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Wang Q, Huang YX, Liu L, Zhao XH, Sun Y, Mao X, Li SW. Pancreatic islet transplantation: current advances and challenges. Front Immunol 2024; 15:1391504. [PMID: 38887292 PMCID: PMC11180903 DOI: 10.3389/fimmu.2024.1391504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
Diabetes is a prevalent chronic disease that traditionally requires severe reliance on medication for treatment. Oral medication and exogenous insulin can only temporarily maintain blood glucose levels and do not cure the disease. Most patients need life-long injections of exogenous insulin. In recent years, advances in islet transplantation have significantly advanced the treatment of diabetes, allowing patients to discontinue exogenous insulin and avoid complications.Long-term follow-up results from recent reports on islet transplantation suggest that they provide significant therapeutic benefit although patients still require immunotherapy, suggesting the importance of future transplantation strategies. Although organ shortage remains the primary obstacle for the development of islet transplantation, new sources of islet cells, such as stem cells and porcine islet cells, have been proposed, and are gradually being incorporated into clinical research. Further research on new transplantation sites, such as the subcutaneous space and mesenteric fat, may eventually replace the traditional portal vein intra-islet cell infusion. Additionally, the immunological rejection reaction in islet transplantation will be resolved through the combined application of immunosuppressant agents, islet encapsulation technology, and the most promising mesenchymal stem cells/regulatory T cell and islet cell combined transplantation cell therapy. This review summarizes the progress achieved in islet transplantation, and discusses the research progress and potential solutions to the challenges faced.
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Affiliation(s)
- Qi Wang
- Department of Hepatobiliary and Pancreatic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yu-xi Huang
- Department of Hepatobiliary and Pancreatic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao-hong Zhao
- Department of Pharmacy, Taizhou Hospital, Zhejiang University, Taizhou, Zhejiang, China
| | - Yi Sun
- MRL Global Medical Affairs, MSD China, Shanghai, China
| | - Xinli Mao
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Shao-wei Li
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
- Key Laboratory of Minimally Invasive Techniques and Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
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2
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Osonoi S, Takebe T. Organoid-guided precision hepatology for metabolic liver disease. J Hepatol 2024; 80:805-821. [PMID: 38237864 DOI: 10.1016/j.jhep.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 03/09/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease affects millions of people worldwide. Progress towards a definitive cure has been incremental and treatment is currently limited to lifestyle modification. Hepatocyte-specific lipid accumulation is the main trigger of lipotoxic events, driving inflammation and fibrosis. The underlying pathology is extraordinarily heterogenous, and the manifestations of steatohepatitis are markedly influenced by metabolic communications across non-hepatic organs. Synthetic human tissue models have emerged as powerful platforms to better capture the mechanistic diversity in disease progression, while preserving person-specific genetic traits. In this review, we will outline current research efforts focused on integrating multiple synthetic tissue models of key metabolic organs, with an emphasis on organoid-based systems. By combining functional genomics and population-scale en masse profiling methodologies, human tissues derived from patients can provide insights into personalised genetic, transcriptional, biochemical, and metabolic states. These collective efforts will advance our understanding of steatohepatitis and guide the development of rational solutions for mechanism-directed diagnostic and therapeutic investigation.
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Affiliation(s)
- Sho Osonoi
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Endocrinology and Metabolism, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Japan
| | - Takanori Takebe
- Center for Stem Cell and Organoid Medicine (CuSTOM), Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; WPI Premium Institute for Human Metaverse Medicine (WPI-PRIMe) and Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.
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3
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Li Q, Liu R, Lin Z, Zhang X, Silva IG, Pollock SD, Alvarez-Dominguez JR, Liu J. Cyborg islets: implanted flexible electronics reveal principles of human islet electrical maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585551. [PMID: 38562695 PMCID: PMC10983936 DOI: 10.1101/2024.03.18.585551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Flexible electronics implanted during tissue formation enable chronic studies of tissue-wide electrophysiology. Here, we integrate tissue-like stretchable electronics during organogenesis of human stem cell-derived pancreatic islets, stably tracing single-cell extracellular spike bursting dynamics over months of functional maturation. Adapting spike sorting methods from neural studies reveals maturation-dependent electrical patterns of α and β-like (SC-α and β) cells, and their stimulus-coupled dynamics. We identified two major electrical states for both SC-α and β cells, distinguished by their glucose threshold for action potential firing. We find that improved hormone stimulation capacity during extended culture reflects increasing numbers of SC-α/β cells in low basal firing states, linked to energy and hormone metabolism gene upregulation. Continuous recording during further maturation by entrainment to daily feeding cycles reveals that circadian islet-level hormone secretion rhythms reflect sustained and coordinate oscillation of cell-level SC-α and β electrical activities. We find that this correlates with cell-cell communication and exocytic network induction, indicating a role for circadian rhythms in coordinating system-level stimulus-coupled responses. Cyborg islets thus reveal principles of electrical maturation that will be useful to build fully functional in vitro islets for research and therapeutic applications.
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4
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024:1-30. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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5
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Parasram K, Zuccato A, Shin M, Willms R, DeVeale B, Foley E, Karpowicz P. The emergence of circadian timekeeping in the intestine. Nat Commun 2024; 15:1788. [PMID: 38413599 PMCID: PMC10899604 DOI: 10.1038/s41467-024-45942-4] [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: 06/12/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
The circadian clock is a molecular timekeeper, present from cyanobacteria to mammals, that coordinates internal physiology with the external environment. The clock has a 24-h period however development proceeds with its own timing, raising the question of how these interact. Using the intestine of Drosophila melanogaster as a model for organ development, we track how and when the circadian clock emerges in specific cell types. We find that the circadian clock begins abruptly in the adult intestine and gradually synchronizes to the environment after intestinal development is complete. This delayed start occurs because individual cells at earlier stages lack the complete circadian clock gene network. As the intestine develops, the circadian clock is first consolidated in intestinal stem cells with changes in Ecdysone and Hnf4 signalling influencing the transcriptional activity of Clk/cyc to drive the expression of tim, Pdp1, and vri. In the mature intestine, stem cell lineage commitment transiently disrupts clock activity in differentiating progeny, mirroring early developmental clock-less transitions. Our data show that clock function and differentiation are incompatible and provide a paradigm for studying circadian clocks in development and stem cell lineages.
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Affiliation(s)
- Kathyani Parasram
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Amy Zuccato
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Minjeong Shin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Reegan Willms
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Brian DeVeale
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Edan Foley
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada.
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6
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Bevacqua RJ, Zhao W, Merheb E, Kim SH, Marson A, Gloyn AL, Kim SK. Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein. iScience 2024; 27:108693. [PMID: 38205242 PMCID: PMC10777115 DOI: 10.1016/j.isci.2023.108693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/27/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Successful genome editing in primary human islets could reveal features of the genetic regulatory landscape underlying β cell function and diabetes risk. Here, we describe a CRISPR-based strategy to interrogate functions of predicted regulatory DNA elements using electroporation of a complex of Cas9 ribonucleoprotein (Cas9 RNP) and guide RNAs into primary human islet cells. We successfully targeted coding regions including the PDX1 exon 1, and non-coding DNA linked to diabetes susceptibility. CRISPR-Cas9 RNP approaches revealed genetic targets of regulation by DNA elements containing candidate diabetes risk SNPs, including an in vivo enhancer of the MPHOSPH9 gene. CRISPR-Cas9 RNP multiplexed targeting of two cis-regulatory elements linked to diabetes risk in PCSK1, which encodes an endoprotease crucial for Insulin processing, also demonstrated efficient simultaneous editing of PCSK1 regulatory elements, resulting in impaired β cell PCSK1 regulation and Insulin secretion. Multiplex CRISPR-Cas9 RNP provides powerful approaches to investigate and elucidate human islet cell gene regulation in health and diabetes.
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Affiliation(s)
- Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Diabetes, Obesity and Metabolism Institute (DOMI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weichen Zhao
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emilio Merheb
- Diabetes, Obesity and Metabolism Institute (DOMI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seung Hyun Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology and Northern California JDRF Center of Excellence, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anna L Gloyn
- Department of Pediatrics (Endocrinology) and of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
- Northern California JDRF Center of Excellence, Stanford University School of Medicine, Stanford, CA 94305, USA
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7
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Weidemann BJ, Marcheva B, Kobayashi M, Omura C, Newman MV, Kobayashi Y, Waldeck NJ, Perelis M, Lantier L, McGuinness OP, Ramsey KM, Stein RW, Bass J. Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity. Cell Metab 2024; 36:90-102.e7. [PMID: 38171340 PMCID: PMC10793877 DOI: 10.1016/j.cmet.2023.11.018] [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: 11/07/2022] [Revised: 07/17/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Interactions between lineage-determining and activity-dependent transcription factors determine single-cell identity and function within multicellular tissues through incompletely known mechanisms. By assembling a single-cell atlas of chromatin state within human islets, we identified β cell subtypes governed by either high or low activity of the lineage-determining factor pancreatic duodenal homeobox-1 (PDX1). β cells with reduced PDX1 activity displayed increased chromatin accessibility at latent nuclear factor κB (NF-κB) enhancers. Pdx1 hypomorphic mice exhibited de-repression of NF-κB and impaired glucose tolerance at night. Three-dimensional analyses in tandem with chromatin immunoprecipitation (ChIP) sequencing revealed that PDX1 silences NF-κB at circadian and inflammatory enhancers through long-range chromatin contacts involving SIN3A. Conversely, Bmal1 ablation in β cells disrupted genome-wide PDX1 and NF-κB DNA binding. Finally, antagonizing the interleukin (IL)-1β receptor, an NF-κB target, improved insulin secretion in Pdx1 hypomorphic islets. Our studies reveal functional subtypes of single β cells defined by a gradient in PDX1 activity and identify NF-κB as a target for insulinotropic therapy.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikoto Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marsha V Newman
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nathan J Waldeck
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Louise Lantier
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Owen P McGuinness
- Vanderbilt-NIH Mouse Metabolic Phenotyping Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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Pollock SD, Galicia-Silva IM, Liu M, Gruskin ZL, Alvarez-Dominguez JR. Scalable generation of 3D pancreatic islet organoids from human pluripotent stem cells in suspension bioreactors. STAR Protoc 2023; 4:102580. [PMID: 37738117 PMCID: PMC10519857 DOI: 10.1016/j.xpro.2023.102580] [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: 06/05/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023] Open
Abstract
Here, we present a protocol for producing 3D pancreatic-like organoids from human pluripotent stem cells in suspension bioreactors. We describe scalable techniques for generating 10,000-100,000 organoids that further mature in 4-5 weeks into α- and β-like cells with glucose-responsive insulin and glucagon release. We detail procedures for culturing, passaging, and cryopreserving stem cells as suspended clusters and specify growth media and differentiation factors for differentiation. Finally, we discuss functional assays for research applications. For complete details on the use and execution of this protocol, please refer to Alvarez-Dominguez et al.1.
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Affiliation(s)
- Samuel D Pollock
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Israeli M Galicia-Silva
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mai Liu
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zoe L Gruskin
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Juan R Alvarez-Dominguez
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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9
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Pasquier A, Pastore N, D'Orsi L, Colonna R, Esposito A, Maffia V, De Cegli R, Mutarelli M, Ambrosio S, Tufano G, Grimaldi A, Cesana M, Cacchiarelli D, Delalleau N, Napolitano G, Ballabio A. TFEB and TFE3 control glucose homeostasis by regulating insulin gene expression. EMBO J 2023; 42:e113928. [PMID: 37712288 PMCID: PMC10620765 DOI: 10.15252/embj.2023113928] [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: 03/02/2023] [Revised: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 09/16/2023] Open
Abstract
To fulfill their function, pancreatic beta cells require precise nutrient-sensing mechanisms that control insulin production. Transcription factor EB (TFEB) and its homolog TFE3 have emerged as crucial regulators of the adaptive response of cell metabolism to environmental cues. Here, we show that TFEB and TFE3 regulate beta-cell function and insulin gene expression in response to variations in nutrient availability. We found that nutrient deprivation in beta cells promoted TFEB/TFE3 activation, which resulted in suppression of insulin gene expression. TFEB overexpression was sufficient to inhibit insulin transcription, whereas beta cells depleted of both TFEB and TFE3 failed to suppress insulin gene expression in response to amino acid deprivation. Interestingly, ChIP-seq analysis showed binding of TFEB to super-enhancer regions that regulate insulin transcription. Conditional, beta-cell-specific, Tfeb-overexpressing, and Tfeb/Tfe3 double-KO mice showed severe alteration of insulin transcription, secretion, and glucose tolerance, indicating that TFEB and TFE3 are important physiological mediators of pancreatic function. Our findings reveal a nutrient-controlled transcriptional mechanism that regulates insulin production, thus playing a key role in glucose homeostasis at both cellular and organismal levels.
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Affiliation(s)
- Adrien Pasquier
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | - Nunzia Pastore
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Luca D'Orsi
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | - Rita Colonna
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | | | - Veronica Maffia
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | | | - Margherita Mutarelli
- Institute of Applied Sciences and Intelligent SystemsNational Research Council (ISASI‐CNR)PozzuoliItaly
| | | | - Gennaro Tufano
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | | | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- School for Advanced Studies, Genomics and Experimental Medicine ProgramUniversity of Naples "Federico II"NaplesItaly
| | | | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- School for Advanced Studies, Genomics and Experimental Medicine ProgramUniversity of Naples "Federico II"NaplesItaly
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM)NaplesItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- School for Advanced Studies, Genomics and Experimental Medicine ProgramUniversity of Naples "Federico II"NaplesItaly
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTXUSA
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Wu H, Liu X, Jiang W, Hu C, Wang X, Tian Z, Gu W, Sun C, Han T, Wei W. The rest-activity rhythm, genetic susceptibility and risk of type 2 diabetes: A prospective study in UK Biobank. Diabetes Obes Metab 2023; 25:3366-3376. [PMID: 37654212 DOI: 10.1111/dom.15236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
AIMS This study aims to examine the association between the rest-activity rhythm (RAR) and the incidence of type 2 diabetes (T2D). MATERIALS AND METHODS In total, 97 503 participants without diabetes in the UK Biobank cohort were recruited. Wearable accelerometry was used to monitor circadian behaviour. The parameters of RAR including inter-daily stability, intra-daily variability, relative amplitude (RA), most active continuous 10 h period (M10), and least active continuous 5 h period (L5) were calculated to evaluate the robustness and regularity of the RAR. The weighted polygenic risk score for T2D (T2D-PRS) was calculated. Cox proportion hazards models were used to evaluate the survival relationship and the joint and interaction effects of RAR parameters and T2D-PRS on the occurrence of T2D. RESULTS During 692 257 person-years follow-ups, a total of 2434 participants were documented. After adjustment for potential confounders, compared with participants in the highest quartile of RA and M10, the participants in the lowest quartile had a greater risk of T2D (HRRA = 2.06, 95% CI: 1.76-2.41; HRM10 = 1.33, 95% CI: 1.19-1.49). Meanwhile, the highest quartile of L5 was related to a higher risk of T2D (HR = 1.78, 95% CI: 1.55-2.24). The joint analysis showed that the high T2D-PRS with the lowest quartile of RA and M10, or highest quartile of L5 jointly increased the risk of T2D (HRRA = 4.46, 95% CI: 3.36-6.42; HRM10 = 3.15, 95% CI: 2.29-4.32; HRL5 = 3.09, 95% CI: 2.40-3.99). No modification effects of T2D-PRS on the association between the RAR parameters and risk of T2D were observed (p > .05). CONCLUSION The unbalanced RAR are associated with a greater risk of T2D, which are independent of known risk factors of T2D.
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Affiliation(s)
- Huanyu Wu
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Xin Liu
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Wenbo Jiang
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Cong Hu
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Xuanyang Wang
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhen Tian
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Wenbo Gu
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Changhao Sun
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Tianshu Han
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
| | - Wei Wei
- National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
- College of Pharmacy Key Laboratory of Cardiovascular Research, Department of Pharmacology, Ministry of Education, Harbin Medical University, Harbin, China
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11
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Lyu X, Rowley MJ, Kulik MJ, Dalton S, Corces VG. Regulation of CTCF loop formation during pancreatic cell differentiation. Nat Commun 2023; 14:6314. [PMID: 37813869 PMCID: PMC10562423 DOI: 10.1038/s41467-023-41964-6] [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: 04/13/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
Transcription reprogramming during cell differentiation involves targeting enhancers to genes responsible for establishment of cell fates. To understand the contribution of CTCF-mediated chromatin organization to cell lineage commitment, we analyzed 3D chromatin architecture during the differentiation of human embryonic stem cells into pancreatic islet organoids. We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of H3K9me3 to H3K9me2, demethylation of DNA, recruitment of pioneer factors, and positioning of nucleosomes flanking the new CTCF sites. Existing CTCF sites not involved in loop formation become functional loop anchors via the establishment of new cohesin loading sites containing NIPBL and YY1 at sites between the new anchors. In both cases, formation of new CTCF loops leads to strengthening of enhancer promoter interactions and increased transcription of genes adjacent to loop anchors. These results suggest an important role for CTCF and cohesin in controlling gene expression during cell differentiation.
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Affiliation(s)
- Xiaowen Lyu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Michael J Kulik
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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12
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Toren E, Kepple JD, Coutinho KV, Poole SO, Deeba IM, Pierre TH, Liu Y, Bethea MM, Hunter CS. The SSBP3 co-regulator is required for glucose homeostasis, pancreatic islet architecture, and beta-cell identity. Mol Metab 2023; 76:101785. [PMID: 37536498 PMCID: PMC10448474 DOI: 10.1016/j.molmet.2023.101785] [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: 05/15/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
OBJECTIVE Transcriptional complex activity drives the development and function of pancreatic islet cells to allow for proper glucose regulation. Prior studies from our lab and others highlighted that the LIM-homeodomain transcription factor (TF), Islet-1 (Isl1), and its interacting co-regulator, Ldb1, are vital effectors of developing and adult β-cells. We further found that a member of the Single Stranded DNA-Binding Protein (SSBP) co-regulator family, SSBP3, interacts with Isl1 and Ldb1 in β-cells and primary islets (mouse and human) to impact β-cell target genes MafA and Glp1R in vitro. Members of the SSBP family stabilize TF complexes by binding directly to Ldb1 and protecting the complex from ubiquitin-mediated turnover. In this study, we hypothesized that SSBP3 has critical roles in pancreatic islet cell function in vivo, similar to the Isl1::Ldb1 complex. METHODS We first developed a novel SSBP3 LoxP allele mouse line, where Cre-mediated recombination imparts a predicted early protein termination. We bred this mouse with constitutive Cre lines (Pdx1- and Pax6-driven) to recombine SSBP3 in the developing pancreas and islet (SSBP3ΔPanc and SSBP3ΔIslet), respectively. We assessed glucose tolerance and used immunofluorescence to detect changes in islet cell abundance and markers of β-cell identity and function. Using an inducible Cre system, we also deleted SSBP3 in the adult β-cell, a model termed SSBP3Δβ-cell. We measured glucose tolerance as well as glucose-stimulated insulin secretion (GSIS), both in vivo and in isolated islets in vitro. Using islets from control and SSBP3Δβ-cell we conducted RNA-Seq and compared our results to published datasets for similar β-cell specific Ldb1 and Isl1 knockouts to identify commonly regulated target genes. RESULTS SSBP3ΔPanc and SSBP3ΔIslet neonates present with hyperglycemia. SSBP3ΔIslet mice are glucose intolerant by P21 and exhibit a reduction of β-cell maturity markers MafA, Pdx1, and UCN3. We observe disruptions in islet cell architecture with an increase in glucagon+ α-cells and ghrelin+ ε-cells at P10. Inducible loss of β-cell SSBP3 in SSBP3Δβ-cell causes hyperglycemia, glucose intolerance, and reduced GSIS. Transcriptomic analysis of 14-week-old SSBP3Δβ-cell islets revealed a decrease in β-cell function gene expression (Ins, MafA, Ucn3), increased stress and dedifferentiation markers (Neurogenin-3, Aldh1a3, Gastrin), and shared differentially expressed genes between SSBP3, Ldb1, and Isl1 in adult β-cells. CONCLUSIONS SSBP3 drives proper islet identity and function, where its loss causes altered islet-cell abundance and glucose homeostasis. β-Cell SSBP3 is required for GSIS and glucose homeostasis, at least partially through shared regulation of Ldb1 and Isl1 target genes.
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Affiliation(s)
- Eliana Toren
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jessica D Kepple
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kristen V Coutinho
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Samuel O Poole
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Iztiba M Deeba
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tanya H Pierre
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yanping Liu
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Maigen M Bethea
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chad S Hunter
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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13
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Bevacqua RJ, Zhao W, Merheb E, Kim SH, Marson A, Gloyn AL, Kim SK. Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558090. [PMID: 37745551 PMCID: PMC10516051 DOI: 10.1101/2023.09.16.558090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Successful genome editing in primary human islets could reveal features of the genetic regulatory landscape underlying β cell function and diabetes risk. Here, we describe a CRISPR-based strategy to interrogate functions of predicted regulatory DNA elements using electroporation of a complex of Cas9 ribonucleoprotein (Cas9 RNP) and guide RNAs into primary human islet cells. We successfully targeted coding regions including the PDX1 exon 1, and non-coding DNA linked to diabetes susceptibility. CRISPR/Cas9 RNP approaches revealed genetic targets of regulation by DNA elements containing candidate diabetes risk SNPs, including an in vivo enhancer of the MPHOSPH9 gene. CRISPR/Cas9 RNP multiplexed targeting of two cis-regulatory elements linked to diabetes risk in PCSK1, which encodes an endoprotease crucial for insulin processing, also demonstrated efficient simultaneous editing of PCSK1 regulatory elements, resulting in impaired β cell PCSK1 regulation and insulin secretion. Multiplex CRISPR/Cas9 RNP provides powerful approaches to investigate and elucidate human islet cell gene regulation in health and diabetes.
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Affiliation(s)
- Romina J. Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Diabetes, Obesity and Metabolism Institute (DOMI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Regenerative Biology and Stem Cell Institute, New York, NY, United States
| | - Weichen Zhao
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emilio Merheb
- Diabetes, Obesity and Metabolism Institute (DOMI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seung Hyun Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology and Northern California JDRF Center of Excellence, University of California at San Francisco, CA, 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anna L. Gloyn
- Department of Pediatrics (Endocrinology) and of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Northern California JDRF Center of Excellence, Stanford University School of Medicine, Stanford, CA, 94305, USA
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14
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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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15
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Dos Santos C, Shrestha S, Cottam M, Perkins G, Lev-Ram V, Roy B, Acree C, Kim KY, Deerinck T, Cutler M, Dean D, Cartailler JP, MacDonald PE, Hetzer M, Ellisman M, E Drigo RA. Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554369. [PMID: 37662336 PMCID: PMC10473730 DOI: 10.1101/2023.08.23.554369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Caloric restriction (CR) extends organismal lifespan and health span by improving glucose homeostasis mechanisms. How CR affects organellar structure and function of pancreatic beta cells over the lifetime of the animal remains unknown. Here, we used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis link this transcriptional phenotype to transcription factors involved in beta cell identity (Mafa) and homeostasis (Atf6). Imaging metabolomics further demonstrates that CR beta cells are more energetically competent. In fact, high-resolution light and electron microscopy indicates that CR reduces beta cell mitophagy and increases mitochondria mass, increasing mitochondrial ATP generation. Finally, we show that long-term CR delays the onset of beta cell aging and senescence to promote longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cells during aging and diabetes.
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Affiliation(s)
- Cristiane Dos Santos
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Shristi Shrestha
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Matthew Cottam
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Guy Perkins
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Varda Lev-Ram
- University of California San Diego, Department of Pharmacology, School of Medicine. La Jolla, CA USA
| | - Birbickram Roy
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Christopher Acree
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Keun-Young Kim
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Thomas Deerinck
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Melanie Cutler
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | - Danielle Dean
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
| | | | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Martin Hetzer
- Institute of Science and Technology Austria (ISTA), Vienna, Austria
| | - Mark Ellisman
- National Center for Imaging and Microscopy Research, University of California San Diego, La Jolla, CA USA
| | - Rafael Arrojo E Drigo
- Vanderbilt University, Department of Molecular Physiology and Biophysics, Nashville, TN USA
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16
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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight 2023; 8:e164720. [PMID: 37463053 PMCID: PMC10543710 DOI: 10.1172/jci.insight.164720] [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] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Optimal lung repair and regeneration are essential for recovery from viral infections, including influenza A virus (IAV). We have previously demonstrated that acute inflammation and mortality induced by IAV is under circadian control. However, it is not known whether the influence of the circadian clock persists beyond the acute outcomes. Here, we utilize the UK Biobank to demonstrate an association between poor circadian rhythms and morbidity from lower respiratory tract infections, including the need for hospitalization and mortality after discharge; this persists even after adjusting for common confounding factors. Furthermore, we use a combination of lung organoid assays, single-cell RNA sequencing, and IAV infection in different models of clock disruption to investigate the role of the circadian clock in lung repair and regeneration. We show that lung organoids have a functional circadian clock and the disruption of this clock impairs regenerative capacity. Finally, we find that the circadian clock acts through distinct pathways in mediating lung regeneration - in tracheal cells via the Wnt/β-catenin pathway and through IL-1β in alveolar epithelial cells. We speculate that adding a circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes.
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Affiliation(s)
- Amruta Naik
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Oindrila Paul
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yasmine Issah
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Utham K. Valekunja
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Soon Y. Tang
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Akhilesh B. Reddy
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Thomas G. Brooks
- Institute of Translational Medicine and Therapeutics (ITMAT), and
| | - Fatima Chaudhry
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Department of Genetics
| | - Garret A. FitzGerald
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amita Sehgal
- Institute of Translational Medicine and Therapeutics (ITMAT), and
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, and
| | - G. Scott Worthen
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David B. Frank
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Edward E. Morrisey
- Penn-CHOP Lung Biology Institute
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Systems Pharmacology, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn-CHOP Lung Biology Institute
- Department of Pediatrics
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17
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Montalvo AP, Gruskin ZL, Leduc A, Liu M, Gao Z, Ahn JH, Straubhaar JR, Slavov N, Alvarez-Dominguez JR. An adult clock component links circadian rhythms to pancreatic β-cell maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552890. [PMID: 37609178 PMCID: PMC10441398 DOI: 10.1101/2023.08.11.552890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
How ubiquitous circadian clocks orchestrate tissue-specific outputs is not well understood. Pancreatic β cell-autonomous clocks attune insulin secretion to daily energy cycles, and desynchrony from genetic or behavioral disruptions raises type 2 diabetes risk. We show that the transcription factor DEC1, a clock component induced in adult β cells, coordinates their glucose responsiveness by synchronizing energy metabolism and secretory gene oscillations. Dec1-ablated mice develop lifelong hypo-insulinemic diabetes, despite normal islet formation and intact circadian Clock and Bmal1 activators. DEC1, but not CLOCK/BMAL1, binds maturity-linked genes that mediate respiratory metabolism and insulin exocytosis, and Dec1 loss disrupts their transcription synchrony. Accordingly, β-cell Dec1 ablation causes hypo-insulinemia due to immature glucose responsiveness, dampening insulin rhythms. Thus, Dec1 links circadian clockwork to the β-cell maturation process, aligning metabolism to diurnal energy cycles.
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Affiliation(s)
- Ana P Montalvo
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Zoe L Gruskin
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrew Leduc
- Departments of Bioengineering and Biology, Single-Cell Proteomics Center and Barnett Institute, Northeastern University, Boston, MA 02115, USA
| | - Mai Liu
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zihan Gao
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - June H Ahn
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Juerg R Straubhaar
- Bioinformatics Center, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Nikolai Slavov
- Departments of Bioengineering and Biology, Single-Cell Proteomics Center and Barnett Institute, Northeastern University, Boston, MA 02115, USA
| | - Juan R Alvarez-Dominguez
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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18
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Jiménez S, Schreiber V, Mercier R, Gradwohl G, Molina N. Characterization of cell-fate decision landscapes by estimating transcription factor dynamics. CELL REPORTS METHODS 2023; 3:100512. [PMID: 37533652 PMCID: PMC10391345 DOI: 10.1016/j.crmeth.2023.100512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023]
Abstract
Time-specific modulation of gene expression during differentiation by transcription factors promotes cell diversity. However, estimating their dynamic regulatory activity at the single-cell level and in a high-throughput manner remains challenging. We present FateCompass, an integrative approach that utilizes single-cell transcriptomics data to identify lineage-specific transcription factors throughout differentiation. By combining a probabilistic framework with RNA velocities or differentiation potential, we estimate transition probabilities, while a linear model of gene regulation is employed to compute transcription factor activities. Considering dynamic changes and correlations of expression and activities, FateCompass identifies lineage-specific regulators. Our validation using in silico data and application to pancreatic endocrine cell differentiation datasets highlight both known and potentially novel lineage-specific regulators. Notably, we uncovered undescribed transcription factors of an enterochromaffin-like population during in vitro differentiation toward ß-like cells. FateCompass provides a valuable framework for hypothesis generation, advancing our understanding of the gene regulatory networks driving cell-fate decisions.
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Affiliation(s)
- Sara Jiménez
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Valérie Schreiber
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Reuben Mercier
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Gérard Gradwohl
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Nacho Molina
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
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19
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Sato S, Hishida T, Kinouchi K, Hatanaka F, Li Y, Nguyen Q, Chen Y, Wang PH, Kessenbrock K, Li W, Izpisua Belmonte JC, Sassone-Corsi P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming. Cell Rep 2023; 42:112590. [PMID: 37261952 DOI: 10.1016/j.celrep.2023.112590] [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: 08/23/2022] [Revised: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Distinct metabolic conditions rewire circadian-clock-controlled signaling pathways leading to the de novo construction of signal transduction networks. However, it remains unclear whether metabolic hallmarks unique to pluripotent stem cells (PSCs) are connected to clock functions. Reprogramming somatic cells to a pluripotent state, here we highlighted non-canonical functions of the circadian repressor CRY1 specific to PSCs. Metabolic reprogramming, including AMPK inactivation and SREBP1 activation, was coupled with the accumulation of CRY1 in PSCs. Functional assays verified that CRY1 is required for the maintenance of self-renewal capacity, colony organization, and metabolic signatures. Genome-wide occupancy of CRY1 identified CRY1-regulatory genes enriched in development and differentiation in PSCs, albeit not somatic cells. Last, cells lacking CRY1 exhibit differential gene expression profiles during induced PSC (iPSC) reprogramming, resulting in impaired iPSC reprogramming efficiency. Collectively, these results suggest the functional implication of CRY1 in pluripotent reprogramming and ontogenesis, thereby dictating PSC identity.
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Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Fumiaki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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20
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Trinh LT, Osipovich AB, Liu B, Shrestha S, Cartailler JP, Wright CVE, Magnuson MA. Single-Cell RNA Sequencing of Sox17-Expressing Lineages Reveals Distinct Gene Regulatory Networks and Dynamic Developmental Trajectories. Stem Cells 2023; 41:643-657. [PMID: 37085274 PMCID: PMC10465087 DOI: 10.1093/stmcls/sxad030] [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: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023]
Abstract
During early embryogenesis, the transcription factor SOX17 contributes to hepato-pancreato-biliary system formation and vascular-hematopoietic emergence. To better understand Sox17 function in the developing endoderm and endothelium, we developed a dual-color temporal lineage-tracing strategy in mice combined with single-cell RNA sequencing to analyze 6934 cells from Sox17-expressing lineages at embryonic days 9.0-9.5. Our analyses showed 19 distinct cellular clusters combined from all 3 germ layers. Differential gene expression, trajectory and RNA-velocity analyses of endothelial cells revealed a heterogenous population of uncommitted and specialized endothelial subtypes, including 2 hemogenic populations that arise from different origins. Similarly, analyses of posterior foregut endoderm revealed subsets of hepatic, pancreatic, and biliary progenitors with overlapping developmental potency. Calculated gene-regulatory networks predict gene regulons that are dominated by cell type-specific transcription factors unique to each lineage. Vastly different Sox17 regulons found in endoderm versus endothelial cells support the differential interactions of SOX17 with other regulatory factors thereby enabling lineage-specific regulatory actions.
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Affiliation(s)
- Linh T Trinh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Bryan Liu
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, USA
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Christopher V E Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
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21
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Shilleh AH, Beard S, Russ HA. Enrichment of stem cell-derived pancreatic beta-like cells and controlled graft size through pharmacological removal of proliferating cells. Stem Cell Reports 2023; 18:1284-1294. [PMID: 37315522 DOI: 10.1016/j.stemcr.2023.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
Transplantation of limited human cadaveric islets into type 1 diabetic patients results in ∼35 months of insulin independence. Direct differentiation of stem cell-derived insulin-producing beta-like cells (sBCs) that can reverse diabetes in animal models effectively removes this shortage constraint, but uncontrolled graft growth remains a concern. Current protocols do not generate pure sBCs, but consist of only 20%-50% insulin-expressing cells with additional cell types present, some of which are proliferative. Here, we show the selective ablation of proliferative cells marked by SOX9 by simple pharmacological treatment in vitro. This treatment concomitantly enriches for sBCs by ∼1.7-fold. Treated sBC clusters show improved function in vitro and in vivo transplantation controls graft size. Overall, our study provides a convenient and effective approach to enrich for sBCs while minimizing the presence of unwanted proliferative cells and thus has important implications for current cell therapy approaches.
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Affiliation(s)
- Ali H Shilleh
- Barbara-Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Scott Beard
- Barbara-Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Holger A Russ
- Barbara-Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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22
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Augsornworawat P, Hogrebe NJ, Ishahak M, Schmidt MD, Marquez E, Maestas MM, Veronese-Paniagua DA, Gale SE, Miller JR, Velazco-Cruz L, Millman JR. Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification. Nat Cell Biol 2023; 25:904-916. [PMID: 37188763 PMCID: PMC10264244 DOI: 10.1038/s41556-023-01150-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023]
Abstract
Insulin-producing β cells created from human pluripotent stem cells have potential as a therapy for insulin-dependent diabetes, but human pluripotent stem cell-derived islets (SC-islets) still differ from their in vivo counterparts. To better understand the state of cell types within SC-islets and identify lineage specification deficiencies, we used single-nucleus multi-omic sequencing to analyse chromatin accessibility and transcriptional profiles of SC-islets and primary human islets. Here we provide an analysis that enabled the derivation of gene lists and activity for identifying each SC-islet cell type compared with primary islets. Within SC-islets, we found that the difference between β cells and awry enterochromaffin-like cells is a gradient of cell states rather than a stark difference in identity. Furthermore, transplantation of SC-islets in vivo improved cellular identities overtime, while long-term in vitro culture did not. Collectively, our results highlight the importance of chromatin and transcriptional landscapes during islet cell specification and maturation.
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Affiliation(s)
- Punn Augsornworawat
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Nathaniel J Hogrebe
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Mason D Schmidt
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Erica Marquez
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Marlie M Maestas
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Daniel A Veronese-Paniagua
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Sarah E Gale
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Julia R Miller
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Leonardo Velazco-Cruz
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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23
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Zhu H, Wang G, Nguyen-Ngoc KV, Kim D, Miller M, Goss G, Kovsky J, Harrington AR, Saunders DC, Hopkirk AL, Melton R, Powers AC, Preissl S, Spagnoli FM, Gaulton KJ, Sander M. Understanding cell fate acquisition in stem-cell-derived pancreatic islets using single-cell multiome-inferred regulomes. Dev Cell 2023; 58:727-743.e11. [PMID: 37040771 PMCID: PMC10175223 DOI: 10.1016/j.devcel.2023.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 01/06/2023] [Accepted: 03/14/2023] [Indexed: 04/13/2023]
Abstract
Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem-cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and pancreas from childhood and adult donors for comparison. We delineate major cell types, define their regulomes, and describe spatiotemporal gene regulatory relationships between transcription factors. CDX2 emerged as a regulator of enterochromaffin-like cells, which we show resemble a transient, previously unrecognized, serotonin-producing pre-β cell population in fetal pancreas, arguing against a proposed non-pancreatic origin. Furthermore, we observe insufficient activation of signal-dependent transcriptional programs during in vitro β cell maturation and identify sex hormones as drivers of β cell proliferation in childhood. Altogether, our analysis provides a comprehensive understanding of cell fate acquisition in stem-cell-derived islets and a framework for manipulating cell identities and maturity.
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Affiliation(s)
- Han Zhu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Gaowei Wang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Kim-Vy Nguyen-Ngoc
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Dongsu Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Georgina Goss
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Jenna Kovsky
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Austin R Harrington
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232-0475, USA
| | - Alexander L Hopkirk
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232-0475, USA
| | - Rebecca Melton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232-0475, USA; Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212-2637, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Maike Sander
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0653, USA; Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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24
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Hogrebe NJ, Ishahak M, Millman JR. Developments in stem cell-derived islet replacement therapy for treating type 1 diabetes. Cell Stem Cell 2023; 30:530-548. [PMID: 37146579 PMCID: PMC10167558 DOI: 10.1016/j.stem.2023.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
The generation of islet-like endocrine clusters from human pluripotent stem cells (hPSCs) has the potential to provide an unlimited source of insulin-producing β cells for the treatment of diabetes. In order for this cell therapy to become widely adopted, highly functional and well-characterized stem cell-derived islets (SC-islets) need to be manufactured at scale. Furthermore, successful SC-islet replacement strategies should prevent significant cell loss immediately following transplantation and avoid long-term immune rejection. This review highlights the most recent advances in the generation and characterization of highly functional SC-islets as well as strategies to ensure graft viability and safety after transplantation.
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Affiliation(s)
- Nathaniel J Hogrebe
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA.
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.
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25
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Tan C, Ding M, Zheng YW. The Values and Perspectives of Organoids in the Field of Metabolic Syndrome. Int J Mol Sci 2023; 24:ijms24098125. [PMID: 37175830 PMCID: PMC10179392 DOI: 10.3390/ijms24098125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Metabolic syndrome (MetS) has become a global health problem, and the prevalence of obesity at all stages of life makes MetS research increasingly important and urgent. However, as a comprehensive and complex disease, MetS has lacked more appropriate research models. The advent of organoids provides an opportunity to address this issue. However, it should be noted that organoids are still in their infancy. The main drawbacks are a lack of maturity, complexity, and the inability to standardize large-scale production. Could organoids therefore be a better choice for studying MetS than other models? How can these limitations be overcome? Here, we summarize the available data to present current progress on pancreatic and hepatobiliary organoids and to answer these open questions. Organoids are of human origin and contain a variety of human cell types necessary to mimic the disease characteristics of MetS in their development. Taken together with the discovery of hepatobiliary progenitors in situ, the dedifferentiation of beta cells in diabetes, and studies on hepatic macrophages, we suggest that promoting endogenous regeneration has the potential to prevent the development of end-stage liver and pancreatic lesions caused by MetS and outline the direction of future research in this field.
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Affiliation(s)
- Chen Tan
- Institute of Regenerative Medicine, Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China
| | - Min Ding
- Institute of Regenerative Medicine, Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China
| | - Yun-Wen Zheng
- Institute of Regenerative Medicine, Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, China
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda 278-8510, Japan
- School of Medicine, Yokohama City University, Yokohama 234-0006, Japan
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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26
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Mawla AM, van der Meulen T, Huising MO. Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers. BMC Genomics 2023; 24:202. [PMID: 37069576 PMCID: PMC10108528 DOI: 10.1186/s12864-023-09293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/03/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene expression signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. However, chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. RESULTS Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we not only confirm and visualize previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin, but identify novel regions as well. We compiled our chromatin accessibility data in a freely accessible database of common endocrine- and cell specific-enhancer regions that can be navigated with minimal bioinformatics expertise. CONCLUSIONS Both alpha and delta cells appear poised, but repressed, from becoming beta cells in murine pancreatic islets. These data broadly support earlier findings on the plasticity in identity of non-beta cells under certain circumstances. Furthermore, differential chromatin accessibility shows preferentially enriched distal-intergenic regions in beta cells, when compared to either alpha or delta cells.
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Affiliation(s)
- Alex M Mawla
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Talitha van der Meulen
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark O Huising
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
- Department of Physiology and Membrane Biology, School of Medicine, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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27
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Tremmel DM, Mikat AE, Gupta S, Mitchell SA, Curran AM, Menadue JA, Odorico JS, Sackett SD. Validating expression of beta cell maturation-associated genes in human pancreas development. Front Cell Dev Biol 2023; 11:1103719. [PMID: 36846594 PMCID: PMC9945361 DOI: 10.3389/fcell.2023.1103719] [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: 11/20/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
The identification of genes associated with human pancreatic beta cell maturation could stimulate a better understanding of normal human islet development and function, be informative for improving stem cell-derived islet (SC-islet) differentiation, and facilitate the sorting of more mature beta cells from a pool of differentiated cells. While several candidate factors to mark beta cell maturation have been identified, much of the data supporting these markers come from animal models or differentiated SC-islets. One such marker is Urocortin-3 (UCN3). In this study, we provide evidence that UCN3 is expressed in human fetal islets well before the acquisition of functional maturation. When SC-islets expressing significant levels of UCN3 were generated, the cells did not exhibit glucose-stimulated insulin secretion, indicating that UCN3 expression is not correlated with functional maturation in these cells. We utilized our tissue bank and SC-islet resources to test an array of other candidate maturation-associated genes, and identified CHGB, G6PC2, FAM159B, GLUT1, IAPP and ENTPD3 as markers with expression patterns that correlate developmentally with the onset of functional maturation in human beta cells. We also find that human beta cell expression of ERO1LB, HDAC9, KLF9, and ZNT8 does not change between fetal and adult stages.
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Affiliation(s)
- Daniel M. Tremmel
- *Correspondence: Daniel M. Tremmel, ; Sara Dutton Sackett, ; Jon S. Odorico,
| | - Anna E. Mikat
- University of Wisconsin-Madison, Department of Surgery, Transplantation Division, Madison, WI, United States
| | - Sakar Gupta
- University of Wisconsin-Madison, Department of Surgery, Transplantation Division, Madison, WI, United States
| | - Samantha A. Mitchell
- University of Wisconsin-Madison, Department of Surgery, Transplantation Division, Madison, WI, United States
| | - Andrew M. Curran
- University of Wisconsin-Madison, Department of Surgery, Transplantation Division, Madison, WI, United States
| | - Jenna A. Menadue
- University of Wisconsin-Madison, Department of Surgery, Transplantation Division, Madison, WI, United States
| | - Jon S. Odorico
- *Correspondence: Daniel M. Tremmel, ; Sara Dutton Sackett, ; Jon S. Odorico,
| | - Sara Dutton Sackett
- *Correspondence: Daniel M. Tremmel, ; Sara Dutton Sackett, ; Jon S. Odorico,
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28
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Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 2023; 12:e83077. [PMID: 36719724 PMCID: PMC9889090 DOI: 10.7554/elife.83077] [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] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.
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Affiliation(s)
- Alexandro Landshammer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Christian Much
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - René Buschow
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - Alina Rose
- Helmholtz Institute for Metabolic, Obesity and Vascular ResearchLeipzigGermany
| | - Hua-Jun Wu
- Department of Data Science, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bjoern Braendl
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Rosaria Tornisiello
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Krishna Mohan Parsi
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jack Huey
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy Core FacilityBerlinGermany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Core FacilityBerlinGermany
| | - René Maehr
- Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center and Peking University Cancer Hospital and InstituteBeijingChina
- Diabetes Center of Excellence, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Franziska Michor
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Data Science, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public HealthBostonUnited States
- The Ludwig Center at Harvard, Boston, MA 02215, USA, and Center for Cancer Evolution, Dana-Farber Cancer InstituteBostonUnited States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers InstituteBoulderUnited States
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
- Institute of Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
- Department of Stem Cell and Regenerative Biology, Harvard UniversityCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
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29
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Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies. Dev Cell 2023; 58:3-17.e8. [PMID: 36516856 PMCID: PMC7614300 DOI: 10.1016/j.devcel.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
In many developing tissues, the patterns of gene expression that assign cell fate are organized by graded secreted signals. Cis-regulatory elements (CREs) interpret these signals to control gene expression, but how this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen sonic hedgehog (Shh) patterns neural progenitors. We identify two distinct ways in which CREs translate graded Shh into differential gene expression in mouse neural progenitors. In most progenitors, a common set of CREs control gene activity by integrating cell-type-specific inputs. By contrast, the most ventral progenitors use a unique set of CREs, established by the pioneer factor FOXA2. This parallels the role of FOXA2 in endoderm, where FOXA2 binds some of the same sites. Together, the data identify distinct cis-regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2 across tissues.
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30
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Olaniru OE, Kadolsky U, Kannambath S, Vaikkinen H, Fung K, Dhami P, Persaud SJ. Single-cell transcriptomic and spatial landscapes of the developing human pancreas. Cell Metab 2023; 35:184-199.e5. [PMID: 36513063 DOI: 10.1016/j.cmet.2022.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
Current differentiation protocols have not been successful in reproducibly generating fully functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single-cell RNA sequencing with spatial transcriptomics at multiple developmental time points and revealed distinct temporal-spatial gene cascades. Cell trajectory inference identified endocrine progenitor populations and branch-specific genes as the progenitors differentiate toward alpha or beta cells. Spatial differentiation trajectories indicated that Schwann cells are spatially co-located with endocrine progenitors, and cell-cell connectivity analysis predicted that they may interact via L1CAM-EPHB2 signaling. Our integrated approach enabled us to identify heterogeneity and multiple lineage dynamics within the mesenchyme, showing that it contributed to the exocrine acinar cell state. Finally, we have generated an interactive web resource for investigating human pancreas development for the research community.
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Affiliation(s)
- Oladapo Edward Olaniru
- Department of Diabetes, School of Cardiovascular and Metabolic Medicine & Sciences, King's College London, Guy's Campus, London SE1 1UL, UK.
| | - Ulrich Kadolsky
- Genomics Research Platform and Single Cell Laboratory, Biomedical Research Centre, Guy's and St. Thomas' NHS Trust, London, UK; Genomics WA, University of Western Australia, Harry Perkins Institute of Medical Research and Telethon Kids Institute QEII Campus, Nedlands, Perth, WA 6009, Australia
| | - Shichina Kannambath
- Genomics Research Platform and Single Cell Laboratory, Biomedical Research Centre, Guy's and St. Thomas' NHS Trust, London, UK
| | - Heli Vaikkinen
- Genomics Research Platform and Single Cell Laboratory, Biomedical Research Centre, Guy's and St. Thomas' NHS Trust, London, UK
| | - Kathy Fung
- Genomics Research Platform and Single Cell Laboratory, Biomedical Research Centre, Guy's and St. Thomas' NHS Trust, London, UK
| | - Pawan Dhami
- Genomics Research Platform and Single Cell Laboratory, Biomedical Research Centre, Guy's and St. Thomas' NHS Trust, London, UK
| | - Shanta J Persaud
- Department of Diabetes, School of Cardiovascular and Metabolic Medicine & Sciences, King's College London, Guy's Campus, London SE1 1UL, UK.
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31
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Ouchi R, Koike H. Modeling human liver organ development and diseases with pluripotent stem cell-derived organoids. Front Cell Dev Biol 2023; 11:1133534. [PMID: 36875751 PMCID: PMC9974642 DOI: 10.3389/fcell.2023.1133534] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
The discoveries of human pluripotent stem cells (PSCs) including embryonic stem cells and induced pluripotent stem cells (iPSCs) has led to dramatic advances in our understanding of basic human developmental and cell biology and has also been applied to research aimed at drug discovery and development of disease treatments. Research using human PSCs has been largely dominated by studies using two-dimensional cultures. In the past decade, however, ex vivo tissue "organoids," which have a complex and functional three-dimensional structure similar to human organs, have been created from PSCs and are now being used in various fields. Organoids created from PSCs are composed of multiple cell types and are valuable models with which it is better to reproduce the complex structures of living organs and study organogenesis through niche reproduction and pathological modeling through cell-cell interactions. Organoids derived from iPSCs, which inherit the genetic background of the donor, are helpful for disease modeling, elucidation of pathophysiology, and drug screening. Moreover, it is anticipated that iPSC-derived organoids will contribute significantly to regenerative medicine by providing treatment alternatives to organ transplantation with which the risk of immune rejection is low. This review summarizes how PSC-derived organoids are used in developmental biology, disease modeling, drug discovery, and regenerative medicine. Highlighted is the liver, an organ that play crucial roles in metabolic regulation and is composed of diverse cell types.
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Affiliation(s)
- Rie Ouchi
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroyuki Koike
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
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32
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Chu CMJ, Modi H, Ellis C, Krentz NAJ, Skovsø S, Zhao YB, Cen H, Noursadeghi N, Panzhinskiy E, Hu X, Dionne DA, Xia YH, Xuan S, Huising MO, Kieffer TJ, Lynn FC, Johnson JD. Dynamic Ins2 Gene Activity Defines β-Cell Maturity States. Diabetes 2022; 71:2612-2631. [PMID: 36170671 DOI: 10.2337/db21-1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Transcriptional and functional cellular specialization has been described for insulin-secreting β-cells of the endocrine pancreas. However, it is not clear whether β-cell heterogeneity is stable or reflects dynamic cellular states. We investigated the temporal kinetics of endogenous insulin gene activity using live cell imaging, with complementary experiments using FACS and single-cell RNA sequencing, in β-cells from Ins2GFP knockin mice. In vivo staining and FACS analysis of islets from Ins2GFP mice confirmed that at a given moment, ∼25% of β-cells exhibited significantly higher activity at the evolutionarily conserved insulin gene, Ins2. Live cell imaging over days captured Ins2 gene activity dynamics in single β-cells. Autocorrelation analysis revealed a subset of oscillating cells, with mean oscillation periods of 17 h. Increased glucose concentrations stimulated more cells to oscillate and resulted in higher average Ins2 gene activity per cell. Single-cell RNA sequencing showed that Ins2(GFP)HIGH β-cells were enriched for markers of β-cell maturity. Ins2(GFP)HIGH β-cells were also significantly less viable at all glucose concentrations and in the context of endoplasmic reticulum stress. Collectively, our results demonstrate that the heterogeneity of insulin production, observed in mouse and human β-cells, can be accounted for by dynamic states of insulin gene activity.
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Affiliation(s)
- Chieh Min Jamie Chu
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Honey Modi
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Cara Ellis
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Nicole A J Krentz
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, Canada
| | - Søs Skovsø
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Yiwei Bernie Zhao
- Biomedical Research Centre, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Haoning Cen
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Nilou Noursadeghi
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Evgeniy Panzhinskiy
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Xiaoke Hu
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Derek A Dionne
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Yi Han Xia
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Shouhong Xuan
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Mark O Huising
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA
| | - Timothy J Kieffer
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
| | - Francis C Lynn
- BC Children's Hospital Research Institute, Department of Surgery, University of British Columbia, Vancouver, Canada
| | - James D Johnson
- Diabetes Focus Team, Life Sciences Institute, Departments of Cellular and Physiological Sciences and Surgery, University of British Columbia, Vancouver, Canada
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33
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Abstract
Metabolic diseases, including obesity, diabetes mellitus and cardiovascular disease, are a major threat to health in the modern world, but efforts to understand the underlying mechanisms and develop rational treatments are limited by the lack of appropriate human model systems. Notably, advances in stem cell and organoid technology allow the generation of cellular models that replicate the histological, molecular and physiological properties of human organs. Combined with marked improvements in gene editing tools, human stem cells and organoids provide unprecedented systems for studying mechanisms of metabolic diseases. Here, we review progress made over the past decade in the generation and use of stem cell-derived metabolic cell types and organoids in metabolic disease research, especially obesity and liver diseases. In particular, we discuss the limitations of animal models and the advantages of stem cells and organoids, including their application to metabolic diseases. We also discuss mechanisms of drug action, understanding the efficacy and toxicity of existing therapies, screening for new treatments and pursuing personalized therapies. We highlight the potential of combining stem cell-derived organoids with gene editing and functional genomics to revolutionize the approach to finding treatments for metabolic diseases.
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Affiliation(s)
- Wenxiang Hu
- Department of Basic Research, Guangzhou Laboratory, Guangdong, China.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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34
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Leavens KF, Alvarez-Dominguez JR, Vo LT, Russ HA, Parent AV. Stem cell-based multi-tissue platforms to model human autoimmune diabetes. Mol Metab 2022; 66:101610. [PMID: 36209784 PMCID: PMC9587366 DOI: 10.1016/j.molmet.2022.101610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic insulin-producing β cells are specifically destroyed by the immune system. Understanding the initiation and progression of human T1D has been hampered by the lack of appropriate models that can reproduce the complexity and heterogeneity of the disease. The development of platforms combining multiple human pluripotent stem cell (hPSC) derived tissues to model distinct aspects of T1D has the potential to provide critical novel insights into the etiology and pathogenesis of the human disease. SCOPE OF REVIEW In this review, we summarize the state of hPSC differentiation approaches to generate cell types and tissues relevant to T1D, with a particular focus on pancreatic islet cells, T cells, and thymic epithelium. We present current applications as well as limitations of using these hPSC-derived cells for disease modeling and discuss efforts to optimize platforms combining multiple cell types to model human T1D. Finally, we outline remaining challenges and emphasize future improvements needed to accelerate progress in this emerging field of research. MAJOR CONCLUSIONS Recent advances in reprogramming approaches to create patient-specific induced pluripotent stem cell lines (iPSCs), genome engineering technologies to efficiently modify DNA of hPSCs, and protocols to direct their differentiation into mature cell types have empowered the use of stem cell derivatives to accurately model human disease. While challenges remain before complex interactions occurring in human T1D can be modeled with these derivatives, experiments combining hPSC-derived β cells and immune cells are already providing exciting insight into how these cells interact in the context of T1D, supporting the viability of this approach.
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Affiliation(s)
- Karla F Leavens
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania and Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Juan R Alvarez-Dominguez
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Holger A Russ
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Audrey V Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
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35
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Beucher A, Miguel-Escalada I, Balboa D, De Vas MG, Maestro MA, Garcia-Hurtado J, Bernal A, Gonzalez-Franco R, Vargiu P, Heyn H, Ravassard P, Ortega S, Ferrer J. The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A. Nat Cell Biol 2022; 24:1528-1540. [PMID: 36202974 PMCID: PMC9586874 DOI: 10.1038/s41556-022-00996-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/16/2022] [Indexed: 11/08/2022]
Abstract
The biological purpose of long non-coding RNAs (lncRNAs) is poorly understood. Haploinsufficient mutations in HNF1A homeobox A (HNF1A), encoding a homeodomain transcription factor, cause diabetes mellitus. Here, we examine HASTER, the promoter of an lncRNA antisense to HNF1A. Using mouse and human models, we show that HASTER maintains cell-specific physiological HNF1A concentrations through positive and negative feedback loops. Pancreatic β cells from Haster mutant mice consequently showed variegated HNF1A silencing or overexpression, resulting in hyperglycaemia. HASTER-dependent negative feedback was essential to prevent HNF1A binding to inappropriate genomic regions. We demonstrate that the HASTER promoter DNA, rather than the lncRNA, modulates HNF1A promoter-enhancer interactions in cis and thereby regulates HNF1A transcription. Our studies expose a cis-regulatory element that is unlike classic enhancers or silencers, it stabilizes the transcription of its target gene and ensures the fidelity of a cell-specific transcription factor program. They also show that disruption of a mammalian lncRNA promoter can cause diabetes mellitus.
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Affiliation(s)
- Anthony Beucher
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Irene Miguel-Escalada
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Diego Balboa
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Matías G De Vas
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Miguel Angel Maestro
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Javier Garcia-Hurtado
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Aina Bernal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Roser Gonzalez-Franco
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | - Holger Heyn
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Philippe Ravassard
- Biotechnology and Biotherapy Team, Institut du Cerveau et de la Moelle, CNRS UMR7225, INSERM U975, University Pierre et Marie Curie, Paris, France
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jorge Ferrer
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain.
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36
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Su C, Gao L, May CL, Pippin JA, Boehm K, Lee M, Liu C, Pahl MC, Golson ML, Naji A, Grant SFA, Wells AD, Kaestner KH. 3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk. Cell Metab 2022; 34:1394-1409.e4. [PMID: 36070683 PMCID: PMC9664375 DOI: 10.1016/j.cmet.2022.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 12/20/2022]
Abstract
Three-dimensional (3D) chromatin organization maps help dissect cell-type-specific gene regulatory programs. Furthermore, 3D chromatin maps contribute to elucidating the pathogenesis of complex genetic diseases by connecting distal regulatory regions and genetic risk variants to their respective target genes. To understand the cell-type-specific regulatory architecture of diabetes risk, we generated transcriptomic and 3D epigenomic profiles of human pancreatic acinar, alpha, and beta cells using single-cell RNA-seq, single-cell ATAC-seq, and high-resolution Hi-C of sorted cells. Comparisons of these profiles revealed differential A/B (open/closed) chromatin compartmentalization, chromatin looping, and transcriptional factor-mediated control of cell-type-specific gene regulatory programs. We identified a total of 4,750 putative causal-variant-to-target-gene pairs at 194 type 2 diabetes GWAS signals using pancreatic 3D chromatin maps. We found that the connections between candidate causal variants and their putative target effector genes are cell-type stratified and emphasize previously underappreciated roles for alpha and acinar cells in diabetes pathogenesis.
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Affiliation(s)
- Chun Su
- Division of Human Genetics and Endocrinology & Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Long Gao
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine L May
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James A Pippin
- Division of Human Genetics and Endocrinology & Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Keith Boehm
- Division of Human Genetics and Endocrinology & Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michelle Lee
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chengyang Liu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew C Pahl
- Division of Human Genetics and Endocrinology & Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maria L Golson
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ali Naji
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Division of Human Genetics and Endocrinology & Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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37
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Miguel-Escalada I, Maestro MÁ, Balboa D, Elek A, Bernal A, Bernardo E, Grau V, García-Hurtado J, Sebé-Pedrós A, Ferrer J. Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster. Dev Cell 2022; 57:1922-1936.e9. [PMID: 35998583 PMCID: PMC9426562 DOI: 10.1016/j.devcel.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/30/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022]
Abstract
Sequence variants in cis-acting enhancers are important for polygenic disease, but their role in Mendelian disease is poorly understood. Redundancy between enhancers that regulate the same gene is thought to mitigate the pathogenic impact of enhancer mutations. Recent findings, however, have shown that loss-of-function mutations in a single enhancer near PTF1A cause pancreas agenesis and neonatal diabetes. Using mouse and human genetic models, we show that this enhancer activates an entire PTF1A enhancer cluster in early pancreatic multipotent progenitors. This leading role, therefore, precludes functional redundancy. We further demonstrate that transient expression of PTF1A in multipotent progenitors sets in motion an epigenetic cascade that is required for duct and endocrine differentiation. These findings shed insights into the genome regulatory mechanisms that drive pancreas differentiation. Furthermore, they reveal an enhancer that acts as a regulatory master key and is thus vulnerable to pathogenic loss-of-function mutations. The pancreas agenesis enhancer (EnhP) activates PTF1A in early pancreatic progenitors EnhP also activates other progenitor PTF1A enhancers This master key function explains why EnhP is vulnerable to loss-of-function mutations Transient PTF1A expression in progenitors controls pancreas growth and endocrinogenesis
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Affiliation(s)
- Irene Miguel-Escalada
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain.
| | - Miguel Ángel Maestro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Diego Balboa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Aina Bernal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Edgar Bernardo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Vanessa Grau
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Javier García-Hurtado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Spain; Genetics and Genomics Section, Department of Metabolism, Digestion and Reproduction, National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, Imperial College London, London W12 0NN, UK; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
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Taleb Z, Karpowicz P. Circadian regulation of digestive and metabolic tissues. Am J Physiol Cell Physiol 2022; 323:C306-C321. [PMID: 35675638 DOI: 10.1152/ajpcell.00166.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The circadian clock is a self-sustained molecular timekeeper that drives 24-h (circadian) rhythms in animals. The clock governs important aspects of behavior and physiology including wake/sleep activity cycles that regulate the activity of metabolic and digestive systems. Light/dark cycles (photoperiod) and cycles in the time of feeding synchronize the circadian clock to the surrounding environment, providing an anticipatory benefit that promotes digestive health. The availability of animal models targeting the genetic components of the circadian clock has made it possible to investigate the circadian clock's role in cellular functions. Circadian clock genes have been shown to regulate the physiological function of hepatocytes, gastrointestinal cells, and adipocytes; disruption of the circadian clock leads to the exacerbation of liver diseases and liver cancer, inflammatory bowel disease and colorectal cancer, and obesity. Previous findings provide strong evidence that the circadian clock plays an integral role in digestive/metabolic disease pathogenesis, hence, the circadian clock is a necessary component in metabolic and digestive health and homeostasis. Circadian rhythms and circadian clock function provide an opportunity to improve the prevention and treatment of digestive and metabolic diseases by aligning digestive system tissue with the 24-h day.
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Affiliation(s)
- Zainab Taleb
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
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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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Toren E, Liu Y, Bethea M, Wade A, Hunter CS. The Ldb1 transcriptional co-regulator is required for establishment and maintenance of the pancreatic endocrine lineage. FASEB J 2022; 36:e22460. [PMID: 35881062 PMCID: PMC9397370 DOI: 10.1096/fj.202200410r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/26/2022] [Accepted: 07/08/2022] [Indexed: 11/11/2022]
Abstract
Pancreatic islet cell development is regulated by transcription factors (TFs) that mediate embryonic progenitor differentiation toward mature endocrine cells. Prior studies from our lab and others showed that the islet-enriched TF, Islet-1 (Isl1), interacts with the broadly-expressed transcriptional co-regulator, Ldb1, to regulate islet cell maturation and postnhyperatal function (by embryonic day (E)18.5). However, Ldb1 is expressed in the developing pancreas prior to Isl1 expression, notably in multipotent progenitor cells (MPCs) marked by Pdx1 and endocrine progenitors (EPs) expressing Neurogenin-3 (Ngn3). MPCs give rise to the endocrine and exocrine pancreas, while Ngn3+ EPs specify pancreatic islet endocrine cells. We hypothesized that Ldb1 is required for progenitor identity in MPC and EP populations during development to impact islet appearance and function. To test this, we generated a whole-pancreas Ldb1 knockout, termed Ldb1ΔPanc , and observed severe developmental and postnatal pancreas defects including disorganized progenitor pools, a significant reduction of Ngn3-expressing EPs, Pdx1HI β-cells, and early hormone+ cells. Ldb1ΔPanc neonates presented with severe hyperglycemia, hypoinsulinemia, and drastically reduced hormone expression in islets, yet no change in total pancreas mass. This supports the endocrine-specific actions of Ldb1. Considering this, we also developed an endocrine-enriched model of Ldb1 loss, termed Ldb1ΔEndo . We observed similar dysglycemia in this model, as well as a loss of islet identity markers. Through in vitro and in vivo chromatin immunoprecipitation experiments, we found that Ldb1 occupies key Pdx1 and Ngn3 promoter domains. Our findings provide insight into novel regulation of endocrine cell differentiation that may be vital toward improving cell-based diabetes therapies.
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Affiliation(s)
- Eliana Toren
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yanping Liu
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maigen Bethea
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alexa Wade
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chad S Hunter
- Comprehensive Diabetes Center and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Kwak D, Olsen PA, Danielsen A, Jensenius AR. A trio of biological rhythms and their relevance in rhythmic mechanical stimulation of cell cultures. Front Psychol 2022; 13:867191. [PMID: 35967633 PMCID: PMC9374063 DOI: 10.3389/fpsyg.2022.867191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
The primary aim of this article is to provide a biological rhythm model based on previous theoretical and experimental findings to promote more comprehensive studies of rhythmic mechanical stimulation of cell cultures, which relates to tissue engineering and regenerative medicine fields. Through an interdisciplinary approach where different standpoints from biology and musicology are combined, we explore some of the core rhythmic features of biological and cellular rhythmic processes and present them as a trio model that aims to afford a basic but fundamental understanding of the connections between various biological rhythms. It is vital to highlight such links since rhythmic mechanical stimulation and its effect on cell cultures are vastly underexplored even though the cellular response to mechanical stimuli (mechanotransduction) has been studied widely and relevant experimental evidence suggests mechanotransduction processes are rhythmic.
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Affiliation(s)
- Dongho Kwak
- Department of Musicology, RITMO Centre for Interdisciplinary Studies in Rhythm, Time and Motion, University of Oslo, Oslo, Norway
- *Correspondence: Dongho Kwak,
| | - Petter Angell Olsen
- Hybrid Technology Hub-Centre for Organ on a Chip-Technology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Unit for Cell Signaling, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Anne Danielsen
- Department of Musicology, RITMO Centre for Interdisciplinary Studies in Rhythm, Time and Motion, University of Oslo, Oslo, Norway
| | - Alexander Refsum Jensenius
- Department of Musicology, RITMO Centre for Interdisciplinary Studies in Rhythm, Time and Motion, University of Oslo, Oslo, Norway
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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: 5] [Impact Index Per Article: 2.5] [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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Alachkar A, Lee J, Asthana K, Vakil Monfared R, Chen J, Alhassen S, Samad M, Wood M, Mayer EA, Baldi P. The hidden link between circadian entropy and mental health disorders. Transl Psychiatry 2022; 12:281. [PMID: 35835742 PMCID: PMC9283542 DOI: 10.1038/s41398-022-02028-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The high overlapping nature of various features across multiple mental health disorders suggests the existence of common psychopathology factor(s) (p-factors) that mediate similar phenotypic presentations across distinct but relatable disorders. In this perspective, we argue that circadian rhythm disruption (CRD) is a common underlying p-factor that bridges across mental health disorders within their age and sex contexts. We present and analyze evidence from the literature for the critical roles circadian rhythmicity plays in regulating mental, emotional, and behavioral functions throughout the lifespan. A review of the literature shows that coarse CRD, such as sleep disruption, is prevalent in all mental health disorders at the level of etiological and pathophysiological mechanisms and clinical phenotypical manifestations. Finally, we discuss the subtle interplay of CRD with sex in relation to these disorders across different stages of life. Our perspective highlights the need to shift investigations towards molecular levels, for instance, by using spatiotemporal circadian "omic" studies in animal models to identify the complex and causal relationships between CRD and mental health disorders.
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Affiliation(s)
- Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA, USA. .,Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA. .,Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA, USA.
| | - Justine Lee
- grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA USA
| | - Kalyani Asthana
- grid.266093.80000 0001 0668 7243Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA USA
| | - Roudabeh Vakil Monfared
- grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA USA
| | - Jiaqi Chen
- grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA USA
| | - Sammy Alhassen
- grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA USA
| | - Muntaha Samad
- grid.266093.80000 0001 0668 7243Institute for Genomics and Bioinformatics, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA USA
| | - Marcelo Wood
- grid.266093.80000 0001 0668 7243Institute for Genomics and Bioinformatics, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Department of Neurobiology and Behavior, School of Biological Sciences, University of California, Irvine, CA USA
| | - Emeran A. Mayer
- grid.266093.80000 0001 0668 7243Institute for Genomics and Bioinformatics, University of California, Irvine, CA USA ,grid.19006.3e0000 0000 9632 6718G. Oppenheimer Center of Neurobiology of Stress & Resilience and Goldman Luskin Microbiome Center, Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, CA USA
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA. .,Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA, USA. .,Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA, USA.
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Targeting NMDA receptors in neuropsychiatric disorders by drug screening on human neurons derived from pluripotent stem cells. Transl Psychiatry 2022; 12:243. [PMID: 35680847 PMCID: PMC9184461 DOI: 10.1038/s41398-022-02010-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 01/04/2023] Open
Abstract
NMDA receptors (NMDARs), a prominent subtype of glutamatergic receptors, are implicated in the pathogenesis and development of neuropsychiatric disorders such as epilepsy, intellectual disability, autism spectrum disorder, and schizophrenia, and are therefore a potential therapeutic target in treating these disorders. Neurons derived from induced pluripotent stem cells (iPSCs) have provided the opportunity to investigate human NMDARs in their native environment. In this review, we describe the expression, function, and regulation of NMDARs in human iPSC-derived neurons and discuss approaches for utilizing human neurons for identifying potential drugs that target NMDARs in the treatment of neuropsychiatric disorders. A challenge in studying NMDARs in human iPSC-derived neurons is a predominance of those receptors containing the GluN2B subunit and low synaptic expression, suggesting a relatively immature phenotype of these neurons and delayed development of functional NMDARs. We outline potential approaches for improving neuronal maturation of human iPSC-derived neurons and accelerating the functional expression of NMDARs. Acceleration of functional expression of NMDARs in human iPSC-derived neurons will improve the modeling of neuropsychiatric disorders and facilitate the discovery and development of novel therapeutics targeting NMDARs for the treatment of these disorders.
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Abstract
The ability to maintain normoglycaemia, through glucose-sensitive insulin release, is a key aspect of postnatal beta cell function. However, terminally differentiated beta cell identity does not necessarily imply functional maturity. Beta cell maturation is therefore a continuation of beta cell development, albeit a process that occurs postnatally in mammals. Although many important features have been identified in the study of beta cell maturation, as of yet no unified mechanistic model of beta cell functional maturity exists. Here, we review recent findings about the underlying mechanisms of beta cell functional maturation. These findings include systemic hormonal and nutritional triggers that operate through energy-sensing machinery shifts within beta cells, resulting in primed metabolic states that allow for appropriate glucose trafficking and, ultimately, insulin release. We also draw attention to the expansive synergistic nature of these pathways and emphasise that beta cell maturation is dependent on overlapping regulatory and metabolic networks.
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Affiliation(s)
- Tom Barsby
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
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Basile G, Qadir MMF, Mauvais-Jarvis F, Vetere A, Shoba V, Modell AE, Pastori RL, Russ HA, Wagner BK, Dominguez-Bendala J. Emerging diabetes therapies: Bringing back the β-cells. Mol Metab 2022; 60:101477. [PMID: 35331962 PMCID: PMC8987999 DOI: 10.1016/j.molmet.2022.101477] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Stem cell therapies are finally coming of age as a viable alternative to pancreatic islet transplantation for the treatment of insulin-dependent diabetes. Several clinical trials using human embryonic stem cell (hESC)-derived β-like cells are currently underway, with encouraging preliminary results. Remaining challenges notwithstanding, these strategies are widely expected to reduce our reliance on human isolated islets for transplantation procedures, making cell therapies available to millions of diabetic patients. At the same time, advances in our understanding of pancreatic cell plasticity and the molecular mechanisms behind β-cell replication and regeneration have spawned a multitude of translational efforts aimed at inducing β-cell replenishment in situ through pharmacological means, thus circumventing the need for transplantation. SCOPE OF REVIEW We discuss here the current state of the art in hESC transplantation, as well as the parallel quest to discover agents capable of either preserving the residual mass of β-cells or inducing their proliferation, transdifferentiation or differentiation from progenitor cells. MAJOR CONCLUSIONS Stem cell-based replacement therapies in the mold of islet transplantation are already around the corner, but a permanent cure for type 1 diabetes will likely require the endogenous regeneration of β-cells aided by interventions to restore the immune balance. The promise of current research avenues and a strong pipeline of clinical trials designed to tackle these challenges bode well for the realization of this goal.
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Affiliation(s)
- G Basile
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - M M F Qadir
- Tulane University School of Medicine, New Orleans, LA, USA; Southeast Louisiana Veterans Affairs Medical Center, New Orleans, LA, USA
| | - F Mauvais-Jarvis
- Tulane University School of Medicine, New Orleans, LA, USA; Southeast Louisiana Veterans Affairs Medical Center, New Orleans, LA, USA
| | - A Vetere
- Broad Institute, Cambridge, MA, USA
| | - V Shoba
- Broad Institute, Cambridge, MA, USA
| | | | - R L Pastori
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - H A Russ
- Barbara Davis Center for Diabetes, Colorado University Anschutz Medical Campus, Aurora, CO, USA.
| | | | - J Dominguez-Bendala
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
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Yoshihara E. Adapting Physiology in Functional Human Islet Organogenesis. Front Cell Dev Biol 2022; 10:854604. [PMID: 35557947 PMCID: PMC9086403 DOI: 10.3389/fcell.2022.854604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/22/2022] [Indexed: 01/07/2023] Open
Abstract
Generation of three-dimensional (3D)-structured functional human islets is expected to be an alternative cell source for cadaveric human islet transplantation for the treatment of insulin-dependent diabetes. Human pluripotent stem cells (hPSCs), such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), offer infinite resources for newly synthesized human islets. Recent advancements in hPSCs technology have enabled direct differentiation to human islet-like clusters, which can sense glucose and secrete insulin, and those islet clusters can ameliorate diabetes when transplanted into rodents or non-human primates (NHPs). However, the generated hPSC-derived human islet-like clusters are functionally immature compared with primary human islets. There remains a challenge to establish a technology to create fully functional human islets in vitro, which are functionally and transcriptionally indistinguishable from cadaveric human islets. Understanding the complex differentiation and maturation pathway is necessary to generate fully functional human islets for a tremendous supply of high-quality human islets with less batch-to-batch difference for millions of patients. In this review, I summarized the current progress in the generation of 3D-structured human islets from pluripotent stem cells and discussed the importance of adapting physiology for in vitro functional human islet organogenesis and possible improvements with environmental cues.
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Affiliation(s)
- Eiji Yoshihara
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States.,David Geffen School of Medicine at University of California, Los Angeles, CA, United States
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48
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Shao Y, Fu J. Engineering multiscale structural orders for high-fidelity embryoids and organoids. Cell Stem Cell 2022; 29:722-743. [PMID: 35523138 PMCID: PMC9097334 DOI: 10.1016/j.stem.2022.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.
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Affiliation(s)
- Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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49
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Tremmel DM, Sackett SD, Feeney AK, Mitchell SA, Schaid MD, Polyak E, Chlebeck PJ, Gupta S, Kimple ME, Fernandez LA, Odorico JS. A human pancreatic ECM hydrogel optimized for 3-D modeling of the islet microenvironment. Sci Rep 2022; 12:7188. [PMID: 35504932 PMCID: PMC9065104 DOI: 10.1038/s41598-022-11085-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
Extracellular matrix (ECM) plays a multitude of roles, including supporting cells through structural and biochemical interactions. ECM is damaged in the process of isolating human islets for clinical transplantation and basic research. A platform in which islets can be cultured in contact with natural pancreatic ECM is desirable to better understand and support islet health, and to recapitulate the native islet environment. Our study demonstrates the derivation of a practical and durable hydrogel from decellularized human pancreas that supports human islet survival and function. Islets embedded in this hydrogel show increased glucose- and KCl-stimulated insulin secretion, and improved mitochondrial function compared to islets cultured without pancreatic matrix. In extended culture, hydrogel co-culture significantly reduced levels of apoptosis compared to suspension culture and preserved controlled glucose-responsive function. Isolated islets displayed altered endocrine and non-endocrine cell arrangement compared to in situ islets; hydrogel preserved an islet architecture more similar to that observed in situ. RNA sequencing confirmed that gene expression differences between islets cultured in suspension and hydrogel largely fell within gene ontology terms related to extracellular signaling and adhesion. Natural pancreatic ECM improves the survival and physiology of isolated human islets.
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Affiliation(s)
- Daniel M Tremmel
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sara Dutton Sackett
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
| | - Austin K Feeney
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha A Mitchell
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael D Schaid
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Erzsebet Polyak
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Peter J Chlebeck
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Sakar Gupta
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Michelle E Kimple
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | | | - Jon S Odorico
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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He X, Di R, Guo X, Cao X, Zhou M, Li X, Xia Q, Wang X, Zhang J, Zhang X, Liu Q, Chu M. Transcriptomic Changes of Photoperiodic Response in the Hypothalamus Were Identified in Ovariectomized and Estradiol-Treated Sheep. Front Mol Biosci 2022; 9:848144. [PMID: 35480892 PMCID: PMC9036065 DOI: 10.3389/fmolb.2022.848144] [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: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 01/11/2023] Open
Abstract
Accurate timing of seasonal changes is an essential ability for an animal’s survival, and the change in the photoperiod is the key factor affecting reproductive seasonality in mammals. Emerging evidence has suggested that multiple hypothalamic genes participate in the photoperiod-induced regulation of reproductive activities in sheep, but the mechanism is still unclear. In this study, we initially examined the plasma level of two major reproductive hormones, namely, follicle-stimulating hormone (FSH) and prolactin (PRL), under different photoperiods in ovariectomized and estradiol-treated (OVX + E2) sheep using radioimmunoassay (RIA). Of the two hormones, the concentration of PRL significantly increased with the extension of the photoperiod, while FSH showed the opposite trend. Subsequently, an examination of the transcriptomic variation between the short photoperiod (SP) and long photoperiod (LP) was conducted. Differential expression analyses and functional annotation showed that several key genes in the insulin secretion (VAMP2, PRKACB, PRKCG, and PLCB1), GnRH (MAPK13, CGA, CDC42, ATF4, and LHB) pathways, and circadian entrainment (KCNJ5, PER1, GNB2, MTNR1A, and RASD1), as well as numerous lncRNAs, including XR_173257.3, XR_173415.3, XR_001435315.1, XR_001024596.2, and XR_001023464.2, were shown potentially vital for the hypothalamic photoperiodic response. Four of the differentially expressed mRNAs and lncRNAs were validated by qPCR. The constructed mRNA–mRNA interaction networks further revealed that transcripts potentially participated in hypothalamic thyroid hormone synthesis, endocrine resistance, and neuroactive ligand–receptor interactions. The interactome analysis of lncRNAs and their targets implied that XR_173257.3 and its target arylalkylamine N-acetyltransferase (AANAT) and XR_173415.3 and its target TH might participate in the regulation of seasonal reproduction. Together, the changes in reproductive hormones and transcriptome will help to determine the important photoperiod-induced lncRNAs and mRNAs and provide a valuable resource for further research on reproductive seasonality in sheep.
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Affiliation(s)
- Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofei Guo
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaohan Cao
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Zhou
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyu Li
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Qiuyue Liu, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Qiuyue Liu, ; Mingxing Chu,
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