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Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D. CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. Cell Rep 2024; 43:114640. [PMID: 39163202 DOI: 10.1016/j.celrep.2024.114640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024] Open
Abstract
Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challenging. To identify enhancers pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers identified, we focused on an enhancer we named ONECUT1e-664kb, ∼664 kb from the ONECUT1 promoter. Previous studies have linked ONECUT1 coding mutations to pancreatic hypoplasia and neonatal diabetes. We found that homozygous deletion of ONECUT1e-664kb in hPSCs leads to a near-complete loss of ONECUT1 expression and impaired pancreatic differentiation. ONECUT1e-664kb contains a type 2 diabetes-associated variant (rs528350911) disrupting a GATA motif. Introducing the risk variant into hPSCs reduced binding of key pancreatic transcription factors (GATA4, GATA6, and FOXA2), supporting its causal role in diabetes. This work highlights the utility of unbiased enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.
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Affiliation(s)
- Samuel Joseph Kaplan
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wilfred Wong
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jielin Yan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hyein S Cho
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qianzi Li
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiahui Zhao
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jayanti Leslie-Iyer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan Kazakov
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dylan Murphy
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kushal K Dey
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Effie Apostolou
- Meyer Cancer Center, Division of Neuro-Oncology, Department of Neurology, Sandra and Edward Meyer Cancer Center, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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2
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Robertson CC, Elgamal RM, Henry-Kanarek BA, Arvan P, Chen S, Dhawan S, Eizirik DL, Kaddis JS, Vahedi G, Parker SCJ, Gaulton KJ, Soleimanpour SA. Untangling the genetics of beta cell dysfunction and death in type 1 diabetes. Mol Metab 2024; 86:101973. [PMID: 38914291 PMCID: PMC11283044 DOI: 10.1016/j.molmet.2024.101973] [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: 03/14/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex multi-system disease which arises from both environmental and genetic factors, resulting in the destruction of insulin-producing pancreatic beta cells. Over the past two decades, human genetic studies have provided new insight into the etiology of T1D, including an appreciation for the role of beta cells in their own demise. SCOPE OF REVIEW Here, we outline models supported by human genetic data for the role of beta cell dysfunction and death in T1D. We highlight the importance of strong evidence linking T1D genetic associations to bona fide candidate genes for mechanistic and therapeutic consideration. To guide rigorous interpretation of genetic associations, we describe molecular profiling approaches, genomic resources, and disease models that may be used to construct variant-to-gene links and to investigate candidate genes and their role in T1D. MAJOR CONCLUSIONS We profile advances in understanding the genetic causes of beta cell dysfunction and death at individual T1D risk loci. We discuss how genetic risk prediction models can be used to address disease heterogeneity. Further, we present areas where investment will be critical for the future use of genetics to address open questions in the development of new treatment and prevention strategies for T1D.
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Affiliation(s)
- Catherine C Robertson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ruth M Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Belle A Henry-Kanarek
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Peter Arvan
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA; Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Scott A Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA.
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3
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Ibrahim H, Balboa D, Saarimäki-Vire J, Montaser H, Dyachok O, Lund PE, Omar-Hmeadi M, Kvist J, Dwivedi OP, Lithovius V, Barsby T, Chandra V, Eurola S, Ustinov J, Tuomi T, Miettinen PJ, Barg S, Tengholm A, Otonkoski T. RFX6 haploinsufficiency predisposes to diabetes through impaired beta cell function. Diabetologia 2024; 67:1642-1662. [PMID: 38743124 PMCID: PMC11343796 DOI: 10.1007/s00125-024-06163-y] [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: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
AIMS/HYPOTHESIS Regulatory factor X 6 (RFX6) is crucial for pancreatic endocrine development and differentiation. The RFX6 variant p.His293LeufsTer7 is significantly enriched in the Finnish population, with almost 1:250 individuals as a carrier. Importantly, the FinnGen study indicates a high predisposition for heterozygous carriers to develop type 2 and gestational diabetes. However, the precise mechanism of this predisposition remains unknown. METHODS To understand the role of this variant in beta cell development and function, we used CRISPR technology to generate allelic series of pluripotent stem cells. We created two isogenic stem cell models: a human embryonic stem cell model; and a patient-derived stem cell model. Both were differentiated into pancreatic islet lineages (stem-cell-derived islets, SC-islets), followed by implantation in immunocompromised NOD-SCID-Gamma mice. RESULTS Stem cell models of the homozygous variant RFX6-/- predictably failed to generate insulin-secreting pancreatic beta cells, mirroring the phenotype observed in Mitchell-Riley syndrome. Notably, at the pancreatic endocrine stage, there was an upregulation of precursor markers NEUROG3 and SOX9, accompanied by increased apoptosis. Intriguingly, heterozygous RFX6+/- SC-islets exhibited RFX6 haploinsufficiency (54.2% reduction in protein expression), associated with reduced beta cell maturation markers, altered calcium signalling and impaired insulin secretion (62% and 54% reduction in basal and high glucose conditions, respectively). However, RFX6 haploinsufficiency did not have an impact on beta cell number or insulin content. The reduced insulin secretion persisted after in vivo implantation in mice, aligning with the increased risk of variant carriers to develop diabetes. CONCLUSIONS/INTERPRETATION Our allelic series isogenic SC-islet models represent a powerful tool to elucidate specific aetiologies of diabetes in humans, enabling the sensitive detection of aberrations in both beta cell development and function. We highlight the critical role of RFX6 in augmenting and maintaining the pancreatic progenitor pool, with an endocrine roadblock and increased cell death upon its loss. We demonstrate that RFX6 haploinsufficiency does not affect beta cell number or insulin content but does impair function, predisposing heterozygous carriers of loss-of-function variants to diabetes. DATA AVAILABILITY Ultra-deep bulk RNA-seq data for pancreatic differentiation stages 3, 5 and 7 of H1 RFX6 genotypes are deposited in the Gene Expression Omnibus database with accession code GSE234289. Original western blot images are deposited at Mendeley ( https://data.mendeley.com/datasets/g75drr3mgw/2 ).
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Affiliation(s)
- Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Diego Balboa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Oleg Dyachok
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Per-Eric Lund
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | | | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Om P Dwivedi
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Väinö Lithovius
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tom Barsby
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vikash Chandra
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Solja Eurola
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jarkko Ustinov
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Finland
- Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Päivi J Miettinen
- Department of Pediatrics, Helsinki University Hospital, Helsinki, Finland
| | - Sebastian Barg
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Anders Tengholm
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Pediatrics, Helsinki University Hospital, Helsinki, Finland.
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4
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Zhao J, Liang S, Cen HH, Li Y, Baker RK, Ruprai B, Gao G, Zhang C, Ren H, Tang C, Chen L, Liu Y, Lynn FC, Johnson JD, Kieffer TJ. PDX1+ cell budding morphogenesis in a stem cell-derived islet spheroid system. Nat Commun 2024; 15:5894. [PMID: 39003281 PMCID: PMC11246529 DOI: 10.1038/s41467-024-50109-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024] Open
Abstract
Remarkable advances in protocol development have been achieved to manufacture insulin-secreting islets from human pluripotent stem cells (hPSCs). Distinct from current approaches, we devised a tunable strategy to generate islet spheroids enriched for major islet cell types by incorporating PDX1+ cell budding morphogenesis into staged differentiation. In this process that appears to mimic normal islet morphogenesis, the differentiating islet spheroids organize with endocrine cells that are intermingled or arranged in a core-mantle architecture, accompanied with functional heterogeneity. Through in vitro modelling of human pancreas development, we illustrate the importance of PDX1 and the requirement for EphB3/4 signaling in eliciting cell budding morphogenesis. Using this new approach, we model Mitchell-Riley syndrome with RFX6 knockout hPSCs illustrating unexpected morphogenesis defects in the differentiation towards islet cells. The tunable differentiation system and stem cell-derived islet models described in this work may facilitate addressing fundamental questions in islet biology and probing human pancreas diseases.
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Affiliation(s)
- Jia Zhao
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada.
| | - Shenghui Liang
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Haoning Howard Cen
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Yanjun Li
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
| | - Robert K Baker
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Balwinder Ruprai
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Guang Gao
- Imaging Core Facility, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Chloe Zhang
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Huixia Ren
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Liangyi Chen
- Institute of Molecular Medicine, School of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, South China Normal University, 510631, Guangzhou, China
- Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, 510631, Guangzhou, China
| | - Francis C Lynn
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - James D Johnson
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Timothy J Kieffer
- Life Sciences Institute, Departments of Cellular & Physiological Sciences and Surgery, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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5
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Chernysheva МB, Ruchko ЕS, Karimova МV, Vorotelyak ЕA, Vasiliev АV. Development, regeneration, and physiological expansion of functional β-cells: Cellular sources and regulators. Front Cell Dev Biol 2024; 12:1424278. [PMID: 39045459 PMCID: PMC11263198 DOI: 10.3389/fcell.2024.1424278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Pancreatic regeneration is a complex process observed in both normal and pathological conditions. The aim of this review is to provide a comprehensive understanding of the emergence of a functionally active population of insulin-secreting β-cells in the adult pancreas. The renewal of β-cells is governed by a multifaceted interaction between cellular sources of genetic and epigenetic factors. Understanding the development and heterogeneity of β-cell populations is crucial for functional β-cell regeneration. The functional mass of pancreatic β-cells increases in situations such as pregnancy and obesity. However, the specific markers of mature β-cell populations and postnatal pancreatic progenitors capable of increasing self-reproduction in these conditions remain to be elucidated. The capacity to regenerate the β-cell population through various pathways, including the proliferation of pre-existing β-cells, β-cell neogenesis, differentiation of β-cells from a population of progenitor cells, and transdifferentiation of non-β-cells into β-cells, reveals crucial molecular mechanisms for identifying cellular sources and inducers of functional cell renewal. This provides an opportunity to identify specific cellular sources and mechanisms of regeneration, which could have clinical applications in treating various pathologies, including in vitro cell-based technologies, and deepen our understanding of regeneration in different physiological conditions.
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Affiliation(s)
- М. B. Chernysheva
- Cell Biology Laboratory, Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Е. S. Ruchko
- Cell Biology Laboratory, Koltzov Institute of Developmental Biology, Moscow, Russia
| | - М. V. Karimova
- Cell Biology Laboratory, Koltzov Institute of Developmental Biology, Moscow, Russia
- Department of Biology and Biotechnologies Charles Darwin, The Sapienza University of Rome, Rome, Italy
| | - Е. A. Vorotelyak
- Cell Biology Laboratory, Koltzov Institute of Developmental Biology, Moscow, Russia
| | - А. V. Vasiliev
- Cell Biology Laboratory, Koltzov Institute of Developmental Biology, Moscow, Russia
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6
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Li Y, Xu M, Chen J, Huang J, Cao J, Chen H, Zhang J, Luo Y, Wang Y, Sun J. Ameliorating and refining islet organoids to illuminate treatment and pathogenesis of diabetes mellitus. Stem Cell Res Ther 2024; 15:188. [PMID: 38937834 PMCID: PMC11210168 DOI: 10.1186/s13287-024-03780-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
Diabetes mellitus, a significant global public health challenge, severely impacts human health worldwide. The organoid, an innovative in vitro three-dimensional (3D) culture model, closely mimics tissues or organs in vivo. Insulin-secreting islet organoid, derived from stem cells induced in vitro with 3D structures, has emerged as a potential alternative for islet transplantation and as a possible disease model that mirrors the human body's in vivo environment, eliminating species difference. This technology has gained considerable attention for its potential in diabetes treatment. Despite advances, the process of stem cell differentiation into islet organoid and its cultivation demonstrates deficiencies, prompting ongoing efforts to develop more efficient differentiation protocols and 3D biomimetic materials. At present, the constructed islet organoid exhibit limitations in their composition, structure, and functionality when compared to natural islets. Consequently, further research is imperative to achieve a multi-tissue system composition and improved insulin secretion functionality in islet organoid, while addressing transplantation-related safety concerns, such as tumorigenicity, immune rejection, infection, and thrombosis. This review delves into the methodologies and strategies for constructing the islet organoid, its application in diabetes treatment, and the pivotal scientific challenges within organoid research, offering fresh perspectives for a deeper understanding of diabetes pathogenesis and the development of therapeutic interventions.
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Affiliation(s)
- Yushan Li
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Meiqi Xu
- Department of Biomedical Engineering, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Jiali Chen
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiansong Huang
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiaying Cao
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Huajing Chen
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiayi Zhang
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yukun Luo
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yazhuo Wang
- Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
| | - Jia Sun
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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7
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Sanchez JG, Rankin S, Paul E, McCauley HA, Kechele DO, Enriquez JR, Jones NH, Greeley SAW, Letourneau-Friedberg L, Zorn AM, Krishnamurthy M, Wells JM. RFX6 regulates human intestinal patterning and function upstream of PDX1. Development 2024; 151:dev202529. [PMID: 38587174 PMCID: PMC11128285 DOI: 10.1242/dev.202529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/09/2024]
Abstract
The gastrointestinal (GI) tract is complex and consists of multiple organs with unique functions. Rare gene variants can cause congenital malformations of the human GI tract, although the molecular basis of these has been poorly studied. We identified a patient with compound-heterozygous variants in RFX6 presenting with duodenal malrotation and atresia, implicating RFX6 in development of the proximal intestine. To identify how mutations in RFX6 impact intestinal patterning and function, we derived induced pluripotent stem cells from this patient to generate human intestinal organoids (HIOs). We identified that the duodenal HIOs and human tissues had mixed regional identity, with gastric and ileal features. CRISPR-mediated correction of RFX6 restored duodenal identity. We then used gain- and loss-of-function and transcriptomic approaches in HIOs and Xenopus embryos to identify that PDX1 is a downstream transcriptional target of RFX6 required for duodenal development. However, RFX6 had additional PDX1-independent transcriptional targets involving multiple components of signaling pathways that are required for establishing early regional identity in the GI tract. In summary, we have identified RFX6 as a key regulator in intestinal patterning that acts by regulating transcriptional and signaling pathways.
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Affiliation(s)
- J. Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Scott Rankin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Emily Paul
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Heather A. McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Jacob R. Enriquez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Nana-Hawa Jones
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siri A. W. Greeley
- Division of Endocrinology, University of Chicago, Chicago, IL 60637, USA
| | | | - Aaron M. Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Mansa Krishnamurthy
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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8
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Jarc L, Bandral M, Zanfrini E, Lesche M, Kufrin V, Sendra R, Pezzolla D, Giannios I, Khattak S, Neumann K, Ludwig B, Gavalas A. Regulation of multiple signaling pathways promotes the consistent expansion of human pancreatic progenitors in defined conditions. eLife 2024; 12:RP89962. [PMID: 38180318 PMCID: PMC10945307 DOI: 10.7554/elife.89962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The unlimited expansion of human progenitor cells in vitro could unlock many prospects for regenerative medicine. However, it remains an important challenge as it requires the decoupling of the mechanisms supporting progenitor self-renewal and expansion from those mechanisms promoting their differentiation. This study focuses on the expansion of human pluripotent stem (hPS) cell-derived pancreatic progenitors (PP) to advance novel therapies for diabetes. We obtained mechanistic insights into PP expansion requirements and identified conditions for the robust and unlimited expansion of hPS cell-derived PP cells under GMP-compliant conditions through a hypothesis-driven iterative approach. We show that the combined stimulation of specific mitogenic pathways, suppression of retinoic acid signaling, and inhibition of selected branches of the TGFβ and Wnt signaling pathways are necessary for the effective decoupling of PP proliferation from differentiation. This enabled the reproducible, 2000-fold, over 10 passages and 40-45 d, expansion of PDX1+/SOX9+/NKX6-1+ PP cells. Transcriptome analyses confirmed the stabilization of PP identity and the effective suppression of differentiation. Using these conditions, PDX1+/SOX9+/NKX6-1+ PP cells, derived from different, both XY and XX, hPS cell lines, were enriched to nearly 90% homogeneity and expanded with very similar kinetics and efficiency. Furthermore, non-expanded and expanded PP cells, from different hPS cell lines, were differentiated in microwells into homogeneous islet-like clusters (SC-islets) with very similar efficiency. These clusters contained abundant β-cells of comparable functionality as assessed by glucose-stimulated insulin secretion assays. These findings established the signaling requirements to decouple PP proliferation from differentiation and allowed the consistent expansion of hPS cell-derived PP cells. They will enable the establishment of large banks of GMP-produced PP cells derived from diverse hPS cell lines. This approach will streamline SC-islet production for further development of the differentiation process, diabetes research, personalized medicine, and cell therapies.
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Affiliation(s)
- Luka Jarc
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Manuj Bandral
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Elisa Zanfrini
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Mathias Lesche
- Dresden Concept Genome Centre (DcGC), TU DresdenDresdenGermany
- Center for Molecular and Cellular Bioengineering (CMCB) Technology Platform, TU DresdenDresdenGermany
| | - Vida Kufrin
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
| | - Raquel Sendra
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
| | - Daniela Pezzolla
- German Centre for Diabetes Research (DZD)MunichGermany
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU DresdenDresdenGermany
| | - Ioannis Giannios
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Shahryar Khattak
- Stem Cell Engineering Facility, (SCEF), CRTD, Faculty of Medicine, TU DresdenDresdenGermany
| | - Katrin Neumann
- Stem Cell Engineering Facility, (SCEF), CRTD, Faculty of Medicine, TU DresdenDresdenGermany
| | - Barbara Ludwig
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU DresdenDresdenGermany
- Department of Medicine III, University Hospital Carl Gustav Carus and Faculty of Medicine, TU DresdenDresdenGermany
| | - Anthony Gavalas
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
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9
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Nakamura T, Fujikura J, Ito R, Keidai Y, Inagaki N. Human RFX6 regulates endoderm patterning at the primitive gut tube stage. PNAS NEXUS 2024; 3:pgae001. [PMID: 38239755 PMCID: PMC10794167 DOI: 10.1093/pnasnexus/pgae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024]
Abstract
Transcriptional factor RFX6 is known to be a causal gene of Mitchell-Riley syndrome (MRS), an autosomal recessive neonatal diabetes associated with pancreatic hypoplasia and intestinal atresia/malformation. The morphological defects are limited to posterior foregut and mid-hindgut endodermal lineages and do not occur in the anterior foregut lineage; the mechanism remains to be fully elucidated. In this study, we generated RFX6+/eGFP heterozygous knockin and RFX6eGFP/eGFP homozygous knockin/knockout human-induced pluripotent stem cell (hiPSC) lines and performed in vitro endoderm differentiation to clarify the role of RFX6 in early endoderm development. RFX6 expression was found to surge at the primitive gut tube (PGT) stage in comparison with that in the undifferentiated or definitive endoderm stage. At the PGT stage, the expression of PDX1 and CDX2, posterior foregut and mid-hindgut master regulators, respectively, was decreased by the RFX6 deficit. PDX1+ and CDX2+ cells were mostly green fluorescent protein (GFP)+ in RFX6+/eGFP hiPSCs, but their cell number was markedly decreased in RFX6eGFP/eGFP hiPSCs. The expression of SOX2, an anterior foregut marker, was not affected by the RFX6 deficit. In addition, we found a putative RFX6-binding X-box motif using cap analysis of gene expression-seq and the motif-containing sequences in the enhancer regions of PDX1 and CDX2 bound to RFX6 in vitro. Thus, RFX6 regulates the ParaHox genes PDX1 and CDX2 but does not affect SOX2 in early endodermal differentiation, suggesting that defects in early stage endoderm patterning account for the morphological pathology of MRS.
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Affiliation(s)
- Toshihiro Nakamura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Junji Fujikura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ryo Ito
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yamato Keidai
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Medical Research Institute, Kitano Hospital, PIIF Tazuke-kofukai, Osaka 530-8480, Japan
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10
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Zhao Z, D’Oliveira Albanus R, Taylor H, Tang X, Han Y, Orchard P, Varshney A, Zhang T, Manickam N, Erdos M, Narisu N, Taylor L, Saavedra X, Zhong A, Li B, Zhou T, Naji A, Liu C, Collins F, Parker SCJ, Chen S. An integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D associated genes and regulatory signals. RESEARCH SQUARE 2023:rs.3.rs-3343318. [PMID: 37886586 PMCID: PMC10602166 DOI: 10.21203/rs.3.rs-3343318/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Genome wide association studies (GWAS) have identified over 100 signals associated with type 1 diabetes (T1D). However, translating any given T1D GWAS signal into mechanistic insights, including putative causal variants and the context (cell type and cell state) in which they function, has been limited. Here, we present a comprehensive multi-omic integrative analysis of single-cell/nucleus resolution profiles of gene expression and chromatin accessibility in healthy and autoantibody+ (AAB+) human islets, as well as islets under multiple T1D stimulatory conditions. We broadly nominate effector cell types for all T1D GWAS signals. We further nominated higher-resolution contexts, including effector cell types, regulatory elements, and genes for three independent T1D risk variants acting through islet cells within the pancreas at the DLK1/MEG3, RASGRP1, and TOX loci. Subsequently, we created isogenic gene knockouts DLK1-/-, RASGRP1-/-, and TOX-/-, and the corresponding regulatory region knockout, RASGRP1Δ, and DLK1Δ hESCs. Loss of RASGRP1 or DLK1, as well as knockout of the regulatory region of RASGRP1 or DLK1, increased β cell apoptosis. Additionally, pancreatic β cells derived from isogenic hESCs carrying the risk allele of rs3783355A/A exhibited increased β cell death. Finally, RNA-seq and ATAC-seq identified five genes upregulated in both RASGRP1-/- and DLK1-/- β-like cells, four of which are associated with T1D. Together, this work reports an integrative approach for combining single cell multi-omics, GWAS, and isogenic hESC-derived β-like cells to prioritize the T1D associated signals and their underlying context-specific cell types, genes, SNPs, and regulatory elements, to illuminate biological functions and molecular mechanisms.
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Affiliation(s)
- Zeping Zhao
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | | | - Henry Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | - Yuling Han
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tuo Zhang
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Nandini Manickam
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mike Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaxia Saavedra
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Aaron Zhong
- Genomic Resource Core Facility, Weill Cornell Medical College, NY 10065, USA
| | - Bo Li
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
| | - Ting Zhou
- Genomic Resource Core Facility, Weill Cornell Medical College, NY 10065, USA
| | - Ali Naji
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA19104, USA
| | - Chengyang Liu
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA19104, USA
| | - Francis Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen CJ Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Ave, New York, NY 15 10065, USA
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11
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Vanheer L, Fantuzzi F, To SK, Schiavo A, Van Haele M, Ostyn T, Haesen T, Yi X, Janiszewski A, Chappell J, Rihoux A, Sawatani T, Roskams T, Pattou F, Kerr-Conte J, Cnop M, Pasque V. Inferring regulators of cell identity in the human adult pancreas. NAR Genom Bioinform 2023; 5:lqad068. [PMID: 37435358 PMCID: PMC10331937 DOI: 10.1093/nargab/lqad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/17/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
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 and cell states 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. BHLHE41 depletion induced apoptosis in primary pancreatic 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 and cell states in the human adult pancreas.
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Affiliation(s)
| | | | - San Kit To
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Andrea Schiavo
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Matthias Van Haele
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tessa Ostyn
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tine Haesen
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrien Rihoux
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Toshiaki Sawatani
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Francois Pattou
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Julie Kerr-Conte
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Miriam Cnop
- Correspondence may also be addressed to Miriam Cnop. Tel: +32 2 555 6305; Fax: +32 2 555 6239;
| | - Vincent Pasque
- To whom correspondence should be addressed. Tel: +32 16 376283; Fax: +32 16 330827;
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12
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Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Nat Genet 2023; 55:1336-1346. [PMID: 37488417 PMCID: PMC11012226 DOI: 10.1038/s41588-023-01450-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Comprehensive enhancer discovery is challenging because most enhancers, especially those contributing to complex diseases, have weak effects on gene expression. Our gene regulatory network modeling identified that nonlinear enhancer gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Using human embryonic stem cell definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. We discovered a comprehensive set of enhancers for each of the core endoderm-specifying transcription factors. Many enhancers had strong effects mid-transition but weak effects post-transition, consistent with the nonlinear temporal responses to enhancer perturbation predicted by the modeling. Integrating three-dimensional genomic information, we were able to develop a CTCF-loop-constrained Interaction Activity model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Our study provides generalizable strategies for sensitive and systematic enhancer discovery in both normal and pathological cell state transitions.
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Affiliation(s)
- Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jielin Yan
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Jin Woo Oh
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Wang Xi
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Wilfred Wong
- Computational & Systems Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Hyein S Cho
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Dylan Murphy
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Ronald Cutler
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bess P Rosen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Rachel A Glenn
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Tingxu Chen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Qing V Li
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Effie Apostolou
- Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York City, NY, USA.
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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13
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Atwell S, Waibel DJE, Boushehri SS, Wiedenmann S, Marr C, Meier M. Label-free imaging of 3D pluripotent stem cell differentiation dynamics on chip. CELL REPORTS METHODS 2023; 3:100523. [PMID: 37533640 PMCID: PMC10391578 DOI: 10.1016/j.crmeth.2023.100523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/09/2023] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
Massive, parallelized 3D stem cell cultures for engineering in vitro human cell types require imaging methods with high time and spatial resolution to fully exploit technological advances in cell culture technologies. Here, we introduce a large-scale integrated microfluidic chip platform for automated 3D stem cell differentiation. To fully enable dynamic high-content imaging on the chip platform, we developed a label-free deep learning method called Bright2Nuc to predict in silico nuclear staining in 3D from confocal microscopy bright-field images. Bright2Nuc was trained and applied to hundreds of 3D human induced pluripotent stem cell cultures differentiating toward definitive endoderm on a microfluidic platform. Combined with existing image analysis tools, Bright2Nuc segmented individual nuclei from bright-field images, quantified their morphological properties, predicted stem cell differentiation state, and tracked the cells over time. Our methods are available in an open-source pipeline, enabling researchers to upscale image acquisition and phenotyping of 3D cell culture.
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Affiliation(s)
- Scott Atwell
- Helmholtz Pioneer Campus, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Dominik Jens Elias Waibel
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Life Sciences, Technical University of Munich, Weihenstephan, Germany
| | - Sayedali Shetab Boushehri
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Munich, Germany
- Data & Analytics, Pharmaceutical Research and Early Development, Roche Innovation Center Munich (RICM), Penzberg, Germany
| | - Sandra Wiedenmann
- Helmholtz Pioneer Campus, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
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14
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de la O S, Yao X, Chang S, Liu Z, Sneddon JB. Single-cell chromatin accessibility of developing murine pancreas identifies cell state-specific gene regulatory programs. Mol Metab 2023; 73:101735. [PMID: 37178817 PMCID: PMC10230264 DOI: 10.1016/j.molmet.2023.101735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Numerous studies have characterized the existence of cell subtypes, along with their corresponding transcriptional profiles, within the developing mouse pancreas. The upstream mechanisms that initiate and maintain gene expression programs across cell states, however, remain largely unknown. Here, we generate single-nucleus ATAC-Sequencing data of developing murine pancreas and perform an integrated, multi-omic analysis of both chromatin accessibility and RNA expression to describe the chromatin landscape of the developing pancreas at both E14.5 and E17.5 at single-cell resolution. We identify candidate transcription factors regulating cell fate and construct gene regulatory networks of active transcription factor binding to regulatory regions of downstream target genes. This work serves as a valuable resource for the field of pancreatic biology in general and contributes to our understanding of lineage plasticity among endocrine cell types. In addition, these data identify which epigenetic states should be represented in the differentiation of stem cells to the pancreatic beta cell fate to best recapitulate in vitro the gene regulatory networks that are critical for progression along the beta cell lineage in vivo.
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Affiliation(s)
- Sean de la O
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Xinkai Yao
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sean Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Zhe Liu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Julie B Sneddon
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.
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15
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Pulecio J, Tayyebi Z, Liu D, Wong W, Luo R, Damodaran JR, Kaplan S, Cho H, Yan J, Murphy D, Rickert RW, Shukla A, Zhong A, González F, Yang D, Li W, Zhou T, Apostolou E, Leslie CS, Huangfu D. Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544990. [PMID: 37398096 PMCID: PMC10312725 DOI: 10.1101/2023.06.14.544990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes. They lack typical enhancer-associated histone modifications but show enriched occupancy of pluripotent transcription factors, DNA demethylation factors, and histone deacetylases. TET1 and QSER1 protect CCRs from excessive DNA methylation, while HDAC1 family members prevent premature activation. This "push and pull" feature resembles bivalent domains at developmental gene promoters but involves distinct molecular mechanisms. Our study provides new insights into pluripotency regulation and cellular plasticity in development and disease. One sentence summary We report a class of distal regulatory regions distinct from enhancers that confer human embryonic stem cells with the competence to rapidly activate the expression of lineage-specific genes.
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16
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Beydag-Tasöz BS, Yennek S, Grapin-Botton A. Towards a better understanding of diabetes mellitus using organoid models. Nat Rev Endocrinol 2023; 19:232-248. [PMID: 36670309 PMCID: PMC9857923 DOI: 10.1038/s41574-022-00797-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/19/2022] [Indexed: 01/22/2023]
Abstract
Our understanding of diabetes mellitus has benefited from a combination of clinical investigations and work in model organisms and cell lines. Organoid models for a wide range of tissues are emerging as an additional tool enabling the study of diabetes mellitus. The applications for organoid models include studying human pancreatic cell development, pancreatic physiology, the response of target organs to pancreatic hormones and how glucose toxicity can affect tissues such as the blood vessels, retina, kidney and nerves. Organoids can be derived from human tissue cells or pluripotent stem cells and enable the production of human cell assemblies mimicking human organs. Many organ mimics relevant to diabetes mellitus are already available, but only a few relevant studies have been performed. We discuss the models that have been developed for the pancreas, liver, kidney, nerves and vasculature, how they complement other models, and their limitations. In addition, as diabetes mellitus is a multi-organ disease, we highlight how a merger between the organoid and bioengineering fields will provide integrative models.
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Affiliation(s)
- Belin Selcen Beydag-Tasöz
- The Novo Nordisk Foundation Center for Stem Cell Biology, Copenhagen, Denmark
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Siham Yennek
- The Novo Nordisk Foundation Center for Stem Cell Biology, Copenhagen, Denmark
| | - Anne Grapin-Botton
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Paul Langerhans Institute Dresden, Dresden, Germany.
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17
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Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho H, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn R, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531569. [PMID: 36945628 PMCID: PMC10028945 DOI: 10.1101/2023.03.07.531569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Comprehensive enhancer discovery is challenging because most enhancers, especially those affected in complex diseases, have weak effects on gene expression. Our network modeling revealed that nonlinear enhancer-gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Utilizing hESC definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. The screen discovered a comprehensive set of enhancers (4 to 9 per locus) for each of the core endoderm lineage-specifying transcription factors, and many enhancers had strong effects mid-transition but weak effects post-transition. Through integrating enhancer activity measurements and three-dimensional enhancer-promoter interaction information, we were able to develop a CTCF loop-constrained Interaction Activity (CIA) model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Our study provides generalizable strategies for sensitive and more comprehensive enhancer discovery in both normal and pathological cell state transitions.
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18
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Halliez C, Ibrahim H, Otonkoski T, Mallone R. In vitro beta-cell killing models using immune cells and human pluripotent stem cell-derived islets: Challenges and opportunities. Front Endocrinol (Lausanne) 2023; 13:1076683. [PMID: 36726462 PMCID: PMC9885197 DOI: 10.3389/fendo.2022.1076683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Type 1 diabetes (T1D) is a disease of both autoimmunity and β-cells. The β-cells play an active role in their own demise by mounting defense mechanisms that are insufficient at best, and that can become even deleterious in the long term. This complex crosstalk is important to understanding the physiological defense mechanisms at play in healthy conditions, their alterations in the T1D setting, and therapeutic agents that may boost such mechanisms. Robust protocols to develop stem-cell-derived islets (SC-islets) from human pluripotent stem cells (hPSCs), and islet-reactive cytotoxic CD8+ T-cells from peripheral blood mononuclear cells offer unprecedented opportunities to study this crosstalk. Challenges to develop in vitro β-cell killing models include the cluster morphology of SC-islets, the relatively weak cytotoxicity of most autoimmune T-cells and the variable behavior of in vitro expanded CD8+ T-cells. These challenges may however be highly rewarding in light of the opportunities offered by such models. Herein, we discuss these opportunities including: the β-cell/immune crosstalk in an islet microenvironment; the features that make β-cells more sensitive to autoimmunity; therapeutic agents that may modulate β-cell vulnerability; and the possibility to perform analyses in an autologous setting, i.e., by generating T-cell effectors and SC-islets from the same donor.
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Affiliation(s)
- Clémentine Halliez
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
- Department of Pediatrics, Helsinki University Hospital, Helsinki, Finland
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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19
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Ching C, Iich E, Teo AKK. Harnessing Human Pluripotent Stem Cell-Derived Pancreatic In Vitro Models for High-Throughput Toxicity Testing and Diabetes Drug Discovery. Handb Exp Pharmacol 2023; 281:301-332. [PMID: 37306817 DOI: 10.1007/164_2023_655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The long-standing goals in diabetes research are to improve β-cell survival, functionality and increase β-cell mass. Current strategies to manage diabetes progression are still not ideal for sustained maintenance of normoglycemia, thereby increasing demand for the development of novel drugs. Available pancreatic cell lines, cadaveric islets, and their culture methods and formats, either 2D or 3D, allow for multiple avenues of experimental design to address diverse aims in the research setting. More specifically, these pancreatic cells have been employed in toxicity testing, diabetes drug screens, and with careful curation, can be optimized for use in efficient high-throughput screenings (HTS). This has since spearheaded the understanding of disease progression and related mechanisms, as well as the discovery of potential drug candidates which could be the cornerstone for diabetes treatment. This book chapter will touch on the pros and cons of the most widely used pancreatic cells, including the more recent human pluripotent stem cell-derived pancreatic cells, and HTS strategies (cell models, design, readouts) that can be used for the purpose of toxicity testing and diabetes drug discovery.
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Affiliation(s)
- Carmen Ching
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elhadi Iich
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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20
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Sackett SD, Kaplan SJ, Mitchell SA, Brown ME, Burrack AL, Grey S, Huangfu D, Odorico J. Genetic Engineering of Immune Evasive Stem Cell-Derived Islets. Transpl Int 2022; 35:10817. [PMID: 36545154 PMCID: PMC9762357 DOI: 10.3389/ti.2022.10817] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Genome editing has the potential to revolutionize many investigative and therapeutic strategies in biology and medicine. In the field of regenerative medicine, one of the leading applications of genome engineering technology is the generation of immune evasive pluripotent stem cell-derived somatic cells for transplantation. In particular, as more functional and therapeutically relevant human pluripotent stem cell-derived islets (SCDI) are produced in many labs and studied in clinical trials, there is keen interest in studying the immunogenicity of these cells and modulating allogeneic and autoimmune immune responses for therapeutic benefit. Significant experimental work has already suggested that elimination of Human Leukocytes Antigen (HLA) expression and overexpression of immunomodulatory genes can impact survival of a variety of pluripotent stem cell-derived somatic cell types. Limited work published to date focuses on stem cell-derived islets and work in a number of labs is ongoing. Rapid progress is occurring in the genome editing of human pluripotent stem cells and their progeny focused on evading destruction by the immune system in transplantation models, and while much research is still needed, there is no doubt the combined technologies of genome editing and stem cell therapy will profoundly impact transplantation medicine in the future.
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Affiliation(s)
- Sara D. Sackett
- Division of Transplantation, Department of Surgery, UW Transplant Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States,*Correspondence: Sara D. Sackett,
| | - Samuel J. Kaplan
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, United States
| | - Samantha A. Mitchell
- Division of Transplantation, Department of Surgery, UW Transplant Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Matthew E. Brown
- Division of Transplantation, Department of Surgery, UW Transplant Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Adam L. Burrack
- Department of Microbiology and Immunology, Medical School, University of Minnesota, Minneapolis, MN,Center for Immunology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Shane Grey
- Immunology Division, Garvan Institute of Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
| | - Danwei Huangfu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jon Odorico
- Division of Transplantation, Department of Surgery, UW Transplant Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
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21
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CRISPR/Cas9-engineered mesenchymal stromal/stem cells and their extracellular vesicles: A new approach to overcoming cell therapy limitations. Biomed Pharmacother 2022; 156:113943. [DOI: 10.1016/j.biopha.2022.113943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
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22
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Grapin-Botton A, Kim YH. Pancreas organoid models of development and regeneration. Development 2022; 149:278610. [DOI: 10.1242/dev.201004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Organoids have become one of the fastest progressing and applied models in biological and medical research, and various organoids have now been developed for most of the organs of the body. Here, we review the methods developed to generate pancreas organoids in vitro from embryonic, fetal and adult cells, as well as pluripotent stem cells. We discuss how these systems have been used to learn new aspects of pancreas development, regeneration and disease, as well as their limitations and potential for future discoveries.
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Affiliation(s)
- Anne Grapin-Botton
- Max Planck Institute of Molecular Cell Biology and Genetics 1 , Dresden D-01307 , Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at The University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden 2 , Dresden D-01307 , Germany
- Cluster of Excellence Physics of Life, TU Dresden 3 , 01062 Dresden , Germany
| | - Yung Hae Kim
- Max Planck Institute of Molecular Cell Biology and Genetics 1 , Dresden D-01307 , Germany
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23
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Krishnamurthy M, Kechele DO, Broda T, Zhang X, Enriquez JR, McCauley HA, Sanchez JG, McCracken K, Palermo J, Bernieh A, Collins MH, Thomas IH, Neef HC, Heider A, Dauber A, Wells JM. Using Human Induced Pluripotent Stem Cell-Derived Organoids to Identify New Pathologies in Patients With PDX1 Mutations. Gastroenterology 2022; 163:1053-1063.e7. [PMID: 35803312 PMCID: PMC9724632 DOI: 10.1053/j.gastro.2022.06.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Two patients with homozygous mutations in PDX1 presented with pancreatic agenesis, chronic diarrhea, and poor weight gain, the causes of which were not identified through routine clinical testing. We aimed to perform a deep analysis of the stomach and intestine using organoids derived from induced pluripotent stem cells from PDX1188delC/188delC patients. METHODS Gastric fundic, antral, and duodenal organoids were generated using induced pluripotent stem cell lines from a PDX1188delC/188delC patient and an isogenic induced pluripotent stem cell line where the PDX1 point mutation was corrected. RESULTS Patient-derived PDX1188delC/188delC antral organoids exhibited an intestinal phenotype, whereas intestinal organoids underwent gastric metaplasia with significant reduction in enteroendocrine cells. This prompted a re-examination of gastric and intestinal biopsy specimens from both PDX1188delC/188delC patients, which recapitulated the organoid phenotypes. Moreover, antral biopsy specimens also showed increased parietal cells and lacked G cells, suggesting loss of antral identity. All organoid pathologies were reversed upon CRISPR-mediated correction of the mutation. CONCLUSIONS These patients will now be monitored for the progression of metaplasia and gastrointestinal complications that might be related to the reduced gastric and intestinal endocrine cells. This study demonstrates the utility of organoids in diagnosing uncovered pathologies.
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Affiliation(s)
- Mansa Krishnamurthy
- Division of Endocrinology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Daniel O Kechele
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Taylor Broda
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Xinghao Zhang
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacob R Enriquez
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Heather A McCauley
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - J Guillermo Sanchez
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Kyle McCracken
- Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Joseph Palermo
- Division of Gastroenterology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Anas Bernieh
- Division of Pathology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Margaret H Collins
- Division of Pathology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Inas H Thomas
- Division of Pediatric Endocrinology, University of Michigan, Ann Arbor, Michigan
| | - Haley C Neef
- Division of Pediatric Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Amer Heider
- Division of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Andrew Dauber
- Division of Endocrinology, Children's National Hospital, Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC
| | - James M Wells
- Division of Endocrinology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Developmental Biology; Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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24
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25
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González BJ, Zhao H, Niu J, Williams DJ, Lee J, Goulbourne CN, Xing Y, Wang Y, Oberholzer J, Blumenkrantz MH, Chen X, LeDuc CA, Chung WK, Colecraft HM, Gromada J, Shen Y, Goland RS, Leibel RL, Egli D. Reduced calcium levels and accumulation of abnormal insulin granules in stem cell models of HNF1A deficiency. Commun Biol 2022; 5:779. [PMID: 35918471 PMCID: PMC9345898 DOI: 10.1038/s42003-022-03696-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mutations in HNF1A cause Maturity Onset Diabetes of the Young (HNF1A-MODY). To understand mechanisms of β-cell dysfunction, we generated stem cell-derived pancreatic endocrine cells with hypomorphic mutations in HNF1A. HNF1A-deficient β-cells display impaired basal and glucose stimulated-insulin secretion, reduced intracellular calcium levels in association with a reduction in CACNA1A expression, and accumulation of abnormal insulin granules in association with SYT13 down-regulation. Knockout of CACNA1A and SYT13 reproduce the relevant phenotypes. In HNF1A deficient β-cells, glibenclamide, a sulfonylurea drug used in the treatment of HNF1A-MODY patients, increases intracellular calcium, and restores insulin secretion. While insulin secretion defects are constitutive in β-cells null for HNF1A, β-cells heterozygous for hypomorphic HNF1A (R200Q) mutations lose the ability to secrete insulin gradually; this phenotype is prevented by correction of the mutation. Our studies illuminate the molecular basis for the efficacy of treatment of HNF1A-MODY with sulfonylureas, and suggest promise for the use of cell therapies.
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Affiliation(s)
- Bryan J González
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Institute of Human Nutrition, Columbia University Medical Center, New York, NY, 10032, USA
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jacqueline Niu
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Damian J Williams
- Stem Cell Core Facility, Department of Rehabilitation and Regenerative Medicine, Columbia University, New York, NY, 10032, USA
| | - Jaeyop Lee
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Chris N Goulbourne
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Yuan Xing
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Yong Wang
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jose Oberholzer
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Maria H Blumenkrantz
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Xiaojuan Chen
- Columbia Center for Translational Immunology, Department of Surgery, Columbia University Medical Center, New York, NY, 10032, USA
| | - Charles A LeDuc
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Wendy K Chung
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jesper Gromada
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA.,Vertex Cell and Genetic Therapies, Watertown, MA, 02472, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Robin S Goland
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
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26
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Jin W, Jiang W. Stepwise differentiation of functional pancreatic β cells from human pluripotent stem cells. CELL REGENERATION 2022; 11:24. [PMID: 35909206 PMCID: PMC9339430 DOI: 10.1186/s13619-022-00125-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022]
Abstract
Pancreatic β cells differentiated from stem cells provide promise for cell replacement therapy of diabetes. Human pluripotent stem cells could be differentiated into definitive endoderm, followed by pancreatic progenitors, and then subjected to endocrinal differentiation and maturation in a stepwise fashion. Many achievements have been made in making pancreatic β cells from human pluripotent stem cells in last two decades, and a couple of phase I/II clinical trials have just been initiated. Here, we overview the major progresses in differentiating pancreatic β cells from human pluripotent stem cells with the focus on recent technical advances in each differentiation stage, and briefly discuss the current limitations as well.
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27
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N 6-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis. Nat Commun 2022; 13:4148. [PMID: 35851388 PMCID: PMC9293889 DOI: 10.1038/s41467-022-31698-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
Pancreatic differentiation from human pluripotent stem cells (hPSCs) provides promising avenues for investigating development and treating diseases. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification and plays pivotal roles in regulation of mRNA metabolism, while its functions remain elusive. Here, we profile the dynamic landscapes of m6A transcriptome-wide during pancreatic differentiation. Next, we generate knockout hPSC lines of the major m6A demethylase ALKBH5, and find that ALKBH5 plays significant regulatory roles in pancreatic organogenesis. Mechanistic studies reveal that ALKBH5 deficiency reduces the mRNA stability of key pancreatic transcription factors in an m6A and YTHDF2-dependent manner. We further identify that ALKBH5 cofactor α-ketoglutarate can be applied to enhance differentiation. Collectively, our findings identify ALKBH5 as an essential regulator of pancreatic differentiation and highlight that m6A modification-mediated mRNA metabolism presents an important layer of regulation during cell-fate specification and holds great potentials for translational applications. Ma et al. profile the dynamic landscape of m6A during pancreatic differentiation, and identify ALKBH5 as an essential m6A regulator supporting pancreatic differentiation, indicating a role for m6A-mediated mRNA metabolism in cell-fate specification.
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ZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes. Nat Commun 2022; 13:4142. [PMID: 35842441 PMCID: PMC9288460 DOI: 10.1038/s41467-022-31829-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 07/04/2022] [Indexed: 12/21/2022] Open
Abstract
Human embryonic stem cell-derived β cells (SC-β cells) hold great promise for treatment of diabetes, yet how to achieve functional maturation and protect them against metabolic stresses such as glucotoxicity and lipotoxicity remains elusive. Our single-cell RNA-seq analysis reveals that ZnT8 loss of function (LOF) accelerates the functional maturation of SC-β cells. As a result, ZnT8 LOF improves glucose-stimulated insulin secretion (GSIS) by releasing the negative feedback of zinc inhibition on insulin secretion. Furthermore, we demonstrate that ZnT8 LOF mutations endow SC-β cells with resistance to lipotoxicity/glucotoxicity-triggered cell death by alleviating endoplasmic reticulum (ER) stress through modulation of zinc levels. Importantly, transplantation of SC-β cells with ZnT8 LOF into mice with preexisting diabetes significantly improves glycemia restoration and glucose tolerance. These findings highlight the beneficial effect of ZnT8 LOF on the functional maturation and survival of SC-β cells that are useful as a potential source for cell replacement therapies. Immature function and fragility hinder application of hESC-derived β cells (SC-β cell) for diabetes cell therapy. Here, the authors identify ZnT8 as a gene editing target to enhance the insulin secretion and cell survival under metabolic stress by abolishing zinc transport in SC-β cells.
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29
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Wang Y, Yu M, Hao K, Lei W, Tang M, Hu S. Cardiomyocyte Maturation-the Road is not Obstructed. Stem Cell Rev Rep 2022; 18:2966-2981. [PMID: 35788883 DOI: 10.1007/s12015-022-10407-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/29/2022]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) represent one of the most promising ways to treat cardiovascular diseases. High-purity cardiomyocytes (CM) from different cell sources could be obtained at present. However, the immature nature of these cardiomyocytes hinders its further clinical application. From immature to mature state, it involves structural, functional, and metabolic changes in cardiomyocytes. Generally, two types of culturing (2D and 3D) systems have been reported to induce cardiomyocyte maturation. 2D culture mainly achieves the maturation of cardiomyocytes through long-term culture, co-culture, supplementation of small molecule compounds, and the application of biophysical cues. The combined use of biomaterial's surface topography and biophysical cues also facilitates the maturation of cardiomyocytes. Cardiomyocyte maturation is a complex process involving many signaling pathways, and current methods fail to fully reproduce this process. Therefore, analyzing the signaling pathway network related to the maturation and producing hPSC-CMs with adult-like phenotype is a challenge. In this review, we summarized the structural and functional differences between hPSC-CMs and mature cardiomyocytes, and introduced various methods to induce cardiomyocyte maturation.
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Affiliation(s)
- Yaning Wang
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China
| | - Miao Yu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China
| | - Kaili Hao
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China
| | - Wei Lei
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China
| | - Mingliang Tang
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China.
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, 215000, China.
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Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan SJ, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie CS, Huangfu D. CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Nat Cell Biol 2022; 24:1064-1076. [PMID: 35787684 PMCID: PMC9283336 DOI: 10.1038/s41556-022-00946-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/25/2022] [Indexed: 01/07/2023]
Abstract
The pancreas and liver arise from a common pool of progenitors. However, the underlying mechanisms that drive their lineage diversification from the foregut endoderm are not fully understood. To tackle this question, we undertook a multifactorial approach that integrated human pluripotent-stem-cell-guided differentiation, genome-scale CRISPR-Cas9 screening, single-cell analysis, genomics and proteomics. We discovered that HHEX, a transcription factor (TF) widely recognized as a key regulator of liver development, acts as a gatekeeper of pancreatic lineage specification. HHEX deletion impaired pancreatic commitment and unleashed an unexpected degree of cellular plasticity towards the liver and duodenum fates. Mechanistically, HHEX cooperates with the pioneer TFs FOXA1, FOXA2 and GATA4, shared by both pancreas and liver differentiation programmes, to promote pancreas commitment, and this cooperation restrains the shared TFs from activating alternative lineages. These findings provide a generalizable model for how gatekeeper TFs like HHEX orchestrate lineage commitment and plasticity restriction in broad developmental contexts.
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Affiliation(s)
- Dapeng Yang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hyunwoo Cho
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Zakieh Tayyebi
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Abhijit Shukla
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Renhe Luo
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gary Dixon
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA,Present address: Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Valeria Ursu
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37203, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samuel J. Kaplan
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Qing V. Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jiwoon Park
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA,Division of Gastroenterology and Hepatology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Zengrong Zhu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bess P. Rosen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Julian Pulecio
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Zhong-Dong Shi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Robert E. Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christopher V. Wright
- Vanderbilt University Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37203, USA
| | - Christina S. Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Correspondence to: (DH), (CSL)
| | - Danwei Huangfu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA,Correspondence to: (DH), (CSL)
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31
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Stem Cell-Derived Islets for Type 2 Diabetes. Int J Mol Sci 2022; 23:ijms23095099. [PMID: 35563490 PMCID: PMC9105352 DOI: 10.3390/ijms23095099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Since the discovery of insulin a century ago, insulin injection has been a primary treatment for both type 1 (T1D) and type 2 diabetes (T2D). T2D is a complicated disea se that is triggered by the dysfunction of insulin-producing β cells and insulin resistance in peripheral tissues. Insulin injection partially compensates for the role of endogenous insulin which promotes glucose uptake, lipid synthesis and organ growth. However, lacking the continuous, rapid, and accurate glucose regulation by endogenous functional β cells, the current insulin injection therapy is unable to treat the root causes of the disease. Thus, new technologies such as human pluripotent stem cell (hPSC)-derived islets are needed for both identifying the key molecular and genetic causes of T2D and for achieving a long-term treatment. This perspective review will provide insight into the efficacy of hPSC-derived human islets for treating and understanding T2D. We discuss the evidence that β cells should be the primary target for T2D treatment, the use of stem cells for the modeling of T2D and the potential use of hPSC-derived islet transplantation for treating T2D.
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32
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Greenough MA, Lane DJR, Balez R, Anastacio HTD, Zeng Z, Ganio K, McDevitt CA, Acevedo K, Belaidi AA, Koistinaho J, Ooi L, Ayton S, Bush AI. Selective ferroptosis vulnerability due to familial Alzheimer’s disease presenilin mutations. Cell Death Differ 2022; 29:2123-2136. [PMID: 35449212 PMCID: PMC9613996 DOI: 10.1038/s41418-022-01003-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractMutations in presenilin 1 and 2 (PS1 and PS2) cause autosomal dominant familial Alzheimer’s disease (FAD). Ferroptosis has been implicated as a mechanism of neurodegeneration in AD since neocortical iron burden predicts Alzheimer’s disease (AD) progression. We found that loss of the presenilins dramatically sensitizes multiple cell types to ferroptosis, but not apoptosis. FAD causal mutations of presenilins similarly sensitizes cells to ferroptosis. The presenilins promote the expression of GPX4, the selenoprotein checkpoint enzyme that blocks ferroptosis by quenching the membrane propagation of lethal hydroperoxyl radicals. Presenilin γ-secretase activity cleaves Notch-1 to signal LRP8 expression, which then controls GPX4 expression by regulating the supply of selenium into the cell since LRP8 is the uptake receptor for selenoprotein P. Selenium uptake is thus disrupted by presenilin FAD mutations, suppressing GPX4 expression. Therefore, presenilin mutations may promote neurodegeneration by derepressing ferroptosis, which has implications for disease-modifying therapeutics.
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Barbetti F, Rapini N, Schiaffini R, Bizzarri C, Cianfarani S. The application of precision medicine in monogenic diabetes. Expert Rev Endocrinol Metab 2022; 17:111-129. [PMID: 35230204 DOI: 10.1080/17446651.2022.2035216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/25/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Monogenic diabetes, a form of diabetes mellitus, is caused by a mutation in a single gene and may account for 1-2% of all clinical forms of diabetes. To date, more than 40 loci have been associated with either isolated or syndromic monogenic diabetes. AREAS COVERED While the request of a genetic test is mandatory for cases with diabetes onset in the first 6 months of life, a decision may be difficult for childhood or adolescent diabetes. In an effort to assist the clinician in this task, we have grouped monogenic diabetes genes according to the age of onset (or incidental discovery) of hyperglycemia and described the additional clinical features found in syndromic diabetes. The therapeutic options available are reviewed. EXPERT OPINION Technical improvements in DNA sequencing allow for rapid, simultaneous analysis of all genes involved in monogenic diabetes, progressively shrinking the area of unsolved cases. However, the complexity of the analysis of genetic data requires close cooperation between the geneticist and the diabetologist, who should play a proactive role by providing a detailed clinical phenotype that might match a specific disease gene.
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Affiliation(s)
- Fabrizio Barbetti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- Diabetology and Growth Disorders Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Novella Rapini
- Diabetology and Growth Disorders Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Riccardo Schiaffini
- Diabetology and Growth Disorders Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carla Bizzarri
- Diabetology and Growth Disorders Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Cianfarani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Dipartimento Pediatrico Universitario Ospedaliero, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy
- Department of Women's and Children Health, Karolisnska Institute and University Hospital, Sweden
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34
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Yu G, Zhang M, Gao L, Zhou Y, Qiao L, Yin J, Wang Y, Zhou J, Ye H. Far-red light-activated human islet-like designer cells enable sustained fine-tuned secretion of insulin for glucose control. Mol Ther 2022; 30:341-354. [PMID: 34530162 PMCID: PMC8753431 DOI: 10.1016/j.ymthe.2021.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 01/07/2023] Open
Abstract
Diabetes affects almost half a billion people, and all individuals with type 1 diabetes (T1D) and a large portion of individuals with type 2 diabetes rely on self-administration of the peptide hormone insulin to achieve glucose control. However, this treatment modality has cumbersome storage and equipment requirements and is susceptible to fatal user error. Here, reasoning that a cell-based therapy could be coupled to an external induction circuit for blood glucose control, as a proof of concept we developed far-red light (FRL)-activated human islet-like designer (FAID) cells and demonstrated how FAID cell implants achieved safe and sustained glucose control in diabetic model mice. Specifically, by introducing a FRL-triggered optogenetic device into human mesenchymal stem cells (hMSCs), which we encapsulated in poly-(l-lysine)-alginate and implanted subcutaneously under the dorsum of T1D model mice, we achieved FRL illumination-inducible secretion of insulin that yielded improvements in glucose tolerance and sustained blood glucose control over traditional insulin glargine treatment. Moreover, the FAID cell implants attenuated both oxidative stress and development of multiple diabetes-related complications in kidneys. This optogenetics-controlled "living cell factory" platform could be harnessed to develop multiple synthetic designer therapeutic cells to achieve long-term yet precisely controllable drug delivery.
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Affiliation(s)
- Guiling Yu
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Mingliang Zhang
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ling Gao
- Department of Endocrinology, Renmin Hospital of Wuhan University, Wuhan 430061, China
| | - Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Longliang Qiao
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yiwen Wang
- Electron Microscopy Center, School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jian Zhou
- Department of Endocrinology and Metabolism, Shanghai Clinical Center for Diabetes, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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35
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Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022; 23:501. [PMID: 35008927 PMCID: PMC8745644 DOI: 10.3390/ijms23010501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic β cell dysfunction is a central component of diabetes progression. During the last decades, the genetic basis of several monogenic forms of diabetes has been recognized. Genome-wide association studies (GWAS) have also facilitated the identification of common genetic variants associated with an increased risk of diabetes. These studies highlight the importance of impaired β cell function in all forms of diabetes. However, how most of these risk variants confer disease risk, remains unanswered. Understanding the specific contribution of genetic variants and the precise role of their molecular effectors is the next step toward developing treatments that target β cell dysfunction in the era of personalized medicine. Protocols that allow derivation of β cells from pluripotent stem cells, represent a powerful research tool that allows modeling of human development and versatile experimental designs that can be used to shed some light on diabetes pathophysiology. This article reviews different models to study the genetic basis of β cell dysfunction, focusing on the recent advances made possible by stem cell applications in the field of diabetes research.
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Affiliation(s)
- Alberto Bartolomé
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
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36
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Memon B, Abdelalim EM. OUP accepted manuscript. Stem Cells Transl Med 2022; 11:704-714. [PMID: 35640144 PMCID: PMC9299517 DOI: 10.1093/stcltm/szac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 04/09/2022] [Indexed: 11/14/2022] Open
Abstract
Although genome profiling provides important genetic and phenotypic details for applying precision medicine to diabetes, it is imperative to integrate in vitro human cell models, accurately recapitulating the genetic alterations associated with diabetes. The absence of the appropriate preclinical human models and the unavailability of genetically relevant cells substantially limit the progress in developing personalized treatment for diabetes. Human pluripotent stem cells (hPSCs) provide a scalable source for generating diabetes-relevant cells carrying the genetic signatures of the patients. Remarkably, allogenic hPSC-derived pancreatic progenitors and β cells are being used in clinical trials with promising preliminary results. Autologous hiPSC therapy options exist for those with monogenic and type 2 diabetes; however, encapsulation or immunosuppression must be accompanied with in the case of type 1 diabetes. Furthermore, genome-wide association studies-identified candidate variants can be introduced in hPSCs for deciphering the associated molecular defects. The hPSC-based disease models serve as excellent resources for drug development facilitating personalized treatment. Indeed, hPSC-based diabetes models have successfully provided valuable knowledge by modeling different types of diabetes, which are discussed in this review. Herein, we also evaluate their strengths and shortcomings in dissecting the underlying pathogenic molecular mechanisms and discuss strategies for improving hPSC-based disease modeling investigations.
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Affiliation(s)
- Bushra Memon
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Essam M Abdelalim
- Corresponding author: Essam M. Abdelalim, Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa, University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar. Tel: +974 445 46432; Fax: +974 445 41770;
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Dabi YT, Degechisa ST. Genome Editing and Human Pluripotent Stem Cell Technologies for in vitro Monogenic Diabetes Modeling. Diabetes Metab Syndr Obes 2022; 15:1785-1797. [PMID: 35719247 PMCID: PMC9199525 DOI: 10.2147/dmso.s366967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/08/2022] [Indexed: 12/01/2022] Open
Abstract
Diabetes is a metabolic disease characterized by chronic hyperglycemia. Polygenic diabetes, which encompasses type-1 and type-2 diabetes, is the most prevalent kind of diabetes and is caused by a combination of different genetic and environmental factors, whereas rare phenotype monogenic diabetes is caused by a single gene mutation. Monogenic diabetes includes Neonatal diabetes mellitus and Maturity-onset diabetes of the young. The majority of our current knowledge about the pathogenesis of diabetes stems from studies done on animal models. However, the genetic difference between these creatures and humans makes it difficult to mimic human clinical pathophysiology, limiting their value in modeling key aspects of human disease. Human pluripotent stem cell technologies combined with genome editing techniques have been shown to be better alternatives for creating in vitro models that can provide crucial knowledge about disease etiology. This review paper addresses genome editing and human pluripotent stem cell technologies for in vitro monogenic diabetes modeling.
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Affiliation(s)
- Yosef Tsegaye Dabi
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Science, Wollega University, Nekemte, Ethiopia
- Correspondence: Yosef Tsegaye Dabi, Email
| | - Sisay Teka Degechisa
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
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38
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Lorberbaum DS, Sarbaugh D, Sussel L. Leveraging the strengths of mice, human stem cells, and organoids to model pancreas development and diabetes. Front Endocrinol (Lausanne) 2022; 13:1042611. [PMID: 36339450 PMCID: PMC9634409 DOI: 10.3389/fendo.2022.1042611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022] Open
Abstract
Diabetes is an epidemic with increasing incidence across the world. Most individuals who are afflicted by this disease have type 2 diabetes, but there are many who suffer from type 1, an autoimmune disorder. Both types of diabetes have complex genetic underpinnings that are further complicated by epigenetic and environmental factors. A less prevalent and often under diagnosed subset of diabetes cases are characterized by single genetic mutations and include Maturity Onset Diabetes of the Young (MODY) and Neonatal Diabetes Mellitus (NDM). While the mode of action and courses of treatment for all forms of diabetes are distinct, the diseases all eventually result in the dysfunction and/or death of the pancreatic β cell - the body's source of insulin. With loss of β cell function, blood glucose homeostasis is disrupted, and life-threatening complications arise. In this review, we focus on how model systems provide substantial insights into understanding β cell biology to inform our understanding of all forms of diabetes. The strengths and weaknesses of animal, hPSC derived β-like cell, and organoid models are considered along with discussion of GATA6, a critical transcription factor frequently implicated in pancreatic dysfunction with developmental origins; experimental studies of GATA6 have highlighted the advantages and disadvantages of how each of these model systems can be used to inform our understanding of β cell specification and function in health and disease.
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39
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Scoville DW, Jetten AM. GLIS3: A Critical Transcription Factor in Islet β-Cell Generation. Cells 2021; 10:cells10123471. [PMID: 34943978 PMCID: PMC8700524 DOI: 10.3390/cells10123471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Understanding of pancreatic islet biology has greatly increased over the past few decades based in part on an increased understanding of the transcription factors that guide this process. One such transcription factor that has been increasingly tied to both β-cell development and the development of diabetes in humans is GLIS3. Genetic deletion of GLIS3 in mice and humans induces neonatal diabetes, while single nucleotide polymorphisms (SNPs) in GLIS3 have been associated with both Type 1 and Type 2 diabetes. As a significant progress has been made in understanding some of GLIS3’s roles in pancreas development and diabetes, we sought to compare current knowledge on GLIS3 within the pancreas to that of other islet enriched transcription factors. While GLIS3 appears to regulate similar genes and pathways to other transcription factors, its unique roles in β-cell development and maturation make it a key target for future studies and therapy.
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40
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Ardila Riveros JC, Blöchinger AK, Atwell S, Moussus M, Compera N, Rajabnia O, Georgiev T, Lickert H, Meier M. Automated optimization of endoderm differentiation on chip. LAB ON A CHIP 2021; 21:4685-4695. [PMID: 34751293 PMCID: PMC8613673 DOI: 10.1039/d1lc00565k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/12/2021] [Indexed: 06/02/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) can serve as an unlimited source to rebuild organotypic tissues in vitro. Successful engineering of functional cell types and complex organ structures outside the human body requires knowledge of the chemical, temporal, and spatial microenvironment of their in vivo counterparts. Despite an increased understanding of mouse and human embryonic development, screening approaches are still required for the optimization of stem cell differentiation protocols to gain more functional mature cell types. The liver, lung, pancreas, and digestive tract originate from the endoderm germ layer. Optimization and specification of the earliest differentiation step, which is the definitive endoderm (DE), is of central importance for generating cell types of these organs because off-target cell types will propagate during month-long cultivation steps and reduce yields. Here, we developed a microfluidic large-scale integration (mLSI) chip platform for combined automated three-dimensional (3D) cell culturing and high-throughput imaging to investigate anterior/posterior patterns occurring during hiPSC differentiation into DE cells. Integration of 3D cell cultures with a diameter of 150 μm was achieved using a U-shaped pneumatic membrane valve, which was geometrically optimized and fluidically characterized. Upon parallelization of 32 fluidically individually addressable cell culture unit cells with a total of 128 3D cell cultures, complex and long-term DE differentiation protocols could be automated. Real-time bright-field imaging was used to analyze cell growth during DE differentiation, and immunofluorescence imaging on optically cleared 3D cell cultures was used to determine the DE differentiation yield. By systematically alternating transforming growth factor β (TGF-β) and WNT signaling agonist concentrations and temporal stimulation, we showed that even under similar DE differentiation yields, there were patterning differences in the 3D cell cultures, indicating possible differentiation differences between established DE protocols. The automated mLSI chip platform with the general analytical workflow for 3D stem cell cultures offers the optimization of in vitro generation of various cell types for cell replacement therapies.
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Affiliation(s)
| | - Anna Karolina Blöchinger
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Scott Atwell
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany.
| | - Michel Moussus
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany.
| | - Nina Compera
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany.
| | - Omid Rajabnia
- Laboratory for MEMS Application, IMTEK-Department of Microsystems Engineering, University of Freiburg, Germany
| | - Tihomir Georgiev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany.
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Munich, Germany.
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
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41
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Heller S, Li Z, Lin Q, Geusz R, Breunig M, Hohwieler M, Zhang X, Nair GG, Seufferlein T, Hebrok M, Sander M, Julier C, Kleger A, Costa IG. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation. Commun Biol 2021; 4:1298. [PMID: 34789845 PMCID: PMC8599846 DOI: 10.1038/s42003-021-02818-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/24/2021] [Indexed: 02/07/2023] Open
Abstract
Cell type specification during pancreatic development is tightly controlled by a transcriptional and epigenetic network. The precise role of most transcription factors, however, has been only described in mice. To convey such concepts to human pancreatic development, alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells can be employed. Here, we analyzed stage-specific RNA-, ChIP-, and ATAC-sequencing data to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreatic differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreatic transcription factors and indicate ONECUT1 as a crucial fate regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification. The dissection of the transcriptional and regulatory circuitry revealed an important role for ONECUT1 within such network and will serve as resource to study human development and disease.
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Affiliation(s)
- Sandra Heller
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Zhijian Li
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, RWTH Aachen University Medical School, Aachen, Germany
| | - Qiong Lin
- grid.420044.60000 0004 0374 4101Bayer AG, Research & Development, Pharmaceuticals, Bioinformatics, Berlin, Germany
| | - Ryan Geusz
- grid.266100.30000 0001 2107 4242Pediatric Diabetes Research Center (PDRC) at the University of California, San Diego, USA
| | - Markus Breunig
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Meike Hohwieler
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Xi Zhang
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Gopika G. Nair
- grid.266102.10000 0001 2297 6811Diabetes Center at the University of California, San Francisco, USA
| | - Thomas Seufferlein
- grid.410712.1Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Matthias Hebrok
- grid.266102.10000 0001 2297 6811Diabetes Center at the University of California, San Francisco, USA
| | - Maike Sander
- grid.266100.30000 0001 2107 4242Pediatric Diabetes Research Center (PDRC) at the University of California, San Diego, USA
| | - Cécile Julier
- grid.4444.00000 0001 2112 9282Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR-8104, Paris, France
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany.
| | - Ivan G. Costa
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, RWTH Aachen University Medical School, Aachen, Germany
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Nihad M, Shenoy P S, Bose B. Cell therapy research for Diabetes: Pancreatic β cell differentiation from pluripotent stem cells. Diabetes Res Clin Pract 2021; 181:109084. [PMID: 34673084 DOI: 10.1016/j.diabres.2021.109084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells (PSCs), both embryonic and induced pluripotent stem cells (iPSCs), have been differentiated into pancreatic β isletsin vitrofor more than a decade. The idea is to get enough β cells for cell transplantation for diabetics. Finding a standard cell therapy for diabetes is essential because of the logarithmic increase in the global population of people with diabetes and the insufficient availability of the human cadaveric pancreas. Moreover, with better insights into developmental biology, thein vitroβ cell differentiation protocols have depended on thein vivoβ cell organogenesis. Various protocols for pancreatic β cell differentiation have been developed. Such protocols are based on the modulation of cell signalling pathways with growth factors, small molecules, RNAi approaches, directed differentiation using transcription factors, genome editing. Growth factor free differentiation protocols, epigenetic modulations, 3D differentiation approaches, and encapsulation strategies have also been reported for better glycemic control and endocrine modulations. Here, we have reviewed various aforementionedin vitroβ cell differentiation protocols from human PSCs, their respective comparisons, challenges, past, present, and future. The literature has been reviewed primarily from PubMed from the year 2000 till date using the mentioned keywords.
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Affiliation(s)
- Muhammad Nihad
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Pincode-575 018, Karnataka, India
| | - Sudheer Shenoy P
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Pincode-575 018, Karnataka, India
| | - Bipasha Bose
- Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Pincode-575 018, Karnataka, India.
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43
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Li J, Wei T, Zhang J, Liang T. Intraductal Papillary Mucinous Neoplasms of the Pancreas: A Review of Their Genetic Characteristics and Mouse Models. Cancers (Basel) 2021; 13:cancers13215296. [PMID: 34771461 PMCID: PMC8582516 DOI: 10.3390/cancers13215296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Pancreatic cancer is one of the deadliest cancers with the lowest survival rate. Little progress has been achieved in prolonging the survival for patients with pancreatic adenocarcinoma. Hence, special attention should be paid to pre-cancerous lesions, for instance, an intraductal papillary mucinous neoplasm (IPMN). Here, we reviewed its genetic characteristics and the mouse models involving mutations in specific pathways, and updated our current perception of how this lesion develops into a precursor of invasive cancer. Abstract The intraductal papillary mucinous neoplasm (IPMN) is attracting research attention because of its increasing incidence and proven potential to progress into invasive pancreatic ductal adenocarcinoma (PDAC). In this review, we summarized the key signaling pathways or protein complexes (GPCR, TGF, SWI/SNF, WNT, and PI3K) that appear to be involved in IPMN pathogenesis. In addition, we collected information regarding all the genetic mouse models that mimic the human IPMN phenotype with specific immunohistochemistry techniques. The mouse models enable us to gain insight into the complex mechanism of the origin of IPMN, revealing that it can be developed from both acinar cells and duct cells according to different models. Furthermore, recent genomic studies describe the potential mechanism by which heterogeneous IPMN gives rise to malignant carcinoma through sequential, branch-off, or de novo approaches. The most intractable problem is that the risk of malignancy persists to some extent even if the primary IPMN is excised with a perfect margin, calling for the re-evaluation and improvement of diagnostic, pre-emptive, and therapeutic measures.
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Affiliation(s)
- Jin Li
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China; (J.L.); (T.W.); (J.Z.)
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou 310000, China
- Innovation Center for the Study of Pancreatic Diseases, Hangzhou 310000, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary & Pancreatic Diseases, Hangzhou 310000, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China; (J.L.); (T.W.); (J.Z.)
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou 310000, China
- Innovation Center for the Study of Pancreatic Diseases, Hangzhou 310000, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary & Pancreatic Diseases, Hangzhou 310000, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Jian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China; (J.L.); (T.W.); (J.Z.)
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou 310000, China
- Innovation Center for the Study of Pancreatic Diseases, Hangzhou 310000, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary & Pancreatic Diseases, Hangzhou 310000, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, School of Medicine, The First Affiliated Hospital of Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China; (J.L.); (T.W.); (J.Z.)
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou 310000, China
- Innovation Center for the Study of Pancreatic Diseases, Hangzhou 310000, China
- Zhejiang Provincial Clinical Research Center for the Study of Hepatobiliary & Pancreatic Diseases, Hangzhou 310000, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel./Fax: +86-571-87236688
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Yang D, Patel S, Szlachcic WJ, Chmielowiec J, Scaduto D, Putluri N, Sreekumar A, Suliburk J, Metzker M, Balasubramanyam A, Borowiak M. Pancreatic Differentiation of Stem Cells Reveals Pathogenesis of a Syndrome of Ketosis-Prone Diabetes. Diabetes 2021; 70:2419-2429. [PMID: 34344789 PMCID: PMC8576504 DOI: 10.2337/db20-1293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022]
Abstract
Genetic analysis of an adult patient with an unusual course of ketosis-prone diabetes (KPD) and lacking islet autoantibodies demonstrated a nucleotide variant in the 5'-untranslated region (UTR) of PDX1, a β-cell development gene. When differentiated to the pancreatic lineage, his induced pluripotent stem cells stalled at the definitive endoderm (DE) stage. Metabolomics analysis of the cells revealed that this was associated with leucine hypersensitivity during transition from the DE to the pancreatic progenitor (PP) stage, and RNA sequencing showed that defects in leucine-sensitive mTOR pathways contribute to the differentiation deficiency. CRISPR/Cas9 manipulation of the PDX1 variant demonstrated that it is necessary and sufficient to confer leucine sensitivity and the differentiation block, likely due to disruption of binding of the transcriptional regulator NFY to the PDX1 5'-UTR, leading to decreased PDX1 expression at the early PP stage. Thus, the combination of an underlying defect in leucine catabolism characteristic of KPD with a functionally relevant heterozygous variant in a critical β-cell gene that confers increased leucine sensitivity and inhibits endocrine cell differentiation resulted in the phenotype of late-onset β-cell failure in this patient. We define the molecular pathogenesis of a diabetes syndrome and demonstrate the power of multiomics analysis of patient-specific stem cells for clinical discovery.
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Affiliation(s)
- Diane Yang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- McNair Medical Institute, Baylor College of Medicine, Houston, TX
| | - Sanjeet Patel
- Division of Cardiothoracic Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | | | - Nagireddy Putluri
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Arun Sreekumar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - James Suliburk
- Department of Surgery, Baylor College of Medicine, Houston, TX
| | | | - Ashok Balasubramanyam
- Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX
| | - Malgorzata Borowiak
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- McNair Medical Institute, Baylor College of Medicine, Houston, TX
- Adam Mickiewicz University, Poznan, Poland
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Abstract
This review focuses on the human pancreatic islet-including its structure, cell composition, development, function, and dysfunction. After providing a historical timeline of key discoveries about human islets over the past century, we describe new research approaches and technologies that are being used to study human islets and how these are providing insight into human islet physiology and pathophysiology. We also describe changes or adaptations in human islets in response to physiologic challenges such as pregnancy, aging, and insulin resistance and discuss islet changes in human diabetes of many forms. We outline current and future interventions being developed to protect, restore, or replace human islets. The review also highlights unresolved questions about human islets and proposes areas where additional research on human islets is needed.
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Affiliation(s)
- John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marcela Brissova
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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46
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Shrestha S, Saunders DC, Walker JT, Camunas-Soler J, Dai XQ, Haliyur R, Aramandla R, Poffenberger G, Prasad N, Bottino R, Stein R, Cartailler JP, Parker SC, MacDonald PE, Levy SE, Powers AC, Brissova M. Combinatorial transcription factor profiles predict mature and functional human islet α and β cells. JCI Insight 2021; 6:e151621. [PMID: 34428183 PMCID: PMC8492318 DOI: 10.1172/jci.insight.151621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Islet-enriched transcription factors (TFs) exert broad control over cellular processes in pancreatic α and β cells, and changes in their expression are associated with developmental state and diabetes. However, the implications of heterogeneity in TF expression across islet cell populations are not well understood. To define this TF heterogeneity and its consequences for cellular function, we profiled more than 40,000 cells from normal human islets by single-cell RNA-Seq and stratified α and β cells based on combinatorial TF expression. Subpopulations of islet cells coexpressing ARX/MAFB (α cells) and MAFA/MAFB (β cells) exhibited greater expression of key genes related to glucose sensing and hormone secretion relative to subpopulations expressing only one or neither TF. Moreover, all subpopulations were identified in native pancreatic tissue from multiple donors. By Patch-Seq, MAFA/MAFB-coexpressing β cells showed enhanced electrophysiological activity. Thus, these results indicate that combinatorial TF expression in islet α and β cells predicts highly functional, mature subpopulations.
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Affiliation(s)
- Shristi Shrestha
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Creative Data Solutions, Vanderbilt Center for Stem Cell Biology, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Joan Camunas-Soler
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Xiao-Qing Dai
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Rachana Haliyur
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Radhika Aramandla
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Rita Bottino
- Imagine Pharma, Devon, Pennsylvania, USA.,Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, Pennsylvania, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Stephen Cj Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick E MacDonald
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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47
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Agrawal A, Narayan G, Gogoi R, Thummer RP. Recent Advances in the Generation of β-Cells from Induced Pluripotent Stem Cells as a Potential Cure for Diabetes Mellitus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1347:1-27. [PMID: 34426962 DOI: 10.1007/5584_2021_653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Diabetes mellitus (DM) is a group of metabolic disorders characterized by high blood glucose levels due to insufficient insulin secretion, insulin action, or both. The present-day solution to diabetes mellitus includes regular administration of insulin, which brings about many medical complications in diabetic patients. Although islet transplantation from cadaveric subjects was proposed to be a permanent cure, the increased risk of infections, the need for immunosuppressive drugs, and their unavailability had restricted its use. To overcome this, the generation of renewable and transplantable β-cells derived from autologous induced pluripotent stem cells (iPSCs) has gained enormous interest as a potential therapeutic strategy to treat diabetes mellitus permanently. To date, extensive research has been undertaken to derive transplantable insulin-producing β-cells (iβ-cells) from iPSCs in vitro by recapitulating the in vivo developmental process of the pancreas. This in vivo developmental process relies on transcription factors, signaling molecules, growth factors, and culture microenvironment. This review highlights the various factors facilitating the generation of mature β-cells from iPSCs. Moreover, this review also describes the generation of pancreatic progenitors and β-cells from diabetic patient-specific iPSCs, exploring the potential of the diabetes disease model and drug discovery. In addition, the applications of genome editing strategies have also been discussed to achieve patient-specific diabetes cell therapy. Last, we have discussed the current challenges and prospects of iPSC-derived β-cells to improve the relative efficacy of the available treatment of diabetes mellitus.
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Affiliation(s)
- Akriti Agrawal
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Gloria Narayan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ranadeep Gogoi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network. Mol Metab 2021; 53:101313. [PMID: 34352411 PMCID: PMC8387919 DOI: 10.1016/j.molmet.2021.101313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 01/17/2023] Open
Abstract
Objective Mice lacking the bHLH transcription factor (TF) Neurog3 do not form pancreatic islet cells, including insulin-secreting beta cells, the absence of which leads to diabetes. In humans, homozygous mutations of NEUROG3 manifest with neonatal or childhood diabetes. Despite this critical role in islet cell development, the precise function of and downstream genetic programs regulated directly by NEUROG3 remain elusive. Therefore, we mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (hiPSC)–derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. Methods We generated a novel hiPSC line (NEUROG3-HA-P2A-Venus) where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. We used the CUT&RUN technique to map NEUROG3 occupancy and epigenetic marks in pancreatic endocrine progenitors (PEP) that were differentiated from this hiPSC line. We integrated NEUROG3 occupancy data with chromatin status and gene expression in PEPs as well as their NEUROG3-dependence. In addition, we investigated whether NEUROG3 binds type 2 diabetes mellitus (T2DM)–associated variants at the PEP stage. Results CUT&RUN revealed a total of 863 NEUROG3 binding sites assigned to 1263 unique genes. NEUROG3 occupancy was found at promoters as well as at distant cis-regulatory elements that frequently overlapped within PEP active enhancers. De novo motif analyses defined a NEUROG3 consensus binding motif and suggested potential co-regulation of NEUROG3 target genes by FOXA or RFX transcription factors. We found that 22% of the genes downregulated in NEUROG3−/− PEPs, and 10% of genes enriched in NEUROG3-Venus positive endocrine cells were bound by NEUROG3 and thus likely to be directly regulated. NEUROG3 binds to 138 transcription factor genes, some with important roles in islet cell development or function, such as NEUROD1, PAX4, NKX2-2, SOX4, MLXIPL, LMX1B, RFX3, and NEUROG3 itself, and many others with unknown islet function. Unexpectedly, we uncovered that NEUROG3 targets genes critical for insulin secretion in beta cells (e.g., GCK, ABCC8/KCNJ11, CACNA1A, CHGA, SCG2, SLC30A8, and PCSK1). Thus, analysis of NEUROG3 occupancy suggests that the transient expression of NEUROG3 not only promotes islet destiny in uncommitted pancreatic progenitors, but could also initiate endocrine programs essential for beta cell function. Lastly, we identified eight T2DM risk SNPs within NEUROG3-bound regions. Conclusion Mapping NEUROG3 genome occupancy in PEPs uncovered unexpectedly broad, direct control of the endocrine genes, raising novel hypotheses on how this master regulator controls islet and beta cell differentiation. NEUROG3 CUT&RUN analysis revealed 1263 target genes in human pancreatic endocrine progenitors (PEPs). NEUROG3 binding sites overlap with active chromatin regions in PEPs. 1/5 of the genes downregulated in NEUROG3−/− hESC-derived PEPs are bound by NEUROG3. NEUROG3 targets islet-specific TFs and regulators of insulin secretion. Several T2DM risk alleles lie within NEUROG3-bound regions.
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49
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Burgos JI, Vallier L, Rodríguez-Seguí SA. Monogenic Diabetes Modeling: In Vitro Pancreatic Differentiation From Human Pluripotent Stem Cells Gains Momentum. Front Endocrinol (Lausanne) 2021; 12:692596. [PMID: 34295307 PMCID: PMC8290520 DOI: 10.3389/fendo.2021.692596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
The occurrence of diabetes mellitus is characterized by pancreatic β cell loss and chronic hyperglycemia. While Type 1 and Type 2 diabetes are the most common types, rarer forms involve mutations affecting a single gene. This characteristic has made monogenic diabetes an interesting disease group to model in vitro using human pluripotent stem cells (hPSCs). By altering the genotype of the original hPSCs or by deriving human induced pluripotent stem cells (hiPSCs) from patients with monogenic diabetes, changes in the outcome of the in vitro differentiation protocol can be analyzed in detail to infer the regulatory mechanisms affected by the disease-associated genes. This approach has been so far applied to a diversity of genes/diseases and uncovered new mechanisms. The focus of the present review is to discuss the latest findings obtained by modeling monogenic diabetes using hPSC-derived pancreatic cells generated in vitro. We will specifically focus on the interpretation of these studies, the advantages and limitations of the models used, and the future perspectives for improvement.
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Affiliation(s)
- Juan Ignacio Burgos
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ludovic Vallier
- Wellcome-Medical Research Council Cambridge Stem Cell Institute and Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Santiago A. Rodríguez-Seguí
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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50
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Eksi YE, Sanlioglu AD, Akkaya B, Ozturk BE, Sanlioglu S. Genome engineering and disease modeling via programmable nucleases for insulin gene therapy: Promises of CRISPR/Cas9 technology. World J Stem Cells 2021; 13:485-502. [PMID: 34249224 PMCID: PMC8246254 DOI: 10.4252/wjsc.v13.i6.485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/02/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Targeted genome editing is a continually evolving technology employing programmable nucleases to specifically change, insert, or remove a genomic sequence of interest. These advanced molecular tools include meganucleases, zinc finger nucleases, transcription activator-like effector nucleases and RNA-guided engineered nucleases (RGENs), which create double-strand breaks at specific target sites in the genome, and repair DNA either by homologous recombination in the presence of donor DNA or via the error-prone non-homologous end-joining mechanism. A recently discovered group of RGENs known as CRISPR/Cas9 gene-editing systems allowed precise genome manipulation revealing a causal association between disease genotype and phenotype, without the need for the reengineering of the specific enzyme when targeting different sequences. CRISPR/Cas9 has been successfully employed as an ex vivo gene-editing tool in embryonic stem cells and patient-derived stem cells to understand pancreatic beta-cell development and function. RNA-guided nucleases also open the way for the generation of novel animal models for diabetes and allow testing the efficiency of various therapeutic approaches in diabetes, as summarized and exemplified in this manuscript.
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Affiliation(s)
- Yunus E Eksi
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Ahter D Sanlioglu
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Bahar Akkaya
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
| | - Bilge Esin Ozturk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Salih Sanlioglu
- Department of Gene and Cell Therapy, Akdeniz University Faculty of Medicine, Antalya 07058, Turkey
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