1
|
Ewald JD, Lu Y, Ellis CE, Worton J, Kolic J, Sasaki S, Zhang D, Dos Santos T, Spigelman AF, Bautista A, Dai XQ, Lyon JG, Smith NP, Wong JM, Rajesh V, Sun H, Sharp SA, Rogalski JC, Moravcova R, Cen HH, Manning Fox JE, Consortium HDAS, Atlas E, Bruin JE, Mulvihill EE, Verchere CB, Foster LJ, Gloyn AL, Johnson JD, Pepper AR, Lynn FC, Xia J, MacDonald PE. HumanIslets: An integrated platform for human islet data access and analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599613. [PMID: 38948734 PMCID: PMC11212983 DOI: 10.1101/2024.06.19.599613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Comprehensive molecular and cellular phenotyping of human islets can enable deep mechanistic insights for diabetes research. We established the Human Islet Data Analysis and Sharing (HI-DAS) consortium to advance goals in accessibility, usability, and integration of data from human islets isolated from donors with and without diabetes at the Alberta Diabetes Institute (ADI) IsletCore. Here we introduce HumanIslets.com , an open resource for the research community. This platform, which presently includes data on 547 human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at the donor, islet and single-cell levels. As an example of the analytic capacity of this resource we show a dissociation between cell culture effects on transcript and protein expression, and an approach to correct for exocrine contamination found in hand-picked islets. Finally, we provide an example workflow and visualization that highlights links between type 2 diabetes status, SERCA3b Ca 2+ -ATPase levels at the transcript and protein level, insulin secretion and islet cell phenotypes. HumanIslets.com provides a growing and adaptable set of resources and tools to support the metabolism and diabetes research community.
Collapse
|
2
|
Li J, Zhu J, Deng Y, Reck EC, Walker EM, Sidarala V, Hubers DL, Pasmooij MB, Shin CS, Bandesh K, Motakis E, Nargund S, Kursawe R, Basrur V, Nesvizhskii AI, Stitzel ML, Chan DC, Soleimanpour SA. LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597215. [PMID: 38895283 PMCID: PMC11185607 DOI: 10.1101/2024.06.03.597215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Proteotoxicity is a contributor to the development of type 2 diabetes (T2D), but it is unknown whether protein misfolding in T2D is generalized or has special features. Here, we report a robust accumulation of misfolded proteins within the mitochondria of human pancreatic islets in T2D and elucidate its impact on β cell viability. Surprisingly, quantitative proteomics studies of protein aggregates reveal that human islets from donors with T2D have a signature more closely resembling mitochondrial rather than ER protein misfolding. The matrix protease LonP1 and its chaperone partner mtHSP70 were among the proteins enriched in protein aggregates. Deletion of LONP1 in mice yields mitochondrial protein misfolding and reduced respiratory function, ultimately leading to β cell apoptosis and hyperglycemia. Intriguingly, LONP1 gain of function ameliorates mitochondrial protein misfolding and restores human β cell survival following glucolipotoxicity via a protease-independent effect requiring LONP1-mtHSP70 chaperone activity. Thus, LONP1 promotes β cell survival and prevents hyperglycemia by facilitating mitochondrial protein folding. These observations may open novel insights into the nature of impaired proteostasis on β cell loss in the pathogenesis of T2D that could be considered as future therapeutic targets.
Collapse
|
3
|
Swaminathan G, Saito T, Husain SZ. Exploiting open source omics data to advance pancreas research. JOURNAL OF PANCREATOLOGY 2024; 7:21-27. [PMID: 38524857 PMCID: PMC10959533 DOI: 10.1097/jp9.0000000000000173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/03/2024] [Indexed: 03/26/2024] Open
Abstract
The "omics" revolution has transformed the biomedical research landscape by equipping scientists with the ability to interrogate complex biological phenomenon and disease processes at an unprecedented level. The volume of "big" data generated by the different omics studies such as genomics, transcriptomics, proteomics, and metabolomics has led to the concurrent development of computational tools to enable in silico analysis and aid data deconvolution. Considering the intensive resources and high costs required to generate and analyze big data, there has been centralized, collaborative efforts to make the data and analysis tools freely available as "Open Source," to benefit the wider research community. Pancreatology research studies have contributed to this "big data rush" and have additionally benefitted from utilizing the open source data as evidenced by the increasing number of new research findings and publications that stem from such data. In this review, we briefly introduce the evolution of open source omics data, data types, the "FAIR" guiding principles for data management and reuse, and centralized platforms that enable free and fair data accessibility, availability, and provide tools for omics data analysis. We illustrate, through the case study of our own experience in mining pancreatitis omics data, the power of repurposing open source data to answer translationally relevant questions in pancreas research.
Collapse
Affiliation(s)
- Gayathri Swaminathan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Toshie Saito
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Sohail Z. Husain
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| |
Collapse
|
4
|
Christoffersson G, Fousteri G. Editorial: Footprints of immune cells in the type 1 diabetic pancreas, volume II. Front Endocrinol (Lausanne) 2024; 15:1367245. [PMID: 38379865 PMCID: PMC10877058 DOI: 10.3389/fendo.2024.1367245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
| | - Georgia Fousteri
- Division of Immunology, Transplantation, and Infectious Diseases, Diabetes Research Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Hospital, Milan, Italy
| |
Collapse
|
5
|
Cantley J, Eizirik DL, Latres E, Dayan CM. Islet cells in human type 1 diabetes: from recent advances to novel therapies - a symposium-based roadmap for future research. J Endocrinol 2023; 259:e230082. [PMID: 37493471 PMCID: PMC10502961 DOI: 10.1530/joe-23-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
There is a growing understanding that the early phases of type 1 diabetes (T1D) are characterised by a deleterious dialogue between the pancreatic beta cells and the immune system. This, combined with the urgent need to better translate this growing knowledge into novel therapies, provided the background for the JDRF-DiabetesUK-INNODIA-nPOD symposium entitled 'Islet cells in human T1D: from recent advances to novel therapies', which took place in Stockholm, Sweden, in September 2022. We provide in this article an overview of the main themes addressed in the symposium, pointing to both promising conclusions and key unmet needs that remain to be addressed in order to achieve better approaches to prevent or reverse T1D.
Collapse
Affiliation(s)
- J Cantley
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
| | - D L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
| | - E Latres
- JDRF International, New York, NY, USA
| | - C M Dayan
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
| | - the JDRF-DiabetesUK-INNODIA-nPOD Stockholm Symposium 2022
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
- JDRF International, New York, NY, USA
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
6
|
Shapira SN, Naji A, Atkinson MA, Powers AC, Kaestner KH. Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. Cell Metab 2022; 34:1906-1913. [PMID: 36206763 PMCID: PMC9742126 DOI: 10.1016/j.cmet.2022.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/26/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
In this perspective, we provide an overview of a recently established National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) initiative, the Human Pancreas Analysis Program for Type 2 Diabetes (HPAP-T2D). This program is designed to define the molecular pathogenesis of islet dysfunction by studying human pancreatic tissue samples from organ donors with T2D. HPAP-T2D generates detailed datasets of physiological, histological, transcriptomic, epigenomic, and genomic information. Importantly, all data collected, generated, and analyzed by HPAP-T2D are made immediately and freely available through a centralized database, PANC-DB, thus providing a comprehensive data resource for the diabetes research community.
Collapse
Affiliation(s)
- Suzanne N Shapira
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA; The Human Pancreas Analysis Program (RRID: SCR_016202)
| | - Ali Naji
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Human Pancreas Analysis Program (RRID: SCR_016202)
| | - Mark A Atkinson
- Departments of Pathology, Immunology, and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL 32610, USA; The Human Pancreas Analysis Program (RRID: SCR_016202)
| | - Alvin C Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA; The Human Pancreas Analysis Program (RRID: SCR_016202).
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA; The Human Pancreas Analysis Program (RRID: SCR_016202).
| |
Collapse
|
7
|
Morgan NG, Richardson SJ, Powers AC, Saunders DC, Brissova M. Images From the Exeter Archival Diabetes Biobank Now Accessible via Pancreatlas. Diabetes Care 2022; 45:e174-e175. [PMID: 36239401 PMCID: PMC9862522 DOI: 10.2337/dc22-1613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Noel G Morgan
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, U.K
| | - Sarah J Richardson
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, U.K
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN.,Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN.,VA Tennessee Valley Healthcare System, Nashville, TN
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Marcela Brissova
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| |
Collapse
|
8
|
Glorieux L, Sapala A, Willnow D, Moulis M, Salowka A, Darrigrand JF, Edri S, Schonblum A, Sakhneny L, Schaumann L, Gómez HF, Lang C, Conrad L, Guillemot F, Levenberg S, Landsman L, Iber D, Pierreux CE, Spagnoli FM. Development of a 3D atlas of the embryonic pancreas for topological and quantitative analysis of heterologous cell interactions. Development 2022; 149:274013. [PMID: 35037942 PMCID: PMC8918780 DOI: 10.1242/dev.199655] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023]
Abstract
Generating comprehensive image maps, while preserving spatial three-dimensional (3D) context, is essential in order to locate and assess quantitatively specific cellular features and cell-cell interactions during organ development. Despite recent advances in 3D imaging approaches, our current knowledge of the spatial organization of distinct cell types in the embryonic pancreatic tissue is still largely based on two-dimensional histological sections. Here, we present a light-sheet fluorescence microscopy approach to image the pancreas in three dimensions and map tissue interactions at key time points in the mouse embryo. We demonstrate the utility of the approach by providing volumetric data, 3D distribution of three main cellular components (epithelial, mesenchymal and endothelial cells) within the developing pancreas, and quantification of their relative cellular abundance within the tissue. Interestingly, our 3D images show that endocrine cells are constantly and increasingly in contact with endothelial cells forming small vessels, whereas the interactions with mesenchymal cells decrease over time. These findings suggest distinct cell-cell interaction requirements for early endocrine cell specification and late differentiation. Lastly, we combine our image data in an open-source online repository (referred to as the Pancreas Embryonic Cell Atlas). Summary: A light-sheet fluorescence microscopy approach is used for 3D imaging of the pancreas and to quantitatively map its interactions with surrounding tissues at key development time points in the mouse embryo.
Collapse
Affiliation(s)
- Laura Glorieux
- Cell Biology Unit, de Duve Institute, UCLouvain, Woluwe 1200, Belgium
| | - Aleksandra Sapala
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | - David Willnow
- Centre for Stem Cell and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - Manon Moulis
- Cell Biology Unit, de Duve Institute, UCLouvain, Woluwe 1200, Belgium
| | - Anna Salowka
- Centre for Stem Cell and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - Jean-Francois Darrigrand
- Centre for Stem Cell and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - Shlomit Edri
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Anat Schonblum
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lina Sakhneny
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Laura Schaumann
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | - Harold F Gómez
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | - Christine Lang
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | - Lisa Conrad
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | | | - Shulamit Levenberg
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Limor Landsman
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dagmar Iber
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.,Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland
| | | | - Francesca M Spagnoli
- Centre for Stem Cell and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| |
Collapse
|
9
|
Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen YA, Lin JR, Santagata S, Sorger PK, Pfister H. Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2022; 28:259-269. [PMID: 34606456 PMCID: PMC8805697 DOI: 10.1109/tvcg.2021.3114786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular information plus cell and tissue morphology using antibody staining. This provides unique insight into disease biology and promises to help with the design of patient-specific therapies. However, a substantial gap remains with respect to visualizing the resulting multivariate image data and effectively supporting pathology workflows in digital environments on screen. We, therefore, developed Scope2Screen, a scalable software system for focus+context exploration and annotation of whole-slide, high-plex, tissue images. Our approach scales to analyzing 100GB images of 109 or more pixels per channel, containing millions of individual cells. A multidisciplinary team of visualization experts, microscopists, and pathologists identified key image exploration and annotation tasks involving finding, magnifying, quantifying, and organizing regions of interest (ROIs) in an intuitive and cohesive manner. Building on a scope-to-screen metaphor, we present interactive lensing techniques that operate at single-cell and tissue levels. Lenses are equipped with task-specific functionality and descriptive statistics, making it possible to analyze image features, cell types, and spatial arrangements (neighborhoods) across image channels and scales. A fast sliding-window search guides users to regions similar to those under the lens; these regions can be analyzed and considered either separately or as part of a larger image collection. A novel snapshot method enables linked lens configurations and image statistics to be saved, restored, and shared with these regions. We validate our designs with domain experts and apply Scope2Screen in two case studies involving lung and colorectal cancers to discover cancer-relevant image features.
Collapse
|
10
|
de Boer P, Giepmans BN. State-of-the-art microscopy to understand islets of Langerhans: what to expect next? Immunol Cell Biol 2021; 99:509-520. [PMID: 33667022 PMCID: PMC8252556 DOI: 10.1111/imcb.12450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
The discovery of Langerhans and microscopic description of islets in the pancreas were crucial steps in the discovery of insulin. Over the past 150 years, many discoveries in islet biology and type 1 diabetes have been made using powerful microscopic techniques. In the past decade, combination of new probes, animal and tissue models, application of new biosensors and automation of light and electron microscopic methods and other (sub)cellular imaging modalities have proven their potential in understanding the beta cell under (patho)physiological conditions. The imaging evolution, from fluorescent jellyfish to real‐time intravital functional imaging, the revolution in automation and data handling and the increased resolving power of analytical imaging techniques are now converging. Here, we review innovative approaches that address islet biology from new angles by studying cells and molecules at high spatiotemporal resolution and in live models. Broad implementation of these cellular imaging techniques will shed new light on cause/consequence of (mal)function in islets of Langerhans in the years to come.
Collapse
Affiliation(s)
- Pascal de Boer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben Ng Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| |
Collapse
|