201
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Wu B, Hao Y, Shi J, Geng N, Li T, Chen Y, Sun Z, Zheng L, Li H, Li N, Zhang X, Sun Y. Association between xanthine dehydrogenase tag single nucleotide polymorphisms and essential hypertension. Mol Med Rep 2015; 12:5685-90. [PMID: 26239312 PMCID: PMC4581766 DOI: 10.3892/mmr.2015.4135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 06/26/2015] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to investigate the association between xanthine dehydrogenase (XDH) gene polymorphism and essential hypertension in the rural Han Chinese population of Fuxin, Liaoning. Han Chinese individuals, who had lived in rural areas of Fuxin, were selected as subjects for the present study. A total of 521 unrelated patients with hypertension were selected, along with a further 533 unrelated individuals with normal blood pressure, in order to serve as controls. Five tag single nucleotide polymorphisms (SNP) of the XDH gene were selected. An estimation of SNP allele frequency was determined using DNA pooling and pyrosequencing methods. Prior to Bonferroni correction, T allele frequency for rs206811 was significantly higher in patients with hypertension, as compared with the controls (64.1 vs. 59.4%; P=0.031); C allele frequency for rs1042039 was significantly higher in patients with hypertension, as compared with the controls (66.1 vs. 60.6%; P=0.011), C allele frequency for rs1054889 was significantly lower in patients with hypertension, as compared with the controls (38.8 vs. 44.8%; P=0.007); and A allele frequency for rs2073316 was significantly lower in patients with hypertension, as compared with the controls (29.2 vs. 34.4%; P=0.013). However, once a Bonferroni correction for multiple testing was applied, the XDH gene polymorphisms rs1042039, rs1054889, and rs2073316 were shown to be associated with hypertension (P=0.044, 0.035, and 0.039, respectively). These results suggest that the XDH gene polymorphisms rs1042039, rs1054889, and rs2073316 may be associated with hypertension in the rural Han Chinese population.
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Affiliation(s)
- Baogang Wu
- Department of Geriatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ying Hao
- Department of Geriatrics, Jinqiu Hospital, Shenyang, Liaoning 110016, P.R. China
| | - Jin Shi
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ning Geng
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Tiejun Li
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yanli Chen
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Zhaoqing Sun
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Liqiang Zheng
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Hong Li
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Naijing Li
- Department of Geriatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xingang Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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202
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Salfati E, Morrison AC, Boerwinkle E, Chakravarti A. Direct Estimates of the Genomic Contributions to Blood Pressure Heritability within a Population-Based Cohort (ARIC). PLoS One 2015; 10:e0133031. [PMID: 26162070 PMCID: PMC4498745 DOI: 10.1371/journal.pone.0133031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/23/2015] [Indexed: 01/11/2023] Open
Abstract
Blood pressure (BP) is a heritable trait with multiple environmental and genetic contributions, with current heritability estimates from twin and family studies being ~ 40%. Here, we use genome-wide polymorphism data from the Atherosclerosis Risk in Communities (ARIC) study to estimate BP heritability from genomic relatedness among cohort members. We utilized data on 6,365,596 and 9,578,528 genotyped and imputed common single nucleotide polymorphisms (SNPs), in 8,901 European ancestry (EA) and 2,860 African Ancestry (AA) ARIC participants, respectively, and a mixed linear model for analyses, to make four observations. First, for BP measurements, the heritability is ~20%/~50% and ~27%/~39% for systolic (SBP)/diastolic (DBP) blood pressure in European and African ancestry individuals, respectively, consistent with prior studies. Second, common variants with allele frequency >10% recapitulate most of the BP heritability in these data. Third, the vast majority of BP heritability varies by chromosome, depending on its length, and is largely concentrated in noncoding genomic regions annotated as DNaseI hypersensitive sites (DHSs). Fourth, the majority of this heritability arises from loci not harboring currently known cardiovascular and renal genes. Recent meta-analyses of large-scale genome-wide association studies (GWASs) and admixture mapping have identified ~50 loci associated with BP and hypertension (HTN), and yet they account for only a small fraction (~2%) of the heritability.
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Affiliation(s)
- Elias Salfati
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, United States of America; Université Paris Descartes, Sorbonne Paris Cite, 75005, Paris, France
| | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, 77030, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, 77030, United States of America
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, United States of America
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203
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Walsh SP, Shahripour A, Tang H, Teumelsan N, Frie J, Zhu Y, Priest BT, Swensen AM, Liu J, Margulis M, Visconti R, Weinglass A, Felix JP, Brochu RM, Bailey T, Thomas-Fowlkes B, Alonso-Galicia M, Zhou X, Pai LY, Corona A, Hampton C, Hernandez M, Bentley R, Chen J, Shah K, Metzger J, Forrest M, Owens K, Tong V, Ha S, Roy S, Kaczorowski GJ, Yang L, Parmee E, Garcia ML, Sullivan K, Pasternak A. Discovery of a Potent and Selective ROMK Inhibitor with Pharmacokinetic Properties Suitable for Preclinical Evaluation. ACS Med Chem Lett 2015; 6:747-52. [PMID: 26191360 DOI: 10.1021/ml500440u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/07/2015] [Indexed: 12/12/2022] Open
Abstract
A new subseries of ROMK inhibitors exemplified by 28 has been developed from the initial screening hit 1. The excellent selectivity for ROMK inhibition over related ion channels and pharmacokinetic properties across preclinical species support further preclinical evaluation of 28 as a new mechanism diuretic. Robust pharmacodynamic effects in both SD rats and dogs have been demonstrated.
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Affiliation(s)
- Shawn P. Walsh
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Aurash Shahripour
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Haifeng Tang
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Nardos Teumelsan
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jessica Frie
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Yuping Zhu
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lihu Yang
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Emma Parmee
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | | | | | - Alexander Pasternak
- Discovery Chemistry, ‡Department of Pharmacology, §Department of Cardiometabolic
Diseases, ∥Pharmacokinetic, Pharmacodynamics and Drug Metabolism, ⊥Department of Chemistry
Modeling and Informatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
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204
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Hunter RW, Ivy JR, Flatman PW, Kenyon CJ, Craigie E, Mullins LJ, Bailey MA, Mullins JJ. Hypertrophy in the Distal Convoluted Tubule of an 11β-Hydroxysteroid Dehydrogenase Type 2 Knockout Model. J Am Soc Nephrol 2015; 26:1537-48. [PMID: 25349206 PMCID: PMC4483573 DOI: 10.1681/asn.2013060634] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/12/2014] [Indexed: 11/03/2022] Open
Abstract
Na(+) transport in the renal distal convoluted tubule (DCT) by the thiazide-sensitive NaCl cotransporter (NCC) is a major determinant of total body Na(+) and BP. NCC-mediated transport is stimulated by aldosterone, the dominant regulator of chronic Na(+) homeostasis, but the mechanism is controversial. Transport may also be affected by epithelial remodeling, which occurs in the DCT in response to chronic perturbations in electrolyte homeostasis. Hsd11b2(-/-) mice, which lack the enzyme 11β-hydroxysteroid dehydrogenase type 2 (11βHSD2) and thus exhibit the syndrome of apparent mineralocorticoid excess, provided an ideal model in which to investigate the potential for DCT hypertrophy to contribute to Na(+) retention in a hypertensive condition. The DCTs of Hsd11b2(-/-) mice exhibited hypertrophy and hyperplasia and the kidneys expressed higher levels of total and phosphorylated NCC compared with those of wild-type mice. However, the striking structural and molecular phenotypes were not associated with an increase in the natriuretic effect of thiazide. In wild-type mice, Hsd11b2 mRNA was detected in some tubule segments expressing Slc12a3, but 11βHSD2 and NCC did not colocalize at the protein level. Thus, the phosphorylation status of NCC may not necessarily equate to its activity in vivo, and the structural remodeling of the DCT in the knockout mouse may not be a direct consequence of aberrant corticosteroid signaling in DCT cells. These observations suggest that the conventional concept of mineralocorticoid signaling in the DCT should be revised to recognize the complexity of NCC regulation by corticosteroids.
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Affiliation(s)
- Robert W Hunter
- British Heart Foundation Centre for Cardiovascular Science and
| | - Jessica R Ivy
- British Heart Foundation Centre for Cardiovascular Science and
| | - Peter W Flatman
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Eilidh Craigie
- British Heart Foundation Centre for Cardiovascular Science and
| | - Linda J Mullins
- British Heart Foundation Centre for Cardiovascular Science and
| | | | - John J Mullins
- British Heart Foundation Centre for Cardiovascular Science and
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205
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Classical Bartter syndrome – A case report. INDIAN JOURNAL OF MEDICAL SPECIALITIES 2015. [DOI: 10.1016/j.injms.2015.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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206
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Schröder K, Müller D. [Electrolyte disorders as a hallmark of monogenetic diseases]. Internist (Berl) 2015; 56:739-44. [PMID: 26078045 DOI: 10.1007/s00108-015-3672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In daily clinical practice, the term electrolyte generally refers to sodium, potassium, chloride, calcium, and magnesium ions. In addition to their many functions, such as neuronal and muscular transmission, some electrolytes also contribute to osmolality and maintenance of electrochemical gradients, which, in turn enable many transport processes. The absorption and reabsorption of electrolytes occurs via polarized cell assemblies, i.e., epithelia. Besides the intestine (absorption), the most important organ is the kidney. Here, following glomerular filtration, electrolytes are reabsorbed via trans- and paracellular mechanisms along the renal tubular system. In the past, the identification and elucidation of transport-associated monogenetic disorders has contributed tremendously to our understanding of the physiology and pathophysiology of such transport mechanisms. Sodium reabsorption mechanisms along the tubular system have been characterized by means of pharmacological compounds for a long time. However, only with the development of novel molecular genetic tools and approaches has it been possible to clarify the genetic basis of distinct diseases. As examples, we discuss here Bartter and Gitelman syndrome, and other sodium disorders such as pseudohypoaldosteronism and Liddle Syndrome. Diagnosis, clinical presentation, and therapy are briefly described. Furthermore, examples of magnesium homeostasis disorders are also presented, the molecular mechanisms and pathophysiology of which could also be characterized by the identification of different human mutations.
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Affiliation(s)
- K Schröder
- Klinik für Pädiatrie mit Schwerpunkt Nephrologie, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353, Berlin, Deutschland
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207
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Abstract
Until recently, significant advances in our understanding of the mechanisms of blood pressure regulation arose from studies of monogenic forms of hypertension and hypotension, which identified rare variants that primarily alter renal salt handling. Genome-wide association and exome sequencing studies over the past 6 years have resulted in an unparalleled burst of discovery in the genetics of blood pressure regulation and hypertension. More importantly, genome-wide association studies, while expanding the list of common genetic variants associated with blood pressure and hypertension, are also uncovering novel pathways of blood pressure regulation that augur a new era of novel drug development, repurposing, and stratification in the management of hypertension. In this review, we describe the current state of the art of the genetic and molecular basis of blood pressure and hypertension.
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Affiliation(s)
- Sandosh Padmanabhan
- From the Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, United Kingdom (S.P., A.F.D.); and Queen Mary University of London, Barts and The London School of Medicine, Clinical Pharmacology, London, United Kingdom (M.C.)
| | - Mark Caulfield
- From the Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, United Kingdom (S.P., A.F.D.); and Queen Mary University of London, Barts and The London School of Medicine, Clinical Pharmacology, London, United Kingdom (M.C.)
| | - Anna F Dominiczak
- From the Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, United Kingdom (S.P., A.F.D.); and Queen Mary University of London, Barts and The London School of Medicine, Clinical Pharmacology, London, United Kingdom (M.C.).
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208
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Martelli A, Testai L, Breschi MC, Calderone V. Inhibitors of the renal outer medullary potassium channel: a patent review. Expert Opin Ther Pat 2015; 25:1035-51. [PMID: 26004420 DOI: 10.1517/13543776.2015.1050792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Hypertension represents a substantial cardiovascular risk factor. Among anti-hypertensive drugs, diuretics play an important role. Nevertheless, they present adverse effects such as hypokalemia or hyperkalemia. In this panorama, inhibitors of the renal outer medullary potassium (ROMK) channels are emerging because they are predicted to give a diuretic/natriuretic activity higher than that provided by loop diuretics, without hypokaliemic and hyperkaliemic side effects. AREAS COVERED This article reviews the current literature, including all the patents published in the field of inhibitors of the ROMK channels for the treatment of hypertension, heart failure and correlated diseases. The patent examination has been carried out using electronic databases Espacenet. EXPERT OPINION Although anti-hypertensive drugs armamentarium enumerates a plethora of therapeutic classes, including diuretics, the novel class of ROMK inhibitors may find a place in this crowded market, because of the diuretic/natriuretic effects, devoid of worrying influence on potassium balance. The patent examination highlights, as a strength, the individuation of a successful template: almost all the compounds show noteworthy potency. However, only few selected compounds underwent an in vivo investigation of diuretic and anti-hypertensive activities, and no data on the hERG channel are given in these patents.
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Affiliation(s)
- Alma Martelli
- a 1 Department of Pharmacy , via Bonanno 6, I-56126, Pisa, Italy +39 50 2219598 ; +39 50 2210680 ;
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Cardiovascular consequences of a polygenetic component of blood pressure in an urban-based longitudinal study: the Malmö diet and cancer. J Hypertens 2015; 32:1424-8; discussion 1428. [PMID: 24879493 DOI: 10.1097/hjh.0000000000000209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND A recently published genome wide association study identified 29 single nucleotide polymorphisms (SNPs) influencing blood pressure (BP). Case-control studies suggest that a genetic risk score (GRS) based on these 29 SNPs affect the risk of cardiovascular disease (CVD), but its role for CVD at population level is unknown. Here, we prospectively evaluate the impact of this polygenetic BP component on CVD morbidity and mortality in a large urban-based middle-aged population. METHOD The 29 previously BP associated SNPs were genotyped in the Swedish Malmö Diet and Cancer Study; (n = 27,003 with at least 24 valid SNPs). The number of BP elevating alleles of each SNPs, weighted by their effect size in the discovery studies, was summed into a BP-GRS. RESULTS Using regression models, we found significant associations of the BP-GRS, cross-sectionally, with BP and hypertension prevalence, prospectively, with incident cardiovascular morbidity and mortality during 14.2 ± 3.2 years of follow-up. After adjustment for traditional cardiovascular risk factors (TRF), including hypertension, the BP-GRS remained significantly associated only with CVDs [in terms of strokes and coronary artery disease; hazard ratio 1.15; 95% confidence interval (CI) 1.06-1.24 comparing the third vs. first tertile; P = 0.003]. Calibration, discrimination and reclassification analyses did not show a meaningful increment in prediction using the BP-GRS in addition to the model encompassing only the TRF. CONCLUSION The polygenetic component of BP influences risk of cardiovascular morbidity and mortality. However, the effect size is small and unlikely to be useful for prediction at the population level.
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210
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Koulouridis E, Koulouridis I. Molecular pathophysiology of Bartter's and Gitelman's syndromes. World J Pediatr 2015; 11:113-25. [PMID: 25754753 DOI: 10.1007/s12519-015-0016-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND In the last two decades, progress in cytogenetic and genome research has enabled investigators to unravel the underlying molecular mechanisms of inherited tubulopathies such as Bartter's and Gitelman's syndromes and helped physicians to better understand not only these two pathologic entities but also renal pathophysiology and salt sensitive hypertension. DATA SOURCES Articles collected from PubMed and open access journals included original articles, research articles, and comprehensive reviews. They were evaluated by the authors with an special emphasis on originality and up to date information about molecular pathophysiology. RESULTS Bartter's and Gitelman's syndromes are two different inherited salt loosing tubulopathies. They are characterized by various inability of distal nephron to reabsorb sodium chloride with resultant extarcellular volume contraction and increased activity of the renin angiotensin aldosterone system. Hypokalemic metabolic alkalosis is a common feature of these two forms of tubulopathies. Hypercalciuria characterizes the majority of Bartter's syndrome, and hypomagnesemia with hypocalciuria characterizes Gitelman's syndrome. Low blood pressure is a common feature among patients who suffered from these tubulopathies. Bartter's syndromes encompass a heterogeneous group of ion channels defects localized at the thick ascending limp of Henle's loop with resultant loss of function of sodium-potassium-2 chloride cotransporter. These defects result in the impairment of the countercurrent multiplication system of the kidney as well as calcium, potassium and acid base disturbances which in the majority of cases are proved lethal especially in the antenatal and/or immediate postnatal life period. The underlying pathology in Gitelman's syndrome is defined to the distal convoluted tubule and is related to loss of function of the sodium-chloride cotransporter. The results of this defect encompass the inability of extracellular volume homeostasis, magnesium and potassium conservation, and acid base disturbances which are generally mild and in the majority of cases are not life-threatening. CONCLUSIONS Recent advances in molecular pathophysiology of Bartter's and Gitelman's syndromes have helped physicians to better understand the underlying mechanisms of these pathologic entities which remain obscure. Data collected from experiments among genetically manipulated animals enable us to better understand the pathophysiology of mammalian kidney and the underlying mechanisms of salt sensitive hypertension and to lay a foundation for the future development of new drugs, especially diuretics and antihypertensive drugs.
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211
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Wang L, Dong C, Xi YG, Su X. Thiazide-sensitive Na+-Cl- cotransporter: genetic polymorphisms and human diseases. Acta Biochim Biophys Sin (Shanghai) 2015; 47:325-34. [PMID: 25841442 DOI: 10.1093/abbs/gmv020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 02/26/2015] [Indexed: 12/16/2022] Open
Abstract
The thiazide-sensitive Na(+)-Cl(-) cotransporter (TSC) is responsible for the major sodium chloride reabsorption pathway, which is located in the apical membrane of the epithelial cells of the distal convoluted tubule. TSC is involved in several physiological activities including transepithelial ion absorption and secretion, cell volume regulation, and setting intracellular Cl(-) concentration below or above its electrochemical potential equilibrium. In addition, TSC serves as the target of thiazide-type diuretics that are the first line of therapy for the treatment of hypertension in the clinic, and its mutants are also reported to be associated with the hereditary disease, Gitelman's syndrome. This review aims to summarize the publications with regard to the TSC by focusing on the association between TSC mutants and human hypertension as well as Gitelman's syndrome.
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Affiliation(s)
- Linghong Wang
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot 010050, China
| | - Chao Dong
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot 010050, China
| | - Ya-Guang Xi
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot 010050, China
| | - Xiulan Su
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot 010050, China
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212
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Zhang F, Xu Y, Shugart YY, Yue W, Qi G, Yuan G, Cheng Z, Yao J, Wang J, Wang G, Cao H, Guo W, Zhou Z, Wang Z, Tian L, Jin C, Yuan J, Liu C, Zhang D. Converging evidence implicates the abnormal microRNA system in schizophrenia. Schizophr Bull 2015; 41:728-35. [PMID: 25429046 PMCID: PMC4393688 DOI: 10.1093/schbul/sbu148] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Previous findings are inconsistent; yet, converging evidence suggests an association between schizophrenia (SZ) and the impairment of posttranscriptional regulation of brain development through microRNA (miRNA) systems. METHODS This study aims to (1) compare the overall frequency of 121 rare variants (RVs) in 59 genes associated with the miRNA system in genome-wide association studies (GWAS)-derived data including 768 SZ cases and 1348 healthy controls and validated in an independent GWAS data including 1802 SZ cases and 1447 controls; (2) profile genome-wide miRNA expression in blood collected from 15 early-onset SZ (EOS) cases and 15 healthy controls; and (3) construct a miRNA-messenger RNA (mRNA) regulatory network using our previous genome-wide mRNA expression data generated from a separate sample of 18 EOS cases and 12 healthy controls. RESULTS Our findings indicate that: (1) In genes associated with the control of miRNAs, there are approximately 50% more RVs in SZ cases than in controls (P ≤ 2.62E-10); (2) The observed lower miRNA activity in EOS patients compared with the healthy controls suggests that miRNAs are abnormally downregulated; (3) There exists a predicted regulatory network among some downregulated miRNAs and some upregulated mRNAs. CONCLUSIONS Collectively, results from all 3 lines of evidence, suggest that the genetically based dysregulation of miRNA systems undermines miRNAs' inhibitory effects, resulting in the abnormal upregulation of genome transcription in the development of SZ.
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Affiliation(s)
| | - Yong Xu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China;,These authors contributed equally to this work
| | - Yin Yao Shugart
- Division of Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD;,Department of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD;,These authors contributed equally to this work
| | - Weihua Yue
- Department of Psychiatry, The Sixth Affiliated Hospital and Institute for Mental Health of Peking University/Key Laboratory of Mental Health, Ministry of Health, Beijing, China;,These authors contributed equally to this work
| | - Guoyang Qi
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Guozhen Yuan
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Zaohuo Cheng
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Jianjun Yao
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Jidong Wang
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Guoqiang Wang
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Hongbao Cao
- Division of Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD
| | - Wei Guo
- Division of Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD
| | - Zhenhe Zhou
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Zhiqiang Wang
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Lin Tian
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Chunhui Jin
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Jianmin Yuan
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Chenxing Liu
- Department of Psychiatry, The Sixth Affiliated Hospital and Institute for Mental Health of Peking University/Key Laboratory of Mental Health, Ministry of Health, Beijing, China
| | - Dai Zhang
- Department of Psychiatry, The Sixth Affiliated Hospital and Institute for Mental Health of Peking University/Key Laboratory of Mental Health, Ministry of Health, Beijing, China; Peking-Tsinghua Center for Life Sciences/PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
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213
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Grimm PR, Lazo-Fernandez Y, Delpire E, Wall SM, Dorsey SG, Weinman EJ, Coleman R, Wade JB, Welling PA. Integrated compensatory network is activated in the absence of NCC phosphorylation. J Clin Invest 2015; 125:2136-50. [PMID: 25893600 DOI: 10.1172/jci78558] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022] Open
Abstract
Thiazide diuretics are used to treat hypertension; however, compensatory processes in the kidney can limit antihypertensive responses to this class of drugs. Here, we evaluated compensatory pathways in SPAK kinase-deficient mice, which are unable to activate the thiazide-sensitive sodium chloride cotransporter NCC (encoded by Slc12a3). Global transcriptional profiling, combined with biochemical, cell biological, and physiological phenotyping, identified the gene expression signature of the response and revealed how it establishes an adaptive physiology. Salt reabsorption pathways were created by the coordinate induction of a multigene transport system, involving solute carriers (encoded by Slc26a4, Slc4a8, and Slc4a9), carbonic anhydrase isoforms, and V-type H⁺-ATPase subunits in pendrin-positive intercalated cells (PP-ICs) and ENaC subunits in principal cells (PCs). A distal nephron remodeling process and induction of jagged 1/NOTCH signaling, which expands the cortical connecting tubule with PCs and replaces acid-secreting α-ICs with PP-ICs, were partly responsible for the compensation. Salt reabsorption was also activated by induction of an α-ketoglutarate (α-KG) paracrine signaling system. Coordinate regulation of a multigene α-KG synthesis and transport pathway resulted in α-KG secretion into pro-urine, as the α-KG-activated GPCR (Oxgr1) increased on the PP-IC apical surface, allowing paracrine delivery of α-KG to stimulate salt transport. Identification of the integrated compensatory NaCl reabsorption mechanisms provides insight into thiazide diuretic efficacy.
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214
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Zuo X, Sun L, Yin X, Gao J, Sheng Y, Xu J, Zhang J, He C, Qiu Y, Wen G, Tian H, Zheng X, Liu S, Wang W, Li W, Cheng Y, Liu L, Chang Y, Wang Z, Li Z, Li L, Wu J, Fang L, Shen C, Zhou F, Liang B, Chen G, Li H, Cui Y, Xu A, Yang X, Hao F, Xu L, Fan X, Li Y, Wu R, Wang X, Liu X, Zheng M, Song S, Ji B, Fang H, Yu J, Sun Y, Hui Y, Zhang F, Yang R, Yang S, Zhang X. Whole-exome SNP array identifies 15 new susceptibility loci for psoriasis. Nat Commun 2015; 6:6793. [PMID: 25854761 PMCID: PMC4403312 DOI: 10.1038/ncomms7793] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 02/28/2015] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWASs) have reproducibly associated ∼40 susceptibility loci with psoriasis. However, the missing heritability is evident and the contributions of coding variants have not yet been systematically evaluated. Here, we present a large-scale whole-exome array analysis for psoriasis consisting of 42,760 individuals. We discover 16 SNPs within 15 new genes/loci associated with psoriasis, including C1orf141, ZNF683, TMC6, AIM2, IL1RL1, CASR, SON, ZFYVE16, MTHFR, CCDC129, ZNF143, AP5B1, SYNE2, IFNGR2 and 3q26.2-q27 (P<5.00 × 10(-08)). In addition, we also replicate four known susceptibility loci TNIP1, NFKBIA, IL12B and LCE3D-LCE3E. These susceptibility variants identified in the current study collectively account for 1.9% of the psoriasis heritability. The variant within AIM2 is predicted to impact protein structure. Our findings increase the number of genetic risk factors for psoriasis and highlight new and plausible biological pathways in psoriasis.
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Affiliation(s)
- Xianbo Zuo
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, No.2 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, No.2 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Xianyong Yin
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, No.2 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Jinping Gao
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Yujun Sheng
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People’s Hospital, Beijing 100044, China
| | - Chundi He
- Department of Dermatology, No.1 Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Ying Qiu
- Department of Dermatology, Jining No. 1 People’s Hospital, Jining, Shandong 272011, China
| | - Guangdong Wen
- Department of Dermatology, Peking University People’s Hospital, Beijing 100044, China
| | - Hongqing Tian
- Shandong Provincial Institute of Dermatology and Venereology, Jinan, Shandong 250022, China
| | - Xiaodong Zheng
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Shengxiu Liu
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Wenjun Wang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Weiran Li
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Yuyan Cheng
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Longdan Liu
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Yan Chang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Zaixing Wang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Zenggang Li
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Longnian Li
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Jianping Wu
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Ling Fang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Changbing Shen
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Fusheng Zhou
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Bo Liang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Gang Chen
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Hui Li
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Yong Cui
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Aie Xu
- The Third People's Hospital of Hangzhou, Hangzhou, Zhejiang 310009, China
| | - Xueqin Yang
- Department of Dermatology, General Hospital of PLA Air Force, Beijing 100036, China
| | - Fei Hao
- Department of Dermatology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Limin Xu
- Department of Dermatology, Tianjin Changzheng Hospital, Tianjin 300106, China
| | - Xing Fan
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Yuzhen Li
- Department of Dermatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Rina Wu
- Department of Dermatology, The Affiliated Hospital of Inner Mongolia Medical College, Huhehot, Inner Mongolia 010050, China
| | - Xiuli Wang
- Shanghai Skin Diseases and STD Hospital, Shanghai 200050, China
| | - Xiaoming Liu
- Department of Dermatology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, China
| | - Min Zheng
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhenjiang 310009, China
| | - Shunpeng Song
- Department of Dermatology, Dalian Dermatosis Hosptial, Liaoning 116011, China
| | - Bihua Ji
- Department of Dermatology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241000, China
| | - Hong Fang
- Department of Dermatology, The First Affiliated Hospital of Zhejiang University School of Medicine, Zhenjiang 310006, China
| | - Jianbin Yu
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yongxin Sun
- Department of Dermatology, Anshan Tanggangzi hosptial, Liaoning 210300, China
| | - Yan Hui
- Department of Dermatology, First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830054, China
| | - Furen Zhang
- Shandong Provincial Institute of Dermatology and Venereology, Jinan, Shandong 250022, China
| | - Rongya Yang
- Department of Dermatology, General Hospital of Beijing Military Command, Beijing 100010, China
| | - Sen Yang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, No.2 Hospital, Anhui Medical University, Hefei, Anhui 230022, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, Anhui 230032, China
- State Key Lab Incubation of Dermatology, Ministry of Science and Technology, Hefei, Anhui 230032, China
- Key Lab of Dermatology, Ministry of Education, Hefei, Anhui 230032, China
- Key Lab of Gene Resources Utilization for Severe Inherited Disorders, Anhui 230032, China
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215
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Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJH, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JBA, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One 2015; 10:e0122271. [PMID: 25849893 PMCID: PMC4388675 DOI: 10.1371/journal.pone.0122271] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.
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Affiliation(s)
- Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine P. Liao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert R. Graham
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeffrey D. Greenberg
- New York University Hospital for Joint Diseases, New York, New York, United States of America
| | - Steve Eyre
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Jing Cui
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Lee
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Dimitrios A. Pappas
- Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
| | - Joel M. Kremer
- The Albany Medical College and The Center for Rheumatology, Albany, New York, United States of America
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Marieke J. H. Coenen
- Radboud university medical center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Barbara Franke
- Radboud University Medical Center, Donders Centre for Neurosciences, Department of Psychiatry and Human Genetics, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Xavier Mariette
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Corrine Richard-Miceli
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Helena Canhão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - João E. Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Niek de Vries
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P. Tak
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - J. Bart A. Crusius
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Michael T. Nurmohamed
- Amsterdam Rheumatology and Immunology Center, Department of Rheumatology, Reade, Amsterdam, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ted R. Mikuls
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yukinori Okada
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eli A. Stahl
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - David E. Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tracie L. Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda L. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Roman Kosoy
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Michael Ransom
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Tushar R. Bhangale
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Ward Ortmann
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Andrew Cagan
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Vivian Gainer
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Elizabeth W. Karlson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac Kohane
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Shawn N. Murphy
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, 18100, Spain
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
- Genetics Department, University Medical Center and Groningen University, Groningen, The Netherlands
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael F. Seldin
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Timothy Behrens
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
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216
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Wang X, Zhang S, Li Y, Li M, Sha Q. A powerful approach to test an optimally weighted combination of rare variants in admixed populations. Genet Epidemiol 2015; 39:294-305. [PMID: 25758547 DOI: 10.1002/gepi.21894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 01/09/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
Population stratification has long been recognized as an issue in genetic association studies because unrecognized population stratification can lead to both false-positive and false-negative findings and can obscure true association signals if not appropriately corrected. This issue can be even worse in rare variant association analyses because rare variants often demonstrate stronger and potentially different patterns of stratification than common variants. To correct for population stratification in genetic association studies, we proposed a novel method to Test the effect of an Optimally Weighted combination of variants in Admixed populations (TOWA) in which the analytically derived optimal weights can be calculated from existing phenotype and genotype data. TOWA up weights rare variants and those variants that have strong associations with the phenotype. Additionally, it can adjust for the direction of the association, and allows for local ancestry difference among study subjects. Extensive simulations show that the type I error rate of TOWA is under control in the presence of population stratification and it is more powerful than existing methods. We have also applied TOWA to a real sequencing data. Our simulation studies as well as real data analysis results indicate that TOWA is a useful tool for rare variant association analyses in admixed populations.
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Affiliation(s)
- Xuexia Wang
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
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217
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Cheng CJ, Sung CC, Huang CL, Lin SH. Inward-rectifying potassium channelopathies: new insights into disorders of sodium and potassium homeostasis. Pediatr Nephrol 2015; 30:373-83. [PMID: 24899236 DOI: 10.1007/s00467-014-2764-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/11/2013] [Accepted: 01/10/2014] [Indexed: 11/30/2022]
Abstract
Inward-rectifying potassium (Kir) channels allow more inward than outward potassium flux when channels are open in mammalian cells. At physiological resting membrane potentials, however, they predominantly mediate outward potassium flux and play important roles in regulating the resting membrane potential in diverse cell types and potassium secretion in the kidneys. Mutations of Kir channels cause human hereditary diseases collectively called Kir channelopathies, many of which are characterized by disorders of sodium and potassium homeostasis. Studies on these genetic Kir channelopathies have shed light on novel pathophysiological mechanisms, including renal sodium and potassium handling, potassium shifting in skeletal muscles, and aldosterone production in the adrenal glands. Here, we review several recent advances in Kir channels and their clinical implications in sodium and potassium homeostasis.
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Affiliation(s)
- Chih-Jen Cheng
- Department of Medicine, Division of Nephrology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan
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218
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Rossier BC, Baker ME, Studer RA. Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited. Physiol Rev 2015; 95:297-340. [PMID: 25540145 DOI: 10.1152/physrev.00011.2014] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription and translation require a high concentration of potassium across the entire tree of life. The conservation of a high intracellular potassium was an absolute requirement for the evolution of life on Earth. This was achieved by the interplay of P- and V-ATPases that can set up electrochemical gradients across the cell membrane, an energetically costly process requiring the synthesis of ATP by F-ATPases. In animals, the control of an extracellular compartment was achieved by the emergence of multicellular organisms able to produce tight epithelial barriers creating a stable extracellular milieu. Finally, the adaptation to a terrestrian environment was achieved by the evolution of distinct regulatory pathways allowing salt and water conservation. In this review we emphasize the critical and dual role of Na(+)-K(+)-ATPase in the control of the ionic composition of the extracellular fluid and the renin-angiotensin-aldosterone system (RAAS) in salt and water conservation in vertebrates. The action of aldosterone on transepithelial sodium transport by activation of the epithelial sodium channel (ENaC) at the apical membrane and that of Na(+)-K(+)-ATPase at the basolateral membrane may have evolved in lungfish before the emergence of tetrapods. Finally, we discuss the implication of RAAS in the origin of the present pandemia of hypertension and its associated cardiovascular diseases.
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Affiliation(s)
- Bernard C Rossier
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Michael E Baker
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Romain A Studer
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
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219
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Franceschini N, Chasman DI, Cooper-DeHoff RM, Arnett DK. Genetics, ancestry, and hypertension: implications for targeted antihypertensive therapies. Curr Hypertens Rep 2015; 16:461. [PMID: 24903233 DOI: 10.1007/s11906-014-0461-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hypertension is the most common chronic condition seen by physicians in ambulatory care and a condition for which life-long medications are commonly prescribed. There is evidence for genetic factors influencing blood pressure variation in populations and response to medications. This review summarizes recent genetic discoveries that surround blood pressure, hypertension, and antihypertensive drug response from genome-wide association studies, while highlighting ancestry-specific findings and any potential implication for drug therapy targets. Genome-wide association studies have identified several novel loci for inter-individual variation of blood pressure and hypertension risk in the general population. Evidence from pharmacogenetic studies suggests that genes influence the blood pressure response to antihypertensive drugs, although results are somewhat inconsistent across studies. There is still much work that remains to be done to identify genes both for efficacy and adverse events of antihypertensive medications.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, 137 E. Franklin St., Suite 306, Chapel Hill, NC, USA,
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220
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Guey LT, Kravic J, Melander O, Burtt NP, Laramie JM, Lyssenko V, Jonsson A, Lindholm E, Tuomi T, Isomaa B, Nilsson P, Almgren P, Kathiresan S, Groop L, Seymour AB, Altshuler D, Voight BF. Power in the phenotypic extremes: a simulation study of power in discovery and replication of rare variants. Genet Epidemiol 2015; 35:236-46. [PMID: 21308769 DOI: 10.1002/gepi.20572] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 11/17/2010] [Accepted: 01/10/2011] [Indexed: 12/19/2022]
Abstract
Next-generation sequencing technologies are making it possible to study the role of rare variants in human disease. Many studies balance statistical power with cost-effectiveness by (a) sampling from phenotypic extremes and (b) utilizing a two-stage design. Two-stage designs include a broad-based discovery phase and selection of a subset of potential causal genes/variants to be further examined in independent samples. We evaluate three parameters: first, the gain in statistical power due to extreme sampling to discover causal variants; second, the informativeness of initial (Phase I) association statistics to select genes/variants for follow-up; third, the impact of extreme and random sampling in (Phase 2) replication. We present a quantitative method to select individuals from the phenotypic extremes of a binary trait, and simulate disease association studies under a variety of sample sizes and sampling schemes. First, we find that while studies sampling from extremes have excellent power to discover rare variants, they have limited power to associate them to phenotype—suggesting high false-negative rates for upcoming studies. Second, consistent with previous studies, we find that the effect sizes estimated in these studies are expected to be systematically larger compared with the overall population effect size; in a well-cited lipids study, we estimate the reported effect to be twofold larger. Third, replication studies require large samples from the general population to have sufficient power; extreme sampling could reduce the required sample size as much as fourfold. Our observations offer practical guidance for the design and interpretation of studies that utilize extreme sampling.
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Affiliation(s)
- Lin T Guey
- Applied Quantitative Genotherapeutics, Pfizer Biotherapeutics, Cambridge, MA 02144, USA
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221
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Basson JJ, de Las Fuentes L, Rao DC. Single nucleotide polymorphism-single nucleotide polymorphism interactions among inflammation genes in the genetic architecture of blood pressure in the Framingham Heart Study. Am J Hypertens 2015; 28:248-55. [PMID: 25063733 DOI: 10.1093/ajh/hpu132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Hypertension is a major global health burden, but, although systolic and diastolic blood pressure (BP) each have estimated heritability of at least 30%, <3% of their variance has been attributed to particular genetic variants. Few studies have shown interactions between pairs of single nucleotide polymorphisms (SNPs) to be associated with BP. Although many studies use a Bonferroni correction for multiple testing to control type I error, thereby potentially reducing power, false discovery rate (FDR) approaches are also used in genome-wide studies. Renal ion balance genes have been associated with BP regulation, but, although inflammation has been studied in connection with BP, few studies have reported associations between inflammation genes and BP. METHODS We analyzed SNP-SNP interactions among 31 SNPs from genes involved in renal ion balance and 30 SNPs from genes involved in inflammation using data from the Framingham Heart Study. RESULTS No evidence of association was found for interactions among renal ion balance SNPs for either systolic or diastolic BP. A group of 3 interactions involving 6 inflammation genes (IKBKB-NFKBIA, IKBKE-CHUK, and ADIPOR2-RETN) showed evidence of association with diastolic BP with an FDR of 4.2%; no single interaction reached experiment-wide significance. CONCLUSIONS This study identified promising and biologically plausible candidates for interactions between inflammation genes that may be associated with DBP. Analysis using the FDR may allow detection of signals in the presence of modest noise (false positives) that a stringent approach based on Bonferroni-corrected P value thresholds may miss.
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Affiliation(s)
- Jacob J Basson
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Lisa de Las Fuentes
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA; Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
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222
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Mistry V, Bockett NA, Levine AP, Mirza MM, Hunt KA, Ciclitira PJ, Hummerich H, Neuhausen SL, Simpson MA, Plagnol V, van Heel DA. Exome sequencing of 75 individuals from multiply affected coeliac families and large scale resequencing follow up. PLoS One 2015; 10:e0116845. [PMID: 25635822 PMCID: PMC4312029 DOI: 10.1371/journal.pone.0116845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/24/2014] [Indexed: 11/19/2022] Open
Abstract
Coeliac disease (CeD) is a highly heritable common autoimmune disease involving chronic small intestinal inflammation in response to dietary wheat. The human leukocyte antigen (HLA) region, and 40 newer regions identified by genome wide association studies (GWAS) and dense fine mapping, account for ∼40% of the disease heritability. We hypothesized that in pedigrees with multiple individuals with CeD rare [minor allele frequency (MAF) <0.5%] mutations of larger effect size (odds ratios of ∼2-5) might exist. We sequenced the exomes of 75 coeliac individuals of European ancestry from 55 multiply affected families. We selected interesting variants and genes for further follow up using a combination of: an assessment of shared variants between related subjects, a model-free linkage test, and gene burden tests for multiple, potentially causal, variants. We next performed highly multiplexed amplicon resequencing of all RefSeq exons from 24 candidate genes selected on the basis of the exome sequencing data in 2,248 unrelated coeliac cases and 2,230 controls. 1,335 variants with a 99.9% genotyping call rate were observed in 4,478 samples, of which 939 were present in coding regions of 24 genes (Ti/Tv 2.99). 91.7% of coding variants were rare (MAF <0.5%) and 60% were novel. Gene burden tests performed on rare functional variants identified no significant associations (p<1×10(-3)) in the resequenced candidate genes. Our strategy of sequencing multiply affected families with deep follow up of candidate genes has not identified any new CeD risk mutations.
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Affiliation(s)
- Vanisha Mistry
- Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
- * E-mail:
| | - Nicholas A. Bockett
- Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
| | - Adam P. Levine
- Division of Medicine, University College London, London, WC1E 6JF, United Kingdom
| | - Muddassar M. Mirza
- UCL Advanced Diagnostics, Molecular Profiling Laboratory, Sarah Cannon-UCL Laboratories, Ground Floor, Shropshire House, 1 Capper Street, London, WC1E 6JA, United Kingdom
| | - Karen A. Hunt
- Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
| | - Paul J. Ciclitira
- King’s College London, Division of Diabetes and Nutritional Sciences, Gastroenterology, The Rayne Institute, St Thomas’ Hospital, Westminster Bridge Road, London SE1 7EH, United Kingdom
| | - Holger Hummerich
- Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, United States of America
| | - Michael A. Simpson
- Division of Genetics and Molecular Medicine, Kings College London School of Medicine, 8 Floor Tower Wing, Guy’s Hospital, London SE1 9RY, United Kingdom
| | - Vincent Plagnol
- University College London Genetics Institute, Gower Street, London WC1E 6BT, United Kingdom
| | - David A. van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
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223
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Pearce D, Soundararajan R, Trimpert C, Kashlan OB, Deen PM, Kohan DE. Collecting duct principal cell transport processes and their regulation. Clin J Am Soc Nephrol 2015; 10:135-46. [PMID: 24875192 PMCID: PMC4284417 DOI: 10.2215/cjn.05760513] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The principal cell of the kidney collecting duct is one of the most highly regulated epithelial cell types in vertebrates. The effects of hormonal, autocrine, and paracrine factors to regulate principal cell transport processes are central to the maintenance of fluid and electrolyte balance in the face of wide variations in food and water intake. In marked contrast with the epithelial cells lining the proximal tubule, the collecting duct is electrically tight, and ion and osmotic gradients can be very high. The central role of principal cells in salt and water transport is reflected by their defining transporters-the epithelial Na(+) channel (ENaC), the renal outer medullary K(+) channel, and the aquaporin 2 (AQP2) water channel. The coordinated regulation of ENaC by aldosterone, and AQP2 by arginine vasopressin (AVP) in principal cells is essential for the control of plasma Na(+) and K(+) concentrations, extracellular fluid volume, and BP. In addition to these essential hormones, additional neuronal, physical, and chemical factors influence Na(+), K(+), and water homeostasis. Notably, a variety of secreted paracrine and autocrine agents such as bradykinin, ATP, endothelin, nitric oxide, and prostaglandin E2 counterbalance and limit the natriferic effects of aldosterone and the water-retaining effects of AVP. Considerable recent progress has improved our understanding of the transporters, receptors, second messengers, and signaling events that mediate principal cell responses to changing environments in health and disease. This review primarily addresses the structure and function of the key transporters and the complex interplay of regulatory factors that modulate principal cell ion and water transport.
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Affiliation(s)
- David Pearce
- Division of Nephrology, Department of Medicine, University of California, San Francisco, California
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, Texas
| | - Christiane Trimpert
- Department of Physiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ossama B. Kashlan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Peter M.T. Deen
- Department of Physiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Donald E. Kohan
- Division of Nephrology, University of Utah Health Sciences Center, Salt Lake City, Utah
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224
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Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe JS, Cox NJ, Cook EH, Li C, Chen W, Li B. A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. ACTA ACUST UNITED AC 2015; 31:1452-9. [PMID: 25568282 DOI: 10.1093/bioinformatics/btu860] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/23/2014] [Indexed: 12/30/2022]
Abstract
MOTIVATION A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models. RESULTS In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants. AVAILABILITY AND IMPLEMENTATION We implemented gTDT in C++ and the source code and the detailed usage are available on the authors' website (https://medschool.vanderbilt.edu/cgg). CONTACT bingshan.li@vanderbilt.edu or wei.chen@chp.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaowei Zhan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xue Zhong
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James S Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nancy J Cox
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Edwin H Cook
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chun Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
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Glahn DC, Williams JT, McKay DR, Knowles EE, Sprooten E, Mathias SR, Curran JE, Kent JW, Carless MA, Göring HHH, Dyer TD, Woolsey MD, Winkler AM, Olvera RL, Kochunov P, Fox PT, Duggirala R, Almasy L, Blangero J. Discovering schizophrenia endophenotypes in randomly ascertained pedigrees. Biol Psychiatry 2015; 77:75-83. [PMID: 25168609 PMCID: PMC4261014 DOI: 10.1016/j.biopsych.2014.06.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/08/2014] [Accepted: 06/15/2014] [Indexed: 01/21/2023]
Abstract
BACKGROUND Although case-control approaches are beginning to disentangle schizophrenia's complex polygenic burden, other methods will likely be necessary to fully identify and characterize risk genes. Endophenotypes, traits genetically correlated with an illness, can help characterize the impact of risk genes by providing genetically relevant traits that are more tractable than the behavioral symptoms that classify mental illness. Here, we present an analytic approach for discovering and empirically validating endophenotypes in extended pedigrees with very few affected individuals. Our approach indexes each family member's risk as a function of shared genetic kinship with an affected individual, often referred to as the coefficient of relatedness. To demonstrate the utility of this approach, we search for neurocognitive and neuroanatomic endophenotypes for schizophrenia in large unselected multigenerational pedigrees. METHODS A fixed-effects test within the variance component framework was performed on neurocognitive and cortical surface area traits in 1606 Mexican-American individuals from large, randomly ascertained extended pedigrees who participated in the Genetics of Brain Structure and Function study. As affecteds were excluded from analyses, results were not influenced by disease state or medication usage. RESULTS Despite having sampled just 6 individuals with schizophrenia, our sample provided 233 individuals at various levels of genetic risk for the disorder. We identified three neurocognitive measures (digit-symbol substitution, facial memory, and emotion recognition) and six medial temporal and prefrontal cortical surfaces associated with liability for schizophrenia. CONCLUSIONS With our novel analytic approach, one can discover and rank endophenotypes for schizophrenia, or any heritable disease, in randomly ascertained pedigrees.
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Affiliation(s)
- David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut.
| | - Jeff T Williams
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - D Reese McKay
- Department of Psychiatry, Yale University School of Medicine, New Haven; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
| | - Emma E Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
| | - Emma Sprooten
- Department of Psychiatry, Yale University School of Medicine, New Haven; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
| | - Samuel R Mathias
- Department of Psychiatry, Yale University School of Medicine, New Haven; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, Hartford, Connecticut
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Melanie A Carless
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Thomas D Dyer
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Mary D Woolsey
- Research Imaging Institute, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | - Anderson M Winkler
- Centre for Functional MRI of the Brain, University of Oxford, Oxford, United Kingdom
| | - Rene L Olvera
- Department of Psychiatry, University of Texas Health Science Center San Antonio, San Antonio, Texas
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland
| | - Peter T Fox
- Research Imaging Institute, University of Texas Health Science Center San Antonio, San Antonio, Texas; State Key Laboratory for Brain and Cognitive Sciences, University of Hong Kong
| | - Ravi Duggirala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
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226
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Brunetti A, Brunetti FS, Chiefari E. Pharmacogenetics of type 2 diabetes mellitus: An example of success in clinical and translational medicine. World J Transl Med 2014; 3:141-149. [DOI: 10.5528/wjtm.v3.i3.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/25/2014] [Accepted: 11/03/2014] [Indexed: 02/05/2023] Open
Abstract
The pharmacological interventions currently available to control type 2 diabetes mellitus (T2DM) show a wide interindividual variability in drug response, emphasizing the importance of a personalized, more effective medical treatment for each individual patient. In this context, a growing interest has emerged in recent years and has focused on pharmacogenetics, a discipline aimed at understanding the variability in patients’ drug response, making it possible to predict which drug is best for each patient and at what doses. Recent pharmacological and clinical evidences indicate that genetic polymorphisms (or genetic variations) of certain genes can adversely affect drug response and therapeutic efficacy of oral hypoglycemic agents in patients with T2DM, through pharmacokinetic- and/or pharmacodynamic-based mechanisms that may reduce the therapeutic effects or increase toxicity. For example, genetic variants in genes encoding enzymes of the cytochrome P-450 superfamily, or proteins of the ATP-sensitive potassium channel on the beta-cell of the pancreas, are responsible for the interindividual variability of drug response to sulfonylureas in patients with T2DM. Instead, genetic variants in the genes that encode for the organic cation transporters of metformin have been related to changes in both pharmacodynamic and pharmacokinetic responses to metformin in metformin-treated patients. Thus, based on the individual’s genotype, the possibility, in these subjects, of a personalized therapy constitutes the main goal of pharmacogenetics, directly leading to the development of the right medicine for the right patient. Undoubtedly, this represents an integral part of the translational medicine network.
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Spataro N, Calafell F, Cervera-Carles L, Casals F, Pagonabarraga J, Pascual-Sedano B, Campolongo A, Kulisevsky J, Lleó A, Navarro A, Clarimón J, Bosch E. Mendelian genes for Parkinson's disease contribute to the sporadic forms of the disease†. Hum Mol Genet 2014; 24:2023-34. [PMID: 25504046 DOI: 10.1093/hmg/ddu616] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laura Cervera-Carles
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Ferran Casals
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Javier Pagonabarraga
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Berta Pascual-Sedano
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Antònia Campolongo
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jaime Kulisevsky
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain, Health Sciences Department, Universitat Oberta de Catalunya, Catalonia, Spain
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain, National Institute for Bioinformatics (INB), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain and Center for Genomic Regulation (CRG), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Jordi Clarimón
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain, Center for Networking Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain,
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228
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Luft FC. Clinical salt deficits. Pflugers Arch 2014; 467:559-63. [PMID: 25471347 DOI: 10.1007/s00424-014-1643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 11/25/2022]
Abstract
Salt retention or salt deficit has a bearing on the body fluid volume. Both states are clinically difficult to recognize and quantitate. Salt deficit is particularly cumbersome in that regard since orthostatic blood pressure, heart rate changes, and simple physical inspection are inaccurate and unreliable. Salt deficit can be acute such as after hemorrhage or massive diarrhea, or more chronic as observed in Addison's disease, failure of renal sodium chloride transporters, drug-related effects, or distal nephron disease. Molecular genetics has given us important new insights into salt deficit syndromes. Recent recognition of a novel sodium storage compartment involving sodium binding to proteoglycans adds to the overall complexity of these syndromes.
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Affiliation(s)
- Friedrich C Luft
- Experimental and Clinical Research Center, a joint cooperation between the Max-Delbrück Center for Molecular Medicine and the Charité Medical Faculty, Lindenbergerweg 80, 13125, Berlin, Germany,
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229
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Corbetta S, Raimondo F, Tedeschi S, Syrèn ML, Rebora P, Savoia A, Baldi L, Bettinelli A, Pitto M. Urinary exosomes in the diagnosis of Gitelman and Bartter syndromes. Nephrol Dial Transplant 2014; 30:621-30. [DOI: 10.1093/ndt/gfu362] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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230
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Franceschini N, Tao R, Liu L, Rutherford S, Haack K, Almasy L, Göring HH, Laston S, Lee ET, Best LG, Fabsitz R, Cole SA, North KE. Mapping of a blood pressure QTL on chromosome 17 in American Indians of the strong heart family study. BMC Cardiovasc Disord 2014; 14:158. [PMID: 25387527 PMCID: PMC4246441 DOI: 10.1186/1471-2261-14-158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/18/2014] [Indexed: 01/11/2023] Open
Abstract
Background Blood pressure (BP) is a complex trait, with a heritability of 30 to 40%. Several genome wide associated BP loci explain only a small fraction of the phenotypic variation. Family studies can provide an important tool for gene discovery by utilizing trait and genetic transmission information among relative-pairs. We have previously described a quantitative trait locus at chromosome 17q25.3 influencing systolic BP in American Indians of the Strong Heart Family Study (SHFS). This locus has been reported to associate with variation in BP traits in family studies of Europeans, African Americans and Hispanics. Methods To follow-up persuasive linkage findings at this locus, we performed comprehensive genotyping in the 1-LOD unit support interval region surrounding this QTL using a multi-step strategy. We first genotyped 1,334 single nucleotide polymorphisms (SNPs) in 928 individuals from families that showed evidence of linkage for BP. We then genotyped a second panel of 306 SNPs in all SHFS participants (N = 3,807) for genes that displayed the strongest evidence of association in the region, and, in a third step, included additional genotyping to better cover the genes of interest and to interrogate plausible candidate genes in the region. Results Three genes had multiple SNPs marginally associated with systolic BP (TBC1D16, HRNBP3 and AZI1). In BQTN analysis, used to estimate the posterior probability that any variant in each gene had an effect on the phenotype, AZI1 showed the most prominent findings (posterior probability of 0.66). Importantly, upon correction for multiple testing, none of our study findings could be distinguished from chance. Conclusion Our findings demonstrate the difficulty of follow-up studies of linkage studies for complex traits, particularly in the context of low powered studies and rare variants underlying linkage peaks. Electronic supplementary material The online version of this article (doi:10.1186/1471-2261-14-158) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
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Johnson RJ, Lanaspa MA, Gabriela Sánchez-Lozada L, Rodriguez-Iturbe B. The discovery of hypertension: evolving views on the role of the kidneys, and current hot topics. Am J Physiol Renal Physiol 2014; 308:F167-78. [PMID: 25377913 DOI: 10.1152/ajprenal.00503.2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Primary hypertension is increasingly common and is associated with significant morbidity. Here, we review the history of its discovery and rise during the last century with an emphasis on studies trying to identify its cause. Early studies identified a defect in sodium excretion by the kidney as being central to the pathogenesis. Recent studies have focused on a variety of genetic, congenital (fetal programming), and acquired mechanisms for causing the defect in natriuresis. Certain risk factors are apparent, including genetic polymorphisms that regulate sodium excretion, a congenital reduction in nephron number, obesity and hyperleptinemia, an elevated sympathetic nervous system, diet (salt and fructose), and metabolic (hyperuricemia) mechanisms. The kidney shows evidence for renal arteriolar vasoconstriction, an intrarenal inflammatory response, local oxidative stress, and intrarenal activation of the renin-angiotensin system. Recent studies suggest that intrarenal T cells have an important role in causing hypertension to be persistent, likely due to the induction of a local autoimmune response to neoantigens such as heat shock protein 70 and protein aggregates formed by isoketals resulting from lipid peroxidation. Salt retention due to impairment in pressure-diuresis leads to the release of cardiotonic steroids and central nervous system effects that cause systemic vasoconstriction and a rise in blood pressure. Some recent studies suggest that salt may increase blood pressure not simply by effects on extracellular volume but rather as a consequence of hyperosmolarity. These new insights could lead to new approaches for the prevention and treatment of this important disease.
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Affiliation(s)
- Richard J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, Colorado;
| | - Miguel A Lanaspa
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, Colorado
| | - L Gabriela Sánchez-Lozada
- Laboratory of Renal Physiopathology, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico; and
| | - Bernardo Rodriguez-Iturbe
- Hospital Universitario y Universidad del Zulia; and Instituto Venezolano de Investigaciones Científicas (IVIC)-Zulia, Maracaibo, Venezuela
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232
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Lee SH, Kang MI, Ahn SH, Lim KH, Lee GE, Shin ES, Lee JE, Kim BJ, Cho EH, Kim SW, Kim TH, Kim HJ, Yoon KH, Lee WC, Kim GS, Koh JM, Kim SY. Common and rare variants in the exons and regulatory regions of osteoporosis-related genes improve osteoporotic fracture risk prediction. J Clin Endocrinol Metab 2014; 99:E2400-11. [PMID: 25119311 DOI: 10.1210/jc.2014-1584] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
CONTEXT Osteoporotic fracture risk is highly heritable, but genome-wide association studies have explained only a small proportion of the heritability to date. Genetic data may improve prediction of fracture risk in osteopenic subjects and assist early intervention and management. OBJECTIVE To detect common and rare variants in coding and regulatory regions related to osteoporosis-related traits, and to investigate whether genetic profiling improves the prediction of fracture risk. DESIGN AND SETTING This cross-sectional study was conducted in three clinical units in Korea. PARTICIPANTS Postmenopausal women with extreme phenotypes (n = 982) were used for the discovery set, and 3895 participants were used for the replication set. MAIN OUTCOME MEASURE We performed targeted resequencing of 198 genes. Genetic risk scores from common variants (GRS-C) and from common and rare variants (GRS-T) were calculated. RESULTS Nineteen common variants in 17 genes (of the discovered 34 functional variants in 26 genes) and 31 rare variants in five genes (of the discovered 87 functional variants in 15 genes) were associated with one or more osteoporosis-related traits. Accuracy of fracture risk classification was improved in the osteopenic patients by adding GRS-C to fracture risk assessment models (6.8%; P < .001) and was further improved by adding GRS-T (9.6%; P < .001). GRS-C improved classification accuracy for vertebral and nonvertebral fractures by 7.3% (P = .005) and 3.0% (P = .091), and GRS-T further improved accuracy by 10.2% (P < .001) and 4.9% (P = .008), respectively. CONCLUSIONS Our results suggest that both common and rare functional variants may contribute to osteoporotic fracture and that adding genetic profiling data to current models could improve the prediction of fracture risk in an osteopenic individual.
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Affiliation(s)
- Seung Hun Lee
- Division of Endocrinology and Metabolism (S.H.L., S.H.A., K.-H.L., B.-J.K., G.S.K., J.-M.K.), Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea; Department of Endocrinology and Metabolism (M.I.K., K.-H.Y.), The Catholic University of Korea, College of Medicine, Seoul 137-701, Korea; DNA Link (G.E.L., E.-S.S., J.-E.L.), Seoul 138-736, Korea; Department of Internal Medicine (E.-H.C., S.-W.K.), Kangwon National University College of Medicine, Chuncheon 200-722, Korea; Skeletal Diseases Genome Research Center and Department of Orthopedic Surgery (T.-H.K., H.-J.K., S.-Y.K.), Kyungpook National University School of Medicine, Daegu 702-701, Korea; and Department of Preventive Medicine (W.C.L.), The Catholic University of Korea, College of Medicine, Seoul 137-701, Korea
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Castrop H, Schießl IM. Physiology and pathophysiology of the renal Na-K-2Cl cotransporter (NKCC2). Am J Physiol Renal Physiol 2014; 307:F991-F1002. [PMID: 25186299 DOI: 10.1152/ajprenal.00432.2014] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Na-K-2Cl cotransporter (NKCC2; BSC1) is located in the apical membrane of the epithelial cells of the thick ascending limb of the loop of Henle (TAL). NKCC2 facilitates ∼20–25% of the reuptake of the total filtered NaCl load. NKCC2 is therefore one of the transport proteins with the highest overall reabsorptive capacity in the kidney. Consequently, even subtle changes in NKCC2 transport activity considerably alter the renal reabsorptive capacity for NaCl and eventually lead to perturbations of the salt and water homoeostasis. In addition to facilitating the bulk reabsorption of NaCl in the TAL, NKCC2 transport activity in the macula densa cells of the TAL constitutes the initial step of the tubular-vascular communication within the juxtaglomerular apparatus (JGA); this communications allows the TAL to modulate the preglomerular resistance of the afferent arteriole and the renin secretion from the granular cells of the JGA. This review provides an overview of our current knowledge with respect to the general functions of NKCC2, the modulation of its transport activity by different regulatory mechanisms, and new developments in the pathophysiology of NKCC2-dependent renal NaCl transport.
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Affiliation(s)
- Hayo Castrop
- Institute of Physiology, University of Regensburg, Regensburg, Germany
| | - Ina Maria Schießl
- Institute of Physiology, University of Regensburg, Regensburg, Germany
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234
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Satten GA, Biswas S, Papachristou C, Turkmen A, König IR. Population-based association and gene by environment interactions in Genetic Analysis Workshop 18. Genet Epidemiol 2014; 38 Suppl 1:S49-56. [PMID: 25112188 DOI: 10.1002/gepi.21825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the past decade, genome-wide association studies have been successful in identifying genetic loci that play a role in many complex diseases. Despite this, it has become clear that for many traits, investigation of single common variants does not give a complete picture of the genetic contribution to the phenotype. Therefore a number of new approaches are currently being investigated to further the search for susceptibility loci or regions. We summarize the contributions to Genetic Analysis Workshop 18 (GAW18) that concern this search using methods for population-based association analysis. Many of the members of our GAW18 working group made use of data types that have only recently become available through the use of next-generation sequencing technologies, with many focusing on the investigation of rare variants instead of or in combination with common variants. Some contributors used a haplotype-based approach, which to date has been used relatively infrequently but may become more important for analyzing rare variant association data. Others analyzed gene-gene or gene-environment interactions, where novel statistical approaches were needed to make the best use of the available information without requiring an excessive computational burden. GAW18 provided participants with the chance to make use of state-of-the-art data, statistical techniques, and technology. We report here some of the experiences and conclusions that were reached by workshop participants who analyzed the GAW18 data as a population-based association study.
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Affiliation(s)
- Glen A Satten
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Wei C, Li M, He Z, Vsevolozhskaya O, Schaid DJ, Lu Q. A weighted U-statistic for genetic association analyses of sequencing data. Genet Epidemiol 2014; 38:699-708. [PMID: 25331574 DOI: 10.1002/gepi.21864] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 12/13/2022]
Abstract
With advancements in next-generation sequencing technology, a massive amount of sequencing data is generated, which offers a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex diseases. Nevertheless, the high-dimensional sequencing data poses a great challenge for statistical analysis. The association analyses based on traditional statistical methods suffer substantial power loss because of the low frequency of genetic variants and the extremely high dimensionality of the data. We developed a Weighted U Sequencing test, referred to as WU-SEQ, for the high-dimensional association analysis of sequencing data. Based on a nonparametric U-statistic, WU-SEQ makes no assumption of the underlying disease model and phenotype distribution, and can be applied to a variety of phenotypes. Through simulation studies and an empirical study, we showed that WU-SEQ outperformed a commonly used sequence kernel association test (SKAT) method when the underlying assumptions were violated (e.g., the phenotype followed a heavy-tailed distribution). Even when the assumptions were satisfied, WU-SEQ still attained comparable performance to SKAT. Finally, we applied WU-SEQ to sequencing data from the Dallas Heart Study (DHS), and detected an association between ANGPTL 4 and very low density lipoprotein cholesterol.
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Affiliation(s)
- Changshuai Wei
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, United States of America; Department of Biostatistics and Epidemiology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
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A genetic risk score for hypertension associates with the risk of ischemic stroke in a Swedish case-control study. Eur J Hum Genet 2014; 23:969-74. [PMID: 25293721 DOI: 10.1038/ejhg.2014.212] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/21/2014] [Accepted: 09/05/2014] [Indexed: 12/31/2022] Open
Abstract
Genetic risk scores (GRS), summing up the total effect of several single-nucleotide polymorphisms (SNPs) in genes associated with either coronary risk or cardiovascular risk factors, have been tested for association with ischemic stroke with conflicting results. Recently an association was found between a GRS based on 29 SNPs discovered by genome-wide association studies and hypertension. The aim of our study was to investigate the possible association of the same GRS with ischemic stroke on top of other 'traditional risk factors', also testing its potential improvement in indices of discrimination and reclassification, in a Swedish case-control study. Twenty-nine SNPs were genotyped in 3677 stroke cases and 2415 controls included in the Lund Stroke Register (LSR), the Malmö Diet and Cancer (MDC) study and the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS). The analysis was conducted in the combined sample, and separately for the three studies. After adjustment for hypertension, diabetes mellitus and smoking habits, the GRS was associated with ischemic stroke in the combined sample (OR (95% CI) 1.086 (1.029-1.147) per SD increase in the GRS P=0.003) with similar trends in all three samples: LSR (1.050 (0.967-1.140); P=0.25), MDC (1.168 (1.060-1.288); P=0.002) and SAHLSIS (1.124 (0.997-1.267); P=0.055). Measures of risk discrimination and reclassification improved marginally using the GRS. A blood pressure GRS is independently associated with ischemic stroke risk in three Swedish case-control studies, however, the effect size is low and adds marginally to prediction of stroke on top of traditional risk factors including hypertension.
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Xing C, Dupuis J, Cupples LA. Performance of statistical methods on CHARGE targeted sequencing data. BMC Genet 2014; 15:104. [PMID: 25277365 PMCID: PMC4197341 DOI: 10.1186/s12863-014-0104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background The CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Sequencing Project is a national, collaborative effort from 3 studies: Framingham Heart Study (FHS), Cardiovascular Health Study (CHS), and Atherosclerosis Risk in Communities (ARIC). It uses a case-cohort design, whereby a random sample of study participants is enriched with participants in extremes of traits. Although statistical methods are available to investigate the role of rare variants, few have evaluated their performance in a case-cohort design. Results We evaluate several methods, including the sequence kernel association test (SKAT), Score-Seq, and weighted (Madsen and Browning) and unweighted burden tests. Using genotypes from the CHARGE targeted-sequencing project for FHS (n = 1096), we simulate phenotypes in a large population for 11 correlated traits and then sample individuals to mimic the CHARGE Sequencing study design. We evaluate type I error and power for 77 targeted regions. Conclusions We provide some guidelines on the performance of these aggregate-based tests to detect associations with rare variants when applied to case-cohort study designs, using CHARGE targeted sequencing data. Type I error is conservative when we consider variants with minor allele frequency (MAF) < 1%. Power is generally low, although it is relatively larger for Score-Seq. Greater numbers of causal variants and a greater proportion of variance improve the power, but it tends to be lower in the presence of bi-directionality of effects of causal genotypes, especially for Score-Seq. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0104-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuanhua Xing
- Department of Biostatistics, Boston University, Boston, MA, USA.
| | - Josée Dupuis
- Department of Biostatistics, Boston University, Boston, MA, USA. .,Framingham Heart Study, Framingham, MA, USA.
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University, Boston, MA, USA. .,Framingham Heart Study, Framingham, MA, USA.
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Yeo NC, O'Meara CC, Bonomo JA, Veth KN, Tomar R, Flister MJ, Drummond IA, Bowden DW, Freedman BI, Lazar J, Link BA, Jacob HJ. Shroom3 contributes to the maintenance of the glomerular filtration barrier integrity. Genome Res 2014; 25:57-65. [PMID: 25273069 PMCID: PMC4317173 DOI: 10.1101/gr.182881.114] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWAS) identify regions of the genome correlated with disease risk but are restricted in their ability to identify the underlying causative mechanism(s). Thus, GWAS are useful "roadmaps" that require functional analysis to establish the genetic and mechanistic structure of a particular locus. Unfortunately, direct functional testing in humans is limited, demonstrating the need for complementary approaches. Here we used an integrated approach combining zebrafish, rat, and human data to interrogate the function of an established GWAS locus (SHROOM3) lacking prior functional support for chronic kidney disease (CKD). Congenic mapping and sequence analysis in rats suggested Shroom3 was a strong positional candidate gene. Transferring a 6.1-Mb region containing the wild-type Shroom3 gene significantly improved the kidney glomerular function in FHH (fawn-hooded hypertensive) rat. The wild-type Shroom3 allele, but not the FHH Shroom3 allele, rescued glomerular defects induced by knockdown of endogenous shroom3 in zebrafish, suggesting that the FHH Shroom3 allele is defective and likely contributes to renal injury in the FHH rat. We also show for the first time that variants disrupting the actin-binding domain of SHROOM3 may cause podocyte effacement and impairment of the glomerular filtration barrier.
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Affiliation(s)
- Nan Cher Yeo
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Caitlin C O'Meara
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Jason A Bonomo
- Department of Molecular Medicine and Translational Science, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Kerry N Veth
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Ritu Tomar
- Nephrology Division, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Michael J Flister
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Iain A Drummond
- Nephrology Division, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Barry I Freedman
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA; Department of Internal Medicine - Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Jozef Lazar
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Howard J Jacob
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Abstract
A major impetus to initiating the Human Genome Project was the belief that information encoded in the human genome would "accelerate progress in understanding disease pathogenesis and in developing new approaches to diagnosis, treatment, and prevention in many areas of medicine". Alopecia areata (AA) is a notable example of how understanding the genetic basis of a disease can have an impact on the care of patients in a relatively short time. Our first genome-wide association study in AA identified an initial set of common variants that increase risk of AA, some of which are shared with other autoimmune diseases. Thus, there has already been rapid progress in the translation of this information into new therapeutic strategies for patients, as drugs are already on the market for some of these disorders that can now be tested in AA. Informed by the progress achieved with genetic studies for mechanistically aligned autoimmune diseases, we are poised to carry this work forward and interrogate the underlying disease mechanisms in AA. Importantly, future genetic studies aimed at identifying additional susceptibility genes will further establish the foundation for the application of precision medicine in the care of AA patients.
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McCarthy NS, Vangjeli C, Cavalleri GL, Delanty N, Shianna KV, Surendran P, O'Brien E, Munroe PB, Masca N, Tomaszewski M, Samani NJ, Stanton AV. Two further blood pressure loci identified in ion channel genes with a gene-centric approach. ACTA ACUST UNITED AC 2014; 7:873-9. [PMID: 25210050 DOI: 10.1161/circgenetics.113.000190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Blood pressure (BP) is highly heritable, but our understanding of the genetic causes underlying variations in BP is incomplete. In this study, we explored whether novel loci associated with BP could be identified using a genecentric approach in 3 community-based cohorts with accurate BP measurements. METHODS AND RESULTS Genotyping of 1857 single nucleotide polymorphisms (SNPs) in 91 ion channel genes was performed in a discovery cohort (n=358). Thirty-four SNPs associated with BP traits (P≤0.01) were followed up in an independent population (n=387); significant SNPs from this analysis were looked up in another independent population (n=1010) and meta-analyzed. Repeated clinic and ambulatory measurements were available for all but the discovery cohort (clinic only). Association analyses were performed, with systolic, diastolic, and pulse pressures as quantitative traits, adjusting for age and sex. Quantile-quantile plots indicated that the genecentric approach resulted in an inflation of association signals. Of the 29 SNPs taken forward from the discovery cohort, 2 SNPs were associated with BP phenotypes with the same direction of effect, with experiment-wide significance, in follow-up cohort I. These were rs2228291, in the chloride channel gene CLCN2, and rs10513488, in the potassium channel gene KCNAB1. Both associations were subsequently replicated in follow-up cohort II. CONCLUSIONS Using a genecentric design and 3 well-phenotyped populations, this study identified 2 previously unreported, biologically plausible, genetic associations with BP. These results suggest that dense genotyping of genes, in pathways known to influence BP, could add to candidate-gene and Genome Wide Association studies in further explaining BP heritability.
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Affiliation(s)
- Nina S McCarthy
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Ciara Vangjeli
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Gianpiero L Cavalleri
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Norman Delanty
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Kevin V Shianna
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Praveen Surendran
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Eoin O'Brien
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Patricia B Munroe
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Nicholas Masca
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Maciej Tomaszewski
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Nilesh J Samani
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.)
| | - Alice V Stanton
- From the Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland (N.S.M., C.V., G.L.C., N.D., P.S., A.V.S.); Centre for Genetic Origins of Health and Disease, University of Western Australia, Perth, Australia (N.S.M.); Blood Pressure Unit and Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland (N.D., A.V.S.); Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, NC (K.V.S.); Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland (P.S., E.O.B.); Centre for Clinical Pharmacology, William Harvey Research Institute, Barts and the London Medical School, and Barts NIHR Biomedical Research Unit, London (P.B.M.); and Department of Cardiovascular Sciences, University of Leicester, and Leicester National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom (N.M., M.T., N.J.S.).
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Zhang Q, Wang L, Koboldt D, Boreki IB, Province MA. Adjusting family relatedness in data-driven burden test of rare variants. Genet Epidemiol 2014; 38:722-7. [PMID: 25169066 DOI: 10.1002/gepi.21848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 07/01/2014] [Accepted: 07/16/2014] [Indexed: 11/08/2022]
Abstract
Family data represent a rich resource for detecting association between rare variants (RVs) and human traits. However, most RV association analysis methods developed in recent years are data-driven burden tests which can adaptively learn weights from data but require permutation to evaluate significance, thus are not readily applicable to family data, because random permutation will destroy family structure. Direct application of these methods to family data may result in a significant inflation of false positives. To overcome this issue, we have developed a generalized, weighted sum mixed model (WSMM), and corresponding computational techniques that can incorporate family information into data-driven burden tests, and allow adaptive and efficient permutation test in family data. Using simulated and real datasets, we demonstrate that the WSMM method can be used to appropriately adjust for genetic relatedness among family members and has a good control for the inflation of false positives. We compare WSMM with a nondata-driven, family-based Sequence Kernel Association Test (famSKAT), showing that WSMM has significantly higher power in some cases. WSMM provides a generalized, flexible framework for adapting different data-driven burden tests to analyze data with any family structures, and it can be extended to binary and time-to-onset traits, with or without covariates.
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Affiliation(s)
- Qunyuan Zhang
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Luft FC. Preparation for hypertension specialists: genomics reveals the pathogenesis of hypertension. ACTA ACUST UNITED AC 2014; 8:607-11. [PMID: 25151324 DOI: 10.1016/j.jash.2014.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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243
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Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes. Proc Natl Acad Sci U S A 2014; 111:13127-32. [PMID: 25157153 DOI: 10.1073/pnas.1410428111] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARG) is a master transcriptional regulator of adipocyte differentiation and a canonical target of antidiabetic thiazolidinedione medications. In rare families, loss-of-function (LOF) mutations in PPARG are known to cosegregate with lipodystrophy and insulin resistance; in the general population, the common P12A variant is associated with a decreased risk of type 2 diabetes (T2D). Whether and how rare variants in PPARG and defects in adipocyte differentiation influence risk of T2D in the general population remains undetermined. By sequencing PPARG in 19,752 T2D cases and controls drawn from multiple studies and ethnic groups, we identified 49 previously unidentified, nonsynonymous PPARG variants (MAF < 0.5%). Considered in aggregate (with or without computational prediction of functional consequence), these rare variants showed no association with T2D (OR = 1.35; P = 0.17). The function of the 49 variants was experimentally tested in a novel high-throughput human adipocyte differentiation assay, and nine were found to have reduced activity in the assay. Carrying any of these nine LOF variants was associated with a substantial increase in risk of T2D (OR = 7.22; P = 0.005). The combination of large-scale DNA sequencing and functional testing in the laboratory reveals that approximately 1 in 1,000 individuals carries a variant in PPARG that reduces function in a human adipocyte differentiation assay and is associated with a substantial risk of T2D.
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244
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Abstract
Hypertension has become a major global health burden due to its high prevalence and associated increase in risk of cardiovascular disease and premature death. It is well established that hypertension is determined by both genetic and environmental factors and their complex interactions. Recent large-scale meta-analyses of genome-wide association studies (GWAS) have successfully identified a total of 38 loci which achieved genome-wide significance (P < 5 × 10(-8)) for their association with blood pressure (BP). Although the heritability of BP explained by these loci is very limited, GWAS meta-analyses have elicited renewed optimism in hypertension genomics research, highlighting novel pathways influencing BP and elucidating genetic mechanisms underlying BP regulation. This review summarizes evolving progress in the rapidly moving field of hypertension genetics and highlights several promising approaches for dissecting the remaining heritability of BP. It also discusses the future translation of genetic findings to hypertension treatment and prevention.
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245
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Kemter E, Rathkolb B, Becker L, Bolle I, Busch DH, Dalke C, Elvert R, Favor J, Graw J, Hans W, Ivandic B, Kalaydjiev S, Klopstock T, Rácz I, Rozman J, Schrewe A, Schulz H, Zimmer A, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Wolf E, Aigner B. Standardized, systemic phenotypic analysis of Slc12a1I299F mutant mice. J Biomed Sci 2014; 21:68. [PMID: 25084970 PMCID: PMC4237776 DOI: 10.1186/s12929-014-0068-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/17/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Type I Bartter syndrome is a recessive human nephropathy caused by loss-of-function mutations in the SLC12A1 gene coding for the Na+-K+-2Cl- cotransporter NKCC2. We recently established the mutant mouse line Slc12a1I299F exhibiting kidney defects highly similar to the late-onset manifestation of this hereditary human disease. Besides the kidney defects, low blood pressure and osteopenia were revealed in the homozygous mutant mice which were also described in humans. Beside its strong expression in the kidney, NKCC2 has been also shown to be expressed in other tissues in rodents i.e. the gastrointestinal tract, pancreatic beta cells, and specific compartments of the ear, nasal tissue and eye. RESULTS To examine if, besides kidney defects, further organ systems and/or metabolic pathways are affected by the Slc12a1I299F mutation as primary or secondary effects, we describe a standardized, systemic phenotypic analysis of the mutant mouse line Slc12a1I299F in the German Mouse Clinic. Slc12a1I299F homozygous mutant mice and Slc12a1I299F heterozygous mutant littermates as controls were tested at the age of 4-6 months. Beside the already published changes in blood pressure and bone metabolism, a significantly lower body weight and fat content were found as new phenotypes for Slc12a1I299F homozygous mutant mice. Small additional effects included a mild erythropenic anemia in homozygous mutant males as well as a slight hyperalgesia in homozygous mutant females. For other functions, such as immunology, lung function and neurology, no distinct alterations were observed. CONCLUSIONS In this systemic analysis no clear primary effects of the Slc12a1I299F mutation appeared for the organs other than the kidneys where Slc12a1 expression has been described. On the other hand, long-term effects additional and/or secondary to the kidney lesions might also appear in humans harboring SLC12A1 mutations.
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Eladari D, Chambrey R, Picard N, Hadchouel J. Electroneutral absorption of NaCl by the aldosterone-sensitive distal nephron: implication for normal electrolytes homeostasis and blood pressure regulation. Cell Mol Life Sci 2014; 71:2879-95. [PMID: 24556999 PMCID: PMC11113337 DOI: 10.1007/s00018-014-1585-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/28/2014] [Accepted: 02/05/2014] [Indexed: 01/10/2023]
Abstract
Sodium absorption by the distal part of the nephron, i.e., the distal convoluted tubule, the connecting tubule, and the collecting duct, plays a major role in the control of homeostasis by the kidney. In this part of the nephron, sodium transport can either be electroneutral or electrogenic. The study of electrogenic Na(+) absorption, which is mediated by the epithelial sodium channel (ENaC), has been the focus of considerable interest because of its implication in sodium, potassium, and acid-base homeostasis. However, recent studies have highlighted the crucial role played by electroneutral NaCl absorption in the regulation of the body content of sodium chloride, which in turn controls extracellular fluid volume and blood pressure. Here, we review the identification and characterization of the NaCl cotransporter (NCC), the molecule accounting for the main part of electroneutral NaCl absorption in the distal nephron, and its regulators. We also discuss recent work describing the identification of a novel "NCC-like" transport system mediated by pendrin and the sodium-driven chloride/bicarbonate exchanger (NDCBE) in the β-intercalated cells of the collecting system.
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Affiliation(s)
- Dominique Eladari
- Department of Physiology, Hopital Européen Georges Pompidou, AP-HP, 56 rue Leblanc, 75015, Paris, France,
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Alessi DR, Zhang J, Khanna A, Hochdörfer T, Shang Y, Kahle KT. The WNK-SPAK/OSR1 pathway: master regulator of cation-chloride cotransporters. Sci Signal 2014; 7:re3. [PMID: 25028718 DOI: 10.1126/scisignal.2005365] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The WNK-SPAK/OSR1 kinase complex is composed of the kinases WNK (with no lysine) and SPAK (SPS1-related proline/alanine-rich kinase) or the SPAK homolog OSR1 (oxidative stress-responsive kinase 1). The WNK family senses changes in intracellular Cl(-) concentration, extracellular osmolarity, and cell volume and transduces this information to sodium (Na(+)), potassium (K(+)), and chloride (Cl(-)) cotransporters [collectively referred to as CCCs (cation-chloride cotransporters)] and ion channels to maintain cellular and organismal homeostasis and affect cellular morphology and behavior. Several genes encoding proteins in this pathway are mutated in human disease, and the cotransporters are targets of commonly used drugs. WNKs stimulate the kinases SPAK and OSR1, which directly phosphorylate and stimulate Cl(-)-importing, Na(+)-driven CCCs or inhibit the Cl(-)-extruding, K(+)-driven CCCs. These coordinated and reciprocal actions on the CCCs are triggered by an interaction between RFXV/I motifs within the WNKs and CCCs and a conserved carboxyl-terminal docking domain in SPAK and OSR1. This interaction site represents a potentially druggable node that could be more effective than targeting the cotransporters directly. In the kidney, WNK-SPAK/OSR1 inhibition decreases epithelial NaCl reabsorption and K(+) secretion to lower blood pressure while maintaining serum K(+). In neurons, WNK-SPAK/OSR1 inhibition could facilitate Cl(-) extrusion and promote γ-aminobutyric acidergic (GABAergic) inhibition. Such drugs could have efficacy as K(+)-sparing blood pressure-lowering agents in essential hypertension, nonaddictive analgesics in neuropathic pain, and promoters of GABAergic inhibition in diseases associated with neuronal hyperactivity, such as epilepsy, spasticity, neuropathic pain, schizophrenia, and autism.
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Affiliation(s)
- Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Jinwei Zhang
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Arjun Khanna
- Department of Neurosurgery, Massachusetts General Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Hochdörfer
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Yuze Shang
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, and Harvard Medical School, Boston, MA 02115, USA. Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA.
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248
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Edwards JS, Atlas SR, Wilson SM, Cooper CF, Luo L, Stidley CA. Integrated statistical and pathway approach to next-generation sequencing analysis: a family-based study of hypertension. BMC Proc 2014; 8:S104. [PMID: 25519358 PMCID: PMC4143684 DOI: 10.1186/1753-6561-8-s1-s104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome wide association studies (GWAS) have been used to search for associations between genetic variants and a phenotypic trait of interest. New technologies, such as next-generation sequencing, hold the potential to revolutionize GWAS. However, millions of polymorphisms are identified with next-generation sequencing technology. Consequently, researchers must be careful when performing such a large number of statistical tests, and corrections are typically made to account for multiple testing. Additionally, for typical GWAS, the p value cutoff is set quite low (approximately <10−8). As a result of this p value stringency, it is likely that there are many true associations that do not meet this threshold. To account for this we have incorporated a priori biological knowledge to help identify true associations that may not have reached statistical significance. We propose the application of a pipelined series of statistical and bioinformatic methods, to enable the assessment of the association of genetic polymorphisms with a disease phenotype--here, hypertension--as well as the identification of statistically significant pathways of genes that may play a role in the disease process.
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Affiliation(s)
- Jeremy S Edwards
- Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Susan R Atlas
- Physics and Astronomy, Center for Advanced Research Computing, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Susan M Wilson
- Center for Advanced Research Computing, University of New Mexico Cancer Center, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Candice F Cooper
- Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, 1 University of New Mexico, University of New Mexico Cancer Center, Albuquerque, NM 87131, USA
| | - Li Luo
- University of New Mexico Cancer Center, Internal Medicine, 1 University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Christine A Stidley
- University of New Mexico Cancer Center, Internal Medicine, 1 University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Moutsianas L, Morris AP. Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits. Brief Funct Genomics 2014; 13:362-70. [PMID: 24916163 PMCID: PMC4168660 DOI: 10.1093/bfgp/elu012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies have been successful in identifying common variants that impact complex human traits and diseases. However, despite this success, the joint effects of these variants explain only a small proportion of the genetic variance in these phenotypes, leading to speculation that rare genetic variation might account for much of the ‘missing heritability’. Consequently, there has been an exciting period of research and development into the methodology for the analysis of rare genetic variants, typically by considering their joint effects on complex traits within the same functional unit or genomic region. In this review, we describe a general framework for modelling the joint effects of rare genetic variants on complex traits in association studies of unrelated individuals. We summarise a range of widely used association tests that have been developed from this model and provide an overview of the relative performance of these approaches from published simulation studies.
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250
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Abstract
At least 10% of adults and nearly all children who receive renal-replacement therapy have an inherited kidney disease. These patients rarely die when their disease progresses and can remain alive for many years because of advances in organ-replacement therapy. However, these disorders substantially decrease their quality of life and have a large effect on health-care systems. Since the kidneys regulate essential homoeostatic processes, inherited kidney disorders have multisystem complications, which add to the usual challenges for rare disorders. In this review, we discuss the nature of rare inherited kidney diseases, the challenges they pose, and opportunities from technological advances, which are well suited to target the kidney. Mechanistic insights from rare disorders are relevant for common disorders such as hypertension, kidney stones, cardiovascular disease, and progression of chronic kidney disease.
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Affiliation(s)
- Olivier Devuyst
- Division of Nephrology, Université catholique de Louvain, Brussels, Belgium; Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| | - Nine V A M Knoers
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Giuseppe Remuzzi
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso and Unit of Nephrology and Dialysis, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Franz Schaefer
- Pediatric Nephrology Division, Center for Pediatric and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
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