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Saraswathi V, Ai W, Kumar V, Sharma K, Gopal T, Kumar N, Malhi H, Sehrawat T, Desouza CV. A Pilot Study on the Proteomics Profile of Serum Exosome-Enriched Extracellular Vesicles from Normal versus Individuals with Obesity-Related Insulin Resistance. Biomedicines 2024; 12:799. [PMID: 38672154 PMCID: PMC11048419 DOI: 10.3390/biomedicines12040799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
OBJECTIVE Circulating exosome-enriched extracellular vesicles (EVs) have drawn considerable importance in obesity-related insulin-resistance (IR). We sought to compare the proteomics profile of serum exosomes from normal individuals and those with obesity and IR. METHODS We isolated serum exosomes from male subjects with obesity and insulin resistance (Ob-IR, HOMA-IR > 2.0) and lean/overweight insulin-sensitive (Normal (N), HOMA-IR < 2.0) individuals. The differential protein expression between the two groups was detected by a label-free quantitative mass spectrometry analysis followed by GO annotation and ingenuity pathway analysis (IPA). RESULTS We identified 23 upregulated and 46 downregulated proteins between Ob-IR and N groups. Some of these proteins are involved in altering insulin signaling (VPS13C, TBC1D32, TTR, and ADIPOQ), inflammation (NFκB and CRP), and B-cell proliferation/activation (IGLV4-69, IGKV1D-13, and IGHV4-28). GO analysis revealed that the differentially expressed proteins (DEPs) are mainly involved in regulating immune cell activation and are located in extracellular space. IPA analysis showed that top molecules mediating IR, inflammation and B-cell activation were upregulated in Ob-IR subjects compared to N subjects. CONCLUSIONS Serum exosomal proteins can be used as biomarkers to identify the future risk of diabetes and a therapeutic target to prevent or slow down the progression of diabetes in high-risk individuals.
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Affiliation(s)
- Viswanathan Saraswathi
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA; (V.S.); (W.A.); (T.G.); (N.K.)
- Department of Internal Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Weilun Ai
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA; (V.S.); (W.A.); (T.G.); (N.K.)
- Department of Internal Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vikas Kumar
- Department of Genetics Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (V.K.); (K.S.)
| | - Kanika Sharma
- Department of Genetics Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (V.K.); (K.S.)
| | - Thiyagarajan Gopal
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA; (V.S.); (W.A.); (T.G.); (N.K.)
- Department of Internal Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Narendra Kumar
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA; (V.S.); (W.A.); (T.G.); (N.K.)
- Department of Internal Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Harmeet Malhi
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA (T.S.)
| | - Tejasav Sehrawat
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA (T.S.)
| | - Cyrus V. Desouza
- VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA; (V.S.); (W.A.); (T.G.); (N.K.)
- Department of Internal Medicine, Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Di Pietro P, Abate AC, Prete V, Damato A, Venturini E, Rusciano MR, Izzo C, Visco V, Ciccarelli M, Vecchione C, Carrizzo A. C2CD4B Evokes Oxidative Stress and Vascular Dysfunction via a PI3K/Akt/PKCα-Signaling Pathway. Antioxidants (Basel) 2024; 13:101. [PMID: 38247525 PMCID: PMC10812653 DOI: 10.3390/antiox13010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
High glucose-induced endothelial dysfunction is an important pathological feature of diabetic vasculopathy. While genome-wide studies have identified an association between type 2 diabetes mellitus (T2DM) and increased expression of a C2 calcium-dependent domain containing 4B (C2CD4B), no study has yet explored the possible direct effect of C2CD4B on vascular function. Vascular reactivity studies were conducted using a pressure myograph, and nitric oxide and oxidative stress were assessed through difluorofluorescein diacetate and dihydroethidium, respectively. We demonstrate that high glucose upregulated both mRNA and protein expression of C2CD4B in mice mesenteric arteries in a time-dependent manner. Notably, the inhibition of C2CD4B expression by genetic knockdown efficiently prevented hyperglycemia-induced oxidative stress, endothelial dysfunction, and loss of nitric oxide (NO) bioavailability. Recombinant C2CD4B evoked endothelial dysfunction of mice mesenteric arteries, an effect associated with increased reactive oxygen species (ROS) and decreased NO production. In isolated human umbilical vein endothelial cells (HUVECs), C2CD4B increased phosphorylation of endothelial nitric oxide synthase (eNOS) at the inhibitory site Thr495 and reduced eNOS dimerization. Pharmacological inhibitors of phosphoinositide 3-kinase (PI3K), Akt, and PKCα effectively attenuated oxidative stress, NO reduction, impairment of endothelial function, and eNOS uncoupling induced by C2CD4B. These data demonstrate, for the first time, that C2CD4B exerts a direct effect on vascular endothelium via a phosphoinositide 3-kinase (PI3K)/Akt/PKCα-signaling pathway, providing a new perspective on C2CD4B as a promising therapeutic target for the prevention of oxidative stress in diabetes-induced endothelial dysfunction.
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Affiliation(s)
- Paola Di Pietro
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Angela Carmelita Abate
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Valeria Prete
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Antonio Damato
- Vascular Physiopathology Unit, IRCCS Neuromed, 86077 Pozzilli, Italy; (A.D.); (E.V.)
| | - Eleonora Venturini
- Vascular Physiopathology Unit, IRCCS Neuromed, 86077 Pozzilli, Italy; (A.D.); (E.V.)
| | - Maria Rosaria Rusciano
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Carmine Izzo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Valeria Visco
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
| | - Carmine Vecchione
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
- Vascular Physiopathology Unit, IRCCS Neuromed, 86077 Pozzilli, Italy; (A.D.); (E.V.)
| | - Albino Carrizzo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (P.D.P.); (A.C.A.); (V.P.); (M.R.R.); (C.I.); (V.V.); (M.C.); (C.V.)
- Vascular Physiopathology Unit, IRCCS Neuromed, 86077 Pozzilli, Italy; (A.D.); (E.V.)
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Accili D, Du W, Kitamoto T, Kuo T, McKimpson W, Miyachi Y, Mukhanova M, Son J, Wang L, Watanabe H. Reflections on the state of diabetes research and prospects for treatment. Diabetol Int 2023; 14:21-31. [PMID: 36636157 PMCID: PMC9829952 DOI: 10.1007/s13340-022-00600-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 01/16/2023]
Abstract
Research on the etiology and treatment of diabetes has made substantial progress. As a result, several new classes of anti-diabetic drugs have been introduced in clinical practice. Nonetheless, the number of patients achieving glycemic control targets has not increased for the past 20 years. Two areas of unmet medical need are the restoration of insulin sensitivity and the reversal of pancreatic beta cell failure. In this review, we integrate research advances in transcriptional regulation of insulin action and pathophysiology of beta cell dedifferentiation with their potential impact on prospects of a durable "cure" for patients suffering from type 2 diabetes.
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Affiliation(s)
- Domenico Accili
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Wen Du
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Takumi Kitamoto
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Chiba 260-8670 Japan
| | - Taiyi Kuo
- Department of Neurobiology, Physiology, and Behavior, University of California at Davis, Davis, CA 95616 USA
| | - Wendy McKimpson
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Yasutaka Miyachi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka Japan
| | - Maria Mukhanova
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Jinsook Son
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Liheng Wang
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
| | - Hitoshi Watanabe
- Department of Medicine and Berrie Diabetes Center, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032 USA
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Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
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5
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Mousavy Gharavy SN, Owen BM, Millership SJ, Chabosseau P, Pizza G, Martinez-Sanchez A, Tasoez E, Georgiadou E, Hu M, Fine NHF, Jacobson DA, Dickerson MT, Idevall-Hagren O, Montoya A, Kramer H, Mehta Z, Withers DJ, Ninov N, Gadue PJ, Cardenas-Diaz FL, Cruciani-Guglielmacci C, Magnan C, Ibberson M, Leclerc I, Voz M, Rutter GA. Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis. Diabetologia 2021; 64:850-864. [PMID: 33492421 PMCID: PMC7829492 DOI: 10.1007/s00125-020-05350-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/28/2020] [Indexed: 12/16/2022]
Abstract
AIMS/HYPOTHESIS Variants close to the VPS13C/C2CD4A/C2CD4B locus are associated with altered risk of type 2 diabetes in genome-wide association studies. While previous functional work has suggested roles for VPS13C and C2CD4A in disease development, none has explored the role of C2CD4B. METHODS CRISPR/Cas9-induced global C2cd4b-knockout mice and zebrafish larvae with c2cd4a deletion were used to study the role of this gene in glucose homeostasis. C2 calcium dependent domain containing protein (C2CD)4A and C2CD4B constructs tagged with FLAG or green fluorescent protein were generated to investigate subcellular dynamics using confocal or near-field microscopy and to identify interacting partners by mass spectrometry. RESULTS Systemic inactivation of C2cd4b in mice led to marked, but highly sexually dimorphic changes in body weight and glucose homeostasis. Female C2cd4b mice displayed unchanged body weight compared with control littermates, but abnormal glucose tolerance (AUC, p = 0.01) and defective in vivo, but not in vitro, insulin secretion (p = 0.02). This was associated with a marked decrease in follicle-stimulating hormone levels as compared with wild-type (WT) littermates (p = 0.003). In sharp contrast, male C2cd4b null mice displayed essentially normal glucose tolerance but an increase in body weight (p < 0.001) and fasting blood glucose (p = 0.003) after maintenance on a high-fat and -sucrose diet vs WT littermates. No metabolic disturbances were observed after global inactivation of C2cd4a in mice, or in pancreatic beta cell function at larval stages in C2cd4a null zebrafish. Fasting blood glucose levels were also unaltered in adult C2cd4a-null fish. C2CD4B and C2CD4A were partially localised to the plasma membrane, with the latter under the control of intracellular Ca2+. Binding partners for both included secretory-granule-localised PTPRN2/phogrin. CONCLUSIONS/INTERPRETATION Our studies suggest that C2cd4b may act centrally in the pituitary to influence sex-dependent circuits that control pancreatic beta cell function and glucose tolerance in rodents. However, the absence of sexual dimorphism in the impact of diabetes risk variants argues for additional roles for C2CD4A or VPS13C in the control of glucose homeostasis in humans. DATA AVAILABILITY The datasets generated and/or analysed during the current study are available in the Biorxiv repository ( www.biorxiv.org/content/10.1101/2020.05.18.099200v1 ). RNA-Seq (GSE152576) and proteomics (PXD021597) data have been deposited to GEO ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152576 ) and ProteomeXchange ( www.ebi.ac.uk/pride/archive/projects/PXD021597 ) repositories, respectively.
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Affiliation(s)
- S Neda Mousavy Gharavy
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Bryn M Owen
- Section of Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Steven J Millership
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Pauline Chabosseau
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Grazia Pizza
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Emirhan Tasoez
- DFG-Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Eleni Georgiadou
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Ming Hu
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Nicholas H F Fine
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - David A Jacobson
- Department of Molecular Physiology and Biophysics Vanderbilt University, Nashville, TN, USA
| | - Matthew T Dickerson
- Department of Molecular Physiology and Biophysics Vanderbilt University, Nashville, TN, USA
| | | | - Alex Montoya
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, UK
| | - Holger Kramer
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, UK
| | - Zenobia Mehta
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Campus, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Nikolay Ninov
- DFG-Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
| | - Paul J Gadue
- Children's Hospital of Philadelphia, CTRB, Philadelphia, PA, USA
| | | | | | - Christophe Magnan
- Regulation of Glycemia by Central Nervous System, BFA, UMR 8251, CNRS Université de Paris, Paris, France
| | - Mark Ibberson
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Isabelle Leclerc
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Marianne Voz
- Laboratory of Zebrafish Development and Disease Models, University of Liège (ULg), Liège, Belgium
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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Marselli L, Piron A, Suleiman M, Colli ML, Yi X, Khamis A, Carrat GR, Rutter GA, Bugliani M, Giusti L, Ronci M, Ibberson M, Turatsinze JV, Boggi U, De Simone P, De Tata V, Lopes M, Nasteska D, De Luca C, Tesi M, Bosi E, Singh P, Campani D, Schulte AM, Solimena M, Hecht P, Rady B, Bakaj I, Pocai A, Norquay L, Thorens B, Canouil M, Froguel P, Eizirik DL, Cnop M, Marchetti P. Persistent or Transient Human β Cell Dysfunction Induced by Metabolic Stress: Specific Signatures and Shared Gene Expression with Type 2 Diabetes. Cell Rep 2020; 33:108466. [PMID: 33264613 DOI: 10.1016/j.celrep.2020.108466] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/06/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Pancreatic β cell failure is key to type 2 diabetes (T2D) onset and progression. Here, we assess whether human β cell dysfunction induced by metabolic stress is reversible, evaluate the molecular pathways underlying persistent or transient damage, and explore the relationships with T2D islet traits. Twenty-six islet preparations are exposed to several lipotoxic/glucotoxic conditions, some of which impair insulin release, depending on stressor type, concentration, and combination. The reversal of dysfunction occurs after washout for some, although not all, of the lipoglucotoxic insults. Islet transcriptomes assessed by RNA sequencing and expression quantitative trait loci (eQTL) analysis identify specific pathways underlying β cell failure and recovery. Comparison of a large number of human T2D islet transcriptomes with those of persistent or reversible β cell lipoglucotoxicity show shared gene expression signatures. The identification of mechanisms associated with human β cell dysfunction and recovery and their overlap with T2D islet traits provide insights into T2D pathogenesis, fostering the development of improved β cell-targeted therapeutic strategies.
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Affiliation(s)
- Lorella Marselli
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy.
| | - Anthony Piron
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Maikel L Colli
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Amna Khamis
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille 59000, France
| | - Gaelle R Carrat
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology, and Metabolism, Imperial College, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology, and Metabolism, Imperial College, London, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Marco Bugliani
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Laura Giusti
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy; School of Pharmacy, University of Camerino, Camerino, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy; Centre for Advanced Studies and Technologies (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Mark Ibberson
- Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | | | - Ugo Boggi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56126, Italy; Division of General and Transplant Surgery, Cisanello University Hospital, Pisa 56124, Italy
| | - Paolo De Simone
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56126, Italy; Division of Liver Surgery and Transplantation, Cisanello University Hospital, Pisa 56124, Italy
| | - Vincenzo De Tata
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa 56126, Italy
| | - Miguel Lopes
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Daniela Nasteska
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Carmela De Luca
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Emanuele Bosi
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Pratibha Singh
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Daniela Campani
- Department of Surgical, Medical and Molecular Pathology and the Critical Areas, University of Pisa, Pisa 56126, Italy
| | - Anke M Schulte
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | - Michele Solimena
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden 01307, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Peter Hecht
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Frankfurt, Germany
| | | | | | | | | | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Mickaël Canouil
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille 59000, France
| | - Philippe Froguel
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; WELBIO, Université Libre de Bruxelles, Brussels, Belgium; Indiana Biosciences Research Institute, Indianapolis, IN, USA; Division of Endocrinology, ULB Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels 1070, Belgium; Division of Endocrinology, ULB Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium.
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy.
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7
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Yalçın Çapan Ö, Aydın N, Yılmaz T, Berber E. Whole exome sequencing reveals novel candidate gene variants for MODY. Clin Chim Acta 2020; 510:97-104. [DOI: 10.1016/j.cca.2020.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/20/2020] [Accepted: 07/02/2020] [Indexed: 11/30/2022]
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8
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Hook SC, Chadt A, Heesom KJ, Kishida S, Al-Hasani H, Tavaré JM, Thomas EC. TBC1D1 interacting proteins, VPS13A and VPS13C, regulate GLUT4 homeostasis in C2C12 myotubes. Sci Rep 2020; 10:17953. [PMID: 33087848 PMCID: PMC7578007 DOI: 10.1038/s41598-020-74661-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023] Open
Abstract
Proteins involved in the spaciotemporal regulation of GLUT4 trafficking represent potential therapeutic targets for the treatment of insulin resistance and type 2 diabetes. A key regulator of insulin- and exercise-stimulated glucose uptake and GLUT4 trafficking is TBC1D1. This study aimed to identify proteins that regulate GLUT4 trafficking and homeostasis via TBC1D1. Using an unbiased quantitative proteomics approach, we identified proteins that interact with TBC1D1 in C2C12 myotubes including VPS13A and VPS13C, the Rab binding proteins EHBP1L1 and MICAL1, and the calcium pump SERCA1. These proteins associate with TBC1D1 via its phosphotyrosine binding (PTB) domains and their interactions with TBC1D1 were unaffected by AMPK activation, distinguishing them from the AMPK regulated interaction between TBC1D1 and AMPKα1 complexes. Depletion of VPS13A or VPS13C caused a post-transcriptional increase in cellular GLUT4 protein and enhanced cell surface GLUT4 levels in response to AMPK activation. The phenomenon was specific to GLUT4 because other recycling proteins were unaffected. Our results provide further support for a role of the TBC1D1 PTB domains as a scaffold for a range of Rab regulators, and also the VPS13 family of proteins which have been previously linked to fasting glycaemic traits and insulin resistance in genome wide association studies.
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Affiliation(s)
- Sharon C Hook
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Alexandra Chadt
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Kate J Heesom
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Shosei Kishida
- Department of Biochemistry and Genetics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hadi Al-Hasani
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Jeremy M Tavaré
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elaine C Thomas
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
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9
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Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Identification of C2CD4A as a human diabetes susceptibility gene with a role in β cell insulin secretion. Proc Natl Acad Sci U S A 2019; 116:20033-20042. [PMID: 31527256 DOI: 10.1073/pnas.1904311116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Fine mapping and validation of genes causing β cell failure from susceptibility loci identified in type 2 diabetes genome-wide association studies (GWAS) poses a significant challenge. The VPS13C-C2CD4A-C2CD4B locus on chromosome 15 confers diabetes susceptibility in every ethnic group studied to date. However, the causative gene is unknown. FoxO1 is involved in the pathogenesis of β cell dysfunction, but its link to human diabetes GWAS has not been explored. Here we generated a genome-wide map of FoxO1 superenhancers in chemically identified β cells using 2-photon live-cell imaging to monitor FoxO1 localization. When parsed against human superenhancers and GWAS-derived diabetes susceptibility alleles, this map revealed a conserved superenhancer in C2CD4A, a gene encoding a β cell/stomach-enriched nuclear protein of unknown function. Genetic ablation of C2cd4a in β cells of mice phenocopied the metabolic abnormalities of human carriers of C2CD4A-linked polymorphisms, resulting in impaired insulin secretion during glucose tolerance tests as well as hyperglycemic clamps. C2CD4A regulates glycolytic genes, and notably represses key β cell "disallowed" genes, such as lactate dehydrogenase A We propose that C2CD4A is a transcriptional coregulator of the glycolytic pathway whose dysfunction accounts for the diabetes susceptibility associated with the chromosome 15 GWAS locus.
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11
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Muñoz-Braceras S, Tornero-Écija AR, Vincent O, Escalante R. VPS13A is closely associated with mitochondria and is required for efficient lysosomal degradation. Dis Model Mech 2019; 12:dmm036681. [PMID: 30709847 PMCID: PMC6398486 DOI: 10.1242/dmm.036681] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/22/2019] [Indexed: 12/11/2022] Open
Abstract
Members of the VPS13 family are associated with various human diseases. In particular, the loss of function of VPS13A leads to chorea-acanthocytosis (ChAc), a rare neurodegenerative disease without available curative treatments. Autophagy has been considered a promising therapeutic target because the absence of VPS13A causes a defective autophagy flux. However, the mechanistic details of this deficiency are unknown. Here, we identified Rab7A as an interactor of one of the VPS13 family members in Dictyostelium discoideum and showed that this interaction is conserved between the human homologs VPS13A and RAB7A in HeLa cells. As RAB7A is a key player in endosome trafficking, we addressed the possible function of VPS13A in endosome dynamics and lysosome degradation. Our results suggest that the decrease in autophagy observed in the absence of VPS13A may be the result of a more general defect in endocytic trafficking and lysosomal degradation. Unexpectedly, we found that VPS13A is closely localized to mitochondria, suggesting that the role of VPS13A in the endolysosomal pathway might be related to inter-organelle communication. We show that VPS13A localizes at the interface between mitochondria-endosomes and mitochondria-endoplasmic reticulum and that the presence of membrane contact sites is altered in the absence of VPS13A. Based on these findings, we propose that therapeutic strategies aimed at modulating the endolysosomal pathway could be beneficial in the treatment of ChAc.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sandra Muñoz-Braceras
- Instituto de Investigaciones Biomédicas Alberto Sols, Department of Experimental Models of Human Diseases, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma Madrid (UAM), 28029-Madrid, Spain
| | - Alba R Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, Department of Experimental Models of Human Diseases, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma Madrid (UAM), 28029-Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, Department of Experimental Models of Human Diseases, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma Madrid (UAM), 28029-Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, Department of Experimental Models of Human Diseases, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma Madrid (UAM), 28029-Madrid, Spain
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12
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Soczewka P, Kolakowski D, Smaczynska-de Rooij I, Rzepnikowska W, Ayscough KR, Kaminska J, Zoladek T. Yeast-model-based study identified myosin- and calcium-dependent calmodulin signalling as a potential target for drug intervention in chorea-acanthocytosis. Dis Model Mech 2019; 12:dmm.036830. [PMID: 30635263 PMCID: PMC6361151 DOI: 10.1242/dmm.036830] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/07/2019] [Indexed: 01/03/2023] Open
Abstract
Chorea-acanthocytosis (ChAc) is a rare neurodegenerative disease associated with mutations in the human VPS13A gene. The mechanism of ChAc pathogenesis is unclear. A simple yeast model was used to investigate the function of the single yeast VSP13 orthologue, Vps13. Vps13, like human VPS13A, is involved in vesicular protein transport, actin cytoskeleton organisation and phospholipid metabolism. A newly identified phenotype of the vps13Δ mutant, sodium dodecyl sulphate (SDS) hypersensitivity, was used to screen a yeast genomic library for multicopy suppressors. A fragment of the MYO3 gene, encoding Myo3-N (the N-terminal part of myosin, a protein involved in the actin cytoskeleton and in endocytosis), was isolated. Myo3-N protein contains a motor head domain and a linker. The linker contains IQ motifs that mediate the binding of calmodulin, a negative regulator of myosin function. Amino acid substitutions that disrupt the interaction of Myo3-N with calmodulin resulted in the loss of vps13Δ suppression. Production of Myo3-N downregulated the activity of calcineurin, a protein phosphatase regulated by calmodulin, and alleviated some defects in early endocytosis events. Importantly, ethylene glycol tetraacetic acid (EGTA), which sequesters calcium and thus downregulates calmodulin and calcineurin, was a potent suppressor of vps13Δ. We propose that Myo3-N acts by sequestering calmodulin, downregulating calcineurin and increasing activity of Myo3, which is involved in endocytosis and, together with Osh2/3 proteins, functions in endoplasmic reticulum-plasma membrane contact sites. These results show that defects associated with vps13Δ could be overcome, and point to a functional connection between Vps13 and calcium signalling as a possible target for chemical intervention in ChAc. Yeast ChAc models may uncover the underlying pathological mechanisms, and may also serve as a platform for drug testing. This article has an associated First Person interview with the first author of the paper. Summary: Using the vps13Δ strain, a yeast model of the neurodegenerative disorder chorea-acanthocytosis, we found that its defects can be overcome by reduction of calcineurin activity and/or type-I-myosin activation.
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Affiliation(s)
- Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Damian Kolakowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | | | - Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Kathryn R Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Pawinskiego 5A, 02106 Warsaw, Poland
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13
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Taneera J, Prasad RB, Dhaiban S, Mohammed AK, Haataja L, Arvan P, Hamad M, Groop L, Wollheim CB. Silencing of the FTO gene inhibits insulin secretion: An in vitro study using GRINCH cells. Mol Cell Endocrinol 2018; 472:10-17. [PMID: 29890211 PMCID: PMC6559235 DOI: 10.1016/j.mce.2018.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/14/2018] [Accepted: 06/07/2018] [Indexed: 01/01/2023]
Abstract
Expression of fat mass and obesity-associated gene (FTO) and ADP-ribosylation factor-like 15 (ARL15) in human islets is inversely correlated with HbA1c. However, their impact on insulin secretion is still ambiguous. Here in, we investigated the role of FTO and ARL15 using GRINCH (Glucose-Responsive Insulin-secreting C-peptide-modified Human proinsulin) clonal rat β-cells. GRINCH cells have inserted GFP into the human C-peptide insulin gene. Hence, secreted CpepGFP served to monitor insulin secretion. mRNA silencing of FTO in GRINCH cells showed a significant reduction in glucose but not depolarization-stimulated insulin secretion, whereas ARL15 silencing had no effect. A significant down-regulation of insulin mRNA was observed in FTO knockdown cells. Type-2 Diabetic islets revealed a reduced expression of FTO mRNA. In conclusion, our data suggest that fluorescent CpepGFP released from GRINCH cells may serve as a convenient marker for insulin secretion. Silencing of FTO expression, but not ARL15, inhibits insulin secretion by affecting metabolic signaling.
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Affiliation(s)
- Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; Lund University Diabetes Center, Malmoe, Lund University, Sweden.
| | - Rashmi B Prasad
- Lund University Diabetes Center, Malmoe, Lund University, Sweden
| | - Sarah Dhaiban
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdul Khader Mohammed
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Leena Haataja
- Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, USA
| | - Peter Arvan
- Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, USA
| | - Mawieh Hamad
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Leif Groop
- Lund University Diabetes Center, Malmoe, Lund University, Sweden; Finnish Institute for Molecular Medicine (FIMM), Helsinki University, Finland
| | - Claes B Wollheim
- Lund University Diabetes Center, Malmoe, Lund University, Sweden; Department of Cell Physiology and Metabolism, University Medical Center. Geneva, Switzerland
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14
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Kycia I, Wolford BN, Huyghe JR, Fuchsberger C, Vadlamudi S, Kursawe R, Welch RP, Albanus RD, Uyar A, Khetan S, Lawlor N, Bolisetty M, Mathur A, Kuusisto J, Laakso M, Ucar D, Mohlke KL, Boehnke M, Collins FS, Parker SCJ, Stitzel ML. A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression. Am J Hum Genet 2018; 102:620-635. [PMID: 29625024 DOI: 10.1016/j.ajhg.2018.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/22/2018] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWASs) and functional genomics approaches implicate enhancer disruption in islet dysfunction and type 2 diabetes (T2D) risk. We applied genetic fine-mapping and functional (epi)genomic approaches to a T2D- and proinsulin-associated 15q22.2 locus to identify a most likely causal variant, determine its direction of effect, and elucidate plausible target genes. Fine-mapping and conditional analyses of proinsulin levels of 8,635 non-diabetic individuals from the METSIM study support a single association signal represented by a cluster of 16 strongly associated (p < 10-17) variants in high linkage disequilibrium (r2 > 0.8) with the GWAS index SNP rs7172432. These variants reside in an evolutionarily and functionally conserved islet and β cell stretch or super enhancer; the most strongly associated variant (rs7163757, p = 3 × 10-19) overlaps a conserved islet open chromatin site. DNA sequence containing the rs7163757 risk allele displayed 2-fold higher enhancer activity than the non-risk allele in reporter assays (p < 0.01) and was differentially bound by β cell nuclear extract proteins. Transcription factor NFAT specifically potentiated risk-allele enhancer activity and altered patterns of nuclear protein binding to the risk allele in vitro, suggesting that it could be a factor mediating risk-allele effects. Finally, the rs7163757 proinsulin-raising and T2D risk allele (C) was associated with increased expression of C2CD4B, and possibly C2CD4A, both of which were induced by inflammatory cytokines, in human islets. Together, these data suggest that rs7163757 contributes to genetic risk of islet dysfunction and T2D by increasing NFAT-mediated islet enhancer activity and modulating C2CD4B, and possibly C2CD4A, expression in (patho)physiologic states.
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Affiliation(s)
- Ina Kycia
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Brooke N Wolford
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Jeroen R Huyghe
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Romy Kursawe
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ryan P Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ricardo d'Oliveira Albanus
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Asli Uyar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Shubham Khetan
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nathan Lawlor
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Mohan Bolisetty
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Anubhuti Mathur
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Duygu Ucar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute of Systems Genomics, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael L Stitzel
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute of Systems Genomics, University of Connecticut Health Center, Farmington, CT 06032, USA.
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15
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Lee PH, Lee C, Li X, Wee B, Dwivedi T, Daly M. Principles and methods of in-silico prioritization of non-coding regulatory variants. Hum Genet 2018; 137:15-30. [PMID: 29288389 PMCID: PMC5892192 DOI: 10.1007/s00439-017-1861-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations. We also highlight the limitations of current approaches and discuss the direction of much-needed future research.
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Affiliation(s)
- Phil H Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA.
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Christian Lee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Department of Life Sciences, Harvard University, Cambridge, MA, USA
| | - Xihao Li
- Quantitative Genomics Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brian Wee
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
| | - Tushar Dwivedi
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mark Daly
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Simches Research Building, 185 Cambridge St, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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16
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Ramseyer VD, Kimler VA, Granneman JG. Vacuolar protein sorting 13C is a novel lipid droplet protein that inhibits lipolysis in brown adipocytes. Mol Metab 2017; 7:57-70. [PMID: 29175050 PMCID: PMC5784322 DOI: 10.1016/j.molmet.2017.10.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 12/02/2022] Open
Abstract
Objective Brown adipose tissue (BAT) thermogenesis depends on the mobilization and oxidation of fatty acids from intracellular lipid droplets (LD) within brown adipocytes (BAs); however, the identity and function of LD proteins that control BAT lipolysis remain incomplete. Proteomic analysis of mouse BAT subcellular fractions identified vacuolar protein sorting 13C (VPS13C) as a novel LD protein. The aim of this work was to investigate the role of VPS13C on BA LDs. Methods Biochemical fractionation and high resolution confocal and immuno-transmission electron microscopy (TEM) were used to determine the subcellular distribution of VPS13C in mouse BAT, white adipose tissue, and BA cell culture. Lentivirus-delivered shRNA was used to determine the role of VPS13C in regulating lipolysis and gene expression in cultured BA cells. Results We found that VPS13C is highly expressed in mouse BAT where it is targeted to multilocular LDs in a subspherical subdomain. In inguinal white adipocytes, VPS13C was mainly observed on small LDs and β3-adrenergic stimulation increased VPS13C in this depot. Silencing of VPS13C in cultured BAs decreased LD size and triglyceride content, increased basal free fatty acid release, augmented the expression of thermogenic genes, and enhanced the lipolytic potency and efficacy of isoproterenol. Mechanistically, we found that BA lipolysis required activation of adipose tissue triglyceride lipase (ATGL) and that loss of VPS13C greatly increased the association of ATGL to LDs. Conclusions VPS13C is present on BA LDs where is targeted to a distinct subdomain. VPS13C limits the access of ATGL to LD and loss of VPS13C elevates lipolysis and promotes oxidative gene expression. VPS13C is highly expressed on mouse brown adipose tissue lipid droplets. VPS13C is present on lipid droplets in a unique subspheric pattern. VPS13C silencing in BAs decreases lipid droplet size and triglyceride content. VPS13C silencing in BAs increases lipolysis and oxidative gene expression. VPS13C silencing in BAs enhances ATGL but not HSL targeting to LDs.
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Affiliation(s)
- Vanesa D Ramseyer
- Center for Metabolic Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA
| | | | - James G Granneman
- Center for Metabolic Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA.
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17
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Rzepnikowska W, Flis K, Muñoz-Braceras S, Menezes R, Escalante R, Zoladek T. Yeast and other lower eukaryotic organisms for studies of Vps13 proteins in health and disease. Traffic 2017; 18:711-719. [PMID: 28846184 DOI: 10.1111/tra.12523] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022]
Abstract
Human Vps13 proteins are associated with several diseases, including the neurodegenerative disorder Chorea-acanthocytosis (ChAc), yet the biology of these proteins is still poorly understood. Studies in Saccharomyces cerevisiae, Dictyostelium discoideum, Tetrahymena thermophila and Drosophila melanogaster point to the involvement of Vps13 in cytoskeleton organization, vesicular trafficking, autophagy, phagocytosis, endocytosis, proteostasis, sporulation and mitochondrial functioning. Recent findings show that yeast Vps13 binds to phosphatidylinositol lipids via 4 different regions and functions at membrane contact sites, enlarging the list of Vps13 functions. This review describes the great potential of simple eukaryotes to decipher disease mechanisms in higher organisms and highlights novel insights into the pathological role of Vps13 towards ChAc.
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Affiliation(s)
- Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Regina Menezes
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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18
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Goswami S, Yee SW, Xu F, Sridhar SB, Mosley JD, Takahashi A, Kubo M, Maeda S, Davis RL, Roden DM, Hedderson MM, Giacomini KM, Savic RM. A Longitudinal HbA1c Model Elucidates Genes Linked to Disease Progression on Metformin. Clin Pharmacol Ther 2016; 100:537-547. [PMID: 27415606 PMCID: PMC5534241 DOI: 10.1002/cpt.428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 12/20/2022]
Abstract
One-third of type-2 diabetic patients respond poorly to metformin. Despite extensive research, the impact of genetic and nongenetic factors on long-term outcome is unknown. In this study we combine nonlinear mixed effect modeling with computational genetic methodologies to identify predictors of long-term response. In all, 1,056 patients contributed their genetic, demographic, and long-term HbA1c data. The top nine variants (of 12,000 variants in 267 candidate genes) accounted for approximately one-third of the variability in the disease progression parameter. Average serum creatinine level, age, and weight were determinants of symptomatic response; however, explaining negligible variability. Two single nucleotide polymorphisms (SNPs) in CSMD1 gene (rs2617102, rs2954625) and one SNP in a pharmacologically relevant SLC22A2 gene (rs316009) influenced disease progression, with minor alleles leading to less and more favorable outcomes, respectively. Overall, our study highlights the influence of genetic factors on long-term HbA1c response and provides a computational model, which when validated, may be used to individualize treatment.
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Affiliation(s)
- S Goswami
- University of California, San Francisco, San Francisco, California, USA
| | - S W Yee
- University of California, San Francisco, San Francisco, California, USA
| | - F Xu
- Kaiser Permanente Northern California, Oakland, California, USA
| | - S B Sridhar
- Kaiser Permanente Northern California, Oakland, California, USA
| | - J D Mosley
- Vanderbilt University, Nashville, Tennessee, USA
| | - A Takahashi
- RIKEN Institute, Center for Genomic Medicine, Saitama, Japan
| | - M Kubo
- RIKEN Institute, Center for Genomic Medicine, Saitama, Japan
| | - S Maeda
- RIKEN Institute, Center for Genomic Medicine, Saitama, Japan
| | - R L Davis
- Kaiser Permanente Georgia, Atlanta, Georgia, USA
- Center for Biomedical Informatics, University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - D M Roden
- Vanderbilt University, Nashville, Tennessee, USA
| | - M M Hedderson
- Kaiser Permanente Northern California, Oakland, California, USA
| | - K M Giacomini
- University of California, San Francisco, San Francisco, California, USA.
| | - R M Savic
- University of California, San Francisco, San Francisco, California, USA.
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19
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Mehta ZB, Fine N, Pullen TJ, Cane MC, Hu M, Chabosseau P, Meur G, Velayos-Baeza A, Monaco AP, Marselli L, Marchetti P, Rutter GA. Changes in the expression of the type 2 diabetes-associated gene VPS13C in the β-cell are associated with glucose intolerance in humans and mice. Am J Physiol Endocrinol Metab 2016; 311:E488-507. [PMID: 27329800 PMCID: PMC5005967 DOI: 10.1152/ajpendo.00074.2016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/20/2016] [Indexed: 12/31/2022]
Abstract
Single nucleotide polymorphisms (SNPs) close to the VPS13C, C2CD4A and C2CD4B genes on chromosome 15q are associated with impaired fasting glucose and increased risk of type 2 diabetes. eQTL analysis revealed an association between possession of risk (C) alleles at a previously implicated causal SNP, rs7163757, and lowered VPS13C and C2CD4A levels in islets from female (n = 40, P < 0.041) but not from male subjects. Explored using promoter-reporter assays in β-cells and other cell lines, the risk variant at rs7163757 lowered enhancer activity. Mice deleted for Vps13c selectively in the β-cell were generated by crossing animals bearing a floxed allele at exon 1 to mice expressing Cre recombinase under Ins1 promoter control (Ins1Cre). Whereas Vps13c(fl/fl):Ins1Cre (βVps13cKO) mice displayed normal weight gain compared with control littermates, deletion of Vps13c had little effect on glucose tolerance. Pancreatic histology revealed no significant change in β-cell mass in KO mice vs. controls, and glucose-stimulated insulin secretion from isolated islets was not altered in vitro between control and βVps13cKO mice. However, a tendency was observed in female null mice for lower insulin levels and β-cell function (HOMA-B) in vivo. Furthermore, glucose-stimulated increases in intracellular free Ca(2+) were significantly increased in islets from female KO mice, suggesting impaired Ca(2+) sensitivity of the secretory machinery. The present data thus provide evidence for a limited role for changes in VPS13C expression in conferring altered disease risk at this locus, particularly in females, and suggest that C2CD4A may also be involved.
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Affiliation(s)
- Zenobia B Mehta
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Nicholas Fine
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Timothy J Pullen
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Matthew C Cane
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Ming Hu
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Pauline Chabosseau
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | - Gargi Meur
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom
| | | | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom; and
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom;
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20
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Yang RY, Xue H, Yu L, Velayos-Baeza A, Monaco AP, Liu FT. Identification of VPS13C as a Galectin-12-Binding Protein That Regulates Galectin-12 Protein Stability and Adipogenesis. PLoS One 2016; 11:e0153534. [PMID: 27073999 PMCID: PMC4830523 DOI: 10.1371/journal.pone.0153534] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/30/2016] [Indexed: 01/13/2023] Open
Abstract
Galectin-12, a member of the galectin family of β-galactoside-binding animal lectins, is preferentially expressed in adipocytes and required for adipocyte differentiation in vitro. This protein was recently found to regulate lipolysis, whole body adiposity, and glucose homeostasis in vivo. Here we identify VPS13C, a member of the VPS13 family of vacuolar protein sorting-associated proteins highly conserved throughout eukaryotic evolution, as a major galectin-12-binding protein. VPS13C is upregulated during adipocyte differentiation, and is required for galectin-12 protein stability. Knockdown of Vps13c markedly reduces the steady-state levels of galectin-12 by promoting its degradation through primarily the lysosomal pathway, and impairs adipocyte differentiation. Our studies also suggest that VPS13C may have a broader role in protein quality control. The regulation of galectin-12 stability by VPS13C could potentially be exploited for therapeutic intervention of obesity and related metabolic diseases.
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Affiliation(s)
- Ri-Yao Yang
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
| | - Huiting Xue
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
- School of Life Sciences, Northeast Normal University, Changchun, 130024, People’s Republic of China
| | - Lan Yu
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
| | | | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, OX3 7BN, Oxford, United Kingdom
| | - Fu-Tong Liu
- Department of Dermatology, School of Medicine, University of California-Davis, Sacramento, California, 95817, United States of America
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 115, Taiwan
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21
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Ray D, Pankow JS, Basu S. USAT: A Unified Score-Based Association Test for Multiple Phenotype-Genotype Analysis. Genet Epidemiol 2015; 40:20-34. [PMID: 26638693 DOI: 10.1002/gepi.21937] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWASs) for complex diseases often collect data on multiple correlated endo-phenotypes. Multivariate analysis of these correlated phenotypes can improve the power to detect genetic variants. Multivariate analysis of variance (MANOVA) can perform such association analysis at a GWAS level, but the behavior of MANOVA under different trait models has not been carefully investigated. In this paper, we show that MANOVA is generally very powerful for detecting association but there are situations, such as when a genetic variant is associated with all the traits, where MANOVA may not have any detection power. In these situations, marginal model based methods, however, perform much better than multivariate methods. We investigate the behavior of MANOVA, both theoretically and using simulations, and derive the conditions where MANOVA loses power. Based on our findings, we propose a unified score-based test statistic USAT that can perform better than MANOVA in such situations and nearly as well as MANOVA elsewhere. Our proposed test reports an approximate asymptotic P-value for association and is computationally very efficient to implement at a GWAS level. We have studied through extensive simulations the performance of USAT, MANOVA, and other existing approaches and demonstrated the advantage of using the USAT approach to detect association between a genetic variant and multivariate phenotypes. We applied USAT to data from three correlated traits collected on 5, 816 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC, The ARIC Investigators []) Study and detected some interesting associations.
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Affiliation(s)
- Debashree Ray
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, United States of America
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minnesota, United States of America
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, United States of America
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22
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Genetic variation at glucose and insulin trait loci and response to glucose-insulin-potassium (GIK) therapy: the IMMEDIATE trial. THE PHARMACOGENOMICS JOURNAL 2014; 15:55-62. [PMID: 25135348 DOI: 10.1038/tpj.2014.41] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/29/2014] [Accepted: 06/04/2014] [Indexed: 11/09/2022]
Abstract
The mechanistic effects of intravenous glucose, insulin and potassium (GIK) in cardiac ischemia are not well understood. We conducted a genetic sub-study of the Immediate Myocardial Metabolic Enhancement During Initial Assessment and Treatment in Emergency care (IMMEDIATE) Trial to explore effects of common and rare glucose and insulin-related genetic loci on initial to 6-h and 6- to 12-h change in plasma glucose and potassium. We identified 27 NOTCH2/ADAM30 and 8 C2CD4B variants conferring a 40-57% increase in glucose during the first 6 h of infusion (P<5.96 × 10(-6)). Significant associations were also found for ABCB11 and SLC30A8 single-nucleotide polymorphisms (SNPs) and glucose responses, and an SEC61A2 SNP with a potassium response to GIK. These studies identify genetic factors that may impact the metabolic response to GIK, which could influence treatment benefits in the setting of acute coronary syndromes (ACS).
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23
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Hara K, Shojima N, Hosoe J, Kadowaki T. Genetic architecture of type 2 diabetes. Biochem Biophys Res Commun 2014; 452:213-20. [PMID: 25111817 DOI: 10.1016/j.bbrc.2014.08.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/04/2014] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have identified over 70 loci associated with type 2 diabetes (T2D). Most genetic variants associated with T2D are common variants with modest effects on T2D and are shared with major ancestry groups. To what extent the genetic component of T2D can be explained by common variants relies upon the shape of the genetic architecture of T2D. Fine mapping utilizing populations with different patterns of linkage disequilibrium and functional annotation derived from experiments in relevant tissues are mandatory to track down causal variants responsible for the pathogenesis of T2D.
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Affiliation(s)
- Kazuo Hara
- The Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Nobuhiro Shojima
- The Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Jun Hosoe
- The Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Takashi Kadowaki
- The Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
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24
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Dimas AS, Lagou V, Barker A, Knowles JW, Mägi R, Hivert MF, Benazzo A, Rybin D, Jackson AU, Stringham HM, Song C, Fischer-Rosinsky A, Boesgaard TW, Grarup N, Abbasi FA, Assimes TL, Hao K, Yang X, Lecoeur C, Barroso I, Bonnycastle LL, Böttcher Y, Bumpstead S, Chines PS, Erdos MR, Graessler J, Kovacs P, Morken MA, Narisu N, Payne F, Stancakova A, Swift AJ, Tönjes A, Bornstein SR, Cauchi S, Froguel P, Meyre D, Schwarz PE, Häring HU, Smith U, Boehnke M, Bergman RN, Collins FS, Mohlke KL, Tuomilehto J, Quertemous T, Lind L, Hansen T, Pedersen O, Walker M, Pfeiffer AF, Spranger J, Stumvoll M, Meigs JB, Wareham NJ, Kuusisto J, Laakso M, Langenberg C, Dupuis J, Watanabe RM, Florez JC, Ingelsson E, McCarthy MI, Prokopenko I. Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity. Diabetes 2014; 63:2158-71. [PMID: 24296717 PMCID: PMC4030103 DOI: 10.2337/db13-0949] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition.
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Affiliation(s)
- Antigone S. Dimas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Alexander Fleming, Biomedical Sciences Research Center, Vari, Athens, Greece
| | - Vasiliki Lagou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
| | - Adam Barker
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Joshua W. Knowles
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Reedik Mägi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Marie-France Hivert
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
- General Medicine Division, Massachusetts General Hospital, Boston, MA
| | - Andrea Benazzo
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, MA
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Ci Song
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Antje Fischer-Rosinsky
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
| | | | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fahim A. Abbasi
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Themistocles L. Assimes
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA
| | - Cécile Lecoeur
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, U.K
- University of Cambridge Metabolic Research Laboratories and National Institute for Health Research Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Yvonne Böttcher
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
| | | | - Peter S. Chines
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Michael R. Erdos
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Jurgen Graessler
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Peter Kovacs
- Interdisciplinary Center for Clinical Research Leipzig, Leipzig, Germany
| | - Mario A. Morken
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | | | - Alena Stancakova
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Anke Tönjes
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Stefan R. Bornstein
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Stéphane Cauchi
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
| | - Philippe Froguel
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, U.K
| | - David Meyre
- CNRS UMR8199-Institute of Biology, Pasteur Institute, Lille 2-Droit et Santé University, Lille, France
- Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Peter E.H. Schwarz
- Department of Medicine III, Division of Prevention and Care of Diabetes, University of Dresden, Dresden, Germany
| | - Hans-Ulrich Häring
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, Tübingen, Germany
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Center of Excellence for Metabolic and Cardiovascular Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Richard N. Bergman
- Department of Physiology & Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, MD
| | - Karen L. Mohlke
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Centre for Vascular Prevention, Danube University Krems, Krems, Austria
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thomas Quertemous
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Lars Lind
- Department of Medical Sciences, Akademiska Sjukhuset, Uppsala University, Uppsala, Sweden
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Hagedorn Research Institute, Copenhagen, Denmark
- Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Aarhus, Aarhus, Denmark
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Andreas F.H. Pfeiffer
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition, Nuthetal, Germany
| | - Joachim Spranger
- Charité-Universitätsmedizin Berlin, Department of Endocrinology and Metabolism, Berlin, Germany
| | - Michael Stumvoll
- IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Nicholas J. Wareham
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Claudia Langenberg
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
| | - Richard M. Watanabe
- Departments of Preventive Medicine and Physiology & Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jose C. Florez
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, U.K
- Department of Genomics of Common Disease, Imperial College London, London, U.K
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25
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Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res 2013; 22:1748-59. [PMID: 22955986 PMCID: PMC3431491 DOI: 10.1101/gr.136127.111] [Citation(s) in RCA: 536] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies have been successful in identifying single nucleotide polymorphisms (SNPs) associated with a large number of phenotypes. However, an associated SNP is likely part of a larger region of linkage disequilibrium. This makes it difficult to precisely identify the SNPs that have a biological link with the phenotype. We have systematically investigated the association of multiple types of ENCODE data with disease-associated SNPs and show that there is significant enrichment for functional SNPs among the currently identified associations. This enrichment is strongest when integrating multiple sources of functional information and when highest confidence disease-associated SNPs are used. We propose an approach that integrates multiple types of functional data generated by the ENCODE Consortium to help identify “functional SNPs” that may be associated with the disease phenotype. Our approach generates putative functional annotations for up to 80% of all previously reported associations. We show that for most associations, the functional SNP most strongly supported by experimental evidence is a SNP in linkage disequilibrium with the reported association rather than the reported SNP itself. Our results show that the experimental data sets generated by the ENCODE Consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes.
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Affiliation(s)
- Marc A Schaub
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
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26
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Abstract
Diabetes mellitus type 1 (T1DM) and type 2 (T2DM) are common diseases. To date, it is widely accepted that all forms of DM lead to the loss of beta cells. Therefore, to avoid the debilitating comorbidities when glycemic control cannot be fully achieved, some would argue that beta cell replacement is the only way to cure the disease. Due to organ donor shortage, other cell sources for beta cell replacement strategies have to be employed. Pluripotent stem cells, including embryonic stem (ES) and induced pluripotent stem (iPS) cells offer a valuable alternative to provide the necessary cells to substitute organ transplants but also to serve as a model to study the onset and progression of the disease, resulting in better treatment regimens. This review will summarize recent progress in the establishment of pluripotent stem cells, their differentiation into the pancreatic lineage with a focus on two-dimensional (2D) and three-dimensional (3D) differentiation settings, the special role of iPS cells in the analysis of genetic predispositions to diabetes, and techniques that help to move current approaches to clinical applications. Particular attention, however, is also given to the long-term challenges that have to be addressed before ES or iPS cell-based therapies will become a broadly accepted treatment option.
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Affiliation(s)
- Insa S Schroeder
- JRG Stem Cell Research, Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, D-06108, Halle/Saale, Germany.
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27
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Miyazaki S, Minamida R, Furuyama T, Tashiro F, Yamato E, Inagaki S, Miyazaki JI. Analysis of Foxo1-regulated genes using Foxo1-deficient pancreatic β cells. Genes Cells 2012; 17:758-67. [PMID: 22845550 DOI: 10.1111/j.1365-2443.2012.01625.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/06/2012] [Indexed: 11/27/2022]
Abstract
Several reports have suggested that Foxo1, a key regulator in differentiation, growth and metabolism, is involved in pancreatic β-cell function. However, detailed analyses have been hampered by a lack of Foxo1-deficient β cells. To elucidate Foxo1's function in β cells, we produced a β-cell line with inducible Foxo1 deletion. We generated a conditional knockout mouse line, in which Cre recombinase deletes the Foxo1 gene. We then established a β-cell line from an insulinoma induced in this knockout mouse by the β-cell-specific expression of simian virus 40 T antigen. In this cell line, designated MIN6-Foxo1flox/flox, adenovirus-mediated Cre expression ablates the Foxo1 gene, generating MIN6-Foxo1-KO cells. Using these knockout and floxed cell lines, we found that Foxo1 ablation enhanced the glucose-stimulated insulin secretion (GSIS) at high glucose concentrations and enhanced β-cell proliferation. We also conducted DNA microarray analyses of MIN6-Foxo1-KO cells infected with either an adenovirus vector expressing a constitutively active FOXO1 or a control vector and identified several Foxo1-regulated genes, including some known to be related to β-cell function. These cells should be useful for further studies on Foxo1's roles in β-cells and may lead to novel strategies for treating the impaired insulin secretion in type 2 diabetes mellitus.
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Affiliation(s)
- Satsuki Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
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28
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Abstract
Genome-wide association studies (GWAS) have facilitated a substantial and rapid rise in the number of confirmed genetic susceptibility variants for type 2 diabetes (T2D). Approximately 40 variants have been identified so far, many of which were discovered through GWAS. This success has led to widespread hope that the findings will translate into improved clinical care for the increasing numbers of patients with diabetes. Potential areas or clinical translation include risk prediction and subsequent disease prevention, pharmacogenetics, and the development of novel therapeutics. However, the genetic loci so far identified account for only a small fraction (approximately 10%) of the overall heritable risk for T2D. Uncovering the missing heritability is essential to the progress of T2D genetic studies and to the translation of genetic information into clinical practice.
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Affiliation(s)
- Minako Imamura
- Laboratory for Endocrinology and Metabolism, RIKEN Center for Genomic Medicine, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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