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Antonatos C, Patsatsi A, Zafiriou E, Stavrou EF, Liaropoulos A, Kyriakoy A, Evangelou E, Digka D, Roussaki-Schulze A, Sotiriadis D, Georgiou S, Grafanaki K, Moschonas NΚ, Vasilopoulos Y. Protein network and pathway analysis in a pharmacogenetic study of cyclosporine treatment response in Greek patients with psoriasis. THE PHARMACOGENOMICS JOURNAL 2023; 23:8-13. [PMID: 36229649 DOI: 10.1038/s41397-022-00291-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 02/15/2023]
Abstract
Although cyclosporine comprises a well-established systemic therapy for psoriasis, patients show important heterogeneity in their treatment response. The aim of our study was the pharmacogenetic analysis of 200 Greek patients with psoriasis based on the cyclosporine pathway related protein-protein interaction (PPI) network, reconstructed through the PICKLE meta-database. We genotyped 27 single nucleotide polymorphisms, mapped to 22 key protein nodes of the cyclosporine pathway, via the utilization of the iPLEX®GOLD panel of the MassARRAY® System. Single-SNP analyses showed statistically significant associations between CALM1 rs12885713 (P = 0.0108) and MALT1 rs2874116 (P = 0.0006) polymorphisms with positive response to cyclosporine therapy after correction for multiple comparisons, with the haplotype analyses further enhancing the predictive value of rs12885713 as a pharmacogenetic biomarker for cyclosporine therapy (P = 0.0173). Our findings have the potential to improve our prediction of cyclosporine efficacy and safety in psoriasis patients, as well as provide the framework for the pharmacogenetics of biological therapies in complex diseases.
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Affiliation(s)
- Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, Patras, Greece
| | - Aikaterini Patsatsi
- 2nd Dermatology Department, Medical School, Papageorgiou Hospital, Aristotle University, Thessaloniki, Greece
| | - Efterpi Zafiriou
- Department of Dermatology, University General Hospital Larissa, University of Thessaly, Volos, Greece
| | - Eleana F Stavrou
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, Patras, Greece.,Lab. of General Biology, Medical School, University of Patras, Patras, Greece
| | - Andreas Liaropoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, Patras, Greece
| | - Aikaterini Kyriakoy
- 2nd Dermatology Department, Medical School, Papageorgiou Hospital, Aristotle University, Thessaloniki, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Ioannina, Greece.,Department of Epidemiology & Biostatistics, MRC Centre for Environment and Health, Imperial College London, London, UK.,Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Ioannina, Greece
| | - Danai Digka
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, Patras, Greece
| | - Angeliki Roussaki-Schulze
- Department of Dermatology, University General Hospital Larissa, University of Thessaly, Volos, Greece
| | - Dimitris Sotiriadis
- 2nd Dermatology Department, Medical School, Papageorgiou Hospital, Aristotle University, Thessaloniki, Greece
| | - Sophia Georgiou
- Dermatology Department, Medical School, University of Patras, Patras, Greece
| | - Katerina Grafanaki
- Dermatology Department, Medical School, University of Patras, Patras, Greece
| | - Nicholas Κ Moschonas
- Lab. of General Biology, Medical School, University of Patras, Patras, Greece.,Foundation of Research & Technology, Institute of Chemical Engineering Science (ICE-HT), Patras, Greece
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, Patras, Greece.
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2
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Tziastoudi M, Stefanidis I, Stravodimos K, Zintzaras E. Identification of Chromosomal Regions Linked to Diabetic Nephropathy: A Meta-Analysis of Genome-Wide Linkage Scans. Genet Test Mol Biomarkers 2019; 23:105-117. [DOI: 10.1089/gtmb.2018.0209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Maria Tziastoudi
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Konstantinos Stravodimos
- 1st University Department of Urology, Laiko General Hospital, National and Kapodistrian Athens University, Athens, Greece
| | - Elias Zintzaras
- Department of Biomathematics, Faculty of Medicine, University of Thessaly, Larissa, Greece
- The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts
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3
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Barrett EJ, Liu Z, Khamaisi M, King GL, Klein R, Klein BEK, Hughes TM, Craft S, Freedman BI, Bowden DW, Vinik AI, Casellini CM. Diabetic Microvascular Disease: An Endocrine Society Scientific Statement. J Clin Endocrinol Metab 2017; 102:4343-4410. [PMID: 29126250 PMCID: PMC5718697 DOI: 10.1210/jc.2017-01922] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 01/18/2023]
Abstract
Both type 1 and type 2 diabetes adversely affect the microvasculature in multiple organs. Our understanding of the genesis of this injury and of potential interventions to prevent, limit, or reverse injury/dysfunction is continuously evolving. This statement reviews biochemical/cellular pathways involved in facilitating and abrogating microvascular injury. The statement summarizes the types of injury/dysfunction that occur in the three classical diabetes microvascular target tissues, the eye, the kidney, and the peripheral nervous system; the statement also reviews information on the effects of diabetes and insulin resistance on the microvasculature of skin, brain, adipose tissue, and cardiac and skeletal muscle. Despite extensive and intensive research, it is disappointing that microvascular complications of diabetes continue to compromise the quantity and quality of life for patients with diabetes. Hopefully, by understanding and building on current research findings, we will discover new approaches for prevention and treatment that will be effective for future generations.
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Affiliation(s)
- Eugene J. Barrett
- Division of Endocrinology, Department of Medicine, University of Virginia, Charlottesville, Virginia 22908
| | - Zhenqi Liu
- Division of Endocrinology, Department of Medicine, University of Virginia, Charlottesville, Virginia 22908
| | - Mogher Khamaisi
- Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02215
| | - George L. King
- Section of Vascular Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Barbara E. K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Timothy M. Hughes
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Suzanne Craft
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Barry I. Freedman
- Divisions of Nephrology and Endocrinology, Department of Internal Medicine, Centers for Diabetes Research, and Center for Human Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Donald W. Bowden
- Divisions of Nephrology and Endocrinology, Department of Internal Medicine, Centers for Diabetes Research, and Center for Human Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Aaron I. Vinik
- EVMS Strelitz Diabetes Center, Eastern Virginia Medical Center, Norfolk, Virginia 23510
| | - Carolina M. Casellini
- EVMS Strelitz Diabetes Center, Eastern Virginia Medical Center, Norfolk, Virginia 23510
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4
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Zhang Z, Wu X, Cai T, Gao W, Zhou X, Zhao J, Yao J, Shang H, Dong J, Liao L. Matrix Metalloproteinase 9 Gene Promoter (rs 3918242) Mutation Reduces the Risk of Diabetic Microvascular Complications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:8023-33. [PMID: 26184271 PMCID: PMC4515707 DOI: 10.3390/ijerph120708023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Many studies have evaluated the association between matrix metalloproteinase 9 (MMP9) gene promoter polymorphism and diabetic microvascular complications. However, the results are conflicting and inconclusive. The aim of this meta-analysis was to evaluate the association more precisely. MATERIALS AND METHODS Studies were retrieved from the PubMed, Embase, Medline, China National Knowledge Infrastructure, Web of Science, and Cochrane databases. All statistical analyses were performed using Review Manager 5.2. RESULTS Data were abstracted from four case-control studies that included 446 patients with diabetic microvascular complications and 496 diabetic control subjects. The MMP9-1562 C/T genotype was significantly associated with the risk of diabetic nephropathy after stratification by specific type of microvascular complication (CT + TT vs. CC: OR = 0.42, 95% CI = 0.26-0.69, p = 0.0006; TT vs. CC + CT: OR = 0.37, 95% CI = 0.19-0.76, p = 0.006). CONCLUSIONS This study adds to the evidence that MMP9-1562 T gene mutation might reduce the risk of diabetic nephropathy.
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Affiliation(s)
- Zhongwen Zhang
- Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, 16766 Jingshi Road, Jinan 250014, China.
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Xiaoyun Wu
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Tian Cai
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Weiyi Gao
- Department of Cadres Healthcare, Qilu Hospital of Shandong University, Qingdao 266035, China.
| | - Xiaojun Zhou
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Junyu Zhao
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Jinming Yao
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Hongxia Shang
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
| | - Jianjun Dong
- Division of Endocrinology, Department of Medicine, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Lin Liao
- Division of Endocrinology, Department of Medicine, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014, China.
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Ponomarenko E, Zgoda V, Kopylov A, Poverennaya E, Ilgisonis E, Lisitsa A, Archakov A. The Russian part of the human proteome project:first results and prospects. ACTA ACUST UNITED AC 2015; 61:169-75. [DOI: 10.18097/pbmc20156102169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The article summarizes the achievements of the pilot phase (2010-2014) of the Russian part of the international project “Human Proteome” and identifies the directions for further work on the study of the human chromosome 18 proteome in the framework of the project main phase (2015-2022). The pilot phase of the project was focused on the detection of at least one protein for each chromosome 18 protein-coding gene in three types of the biological material. The application of mass spectrometric detection of proteins by the methods of multiple reactions monitoring (MRM) and gene-centric approach made it possible to detect 95% of master forms of proteins, for 60% of which the quantitative assessment of the protein content was obtained in at least one type of the biological material. The task of the main phase of the project is to measure the proteome size of healthy individuals, taking into account the modified protein forms, providing for both the bioinformatics prediction of the quantity of proteins types and the selective experimental measurement of single proteoforms. Since the ranges of protein concentrations corresponding to the normal physiological state have not been identified, the work of the main phase of the project is focused on the study of clinically healthy individuals. The absence of these data complicates significantly the interpretation of the patients’ blood proteomic profiles and prevents creating diagnostic tests. In the long term prospect, implementation of the project envisages development of a diagnostic test system based on multiple reactions monitoring (MRM) for quantitative measurement of the protein forms associated with some diseases. Development of such test systems will allow predicting the extent of risk of different diseases, diagnosing a disease at its early stage and monitoring the effectiveness of the treatment.
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Affiliation(s)
| | - V.G. Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A.T. Kopylov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - A.V. Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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6
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Alkayyali S, Lyssenko V. Genetics of diabetes complications. Mamm Genome 2014; 25:384-400. [PMID: 25169573 DOI: 10.1007/s00335-014-9543-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/13/2014] [Indexed: 12/11/2022]
Abstract
Chronic hyperglycemia and duration of diabetes are the major risk factors associated with development of micro- and macrovascular complications of diabetes. Although it is believed that hyperglycemia induces damage to the particular cell subtypes, e.g., mesangial cells in the renal glomerulus, capillary endothelial cells in the retina, and neurons and Schwann cells in peripheral nerves, the exact mechanisms underlying these damaging defects are not yet well understood. Clustering of micro- and macrovascular complications in families of patients with diabetes suggests a strong genetic susceptibility. However, until now only a handful number of genetic variants were reported to be associated with either nephropathy (ACE, ELMO1, FRMD3, and AKR1B1) or retinopathy (VEGF, AKR1B1, and EPO), and only a few studies were carried out for genetic susceptibility to cardiovascular diseases (ADIPOQ, GLUL) in patients with diabetes. It is, therefore, obvious that the accumulation of more data from larger studies and better phenotypically characterized cohorts is needed to facilitate genetic discoveries and unravel novel insights into the pathogenesis of diabetic complications.
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Affiliation(s)
- Sami Alkayyali
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Lund, Sweden,
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7
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Stanton RC. Clinical challenges in diagnosis and management of diabetic kidney disease. Am J Kidney Dis 2014; 63:S3-21. [PMID: 24461728 DOI: 10.1053/j.ajkd.2013.10.050] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 10/08/2013] [Indexed: 12/11/2022]
Abstract
Diabetic kidney disease (DKD) is a major and increasing worldwide public health issue. There is a great need for implementing treatments that either prevent or significantly slow the progression of DKD. Although there have been significant improvements in management, the increasing numbers of patients with DKD illustrate that current management is not wholly adequate. The reasons for suboptimal management include the lack of early diagnosis, lack of aggressive interventions, and lack of understanding about which interventions are most successful. There are a number of challenges and controversies regarding the current management of patients with DKD. Understanding of these issues is needed in order to provide the best care to patients with DKD. This article describes some of the clinically important challenges associated with DKD: the current epidemiology and cost burden and the role of biopsy in the diagnosis of DKD. Treatment controversies regarding current pharmacologic and nonpharmacologic approaches are reviewed and recommendations based on the published literature are made.
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Affiliation(s)
- Robert C Stanton
- Kidney and Hypertension Division, Joslin Diabetes Center, Boston, MA.
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Fu J, Akhmedov D, Berdeaux R. The short isoform of the ubiquitin ligase NEDD4L is a CREB target gene in hepatocytes. PLoS One 2013; 8:e78522. [PMID: 24147136 PMCID: PMC3798379 DOI: 10.1371/journal.pone.0078522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/21/2013] [Indexed: 02/02/2023] Open
Abstract
During cycles of fasting and feeding, liver function is regulated by both transcriptional and post-translational events. Regulated protein degradation has recently emerged as a key mechanism to control abundance of specific hepatic proteins under different nutritional conditions. As glucagon signaling through cAMP and PKA is central to glucose output during fasting, we hypothesized that this signaling pathway may also regulate ubiquitin ligases in the fasted state. Here we show that fasting stimuli promote expression of the short isoform of the E3 ubiquitin ligase Nedd4l in primary mouse hepatocytes. Nedd4l-short mRNA and NEDD4L (short isoform) protein accumulate in glucagon-treated primary mouse hepatocytes and in liver tissues during fasting. We identified a functional cAMP response element in the alternate Nedd4l-short promoter; mutation of this element blunts cAMP-induced expression of a Nedd4l reporter construct. CREB occupies the endogenous Nedd4l locus near this element. CREB and its co-activator CRTC2, both activated by fasting stimuli, contribute to glucagon-stimulated Nedd4l-short expression in primary hepatocytes. siRNA-mediated Nedd4l depletion in primary hepatocytes did not affect gluconeogenic gene expression, glucose output or glycogen synthesis. Our findings reveal a new mechanism of Nedd4l transcriptional regulation in liver cells.
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Affiliation(s)
- Jingqi Fu
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Dmitry Akhmedov
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Rebecca Berdeaux
- Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail:
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Association of POL1, MALT1, MC4R, PHLPP and DSEL single nucleotide polymorphisms in chromosome 18q region with type 2 diabetes in Tunisians. Gene 2013; 527:243-7. [DOI: 10.1016/j.gene.2013.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 03/13/2013] [Accepted: 05/06/2013] [Indexed: 12/21/2022]
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Su X, Chen X, Liu L, Chang X, Yu X, Sun K. Intracellular adhesion molecule-1 K469E gene polymorphism and risk of diabetic microvascular complications: a meta-analysis. PLoS One 2013; 8:e69940. [PMID: 23922864 PMCID: PMC3724680 DOI: 10.1371/journal.pone.0069940] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/13/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND A number of studies evaluated the association of intracellular adhesion molecule-1 (ICAM-1) K469E (rs5498, A/G) gene polymorphism with diabetic microvascular complications (DMI) including diabetic nephropathy (DN) and diabetic retinopathy (DR) in different populations. However, the results of individual studies remain conflicting. METHODS A comprehensive search was conducted to identify all eligible studies of the above-mentioned associations. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were assessed using the fixed or random effect model. RESULTS Seven studies involving 3411 subjects were included. Overall, the meta-analysis showed a significant association of the A allele with increased risk of DMI susceptibility in a recessive model (OR = 1.37, 95% CI 1.04-1.80, P = 0.02). In the subgroup analysis stratified by ethnicity, significant association was found in Asians but not in Caucasians (OR = 1.78, 95% CI 1.13-2.81, P = 0.01; OR = 1.10, 95% CI 0.79-1.54, P = 0.58, respectively). Moreover, it showed a significant association between the A allele and risk of DN in a recessive model (OR = 1.25, 95% CI 1.02-1.55, P = 0.04). CONCLUSIONS This meta-analysis suggested that the K469E polymorphism in ICAM-1 gene might affect individual susceptibility to DMI and showed a discrepancy in different ethnicities. Further investigations are needed to validate the association.
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Affiliation(s)
- Xianghui Su
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
| | - Xi Chen
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Lei Liu
- Department of Internal Medicine,Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Xiangyun Chang
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
| | - Xuefeng Yu
- Department of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Kan Sun
- Department of Endocrinology, First Hospital Affiliated to Medical College of Shihezi University, Xinjiang, People’s Republic of China
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11
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Hasstedt SJ, Highland HM, Elbein SC, Hanis CL, Das SK. Five linkage regions each harbor multiple type 2 diabetes genes in the African American subset of the GENNID Study. J Hum Genet 2013; 58:378-83. [PMID: 23552671 PMCID: PMC3692593 DOI: 10.1038/jhg.2013.21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We previously localized type 2 diabetes (T2D)-susceptibility genes to five chromosomal regions through a genome-wide linkage scan of T2D and age of diagnosis (AOD) in the African American subset of the GENNID sample. To follow up these findings, we repeated the linkage and association analysis using genotypes on an additional 9203 fine-mapping single nucleotide polymorphisms (SNPs) selected to tag genes under the linkage peaks. In each of the five regions, we confirmed linkage and inferred the presence of ≥2 susceptibility genes. The evidence of multiple susceptibility genes consisted of: (1) multiple linkage peaks in four of the five regions; and (2) association of T2D and AOD with SNPs within ≥2 genes in every region. The associated genes included 3 previously reported to associate with T2D or related traits (GRB10, NEDD4L, LIPG) and 24 novel candidate genes, including genes in lipid metabolism (ACOXL) and cell-cell and cell-matrix adhesion (MAGI2, CLDN4, CTNNA2).
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Affiliation(s)
- Sandra J Hasstedt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA.
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12
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Lu Q, Wei C, Ye C, Li M, Elston RC. A likelihood ratio-based Mann-Whitney approach finds novel replicable joint gene action for type 2 diabetes. Genet Epidemiol 2012; 36:583-93. [PMID: 22760990 PMCID: PMC3634342 DOI: 10.1002/gepi.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/09/2012] [Accepted: 05/09/2012] [Indexed: 12/29/2022]
Abstract
The potential importance of the joint action of genes, whether modeled with or without a statistical interaction term, has long been recognized. However, identifying such action has been a great challenge, especially when millions of genetic markers are involved. We propose a likelihood ratio-based Mann-Whitney test to search for joint gene action either among candidate genes or genome-wide. It extends the traditional univariate Mann-Whitney test to assess the joint association of genotypes at multiple loci with disease, allowing for high-order statistical interactions. Because only one overall significance test is conducted for the entire analysis, it avoids the issue of multiple testing. Moreover, the approach adopts a computationally efficient algorithm, making a genome-wide search feasible in a reasonable amount of time on a high performance personal computer. We evaluated the approach using both theoretical and real data. By applying the approach to 40 type 2 diabetes (T2D) susceptibility single-nucleotide polymorphisms (SNPs), we identified a four-locus model strongly associated with T2D in the Wellcome Trust (WT) study (permutation P-value < 0.001), and replicated the same finding in the Nurses' Health Study/Health Professionals Follow-Up Study (NHS/HPFS) (P-value = 3.03×10-11). We also conducted a genome-wide search on 385,598 SNPs in the WT study. The analysis took approximately 55 hr on a personal computer, identifying the same first two loci, but overall a different set of four SNPs, jointly associated with T2D (P-value = 1.29×10-5). The nominal significance of this same association reached 4.01×10-6 in the NHS/HPFS.
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Affiliation(s)
- Qing Lu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan
| | - Changshuai Wei
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan
| | - Chengyin Ye
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan
| | - Ming Li
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan
| | - Robert C. Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
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Chakkera HA, Hanson RL, Kobes S, Millis MP, Nelson RG, Knowler WC, Distefano JK. Association of variants in the carnosine peptidase 1 gene (CNDP1) with diabetic nephropathy in American Indians. Mol Genet Metab 2011; 103:185-90. [PMID: 21393041 PMCID: PMC3101283 DOI: 10.1016/j.ymgme.2011.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 01/11/2023]
Abstract
CNDP1 is located on 18q22.3, where linkage with diabetic nephropathy has been observed in several populations, including Pima Indians. However, evidence for association between CNDP1 alleles and diabetic nephropathy is equivocal and population-dependent. This study investigated CNDP1 as a candidate for diabetic kidney disease in Pima Indians. Nineteen tag single nucleotide polymorphisms spanning the CNDP1 locus were selected using genotype data from Chinese individuals in the HapMap resource along with 2 variants previously associated with diabetic nephropathy. All variants were genotyped in 3 different samples including a diabetic end-stage renal disease (ESRD) case-control study, a family-based study of diabetic individuals who participated in the linkage study for nephropathy, and a cohort of diabetic individuals in whom longitudinal measures of glomerular filtration rates (GFR) were performed. There was no statistically significant evidence for association with diabetic ESRD. However, nominal evidence for association was found in the family study, where markers rs12957330 (Odds ratio [OR]=0.29 per copy of G allele; p=0.04) and rs17817077 (OR=0.46 per copy of G allele; p=0.05) were associated with diabetic nephropathy. In addition, markers rs12964454, rs7244647, and rs7229005 were associated with changes in GFR (-8.5ml/min per copy of the G allele; p=0.04; 18.8ml/min per copy of the C allele; p=0.03; and -13.4ml/min per copy of the C allele; p=0.001, respectively). These findings provide nominal evidence supporting a role between CNDP1 variants and diabetic kidney disease.
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Affiliation(s)
- Harini A Chakkera
- Divisions of Nephrology and Transplantation, Mayo Clinic, Phoenix, AZ 85054, USA.
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Bowden DW. Will family studies return to prominence in human genetics and genomics? Rare variants and linkage analysis of complex traits. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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McDonough CW, Palmer ND, Hicks PJ, Roh BH, An SS, Cooke JN, Hester JM, Wing MR, Bostrom MA, Rudock ME, Lewis JP, Talbert ME, Blevins RA, Lu L, Ng MCY, Sale MM, Divers J, Langefeld CD, Freedman BI, Bowden DW. A genome-wide association study for diabetic nephropathy genes in African Americans. Kidney Int 2010; 79:563-72. [PMID: 21150874 DOI: 10.1038/ki.2010.467] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A genome-wide association study was performed using the Affymetrix 6.0 chip to identify genes associated with diabetic nephropathy in African Americans. Association analysis was performed adjusting for admixture in 965 type 2 diabetic African American patients with end-stage renal disease (ESRD) and in 1029 African Americans without type 2 diabetes or kidney disease as controls. The top 724 single nucleotide polymorphisms (SNPs) with evidence of association to diabetic nephropathy were then genotyped in a replication sample of an additional 709 type 2 diabetes-ESRD patients and 690 controls. SNPs with evidence of association in both the original and replication studies were tested in additional African American cohorts consisting of 1246 patients with type 2 diabetes without kidney disease and 1216 with non-diabetic ESRD to differentiate candidate loci for type 2 diabetes-ESRD, type 2 diabetes, and/or all-cause ESRD. Twenty-five SNPs were significantly associated with type 2 diabetes-ESRD in the genome-wide association and initial replication. Although genome-wide significance with type 2 diabetes was not found for any of these 25 SNPs, several genes, including RPS12, LIMK2, and SFI1 are strong candidates for diabetic nephropathy. A combined analysis of all 2890 patients with ESRD showed significant association SNPs in LIMK2 and SFI1 suggesting that they also contribute to all-cause ESRD. Thus, our results suggest that multiple loci underlie susceptibility to kidney disease in African Americans with type 2 diabetes and some may also contribute to all-cause ESRD.
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Affiliation(s)
- Caitrin W McDonough
- Program in Molecular Medicine and Translational Science, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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McEvoy BP, Lind JM, Wang ET, Moyzis RK, Visscher PM, van Holst Pellekaan SM, Wilton AN. Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry. Am J Hum Genet 2010; 87:297-305. [PMID: 20691402 DOI: 10.1016/j.ajhg.2010.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 06/30/2010] [Accepted: 07/16/2010] [Indexed: 12/19/2022] Open
Abstract
Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.
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Affiliation(s)
- Brian P McEvoy
- Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia.
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Abstract
Blood pressure (BP) in the prehypertensive range is associated with an increased risk for cardiovascular (CV) disease. Patients with co-morbidities are at greater risk for chronic kidney disease (CKD) development in the presence of prehypertension. Lifestyle changes can alter the natural history of prehypertension; however, long-term adherence is rare and thus, their impact on outcomes is limited. Pharmacological therapy in patients with prehypertension and demonstrable target organ damage with blockers of the renin-angiotensin system has demonstrated benefits on markers of CKD outcomes such as microalbuminuria. There are no data, however, on 'hard end points' such as doubling of creatinine or need for renal replacement therapy. In patients with diabetes, monitoring changes in albuminuria, along with assessment of BP in the prehypertensive range, is important to optimize early management and impact the attenuation of CKD progression. Data from natural history studies in patients with type 1 diabetes indicate that increases within the microalbuminuria range antedate increases in BP within the prehypertensive range. Even within the microalbuminuria range, however, systolic BP increases above 125 mm Hg are predictive of nephropathy. Thus, nephrologists need to ensure that their colleagues appreciate the importance of not only early BP intervention but also of monitoring albuminuria changes in order to have maximal impact on CKD prevention.
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