigens in human beta -cells, emphasizing the participation of nonconventional translation events in autoimmunity, as occurring in cancer or virus-infected tissues. Using a transcriptome-wide profiling approach to map translation initiation start sites in human beta -cells under standard and inflammatory conditions, we identify a completely new set of polypeptides derived from noncanonical start sites and translation initiation within long noncoding RNA. Our data underline the extreme diversity of the beta -cell translatome and may reveal new functional biomarkers for beta -cell distress, disease prediction and progression, and therapeutic intervention in T1D.Molecular Epidemiolog

Islet stress, degradation and autoimmunity

Transplantation and autoimmunit

Type 1 diabetes mellitus as a disease of the beta-cell (do not blame the immune system?)

Type 1 diabetes mellitus is believed to result from destruction of the insulin-producing beta-cells in pancreatic islets that is mediated by autoimmune mechanisms. The classic view is that autoreactive T cells mistakenly destroy healthy ('innocent') beta-cells. We propose an alternative view in which the beta-cell is the key contributor to the disease. By their nature and function, beta-cells are prone to biosynthetic stress with limited measures for self-defence. beta-Cell stress provokes an immune attack that has considerable negative effects on the source of a vital hormone. This view would explain why immunotherapy at best delays progression of type 1 diabetes mellitus and points to opportunities to use therapies that revitalize beta-cells, in combination with immune intervention strategies, to reverse the disease. We present the case that dysfunction occurs in both the immune system and beta-cells, which provokes further dysfunction, and present the evidence leading to the consensus that islet autoimmunity is an essential component in the pathogenesis of type 1 diabetes mellitus. Next, we build the case for the beta-cell as the trigger of an autoimmune response, supported by analogies in cancer and antitumour immunity. Finally, we synthesize a model ('connecting the dots') in which both beta-cell stress and islet autoimmunity can be harnessed as targets for intervention strategies.This Review examines the evidence that beta-cells are active participants in the dialogue with the immune system during the development of type 1 diabetes mellitus. The authors suggest that therapies targeting beta-cell health, vitality and function might prove essential, in combination with immunotherapy, to change the course of events leading to beta-cell destruction.Therapeutic cell differentiatio