1
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Ji L, Meng Z, Dong X, Wang Q, Jiang Y, Zhang J, Hu D, Guo S, Zhou W, Song W. ICA1 affects APP processing through the PICK1-PKCα signaling pathway. CNS Neurosci Ther 2024; 30:e14754. [PMID: 38884369 PMCID: PMC11181291 DOI: 10.1111/cns.14754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 06/18/2024] Open
Abstract
AIMS Islet cell autoantigen 1 (ICA1) is involved in autoimmune diseases and may affect synaptic plasticity as a neurotransmitter. Databases related to Alzheimer's disease (AD) have shown decreased ICA1 expression in patients with AD. However, the role of ICA1 in AD remains unclear. Here, we report that ICA1 expression is decreased in the brains of patients with AD and an AD mouse model. RESULTS The ICA1 increased the expression of amyloid precursor protein (APP), disintegrin and metalloprotease 10 (ADAM10), and disintegrin and metalloprotease 17 (ADAM17), but did not affect protein half-life or mRNA levels. Transcriptome sequencing analysis showed that ICA1 regulates the G protein-coupled receptor signaling pathway. The overexpression of ICA1 increased PKCα protein levels and phosphorylation. CONCLUSION Our results demonstrated that ICA1 shifts APP processing to non-amyloid pathways by regulating the PICK1-PKCα signaling pathway. Thus, this study suggests that ICA1 is a novel target for the treatment of AD.
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Affiliation(s)
- Liangye Ji
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - ZiJun Meng
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Xiangjun Dong
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Qunxian Wang
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Yanshuang Jiang
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Jie Zhang
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Dongjie Hu
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Shipeng Guo
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Weihui Zhou
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Weihong Song
- Department of Pediatric Research Institute Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation base of Child development and Critical Disorders, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical UniversityChongqingChina
- The Second Affiliated Hospital and Yuying Children's Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang ProvinceWenzhou Medical UniversityWenzhouChina
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health)WenzhouChina
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2
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Neukam M, Sala P, Brunner AD, Ganß K, Palladini A, Grzybek M, Topcheva O, Vasiljević J, Broichhagen J, Johnsson K, Kurth T, Mann M, Coskun Ü, Solimena M. Purification of time-resolved insulin granules reveals proteomic and lipidomic changes during granule aging. Cell Rep 2024; 43:113836. [PMID: 38421874 DOI: 10.1016/j.celrep.2024.113836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Endocrine cells employ regulated exocytosis of secretory granules to secrete hormones and neurotransmitters. Secretory granule exocytosis depends on spatiotemporal variables such as proximity to the plasma membrane and age, with newly generated granules being preferentially released. Despite recent advances, we lack a comprehensive view of the molecular composition of insulin granules and associated changes over their lifetime. Here, we report a strategy for the purification of insulin secretory granules of distinct age from insulinoma INS-1 cells. Tagging the granule-resident protein phogrin with a cleavable CLIP tag, we obtain intact fractions of age-distinct granules for proteomic and lipidomic analyses. We find that the lipid composition changes over time, along with the physical properties of the membrane, and that kinesin-1 heavy chain (KIF5b) as well as Ras-related protein 3a (RAB3a) associate preferentially with younger granules. Further, we identify the Rho GTPase-activating protein (ARHGAP1) as a cytosolic factor associated with insulin granules.
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Affiliation(s)
- Martin Neukam
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| | - Pia Sala
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | | | - Katharina Ganß
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michal Grzybek
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Oleksandra Topcheva
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jovana Vasiljević
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas Kurth
- TU Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Electron Microscopy and Histology Facility, 01307 Dresden, Saxony, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
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3
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Erol ÖD, Şenocak Ş, Aerts-Kaya F. The Role of Rab GTPases in the development of genetic and malignant diseases. Mol Cell Biochem 2024; 479:255-281. [PMID: 37060515 DOI: 10.1007/s11010-023-04727-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
Small GTPases have been shown to play an important role in several cellular functions, including cytoskeletal remodeling, cell polarity, intracellular trafficking, cell-cycle, progression and lipid transformation. The Ras-associated binding (Rab) family of GTPases constitutes the largest family of GTPases and consists of almost 70 known members of small GTPases in humans, which are known to play an important role in the regulation of intracellular membrane trafficking, membrane identity, vesicle budding, uncoating, motility and fusion of membranes. Mutations in Rab genes can cause a wide range of inherited genetic diseases, ranging from neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD) to immune dysregulation/deficiency syndromes, like Griscelli Syndrome Type II (GS-II) and hemophagocytic lymphohistiocytosis (HLH), as well as a variety of cancers. Here, we provide an extended overview of human Rabs, discussing their function and diseases related to Rabs and Rab effectors, as well as focusing on effects of (aberrant) Rab expression. We aim to underline their importance in health and the development of genetic and malignant diseases by assessing their role in cellular structure, regulation, function and biology and discuss the possible use of stem cell gene therapy, as well as targeting of Rabs in order to treat malignancies, but also to monitor recurrence of cancer and metastasis through the use of Rabs as biomarkers. Future research should shed further light on the roles of Rabs in the development of multifactorial diseases, such as diabetes and assess Rabs as a possible treatment target.
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Affiliation(s)
- Özgür Doğuş Erol
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Şimal Şenocak
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Fatima Aerts-Kaya
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey.
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey.
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4
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Chiu SL, Chen CM, Huganir RL. ICA69 regulates activity-dependent synaptic strengthening and learning and memory. Front Mol Neurosci 2023; 16:1171432. [PMID: 37251649 PMCID: PMC10213502 DOI: 10.3389/fnmol.2023.1171432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Long-term potentiation (LTP) is one of the major cellular mechanisms for learning and memory. Activity-dependent increases in surface AMPA receptors (AMPARs) are important for enhanced synaptic efficacy during LTP. Here, we report a novel function of a secretory trafficking protein, ICA69, in AMPAR trafficking, synaptic plasticity, and animal cognition. ICA69 is first identified as a diabetes-associated protein well characterized for its function in the biogenesis of secretory vesicles and trafficking of insulin from ER, Golgi to post-Golgi in pancreatic beta cells. In the brain, ICA69 is found in the AMPAR protein complex through its interaction with PICK1, which binds directly to GluA2 or GluA3 AMPAR subunits. Here, we showed that ICA69 regulates PICK1's distribution in neurons and stability in the mouse hippocampus, which in turn can impact AMPAR function in the brain. Biochemical analysis of postsynaptic density (PSD) proteins from hippocampi of mice lacking ICA69 (Ica1 knockout) and their wild-type littermates revealed comparable AMPAR protein levels. Electrophysiological recording and morphological analysis of CA1 pyramidal neurons from Ica1 knockout also showed normal AMPAR-mediated currents and dendrite architecture, indicating that ICA69 does not regulate synaptic AMPAR function and neuron morphology at the basal state. However, genetic deletion of ICA69 in mice selectively impairs NMDA receptor (NMDAR)-dependent LTP but not LTD at Schaffer collateral to CA1 synapses, which correlates with behavioral deficits in tests of spatial and associative learning and memory. Together, we identified a critical and selective role of ICA69 in LTP, linking ICA69-mediated synaptic strengthening to hippocampus-dependent learning and memory.
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Affiliation(s)
- Shu-Ling Chiu
- Institute of Cellular and Organismic Biology and Neuroscience Program of Academia Sinica (NPAS), Academia Sinica, Taipei, Taiwan
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Chih-Ming Chen
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience and Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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5
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Differentially methylated and expressed genes in familial type 1 diabetes. Sci Rep 2022; 12:11045. [PMID: 35773317 PMCID: PMC9247163 DOI: 10.1038/s41598-022-15304-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
There has recently been a growing interest in examining the role of epigenetic modifications, such as DNA methylation, in the etiology of type 1 diabetes (T1D). This study aimed to delineate differences in methylation patterns between T1D-affected and healthy individuals by examining the genome-wide methylation of individuals from three Arab families from Kuwait with T1D-affected mono-/dizygotic twins and non-twinned siblings. Bisulfite sequencing of DNA from the peripheral blood of the affected and healthy individuals from each of the three families was performed. Methylation profiles of the affected individuals were compared to those of the healthy individuals Principal component analysis on the observed methylation profiling based on base-pair resolution clustered the T1D-affected twins together family-wide. The sites/regions that were differentially methylated between the T1D and healthy samples harbored 84 genes, of which 18 were known to be differentially methylated in T1D individuals compared to healthy individuals in publicly available gene expression data resources. We further validated two of the 18 genes—namely ICA1 and DRAM1 that were hypermethylated in T1D samples compared to healthy samples—for upregulation in T1D samples from an extended study cohort of familial T1D. The study confirmed that the ICA1 and DRAM1 genes are differentially expressed in T1D samples compared to healthy samples.
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6
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Kong C, Ni X, Wang Y, Zhang A, Zhang Y, Lin F, Li S, Lv Y, Zhu J, Yao X, Dai Q, Mo Y, Wang J. ICA69 aggravates ferroptosis causing septic cardiac dysfunction via STING trafficking. Cell Death Dis 2022; 8:187. [PMID: 35397620 PMCID: PMC8994779 DOI: 10.1038/s41420-022-00957-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/03/2022] [Accepted: 03/16/2022] [Indexed: 12/30/2022]
Abstract
Previous studies have demonstrated that cardiomyocyte apoptosis, ferroptosis, and inflammation participate in the progress of sepsis-induced cardiomyopathy (SIC). Although Islet cell autoantigen 69 (ICA69) is an imperative molecule that could regulate inflammation and immune response in numerous illnesses, its function in cardiovascular disease, particularly in SIC, is still elusive. We confirmed that LPS significantly enhanced the expression of ICA69 in wild-type (WT) mice, macrophages, and cardiomyocytes. The knockout of ICA69 in lipopolysaccharide(LPS)-induced mice markedly elevated survival ratio and heart function, while inhibiting cardiac muscle and serum inflammatory cytokines, reactive oxygen (ROS), and ferroptosis biomarkers. Mechanistically, increased expression of ICA69 triggered the production of STING, which further resulted in the production of intracellular lipid peroxidation, eventually triggering ferroptosis and heart injury. Intriguingly, ICA69 deficiency only reversed the ferroptotic marker levels, such as prostaglandin endoperoxide synthase 2 (PTGS2), malonaldehyde (MDA), 4-hydroxynonenal (4HNE), glutathione peroxidase 4 (GPX4), superoxide dismutase (SOD), iron and lipid ROS, but had no effects on the xCT-dependent manner. Additionally, greater ICA69 level was identified in septic patients peripheralblood mononuclear cells (PBMCs) than in normal control groups. Generally, we unveil that ICA69 deficiency can relieve inflammation and ferroptosis in LPS-induced murine hearts and macrophages, making targeting ICA69 in heart a potentially promising treatment method for SIC.
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7
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Andersen RC, Schmidt JH, Rombach J, Lycas MD, Christensen NR, Lund VK, Stapleton DS, Pedersen SS, Olsen MA, Stoklund M, Noes-Holt G, Nielsen TT, Keller MP, Jansen AM, Herlo R, Pietropaolo M, Simonsen JB, Kjærulff O, Holst B, Attie AD, Gether U, Madsen KL. Coding variants identified in diabetic patients alter PICK1 BAR domain function in insulin granule biogenesis. J Clin Invest 2022; 132:144904. [PMID: 35077398 PMCID: PMC8884907 DOI: 10.1172/jci144904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Bin/amphiphysin/Rvs (BAR) domains are positively charged crescent-shaped modules that mediate curvature of negatively charged lipid membranes during remodeling processes. The BAR domain proteins PICK1, ICA69, and the arfaptins have recently been demonstrated to coordinate the budding and formation of immature secretory granules (ISGs) at the trans-Golgi network. Here, we identify 4 coding variants in the PICK1 gene from a whole-exome screening of Danish patients with diabetes that each involve a change in positively charged residues in the PICK1 BAR domain. All 4 coding variants failed to rescue insulin content in INS-1E cells upon knock down of endogenous PICK1. Moreover, 2 variants showed dominant-negative properties. In vitro assays addressing BAR domain function suggested that the coding variants compromised BAR domain function but increased the capacity to cause fission of liposomes. Live confocal microscopy and super-resolution microscopy further revealed that PICK1 resides transiently on ISGs before egress via vesicular budding events. Interestingly, this egress of PICK1 was accelerated in the coding variants. We propose that PICK1 assists in or complements the removal of excess membrane and generic membrane trafficking proteins, and possibly also insulin, from ISGs during the maturation process; and that the coding variants may cause premature budding, possibly explaining their dominant-negative function.
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Affiliation(s)
- Rita C. Andersen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan H. Schmidt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joscha Rombach
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Lycas
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaj R. Christensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Viktor K. Lund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Signe S. Pedersen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias A. Olsen
- Beta Cell Biology Group, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Stoklund
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gith Noes-Holt
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tommas T.E. Nielsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Anna M. Jansen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Herlo
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Massimo Pietropaolo
- Diabetes Research Center, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jens B. Simonsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ole Kjærulff
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L. Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Xiang C, Chen P, Zhang Q, Li Y, Pan Y, Xie W, Sun J, Liu Z. Intestinal microbiota modulates adrenomedullary response through Nod1 sensing in chromaffin cells. iScience 2021; 24:102849. [PMID: 34381974 PMCID: PMC8333343 DOI: 10.1016/j.isci.2021.102849] [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: 02/22/2021] [Revised: 06/07/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
The intestinal microbiota closely interacts with the neuroendocrine system and exerts profound effects on host physiology. Here, we report that nucleotide-binding oligomerization domain 1 (Nod1) ligand derived from intestinal bacteria modulates catecholamine storage and secretion in mouse adrenal chromaffin cells. The cytosolic peptidoglycan receptor Nod1 is involved in chromogranin A (Chga) retention in dense core granules (DCGs) in chromaffin cells. Mechanistically, upon recognizing its ligand, Nod1 localizes to DCGs, and recruits Rab2a, which is critical for Chga and epinephrine retention in DCGs. Depletion of Nod1 ligand or deficiency of Nod1 leads to a profound defect in epinephrine storage in chromaffin cells and subsequently less secretion upon stimulation. The intestine-adrenal medulla cross talk bridged by Nod1 ligand modulates adrenal medullary responses during the immobilization-induced stress response in mice. Thus, our study uncovers a mechanism by which intestinal microbes modulate epinephrine secretion in response to stress, which may provide further understanding of the gut-brain axis.
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Affiliation(s)
- Chen Xiang
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peihua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, CAS; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, CAS, Beijing, 100101, China
| | - Qin Zhang
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yinghui Li
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Pan
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenchun Xie
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Guang Dong Bio-healtech Advanced Co., Ltd., Foshan, 528000, P. R. China
| | - Jianyuan Sun
- University of Chinese Academy of Sciences, Beijing 100049, China
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, CAS; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Biophysics, CAS, Beijing, 100101, China
| | - Zhihua Liu
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Immunology, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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9
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Chen L, Tao F, Zhang Y, Shu C, Xiang W, Yang L, Chen X, Hong Y, Chen B, Li K, Zhang W, Hao K, Ge F, Wang Z, Lyu J. Islet-cell autoantigen 69 accelerates liver regeneration by downregulating Tgfbr1 and attenuating Tgfβ signaling in mice. FEBS Lett 2020; 594:2881-2893. [PMID: 32531799 DOI: 10.1002/1873-3468.13859] [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: 03/10/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 11/08/2022]
Abstract
Regeneration is a unique defense mechanism of liver tissue in response to functional cell loss induced by toxic chemicals or surgical resection. In this study, we found that Islet-cell autoantigen 69 (Ica69) accelerates liver regeneration in mice. Following 70% partial hepatectomy, both Ica69 mRNA and protein are significantly upregulated in mouse hepatocytes at the early stage of liver regeneration. Compared with the wild-type mice, Ica69-deficient mice have more severe liver injury, delayed liver regeneration, and high surgical accidental mortality following hepatectomy. Mechanistically, Ica69 interacts with Pick1 protein to regulate Tgfbr1 protein expression and Tgfβ-induced Smad2 phosphorylation. Our findings suggest that Ica69 in liver tissue is a new potential target for promoting liver regeneration.
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Affiliation(s)
- Linjie Chen
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Fei Tao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
| | | | - Chongyi Shu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
| | - Weiling Xiang
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Leixiang Yang
- Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Xiaopan Chen
- Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Yeting Hong
- Laboratory Medical School, Hangzhou Medical College, China
| | - Bingyu Chen
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Kaiqiang Li
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Wei Zhang
- Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Ke Hao
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Feihang Ge
- Laboratory Medical School, Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Zhen Wang
- Laboratory Medical School, Hangzhou Medical College, China.,Research Center of Blood Transfusion Medicine, Ministry of Education Key Laboratory People's Hospital, People's Hospital of Hangzhou Medical College, China.,Rehabilitation & Sports Medicine Research Institute of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, China
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10
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Korem Kohanim Y, Tendler A, Mayo A, Friedman N, Alon U. Endocrine Autoimmune Disease as a Fragility of Immune Surveillance against Hypersecreting Mutants. Immunity 2020; 52:872-884.e5. [PMID: 32433950 PMCID: PMC7237888 DOI: 10.1016/j.immuni.2020.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/14/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Some endocrine organs are frequent targets of autoimmune attack. Here, we addressed the origin of autoimmune disease from the viewpoint of feedback control. Endocrine tissues maintain mass through feedback loops that balance cell proliferation and removal according to hormone-driven regulatory signals. We hypothesized the existence of a dedicated mechanism that detects and removes mutant cells that missense the signal and therefore hyperproliferate and hypersecrete with potential to disrupt organismal homeostasis. In this mechanism, hypersecreting cells are preferentially eliminated by autoreactive T cells at the cost of a fragility to autoimmune disease. The "autoimmune surveillance of hypersecreting mutants" (ASHM) hypothesis predicts the presence of autoreactive T cells in healthy individuals and the nature of self-antigens as peptides from hormone secretion pathway. It explains why some tissues get prevalent autoimmune disease, whereas others do not and instead show prevalent mutant-expansion disease (e.g., hyperparathyroidism). The ASHM hypothesis is testable, and we discuss experimental follow-up.
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Affiliation(s)
- Yael Korem Kohanim
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avichai Tendler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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11
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Ruhl DA, Bomba-Warczak E, Watson ET, Bradberry MM, Peterson TA, Basu T, Frelka A, Evans CS, Briguglio JS, Basta T, Stowell MHB, Savas JN, Roopra A, Pearce RA, Piper RC, Chapman ER. Synaptotagmin 17 controls neurite outgrowth and synaptic physiology via distinct cellular pathways. Nat Commun 2019; 10:3532. [PMID: 31387992 PMCID: PMC6684635 DOI: 10.1038/s41467-019-11459-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/13/2019] [Indexed: 12/28/2022] Open
Abstract
The synaptotagmin (syt) proteins have been widely studied for their role in regulating fusion of intracellular vesicles with the plasma membrane. Here we report that syt-17, an unusual isoform of unknown function, plays no role in exocytosis, and instead plays multiple roles in intracellular membrane trafficking. Syt-17 is localized to the Golgi complex in hippocampal neurons, where it coordinates import of vesicles from the endoplasmic reticulum to support neurite outgrowth and facilitate axon regrowth after injury. Further, we discovered a second pool of syt-17 on early endosomes in neurites. Loss of syt-17 disrupts endocytic trafficking, resulting in the accumulation of excess postsynaptic AMPA receptors and defective synaptic plasticity. Two distinct pools of syt-17 thus control two crucial, independent membrane trafficking pathways in neurons. Function of syt-17 appears to be one mechanism by which neurons have specialized their secretory and endosomal systems to support the demands of synaptic communication over sprawling neurite arbors. The functional role of synaptotagmin-17 (syt-17) has remained unanswered. In this study, authors demonstrate that syt-17 exists in two distinct pools in hippocampal neurons (Golgi complex and early endosomes), where it served two completely independent functions: controlling neurite outgrowth and synaptic physiology
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Affiliation(s)
- David A Ruhl
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Ewa Bomba-Warczak
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emma T Watson
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Mazdak M Bradberry
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Tabitha A Peterson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, 52242, USA
| | - Trina Basu
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Alyssa Frelka
- Department of Anesthesiology, University of Wisconsin, Madison, WI, 53706, USA
| | - Chantell S Evans
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph S Briguglio
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Tamara Basta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA
| | - Robert A Pearce
- Department of Anesthesiology, University of Wisconsin, Madison, WI, 53706, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, 52242, USA
| | - Edwin R Chapman
- Department of Neuroscience, University of Wisconsin, Madison, WI, 53706, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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12
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Gillingham AK, Bertram J, Begum F, Munro S. In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation. eLife 2019; 8:45916. [PMID: 31294692 PMCID: PMC6639074 DOI: 10.7554/elife.45916] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. The GTPases are precisely controlled by regulators that promote acquisition of GTP (GEFs) or its hydrolysis to GDP (GAPs). We report here MitoID, a method for identifying effectors and regulators by performing in vivo proximity biotinylation with mitochondrially-localized forms of the GTPases. Applying this to 11 human Rab GTPases identified many known effectors and GAPs, as well as putative novel effectors, with examples of the latter validated for Rab2, Rab5, Rab9 and Rab11. MitoID can also efficiently identify effectors and GAPs of Rho and Ras family GTPases such as Cdc42, RhoA, Rheb, and N-Ras, and can identify GEFs by use of GDP-bound forms.
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Affiliation(s)
| | - Jessie Bertram
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Farida Begum
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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13
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Islet-cell autoantigen 69 mediates the antihyperalgesic effects of electroacupuncture on inflammatory pain by regulating spinal glutamate receptor subunit 2 phosphorylation through protein interacting with C-kinase 1 in mice. Pain 2019; 160:712-723. [PMID: 30699097 PMCID: PMC6407810 DOI: 10.1097/j.pain.0000000000001450] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Supplemental Digital Content is Available in the Text. A clear role of ICA69 in mediating the antihyperalgesic effects of electroacupuncture was confirmed, and the ICA69-PICK1-GluR2 molecular mechanism to explain these effects is proposed. Electroacupuncture (EA) is widely used in clinical settings to reduce inflammatory pain. Islet-cell autoantigen 69 (ICA69) has been reported to regulate long-lasting hyperalgesia in mice. ICA69 knockout led to reduced protein interacting with C-kinase 1 (PICK1) expression and increased glutamate receptor subunit 2 (GluR2) phosphorylation at Ser880 in spinal dorsal horn. In this study, we evaluated the role of ICA69 in the antihyperalgesic effects of EA and the underlying mechanism through regulation of GluR2 and PICK1 in spinal dorsal horn. Hyperalgesia was induced in mice with subcutaneous plantar injection of complete Freund adjuvant (CFA) to cause inflammatory pain. Electroacupuncture was then applied for 30 minutes every other day after CFA injection. When compared with CFA group, paw withdrawal frequency of CFA+EA group was significantly decreased. Remarkable increases in Ica1 mRNA expression and ICA69 protein levels on the ipsilateral side were detected in the CFA+EA group. ICA69 expression reached the peak value around day 3. More importantly, ICA69 deletion impaired the antihyperalgesic effects of EA on GluR2-p, but PICK1 deletion could not. Injecting ICA69 peptide into the intrathecal space of ICA69-knockout mice mimicked the effects of EA analgesic and inhibited GluR2-p. Electroacupuncture had no effects on the total protein of PICK1 and GluR2. And, EA could increase the formation of ICA69-PICK1 complexes and decrease the amount of PICK1-GluR2 complexes. Our findings indicate that ICA69 mediates the antihyperalgesic effects of EA on CFA-induced inflammatory pain by regulating spinal GluR2 through PICK1 in mice.
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14
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Berral-Gonzalez A, Riffo-Campos AL, Ayala G. OMICfpp: a fuzzy approach for paired RNA-Seq counts. BMC Genomics 2019; 20:259. [PMID: 30940089 PMCID: PMC6444640 DOI: 10.1186/s12864-019-5496-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it. RESULTS We propose OMICfpp, a method for the statistical analysis of RNA-Seq paired design data. First, we obtain a p-value for each case-control pair using a binomial test. These p-values are aggregated using an ordered weighted average (OWA) with a given orness previously chosen. The aggregated p-value from the original data is compared with the aggregated p-value obtained using the same method applied to random pairs. These new pairs are generated using between-pairs and complete randomization distributions. This randomization p-value is used as a raw p-value to test the differential expression of each gene. The OMICfpp method is evaluated using public data sets of 68 sample pairs from patients with colorectal cancer. We validate our results through bibliographic search of the reported genes and using simulated data set. Furthermore, we compared our results with those obtained by the methods edgeR and DESeq2 for paired samples. Finally, we propose new target genes to validate these as gene expression signatures in colorectal cancer. OMICfpp is available at http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz . CONCLUSIONS Our study shows that OMICfpp is an accurate method for differential expression analysis in RNA-Seq data with paired design. In addition, we propose the use of randomized p-values pattern graphic as a powerful and robust method to select the target genes for experimental validation.
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Affiliation(s)
- Alberto Berral-Gonzalez
- Grupo de Investigación Bioinformática y Genómica Funcional. Laboratorio 19. Centro de Investigación del Cáncer (CiC-IBMCC, Universidad de Salamanca-CSIC, Campus Universitario Miguel de Unamuno s/n, Salamanca, 37007 Spain
| | - Angela L. Riffo-Campos
- Universidad de La Frontera. Centro De Excelencia de Modelación y Computación Científica, C/ Montevideo 740, Temuco, Chile
| | - Guillermo Ayala
- Universidad de Valencia. Departamento de Estadística e Investigación Operativa, Avda. Vicent Andrés Estellés, 1, Burjasot, 46100 Spain
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15
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Cattin-Ortolá J, Topalidou I, Dosey A, Merz AJ, Ailion M. The dense-core vesicle maturation protein CCCP-1 binds RAB-2 and membranes through its C-terminal domain. Traffic 2017; 18:720-732. [PMID: 28755404 DOI: 10.1111/tra.12507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/26/2017] [Accepted: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Dense-core vesicles (DCVs) are secretory organelles that store and release modulatory neurotransmitters from neurons and endocrine cells. Recently, the conserved coiled-coil protein CCCP-1 was identified as a component of the DCV biogenesis pathway in the nematode Caenorhabditis elegans. CCCP-1 binds the small GTPase RAB-2 and colocalizes with it at the trans-Golgi. Here, we report a structure-function analysis of CCCP-1 to identify domains of the protein important for its localization, binding to RAB-2, and function in DCV biogenesis. We find that the CCCP-1 C-terminal domain (CC3) has multiple activities. CC3 is necessary and sufficient for CCCP-1 localization and for binding to RAB-2, and is required for the function of CCCP-1 in DCV biogenesis. In addition, CCCP-1 binds membranes directly through its CC3 domain, indicating that CC3 may comprise a previously uncharacterized lipid-binding motif. We conclude that CCCP-1 is a coiled-coil protein that binds an activated Rab and localizes to the Golgi via its C-terminus, properties similar to members of the golgin family of proteins. CCCP-1 also shares biophysical features with golgins; it has an elongated shape and forms oligomers.
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Affiliation(s)
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Alexey J Merz
- Department of Biochemistry, University of Washington, Seattle, Washington.,Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, Washington
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16
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Mallik B, Dwivedi MK, Mushtaq Z, Kumari M, Verma PK, Kumar V. Regulation of neuromuscular junction organization by Rab2 and its effector ICA69 in Drosophila. Development 2017; 144:2032-2044. [PMID: 28455372 DOI: 10.1242/dev.145920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/19/2017] [Indexed: 12/31/2022]
Abstract
The mechanisms underlying synaptic differentiation, which involves neuronal membrane and cytoskeletal remodeling, are not completely understood. We performed a targeted RNAi-mediated screen of Drosophila BAR-domain proteins and identified islet cell autoantigen 69 kDa (ICA69) as one of the key regulators of morphological differentiation of the larval neuromuscular junction (NMJ). We show that Drosophila ICA69 colocalizes with α-Spectrin at the NMJ. The conserved N-BAR domain of ICA69 deforms liposomes in vitro Full-length ICA69 and the ICAC but not the N-BAR domain of ICA69 induce filopodia in cultured cells. Consistent with its cytoskeleton regulatory role, ICA69 mutants show reduced α-Spectrin immunoreactivity at the larval NMJ. Manipulating levels of ICA69 or its interactor PICK1 alters the synaptic level of ionotropic glutamate receptors (iGluRs). Moreover, reducing PICK1 or Rab2 levels phenocopies ICA69 mutation. Interestingly, Rab2 regulates not only synaptic iGluR but also ICA69 levels. Thus, our data suggest that: (1) ICA69 regulates NMJ organization through a pathway that involves PICK1 and Rab2, and (2) Rab2 functions genetically upstream of ICA69 and regulates NMJ organization and targeting/retention of iGluRs by regulating ICA69 levels.
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Affiliation(s)
- Bhagaban Mallik
- Department of Biological Sciences, AB-3, Indian Institute of Science Education and Research, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Manish Kumar Dwivedi
- Department of Biological Sciences, AB-3, Indian Institute of Science Education and Research, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Zeeshan Mushtaq
- Department of Biological Sciences, AB-3, Indian Institute of Science Education and Research, Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Manisha Kumari
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Vimlesh Kumar
- Department of Biological Sciences, AB-3, Indian Institute of Science Education and Research, Bhauri, Bhopal, Madhya Pradesh 462066, India
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17
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Matsunaga K, Taoka M, Isobe T, Izumi T. Rab2a and Rab27a cooperatively regulate the transition from granule maturation to exocytosis through the dual effector Noc2. J Cell Sci 2016; 130:541-550. [PMID: 27927751 DOI: 10.1242/jcs.195479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Exocytosis of secretory granules entails budding from the trans-Golgi network, sorting and maturation of cargo proteins, and trafficking and fusion to the plasma membrane. Rab27a regulates the late steps in this process, such as granule recruitment to the fusion site, whereas Rab2a functions in the early steps, such as granule biogenesis and maturation. Here, we demonstrate that these two small GTPases simultaneously bind to Noc2 (also known as RPH3AL) in a GTP-dependent manner, although Rab2a binds only after Rab27a has bound. In pancreatic β-cells, the ternary Rab2a-Noc2-Rab27a complex specifically localizes on perinuclear immature granules, whereas the binary Noc2-Rab27a complex localizes on peripheral mature granules. In contrast to the wild type, Noc2 mutants defective in binding to Rab2a or Rab27a fail to promote glucose-stimulated insulin secretion. Although knockdown of any component of the ternary complex markedly inhibits insulin secretion, only knockdown of Rab2a or Noc2, and not that of Rab27a, impairs cargo processing from proinsulin to insulin. These results suggest that the dual effector, Noc2, regulates the transition from Rab2a-mediated granule biogenesis to Rab27a-mediated granule exocytosis.
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Affiliation(s)
- Kohichi Matsunaga
- Laboratory of Molecular Endocrinology and Metabolism, Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Tetsuro Izumi
- Laboratory of Molecular Endocrinology and Metabolism, Department of Molecular Medicine, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan .,Research Program for Signal Transduction, Division of Endocrinology, Metabolism and Signal Research, Gunma University Initiative for Advanced Research, Gunma University, Maebashi 371-8512, Japan
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18
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Topalidou I, Cattin-Ortolá J, Pappas AL, Cooper K, Merrihew GE, MacCoss MJ, Ailion M. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. PLoS Genet 2016; 12:e1006074. [PMID: 27191843 PMCID: PMC4871572 DOI: 10.1371/journal.pgen.1006074] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/30/2016] [Indexed: 12/15/2022] Open
Abstract
The dense-core vesicle is a secretory organelle that mediates the regulated release of peptide hormones, growth factors, and biogenic amines. Dense-core vesicles originate from the trans-Golgi of neurons and neuroendocrine cells, but it is unclear how this specialized organelle is formed and acquires its specific cargos. To identify proteins that act in dense-core vesicle biogenesis, we performed a forward genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We previously reported the identification of two conserved proteins that interact with the small GTPase RAB-2 to control normal dense-core vesicle cargo-sorting. Here we identify several additional conserved factors important for dense-core vesicle cargo sorting: the WD40 domain protein EIPR-1 and the endosome-associated recycling protein (EARP) complex. By assaying behavior and the trafficking of dense-core vesicle cargos, we show that mutants that lack EIPR-1 or EARP have defects in dense-core vesicle cargo-sorting similar to those of mutants in the RAB-2 pathway. Genetic epistasis data indicate that RAB-2, EIPR-1 and EARP function in a common pathway. In addition, using a proteomic approach in rat insulinoma cells, we show that EIPR-1 physically interacts with the EARP complex. Our data suggest that EIPR-1 is a new interactor of the EARP complex and that dense-core vesicle cargo sorting depends on the EARP-dependent trafficking of cargo through an endosomal sorting compartment. Animal cells package and store many important signaling molecules in specialized compartments called dense-core vesicles. Molecules stored in dense-core vesicles include peptide hormones like insulin and small molecule neurotransmitters like dopamine. Defects in the release of these compounds can lead to a wide range of metabolic and mental disorders in humans, including diabetes, depression, and drug addiction. However, it is not well understood how dense-core vesicles are formed in cells and package the appropriate molecules. Here we use a genetic screen in the microscopic worm C. elegans to identify proteins that are important for early steps in the generation of dense-core vesicles, such as packaging the correct molecular cargos in the vesicles. We identify several factors that are conserved between worms and humans and point to a new role for a protein complex that had previously been shown to be important for controlling trafficking in other cellular compartments. The identification of this complex suggests new cellular trafficking events that may be important for the generation of dense-core vesicles.
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Affiliation(s)
- Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jérôme Cattin-Ortolá
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Andrea L. Pappas
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kirsten Cooper
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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19
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Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 2015; 43:10612-22. [PMID: 26578562 PMCID: PMC4678817 DOI: 10.1093/nar/gkv1099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/09/2015] [Indexed: 01/27/2023] Open
Abstract
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to the reference genome. We developed and evaluated an approach to identify ‘hidden’ splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Computational analysis and experimental validation indicate that this approach identifies personal specific splice junctions at a low false positive rate. Applying this approach to an RNA-seq data set of 75 individuals, we identified 506 personal specific splice junctions, among which 437 were novel splice junctions not documented in current human transcript annotations. 94 splice junctions had splice site SNPs associated with GWAS signals of human traits and diseases. These involve genes whose splicing variations have been implicated in diseases (such as OAS1), as well as novel associations between alternative splicing and diseases (such as ICA1). Collectively, our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
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Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Hadžić T, Park D, Abruzzi KC, Yang L, Trigg JS, Rohs R, Rosbash M, Taghert PH. Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED. Nucleic Acids Res 2015; 43:2199-215. [PMID: 25634895 PMCID: PMC4344488 DOI: 10.1093/nar/gku1377] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Neuroendocrine (NE) cells use large dense core vesicles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secretory pathway. The dimmed (DIMM) basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, we have performed two independent genome-wide analyses of DIMM's activities: (i) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of DIMM occupancy and (ii) deep sequencing of purified DIMM neurons to characterize their transcriptional profile. By this combined approach, we showed that DIMM binds to conserved E-boxes in enhancers of 212 genes whose expression is enriched in DIMM-expressing NE cells. DIMM binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical machine learning revealed that flanking regions of putative DIMM binding sites contribute to its DNA binding specificity. DIMM's transcriptional repertoire features at least 20 LDCV constituents. In addition, DIMM notably targets the pro-secretory transcription factor, creb-A, but significantly, DIMM does not target any neuropeptide genes. DIMM therefore prescribes the scale of secretory activity in NE neurons, by a systematic control of both proximal and distal points in the regulated secretory pathway.
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Affiliation(s)
- Tarik Hadžić
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Dongkook Park
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Katharine C Abruzzi
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jennifer S Trigg
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Paul H Taghert
- Department of Anatomy and Neurobiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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21
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Loss of ICA69 Potentiates Long-Lasting Hyperalgesia After Subcutaneous Formalin Injection into the Mouse Hindpaw. Neurochem Res 2014; 40:579-90. [DOI: 10.1007/s11064-014-1503-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/10/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
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22
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Boon ACM, Williams RW, Sinasac DS, Webby RJ. A novel genetic locus linked to pro-inflammatory cytokines after virulent H5N1 virus infection in mice. BMC Genomics 2014; 15:1017. [PMID: 25418976 PMCID: PMC4256927 DOI: 10.1186/1471-2164-15-1017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/22/2014] [Indexed: 12/15/2022] Open
Abstract
Background Genetic variation in the human population is a key determinant of influenza disease severity. A single nucleotide polymorphism in the antiviral gene IFITM3 was linked to outcomes during the 2009 H1N1 pandemic. To identify variant host genes associated with increased virus replication and severe disease, we performed a quantitative trait locus analysis on pro-inflammatory cytokine production 48 hours after intranasal infection with highly pathogenic H5N1 influenza virus. Results Pro-inflammatory cytokines CCL2, TNFα and IFN-α, were measured by ELISA in lung homogenates of DBA/2J (D2), C57BL/6J (B6) and 44 different BXD recombinant inbred mouse strains. Virus titer was also assessed in a subset of these animals. CCL2 (8-fold), TNFα (24-fold) and IFN-α (8-fold) concentrations varied significantly among the different BXD RI strains. Importantly, cytokine concentration correlated very well (r =0.86-0.96, P <0.0001) with virus titer suggesting that early cytokine production is due to increased virus infection and replication. Linkage analysis of cytokine concentration revealed a significant locus on chromosome 6 associated with differences in TNFα, IFN-α and CCL2 cytokine concentration (LRS =26). This locus accounted for nearly 20% of the observed phenotypic variation in the BXD population studied. Sequence and RNA expression analysis identified several candidate host genes containing missense mutations or deletions; Samd9l, Ica1, and Slc25a13. To study the role of Slc25a13, we obtained Slc25a13 knockout line, but upon challenge with H5N1 influenza virus observed no effect on CCL2 production, or morbidity and mortality. Conclusion A novel genetic locus on chromosome 6 modulates early pro-inflammatory cytokine production and virus replication after highly pathogenic influenza virus infection. Candidate genes, Samd9l and Ica1, may be important for the control of influenza virus infection and pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1017) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrianus C M Boon
- Departments of Internal Medicine, Division of Infectious Diseases, Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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23
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Ailion M, Hannemann M, Dalton S, Pappas A, Watanabe S, Hegermann J, Liu Q, Han HF, Gu M, Goulding MQ, Sasidharan N, Schuske K, Hullett P, Eimer S, Jorgensen EM. Two Rab2 interactors regulate dense-core vesicle maturation. Neuron 2014; 82:167-80. [PMID: 24698274 DOI: 10.1016/j.neuron.2014.02.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2014] [Indexed: 12/14/2022]
Abstract
Peptide neuromodulators are released from a unique organelle: the dense-core vesicle. Dense-core vesicles are generated at the trans-Golgi and then sort cargo during maturation before being secreted. To identify proteins that act in this pathway, we performed a genetic screen in Caenorhabditis elegans for mutants defective in dense-core vesicle function. We identified two conserved Rab2-binding proteins: RUND-1, a RUN domain protein, and CCCP-1, a coiled-coil protein. RUND-1 and CCCP-1 colocalize with RAB-2 at the Golgi, and rab-2, rund-1, and cccp-1 mutants have similar defects in sorting soluble and transmembrane dense-core vesicle cargos. RUND-1 also interacts with the Rab2 GAP protein TBC-8 and the BAR domain protein RIC-19, a RAB-2 effector. In summary, a pathway of conserved proteins controls the maturation of dense-core vesicles at the trans-Golgi network.
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Affiliation(s)
- Michael Ailion
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry, University of Washington, Seattle WA, 98195, USA.
| | - Mandy Hannemann
- European Neuroscience Institute, 37077 Göttingen, Germany; International Max Planck Research School Molecular Biology, 37077 Göttingen, Germany
| | - Susan Dalton
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrea Pappas
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Shigeki Watanabe
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Jan Hegermann
- European Neuroscience Institute, 37077 Göttingen, Germany; DFG research Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Qiang Liu
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Hsiao-Fen Han
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mingyu Gu
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Morgan Q Goulding
- Department of Biochemistry, University of Washington, Seattle WA, 98195, USA
| | | | - Kim Schuske
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Patrick Hullett
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Stefan Eimer
- European Neuroscience Institute, 37077 Göttingen, Germany; DFG research Center for Molecular Physiology of the Brain (CMPB), 37077 Göttingen, Germany
| | - Erik M Jorgensen
- Howard Hughes Medical Institute, Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
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Reiterer V, Eyers PA, Farhan H. Day of the dead: pseudokinases and pseudophosphatases in physiology and disease. Trends Cell Biol 2014; 24:489-505. [PMID: 24818526 DOI: 10.1016/j.tcb.2014.03.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022]
Abstract
Pseudophosphatases and pseudokinases are increasingly viewed as integral elements of signaling pathways, and there is mounting evidence that they have frequently retained the ability to interact with cellular 'substrates', and can exert important roles in different diseases. However, these pseudoenzymes have traditionally received scant attention compared to classical kinases and phosphatases. In this review we explore new findings in the emerging pseudokinase and pseudophosphatase fields, and discuss their different modes of action which include exciting new roles as scaffolds, anchors, spatial modulators, traps, and ligand-driven regulators of canonical kinases and phosphatases. Thus, it is now apparent that pseudokinases and pseudophosphatases both support and drive a panoply of signaling networks. Finally, we highlight recent evidence on their involvement in human pathologies, marking them as potential novel drug targets.
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Affiliation(s)
- Veronika Reiterer
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Hesso Farhan
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Department of Biology, University of Konstanz, Konstanz, Germany.
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25
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Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus. Hum Mol Genet 2013; 22:4653-60. [PMID: 23836780 PMCID: PMC3904806 DOI: 10.1093/hmg/ddt293] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
To discover quantitative trait loci for intraocular pressure, a major risk factor for glaucoma and the only modifiable one, we performed a genome-wide association study on a discovery cohort of 2175 individuals from Sydney, Australia. We found a novel association between intraocular pressure and a common variant at 7p21 near to GLCCI1 and ICA1. The findings in this region were confirmed through two UK replication cohorts totalling 4866 individuals (rs59072263, Pcombined = 1.10 × 10−8). A copy of the G allele at this SNP is associated with an increase in mean IOP of 0.45 mmHg (95%CI = 0.30–0.61 mmHg). These results lend support to the implication of vesicle trafficking and glucocorticoid inducibility pathways in the determination of intraocular pressure and in the pathogenesis of primary open-angle glaucoma.
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26
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Cao M, Mao Z, Kam C, Xiao N, Cao X, Shen C, Cheng KKY, Xu A, Lee KM, Jiang L, Xia J. PICK1 and ICA69 control insulin granule trafficking and their deficiencies lead to impaired glucose tolerance. PLoS Biol 2013; 11:e1001541. [PMID: 23630453 PMCID: PMC3635858 DOI: 10.1371/journal.pbio.1001541] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 03/12/2013] [Indexed: 11/19/2022] Open
Abstract
PICK1 and ICA69, proteins containing a BAR domain, regulate the biogenesis and maturation of insulin granules in mice. Diabetes is a metabolic disorder characterized by hyperglycemia. Insulin, which is secreted by pancreatic beta cells, is recognized as the critical regulator of blood glucose, but the molecular machinery responsible for insulin trafficking remains poorly defined. In particular, the roles of cytosolic factors that govern the formation and maturation of insulin granules are unclear. Here we report that PICK1 and ICA69, two cytosolic lipid-binding proteins, formed heteromeric BAR-domain complexes that associated with insulin granules at different stages of their maturation. PICK1-ICA69 heteromeric complexes associated with immature secretory granules near the trans-Golgi network (TGN). A brief treatment of Brefeldin A, which blocks vesicle budding from the Golgi, increased the amount of PICK1 and ICA69 at TGN. On the other hand, mature secretory granules were associated with PICK1 only, not ICA69. PICK1 deficiency in mice caused the complete loss of ICA69 and led to increased food and water intake but lower body weight. Glucose tolerance tests demonstrated that these mutant mice had high blood glucose, a consequence of insufficient insulin. Importantly, while the total insulin level was reduced in PICK1-deficient beta cells, proinsulin was increased. Lastly, ICA69 knockout mice also displayed similar phenotype as the mice deficient in PICK1. Together, our results indicate that PICK1 and ICA69 are key regulators of the formation and maturation of insulin granules.
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Affiliation(s)
- Mian Cao
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhuo Mao
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chuen Kam
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Nan Xiao
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoxing Cao
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chong Shen
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Kenneth K. Y. Cheng
- Department of Medicine and Department of Pharmacology & Pharmacy, University of Hong Kong, Hong Kong, China
| | - Aimin Xu
- Department of Medicine and Department of Pharmacology & Pharmacy, University of Hong Kong, Hong Kong, China
| | - Kwong-Man Lee
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jun Xia
- Division of Life Science, Division of Biomedical Engineering and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China
- * E-mail:
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27
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Holst B, Madsen KL, Jansen AM, Jin C, Rickhag M, Lund VK, Jensen M, Bhatia V, Sørensen G, Madsen AN, Xue Z, Møller SK, Woldbye D, Qvortrup K, Huganir R, Stamou D, Kjærulff O, Gether U. PICK1 deficiency impairs secretory vesicle biogenesis and leads to growth retardation and decreased glucose tolerance. PLoS Biol 2013; 11:e1001542. [PMID: 23630454 PMCID: PMC3635866 DOI: 10.1371/journal.pbio.1001542] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/12/2013] [Indexed: 01/02/2023] Open
Abstract
Two lipid membrane sculpting BAR domain proteins, PICK1 and ICA69, play a key role early in the biogenesis of peptide hormone secretory vesicles and are critical for normal growth and metabolic homeostasis. Secretory vesicles in endocrine cells store hormones such as growth hormone (GH) and insulin before their release into the bloodstream. The molecular mechanisms governing budding of immature secretory vesicles from the trans-Golgi network (TGN) and their subsequent maturation remain unclear. Here, we identify the lipid binding BAR (Bin/amphiphysin/Rvs) domain protein PICK1 (protein interacting with C kinase 1) as a key component early in the biogenesis of secretory vesicles in GH-producing cells. Both PICK1-deficient Drosophila and mice displayed somatic growth retardation. Growth retardation was rescued in flies by reintroducing PICK1 in neurosecretory cells producing somatotropic peptides. PICK1-deficient mice were characterized by decreased body weight and length, increased fat accumulation, impaired GH secretion, and decreased storage of GH in the pituitary. Decreased GH storage was supported by electron microscopy showing prominent reduction in secretory vesicle number. Evidence was also obtained for impaired insulin secretion associated with decreased glucose tolerance. PICK1 localized in cells to immature secretory vesicles, and the PICK1 BAR domain was shown by live imaging to associate with vesicles budding from the TGN and to possess membrane-sculpting properties in vitro. In mouse pituitary, PICK1 co-localized with the BAR domain protein ICA69, and PICK1 deficiency abolished ICA69 protein expression. In the Drosophila brain, PICK1 and ICA69 co-immunoprecipitated and showed mutually dependent expression. Finally, both in a Drosophila model of type 2 diabetes and in high-fat-diet-induced obese mice, we observed up-regulation of PICK1 mRNA expression. Our findings suggest that PICK1, together with ICA69, is critical during budding of immature secretory vesicles from the TGN and thus for vesicular storage of GH and possibly other hormones. The data link two BAR domain proteins to membrane remodeling processes in the secretory pathway of peptidergic endocrine cells and support an important role of PICK1/ICA69 in maintenance of metabolic homeostasis. Regulated secretion of peptide hormones, such as growth hormone (GH) and insulin, represents a fundamental process in controlling physiological homeostasis. In endocrine cells, hormone-containing vesicles bud from the Golgi apparatus to enable storage and regulated release into the blood stream. Here we show that two proteins with a lipid membrane-shaping BAR domain, PICK1 and ICA69, work together in the pituitary gland and the pancreas to facilitate the budding of early secretory vesicle from the Golgi apparatus. The physiological significance of our findings was borne out by showing that mice and Drosophila flies lacking the PICK1 encoding gene have marked growth retardation. PICK1-deficient mice showed increased fat accumulation, reduced body weight and length, as well as reduced glucose clearance from the blood stream. Consistent with these findings, we observed a severe reduction in GH storage in the pituitary and impaired secretion of both insulin and GH in response to physiological stimuli. Finally, we found that PICK1 expression levels were raised in a fly model of type 2 diabetes and in high-fat-diet-induced obese mice. These results indicate that alteration of PICK1 expression might play a role in pathophysiological processes of metabolic diseases and/or in a protective compensatory mechanism.
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Affiliation(s)
- Birgitte Holst
- Laboratory for Molecular Pharmacology, Novo Nordisk Foundation Center for Basic Metabolic Research, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (BH); (OK); (UG)
| | - Kenneth L. Madsen
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anna M. Jansen
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chunyu Jin
- Laboratory for Molecular Pharmacology, Novo Nordisk Foundation Center for Basic Metabolic Research, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mattias Rickhag
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Viktor K. Lund
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten Jensen
- Laboratory for Molecular Pharmacology, Novo Nordisk Foundation Center for Basic Metabolic Research, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vikram Bhatia
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- BioNano Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar Sørensen
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andreas N. Madsen
- Laboratory for Molecular Pharmacology, Novo Nordisk Foundation Center for Basic Metabolic Research, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zhichao Xue
- Laboratory for Molecular Pharmacology, Novo Nordisk Foundation Center for Basic Metabolic Research, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Siri K. Møller
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Woldbye
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy, Department of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Richard Huganir
- Department of Neuroscience, The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dimitrios Stamou
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- BioNano Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ole Kjærulff
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (BH); (OK); (UG)
| | - Ulrik Gether
- Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Molecular Neuropharmacology Laboratory, The Faculty of Health Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (BH); (OK); (UG)
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Arvan P, Pietropaolo M, Ostrov D, Rhodes CJ. Islet autoantigens: structure, function, localization, and regulation. Cold Spring Harb Perspect Med 2012; 2:cshperspect.a007658. [PMID: 22908193 DOI: 10.1101/cshperspect.a007658] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Islet autoantigens associated with autoimmune type 1 diabetes (T1D) are expressed in pancreatic β cells, although many show wider patterns of expression in the neuroendocrine system. Within pancreatic β cells, every T1D autoantigen is in one way or another linked to the secretory pathway. Together, these autoantigens play diverse roles in glucose regulation, metabolism of biogenic amines, as well as the regulation, formation, and packaging of secretory granules. The mechanism(s) by which immune tolerance to islet-cell antigens is lost during the development of T1D, remains unclear. Antigenic peptide creation for immune presentation may potentially link to the secretory biology of β cells in a number of ways, including proteasomal digestion of misfolded products, exocytosis and endocytosis of cell-surface products, or antigen release from dying β cells during normal or pathological turnover. In this context, we evaluate the biochemical nature and immunogenicity of the major autoantigens in T1D including (pro)insulin, GAD65, ZnT8, IA2, and ICA69.
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Affiliation(s)
- Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA.
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TBC-8, a putative RAB-2 GAP, regulates dense core vesicle maturation in Caenorhabditis elegans. PLoS Genet 2012; 8:e1002722. [PMID: 22654674 PMCID: PMC3359978 DOI: 10.1371/journal.pgen.1002722] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 04/04/2012] [Indexed: 02/05/2023] Open
Abstract
Dense core vesicles (DCVs) are thought to be generated at the late Golgi apparatus as immature DCVs, which subsequently undergo a maturation process through clathrin-mediated membrane remodeling events. This maturation process is required for efficient processing of neuropeptides within DCVs and for removal of factors that would otherwise interfere with DCV release. Previously, we have shown that the GTPase, RAB-2, and its effector, RIC-19, are involved in DCV maturation in Caenorhabditis elegans motoneurons. In rab-2 mutants, specific cargo is lost from maturing DCVs and missorted into the endosomal/lysosomal degradation route. Cargo loss could be prevented by blocking endosomal delivery. This suggests that RAB-2 is involved in retention of DCV components during the sorting process at the Golgi-endosomal interface. To understand how RAB-2 activity is regulated at the Golgi, we screened for RAB-2-specific GTPase activating proteins (GAPs). We identified a potential RAB-2 GAP, TBC-8, which is exclusively expressed in neurons and which, when depleted, shows similar DCV maturation defects as rab-2 mutants. We could demonstrate that RAB-2 binds to its putative GAP, TBC-8. Interestingly, TBC-8 also binds to the RAB-2 effector, RIC-19. This interaction appears to be conserved as TBC-8 also interacted with the human ortholog of RIC-19, ICA69. Therefore, we propose that a dynamic ON/OFF cycling of RAB-2 at the Golgi induced by the GAP/effector complex is required for proper DCV maturation.
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Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP, Beems M, Giannoukakis N, Trucco G, Palumbo MO, Solimena M, Pugliese A, Polychronakos C, Trucco M, Pietropaolo M. Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression. J Biol Chem 2012; 287:17882-17893. [PMID: 22447927 PMCID: PMC3366781 DOI: 10.1074/jbc.m111.319020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 03/15/2012] [Indexed: 12/22/2022] Open
Abstract
ICA69 (islet cell autoantigen 69 kDa) is a protein implicated in type 1 diabetes mellitus in both the non-obese diabetic (NOD) mouse model and humans. ICA69 is encoded by the Ica1 gene on mouse chromosome 6 A1-A2. We previously reported reduced ICA69 expression in the thymus of NOD mice compared with thymus of several non-diabetic mouse strains. We propose that reduced thymic ICA69 expression could result from variations in transcriptional regulation of the gene and that polymorphisms within the Ica1 core promoter may partially determine this transcriptional variability. We characterized the functional promoter of Ica1 in NOD mice and compared it with the corresponding portions of Ica1 in non-diabetic C57BL/6 mice. Luciferase reporter constructs demonstrated that the NOD Ica1 promoter region exhibited markedly reduced luciferase expression in transiently transfected medullary thymus epithelial (mTEC(+)) and B-cell (M12)-derived cell lines. However, in a non-diabetic strain, C57BL/6, the Ica1 promoter region was transcriptionally active when transiently transfected into the same cell lines. We concomitantly identified five single nucleotide polymorphisms within the NOD Ica1 promoter. One of these single nucleotide polymorphisms increases the binding affinity for the transcription factor AIRE (autoimmune regulator), which is highly expressed in thymic epithelial cells, where it is known to play a key role regulating self-antigen expression. We conclude that polymorphisms within the NOD Ica1 core promoter may determine AIRE-mediated down-regulation of ICA69 expression in medullary thymic epithelial cells, thus providing a novel mechanistic explanation for the loss of immunologic tolerance to this self-antigen in autoimmunity.
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Affiliation(s)
- Samantha M Bonner
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Susan L Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Yong Fan
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Yigang Chang
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Michael P Morran
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Megan Beems
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Nick Giannoukakis
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224; Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Giuliana Trucco
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Michael O Palumbo
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Michele Solimena
- Department of Molecular Diabetology, Paul Langerhans Institute Dresden, Carl Gustav Carus School of Medicine, Dresden University of Technology, 01307 Dresden, Germany
| | - Alberto Pugliese
- Immunogenetics Program, Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Massimo Trucco
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Massimo Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105.
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Jaschke A, Chung B, Hesse D, Kluge R, Zahn C, Moser M, Petzke KJ, Brigelius-Flohé R, Puchkov D, Koepsell H, Heeren J, Joost HG, Schürmann A. The GTPase ARFRP1 controls the lipidation of chylomicrons in the Golgi of the intestinal epithelium. Hum Mol Genet 2012; 21:3128-42. [PMID: 22505585 PMCID: PMC3384381 DOI: 10.1093/hmg/dds140] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The uptake and processing of dietary lipids by the small intestine is a multistep process that involves several steps including vesicular and protein transport. The GTPase ADP-ribosylation factor-related protein 1 (ARFRP1) controls the ARF-like 1 (ARL1)-mediated Golgi recruitment of GRIP domain proteins which in turn bind several Rab-GTPases. Here, we describe the essential role of ARFRP1 and its interaction with Rab2 in the assembly and lipidation of chylomicrons in the intestinal epithelium. Mice lacking Arfrp1 specifically in the intestine (Arfrp1vil−/−) exhibit an early post-natal growth retardation with reduced plasma triacylglycerol and free fatty acid concentrations. Arfrp1vil−/− enterocytes as well as Arfrp1 mRNA depleted Caco-2 cells absorbed fatty acids normally but secreted chylomicrons with a markedly reduced triacylglycerol content. In addition, the release of apolipoprotein A-I (ApoA-I) was dramatically decreased, and ApoA-I accumulated in the Arfrp1vil−/− epithelium, where it predominantly co-localized with Rab2. The release of chylomicrons from Caco-2 was markedly reduced after the suppression of Rab2, ARL1 and Golgin-245. Thus, the GTPase ARFRP1 and its downstream proteins are required for the lipidation of chylomicrons and the assembly of ApoA-I to these particles in the Golgi of intestinal epithelial cells.
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Affiliation(s)
- Alexander Jaschke
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, D-14558 Nuthetal, Germany
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Larsson S, Resjö S, Gomez MF, James P, Holm C. Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13). J Proteome Res 2012; 11:1264-73. [PMID: 22268682 DOI: 10.1021/pr200957p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Lipids are known to play a crucial role both in the normal control of insulin release and in the deterioration of β-cell function, as observed in type 2 diabetes. Despite this established dual role of lipids, little is known about lipid storage and handling in β-cells. Here, we isolated lipid droplets from oleate-incubated INS-1 832/13 cells and characterized the lipid droplet proteome. In a total of four rounds of droplet isolation and proteomic analysis by HPLC-MS/MS, we identified 96 proteins that were specific to droplets. The proteins fall into six categories based on function or previously observed localization: metabolism, endoplasmic reticulum/ribosomes, mitochondria, vesicle formation and transport, signaling, and miscellaneous. The protein profile reinforces the emerging picture of the lipid droplet as an active and dynamic organelle involved in lipid homeostasis and intracellular trafficking. Proteins belonging to the category mitochondria were highly represented, suggesting that the β-cell mitochondria and lipid droplets form a metabolic unit of potential relevance for insulin secretion.
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Affiliation(s)
- Sara Larsson
- Department of Experimental Medical Science, Division of Diabetes, Metabolism and Endocrinology, Lund Univeristy , BMC C11, SE-221 84 Lund, Sweden.
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Ramírez F, Lawyer G, Albrecht M. Novel search method for the discovery of functional relationships. ACTA ACUST UNITED AC 2011; 28:269-76. [PMID: 22180409 PMCID: PMC3259435 DOI: 10.1093/bioinformatics/btr631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Motivation: Numerous annotations are available that functionally characterize genes and proteins with regard to molecular process, cellular localization, tissue expression, protein domain composition, protein interaction, disease association and other properties. Searching this steadily growing amount of information can lead to the discovery of new biological relationships between genes and proteins. To facilitate the searches, methods are required that measure the annotation similarity of genes and proteins. However, most current similarity methods are focused only on annotations from the Gene Ontology (GO) and do not take other annotation sources into account. Results: We introduce the new method BioSim that incorporates multiple sources of annotations to quantify the functional similarity of genes and proteins. We compared the performance of our method with four other well-known methods adapted to use multiple annotation sources. We evaluated the methods by searching for known functional relationships using annotations based only on GO or on our large data warehouse BioMyn. This warehouse integrates many diverse annotation sources of human genes and proteins. We observed that the search performance improved substantially for almost all methods when multiple annotation sources were included. In particular, our method outperformed the other methods in terms of recall and average precision. Contact:mario.albrecht@mpi-inf.mpg.de Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fidel Ramírez
- Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany
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Wang X, Nath A, Yang X, Portis A, Walton SP, Chan C. Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. PLoS One 2011; 6:e28138. [PMID: 22132232 PMCID: PMC3223234 DOI: 10.1371/journal.pone.0028138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 11/02/2011] [Indexed: 12/27/2022] Open
Abstract
The regulation of complex cellular activities in palmitate treated HepG2 cells, and the ensuing cytotoxic phenotype, involves cooperative interactions between genes. While previous approaches have largely focused on identifying individual target genes, elucidating interacting genes has thus far remained elusive. We applied the concept of information synergy to reconstruct a “gene-cooperativity” network for palmititate-induced cytotoxicity in liver cells. Our approach integrated gene expression data with metabolic profiles to select a subset of genes for network reconstruction. Subsequent analysis of the network revealed insulin signaling as the most significantly enriched pathway, and desmoplakin (DSP) as its top neighbor. We determined that palmitate significantly reduces DSP expression, and treatment with insulin restores the lost expression of DSP. Insulin resistance is a common pathological feature of fatty liver and related ailments, whereas loss of DSP has been noted in liver carcinoma. Reduced DSP expression can lead to loss of cell-cell adhesion via desmosomes, and disrupt the keratin intermediate filament network. Our findings suggest that DSP expression may be perturbed by palmitate and, along with insulin resistance, may play a role in palmitate induced cytotoxicity, and serve as potential targets for further studies on non-alcoholic fatty liver disease (NAFLD).
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Affiliation(s)
- Xuewei Wang
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Aritro Nath
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Xuerui Yang
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Amanda Portis
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Prigent M, Boy-Marcotte E, Chesneau L, Gibson K, Dupré-Crochet S, Tisserand H, Verbavatz JM, Cuif MH. The RabGAP proteins Gyp5p and Gyl1p recruit the BAR domain protein Rvs167p for polarized exocytosis. Traffic 2011; 12:1084-97. [PMID: 21554509 DOI: 10.1111/j.1600-0854.2011.01218.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Rab GTPase-activating proteins (GAP) Gyp5p and Gyl1p are involved in the control of polarized exocytosis at the small-bud stage in Saccharomyces cerevisiae. Both Gyp5p and Gyl1p interact with the N-Bin1/Amphiphysin/Rvs167 (BAR) domain protein Rvs167p, but the biological function of this interaction is unclear. We show here that Gyp5p and Gyl1p recruit Rvs167p to the small-bud tip, where it plays a role in polarized exocytosis. In gyp5Δgyl1Δ cells, Rvs167p is not correctly localized to the small-bud tip. Both P473L mutation in the SH3 domain of Rvs167p and deletion of the proline-rich regions of Gyp5p and Gyl1p disrupt the interaction of Rvs167p with Gyp5p and Gyl1p and impair the localization of Rvs167p to the tips of small buds. We provide evidence for the accumulation of secretory vesicles in small buds of rvs167Δ cells and for defective Bgl2p secretion in rvs167Δ cultures enriched in small-budded cells at 13°C, implicating Rvs167p in polarized exocytosis. Moreover, both the accumulation of secretory vesicles in Rvs167p P473L cells cultured at 13°C and secretion defects in cells producing Gyp5p and Gyl1p without proline-rich regions strongly suggest that the function of Rvs167p in exocytosis depends on its ability to interact with Gyp5p and Gyl1p.
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Affiliation(s)
- Magali Prigent
- Univ Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR8621, Bâtiment 400, Orsay F-91405, France
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Abstract
Intracellular membrane traffic defines a complex network of pathways that connects many of the membrane-bound organelles of eukaryotic cells. Although each pathway is governed by its own set of factors, they all contain Rab GTPases that serve as master regulators. In this review, we discuss how Rabs can regulate virtually all steps of membrane traffic from the formation of the transport vesicle at the donor membrane to its fusion at the target membrane. Some of the many regulatory functions performed by Rabs include interacting with diverse effector proteins that select cargo, promoting vesicle movement, and verifying the correct site of fusion. We describe cascade mechanisms that may define directionality in traffic and ensure that different Rabs do not overlap in the pathways that they regulate. Throughout this review we highlight how Rab dysfunction leads to a variety of disease states ranging from infectious diseases to cancer.
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Affiliation(s)
- Alex H Hutagalung
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
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Barkalifa R, Yagil Y, Yagil C. Sex-specific genetic dissection of diabetes in a rodent model identifies Ica1 and Ndufa4 as major candidate genes. Physiol Genomics 2010; 42:445-55. [PMID: 20530722 DOI: 10.1152/physiolgenomics.00042.2010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The aim of the study was to initiate a sex-specific investigation of the molecular basis of diabetes, using a genomic approach in the Cohen Diabetic rat model of diet-induced Type 2 diabetes. We used an F2 population resulting from a cross between Cohen Diabetic susceptible (CDs) and resistant (CDr) and consisting of 132 males and 159 females to detect relevant QTLs by linkage and cosegregation analyses. To confirm the functional relevance of the QTL, we applied the "chromosome substitution" strategy. We identified candidate genes within the quantitative trait locus (QTL) and studied their differential expression. We sequenced the differentially expressed candidate genes to account for differences in their expression. We confirmed in this new cross in males a previously detected major QTL on rat chromosome 4 (RNO4); we identified in females this major QTL as well. We found three additional diabetes-related QTLs on RNO11, 13, and 20 in females only. We pursued the investigation of the QTL on RNO4 and generated a CDs.4(CDr) consomic strain, which provided us with functional confirmation for the contribution of the QTL to the diabetic phenotype in both sexes. We successfully narrowed the QTL span to 2.6 cM and identified within it six candidate genes, but only two of which, Ica1 (islet cell autoantigen 1) and Ndufa4 (NADH dehydrogenase ubiquinone) were differentially expressed between CDs and CDr. We sequenced the exons and promoter regions of Ica1 and Ndufa4 but did not identify sequence variations between the strains. The detection of the QTL on RNO4 in both sexes suggests involvement of Ica1, Ndufa4, the Golgi apparatus, the mitochondria and genetic susceptibility to dietary-environmental factors in the pathophysiology of diabetes in our model. The additional sex-specific QTLs are likely to account for differences in the diabetic phenotype between the sexes.
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Affiliation(s)
- Ronit Barkalifa
- Faculty of Health Sciences, Ben-Gurion University, Barzilai Medical Center Campus, Ashkelon, Israel
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Abstract
Glucose-stimulated insulin secretion from the islet beta-cell involves a sequence of metabolic events and an interplay between a wide range of signaling pathways leading to the generation of second messengers (e.g., cyclic nucleotides, adenine and guanine nucleotides, soluble lipid messengers) and mobilization of calcium ions. Consequent to the generation of necessary signals, the insulin-laden secretory granules are transported from distal sites to the plasma membrane for fusion and release of their cargo into the circulation. The secretory granule transport underlies precise changes in cytoskeletal architecture involving a well-coordinated cross-talk between various signaling proteins, including small molecular mass GTP-binding proteins (G proteins) and their respective effector proteins. The purpose of this article is to provide an overview of current understanding of the identity of small G proteins (e.g., Cdc42, Rac1, and ARF-6) and their corresponding regulatory factors (e.g., GDP/GTP-exchange factors, GDP-dissociation inhibitors) in the pancreatic beta-cell. Plausible mechanisms underlying regulation of these signaling proteins by insulin secretagogues are also discussed. In addition to their positive modulatory roles, certain small G proteins also contribute to the metabolic dysfunction and demise of the islet beta-cell seen in in vitro and in vivo models of impaired insulin secretion and diabetes. Emerging evidence also suggests significant insulin secretory abnormalities in small G protein knockout animals, further emphasizing vital roles for these proteins in normal health and function of the islet beta-cell. Potential significance of these experimental observations from multiple laboratories and possible avenues for future research in this area of islet research are highlighted.
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Affiliation(s)
- Anjaneyulu Kowluru
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48202-3489, USA.
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Sumakovic M, Hegermann J, Luo L, Husson SJ, Schwarze K, Olendrowitz C, Schoofs L, Richmond J, Eimer S. UNC-108/RAB-2 and its effector RIC-19 are involved in dense core vesicle maturation in Caenorhabditis elegans. ACTA ACUST UNITED AC 2009; 186:897-914. [PMID: 19797081 PMCID: PMC2753160 DOI: 10.1083/jcb.200902096] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Uncoordinated movement in Rab2 mutants is caused by impaired retention of cargo on dense core vesicles, not by defective synaptic vesicle release. (Also see the companion article by Edwards et al. in this issue.) Small guanosine triphosphatases of the Rab family regulate intracellular vesicular trafficking. Rab2 is highly expressed in the nervous system, yet its function in neurons is unknown. In Caenorhabditis elegans, unc-108/rab-2 mutants have been isolated based on their locomotory defects. We show that the locomotion defects of rab-2 mutants are not caused by defects in synaptic vesicle release but by defects in dense core vesicle (DCV) signaling. DCVs in rab-2 mutants are often enlarged and heterogeneous in size; however, their number and distribution are not affected. This implicates Rab2 in the biogenesis of DCVs at the Golgi complex. We demonstrate that Rab2 is required to prevent DCV cargo from inappropriately entering late endosomal compartments during DCV maturation. Finally, we show that RIC-19, the C. elegans orthologue of the human diabetes autoantigen ICA69, is also involved in DCV maturation and is recruited to Golgi membranes by activated RAB-2. Thus, we propose that RAB-2 and its effector RIC-19 are required for neuronal DCV maturation.
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Affiliation(s)
- Marija Sumakovic
- European Neuroscience Institute Goettingen, German Research Foundation Research Center for Molecular Physiology of the Brain, 37077 Goettingen, Germany
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Sol ERM, Hovsepyan M, Bergsten P. Proteins altered by elevated levels of palmitate or glucose implicated in impaired glucose-stimulated insulin secretion. Proteome Sci 2009; 7:24. [PMID: 19607692 PMCID: PMC2732594 DOI: 10.1186/1477-5956-7-24] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 07/16/2009] [Indexed: 01/09/2023] Open
Abstract
Background Development of type 2 diabetes mellitus (T2DM) is characterized by aberrant insulin secretory patterns, where elevated insulin levels at non-stimulatory basal conditions and reduced hormonal levels at stimulatory conditions are major components. To delineate mechanisms responsible for these alterations we cultured INS-1E cells for 48 hours at 20 mM glucose in absence or presence of 0.5 mM palmitate, when stimulatory secretion of insulin was reduced or basal secretion was elevated, respectively. Results After culture, cells were protein profiled by SELDI-TOF-MS and 2D-PAGE. Differentially expressed proteins were discovered and identified by peptide mass fingerprinting. Complimentary protein profiles were obtained by the two approaches with SELDI-TOF-MS being more efficient in separating proteins in the low molecular range and 2D-PAGE in the high molecular range. Identified proteins included alpha glucosidase, calmodulin, gars, glucose-6-phosphate dehydrogenase, heterogenous nuclear ribonucleoprotein A3, lon peptidase, nicotineamide adenine dinucleotide hydrogen (NADH) dehydrogenase, phosphoglycerate kinase, proteasome p45, rab2, pyruvate kinase and t-complex protein. The observed glucose-induced differential protein expression pattern indicates enhanced glucose metabolism, defense against reactive oxygen species, enhanced protein translation, folding and degradation and decreased insulin granular formation and trafficking. Palmitate-induced changes could be related to altered exocytosis. Conclusion The identified altered proteins indicate mechanism important for altered β-cell function in T2DM.
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Affiliation(s)
- E-ri M Sol
- Department of Medical Cell Biology, Uppsala University, Sweden.
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