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Haberman N, Cheung R, Pizza G, Cvetesic N, Nagy D, Maude H, Blazquez L, Lenhard B, Cebola I, Rutter GA, Martinez-Sanchez A. Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. FASEB J 2024; 38:e23885. [PMID: 39139039 PMCID: PMC11378476 DOI: 10.1096/fj.202401078r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell-selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors (TFs) important for β-cell identity, such as FOXA, MAFA or RFX6, and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
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Affiliation(s)
- Nejc Haberman
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Rebecca Cheung
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Grazia Pizza
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Nevena Cvetesic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Dorka Nagy
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Lorea Blazquez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Lee Kong Chian Medical School, Nanyang Technological University, Singapore, Singapore
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
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2
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Laver TW, Wakeling MN, Caswell RC, Bunce B, Yau D, Männistö JME, Houghton JAL, Hopkins JJ, Weedon MN, Saraff V, Kershaw M, Honey EM, Murphy N, Giri D, Nath S, Tangari Saredo A, Banerjee I, Hussain K, Owens NDL, Flanagan SE. Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements. Eur J Hum Genet 2024; 32:813-818. [PMID: 38605124 PMCID: PMC11220097 DOI: 10.1038/s41431-024-01593-z] [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: 09/14/2023] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Persistent congenital hyperinsulinism (HI) is a rare genetically heterogeneous condition characterised by dysregulated insulin secretion leading to life-threatening hypoglycaemia. For up to 50% of affected individuals screening of the known HI genes does not identify a disease-causing variant. Large deletions have previously been used to identify novel regulatory regions causing HI. Here, we used genome sequencing to search for novel large (>1 Mb) deletions in 180 probands with HI of unknown cause and replicated our findings in a large cohort of 883 genetically unsolved individuals with HI using off-target copy number variant calling from targeted gene panels. We identified overlapping heterozygous deletions in five individuals (range 3-8 Mb) spanning chromosome 20p11.2. The pancreatic beta-cell transcription factor gene, FOXA2, a known cause of HI was deleted in two of the five individuals. In the remaining three, we found a minimal deleted region of 2.4 Mb adjacent to FOXA2 that encompasses multiple non-coding regulatory elements that are in conformational contact with FOXA2. Our data suggests that the deletions in these three children may cause disease through the dysregulation of FOXA2 expression. These findings provide new insights into the regulation of FOXA2 in the beta-cell and confirm an aetiological role for chromosome 20p11.2 deletions in syndromic HI.
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Affiliation(s)
- Thomas W Laver
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Matthew N Wakeling
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Richard C Caswell
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Benjamin Bunce
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Daphne Yau
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Jonna M E Männistö
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Health Sciences, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jayne A L Houghton
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jasmin J Hopkins
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Vrinda Saraff
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Melanie Kershaw
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nuala Murphy
- Department of Paediatric Endocrinology, Children's University Hospital, Dublin, Ireland
| | - Dinesh Giri
- Department of Paediatric Endocrinology, Bristol Royal Hospital for Children, Bristol, UK
| | | | | | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Khalid Hussain
- Department of Paediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Nick D L Owens
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK.
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3
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Haberman N, Cheung R, Pizza G, Cvetesic N, Nagy D, Maude H, Blazquez L, Lenhard B, Cebola I, Rutter GA, Martinez-Sanchez A. Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593867. [PMID: 38798508 PMCID: PMC11118353 DOI: 10.1101/2024.05.13.593867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell- selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors important for β-cell identity, such as FOXA, MAFA or RFX6 and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
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4
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Yan D, Lv M, Kong X, Feng L, Ying Y, Liu W, Wang X, Ma X. FXR controls insulin content by regulating Foxa2-mediated insulin transcription. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119655. [PMID: 38135007 DOI: 10.1016/j.bbamcr.2023.119655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Farnesoid X receptor (FXR) is a nuclear ligand-activated receptor of bile acids that plays a role in the modulation of insulin content. However, the underlying molecular mechanisms remain unclear. Forkhead box a2 (Foxa2) is an important nuclear transcription factor in pancreatic β-cells and is involved in β-cell function. We aimed to explore the signaling mechanism downstream of FXR to regulate insulin content and underscore its association with Foxa2 and insulin gene (Ins) transcription. All experiments were conducted on FXR transgenic mice, INS-1 823/13 cells, and diabetic Goto-Kakizaki (GK) rats undergoing sham or Roux-en-Y gastric bypass (RYGB) surgery. Islets from FXR knockout mice and INS-1823/13 cells with FXR knockdown exhibited substantially lower insulin levels than that of controls. This was accompanied by decreased Foxa2 expression and Ins transcription. Conversely, FXR overexpression increased insulin content, concomitant with enhanced Foxa2 expression and Ins transcription in INS-1 823/13 cells. Moreover, FXR knockdown reduced FXR recruitment and H3K27 trimethylation in the Foxa2 promoter. Importantly, Foxa2 overexpression abrogated the adverse effects of FXR knockdown on Ins transcription and insulin content in INS-1 823/13 cells. Notably, RYGB surgery led to improved insulin content in diabetic GK rats, which was accompanied by upregulated FXR and Foxa2 expression and Ins transcription. Collectively, these data suggest that Foxa2 serves as the target gene of FXR in β-cells and mediates FXR-enhanced Ins transcription. Additionally, the upregulated FXR/Foxa2 signaling cascade could contribute to the enhanced insulin content in diabetic GK rats after RYGB.
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Affiliation(s)
- Dan Yan
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China.
| | - Moyang Lv
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, PR China
| | - Xiangchen Kong
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
| | - Linxian Feng
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
| | - Ying Ying
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
| | - Wenjuan Liu
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
| | - Xin Wang
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
| | - Xiaosong Ma
- Shenzhen University Diabetes Institute, Medical School, Shenzhen University, Shenzhen 518060, PR China
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5
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Jarc L, Bandral M, Zanfrini E, Lesche M, Kufrin V, Sendra R, Pezzolla D, Giannios I, Khattak S, Neumann K, Ludwig B, Gavalas A. Regulation of multiple signaling pathways promotes the consistent expansion of human pancreatic progenitors in defined conditions. eLife 2024; 12:RP89962. [PMID: 38180318 PMCID: PMC10945307 DOI: 10.7554/elife.89962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The unlimited expansion of human progenitor cells in vitro could unlock many prospects for regenerative medicine. However, it remains an important challenge as it requires the decoupling of the mechanisms supporting progenitor self-renewal and expansion from those mechanisms promoting their differentiation. This study focuses on the expansion of human pluripotent stem (hPS) cell-derived pancreatic progenitors (PP) to advance novel therapies for diabetes. We obtained mechanistic insights into PP expansion requirements and identified conditions for the robust and unlimited expansion of hPS cell-derived PP cells under GMP-compliant conditions through a hypothesis-driven iterative approach. We show that the combined stimulation of specific mitogenic pathways, suppression of retinoic acid signaling, and inhibition of selected branches of the TGFβ and Wnt signaling pathways are necessary for the effective decoupling of PP proliferation from differentiation. This enabled the reproducible, 2000-fold, over 10 passages and 40-45 d, expansion of PDX1+/SOX9+/NKX6-1+ PP cells. Transcriptome analyses confirmed the stabilization of PP identity and the effective suppression of differentiation. Using these conditions, PDX1+/SOX9+/NKX6-1+ PP cells, derived from different, both XY and XX, hPS cell lines, were enriched to nearly 90% homogeneity and expanded with very similar kinetics and efficiency. Furthermore, non-expanded and expanded PP cells, from different hPS cell lines, were differentiated in microwells into homogeneous islet-like clusters (SC-islets) with very similar efficiency. These clusters contained abundant β-cells of comparable functionality as assessed by glucose-stimulated insulin secretion assays. These findings established the signaling requirements to decouple PP proliferation from differentiation and allowed the consistent expansion of hPS cell-derived PP cells. They will enable the establishment of large banks of GMP-produced PP cells derived from diverse hPS cell lines. This approach will streamline SC-islet production for further development of the differentiation process, diabetes research, personalized medicine, and cell therapies.
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Affiliation(s)
- Luka Jarc
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Manuj Bandral
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Elisa Zanfrini
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Mathias Lesche
- Dresden Concept Genome Centre (DcGC), TU DresdenDresdenGermany
- Center for Molecular and Cellular Bioengineering (CMCB) Technology Platform, TU DresdenDresdenGermany
| | - Vida Kufrin
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
| | - Raquel Sendra
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
| | - Daniela Pezzolla
- German Centre for Diabetes Research (DZD)MunichGermany
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU DresdenDresdenGermany
| | - Ioannis Giannios
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
| | - Shahryar Khattak
- Stem Cell Engineering Facility, (SCEF), CRTD, Faculty of Medicine, TU DresdenDresdenGermany
| | - Katrin Neumann
- Stem Cell Engineering Facility, (SCEF), CRTD, Faculty of Medicine, TU DresdenDresdenGermany
| | - Barbara Ludwig
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU DresdenDresdenGermany
- Department of Medicine III, University Hospital Carl Gustav Carus and Faculty of Medicine, TU DresdenDresdenGermany
| | - Anthony Gavalas
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Centre for Diabetes Research (DZD)MunichGermany
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6
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Mandatori S, Liu Y, Marturia-Navarro J, Hadi M, Henriksen K, Zheng J, Rasmussen LM, Rizza S, Kaestner KH, Issazadeh-Navikas S. PRKAG2.2 is essential for FoxA1 + regulatory T cell differentiation and metabolic rewiring distinct from FoxP3 + regulatory T cells. SCIENCE ADVANCES 2023; 9:eadj8442. [PMID: 38117896 PMCID: PMC10732530 DOI: 10.1126/sciadv.adj8442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/20/2023] [Indexed: 12/22/2023]
Abstract
Forkhead box A1 (FoxA1)+ regulatory T cells (Tregs) exhibit distinct characteristics from FoxP3+ Tregs while equally effective in exerting anti-inflammatory properties. The role of FoxP3+ Tregs in vivo has been challenged, motivating a better understanding of other Tregs in modulating hyperactive immune responses. FoxA1+ Tregs are generated on activation of the transcription factor FoxA1 by interferon-β (IFNβ), an anti-inflammatory cytokine. T cell activation, expansion, and function hinge on metabolic adaptability. We demonstrated that IFNβ promotes a metabolic rearrangement of FoxA1+ Tregs by enhancing oxidative phosphorylation and mitochondria clearance by mitophagy. In response to IFNβ, FoxA1 induces a specific transcription variant of adenosine 5'-monophosphate-activated protein kinase (AMPK) γ2 subunit, PRKAG2.2. This leads to the activation of AMPK signaling, thereby enhancing mitochondrial respiration and mitophagy by ULK1-BNIP3. This IFNβ-FoxA1-PRKAG2.2-BNIP3 axis is pivotal for their suppressive function. The involvement of PRKAG2.2 in FoxA1+ Treg, not FoxP3+ Treg differentiation, underscores the metabolic differences between Treg populations and suggests potential therapeutic targets for autoimmune diseases.
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Affiliation(s)
- Sara Mandatori
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yawei Liu
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joana Marturia-Navarro
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mahdieh Hadi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Henriksen
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jin Zheng
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louise Munk Rasmussen
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Klaus H. Kaestner
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Hudaiberdiev S, Taylor DL, Song W, Narisu N, Bhuiyan RM, Taylor HJ, Tang X, Yan T, Swift AJ, Bonnycastle LL, Consortium DIAMANTE, Chen S, Stitzel ML, Erdos MR, Ovcharenko I, Collins FS. Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits. Proc Natl Acad Sci U S A 2023; 120:e2206612120. [PMID: 37603758 PMCID: PMC10469333 DOI: 10.1073/pnas.2206612120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/19/2023] [Indexed: 08/23/2023] Open
Abstract
Genetic association studies have identified hundreds of independent signals associated with type 2 diabetes (T2D) and related traits. Despite these successes, the identification of specific causal variants underlying a genetic association signal remains challenging. In this study, we describe a deep learning (DL) method to analyze the impact of sequence variants on enhancers. Focusing on pancreatic islets, a T2D relevant tissue, we show that our model learns islet-specific transcription factor (TF) regulatory patterns and can be used to prioritize candidate causal variants. At 101 genetic signals associated with T2D and related glycemic traits where multiple variants occur in linkage disequilibrium, our method nominates a single causal variant for each association signal, including three variants previously shown to alter reporter activity in islet-relevant cell types. For another signal associated with blood glucose levels, we biochemically test all candidate causal variants from statistical fine-mapping using a pancreatic islet beta cell line and show biochemical evidence of allelic effects on TF binding for the model-prioritized variant. To aid in future research, we publicly distribute our model and islet enhancer perturbation scores across ~67 million genetic variants. We anticipate that DL methods like the one presented in this study will enhance the prioritization of candidate causal variants for functional studies.
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Affiliation(s)
- Sanjarbek Hudaiberdiev
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20892
| | - D. Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Wei Song
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20892
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Redwan M. Bhuiyan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT06032
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT06032
| | - Henry J. Taylor
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CambridgeCB1 8RN, UK
| | - Xuming Tang
- Department of Surgery, Weill Cornell Medicine, New York, NY10065
- Center for Genomic Health, Weill Cornell Medicine, New York, NY10065
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Amy J. Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Lori L. Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - DIAMANTE Consortium
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20892
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
- The Jackson Laboratory for Genomic Medicine, Farmington, CT06032
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT06032
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CambridgeCB1 8RN, UK
- Department of Surgery, Weill Cornell Medicine, New York, NY10065
- Center for Genomic Health, Weill Cornell Medicine, New York, NY10065
- Institute of Systems Genomics, University of Connecticut, Farmington, CT06032
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY10065
- Center for Genomic Health, Weill Cornell Medicine, New York, NY10065
| | - Michael L. Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT06032
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT06032
- Institute of Systems Genomics, University of Connecticut, Farmington, CT06032
| | - Michael R. Erdos
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20892
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
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8
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Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep 2023; 42:112821. [PMID: 37467106 DOI: 10.1016/j.celrep.2023.112821] [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: 11/17/2021] [Revised: 11/03/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) enriched in ER+ endocrine-resistant (EndoR) cells. We identify Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, as a strong predictor for poor outcomes of ER+ BC. It is elevated in ER+ metastases vs. primary tumors, irrespective of ESR1 mutations. Genomic ER binding near Secretome14 genes is also increased in mutant ER-expressing or mitogen-treated ER+ BC cells and in ER+ metastatic vs. primary tumors, suggesting a convergent pathway including high growth factor receptor signaling in activating pro-metastatic secretome genes. Our findings uncover H-FOXA1-induced ER reprogramming that drives EndoR and metastasis partly via an H-FOXA1/ER-dependent secretome.
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Affiliation(s)
- Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Resel Pereira
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Chia Liu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Martin J Shea
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lanfang Qin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamika Mitchell
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria L Cataldo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Jamunarani Veeraraghavan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vidyalakshmi Sethunath
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mario Giuliano
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carolina Gutierrez
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1085 Budapest, Hungary; RCNS Cancer Biomarker Research Group, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary
| | - Meghana V Trivedi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA; Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02210, USA
| | - Mothaffar F Rimawi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - C Kent Osborne
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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9
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Rogerson C, Sciacovelli M, Maddalena LA, Pouikli A, Segarra-Mondejar M, Valcarcel-Jimenez L, Schmidt C, Yang M, Ivanova E, Kent J, Mora A, Cheeseman D, Carroll JS, Kelsey G, Frezza C. FOXA2 controls the anti-oxidant response in FH-deficient cells. Cell Rep 2023; 42:112751. [PMID: 37405921 PMCID: PMC10391629 DOI: 10.1016/j.celrep.2023.112751] [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: 10/14/2022] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a cancer syndrome caused by inactivating germline mutations in fumarate hydratase (FH) and subsequent accumulation of fumarate. Fumarate accumulation leads to profound epigenetic changes and the activation of an anti-oxidant response via nuclear translocation of the transcription factor NRF2. The extent to which chromatin remodeling shapes this anti-oxidant response is currently unknown. Here, we explored the effects of FH loss on the chromatin landscape to identify transcription factor networks involved in the remodeled chromatin landscape of FH-deficient cells. We identify FOXA2 as a key transcription factor that regulates anti-oxidant response genes and subsequent metabolic rewiring cooperating without direct interaction with the anti-oxidant regulator NRF2. The identification of FOXA2 as an anti-oxidant regulator provides additional insights into the molecular mechanisms behind cell responses to fumarate accumulation and potentially provides further avenues for therapeutic intervention for HLRCC.
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Affiliation(s)
- Connor Rogerson
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Marco Sciacovelli
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Lucas A Maddalena
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Andromachi Pouikli
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD)
| | - Marc Segarra-Mondejar
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD)
| | - Lorea Valcarcel-Jimenez
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD)
| | - Christina Schmidt
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD)
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD)
| | - Elena Ivanova
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Joshua Kent
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ariane Mora
- School of Chemistry and Molecular Biosciences, University of Queensland, Molecular Biosciences Building 76, St Lucia, QLD 4072, Australia
| | - Danya Cheeseman
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Institute of Metabolic Science - Metabolic Research Laboratories, Cambridge, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD); University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD).
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10
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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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11
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Yu C, Li X, Zhao Y, Hu Y. The role of FOXA family transcription factors in glucolipid metabolism and NAFLD. Front Endocrinol (Lausanne) 2023; 14:1081500. [PMID: 36798663 PMCID: PMC9927216 DOI: 10.3389/fendo.2023.1081500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Abnormal glucose metabolism and lipid metabolism are common pathological processes in many metabolic diseases, such as nonalcoholic fatty liver disease (NAFLD). Many studies have shown that the forkhead box (FOX) protein subfamily FOXA has a role in regulating glucolipid metabolism and is closely related to hepatic steatosis and NAFLD. FOXA exhibits a wide range of functions ranging from the initiation steps of metabolism such as the development of the corresponding metabolic organs and the differentiation of cells, to multiple pathways of glucolipid metabolism, to end-of-life problems of metabolism such as age-related obesity. The purpose of this article is to review and discuss the currently known targets and signal transduction pathways of FOXA in glucolipid metabolism. To provide more experimental evidence and basis for further research and clinical application of FOXA in the regulation of glucolipid metabolism and the prevention and treatment of NAFLD.
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Affiliation(s)
- Chuchu Yu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaojing Li
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Zhao
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yu Zhao, ; Yiyang Hu,
| | - Yiyang Hu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Institute of Liver Diseases, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Clinical Pharmacology, Shuguang Hospital Affifiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yu Zhao, ; Yiyang Hu,
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12
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Warren I, Moeller MM, Guiggey D, Chiang A, Maloy M, Ogoke O, Groth T, Mon T, Meamardoost S, Liu X, Thompson S, Szeglowski A, Thompson R, Chen P, Paulmurugan R, Yarmush ML, Kidambi S, Parashurama N. FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells. FASEB J 2023; 37:e22652. [PMID: 36515690 DOI: 10.1096/fj.202101506rrr] [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: 09/22/2021] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 12/15/2022]
Abstract
FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA factors dictate human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in controlling hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA mediated knockdown of FOXA1/2 in HepG2 cells significantly downregulated albumin (p < .05) and GRN TF gene expression (HNF4α, HEX, HNF1ß, TBX3) (p < .05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid [GSC], FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < .05), all consistent with partial/transient reprograming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility of phenotype. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, with concomitant accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During human pluripotent stem cells (hPSC)-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate that FOXA1/2 controls hepatic and developmental GRN, and their knockdown leads to reprogramming of both differentiation and metabolism, with applications in studies of cancer, differentiation, and organogenesis.
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Affiliation(s)
- Iyan Warren
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Michael M Moeller
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Alexander Chiang
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Mitchell Maloy
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Theodore Groth
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Xiaojun Liu
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Sarah Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Antoni Szeglowski
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ryan Thompson
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Peter Chen
- Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Canary Center for Early Cancer Detection and the Molecular Imaging Program at Stanford, Stanford University, Palo Alto, California, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Srivatsan Kidambi
- Department of Chemical and Biomolecular Engineering, University of Nebraska- Lincoln, Lincoln, Nebraska, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA
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13
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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: 23] [Impact Index Per Article: 11.5] [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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14
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Zhang Z, Piro AL, Allalou A, Alexeeff SE, Dai FF, Gunderson EP, Wheeler MB. Prolactin and Maternal Metabolism in Women With a Recent GDM Pregnancy and Links to Future T2D: The SWIFT Study. J Clin Endocrinol Metab 2022; 107:2652-2665. [PMID: 35666146 PMCID: PMC9387721 DOI: 10.1210/clinem/dgac346] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Prolactin is a multifaceted hormone known to regulate lactation. In women with gestational diabetes mellitus (GDM) history, intensive lactation has been associated with lower relative risk of future type 2 diabetes (T2D). However, the role of prolactin in T2D development and maternal metabolism in women with a recent GDM pregnancy has not been ascertained. OBJECTIVE We examined the relationships among prolactin, future T2D risk, and key clinical and metabolic parameters. METHODS We utilized a prospective GDM research cohort (the SWIFT study) and followed T2D onset by performing 2-hour 75-g research oral glucose tolerance test (OGTT) at study baseline (6-9 weeks postpartum) and again annually for 2 years, and also by retrieving clinical diagnoses of T2D from 2 years through 10 years of follow up from electronic medical records. Targeted metabolomics and lipidomics were applied on fasting plasma samples collected at study baseline from 2-hour 75-g research OGTTs in a nested case-control study (100 future incident T2D cases vs 100 no T2D controls). RESULTS Decreasing prolactin quartiles were associated with increased future T2D risk (adjusted odds ratio 2.48; 95% CI, 0.81-7.58; P = 0.05). In women who maintained normoglycemia during the 10-year follow-up period, higher prolactin at baseline was associated with higher insulin sensitivity (P = 0.038) and HDL-cholesterol (P = 0.01), but lower BMI (P = 0.001) and leptin (P = 0.002). Remarkably, among women who developed future T2D, prolactin was not correlated with a favorable metabolic status (all P > 0.05). Metabolomics and lipidomics showed that lower circulating prolactin strongly correlated with a T2D-high risk lipid profile, with elevated circulating neutral lipids and lower concentrations of specific phospholipids/sphingolipids. CONCLUSION In women with recent GDM pregnancy, low circulating prolactin is associated with specific clinical and metabolic parameters and lipid metabolites linked to a high risk of developing T2D.
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Affiliation(s)
- Ziyi Zhang
- Department of Physiology, Faculty of Medicine, University of Toronto, Ontario M5S 1A8, Canada
- Department of Endocrinology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Anthony L Piro
- Department of Physiology, Faculty of Medicine, University of Toronto, Ontario M5S 1A8, Canada
| | - Amina Allalou
- Department of Physiology, Faculty of Medicine, University of Toronto, Ontario M5S 1A8, Canada
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Feihan F Dai
- Correspondence: Feihan F. Dai, PhD, Department of Physiology, Faculty of Medicine, University of Toronto, 1 King’s College Circle, M5S 1A8 Ontario, Canada.
| | - Erica P Gunderson
- Correspondence: Erica P. Gunderson, PhD, MS, MPH, Division of Research, Kaiser Permanente Northern California, 1 King’s College Circle, M5S 1A8 Oakland, CA, USA.
| | - Michael B Wheeler
- Correspondence: Michael B. Wheeler, PhD, Department of Physiology, Faculty of Medicine, University of Toronto, 1 King’s College Circle, M5S 1A8 Ontario, Canada.
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15
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Lien YC, Pinney SE, Lu XM, Simmons RA. Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets. Endocrinology 2022; 163:6459683. [PMID: 34894232 PMCID: PMC8743043 DOI: 10.1210/endocr/bqab251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 01/05/2023]
Abstract
Intrauterine growth restriction (IUGR) leads to the development of type 2 diabetes in adulthood, and the permanent alterations in gene expression implicate an epigenetic mechanism. Using a rat model of IUGR, we performed TrueSeq-HELP Tagging to assess the association of DNA methylation changes and gene dysregulation in islets. We identified 511 differentially methylated regions (DMRs) and 4377 significantly altered single CpG sites. Integrating the methylome and our published transcriptome data sets resulted in the identification of pathways critical for islet function. The identified DMRs were enriched with transcription factor binding motifs, such as Elk1, Etv1, Foxa1, Foxa2, Pax7, Stat3, Hnf1, and AR. In silico analysis of 3-dimensional chromosomal interactions using human pancreas and islet Hi-C data sets identified interactions between 14 highly conserved DMRs and 35 genes with significant expression changes at an early age, many of which persisted in adult islets. In adult islets, there were far more interactions between DMRs and genes with significant expression changes identified with Hi-C, and most of them were critical to islet metabolism and insulin secretion. The methylome was integrated with our published genome-wide histone modification data sets from IUGR islets, resulting in further characterization of important regulatory regions of the genome altered by IUGR containing both significant changes in DNA methylation and specific histone marks. We identified novel regulatory regions in islets after exposure to IUGR, suggesting that epigenetic changes at key transcription factor binding motifs and other gene regulatory regions may contribute to gene dysregulation and an abnormal islet phenotype in IUGR rats.
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Affiliation(s)
- Yu-Chin Lien
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sara E Pinney
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Perlman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xueqing Maggie Lu
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Perlman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Correspondence: Rebecca A. Simmons, MD, Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, the University of Pennsylvania, BRB II/III, 13th Fl, Rm 1308, 421 Curie Blvd, Philadelphia, PA 19104, USA.
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16
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Kumar A, Sundaram K, Teng Y, Mu J, Sriwastva MK, Zhang L, Hood JL, Yan J, Zhang X, Park JW, Merchant ML, Zhang HG. Ginger nanoparticles mediated induction of Foxa2 prevents high-fat diet-induced insulin resistance. Theranostics 2022; 12:1388-1403. [PMID: 35154496 PMCID: PMC8771553 DOI: 10.7150/thno.62514] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Rationale: The obesity epidemic has expanded globally, due in large part to the increased consumption of high-fat diets (HFD), and has increased the risk of major chronic diseases, including type 2 diabetes. Diet manipulation is the foundation of prevention and treatment of obesity and diabetes. The molecular mechanisms that mediate the diet-based prevention of insulin resistance, however, remain to be identified. Here, we report that treatment with orally administered ginger-derived nanoparticles (GDNP) prevents insulin resistance by restoring homeostasis in gut epithelial Foxa2 mediated signaling in mice fed a high-fat diet (HFD). Methods: Ginger-derived nanoparticles (GDNP) were added into drinking water to treat high-fat diet fed mice for at least one year or throughout their life span. A micro array profile of intestinal, liver and fat tissue of GDNP treated mice was used to analyze their gene expression profile. Genes associated with metabolism or insulin signaling were further quantified using the real time polymerase chain reaction (RT-PCR). Surface plasmon resonance (SPR) was used for determining the interaction between Foxa2 protein and phosphatic acid lipid nanoparticles. Results: HFD-feeding inhibited the expression of Foxa2; the GDNPs increased the expression of Foxa2 and protected Foxa2 against Akt-1 mediated phosphorylation and subsequent inactivation of Foxa2. Increasing expression of Foxa2 leads to altering the composition of intestinal epithelial cell (IEC) exosomes of mice fed a HFD and prevents IEC exosome mediated insulin resistance. Collectively, oral administration of GDNP prevents insulin resistance in HFD mice. Interestingly, oral administration of GDNP also extended the life span of the mice and inhibited skin inflammation. Conclusion: Our findings showed that GDNP treatment can prevent HFD-induced obesity and insulin resistance via protecting the Foxa2 from Akt-1 mediated phosphorylation. GDNP treatment provides an alternative approach based on diet manipulation for the development of therapeutic interventions for obesity.
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Affiliation(s)
- Anil Kumar
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Kumaran Sundaram
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Yun Teng
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Jingyao Mu
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Mukesh K Sriwastva
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Lifeng Zhang
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Joshua L. Hood
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY40202, USA
| | - Jun Yan
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
| | - Xiang Zhang
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY40202, USA
| | - Juw Won Park
- Department of Computer Engineering and Computer Science, University of Louisville, KY40202, USA
- KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
| | - Michael L Merchant
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | - Huang-Ge Zhang
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, KY 40202, USA
- Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
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17
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Khetan S, Kales S, Kursawe R, Jillette A, Ulirsch JC, Reilly SK, Ucar D, Tewhey R, Stitzel ML. Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation. Nat Commun 2021; 12:5242. [PMID: 34475398 PMCID: PMC8413311 DOI: 10.1038/s41467-021-25514-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/10/2021] [Indexed: 11/08/2022] Open
Abstract
Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) at >250 loci in the human genome to type 2 diabetes (T2D) risk. For each locus, identifying the functional variant(s) among multiple SNPs in high linkage disequilibrium is critical to understand molecular mechanisms underlying T2D genetic risk. Using massively parallel reporter assays (MPRA), we test the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 β cells under steady state and pathophysiologic endoplasmic reticulum (ER) stress conditions. We identify 1,982/6,621 (29.9%) SNP-containing elements that activate transcription in MIN6 and 879 SNP alleles that modulate MPRA activity. Multiple T2D-associated SNPs alter the activity of short interspersed nuclear element (SINE)-containing elements that are strongly induced by ER stress. We identify 220 functional variants at 104 T2D association signals, narrowing 54 signals to a single candidate SNP. Together, this study identifies elements driving β cell steady state and ER stress-responsive transcriptional activation, nominates causal T2D SNPs, and uncovers potential roles for repetitive elements in β cell transcriptional stress response and T2D genetics.
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Affiliation(s)
- Shubham Khetan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
| | - Susan Kales
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Jacob C Ulirsch
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Ryan Tewhey
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
- Tufts University School of Medicine, Boston, MA, USA.
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA.
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, USA.
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18
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Bell S, McCarty V, Peng H, Jefri M, Hettige N, Antonyan L, Crapper L, O'Leary LA, Zhang X, Zhang Y, Wu H, Sutcliffe D, Kolobova I, Rosenberger TA, Moquin L, Gratton A, Popic J, Gantois I, Stumpf PS, Schuppert AA, Mechawar N, Sonenberg N, Tremblay ML, Jinnah HA, Ernst C. Lesch-Nyhan disease causes impaired energy metabolism and reduced developmental potential in midbrain dopaminergic cells. Stem Cell Reports 2021; 16:1749-1762. [PMID: 34214487 PMCID: PMC8282463 DOI: 10.1016/j.stemcr.2021.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 10/30/2022] Open
Abstract
Mutations in HPRT1, a gene encoding a rate-limiting enzyme for purine salvage, cause Lesch-Nyhan disease which is characterized by self-injury and motor impairments. We leveraged stem cell and genetic engineering technologies to model the disease in isogenic and patient-derived forebrain and midbrain cell types. Dopaminergic progenitor cells deficient in HPRT showed decreased intensity of all developmental cell-fate markers measured. Metabolic analyses revealed significant loss of all purine derivatives, except hypoxanthine, and impaired glycolysis and oxidative phosphorylation. real-time glucose tracing demonstrated increased shunting to the pentose phosphate pathway for de novo purine synthesis at the expense of ATP production. Purine depletion in dopaminergic progenitor cells resulted in loss of RHEB, impairing mTORC1 activation. These data demonstrate dopaminergic-specific effects of purine salvage deficiency and unexpectedly reveal that dopaminergic progenitor cells are programmed to a high-energy state prior to higher energy demands of terminally differentiated cells.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Vincent McCarty
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Liam Crapper
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Liam A O'Leary
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Ying Zhang
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Diane Sutcliffe
- Department of Neurology, Emory University, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Ilaria Kolobova
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Thad A Rosenberger
- Department of Pharmacology, Physiology, and Therapeutics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Luc Moquin
- Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Alain Gratton
- Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Jelena Popic
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Ilse Gantois
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Patrick S Stumpf
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Andreas A Schuppert
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Naguib Mechawar
- Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Michel L Tremblay
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Hyder A Jinnah
- Department of Neurology, Emory University, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA; Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Carl Ernst
- Psychiatric Genetics Group, McGill University, Montreal, QC, Canada; Department of Psychiatry, McGill University and Douglas Hospital Research Institute, 6875 LaSalle Boulevard, Frank Common Building, Room 2101.2, Montreal, QC H4H 1R3, Canada.
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19
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Dai P, Li J, Chen Y, Zhang L, Zhang X, Wang J, Qi G, Zhang Y. Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis. Front Cell Dev Biol 2021; 9:685494. [PMID: 34262902 PMCID: PMC8273515 DOI: 10.3389/fcell.2021.685494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
The transdifferentiation of adipose-derived mesenchymal stem cells (ADMSCs) into insulin-producing cells (IPCs) is a potential resource for the treatment of diabetes. However, the changes of genes and metabolic pathways on the transdifferentiation of ADMSCs into IPCs are largely unknown. In this study, the transdifferentiation of canine ADMSCs into IPCs was completed using five types of procedures. Absolute Quantitative Transcriptome Sequencing Analysis was performed at different stages of the optimal procedure. A total of 60,151 transcripts were obtained. Differentially expressed genes (DEGs) were divided into five groups: IPC1 vs. ADSC (1169 upregulated genes and 1377 downregulated genes), IPC2 vs. IPC1 (1323 upregulated genes and 803 downregulated genes), IPC3 vs. IPC2 (722 upregulated genes and 680 downregulated genes), IPC4 vs. IPC3 (539 upregulated genes and 1561 downregulated genes), and Beta_cell vs. IPC4 (2816 upregulated genes and 4571 downregulated genes). The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs revealed that many genes and signaling pathways that are essential for transdifferentiation. Hnf1B, Dll1, Pbx1, Rfx3, and Foxa1 were screened out, and the functions of five genes were verified further by overexpression and silence. Foxa1, Pbx1, and Rfx3 exhibited significant effects, can be used as specific key regulatory factors in the transdifferentiation of ADMSCs into IPCs. This study provides a foundation for future work to understand the mechanisms of the transdifferentiation of ADMSCs into IPCs and acquire IPCs with high maturity.
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Affiliation(s)
- Pengxiu Dai
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jiakai Li
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yijing Chen
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Luwen Zhang
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xinke Zhang
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jinglu Wang
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guixiang Qi
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yihua Zhang
- Shaanxi Branch of National Stem Cell Engineering and Technology Centre, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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20
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Theis A, Singer RA, Garofalo D, Paul A, Narayana A, Sussel L. Groucho co-repressor proteins regulate β cell development and proliferation by repressing Foxa1 in the developing mouse pancreas. Development 2021; 148:dev.192401. [PMID: 33658226 DOI: 10.1242/dev.192401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 02/24/2021] [Indexed: 11/20/2022]
Abstract
Groucho-related genes (GRGs) are transcriptional co-repressors that are crucial for many developmental processes. Several essential pancreatic transcription factors are capable of interacting with GRGs; however, the in vivo role of GRG-mediated transcriptional repression in pancreas development is still not well understood. In this study, we used complex mouse genetics and transcriptomic analyses to determine that GRG3 is essential for β cell development, and in the absence of Grg3 there is compensatory upregulation of Grg4 Grg3/4 double mutant mice have severe dysregulation of the pancreas gene program with ectopic expression of canonical liver genes and Foxa1, a master regulator of the liver program. Neurod1, an essential β cell transcription factor and predicted target of Foxa1, becomes downregulated in Grg3/4 mutants, resulting in reduced β cell proliferation, hyperglycemia, and early lethality. These findings uncover novel functions of GRG-mediated repression during pancreas development.
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Affiliation(s)
- Alexandra Theis
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ruth A Singer
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA.,Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY 10032, USA
| | - Diana Garofalo
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Alexander Paul
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA.,Graduate program in Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Anila Narayana
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lori Sussel
- Department of Pediatrics and Cell & Developmental Biology, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA .,Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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21
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Elsayed AK, Younis I, Ali G, Hussain K, Abdelalim EM. Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency. Cell Death Dis 2021; 12:103. [PMID: 33473118 PMCID: PMC7817686 DOI: 10.1038/s41419-021-03390-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 01/30/2023]
Abstract
FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2+/- iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results showed that FOXA2 haploinsufficiency resulted in aberrant expression of genes essential for the differentiation and proper functioning of beta cells. At pancreatic progenitor (PP2) and endocrine progenitor (EPs) stages, transcriptome analysis showed downregulation in genes associated with pancreatic development and diabetes and upregulation in genes associated with nervous system development and WNT signaling pathway. Knockout of FOXA2 in control iPSCs (FOXA2-/- iPSCs) led to severe phenotypes in EPs and beta-cell stages. The expression of NGN3 and its downstream targets at EPs as well as INSUILIN and GLUCAGON at the beta-cell stage, were almost absent in the cells derived from FOXA2-/- iPSCs. These findings indicate that FOXA2 is crucial for human pancreatic endocrine development and its defect may lead to diabetes based on FOXA2 dosage.
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Affiliation(s)
- Ahmed K. Elsayed
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ihab Younis
- grid.418818.c0000 0001 0516 2170Biological Sciences Program, Carnegie Mellon University, Qatar Foundation, Education City, Doha, Qatar
| | - Gowher Ali
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Essam M. Abdelalim
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar ,grid.418818.c0000 0001 0516 2170College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Education City, Doha, Qatar
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22
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Yang J, Liu X, Yuan F, Liu J, Li D, Wei L, Wang X, Yuan L. X-box-binding protein 1 is required for pancreatic development in Xenopus laevis. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1215-1226. [PMID: 33098302 DOI: 10.1093/abbs/gmaa114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 11/14/2022] Open
Abstract
X-box-binding protein 1 (XBP1) is a protein containing the basic leucine zipper structure. It belongs to the cAMP-response element binding protein (CREB)/activating transcription factor transcription factor family. As the main transcription factor, spliced XBP1 (XBP1s) participates in many physiological and pathological processes and plays an important role in embryonic development. Previous studies showed that XBP1-knockout mice died because of pancreatic exocrine function deficiency, indicating that XBP1 plays an important role in pancreatic development. However, the exact role of XBP1 in pancreatic development remains unclear. This study aimed to investigate the role of XBP1 in the pancreatic development of Xenopus laevis embryos. Whole-mount in situ hybridization and quantitative real-time PCR results revealed that the expression levels of pancreatic progenitor marker genes pdx1, p48, ngn3, and sox9 were downregulated in XBP1s morpholino oligonucleotide (MO)-injected embryos. The expression levels of pancreatic exocrine and endocrine marker genes insulin and amylase were also downregulated. Through the overexpression of XBP1s, the phenotype and gene expressions were opposite to those in XBP1s MO-injected embryos. Luciferase and chromatin immunoprecipitation assays showed that XBP1s could bind to the XBP1-binding site in the foxa2 promoter. These results revealed that XBP1 is required in the pancreatic development of Xenopus laevis and might function by regulating foxa2.
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Affiliation(s)
- Jing Yang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Xingjing Liu
- Department of Endocrinology, Zhongda Hospital, Institute of Diabetes, Medical School, Southeast University, Nanjing 210009, China
| | - Fang Yuan
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Jia Liu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Deli Li
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Liyuan Wei
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Xuejun Wang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
| | - Li Yuan
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 210029, China
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23
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Loganathan R, Kim JH, Wells MB, Andrew DJ. Secrets of secretion-How studies of the Drosophila salivary gland have informed our understanding of the cellular networks underlying secretory organ form and function. Curr Top Dev Biol 2020; 143:1-36. [PMID: 33820619 DOI: 10.1016/bs.ctdb.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Secretory organs are critical for organismal survival. Yet, the transcriptional regulatory mechanisms governing their development and maintenance remain unclear for most model secretory organs. The Drosophila embryonic salivary gland (SG) remedies this deficiency as one of the few organs wherein direct connections from the expression of the early patterning genes to cell specification to organ architecture and functional specialization can be made. Few other models of secretion can be accorded this distinction. Studies from the past three decades have made enormous strides in parsing out the roles of distinct transcription factors (TFs) that direct major steps in furnishing this secretory organ. In the first step of specifying the salivary gland, the activity of the Hox factors Sex combs reduced, Extradenticle, and Homothorax activate expression of fork head (fkh), sage, and CrebA, which code for the major suite of TFs that carry forward the task of organ building and maintenance. Then, in the second key step of building the SG, the program for cell fate maintenance and morphogenesis is deployed. Fkh maintains the secretory cell fate by regulating its own expression and that of sage and CrebA. Fkh and Sage maintain secretory cell viability by actively blocking apoptotic cell death. Fkh, along with two other TFs, Hkb and Rib, also coordinates organ morphogenesis, transforming two plates of precursor cells on the embryo surface into elongated internalized epithelial tubes. Acquisition of functional specialization, the third key step, is mediated by CrebA and Fkh working in concert with Sage and yet another TF, Sens. CrebA directly upregulates expression of all of the components of the secretory machinery as well as other genes (e.g., Xbp1) necessary for managing the physiological stress that inexorably accompanies high secretory load. Secretory cargo specificity is controlled by Sage and Sens in collaboration with Fkh. Investigations have also uncovered roles for various signaling pathways, e.g., Dpp signaling, EGF signaling, GPCR signaling, and cytoskeletal signaling, and their interactions within the gene regulatory networks that specify, build, and specialize the SG. Collectively, studies of the SG have expanded our knowledge of secretory dynamics, cell polarity, and cytoskeletal mechanics in the context of organ development and function. Notably, the embryonic SG has made the singular contribution as a model system that revealed the core function of CrebA in scaling up secretory capacity, thus, serving as the pioneer system in which the conserved roles of the mammalian Creb3/3L-family orthologues were first discovered.
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Affiliation(s)
- Rajprasad Loganathan
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ji Hoon Kim
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael B Wells
- Idaho College of Osteopathic Medicine, Meridian, ID, United States
| | - Deborah J Andrew
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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24
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Lam ATN, Aksit MA, Vecchio-Pagan B, Shelton CA, Osorio DL, Anzmann AF, Goff LA, Whitcomb DC, Blackman SM, Cutting GR. Increased expression of anion transporter SLC26A9 delays diabetes onset in cystic fibrosis. J Clin Invest 2020; 130:272-286. [PMID: 31581148 DOI: 10.1172/jci129833] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Diabetes is a common complication of cystic fibrosis (CF) that affects approximately 20% of adolescents and 40%-50% of adults with CF. The age at onset of CF-related diabetes (CFRD) (marked by clinical diagnosis and treatment initiation) is an important measure of the disease process. DNA variants associated with age at onset of CFRD reside in and near SLC26A9. Deep sequencing of the SLC26A9 gene in 762 individuals with CF revealed that 2 common DNA haplotypes formed by the risk variants account for the association with diabetes. Single-cell RNA sequencing (scRNA-Seq) indicated that SLC26A9 is predominantly expressed in pancreatic ductal cells and frequently coexpressed with CF transmembrane conductance regulator (CFTR) along with transcription factors that have binding sites 5' of SLC26A9. These findings were replicated upon reanalysis of scRNA-Seq data from 4 independent studies. DNA fragments derived from the 5' region of SLC26A9-bearing variants from the low-risk haplotype generated 12%-20% higher levels of expression in PANC-1 and CFPAC-1 cells compared with the high- risk haplotype. Taken together, our findings indicate that an increase in SLC26A9 expression in ductal cells of the pancreas delays the age at onset of diabetes, suggesting a CFTR-agnostic treatment for a major complication of CF.
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Affiliation(s)
- Anh-Thu N Lam
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melis A Aksit
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Briana Vecchio-Pagan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - Celeste A Shelton
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Ariel Precision Medicine, Pittsburgh, Pennsylvania, USA
| | - Derek L Osorio
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Arianna F Anzmann
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Loyal A Goff
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Scott M Blackman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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25
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Helman A, Cangelosi AL, Davis JC, Pham Q, Rothman A, Faust AL, Straubhaar JR, Sabatini DM, Melton DA. A Nutrient-Sensing Transition at Birth Triggers Glucose-Responsive Insulin Secretion. Cell Metab 2020; 31:1004-1016.e5. [PMID: 32375022 PMCID: PMC7480404 DOI: 10.1016/j.cmet.2020.04.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/14/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022]
Abstract
A drastic transition at birth, from constant maternal nutrient supply in utero to intermittent postnatal feeding, requires changes in the metabolic system of the neonate. Despite their central role in metabolic homeostasis, little is known about how pancreatic β cells adjust to the new nutritional challenge. Here, we find that after birth β cell function shifts from amino acid- to glucose-stimulated insulin secretion in correlation with the change in the nutritional environment. This adaptation is mediated by a transition in nutrient sensitivity of the mTORC1 pathway, which leads to intermittent mTORC1 activity. Disrupting nutrient sensitivity of mTORC1 in mature β cells reverts insulin secretion to a functionally immature state. Finally, manipulating nutrient sensitivity of mTORC1 in stem cell-derived β cells in vitro strongly enhances their glucose-responsive insulin secretion. These results reveal a mechanism by which nutrients regulate β cell function, thereby enabling a metabolic adaptation for the newborn.
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Affiliation(s)
- Aharon Helman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Andrew L Cangelosi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey C Davis
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Quan Pham
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Arielle Rothman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Aubrey L Faust
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Juerg R Straubhaar
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Douglas A Melton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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26
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Gao B, Xie W, Wu X, Wang L, Guo J. Functionally analyzing the important roles of hepatocyte nuclear factor 3 (FoxA) in tumorigenesis. Biochim Biophys Acta Rev Cancer 2020; 1873:188365. [PMID: 32325165 DOI: 10.1016/j.bbcan.2020.188365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Transcriptional factors (TFs) play a central role in governing gene expression under physiological conditions including the processes of embryonic development, metabolic homeostasis and response to extracellular stimuli. Conceivably, the aberrant dysregulations of TFs would dominantly result in various human disorders including tumorigenesis, diabetes and neurodegenerative diseases. Serving as the most evolutionarily reserved TFs, Fox family TFs have been explored to exert distinct biological functions in neoplastic development, by manipulating diverse gene expression. Recently, among the Fox family members, the pilot roles of FoxAs attract more attention due to their functions as both pioneer factor and transcriptional factor in human tumorigenesis, particularly in the sex-dimorphism tumors. Therefore, the pathological roles of FoxAs in tumorigenesis have been well-explored in modulating inflammation, immune response and metabolic homeostasis. In this review, we comprehensively summarize the impressive progression of FoxA functional annotation, clinical relevance, upstream regulators and downstream effectors, as well as valuable animal models, and highlight the potential strategies to target FoxAs for cancer therapies.
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Affiliation(s)
- Bing Gao
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Xie
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xueji Wu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lei Wang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Guo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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27
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Mohammed I, Al-Khawaga S, Bohanna D, Shabani A, Khan F, Love DR, Nawaz Z, Hussain K. Haploinsufficiency of the FOXA2 associated with a complex clinical phenotype. Mol Genet Genomic Med 2020; 8:e1086. [PMID: 32277595 PMCID: PMC7284027 DOI: 10.1002/mgg3.1086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 12/23/2022] Open
Abstract
Background There are few reports describing the proximal deletions of the short arm of chromosome 20, making it difficult to predict the likely consequences of these deletions. Most previously reported cases have described the association of 20p11.2 deletions with Alagille syndrome, while there are others that include phenotypes such as panhypopituitarism, craniofacial dysmorphism, polysplenia, autism, and Hirschsprung disease. Methods Molecular karyotyping, cytogenetics, and DNA sequencing were undertaken in a child to study the genetic basis of a complex phenotype consisting of craniofacial dysmorphism, ocular abnormalities, ectopic inguinal testes, polysplenia, growth hormone deficiency, central hypothyroidism, and gastrointestinal system anomalies. Results We report the smallest described de novo proximal 20p11.2 deletion, which deletes only the FOXA2 leading to the above complex phenotype. Conclusions Haploinsufficiency of the FOXA2 only gene is associated with a multisystem disorder.
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Affiliation(s)
- Idris Mohammed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Sara Al-Khawaga
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - David Bohanna
- Department of Radiology, Sidra Medicine, Doha, Qatar
| | - Abdusamea Shabani
- Division of Pathology Genetics, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Faiyaz Khan
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Donald R Love
- Department of Radiology, Sidra Medicine, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
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28
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Yang W, Chi Y, Meng Y, Chen Z, Xiang R, Yan H, Yang J. FAM3A plays crucial roles in controlling PDX1 and insulin expressions in pancreatic beta cells. FASEB J 2020; 34:3915-3931. [PMID: 31944392 DOI: 10.1096/fj.201902368rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 11/11/2022]
Abstract
So far, the mechanism that links mitochondrial dysfunction to PDX1 inhibition in the pathogenesis of pancreatic β cell dysfunction under diabetic condition remains largely unclear. This study determined the role of mitochondrial protein FAM3A in regulating PDX1 expression in pancreatic β cells using gain- and loss-of function methods in vitro and in vivo. Within pancreas, FAM3A is highly expressed in β, α, δ, and pp cells of islets. Islet FAM3A expression was correlated with insulin expression under physiological and diabetic conditions. Mice with specific knockout of FAM3A in islet β cells exhibited markedly blunted insulin secretion and glucose intolerance. FAM3A-deficient islets showed significant decrease in PDX1 expression, and insulin expression and secretion. FAM3A overexpression upregulated PDX1 and insulin expressions, and augmented insulin secretion in cultured islets and β cells. Mechanistically, FAM3A enhanced ATP production to elevate cellular Ca2+ level and promote insulin secretion. Furthermore, FAM3A-induced ATP release activated CaM to function as a co-activator of FOXA2, stimulating PDX1 gene transcription. In conclusion, FAM3A plays crucial roles in controlling PDX1 and insulin expressions in pancreatic β cells. Inhibition of FAM3A will trigger mitochondrial dysfunction to repress PDX1 and insulin expressions.
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Affiliation(s)
- Weili Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China.,Beijing Key Laboratory of Diabetes Research and Care, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yujing Chi
- Department of Central Laboratory & Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing, China
| | - Yuhong Meng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Zhenzhen Chen
- State Key Laboratory of Cardiovascular Disease, Hypertension Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Han Yan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Science of the Ministry of Education, Center for Non-coding RNA Medicine, Peking University Health Science Center, Beijing, China
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29
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ZnT8 Haploinsufficiency Impacts MIN6 Cell Zinc Content and β-Cell Phenotype via ZIP-ZnT8 Coregulation. Int J Mol Sci 2019; 20:ijms20215485. [PMID: 31690008 PMCID: PMC6861948 DOI: 10.3390/ijms20215485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/17/2023] Open
Abstract
The zinc transporter ZnT8 (SLC30A8) localises to insulin secretory granules of β-cells where it facilitates zinc uptake for insulin crystallisation. ZnT8 abundance has been linked to β-cell survival and functional phenotype. However, the consequences of ZnT8 haploinsufficiency for β-cell zinc trafficking and function remain unclear. Since investigations in human populations have shown SLC30A8 truncating polymorphisms to decrease the risk of developing Type 2 Diabetes, we hypothesised that ZnT8 haploinsufficiency would improve β-cell function and maintain the endocrine phenotype. We used CRISPR/Cas9 technology to generate ZnT8 haploinsufficient mouse MIN6 β-cells and showed that ZnT8 haploinsufficiency is associated with downregulation of mRNAs for Slc39a8 and Slc39a14, which encode for the zinc importers, Znt- and Irt-related proteins 8 (ZIP8) and 14 (ZIP14), and with lowered total cellular zinc content. ZnT8 haploinsufficiency disrupts expression of a distinct array of important β-cell markers, decreases cellular proliferation via mitogen-activated protein (MAP) kinase cascades and downregulates insulin gene expression. Thus, ZnT8 cooperates with zinc importers of the ZIP family to maintain β-cell zinc homeostasis. In contrast to the hypothesis, lowered ZnT8 expression reduces MIN6 cell survival by affecting zinc-dependent transcription factors that control the β-cell phenotype.
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30
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Identification of C2CD4A as a human diabetes susceptibility gene with a role in β cell insulin secretion. Proc Natl Acad Sci U S A 2019; 116:20033-20042. [PMID: 31527256 DOI: 10.1073/pnas.1904311116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Fine mapping and validation of genes causing β cell failure from susceptibility loci identified in type 2 diabetes genome-wide association studies (GWAS) poses a significant challenge. The VPS13C-C2CD4A-C2CD4B locus on chromosome 15 confers diabetes susceptibility in every ethnic group studied to date. However, the causative gene is unknown. FoxO1 is involved in the pathogenesis of β cell dysfunction, but its link to human diabetes GWAS has not been explored. Here we generated a genome-wide map of FoxO1 superenhancers in chemically identified β cells using 2-photon live-cell imaging to monitor FoxO1 localization. When parsed against human superenhancers and GWAS-derived diabetes susceptibility alleles, this map revealed a conserved superenhancer in C2CD4A, a gene encoding a β cell/stomach-enriched nuclear protein of unknown function. Genetic ablation of C2cd4a in β cells of mice phenocopied the metabolic abnormalities of human carriers of C2CD4A-linked polymorphisms, resulting in impaired insulin secretion during glucose tolerance tests as well as hyperglycemic clamps. C2CD4A regulates glycolytic genes, and notably represses key β cell "disallowed" genes, such as lactate dehydrogenase A We propose that C2CD4A is a transcriptional coregulator of the glycolytic pathway whose dysfunction accounts for the diabetes susceptibility associated with the chromosome 15 GWAS locus.
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31
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Gouda W, Mageed L, Azmy O, Okasha A, Shaker Y, Ashour E. Association of genetic variants in IGF-1 gene with susceptibility to gestational and type 2 diabetes mellitus. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
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32
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Jiang B, Lv Q, Wan W, Le L, Xu L, Hu K, Xiao P. Transcriptome analysis reveals the mechanism of the effect of flower tea Coreopsis tinctoria on hepatic insulin resistance. Food Funct 2019; 9:5607-5620. [PMID: 30370909 DOI: 10.1039/c8fo00965a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-Camellia tea and herbal medicine help prevent the development of diabetes and other metabolic diseases. Previous studies revealed that Coreopsis tinctoria (CT) flower tea increases insulin sensitivity and, in some high-fat diet (HFD)-fed rats, even prevents hepatic metabolic disorders. However, the molecular mechanisms by which CT improves insulin resistance are not known. In this study, six-week-old rats were fed a normal diet (ND), an HFD or an HFD supplemented with CT for 8 weeks. Serum samples were collected, and the livers were extracted for RNA-seq gene expression analysis. Real-time PCR and western blotting further verified the RNA-seq results. In our results, dietary CT ameliorated HFD-induced hepatosteatosis, glucose intolerance, and insulin resistance. In the HFD group, 1667 differentially expressed genes (DEGs) were identified compared with the ND group. In the CT group, 327 DEGs were identified compared with the HFD group. Some of these DEGs were related to insulin signalling, hepatic lipogenesis and glucose homeostasis. This study suggested that insulin resistance with hyperinsulinaemia, and not insulin insufficiency, is an early problem in HFD-fed rats, and CT downregulates insulin secretion genes (e.g., Rasd1, Stxbp1 and Sfxn1). Hepatic gene and protein expression analyses indicated that the regulatory effects of CT on glucose and lipid homeostasis are likely mediated via the Akt/FoxO1 signalling pathway and are regulated by the transcription factors hairy and enhancer of split 1 (HES1) and small heterodimer partner (SHP). Our study provides transcriptomic evidence of the complex pathogenic mechanism involved in hepatic insulin resistance and proves that supplementation with CT improves insulin resistance at a global scale.
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Affiliation(s)
- Baoping Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
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33
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Chen B, Yu J, Lu L, Dong F, Zhou F, Tao X, Sun E. Upregulated forkhead-box A3 elevates the expression of forkhead-box A1 and forkhead-box A2 to promote metastasis in esophageal cancer. Oncol Lett 2019; 17:4351-4360. [PMID: 30944629 DOI: 10.3892/ol.2019.10078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/04/2019] [Indexed: 11/06/2022] Open
Abstract
Esophageal cancer (EC) is one of the most lethal cancers currently known. Members of the forkhead-box A (FOXA) family, including FOXA1 and FOXA2, have been reported to regulate EC progression. However, the role of FOXA3, which is another FOXA member, has not yet been investigated. In the present study, public dataset analyses and immunohistochemistry of 96 samples from patients with EC were performed to determine the potential roles of FOXA3 in EC. The results revealed that FOXA3 was significantly upregulated in EC tumor tissues and Barrett's esophagus tissues. In addition, FOXA3 upregulation was positively associated with tumor invasion, distant metastasis, tumor-node-metastasis stage and shorter overall survival in patients with EC, and multivariate analysis identified FOXA3 as an independent prognostic marker. In vitro experiments demonstrated that the migratory and invasive abilities of EC109 and EC9706 cell lines were inhibited following FOXA3 knockdown. Notably, FOXA3 expression levels were positively correlated with FOXA1 and FOXA2 expression levels according to The Cancer Genome Atlas dataset analysis. Furthermore, FOXA3 knockdown decreased the expression levels of FOXA1 and FOXA2 in EC109 and EC9706 cell lines. Conversely, FOXA1 or FOXA2 overexpression compensated for the effects of FOXA3 knockdown on the migratory and invasive capacities of EC cells. In conclusion, the present study demonstrated that FOXA3 upregulation in EC cells promoted metastasis through regulation of other FOXA members.
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Affiliation(s)
- Bing Chen
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Jiegen Yu
- Department of Management Science, School of Humanities and Management, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Linming Lu
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangyuan Dong
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Fangfang Zhou
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiangxiang Tao
- Department of Pathology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Entao Sun
- Department of Health Inspection and Quarantine, School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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34
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Cañibano-Hernández A, Saenz del Burgo L, Espona-Noguera A, Orive G, Hernández RM, Ciriza J, Pedraz JL. Hyaluronic Acid Promotes Differentiation of Mesenchymal Stem Cells from Different Sources toward Pancreatic Progenitors within Three-Dimensional Alginate Matrixes. Mol Pharm 2019; 16:834-845. [DOI: 10.1021/acs.molpharmaceut.8b01126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alberto Cañibano-Hernández
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Laura Saenz del Burgo
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Albert Espona-Noguera
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Rosa M. Hernández
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - Jesús Ciriza
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
| | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, Vitoria-Gasteiz 01006, Spain
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Reshef YA, Finucane HK, Kelley DR, Gusev A, Kotliar D, Ulirsch JC, Hormozdiari F, Nasser J, O'Connor L, van de Geijn B, Loh PR, Grossman SR, Bhatia G, Gazal S, Palamara PF, Pinello L, Patterson N, Adams RP, Price AL. Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nat Genet 2018; 50:1483-1493. [PMID: 30177862 PMCID: PMC6202062 DOI: 10.1038/s41588-018-0196-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Biological interpretation of genome-wide association study data frequently involves assessing whether SNPs linked to a biological process, for example, binding of a transcription factor, show unsigned enrichment for disease signal. However, signed annotations quantifying whether each SNP allele promotes or hinders the biological process can enable stronger statements about disease mechanism. We introduce a method, signed linkage disequilibrium profile regression, for detecting genome-wide directional effects of signed functional annotations on disease risk. We validate the method via simulations and application to molecular quantitative trait loci in blood, recovering known transcriptional regulators. We apply the method to expression quantitative trait loci in 48 Genotype-Tissue Expression tissues, identifying 651 transcription factor-tissue associations including 30 with robust evidence of tissue specificity. We apply the method to 46 diseases and complex traits (average n = 290 K), identifying 77 annotation-trait associations representing 12 independent transcription factor-trait associations, and characterize the underlying transcriptional programs using gene-set enrichment analyses. Our results implicate new causal disease genes and new disease mechanisms.
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Affiliation(s)
- Yakir A Reshef
- Department of Computer Science, Harvard University, Cambridge, MA, USA.
- Harvard/MIT MD/PhD Program, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | | | - David R Kelley
- California Life Sciences LLC, South San Francisco, CA, USA
| | | | - Dylan Kotliar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Farhad Hormozdiari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luke O'Connor
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
| | - Bryce van de Geijn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Po-Ru Loh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon R Grossman
- Harvard/MIT MD/PhD Program, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaurav Bhatia
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pier Francesco Palamara
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, University of Oxford, Oxford, UK
| | - Luca Pinello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Ryan P Adams
- Google Brain, New York, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Alkes L Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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36
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Zou LS, Erdos MR, Taylor DL, Chines PS, Varshney A, Parker SCJ, Collins FS, Didion JP. BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues. BMC Genomics 2018; 19:390. [PMID: 29792182 PMCID: PMC5966887 DOI: 10.1186/s12864-018-4766-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/08/2018] [Indexed: 01/14/2023] Open
Abstract
Background Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. Results Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data. BoostMe uses a gradient boosting algorithm, XGBoost, and leverages information from multiple samples for prediction. We find that BoostMe outperforms existing algorithms in speed and accuracy when applied to WGBS of human tissues. Furthermore, we show that imputation improves concordance between WGBS and the MethylationEPIC array at low WGBS depth, suggesting improved WGBS accuracy after imputation. Conclusions Our findings support the use of BoostMe as a preprocessing step for WGBS analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4766-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luli S Zou
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - D Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Stephen C J Parker
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - John P Didion
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Ou K, Zhang J, Jiao Y, Wang ZV, Scherer P, Kaestner KH. Overexpression of ST5, an activator of Ras, has no effect on β-cell proliferation in adult mice. Mol Metab 2018; 11:212-217. [PMID: 29650351 PMCID: PMC6001393 DOI: 10.1016/j.molmet.2018.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE Both Type I and Type II diabetes mellitus result from insufficient functional β-cell mass. Efforts to increase β-cell proliferation as a means to restore β-cell mass have been met with limited success. Suppression of Tumorigenicity 5 (ST5) activates Ras/Erk signaling in the presence of Epidermal Growth Factor (EGF). In the pancreatic islet, Ras/Erk signaling is required for augmented β-cell proliferation during pregnancy, suggesting that ST5 is an appealing candidate to enhance adult β-cell proliferation. We aimed to test the hypothesis that overexpression of ST5 drives adult β-cell proliferation. METHODS We utilized a doxycycline-inducible bitransgenic mouse model to activate β-cell-specific expression of human ST5 in adult mice at will. Islet morphology, β-cell proliferation, and β-cell mass in control and ST5-overexpressing (ST5 OE) animals were analyzed by immunofluorescent staining, under basal and two stimulated metabolic states: pregnancy and streptozotocin (STZ)-induced β-cell loss. RESULTS Doxycycline treatment resulted in robust ST5 overexpression in islets from 12-16 week-old ST5 OE animals compared to controls, without affecting the islet morphology and identity of the β-cells. Under both basal and metabolically stimulated pregnancy states, β-cell proliferation and mass were comparable in ST5 OE and control animals. Furthermore, there was no detectable difference in β-cell proliferation between ST5 OE and control animals in response to STZ-induced β-cell loss. CONCLUSIONS We successfully derived an inducible bitransgenic mouse model to overexpress ST5 specifically in β-cells. However, our findings demonstrate that ST5 overexpression by itself has no mitogenic effect on the adult β-cell under basal and metabolically challenged states.
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Affiliation(s)
- Kristy Ou
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Jia Zhang
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yang Jiao
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhao V Wang
- Touchstone Diabetes Center, University of Texas Southwestern, Dallas, TX, 75390, USA
| | - Phillipp Scherer
- Touchstone Diabetes Center, University of Texas Southwestern, Dallas, TX, 75390, USA.
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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38
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Vajravelu ME, Chai J, Krock B, Baker S, Langdon D, Alter C, De León DD. Congenital Hyperinsulinism and Hypopituitarism Attributable to a Mutation in FOXA2. J Clin Endocrinol Metab 2018; 103:1042-1047. [PMID: 29329447 PMCID: PMC6276717 DOI: 10.1210/jc.2017-02157] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/05/2018] [Indexed: 12/14/2022]
Abstract
CONTEXT Persistent hypoglycemia in the newborn period most commonly occurs as a result of hyperinsulinism. The phenotype of hypoketotic hypoglycemia can also result from pituitary hormone deficiencies, including growth hormone and adrenocorticotropic hormone deficiency. Forkhead box A2 (Foxa2) is a transcription factor shown in mouse models to influence insulin secretion by pancreatic β cells. In addition, Foxa2 is involved in regulation of pituitary development, and deletions of FOXA2 have been linked to panhypopituitarism. OBJECTIVE To describe an infant with congenital hyperinsulinism and hypopituitarism as a result of a mutation in FOXA2 and to determine the functional impact of the identified mutation. MAIN OUTCOME MEASURE Difference in wild-type (WT) vs mutant Foxa2 transactivation of target genes that are critical for β cell function (ABCC8, KNCJ11, HADH) and pituitary development (GLI2, NKX2-2, SHH). RESULTS Transactivation by mutant Foxa2 of all genes studied was substantially decreased compared with WT. CONCLUSIONS We report a mutation in FOXA2 leading to congenital hyperinsulinism and hypopituitarism and provide functional evidence of the molecular mechanism responsible for this phenotype.
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Affiliation(s)
- Mary Ellen Vajravelu
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Jinghua Chai
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Bryan Krock
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - Samuel Baker
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
| | - David Langdon
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Craig Alter
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Diva D De León
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia,
Philadelphia, Pennsylvania
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman
School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Correspondence and Reprint Requests: Diva D. De León, MD, Division of Endocrinology and Diabetes, Children’s Hospital
of Philadelphia, 3615 Civic Center Boulevard, Ambramson Research Center, Room 802A,
Philadelphia, Pennsylvania 19104. E-mail:
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39
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Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet 2018; 50:250-258. [PMID: 29358654 PMCID: PMC6517675 DOI: 10.1038/s41588-017-0034-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 12/04/2017] [Indexed: 12/27/2022]
Abstract
Transcription factors are the core drivers of gene regulatory networks that control developmental transitions, therefore a more complete understanding of how they access, alter and maintain tissue-specific gene expression patterns remains an important goal. To systematically dissect molecular components that enable or constrain their activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite a classification as pioneer factors, all three factors demonstrate cell type specific enrichment even under super-physiological expression. However, only FOXA2 and GATA4 display, in both endogenous and ectopic conditions, a low enrichment sampling of additional loci that are occupied in alternative cell types. Co-factor expression can lead to increased pioneer factor binding at subsets of previously sampled target sites. Finally, we demonstrate that FOXA2 occupancy and changes to DNA accessibility at silent cis-regulatory elements can occur when the cell cycle is halted in G1, but subsequent loss of DNA methylation requires DNA replication.
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40
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Whirledge S, Kisanga EP, Taylor RN, Cidlowski JA. Pioneer Factors FOXA1 and FOXA2 Assist Selective Glucocorticoid Receptor Signaling in Human Endometrial Cells. Endocrinology 2017; 158:4076-4092. [PMID: 28938408 PMCID: PMC5695839 DOI: 10.1210/en.2017-00361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/24/2017] [Indexed: 01/10/2023]
Abstract
Successful pregnancy relies on dynamic control of cell signaling to achieve uterine receptivity and the necessary biological changes required for endometrial decidualization, embryo implantation, and fetal development. Glucocorticoids are master regulators of intracellular signaling and can directly regulate embryo implantation and endometrial remodeling during murine pregnancy. In immortalized human uterine cells, we have shown that glucocorticoids and estradiol (E2) coregulate thousands of genes. Recently, glucocorticoids and E2 were shown to coregulate the expression of Left-right determination factor 1 (LEFTY1), previously implicated in the regulation of decidualization. To elucidate the molecular mechanism by which glucocorticoids and E2 regulate the expression of LEFTY1, immortalized and primary human endometrial cells were evaluated for gene expression and receptor recruitment to regulatory regions of the LEFTY1 gene. Glucocorticoid administration induced expression of LEFTY1 messenger RNA and protein and recruitment of the glucocorticoid receptor (GR) and activated polymerase 2 to the promoter of LEFTY1. Glucocorticoid-mediated recruitment of GR was dependent on pioneer factors FOXA1 and FOXA2. E2 was found to antagonize glucocorticoid-mediated induction of LEFTY1 by reducing recruitment of GR, FOXA1, FOXA2, and activated polymerase 2 to the LEFTY1 promoter. Gene expression analysis identified several genes whose glucocorticoid-dependent induction required FOXA1 and FOXA2 in endometrial cells. These results suggest a molecular mechanism by which E2 antagonizes GR-dependent induction of specific genes by preventing the recruitment of the pioneer factors FOXA1 and FOXA2 in a physiologically relevant model.
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Affiliation(s)
- Shannon Whirledge
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut 06520
| | - Edwina P. Kisanga
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut 06520
| | - Robert N. Taylor
- Department of Obstetrics and Gynecology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101
| | - John A. Cidlowski
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
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41
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Chen D, Wang K, Li X, Jiang M, Ni L, Xu B, Chu Y, Wang W, Wang H, Kang H, Wu K, Liang J, Ren G. FOXK1 plays an oncogenic role in the development of esophageal cancer. Biochem Biophys Res Commun 2017; 494:88-94. [PMID: 29050933 DOI: 10.1016/j.bbrc.2017.10.080] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 12/29/2022]
Abstract
Forkhead box k1 (FOXK1) is a member of the FOX class of transcription factors and it is dysregulated in many solid tumors including hepatocellular carcinoma, gastric cancer, colorectal cancer and prostate cancer. However, the expression status of FOXK1 and its clinical significance in esophageal cancer (EC) is still uncertain. Our study aimed at investigating the significance of FOXK1 expression in human EC and its biological function in the development of EC. We found that FOXK1 was overexpressed in EC tissues compared with corresponding non-tumor tissues using immunohistochemistry. And high FOXK1 expression was related to poor differentiation of EC. The Kaplan-Meier curve indicated that high FOXK1 expression may result in poor prognosis of EC patients. Furthermore, overexpression of FOXK1 in EC9706 cell inhibited cell apoptosis and promoted cell proliferation and migration, and suppression of FOXK1 in EC109 cell obtained reverse results. Our data suggest that FOXK1 plays an oncogenic role in EC pathogenesis and can serve as a therapeutic target for patients with EC.
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Affiliation(s)
- Di Chen
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Kai Wang
- Department of Gastroenterology, The 16th Hospital of the People's Liberation Army of China, 219 Tuanjie South Road, A Letai, Xinjiang Province, 836599, China
| | - Xiaowei Li
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Mingzuo Jiang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Lu Ni
- Department of Gastroenterology, The 16th Hospital of the People's Liberation Army of China, 219 Tuanjie South Road, A Letai, Xinjiang Province, 836599, China
| | - Bing Xu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Yi Chu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Weijie Wang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Hua Wang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Huijie Kang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Jie Liang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China.
| | - Gui Ren
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China.
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Jois T, Sleeman MW. The regulation and role of carbohydrate response element-binding protein in metabolic homeostasis and disease. J Neuroendocrinol 2017; 29. [PMID: 28370553 DOI: 10.1111/jne.12473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/20/2022]
Abstract
The transcription factor carbohydrate response element-binding protein (ChREBP) is a member of the basic helix-loop-helix leucine zipper transcription factor family. Under high-glucose conditions, it has a role in regulating the expression of key genes involved in various pathways, including glycolysis, gluconeogenesis and lipogenesis. It does this by forming a tetrameric complex made up of two ChREBP/Mlx heterodimers, which enables it to bind to the carbohydrate response element (ChoRE) in the promoter region of its target genes to regulate transcription. Because ChREBP plays a key role in glucose signalling and metabolism, and aberrations in glucose homeostasis are often present in metabolic diseases, this transcription factor presents itself as an enticing target with respect to further understanding metabolic disease mechanisms and potentially uncovering new therapeutic targets.
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Affiliation(s)
- T Jois
- Department of Physiology, Monash University, Clayton, VIC, Australia
| | - M W Sleeman
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Abdul-Wahed A, Guilmeau S, Postic C. Sweet Sixteenth for ChREBP: Established Roles and Future Goals. Cell Metab 2017; 26:324-341. [PMID: 28768172 DOI: 10.1016/j.cmet.2017.07.004] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/01/2017] [Accepted: 07/12/2017] [Indexed: 12/25/2022]
Abstract
With the identification of ChREBP in 2001, our interest in understanding the molecular control of carbohydrate sensing has surged. While ChREBP was initially studied as a master regulator of lipogenesis in liver and fat tissue, it is now clear that ChREBP functions as a central metabolic coordinator in a variety of cell types in response to environmental and hormonal signals, with wide implications in health and disease. Celebrating its sweet sixteenth birthday, we review here the current knowledge about the function and regulation of ChREBP throughout usual and less explored tissues, to recapitulate ChREBP's role as a whole-body glucose sensor.
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Affiliation(s)
- Aya Abdul-Wahed
- Inserm, U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Sandra Guilmeau
- Inserm, U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Catherine Postic
- Inserm, U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France.
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44
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Wang R, Xu D, Liu R, Zhao L, Hu L, Wu P. Microsatellite and Single Nucleotide Polymorphisms in the Insulin-Like Growth Factor 1 Promoter with Insulin Sensitivity and Insulin Secretion. Med Sci Monit 2017; 23:3722-3736. [PMID: 28761040 PMCID: PMC5549718 DOI: 10.12659/msm.902956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background To investigate associations of the CA microsatellite and rs35767, rs5742612, and rs2288377 polymorphisms and the single nucleotide polymorphism (SNP) haplotypes with and without the CA microsatellite in the IGF1 promoter with insulin sensitivity and secretion. Material/Methods The CA microsatellite and SNPs were genotyped in 389 type 2 diabetes mellitus (T2DM) patients. A 75 g oral glucose tolerance test (OGTT) was given to all the participants. Associations of the genotypes and haplotypes with insulin sensitivity, insulin secretion, glucose tolerance, and insulin-like growth factor 1 (IGF1) were analyzed by ANCOVA (general linear model) and multiple linear regression, after controlling for gender, age, and BMI. Results The CA microsatellite, rs35767 polymorphisms, and SNP haplotypes with or without CA showed no significant association with metabolic parameters. The C allele of rs5742612 was found to be associated with decreased insulin sensitivity (HOMA-S index, β=−0.131, P=0.008; fasting insulin level, β=0.022, P=0.006) and increased insulin secretion (HOMA-B index, β=0.099, P=0.008; insulin AUC, β=0.112, P=0.012). The linear regression model also indicated that the A allele of rs2288377 was associated with decreased insulin sensitivity (HOMA-S index, β=−0.159, P=0.001; fasting insulin, β=0.143, P=0.001) and increased insulin secretion (HOMA-B index, β=0.114, P=0.017; insulin AUC, β=0.042, P=0.002). Conclusions The CA microsatellite and rs35767 have no genotype-related difference in insulin sensitivity or secretion. The rs5742612 and rs2288377 polymorphisms are significantly associated with insulin biology, with the TT genotype exhibiting higher insulin sensitivity and lower insulin secretion compared with carriers of the C allele and A allele, respectively, mostly attributed to the direct functional roles of the two loci.
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Affiliation(s)
- Ruyao Wang
- Graduate School, Tianjin Medical University, Tianjin, China (mainland).,Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Dandan Xu
- Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Rui Liu
- Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Lijie Zhao
- Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Liling Hu
- Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
| | - Ping Wu
- Department of Clinical Laboratory, Tianjin Union Medical Center, Tianjin, China (mainland)
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45
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Cheng M, Liu X, Yang M, Han L, Xu A, Huang Q. Computational analyses of type 2 diabetes-associated loci identified by genome-wide association studies. J Diabetes 2017; 9:362-377. [PMID: 27121852 DOI: 10.1111/1753-0407.12421] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/31/2016] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) of type 2 diabetes (T2D) have discovered a number of loci that contribute to susceptibility to the disease. Future challenges include elucidation of functional mechanisms through which these GWAS-identified loci modulate T2D disease risk. The aim of the present study was to comprehensively characterize T2D associated single nucleotide polymorphisms (SNPs) and genes through computational approaches. METHODS Computational biology approaches used in the present study included comparative genomic analyses and functional annotation using GWAS3D and RegulomeDB, investigation of the effects of T2D-associated SNPs on miRNA binding and protein phosphorylation, and gene ontology, pathway enrichment, protein-protein interaction (PPI) networks and functional module analysis of T2D-associated genes from previously published GWAS. RESULTS Computational analysis identified a number of T2D GWAS-associated SNPs that were located at protein binding sites, including CCCTC-binding factor (CTCF), E1A binding protein p300 (EP300), hepatocyte nuclear factor 4alpha (HNF4A), transcription factor 7 like 2 (TCF7L2), forkhead box A1 (FOXA1) and A2 (FOXA2), and potentially affected the binding of miRNAs and protein phosphorylation. Pathway enrichment analysis confirmed two well-known maturity onset diabetes of the young and T2D pathways, whereas PPI network analysis identified highly interconnected "hub" genes, such as TCF7L2, melatonin receptor 1B (MTNR1B), and solute carrier family 30 (zinc transporter), member 8 (SLC30A8), that created two tight subnetworks. CONCLUSIONS The results provide objectives and clues for future experimental studies and further insights into the molecular pathogenesis of T2D.
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Affiliation(s)
- Mengrong Cheng
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Xinhong Liu
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Mei Yang
- College of Life Sciences, Central China Normal University, Wuhan, China
| | - Lanchun Han
- College of Life Sciences, Central China Normal University, Wuhan, China
- Institute of Public Health and Molecular Medicine Analysis, Central China Normal University, Wuhan, China
| | - Aimin Xu
- Li Cha Chung Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan, China
- Institute of Public Health and Molecular Medicine Analysis, Central China Normal University, Wuhan, China
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Bastidas-Ponce A, Roscioni SS, Burtscher I, Bader E, Sterr M, Bakhti M, Lickert H. Foxa2 and Pdx1 cooperatively regulate postnatal maturation of pancreatic β-cells. Mol Metab 2017; 6:524-534. [PMID: 28580283 PMCID: PMC5444078 DOI: 10.1016/j.molmet.2017.03.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/16/2017] [Accepted: 03/21/2017] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE The transcription factors (TF) Foxa2 and Pdx1 are key regulators of beta-cell (β-cell) development and function. Mutations of these TFs or their respective cis-regulatory consensus binding sites have been linked to maturity diabetes of the young (MODY), pancreas agenesis, or diabetes susceptibility in human. Although Foxa2 has been shown to directly regulate Pdx1 expression during mouse embryonic development, the impact of this gene regulatory interaction on postnatal β-cell maturation remains obscure. METHODS In order to easily monitor the expression domains of Foxa2 and Pdx1 and analyze their functional interconnection, we generated a novel double knock-in homozygous (FVFPBFDHom) fluorescent reporter mouse model by crossing the previously described Foxa2-Venus fusion (FVF) with the newly generated Pdx1-BFP (blue fluorescent protein) fusion (PBF) mice. RESULTS Although adult PBF homozygous animals exhibited a reduction in expression levels of Pdx1, they are normoglycemic. On the contrary, despite normal pancreas and endocrine development, the FVFPBFDHom reporter male animals developed hyperglycemia at weaning age and displayed a reduction in Pdx1 levels in islets, which coincided with alterations in β-cell number and islet architecture. The failure to establish mature β-cells resulted in loss of β-cell identity and trans-differentiation towards other endocrine cell fates. Further analysis suggested that Foxa2 and Pdx1 genetically and functionally cooperate to regulate maturation of adult β-cells. CONCLUSIONS Our data show that the maturation of pancreatic β-cells requires the cooperative function of Foxa2 and Pdx1. Understanding the postnatal gene regulatory network of β-cell maturation will help to decipher pathomechanisms of diabetes and identify triggers to regenerate dedifferentiated β-cell mass.
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Affiliation(s)
- Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Sara S Roscioni
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Erik Bader
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Germany.,Institute of Stem Cell Research, Helmholtz Zentrum München, Germany.,Technical University of Munich, Germany.,German Center for Diabetes Research (DZD), Germany
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Zinovyeva MV, Kuzmich AI, Monastyrskaya GS, Sverdlov ED. The role of FOXA subfamily factors in embryonic development and carcinogenesis of the pancreas. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2017. [DOI: 10.3103/s0891416816030113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Abstract
It has been demonstrated that microfluidic systems allow integration of sampling, reagent mixing, and rapid electrophoretic analysis. They have also proven useful for culturing cells wherein control over the environment allows novel and automated experiments. Here, we describe a microchip-based electrophoresis assay that allows cell culture and hormone monitoring. An online gradient generator can control cell culture condition precisely. This system has been applied for Pancreas islets' glucose sensitivity studies.
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Affiliation(s)
- Shusheng Lu
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA.
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA.
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Han YL, Cao XE, Wang JX, Dong CL, Chen HT. Correlations of microRNA-124a and microRNA-30d with clinicopathological features of breast cancer patients with type 2 diabetes mellitus. SPRINGERPLUS 2016; 5:2107. [PMID: 28066696 PMCID: PMC5179477 DOI: 10.1186/s40064-016-3786-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 12/09/2016] [Indexed: 12/25/2022]
Abstract
This study intends to investigate the correlations of miR-124a and miR-30d with clinicopathological features of breast cancer (BC) patients with type 2 diabetes mellitus (T2DM). A total of 72 BC patients with T2DM (diabetic group) and 144 BC patients without T2DM (non-diabetic group) were enrolled in this study. Blood glucose was detected by glucose oxidase methods. Glycosylated hemoglobin (HbA1c) was measured by high performance liquid chromatography. Fasting insulin (FIns) was measured by chemiluminescent microparticle immunoassay. Automatic biochemical analyzer was used to detect triglyceride, total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C). Estradiol (E2) was detected by radioimmunoassay. Homeostasis model assessment was applied to assess the insulin resistance (HOMA-IR) and β-cell insulin secretion (HOMA-IS). The expressions of miR124a and miR-30d were measured by quantitative real-time polymerase chain reaction (qRT-PCR). There were significant differences in age, the ratio of menopause, body mass index (BMI), HDL-C, TC, 2-h plasma glucose (2hPG), FIns, HbA1c, HOMA-IS and HOMA-IR between the diabetic and non-diabetic groups. The diabetic group had higher incidence of lymph node metastasis than non-diabetic group. The miR-124a expression was down-regulated while the miR-30d expression was up-regulated in BC patients with T2DM. The correlation analysis showed that miR-124a expression was positively correlated with HDL-C, while it was negatively correlated with age, HbA1c, LDL-C and E2. However, the miR-30d expression was negatively correlated with HDL-C but positively correlated with age, HbA1c, LDL-C and E2. In conclusion, miR-124a and miR-30d may be correlated with clinicopathological features of BC patients with T2DM. The miR-124a and miR-30d could serve as novel biomarkers for early diagnosis of BC in patients with T2DM.
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Affiliation(s)
- Yu-Ling Han
- Department of Breast and Thyroid Surgery, Linyi People's Hospital, Linyi, 276000 People's Republic of China
| | - Xian-E Cao
- Department of Geriatrics, Linyi People's Hospital, North Park Road, 200 Meters East of Municipal Party School, Linyi, 276000 Shandong Province People's Republic of China
| | - Ju-Xun Wang
- Linyi City Family Planning Management Station, Linyi, 276000 People's Republic of China
| | - Chun-Ling Dong
- Department of Nurse, Linyi People's Hospital, Linyi, 276000 People's Republic of China
| | - Hong-Tao Chen
- Department of Rheumatism, Linyi People's Hospital, Linyi, 276000 People's Republic of China
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Wruck W, Schröter F, Adjaye J. Meta-Analysis of Transcriptome Data Related to Hippocampus Biopsies and iPSC-Derived Neuronal Cells from Alzheimer's Disease Patients Reveals an Association with FOXA1 and FOXA2 Gene Regulatory Networks. J Alzheimers Dis 2016; 50:1065-82. [PMID: 26890743 DOI: 10.3233/jad-150733] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the incidence of Alzheimer's disease (AD) is continuously increasing in the aging population worldwide, effective therapies are not available. The interplay between causative genetic and environmental factors is partially understood. Meta-analyses have been performed on aspects such as polymorphisms, cytokines, and cognitive training. Here, we propose a meta-analysis approach based on hierarchical clustering analysis of a reliable training set of hippocampus biopsies, which is condensed to a gene expression signature. This gene expression signature was applied to various test sets of brain biopsies and iPSC-derived neuronal cell models to demonstrate its ability to distinguish AD samples from control. Thus, our identified AD-gene signature may form the basis for determination of biomarkers that are urgently needed to overcome current diagnostic shortfalls. Intriguingly, the well-described AD-related genes APP and APOE are not within the signature because their gene expression profiles show a lower correlation to the disease phenotype than genes from the signature. This is in line with the differing characteristics of the disease as early-/late-onset or with/without genetic predisposition. To investigate the gene signature's systemic role(s), signaling pathways, gene ontologies, and transcription factors were analyzed which revealed over-representation of response to stress, regulation of cellular metabolic processes, and reactive oxygen species. Additionally, our results clearly point to an important role of FOXA1 and FOXA2 gene regulatory networks in the etiology of AD. This finding is in corroboration with the recently reported major role of the dopaminergic system in the development of AD and its regulation by FOXA1 and FOXA2.
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