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Abu Khalaf R, Abusaad A, Al-Nawaiseh B, Sabbah D, Albadawi G. Synthesis, Molecular Modeling and Biological Evaluation of Novel Trifluoromethyl Benzamides as Promising CETP Inhibitors. Curr Comput Aided Drug Des 2024; 20:564-574. [PMID: 37165488 DOI: 10.2174/1573409919666230509123852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Hyperlipidemia is considered a major risk factor for the progress of atherosclerosis. OBJECTIVE Cholesteryl ester transfer protein (CETP) facilitates the relocation of cholesterol esters from HDL to LDL. CETP inhibition produces higher HDL and lower LDL levels. METHODS Synthesis of nine benzylamino benzamides 8a-8f and 9a-9c was performed. RESULTS In vitro biological study displayed potential CETP inhibitory activity, where compound 9c had the best activity with an IC50 of 1.03 μM. Induced-fit docking demonstrated that 8a-8f and 9a-9c accommodated the CETP active site and hydrophobic interaction predominated ligand/ CETP complex formation. CONCLUSION Pharmacophore mapping showed that this scaffold endorsed CETP inhibitors features and consequently elaborated the high CETP binding affinity.
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Affiliation(s)
- Reema Abu Khalaf
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Amani Abusaad
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Bara'a Al-Nawaiseh
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Dima Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Ghadeer Albadawi
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
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Khalaf RA, NasrAllah A, Jarrar W, Sabbah DA. Cholesteryl ester transfer protein inhibitory oxoacetamido-benzamide derivatives: Glide docking, pharmacophore mapping, and synthesis. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902022e20028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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3
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Blauw LL, Li-Gao R, Noordam R, de Mutsert R, Trompet S, Berbée JFP, Wang Y, van Klinken JB, Christen T, van Heemst D, Mook-Kanamori DO, Rosendaal FR, Jukema JW, Rensen PCN, Willems van Dijk K. CETP (Cholesteryl Ester Transfer Protein) Concentration: A Genome-Wide Association Study Followed by Mendelian Randomization on Coronary Artery Disease. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002034. [PMID: 29728394 DOI: 10.1161/circgen.117.002034] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/26/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND We aimed to identify independent genetic determinants of circulating CETP (cholesteryl ester transfer protein) to assess causal effects of variation in CETP concentration on circulating lipid concentrations and cardiovascular disease risk. METHODS A genome-wide association discovery and replication study on serum CETP concentration were embedded in the NEO study (Netherlands Epidemiology of Obesity). Based on the independent identified variants, Mendelian randomization was conducted on serum lipids (NEO study) and coronary artery disease (CAD; CARDIoGRAMplusC4D consortium). RESULTS In the discovery analysis (n=4248), we identified 3 independent variants (P<5×10-8) that determine CETP concentration. These single-nucleotide polymorphisms were mapped to CETP and replicated in a separate subpopulation (n=1458). Per-allele increase (SE) in serum CETP was 0.32 (0.02) µg/mL for rs247616-C, 0.35 (0.02) µg/mL for rs12720922-A, and 0.12 (0.02) µg/mL for rs1968905-G. Combined, these 3 variants explained 16.4% of the total variation in CETP concentration. One microgram per milliliter increase in genetically determined CETP concentration strongly decreased high-density lipoprotein cholesterol (-0.23 mmol/L; 95% confidence interval, -0.26 to -0.20), moderately increased low-density lipoprotein cholesterol (0.08 mmol/L; 95% confidence interval, 0.00-0.16), and was associated with an odds ratio of 1.08 (95% confidence interval, 0.94-1.23) for CAD risk. CONCLUSIONS This is the first genome-wide association study identifying independent variants that largely determine CETP concentration. Although high-density lipoprotein cholesterol is not a causal risk factor for CAD, it has been unequivocally demonstrated that low-density lipoprotein cholesterol lowering is proportionally associated with a lower CAD risk. Therefore, the results of our study are fully consistent with the notion that CETP concentration is causally associated with CAD through low-density lipoprotein cholesterol.
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Affiliation(s)
- Lisanne L Blauw
- Department of Internal Medicine, Division of Endocrinology (L.L.B., J.F.P.B., Y.W., P.C.N.R., K.W.v.D.) .,Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.).,Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.)
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.)
| | - Raymond Noordam
- Department of Internal Medicine, Division of Gerontology and Geriatrics (R.N., S.T., D.v.H.)
| | - Renée de Mutsert
- Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.)
| | - Stella Trompet
- Department of Internal Medicine, Division of Gerontology and Geriatrics (R.N., S.T., D.v.H.).,Department of Cardiology (S.T., J.W.J.)
| | - Jimmy F P Berbée
- Department of Internal Medicine, Division of Endocrinology (L.L.B., J.F.P.B., Y.W., P.C.N.R., K.W.v.D.).,Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.)
| | - Yanan Wang
- Department of Internal Medicine, Division of Endocrinology (L.L.B., J.F.P.B., Y.W., P.C.N.R., K.W.v.D.).,Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.)
| | - Jan B van Klinken
- Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.).,Department of Human Genetics (J.B.v.K., K.W.v.D.)
| | - Tim Christen
- Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.)
| | - Diana van Heemst
- Department of Internal Medicine, Division of Gerontology and Geriatrics (R.N., S.T., D.v.H.)
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.).,and Department of Public Health and Primary Care (D.O.M.-K.) Leiden University Medical Center, The Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology (L.L.B., R.L.-G., R.d.M., T.C., D.O.M.-K., F.R.R.)
| | | | - Patrick C N Rensen
- Department of Internal Medicine, Division of Endocrinology (L.L.B., J.F.P.B., Y.W., P.C.N.R., K.W.v.D.).,Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.)
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology (L.L.B., J.F.P.B., Y.W., P.C.N.R., K.W.v.D.).,Einthoven Laboratory for Experimental Vascular Medicine (L.L.B., J.F.P.B., Y.W., J.B.v.K., P.C.N.R., K.W.v.D.).,Department of Human Genetics (J.B.v.K., K.W.v.D.)
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Yu X, Wei B, Su R, Yao J, Feng X, Jiang G, Xie H, Wu J, Xu X, Zhang M, Zheng S, Zhou L. A risk assessment model of acute liver allograft rejection by genetic polymorphism of CD276. Mol Genet Genomic Med 2019; 7:e689. [PMID: 31044564 PMCID: PMC6603397 DOI: 10.1002/mgg3.689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 02/05/2023] Open
Abstract
Background Liver transplantation is an effective therapy for end‐stage liver diseases and acute liver failure. After the operation, however, recipients may suffer grafts loss induced by alloimmune reaction, which is termed as acute allograft rejection. The interaction between costimulatory molecules, CD276, and its ligand, TREML2, promotes T cell‐mediated immune response, as well as acute or chronic allograft rejection. Our research aimed at correlating genetic polymorphisms of CD276/TREML2 with acute rejection, and evaluating its prognostic value of acute rejection after liver transplantation. Methods The study enrolled a total of 388 recipients. Among them, acute allograft rejection was observed in 54 cases. We performed single nucleotide polymorphism genotyping of CD276, including rs11072431, rs11574495, rs12593558, rs12594627, rs2127015, rs3816661 and rs7176654, and TREML2, including rs4714431, rs6915083, rs7754593, and rs9394767 from preoperative peripheral blood genome DNA. Results We found rs2127015 of CD276, rs6915083 and rs7754593 of TREML2, and HBV infection as well were associated with acute rejection. And, rs2127015 influences CD276 expression. Moreover, we established a risk assessment model, composited by statistically proved risk factors. Conclusion By integrating both clinical and genetic variables, liver transplant recipients can be categorized into different risk groups, and might benefit from individualized therapies.
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Affiliation(s)
- Xiaobo Yu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Bajin Wei
- NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Rong Su
- NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Jia Yao
- NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Xiaowen Feng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Guoping Jiang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Min Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou, China
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Liang Y, Kelemen A. Shared polymorphisms and modifiable behavior factors for myocardial infarction and high cholesterol in a retrospective population study. Medicine (Baltimore) 2017; 96:e7683. [PMID: 28906356 PMCID: PMC5604625 DOI: 10.1097/md.0000000000007683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 01/07/2023] Open
Abstract
Genetic and environmental (behavior, clinical, and demographic) factors are associated with increased risks of both myocardial infarction (MI) and high cholesterol (HC). It is known that HC is major risk factor that may cause MI. However, whether there are common single nucleotide polymorphism (SNPs) associated with both MI and HC is not firmly established, and whether there are modulate and modified effects (interactions of genetic and known environmental factors) on either HC or MI, and whether these joint effects improve the predictions of MI, is understudied.The purpose of this study is to identify novel shared SNPs and modifiable environmental factors on MI and HC. We assess whether SNPs from a metabolic pathway related to MI may relate to HC; whether there are moderate effects among SNPs, lifestyle (smoke and drinking), HC, and MI after controlling other factors [gender, body mass index (BMI), and hypertension (HTN)]; and evaluate prediction power of the joint and modulate genetic and environmental factors influencing the MI and HC.This is a retrospective study with residents of Erie and Niagara counties in New York with a history of MI or with no history of MI. The data set includes environmental variables (demographic, clinical, lifestyle). Thirty-one tagSNPs from a metabolic pathway related to MI are genotyped. Generalized linear models (GLMs) with imputation-based analysis are conducted for examining the common effects of tagSNPs and environmental exposures and their interactions on having a history of HC or MI.MI, BMI, and HTN are significant risk factors for HC. HC shows the strongest effect on risk of MI in addition to HTN; gender and smoking status while drinking status shows protective effect on MI. rs16944 (gene IL-1β) and rs17222772 (gene ALOX) increase the risks of HC, while rs17231896 (gene CETP) has protective effects on HC either with or without the clinical, behavioral, demographic factors with different effect sizes that may indicate the existence of moderate or modifiable effects. Further analysis with the inclusions of gene-gene and gene-environmental interactions shows interactions between rs17231896 (CETP) and rs17222772 (ALOX); rs17231896 (CETP) and gender. rs17237890 (CETP) and rs2070744 (NOS3) are found to be significantly associated with risks of MI adjusted by both SNPs and environmental factors. After multiple testing adjustments, these effects diminished as expected. In addition, an interaction between drinking and smoking status is significant. Overall, the prediction power in successfully classifying MI status is increased to 80% with inclusions of all significant tagSNPs and environmental factors and their interactions compared with environmental factors only (72%).Having a history of either HC or MI has significant effects on each other in both directions, in addition to HTN and gender. Genes/SNPs identified from this analysis that are associated with HC may be potentially linked to MI, which could be further examined and validated through haplotype-pairs analysis with appropriate population stratification corrections, and function/pathway regulation analysis to eliminate the limitations of the current analysis.
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Affiliation(s)
| | - Arpad Kelemen
- Department of Organizational Systems and Adult Health, University of Maryland, Baltimore, MD
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Bien SA, Wojcik GL, Zubair N, Gignoux CR, Martin AR, Kocarnik JM, Martin LW, Buyske S, Haessler J, Walker RW, Cheng I, Graff M, Xia L, Franceschini N, Matise T, James R, Hindorff L, Le Marchand L, North KE, Haiman CA, Peters U, Loos RJF, Kooperberg CL, Bustamante CD, Kenny EE, Carlson CS. Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array. PLoS One 2016; 11:e0167758. [PMID: 27973554 PMCID: PMC5156387 DOI: 10.1371/journal.pone.0167758] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/18/2016] [Indexed: 11/25/2022] Open
Abstract
Investigating genetic architecture of complex traits in ancestrally diverse populations is imperative to understand the etiology of disease. However, the current paucity of genetic research in people of African and Latin American ancestry, Hispanic and indigenous peoples in the United States is likely to exacerbate existing health disparities for many common diseases. The Population Architecture using Genomics and Epidemiology, Phase II (PAGE II), Study was initiated in 2013 by the National Human Genome Research Institute to expand our understanding of complex trait loci in ethnically diverse and well characterized study populations. To meet this goal, the Multi-Ethnic Genotyping Array (MEGA) was designed to substantially improve fine-mapping and functional discovery by increasing variant coverage across multiple ethnicities at known loci for metabolic, cardiovascular, renal, inflammatory, anthropometric, and a variety of lifestyle traits. Studying the frequency distribution of clinically relevant mutations, putative risk alleles, and known functional variants across multiple populations will provide important insight into the genetic architecture of complex diseases and facilitate the discovery of novel, sometimes population-specific, disease associations. DNA samples from 51,650 self-identified African ancestry (17,328), Hispanic/Latino (22,379), Asian/Pacific Islander (8,640), and American Indian (653) and an additional 2,650 participants of either South Asian or European ancestry, and other reference panels have been genotyped on MEGA by PAGE II. MEGA was designed as a new resource for studying ancestrally diverse populations. Here, we describe the methodology for selecting trait-specific content for use in multi-ethnic populations and how enriching MEGA for this content may contribute to deeper biological understanding of the genetic etiology of complex disease.
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Affiliation(s)
- Stephanie A. Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (CSC); (SAB)
| | - Genevieve L. Wojcik
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Niha Zubair
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher R. Gignoux
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Alicia R. Martin
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jonathan M. Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lisa W. Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Steven Buyske
- Department of Genetics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ryan W. Walker
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucy Xia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Tara Matise
- Department of Genetics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey, United States of America
| | - Regina James
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Loic Le Marchand
- Department of Epidemiology Program, University of Hawai’i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Charles L. Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (CSC); (SAB)
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Suhy A, Hartmann K, Papp AC, Wang D, Sadee W. Regulation of cholesteryl ester transfer protein expression by upstream polymorphisms: reduced expression associated with rs247616. Pharmacogenet Genomics 2015; 25:394-401. [PMID: 26061659 PMCID: PMC4499003 DOI: 10.1097/fpc.0000000000000151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cholesteryl ester transfer protein (CETP) is involved in reverse cholesterol transport by exchanging cholesteryl esters for triglycerides between high-density lipoprotein and low-density lipoprotein particles, effectively decreasing high-density lipoprotein cholesterol levels. Variants within a large haplotype block upstream of CETP (rs247616, rs173539) have been shown to be significantly associated with reduced expression; however, the underlying mechanism has not been identified. METHODS We analyzed the linkage structure of our top candidate single-nucleotide polymorphism (SNP), rs247616, and assessed each SNP of the haplotype block for potential interactions with transcription factor binding sites. We then used a reporter gene assay to assess the effect of three SNPs (rs247616, rs173539, and rs1723150) on expression in vitro. RESULTS Several variants in the upstream haplotype, including rs247616, rs173539, and rs1723150, disrupt or generate transcription factor binding sites. In reporter gene assays, rs247616 and rs173539 were found to significantly affected expression in HepG2 cells, whereas rs17231506 had no effect. rs247616 decreased expression by 1.7-fold (P<0.0001), whereas rs173539 increased expression by 2.2-fold (P=0.0006). CONCLUSION SNPs rs247616 and rs173539 are in high linkage disequilibrium (R=0.96, D'=1.00) and have the potential to regulate CETP expression. Although opposing effects suggest that regulation of CETP expression could vary between tissues, the minor allele of rs247616 and SNPs in high linkage with it were found to be associated with reduced expression across all tissues.
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Affiliation(s)
- Adam Suhy
- Department of Pharmacology, Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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Chen W, Liu Y, Li H, Chang S, Shu D, Zhang H, Chen F, Xie Q. Intronic deletions of tva receptor gene decrease the susceptibility to infection by avian sarcoma and leukosis virus subgroup A. Sci Rep 2015; 5:9900. [PMID: 25873518 PMCID: PMC4397534 DOI: 10.1038/srep09900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/17/2015] [Indexed: 12/16/2022] Open
Abstract
The group of avian sarcoma and leukosis virus (ASLV) in chickens contains six highly related subgroups, A to E and J. Four genetic loci, tva, tvb, tvc and tvj, encode for corresponding receptors that determine the susceptibility to the ASLV subgroups. The prevalence of ASLV in hosts may have imposed strong selection pressure toward resistance to ASLV infection, and the resistant alleles in all four receptor genes have been identified. In this study, two new alleles of the tva receptor gene, tvar5 and tvar6, with similar intronic deletions were identified in Chinese commercial broilers. These natural mutations delete the deduced branch point signal within the first intron, disrupting mRNA splicing of the tva receptor gene and leading to the retention of intron 1 and introduction of premature TGA stop codons in both the longer and shorter tva isoforms. As a result, decreased susceptibility to subgroup A ASLV in vitro and in vivo was observed in the subsequent analysis. In addition, we identified two groups of heterozygous allele pairs which exhibited quantitative differences in host susceptibility to ASLV-A. This study demonstrated that defective splicing of the tva receptor gene can confer genetic resistance to ASLV subgroup A in the host.
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Affiliation(s)
- Weiguo Chen
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Yang Liu
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Hongxing Li
- College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, P. R. China
| | - Dingming Shu
- Institute of Animal Science, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, P. R. China
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, U.S.A
| | - Feng Chen
- 1] College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China [2] South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, P. R. China
| | - Qingmei Xie
- 1] College of Animal Science, South China Agricultural University &Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P. R. China [2] Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou, 510642, P. R. China [3] South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, P. R. China
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