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El-Hawy MA, Abdelsattar S, Bedair HM, Elsaady DZ, Hola ASA. Single nucleotide polymorphism rs7961894, platelet morphological parameters and lipid profile in children with type 1 diabetes: a potential relationship. Eur J Pediatr 2024; 183:4385-4395. [PMID: 39098887 DOI: 10.1007/s00431-024-05694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/06/2024]
Abstract
Increased cardiovascular risk has been associated with certain platelet morphological parameters, and several single nucleotide polymorphisms (SNPs) have been reported to be linked. Still, little is known about their role among children with type 1 diabetes mellitus (T1DM). So, we aimed to investigate platelet parameters and lipid profile changes in relation to rs7961894 SNP in children with T1DM. Eighty children with T1DM and eighty apparently healthy controls participated in this cross-sectional study. Platelet count, mean platelet volume (MPV), platelet distribution width (PDW), plateletcrit (PCT), HbA1c, triglycerides, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol were measured, and atherogenic indices were calculated. Using a real-time polymerase chain allelic discrimination technique, rs7961894 SNP was genotyped. Children with T1DM had significantly higher MPV, PDW, TC, and LDL-C compared to controls. 25% of patients had rs7961894 CT genotype with significantly higher MPV, PDW, PCT, LDL-C, triglycerides, Castelli's risk index II (CRI II), and atherogenic index of plasma (AIP) compared to CC genotyped patients. MPV correlated significantly with CRI II and AIP, PDW with CRI II, while PCT correlated substantially with HbA1c, LDL-C, CRI II, and AIP. rs7961894 CT genotype was a significant dependent predictor of the changes in MPV, PDW, and PCT in multivariate regression analysis.Conclusion: In children with T1DM, rs7961894 CT genotype is significantly linked to MPV, PDW, and PCT changes, which showed a substantial relationship to CRI II and AIP, highlighting the importance of monitoring these patients to identify potential cardiovascular risks early. What is Known: • Platelets and dyslipidemia are involved in atherosclerosis pathogenesis • Changes in platelet activity and morphological parameters in diabetes mellitus are contradictory • rs7961894 single nucleotide polymorphism is associated with significant changes in mean platelet volume (MPV) with no available data in children What is New: • Children with type 1 diabetes mellitus exhibited significantly higher values of MPV and platelet distribution width (PDW) • rs7961894 CT genotype was a dependent predictor of the changes in MPV, PDW, and plateletcrit (PCT) values • Diabetic children with the rs7961894 CT genotype showed substantial alterations in lipid parameters with a strong correlation between MPV, PDW, and PCT and Castelli's risk index II and the atherogenic index of plasma.
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Affiliation(s)
- Mahmoud A El-Hawy
- Department of Pediatrics, Faculty of Medicine, Menoufia University, Yassin Abdel-Ghafar Street, Shebin El-Kom, Egypt
| | - Shimaa Abdelsattar
- Clinical Biochemistry and Molecular Diagnostics Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | - Hanan M Bedair
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | | | - Ahmed S Abo Hola
- Department of Pediatrics, Faculty of Medicine, Menoufia University, Yassin Abdel-Ghafar Street, Shebin El-Kom, Egypt.
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Ludhiadch A, Sulena, Singh S, Chakraborty S, Sharma D, Kulharia M, Singh P, Munshi A. Genomic Variation Affecting MPV and PLT Count in Association with Development of Ischemic Stroke and Its Subtypes. Mol Neurobiol 2023; 60:6424-6440. [PMID: 37453995 DOI: 10.1007/s12035-023-03460-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Platelets play a significant role in the pathophysiology of ischemic stroke since they are involved in the formation of intravascular thrombus after erosion or rupture of the atherosclerotic plaques. Platelet (PLT) count and mean platelet volume (MPV) are the two significant parameters that affect the functions of platelets. In the current study, MPV and PLT count was evaluated using flow cytometry and a cell counter. SonoClot analysis was carried out to evaluate activated clot timing (ACT), clot rate (CR), and platelet function (PF). Genotyping was carried out using GSA and Sanger sequencing, and expression analysis was performed using RT-PCR. In silico analysis was carried out using the GROMACS tool and UNAFold. The interaction of significant proteins with other proteins was predicted using the STRING database. Ninety-six genes were analyzed, and a significant association of THPO (rs6141) and ARHGEF3 (rs1354034) was observed with the disease and its subtypes. Altered genotypes were associated significantly with increased MPV, decreased PLT count, and CR. Expression analysis revealed a higher expression in patients bearing the variant genotypes of both genes. In silico analysis revealed that mutation in the THPO gene leads to the reduced compactness of protein structure. mRNA encoded by mutated ARHGEF3 gene increases the half-life of mRNA. The two significant proteins interact with many other proteins, especially the ones involved in platelet activation, aggregation, erythropoiesis, megakaryocyte maturation, and cytoskeleton rearrangements, suggesting that they could be important players in the determination of MPV values. In conclusion, the current study demonstrated the role of higher MPV affected by genetic variation in the development of IS and its subtypes. The results of the current study also indicate that higher MPV can be used as a biomarker for the disease and altered genotypes, and higher MPV can be targeted for better therapeutic outcomes.
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Affiliation(s)
- Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Sulena
- Department of Neurology, Guru Gobind Singh Medical College and Hospital, Sadiq Road, Faridkot, Punjab, 151203, India
| | | | - Sudip Chakraborty
- Department of Computational Sciences, School of Basic and Applied Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Dixit Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Mahesh Kulharia
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Paramdeep Singh
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, Punjab, 151001, India
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India.
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Fu B, Pazokitoroudi A, Sudarshan M, Liu Z, Subramanian L, Sankararaman S. Fast kernel-based association testing of non-linear genetic effects for biobank-scale data. Nat Commun 2023; 14:4936. [PMID: 37582955 PMCID: PMC10427662 DOI: 10.1038/s41467-023-40346-2] [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: 03/22/2022] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
Our knowledge of non-linear genetic effects on complex traits remains limited, in part, due to the modest power to detect such effects. While kernel-based tests offer a versatile approach to test for non-linear relationships between sets of genetic variants and traits, current approaches cannot be applied to Biobank-scale datasets containing hundreds of thousands of individuals. We propose, FastKAST, a kernel-based approach that can test for non-linear effects of a set of variants on a quantitative trait. FastKAST provides calibrated hypothesis tests while enabling analysis of Biobank-scale datasets with hundreds of thousands of unrelated individuals from a homogeneous population. We apply FastKAST to 53 quantitative traits measured across ≈ 300 K unrelated white British individuals in the UK Biobank to detect sets of variants with non-linear effects at genome-wide significance.
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Affiliation(s)
- Boyang Fu
- Department of Computer Science, UCLA, Los Angeles, CA, USA.
| | | | - Mukund Sudarshan
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Zhengtong Liu
- Department of Computer Science, UCLA, Los Angeles, CA, USA
| | - Lakshminarayanan Subramanian
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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4
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Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, de Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis GR, Almasy L, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Choquet H, Correa A, Curran JE, Faraday N, Fornage M, Glahn DC, Hou L, Jorgenson E, Kooperberg C, Lewis JP, Lloyd-Jones DM, Loos RJF, Min YI, Mitchell BD, Morrison AC, Nickerson DA, North KE, O'Connell JR, Pankratz N, Psaty BM, Vasan RS, Rich SS, Rotter JI, Smith AV, Smith NL, Tang H, Tracy RP, Conomos MP, Laurie CA, Mathias RA, Li Y, Auer PL, Thornton T, Reiner AP, Johnson AD, Raffield LM. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative. Hum Mol Genet 2022; 31:347-361. [PMID: 34553764 PMCID: PMC8825339 DOI: 10.1093/hmg/ddab252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
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Affiliation(s)
- Amarise Little
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Caitlin McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | | | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ani Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yuan-I Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
- Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA 98108, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | | | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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Ngwa JS, Yanek LR, Kammers K, Kanchan K, Taub MA, Scharpf RB, Faraday N, Becker LC, Mathias RA, Ruczinski I. Secondary analyses for genome-wide association studies using expression quantitative trait loci. Genet Epidemiol 2022; 46:170-181. [PMID: 35312098 PMCID: PMC9086181 DOI: 10.1002/gepi.22448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/19/2021] [Accepted: 01/20/2022] [Indexed: 01/01/2023]
Abstract
Genome-wide association studies (GWAS) have successfully identified thousands of single nucleotide polymorphisms (SNPs) associated with complex traits; however, the identified SNPs account for a fraction of trait heritability, and identifying the functional elements through which genetic variants exert their effects remains a challenge. Recent evidence suggests that SNPs associated with complex traits are more likely to be expression quantitative trait loci (eQTL). Thus, incorporating eQTL information can potentially improve power to detect causal variants missed by traditional GWAS approaches. Using genomic, transcriptomic, and platelet phenotype data from the Genetic Study of Atherosclerosis Risk family-based study, we investigated the potential to detect novel genomic risk loci by incorporating information from eQTL in the relevant target tissues (i.e., platelets and megakaryocytes) using established statistical principles in a novel way. Permutation analyses were performed to obtain family-wise error rates for eQTL associations, substantially lowering the genome-wide significance threshold for SNP-phenotype associations. In addition to confirming the well known association between PEAR1 and platelet aggregation, our eQTL-focused approach identified a novel locus (rs1354034) and gene (ARHGEF3) not previously identified in a GWAS of platelet aggregation phenotypes. A colocalization analysis showed strong evidence for a functional role of this eQTL.
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Affiliation(s)
- Julius S. Ngwa
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Lisa R. Yanek
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Kai Kammers
- Department of OncologyJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | - Kanika Kanchan
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Margaret A. Taub
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Robert B. Scharpf
- Department of OncologyJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Lewis C. Becker
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Rasika A. Mathias
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ingo Ruczinski
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
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6
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The Predictive role of Neutrophil-to-Lymphocyte Ratio (NLR) and Mean Platelet Volume-to-Lymphocyte Ratio (MPVLR) for Cardiovascular Events in Adult Patients with Acute Heart Failure. Mediators Inflamm 2021; 2021:6889733. [PMID: 34671226 PMCID: PMC8523242 DOI: 10.1155/2021/6889733] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/22/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction The inflammatory response plays a potential role for the pathogenesis and adverse outcomes of heart failure (HF). We aimed to explore the predictive role of baseline neutrophil-to-lymphocyte ratio (NLR) and mean platelet volume-to-lymphocyte ratio (MPVLR) on cardiovascular events (CVEs) in patients hospitalized with acute HF. Materials and Methods A retrospective cohort study was conducted in 321 patients with HF between January 2017 and December 2019. The association between their NLR, MPVLR, and combined NLR and MPVLR and CVEs, rehospitalization for HF, in-hospital death, and a composite outcome was explored by survival analysis using a Cox proportional hazard model. They were separately investigated and compared with the area under the receiver operating characteristics curve (AUC). Results Up to the end of the 3-year follow-up, 96 (29.9%) had CVEs, 106 (33.0%) died, 62 (19.3%) were rehospitalized with HF, and 21 (6.5%) died during admission. The NLR and MPVLR were significantly associated with CVEs (adjusted HR for NLR ≥ 3.29, 3.11; 95% CI, 1.98-4.89; MPVLR ≥ 8.57, 2.86; 95% CI, 1.87-4.39), readmissions for HF (adjusted HR for NLR ≥ 3.58, 2.70; 95% CI, 1.58-4.61; MPVLR ≥ 6.43, 2.84; 95% CI,1.59-5.07), in-hospital mortality (adjusted HR for NLR ≥ 3.29, 9.54; 95% CI, 2.19-41.40; MPVLR ≥ 8.57, 7.87; 95% CI, 2.56-24.19), and composite outcome (adjusted HR for NLR ≥ 3.32, 4.76; 95% CI, 3.29-6.89; MPVLR ≥ 7.07, 3.64; 95% CI, 2.58-5.15). The AUC of NLR and MPVLR for CVEs were 0.67 (95% CI, 0.61-0.72) and 0.63 (95% CI, 0.58-0.69). Combined NLR and MPVLR increased the AUC to 0.77 (95% CI, 0.72-0.83) with statistical significance. Conclusion The elevated NLR and MPVLR on admission in patients with acute HF were independently associated with worse CVEs, rehospitalization for HF, in-hospital death, and composite outcomes. These economical biomarkers should be considered in the management and follow-up care of patients with acute HF.
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7
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Babes EE, Zaha DC, Tit DM, Nechifor AC, Bungau S, Andronie-Cioara FL, Behl T, Stoicescu M, Munteanu MA, Rus M, Toma MM, Brisc C. Value of Hematological and Coagulation Parameters as Prognostic Factors in Acute Coronary Syndromes. Diagnostics (Basel) 2021; 11:850. [PMID: 34065132 PMCID: PMC8151317 DOI: 10.3390/diagnostics11050850] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
The values of hematological and coagulation biomarkers were evaluated as predictors of in hospital mortality and complications, in patients with acute coronary syndromes (ACS). This retrospective observational study enrolled 936 ACS subjects admitted to the Clinical Emergency Hospital of Oradea, Romania, between January-December 2019. Hematological and coagulation parameters were obtained at admission. During hospitalization, the following adverse events were recorded: death, ventricular rhythm disturbances, atrial fibrillation, heart failure, re-infarction, and stroke. Accuracy of hematological and coagulation parameters as predictors of adverse outcome were also evaluated. The diagnosis was unstable angina in 442 patients (47.22%), non-ST-elevation myocardial infarction (NSTEMI) in 113 patients (12.1%) and ST-elevation myocardial infarction (STEMI) in 381 patients (40.70%); 87 patients (9.29%) died during hospitalization and 193 (20.7%) developed complications. Predictors for in hospital mortality were as follows: red cell distribution width (RDW) (AUC 0.691, p < 0.0001), white blood cells (WBC) (AUC 0.684, p < 0.0001), neutrophils (NEU) (AUC 0.684, p < 0.0001), and prothrombin time (PT) (AUC 0.765, p < 0.0001). WBC (AUC 0.659, p < 0.0001), NEU (AUC 0.664, p < 0.0001), RDW (AUC 0.669, p < 0.0001), and PT (AUC 0.669, 95% CI 0.622-0.714, p < 0.0001) also had accuracy for complications prediction. RDW had a good ability to predict heart failure in NSTEMI patients (AUC 0.832, p < 0.0001). An acceptable ability to predict ventricular rhythm disturbances occurrence had WBC (AUC 0.758, p < 0.0001) and NEU (AUC 0.772, p < 0.0001). Hematological and coagulation parameters can help in risk stratification of ACS patients. RDW, WBC, NEU, and PT were able to predict mortality and in-hospital complications in ACS patients. RDW has a good accuracy in predicting complications and heart failure in NSTEMI patients. WBC and NEU are good predictors for ventricular rhythm disturbances.
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Affiliation(s)
- Elena Emilia Babes
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (M.S.); (M.A.M.); (M.R.); (C.B.)
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
| | - Dana Carmen Zaha
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy of Oradea, University of Oradea, 410073 Oradea, Romania
| | - Delia Mirela Tit
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania; (D.M.T.); (M.M.T.)
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Aurelia Cristina Nechifor
- Analytical Chemistry and Environmental Engineering Department, Polytechnic University of Bucharest, 011061 Bucharest, Romania;
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania; (D.M.T.); (M.M.T.)
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Felicia Liana Andronie-Cioara
- Department of Psycho-Neuroscience and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India;
| | - Manuela Stoicescu
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (M.S.); (M.A.M.); (M.R.); (C.B.)
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
| | - Mihai Alexandru Munteanu
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (M.S.); (M.A.M.); (M.R.); (C.B.)
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
| | - Marius Rus
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (M.S.); (M.A.M.); (M.R.); (C.B.)
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
| | - Mirela Marioara Toma
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania; (D.M.T.); (M.M.T.)
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Ciprian Brisc
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (M.S.); (M.A.M.); (M.R.); (C.B.)
- Clinical Emergency Hospital of Oradea, 410169 Oradea, Romania;
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8
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Blanc F, Maroilley T, Revilla M, Lemonnier G, Leplat JJ, Billon Y, Ravon L, Bouchez O, Bidanel JP, Bed'Hom B, Pinard-van der Laan MH, Estellé J, Rogel-Gaillard C. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs. Genet Sel Evol 2021; 53:24. [PMID: 33731010 PMCID: PMC7972226 DOI: 10.1186/s12711-021-00614-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs. Results A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumoniae (M. hyo) at weaning (28 days of age), with a booster 21 days later. Vaccine response was assessed by measuring seric M. hyo antibodies (Ab) at 0 (vaccination day), 21 (booster day), 28, 35, and 118 days post-vaccination (dpv). Inter-individual variability of M. hyo Ab levels was observed at all time points and the corresponding heritabilities ranged from 0.46 to 0.57. Ab persistence was higher in females than in males. Genome-wide association studies with a 658 K SNP panel revealed two genomic regions associated with variations of M. hyo Ab levels at 21 dpv at positions where immunity-related genes have been mapped, DAB2IP on chromosome 1, and ASAP1, CYRIB and GSDMC on chromosome 4. We studied covariations of Ab responses with the pre-vaccination blood transcriptome obtained by RNA-Seq for a subset of 82 pigs. Weighted gene correlation network and differential expression analyses between pigs that differed in Ab responses highlighted biological functions that were enriched in heme biosynthesis and platelet activation for low response at 21 dpv, innate antiviral immunity and dendritic cells for high response at 28 and 35 dpv, and cell adhesion and extracellular matrix for high response at 118 dpv. Sparse partial least squares discriminant analysis identified 101 genes that efficiently predicted divergent responders at all time points. We found weak negative correlations of M. hyo Ab levels with body weight traits, which revealed a trade-off that needs to be further explored. Conclusions We confirmed the influence of the host genetics on vaccine effectiveness to M. hyo and provided evidence that the pre-vaccination blood transcriptome co-varies with the Ab response. Our results highlight that both genetic markers and blood biomarkers could be used as potential predictors of vaccine response levels and more studies are required to assess whether they can be exploited in breeding programs.
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Affiliation(s)
- Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Tatiana Maroilley
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Manuel Revilla
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Jacques Leplat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | | | | | - Jean-Pierre Bidanel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Bertrand Bed'Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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Hacein-Bey-Abina S, Estienne M, Bessoles S, Echchakir H, Pederzoli-Ribeil M, Chiron A, Aldaz-Carroll L, Leducq V, Zhang Y, Souyri M, Louache F, Abina AM. Erythropoietin is a major regulator of thrombopoiesis in thrombopoietin-dependent and -independent contexts. Exp Hematol 2020; 88:15-27. [PMID: 32721504 DOI: 10.1016/j.exphem.2020.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/18/2020] [Accepted: 07/22/2020] [Indexed: 01/09/2023]
Abstract
Thrombopoietin (TPO), through activation of its cognate receptor Mpl, is the major regulator of platelet production. However, residual platelets observed in TPO- and Mpl-loss-of-function (LOF) mice suggest the existence of an additional factor to TPO in platelet production. As erythropoietin (EPO) exhibited both in vitro megakaryocytic potential, in association with other early-acting cytokines, and in vivo platelet activation activity, we sought to investigate its role in this setting. Here, we used multiple LOF models to decipher the reciprocal role of EPO and TPO in the regulation of platelet production in TPO-LOF and Mpl-LOF mice and of platelet size heterogeneity in wild-type mice. We first identified EPO as the major thrombopoietic factor in the absence of the TPO-Mpl pathway. Based on the study of several mouse models we found that the EPO-EPO receptor pathway acts on late-stage megakaryopoiesis and is responsible for large-sized platelet production, while the TPO-Mpl pathway promotes small-sized platelet production. On the basis of our data, EPO might be used for thrombocytopenia supportive therapy in congenital amegakaryocytopoiesis. Furthermore, as a distribution skewed toward large platelets is an independent risk factor and a poor prognosis indicator in atherothrombosis, the characterization of EPO's role in the production of large-sized platelets, if confirmed in humans, may open new perspectives in the understanding of the role of EPO-induced platelets in atherothrombosis.
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Affiliation(s)
- Salima Hacein-Bey-Abina
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, Le-Kremlin-Bicêtre, France.
| | | | - Stéphanie Bessoles
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Magali Pederzoli-Ribeil
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | - Andrada Chiron
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, Le-Kremlin-Bicêtre, France
| | - Lydia Aldaz-Carroll
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Yanyan Zhang
- INSERM U1170, CNRS GDR 3697 MicroNiT, Institut Gustave Roussy, Villejuif, France
| | - Michèle Souyri
- INSERM UMRS 1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris, France
| | - Fawzia Louache
- INSERM U1170, CNRS GDR 3697 MicroNiT, Institut Gustave Roussy, Villejuif, France; Université Paris-Sud, Orsay, France
| | - Amine M Abina
- UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France; NOKAD, Evry, France.
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Miller MM, Henninger N, Słowik A. Mean platelet volume and its genetic variants relate to stroke severity and 1-year mortality. Neurology 2020; 95:e1153-e1162. [PMID: 32576634 DOI: 10.1212/wnl.0000000000010105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/28/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To determine whether mean platelet volume (MPV) and selected single nucleotide polymorphisms (SNPs) that have been associated with MPV in genome-wide association studies relate to stroke severity, functional outcome on discharge, and 1-year mortality in patients with ischemic stroke, we retrospectively analyzed 577 patients with first-ever ischemic stroke. METHODS Genotyping of 3 SNPs (rs342293, rs1354034, rs7961894) was performed using a real-time PCR allelic discrimination assay. Multivariable regression was used to determine the association of MPV and MPV-associated SNPs with the NIH Stroke Scale (NIHSS) score on admission, modified Rankin Scale score on discharge, and data on 1-year mortality. RESULTS Rs7961894, but not rs342293 or rs1354034 SNP, was independently associated with an MPV in the highest quartile (MPV Q4). MPV Q4 was associated with significantly greater admission NIHSS (p = 0.006), poor discharge outcome (p = 0.034), and worse 1-year mortality (p = 0.033). After adjustment for pertinent covariates, MPV Q4 remained independently associated with a greater admission NIHSS score (p = 0.025). The T>C variant of rs7961894 SNP was an independent marker of a lower 1-year mortality (hazard ratio, 0.30; 95% confidence interval, 0.13-0.70; p = 0.006) in the studied population. CONCLUSION MPV is a marker of stroke severity and T>C variant of rs7961894 is independently associated with greater MPV in acute phase of ischemic stroke and relates to decreased 1-year mortality after stroke.
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Affiliation(s)
- Małgorzata M Miller
- From the Department of Neurology (M.M.M., A.S.), Jagiellonian University Medical College, Krakow, Poland; and Departments of Neurology and Psychiatry (N.H.), University of Massachusetts Medical School, Worcester.
| | - Nils Henninger
- From the Department of Neurology (M.M.M., A.S.), Jagiellonian University Medical College, Krakow, Poland; and Departments of Neurology and Psychiatry (N.H.), University of Massachusetts Medical School, Worcester
| | - Agnieszka Słowik
- From the Department of Neurology (M.M.M., A.S.), Jagiellonian University Medical College, Krakow, Poland; and Departments of Neurology and Psychiatry (N.H.), University of Massachusetts Medical School, Worcester
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11
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Lin SH, Loftfield E, Sampson JN, Zhou W, Yeager M, Freedman ND, Chanock SJ, Machiela MJ. Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men. Sci Rep 2020; 10:3655. [PMID: 32108144 PMCID: PMC7046668 DOI: 10.1038/s41598-020-59963-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022] Open
Abstract
Mosaic loss of Y chromosome (mLOY) is the most frequently detected somatic copy number alteration in leukocytes of men. In this study, we investigate blood cell counts as a potential mechanism linking mLOY to disease risk in 206,353 UK males. Associations between mLOY, detected by genotyping arrays, and blood cell counts were assessed by multivariable linear models adjusted for relevant risk factors. Among the participants, mLOY was detected in 39,809 men. We observed associations between mLOY and reduced erythrocyte count (−0.009 [−0.014, −0.005] × 1012 cells/L, p = 2.75 × 10−5) and elevated thrombocyte count (5.523 [4.862, 6.183] × 109 cells/L, p = 2.32 × 10−60) and leukocyte count (0.218 [0.198, 0.239] × 109 cells/L, p = 9.22 × 10−95), particularly for neutrophil count (0.174 × [0.158, 0.190]109 cells/L, p = 1.24 × 10−99) and monocyte count (0.021 [0.018 to 0.024] × 109 cells/L, p = 6.93 × 10−57), but lymphocyte count was less consistent (0.016 [0.007, 0.025] × 109 cells/L, p = 8.52 × 10−4). Stratified analyses indicate these associations are independent of the effects of aging and smoking. Our findings provide population-based evidence for associations between mLOY and blood cell counts that should stimulate investigation of the underlying biological mechanisms linking mLOY to cancer and chronic disease risk.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Josh N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.
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12
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Ludhiadch A, Muralidharan A, Balyan R, Munshi A. The molecular basis of platelet biogenesis, activation, aggregation and implications in neurological disorders. Int J Neurosci 2020; 130:1237-1249. [PMID: 32069430 DOI: 10.1080/00207454.2020.1732372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Platelets are anucleated blood constituents, vital for hemostasis and involved in the pathophysiology of several cardiovascular, neurovascular diseases as well as inflammatory processes and metastasis. Over the past few years, the molecular processes that regulate the function of platelets in hemostasis and thrombosis have emerged revealing platelets to be perhaps more complex than may have been expected. The most understood part of platelets is to respond to a blood vessel injury by altering shape, secreting granule contents, and aggregating. These responses, while advantageous for hemostasis, can become detrimental when they root ischemia or infarction. Only a few transcription and signaling factors involved in platelet biogenesis have been identified till date. Platelets encompass an astonishingly complete array of organelles and storage granules including mitochondria, lysosomes, alpha granules, dense granules, a dense tubular system (analogous to the endoplasmic reticulum of nucleated cells); a highly invaginated plasma membrane system known as the open canalicular system (OCS) and large fields of glycogen. Platelets as a model cells to study neurological disorders have been recommended by several researchers since several counterparts exist between platelets and the brain, which make them interesting for studying the neurobiology of various neurological disorders. This review has been compiled with an aim to integrate the latest research on platelet biogenesis, activation and aggregation focusing on the molecular pathways that power and regulate these processes. The dysregulation of important molecular players affecting fluctuating platelet biology and thereby resulting in neurovascular diseases has also been discussed.
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Affiliation(s)
- Abhilash Ludhiadch
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Abhishek Muralidharan
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Renuka Balyan
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
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13
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Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Lin Y, Le Marchand L, Matise TC, Monroe KR, Moreland L, North KE, Park SL, Reiner A, Wallace R, Wilkens LR, Kooperberg C, Ritchie MD, Crawford DC. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS One 2019; 14:e0226771. [PMID: 31891604 PMCID: PMC6938343 DOI: 10.1371/journal.pone.0226771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/11/2022] Open
Abstract
We performed a hypothesis-generating phenome-wide association study (PheWAS) to identify and characterize cross-phenotype associations, where one SNP is associated with two or more phenotypes, between thousands of genetic variants assayed on the Metabochip and hundreds of phenotypes in 5,897 African Americans as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study. The PAGE I study was a National Human Genome Research Institute-funded collaboration of four study sites accessing diverse epidemiologic studies genotyped on the Metabochip, a custom genotyping chip that has dense coverage of regions in the genome previously associated with cardio-metabolic traits and outcomes in mostly European-descent populations. Here we focus on identifying novel phenome-genome relationships, where SNPs are associated with more than one phenotype. To do this, we performed a PheWAS, testing each SNP on the Metabochip for an association with up to 273 phenotypes in the participating PAGE I study sites. We identified 133 putative pleiotropic variants, defined as SNPs associated at an empirically derived p-value threshold of p<0.01 in two or more PAGE study sites for two or more phenotype classes. We further annotated these PheWAS-identified variants using publicly available functional data and local genetic ancestry. Amongst our novel findings is SPARC rs4958487, associated with increased glucose levels and hypertension. SPARC has been implicated in the pathogenesis of diabetes and is also known to have a potential role in fibrosis, a common consequence of multiple conditions including hypertension. The SPARC example and others highlight the potential that PheWAS approaches have in improving our understanding of complex disease architecture by identifying novel relationships between genetic variants and an array of common human phenotypes.
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Affiliation(s)
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Janina M. Jeff
- Illumina, Inc., San Diego, California, United States of America
| | - Alex Frase
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Scott Dudek
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jose-Luis Ambite
- Information Sciences Institute; University of Southern California, Marina del Rey, California, United States of America
| | - Christy L. Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Ewa Deelman
- Information Sciences Institute; University of Southern California, Marina del Rey, California, United States of America
| | | | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucia A. Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chun-Nan Hsu
- Center for Research in Biological Systems, Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | | | - Yi Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Kristine R. Monroe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Larry Moreland
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sungshim L. Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Robert Wallace
- Departments of Epidemiology and Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dana C. Crawford
- Cleveland Institute for Computational Biology, Cleveland, Ohio, United States of America
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Ma X, Jia C, Fu D, Chu M, Ding X, Wu X, Guo X, Pei J, Bao P, Liang C, Yan P. Analysis of Hematological Traits in Polled Yak by Genome-Wide Association Studies Using Individual SNPs and Haplotypes. Genes (Basel) 2019; 10:E463. [PMID: 31212963 PMCID: PMC6627507 DOI: 10.3390/genes10060463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022] Open
Abstract
Yak (Bos grunniens) is an important domestic animal living in high-altitude plateaus. Due to inadequate disease prevention, each year, the yak industry suffers significant economic losses. The identification of causal genes that affect blood- and immunity-related cells could provide preliminary reference guidelines for the prevention of diseases in the population of yaks. The genome-wide association studies (GWASs) utilizing a single-marker or haplotype method were employed to analyze 15 hematological traits in the genome of 315 unrelated yaks. Single-marker GWASs identified a total of 43 significant SNPs, including 35 suggestive and eight genome-wide significant SNPs, associated with nine traits. Haplotype analysis detected nine significant haplotype blocks, including two genome-wide and seven suggestive blocks, associated with seven traits. The study provides data on the genetic variability of hematological traits in the yak. Five essential genes (GPLD1, EDNRA,APOB, HIST1H1E, and HIST1H2BI) were identified, which affect the HCT, HGB, RBC, PDW, PLT, and RDWSD traits and can serve as candidate genes for regulating hematological traits. The results provide a valuable reference to be used in the analysis of blood properties and immune diseases in the yak.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou 730050, China.
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Read RW, Schlauch KA, Elhanan G, Metcalf WJ, Slonim AD, Aweti R, Borkowski R, Grzymski JJ. GWAS and PheWAS of red blood cell components in a Northern Nevadan cohort. PLoS One 2019; 14:e0218078. [PMID: 31194788 PMCID: PMC6564422 DOI: 10.1371/journal.pone.0218078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/21/2019] [Indexed: 01/20/2023] Open
Abstract
In this study, we perform a full genome-wide association study (GWAS) to identify statistically significantly associated single nucleotide polymorphisms (SNPs) with three red blood cell (RBC) components and follow it with two independent PheWASs to examine associations between phenotypic data (case-control status of diagnoses or disease), significant SNPs, and RBC component levels. We first identified associations between the three RBC components: mean platelet volume (MPV), mean corpuscular volume (MCV), and platelet counts (PC), and the genotypes of approximately 500,000 SNPs on the Illumina Infimum DNA Human OmniExpress-24 BeadChip using a single cohort of 4,673 Northern Nevadans. Twenty-one SNPs in five major genomic regions were found to be statistically significantly associated with MPV, two regions with MCV, and one region with PC, with p<5x10-8. Twenty-nine SNPs and nine chromosomal regions were identified in 30 previous GWASs, with effect sizes of similar magnitude and direction as found in our cohort. The two strongest associations were SNP rs1354034 with MPV (p = 2.4x10-13) and rs855791 with MCV (p = 5.2x10-12). We then examined possible associations between these significant SNPs and incidence of 1,488 phenotype groups mapped from International Classification of Disease version 9 and 10 (ICD9 and ICD10) codes collected in the extensive electronic health record (EHR) database associated with Healthy Nevada Project consented participants. Further leveraging data collected in the EHR, we performed an additional PheWAS to identify associations between continuous red blood cell (RBC) component measures and incidence of specific diagnoses. The first PheWAS illuminated whether SNPs associated with RBC components in our cohort were linked with other hematologic phenotypic diagnoses or diagnoses of other nature. Although no SNPs from our GWAS were identified as strongly associated to other phenotypic components, a number of associations were identified with p-values ranging between 1x10-3 and 1x10-4 with traits such as respiratory failure, sleep disorders, hypoglycemia, hyperglyceridemia, GERD and IBS. The second PheWAS examined possible phenotypic predictors of abnormal RBC component measures: a number of hematologic phenotypes such as thrombocytopenia, anemias, hemoglobinopathies and pancytopenia were found to be strongly associated to RBC component measures; additional phenotypes such as (morbid) obesity, malaise and fatigue, alcoholism, and cirrhosis were also identified to be possible predictors of RBC component measures.
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Affiliation(s)
- Robert W. Read
- Applied Innovation Center, Renown Institute for Health Innovation, Desert Research Institute, Reno, NV, United States of America
| | - Karen A. Schlauch
- Applied Innovation Center, Renown Institute for Health Innovation, Desert Research Institute, Reno, NV, United States of America
| | - Gai Elhanan
- Applied Innovation Center, Renown Institute for Health Innovation, Desert Research Institute, Reno, NV, United States of America
| | - William J. Metcalf
- Applied Innovation Center, Renown Institute for Health Innovation, Desert Research Institute, Reno, NV, United States of America
| | | | - Ramsey Aweti
- 23andMe, Inc., Mountain View, CA, United States of America
| | | | - Joseph J. Grzymski
- Applied Innovation Center, Renown Institute for Health Innovation, Desert Research Institute, Reno, NV, United States of America
- Renown Health, Reno, NV, United States of America
- * E-mail:
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16
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Reiner AP, Johnson AD. Platelet Genomics. Platelets 2019. [DOI: 10.1016/b978-0-12-813456-6.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Cao Y, Liu H, Xia SL, Zhang X, Bai H, Yang Q, Li J, Gao L, Jin F, Wei MJ, Lu SL, Xiao J. PTEN downregulates WD repeat‑containing protein 66 in salivary adenoid cystic carcinoma. Oncol Rep 2018; 41:1827-1836. [PMID: 30569117 PMCID: PMC6365686 DOI: 10.3892/or.2018.6931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/30/2018] [Indexed: 11/05/2022] Open
Abstract
Salivary adenoid cystic carcinoma (SACC) is one of the most common types of salivary gland cancer that causes substantial morbidity and mortality. Despite the substantial health burden of SACC, the molecular mechanisms underlying its development and progression remain poorly understood. We previously reported the loss of phosphatase and tensin homolog (PTEN) expression to be common among SACC tumors, and the PTEN deficiency to be correlated with enrichment of epithelial-mesenchymal transition (EMT) genes based on expression array analysis. The aim of the present study was to investigate further the functional function of WD repeat-containing protein 66 (WDR66), one of the enriched EMT genes, in the context of PTEN deficiency and SACC pathogenesis. WDR66 was identified to be required to maintain the EMT phenotype and the expression of cancer stem cell genes in the context of PTEN deficiency. Furthermore, knockdown of WDR66 decreased cellular proliferation, migration and invasion. Finally, WDR66 expression was identified to be inversely associated with PTEN expression and negatively correlated with the overall survival of patients with SACC. Collectively, the results of the present study revealed a novel function of WDR66 in mediating the progression of PTEN-deficient SACCs, thereby suggesting WDR66 inhibition to be a potential therapeutic approach towards successful management of SACC disease progression, particularly against tumors with decreased PTEN expression levels.
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Affiliation(s)
- Yu Cao
- Laboratory of Precision Oncology, China Medical University School of Pharmacy, Shenyang, Liaoning 110122, P.R. China
| | - Han Liu
- Department of Oral Pathology, Dental School, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Shi-Lin Xia
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Xi Zhang
- Department of Oral Pathology, Dental School, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Han Bai
- Department of Oral Pathology, Dental School, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Qian Yang
- Department of Oral Pathology, Dental School, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jiang Li
- Department of Oral Pathology, 9th People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Stomatology, Shanghai 200011, P.R. China
| | - Liwei Gao
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Feng Jin
- Department of Surgical Oncology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Min-Jie Wei
- Laboratory of Precision Oncology, China Medical University School of Pharmacy, Shenyang, Liaoning 110122, P.R. China
| | - Shi-Long Lu
- Laboratory of Precision Oncology, China Medical University School of Pharmacy, Shenyang, Liaoning 110122, P.R. China
| | - Jing Xiao
- Department of Oral Pathology, Dental School, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
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Vasudeva K, Munshi A. Genetics of platelet traits in ischaemic stroke: focus on mean platelet volume and platelet count. Int J Neurosci 2018; 129:511-522. [PMID: 30371123 DOI: 10.1080/00207454.2018.1538991] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Purpose/Aim of the study: The aim of this review is to summarize the role of genetic variants affecting mean platelet volume (MPV) and platelet count (PLT) leading to higher platelet reactivity and in turn to thrombotic events like stroke and cardiovascular diseases. MATERIALS AND METHODS A search was conducted in PUBMED, MEDLINE, EMBASE, PROQUEST, Science Direct, Cochrane Library, and Google Scholar related to the studies focussing on genome-wide association studies (GWAS), whole exome sequencing (WES), whole genome sequencing (WGS), phenome-wide association studies (PheWAS) and multi-omic analysis that have been employed to identify the genetic variants influencing MPV and PLT. RESULTS Antiplatelet agents underscore the crucial role of platelets in the pathogenesis of stroke. Higher platelet reactivity in terms of mean platelet volume (MPV) and platelet count (PLT) contributes significantly to the interindividual variation in platelet reaction at the site of vessel wall injury. Some individuals encounter thrombotic events as platelets get occluded at the site of vessel wall injury whereas others heal the injury without occluding the circulation. Evidence suggests that MPV and PLT have a strong genetic component. High throughput techniques including genome-wide association studies (GWAS), whole exome sequencing (WES), whole genome sequencing (WGS), phenome-wide association studies (PheWAS) and multi-omic analysis have identified different genetic variants influencing MPV and PLT. CONCLUSIONS Identification of complex genetic cross talks affecting PLT and MPV might help to develop novel treatment strategies in treating neurovascular diseases like stroke.
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Affiliation(s)
- Kanika Vasudeva
- a Department of Human Genetics and Molecular Medicine , Central University of Punjab Bathinda , Punjab , India
| | - Anjana Munshi
- a Department of Human Genetics and Molecular Medicine , Central University of Punjab Bathinda , Punjab , India
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Fisher MH, Di Paola J. Genomics and transcriptomics of megakaryocytes and platelets: Implications for health and disease. Res Pract Thromb Haemost 2018; 2:630-639. [PMID: 30349880 PMCID: PMC6178711 DOI: 10.1002/rth2.12129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/03/2018] [Indexed: 01/07/2023] Open
Abstract
The field of megakaryocyte and platelet biology has been transformed with the implementation of high throughput sequencing. The use of modern sequencing technologies has led to the discovery of causative mutations in congenital platelet disorders and has been a useful tool in uncovering many other mechanisms of altered platelet formation and function. Although the understanding of the presence of RNA in platelets is relatively novel, mRNA and miRNA expression profiles are being shown to play an increasingly important role in megakaryopoiesis and platelet function in normal physiology as well as in disease states. Understanding the genetic perturbations underlying platelet dysfunction provides insight into normal megakaryopoiesis and thrombopoiesis, as well as guiding the development of novel therapeutics.
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Affiliation(s)
- Marlie H. Fisher
- Department of PediatricsUniversity of Colorado School of MedicineAuroraColorado
- Medical Scientist Training ProgramUniversity of Colorado School of MedicineAuroraColorado
| | - Jorge Di Paola
- Department of PediatricsUniversity of Colorado School of MedicineAuroraColorado
- Medical Scientist Training ProgramUniversity of Colorado School of MedicineAuroraColorado
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20
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Adam AM, Ali MA, Shah AA, Rizvi AH, Rehan A, Godil A, Abbas AH, Durrani NUA, Shaikh AT, Mallick MSA, Lashari MN. Efficacy of Hematological and Coagulation Parameters in the Diagnosis and Prognosis of Patients with Acute Coronary Syndrome. J Tehran Heart Cent 2018; 13:115-125. [PMID: 30745924 PMCID: PMC6368913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background : The diagnosis and management of acute coronary syndrome (ACS) have improved significantly over the past few decades; however, the recognition of myocardial ischemia still proves to be a dilemma for cardiologists. The aim of this study was to determine the role of hematological and coagulation parameters in the diagnosis and prognosis of patients with ACS. Methods: This prospective study recruited 250 patients with ACS and 250 healthy controls. The diagnostic role of hematological and coagulation parameters was assessed by comparing the patients with ACS with the control group. The relationships between these parameters and mortality were determined by dividing the patients into 2 groups: Group A (discharged) and Group B (patients who died within 30 days of follow-up). Multivariate Cox regression analysis was performed to calculate the hazard ratio (HR). Results: The mean age of the patients was 55.14±10.71 years, and 65.2% of them were male. Prothrombin time (P<0.001), activated partial thromboplastin time (P<0.001), mean platelet volume (MPV) (P<0.001), white blood cell (WBC) count (P<0.001), and red blood cell distribution width (RDW) (P<0.001) were significantly higher in the case group than in the control group. WBC count (P<0.001), RDW (P<0.001), and MPV (P<0.001) were significantly higher in the controls than in the case group. The Cox regression model showed that RDW above 16.55% (HR=6.8), MPV greater than 11.25 fL (HR=2.6), and WBC higher than 10.55×103/μL (HR=6.3) were the independent predictors of mortality. Conclusion: In addition to being the independent predictors of short-term mortality, RDW, WBC, and MPV when used together with the coagulation profile may aid in the diagnosis of ACS in patients presenting with chest pain.
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Affiliation(s)
| | | | | | - Ather Hasan Rizvi
- Dow University of Health Sciences (DUHS), Karachi, Pakistan.,Corresponding Author: Ather Hasan Rizvi, Dow University of Health Sciences (DUHS), 149/E, Block 2, PECHS, Karachi, Pakistan. 75400. Tel: +92 3321312467. Fax: +92 3321312467.E-mail: .
| | - Aiman Rehan
- Dow University of Health Sciences (DUHS), Karachi, Pakistan.
| | - Ansab Godil
- Dow University of Health Sciences (DUHS), Karachi, Pakistan.
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21
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Zhou S, Liang X, Wang N, Shao L, Yu W, Liu M. Association of human platelet antigen polymorphisms with platelet count and mean platelet volume. ACTA ACUST UNITED AC 2018; 23:517-521. [PMID: 29486655 DOI: 10.1080/10245332.2018.1445580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVES Although recent genome-wide association studies have identified a number of single nucleotide polymorphisms associated with platelet count and mean platelet volume (MPV), it is unclear whether polymorphisms in the human platelet antigens (HPA) genes are associated with platelet count and MPV. The aim of this study was to determine the association of the HPA-2, -3, -5 and -15 polymorphisms with platelet count and MPV. METHODS The HPA were genotyped by 5'-nuclease assay in 139 healthy Chinese Han individuals, while platelet count and MPV from the same samples were measured using an hematology cell analyzer. RESULTS The platelet count was significantly lower in the individuals with the HPA-2aa genotype compared to those with HPA-2ab (P = 0.020), and significantly higher in individuals with HPA-5aa and HPA-15aa genotypes compared to those with HPA-5ab (P = 0.045) and HPA-15ab/bb (P = 0.032), respectively. On the other hand, platelet count of individuals with the HPA-3aa and HPA-3ab/bb genotypes did not differ significantly (P = 0.084). The MPV was significantly lower in individuals with HPA-5aa genotype compared to those with HPA-5ab (P = 0.001) but did not differ among the HPA-2, -3 and -15 genotypes. Furthermore, HPA-2, -5 and -15 polymorphisms were identified as independent factors for the platelet count and HPA-5 polymorphism was shown as an independent factor for MPV. CONCLUSIONS This study demonstrates that HPA-2, -5 and -15 polymorphisms are associated with the platelet count while HPA-5 polymorphism is associated with MPV. This finding will further our understanding of the association of HPA polymorphisms with platelet-related diseases.
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Affiliation(s)
- Shihang Zhou
- a Dalian Blood Center , Dalian , People's Republic of China
| | - Xiaohua Liang
- a Dalian Blood Center , Dalian , People's Republic of China
| | - Ni Wang
- a Dalian Blood Center , Dalian , People's Republic of China
| | - Linnan Shao
- a Dalian Blood Center , Dalian , People's Republic of China
| | - Weijian Yu
- a Dalian Blood Center , Dalian , People's Republic of China
| | - Ming Liu
- b Department of Cell Biology , Dalian Medical University , Dalian , People's Republic of China
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Laffan M. Ein genomweiter Ansatz bei Thrombozyten-und Gerinnungsstörungen. Hamostaseologie 2017; 36:161-6. [DOI: 10.5482/hamo-14-11-0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/13/2015] [Indexed: 11/05/2022] Open
Abstract
ZusammenfassungDie Sequenzierung von hunderttausenden menschlichen Exomen und Gesamtgenomen bietet einen immer genaueren und vollständigeren Katalog menschlicher Genvarianten. Die ersten Studien zum Verständnis von Thrombozytenstörungen anhand von genomweiten Daten wurden als genomweite Assoziationsstudien durchgeführt, in denen Loci identifiziert wurden, die mit Variationen der Blutzellparameter assoziiert sind. In diesen Studien wurden Norm-varianten genutzt, um die entsprechenden genetische Variation zu finden. Als nächstes wollten wir die genetische Grundlage von Gerinnungsstörungen untersuchen, die einen Schlüssel für neue Gene liefern könnte, welche Thrombozyten- und Gerinnungsfunktionen steuern. Das BRIDGE-Konsortium (www.bridgestudy. org) wird vom NIHR finanziert und bringt 13 Genforschungsprojekte zu seltenen Krankheiten zusammen. Ziel dieser Projekte ist die Erforschung bislang unterdiagnostizierter seltener Erbkrankheiten und die Identifizierung der zugrunde liegenden Mutationen. Wir verwendeten eine Cluster-Analyse, basierend auf der Human Phenotype Ontology, kombiniert mit Next-Generation Sequenzierungstechniken, um Patienten mit ähnlichen Phänotypen, die vermutlich aus den gleichen Gendefekten hervorgehen, leichter zu identifizieren. Vorläufige Ergebnisse bestätigen dieses Vorgehen in Clustern und ergaben auch eine Reihe neuer Gene, die für die normale und die pathologische Thrombozytenphysiologie wichtig sind.
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Arbesu I, Jilma B, Maurer G, Lang IM, Mannhalter C, Siller-Matula JM. Association between the rs342293 polymorphism and adverse cardiac events in patients undergoing percutaneous coronary intervention. Thromb Haemost 2017; 111:1060-6. [DOI: 10.1160/th13-09-0757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/16/2014] [Indexed: 01/05/2023]
Abstract
SummaryThe single nucleotide polymorphism (SNP) rs342293 has been shown to influence platelet number and mean platelet volume (MPV). We investigated the association between the rs342293 polymorphism and cardiovascular outcome in a prospective cohort study. The rs342293 polymorphism was analysed in 404 patients with coronary artery disease undergoing percutaneous coronary intervention. The rates of cardiac adverse events were recorded during two years of follow-up. The polymorphism was associated with MPV (median 10.1 fL, interquartile range [IQR]: 9.6 to 10.6 in patients with the CC-allele vs 10.4 fL, IQR: 9.9 to 11.1 in G>C SNP carriers; p<0.001), but not with platelet count. Survival analysis indicated that carriers of the rs342293 G variant had a substantially higher risk to develop cardiac adverse events compared with wild type carriers during two years of follow-up (33% vs 22%; adjusted hazard ratio = 1.63, 95% confidence interval = 1.06–2.52, p=0.027). The rs342293 SNP could explain 2.9% of the variability in MPV (p=0.01). In conclusion, patients undergoing coronary stenting who carry the G-variant of the rs342293 SNP which is associated with larger MPV are at higher risk for adverse cardiovascular outcome.
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Christiansen MK, Larsen SB, Nyegaard M, Neergaard-Petersen S, Würtz M, Grove EL, Hvas AM, Jensen HK, Kristensen SD. The SH2B3 and KCNK5 loci may be implicated in regulation of platelet count, volume, and maturity. Thromb Res 2017; 158:86-92. [PMID: 28865245 DOI: 10.1016/j.thromres.2017.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/21/2017] [Accepted: 08/17/2017] [Indexed: 01/11/2023]
Abstract
INTRODUCTION In recent genome-wide association studies, coronary artery disease (CAD) and myocardial infarction (MI) have been linked to a number of genetic variants, but their role in thrombopoiesis is largely unknown. AIM We investigated the association between CAD and MI-associated genetic variants and five thrombopoiesis-related indices: platelet count (PC), mean platelet volume (MPV), immature platelet count (IPC), immature platelet fraction (IPF), and serum thrombopoietin (TPO). METHODS We genotyped 45 genome-wide significant CAD/MI-markers in 879 stable CAD patients. A genetic risk score was calculated to assess the combined risk associated with all the genetic variants. Platelet indices were analysed using the Sysmex XE-2100 haematology analyser. TPO was measured by ELISA. RESULTS Two variants were nominally associated with several indices; for rs10947789 (KCNK5), the adjusted geometric mean was 2% higher for MPV (95% confidence interval: 1-2%, p=0.002), 6% for IPC (0-12%, p=0.033), and 9% for IPF (3-16%, p=0.004) per CAD risk allele. Moreover, an 11% lower TPO (3-19%, p=0.010) was observed. Rs3184504 (SH2B3) was associated with a higher adjusted geometric mean of 3% (1-6%, p=0.003) per CAD risk allele for PC, and an 11% (5-17%, p<0.001) lower TPO. Furthermore, the adjusted IPC was 5% (0-9%, p=0.037) lower per CAD risk allele for PC, whereas IPF levels did not vary across genotypes. CONCLUSION As a novel finding, our study suggests a role for KCNK5 in the regulation of platelet size and maturity. Furthermore, our findings confirm an association between the SH2B3-locus and platelet count.
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Affiliation(s)
- Morten K Christiansen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sanne B Larsen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark.
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Morten Würtz
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Erik L Grove
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Anne-Mette Hvas
- Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik K Jensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Steen D Kristensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark; Faculty of Health, Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Abstract
The last decade has witnessed an explosion in the depth, variety, and amount of human genetic data that can be generated. This revolution in technical and analytical capacities has enabled the genetic investigation of human traits and disease in thousands to now millions of participants. Investigators have taken advantage of these advancements to gain insight into platelet biology and the platelet's role in human disease. To do so, large human genetics studies have examined the association of genetic variation with two quantitative traits measured in many population and patient based cohorts: platelet count (PLT) and mean platelet volume (MPV). This article will review the many human genetic strategies-ranging from genome-wide association study (GWAS), Exomechip, whole exome sequencing (WES), to whole genome sequencing (WGS)-employed to identify genes and variants that contribute to platelet traits. Additionally, we will discuss how these investigations have examined and interpreted the functional implications of these newly identified genetic factors and whether they also impart risk to human disease. The depth and size of genetic, phenotypic, and other -omic data are primed to continue their growth in the coming years and provide unprecedented opportunities to gain critical insights into platelet biology and how platelets contribute to disease.
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Affiliation(s)
- John D Eicher
- a Population Sciences Branch , National Heart Lung and Blood Institute, The Framingham Heart Study , Framingham , MA , USA
| | - Guillaume Lettre
- b Department of Medicine , Université de Montréal , Montréal , Québec , Canada.,c Montreal Heart Institute , Montréal , Québec , Canada
| | - Andrew D Johnson
- a Population Sciences Branch , National Heart Lung and Blood Institute, The Framingham Heart Study , Framingham , MA , USA
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SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume. PLoS One 2017; 12:e0178095. [PMID: 28542600 PMCID: PMC5441597 DOI: 10.1371/journal.pone.0178095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 05/07/2017] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation. We show that the SNP (rs1354034) is located in a DNase I hypersensitive region in human MKs and is an expression quantitative locus (eQTL) associated with ARHGEF3 expression level in human platelets, suggesting that it may be the causal SNP that accounts for the variations observed in human platelet traits and ARHGEF3 expression. In vitro human platelet activation assays revealed that rs1354034 is highly correlated with human platelet activation by ADP. In order to test whether ARHGEF3 plays a role in MK development and/or platelet function, we developed an Arhgef3 KO/LacZ reporter mouse model. Reflecting changes in gene expression, LacZ expression increases during MK maturation in these mice. Although Arhgef3 KO mice have significantly larger platelets, loss of Arhgef3 does not affect baseline MK or platelets nor does it affect platelet function or platelet recovery in response to antibody-mediated platelet depletion compared to littermate controls. In summary, our data suggest that modulation of ARHGEF3 gene expression in humans with a promoter-localized SNP plays a role in human MKs and human platelet function—a finding resulting from the biological follow-up of human genetic studies. Arhgef3 KO mice partially recapitulate the human phenotype.
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27
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Pleines I, Woods J, Chappaz S, Kew V, Foad N, Ballester-Beltrán J, Aurbach K, Lincetto C, Lane RM, Schevzov G, Alexander WS, Hilton DJ, Astle WJ, Downes K, Nurden P, Westbury SK, Mumford AD, Obaji SG, Collins PW, Delerue F, Ittner LM, Bryce NS, Holliday M, Lucas CA, Hardeman EC, Ouwehand WH, Gunning PW, Turro E, Tijssen MR, Kile BT. Mutations in tropomyosin 4 underlie a rare form of human macrothrombocytopenia. J Clin Invest 2017; 127:814-829. [PMID: 28134622 PMCID: PMC5330761 DOI: 10.1172/jci86154] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/01/2016] [Indexed: 01/12/2023] Open
Abstract
Platelets are anuclear cells that are essential for blood clotting. They are produced by large polyploid precursor cells called megakaryocytes. Previous genome-wide association studies in nearly 70,000 individuals indicated that single nucleotide variants (SNVs) in the gene encoding the actin cytoskeletal regulator tropomyosin 4 (TPM4) exert an effect on the count and volume of platelets. Platelet number and volume are independent risk factors for heart attack and stroke. Here, we have identified 2 unrelated families in the BRIDGE Bleeding and Platelet Disorders (BPD) collection who carry a TPM4 variant that causes truncation of the TPM4 protein and segregates with macrothrombocytopenia, a disorder characterized by low platelet count. N-Ethyl-N-nitrosourea–induced (ENU-induced) missense mutations in Tpm4 or targeted inactivation of the Tpm4 locus led to gene dosage–dependent macrothrombocytopenia in mice. All other blood cell counts in Tpm4-deficient mice were normal. Insufficient TPM4 expression in human and mouse megakaryocytes resulted in a defect in the terminal stages of platelet production and had a mild effect on platelet function. Together, our findings demonstrate a nonredundant role for TPM4 in platelet biogenesis in humans and mice and reveal that truncating variants in TPM4 cause a previously undescribed dominant Mendelian platelet disorder.
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Affiliation(s)
- Irina Pleines
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Joanne Woods
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephane Chappaz
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Verity Kew
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nicola Foad
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - José Ballester-Beltrán
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Katja Aurbach
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Center, University of Wuerzburg, Wuerzburg, Germany
| | - Chiara Lincetto
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Rachael M. Lane
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Galina Schevzov
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Warren S. Alexander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Douglas J. Hilton
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - William J. Astle
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Paquita Nurden
- Institut Hospitalo-Universitaire LIRYC, Plateforme Technologique d’Innovation Biomédicale, Hôpital Xavier Arnozan, Pessac, France
| | - Sarah K. Westbury
- School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Samya G. Obaji
- Arthur Bloom Haemophilia Centre, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Peter W. Collins
- Arthur Bloom Haemophilia Centre, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - NIHR BioResource
- NIHR BioResource–Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Fabien Delerue
- Transgenic Animal Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Lars M. Ittner
- Transgenic Animal Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Nicole S. Bryce
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Mira Holliday
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Christine A. Lucas
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Edna C. Hardeman
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource–Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Peter W. Gunning
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom
| | - Marloes R. Tijssen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Benjamin T. Kile
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
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Abstract
Taken together, there is ample evidence of the association of cardiovascular disease, cerebrovascular, and inflammatory disease with single nucleotide variants (SNV) due to their impact on platelet size, number, and function. With the use of electronic medical record (EMR) or other phenotypic-linked bioinformatics sources, the more important "functional" variants are emerging and provide valuable information on their specific role in promoting early onset of disease or poor response to therapeutic measures. This review will focus upon the recognized common polymorphisms or gene variants with small, but functional effects, as it is becoming clear that these contribute to hyper- or hypo-responsive platelet phenotypes. The impact of these gene variants is distinguishable among normal individuals, and they are suspected contributors to increased risk of adverse outcomes in patients with underlying disease. There are thousands of gene variants and environmental factors that may mitigate risk or amplify the potential for disease within each of us. When combined with the environment and epigenetic influences, it is clear that whole-genome sequencing and bioinformatics alone will not be enough to truly predict "risk" or probability, but awareness of their potential influence may be a starting point in selective screening and generating prevention strategies to promote a healthy lifestyle or fine-tune therapeutic choices in the future.
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Affiliation(s)
- Diane Nugent
- a Hematology Advanced Diagnostic Laboratory , CHOC Children's Hospital , Orange , CA , USA.,b Center for Inherited Blood Disorders , Orange , CA.,c UC Irvine Medical School , Irvine , CA , USA
| | - Thomas Kunicki
- a Hematology Advanced Diagnostic Laboratory , CHOC Children's Hospital , Orange , CA , USA.,b Center for Inherited Blood Disorders , Orange , CA.,c UC Irvine Medical School , Irvine , CA , USA
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Identification of ITGA2B and ITGB3 Single-Nucleotide Polymorphisms and Their Influences on the Platelet Function. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5675084. [PMID: 27965976 PMCID: PMC5124636 DOI: 10.1155/2016/5675084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
The aim of the study was to investigate ITGA2B and ITGB3 genetic polymorphisms and to evaluate the variability in the platelet function in healthy Chinese subjects. The genetic sequence of the entire coding region of the ITGA2B and ITGB3 genes was investigated. Adenosine diphosphate-induced platelet aggregation, glycoprotein IIb/IIIa content, bleeding time, and coagulation indexes were detected. Thirteen variants in the ITGA2B locus and 29 variants in the ITGB3 locus were identified in the Chinese population. The rs1009312 and rs2015049 were associated with the mean platelet volume. The rs70940817 was significantly correlated with the prothrombin time. The rs70940817 and rs112188890 were related with the activated partial thromboplastin time, and ITGB3 rs4642 was correlated with the thrombin time and fibrinogen. The minor alleles of rs56197296 and rs5919 were associated with decreased ADP-induced platelet aggregation, and rs55827077 was related with decreased GPIIb/IIIa per platelet. The rs1009312, rs2015049, rs3760364, rs567581451, rs7208170, and rs117052258 were related with bleeding time. Further studies are needed to explore the clinical importance of ITGA2B and ITGB3 SNPs in the platelet function.
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Vasquez LJ, Mann AL, Chen L, Soranzo N. From GWAS to function: lessons from blood cells. ISBT SCIENCE SERIES 2016; 11:211-219. [PMID: 27347004 PMCID: PMC4916502 DOI: 10.1111/voxs.12217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Haematopoiesis, or the process of formation of mature blood cells from committed progenitors, represents an accessible and well-studied paradigm of cell differentiation and lineage specification. Genetic association studies provide a powerful approach to discover new genes, biological pathways and mechanisms underlying haematopoietic development. Here, we highlight recent findings of genomewide association studies (GWAS) linking 145 genomic loci to traits affecting the formation of red and white cells and platelets in European and other ancestries. We present strategies to address the main challenges in GWAS discoveries, particularly to find functional and regulatory effects of genetic variants, and to identify genes through which these genetic variants affect haematological phenotypes. We argue that studies of haematological trait variation provide an ideal paradigm for understanding the function of GWAS-associated variants owing to the accessible nature of cells, simple cellular phenotype and focused efforts to characterize the genetic and epigenetic factors influencing the regulatory landscape in highly pure mature cell populations.
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Affiliation(s)
- L J Vasquez
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK
| | - A L Mann
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK
| | - L Chen
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK; Department of Haematology University of Cambridge Cambridge Biomedical Campus Cambridge UK
| | - N Soranzo
- Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton UK; Department of Haematology University of Cambridge Cambridge Biomedical Campus Cambridge UK
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31
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Eicher JD, Wakabayashi Y, Vitseva O, Esa N, Yang Y, Zhu J, Freedman JE, McManus DD, Johnson AD. Characterization of the platelet transcriptome by RNA sequencing in patients with acute myocardial infarction. Platelets 2015; 27:230-9. [PMID: 26367242 DOI: 10.3109/09537104.2015.1083543] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Transcripts in platelets are largely produced in precursor megakaryocytes but remain physiologically active as platelets translate RNAs and regulate protein/RNA levels. Recent studies using transcriptome sequencing (RNA-seq) characterized the platelet transcriptome in limited number of non-diseased individuals. Here, we expand upon these RNA-seq studies by completing RNA-seq in platelets from 32 patients with acute myocardial infarction (MI). Our goals were to characterize the platelet transcriptome using a population of patients with acute MI and relate gene expression to platelet aggregation measures and ST-segment elevation MI (STEMI) (n = 16) vs. non-STEMI (NSTEMI) (n = 16) subtypes. Similar to other studies, we detected 9565 expressed transcripts, including several known platelet-enriched markers (e.g. PPBP, OST4). Our RNA-seq data strongly correlated with independently ascertained platelet expression data and showed enrichment for platelet-related pathways (e.g. wound response, hemostasis, and platelet activation), as well as actin-related and post-transcriptional processes. Several transcripts displayed suggestively higher (FBXL4, ECHDC3, KCNE1, TAOK2, AURKB, ERG, and FKBP5) and lower (MIAT, PVRL3, and PZP) expression in STEMI platelets compared to NSTEMI. We also identified transcripts correlated with platelet aggregation to TRAP (ATP6V1G2, SLC2A3), collagen (CEACAM1, ITGA2), and ADP (PDGFB, PDGFC, ST3GAL6). Our study adds to current platelet gene expression resources by providing transcriptome-wide analyses in platelets isolated from patients with acute MI. In concert with prior studies, we identify various genes for further study in regards to platelet function and acute MI. Future platelet RNA-seq studies examining more diverse sets of healthy and diseased samples will add to our understanding of platelet thrombotic and non-thrombotic functions.
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Affiliation(s)
- John D Eicher
- a The Framingham Heart Study , Framingham , MA , USA .,b National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch , Bethesda , MD , USA
| | - Yoshiyuki Wakabayashi
- c National Heart, Lung, and Blood Institute, Division of Intramural Research, DNA Sequencing and Genomics Core Laboratory , Bethesda , MD , USA
| | - Olga Vitseva
- d Department of Medicine, Division of Cardiovascular Medicine , University of Massachusetts Medical School , Worcester , MA , USA , and
| | - Nada Esa
- e Memorial Heart and Vascular Center, University of Massachusetts , Worcester , MA , USA
| | - Yanqin Yang
- c National Heart, Lung, and Blood Institute, Division of Intramural Research, DNA Sequencing and Genomics Core Laboratory , Bethesda , MD , USA
| | - Jun Zhu
- c National Heart, Lung, and Blood Institute, Division of Intramural Research, DNA Sequencing and Genomics Core Laboratory , Bethesda , MD , USA
| | - Jane E Freedman
- e Memorial Heart and Vascular Center, University of Massachusetts , Worcester , MA , USA
| | - David D McManus
- e Memorial Heart and Vascular Center, University of Massachusetts , Worcester , MA , USA
| | - Andrew D Johnson
- a The Framingham Heart Study , Framingham , MA , USA .,b National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch , Bethesda , MD , USA
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Kirsten H, Al-Hasani H, Holdt L, Gross A, Beutner F, Krohn K, Horn K, Ahnert P, Burkhardt R, Reiche K, Hackermüller J, Löffler M, Teupser D, Thiery J, Scholz M. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†. Hum Mol Genet 2015; 24:4746-63. [PMID: 26019233 PMCID: PMC4512630 DOI: 10.1093/hmg/ddv194] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/21/2015] [Indexed: 12/24/2022] Open
Abstract
Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait-associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters and enrichment of co-localized functional elements. We found eQTLs for about 85% of analysed genes, and 18% of genes were trans-regulated. Local eSNPs were enriched up to a distance of 5 Mb to the transcript challenging typically implemented ranges of cis-regulations. Pathway enrichment within regulated genes of GWAS-related eSNPs supported functional relevance of identified eQTLs. We demonstrate that nearest genes of GWAS-SNPs might frequently be misleading functional candidates. We identified novel trans-clusters of potential functional relevance for GWAS-SNPs of several phenotypes including obesity-related traits, HDL-cholesterol levels and haematological phenotypes. We used chromatin immunoprecipitation data for demonstrating biological effects. Yet, we show for strongly heritable transcripts that still little trans-chromosomal heritability is explained by all identified trans-eSNPs; however, our data suggest that most cis-heritability of these transcripts seems explained. Dissection of co-localized functional elements indicated a prominent role of SNPs in loci of pseudogenes and non-coding RNAs for the regulation of coding genes. In summary, our study substantially increases the catalogue of human eQTLs and improves our understanding of the complex genetic regulation of gene expression, pathways and disease-related processes.
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Affiliation(s)
- Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases, Cognitive Genetics, Department of Cell Therapy
| | - Hoor Al-Hasani
- Department for Computer Science, Analysis Strategies Group, Department of Diagnostics, Young Investigators Group Bioinformatics and Transcriptomics, Department Proteomics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany and
| | - Lesca Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Arnd Gross
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases
| | - Frank Beutner
- LIFE - Leipzig Research Center for Civilization Diseases, Department of Internal Medicine/Cardiology, Heart Center
| | - Knut Krohn
- Interdisciplinary Center for Clinical Research, Faculty of Medicine and
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases
| | - Ralph Burkhardt
- LIFE - Leipzig Research Center for Civilization Diseases, Institute of Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Kristin Reiche
- Department for Computer Science, RNomics Group, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology- IZI, Leipzig, Germany, Young Investigators Group Bioinformatics and Transcriptomics, Department Proteomics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany and
| | - Jörg Hackermüller
- Department for Computer Science, RNomics Group, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology- IZI, Leipzig, Germany, Young Investigators Group Bioinformatics and Transcriptomics, Department Proteomics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany and
| | - Markus Löffler
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases
| | - Daniel Teupser
- Institute of Laboratory Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Joachim Thiery
- LIFE - Leipzig Research Center for Civilization Diseases, Institute of Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, LIFE - Leipzig Research Center for Civilization Diseases,
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Olteanu AL, Mihaila RG, Catana AC, Flucus O, Bus C, Mihalache M. Platelet indices in Philadelphia-negative chronic myeloproliferative neoplasms / Indicii plachetari de volum în neoplasmele mieloproliferative cronice Philadelphia-negative. REV ROMANA MED LAB 2015. [DOI: 10.1515/rrlm-2015-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractIntroduction: Philadelphia-negative chronic myeloproliferative neoplasms (Ph-MPN): polycythemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) are characterized by an increased rate of thrombosis complications partly due to platelets activation. Large platelets are more active, have an enhanced procoagulant function and have a pathogenic role in arterial and venous thrombosis. In our study we tried to establish if platelet volume indices (MPV, PDW, P-LCR) issued from automated complete blood count determination are significantly different in Ph-MPN patients in comparison to healthy subjects. Materials and methods: Blood cell counts including platelet volume indices were assessed for 102 Ph-MPN and 102 healthy subjects using the impedance method on Sysmex XS 1000i and glucose and lipid profile, were assessed on Architect c 8000. Assessement of JAK2V617 positivity was conducted with amplification refractory mutation system polymerase chain reaction (ARMS-PCR), in whole peripheral blood. Results: Platelet volume indices (PVI) measured with the impedance based method, did not show significant differences in Ph-MPN patients in comparison to healthy controls. We noticed a moderate correlation between these indices and the presence of JAK2V617F mutation. PVI were increased in the small subgroup of patients treated with anagrelide and decreased in patients treated with simvastatin, comparatively with untreated patients. Conclusion: In our study we did not find a significant difference between platelet volume indices from Ph-MPN patients and healthy subjects. Further studies are required to demonstrate correlations between platelet volume indices and JAK2 V617F mutation, treatment with anagrelide and statins, respectively
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Lin DY, Tao R, Kalsbeek W, Zeng D, Gonzalez F, Fernández-Rhodes L, Graff M, Koch G, North K, Heiss G. Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos. Am J Hum Genet 2014; 95:675-88. [PMID: 25480034 DOI: 10.1016/j.ajhg.2014.11.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/11/2014] [Indexed: 12/27/2022] Open
Abstract
The cohort design allows investigators to explore the genetic basis of a variety of diseases and traits in a single study while avoiding major weaknesses of the case-control design. Most cohort studies employ multistage cluster sampling with unequal probabilities to conveniently select participants with desired characteristics, and participants from different clusters might be genetically related. Analysis that ignores the complex sampling design can yield biased estimation of the genetic association and inflation of the type I error. Herein, we develop weighted estimators that reflect unequal selection probabilities and differential nonresponse rates, and we derive variance estimators that properly account for the sampling design and the potential relatedness of participants in different sampling units. We compare, both analytically and numerically, the performance of the proposed weighted estimators with unweighted estimators that disregard the sampling design. We demonstrate the usefulness of the proposed methods through analysis of MetaboChip data in the Hispanic Community Health Study/Study of Latinos, which is the largest health study of the Hispanic/Latino population in the United States aimed at identifying risk factors for various diseases and determining the role of genes and environment in the occurrence of diseases. We provide guidelines on the use of weighted and unweighted estimators, as well as the relevant software.
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Analysis of indel variations in the human disease-associated genes CDKN2AIP, WDR66, USP20 and OR7C2 in a Korean population. J Genet 2014. [DOI: 10.1007/s12041-012-0129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Freyburger G, Labrouche S, Hubert C, Bauduer F. Haemostaseome-associated SNPs: has the thrombotic phenotype a greater influence than ethnicity? GMT study from Aquitaine including Basque individuals. Thromb Haemost 2014; 113:66-76. [PMID: 25374097 DOI: 10.1160/th14-02-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/15/2014] [Indexed: 11/05/2022]
Abstract
The Genetic Markers for Thrombosis (GMT) study compared the relative influence of ethnicity and thrombotic phenotype regarding the distribution of SNPs implicated in haemostasis pathophysiology ("haemostaseome"). We assessed 384 SNPs in three groups, each of 480 subjects: 1) general population of Aquitaine region (Southwestern France) used as control; 2) patients with venous thromboembolism from the same area; and 3) autochthonous Basques, a genetic isolate, who demonstrate unusual characteristics regarding the coagulation system. This study sought to evaluate i) the value of looking for a large number of genes in order to identify new genetic markers of thrombosis, ii) the value of investigating low risk factors and potential preferential associations, iii) the impact of ethnicity on the characterisation of markers for thrombosis. We did not detect any previously unrecognised SNP significantly associated with thrombosis risk or any preferential associations of low-risk factors in patients with thrombosis. The sum of ϰ² values for our 110 significant SNPs demonstrated a smaller genetic distance between patients and controls (321 cumulated ϰ² value) than between Basques and controls (1,570 cumulated ϰ² value). Hence, our study confirms the genetic particularity of Basques especially regarding a significantly lower expression of the non-O blood group (p< 0.0004). This is mitigated by a higher prevalence of factor II Leiden (p< 0.02) while factor V Leiden prevalence does not differ. Numerous other differences covering a wide range of proteins of the haemostaseome may result in an overall different genetic risk for venous thromboembolism.
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Affiliation(s)
- Geneviève Freyburger
- Geneviève Freyburger, Laboratory for Hematology, CHU Pellegrin, 33076 Bordeaux cedex, France, Tel.: +335 57 820 206, Fax: +335 56 79 60 20, E-mail:
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Cvejic A. From genome-wide association study hits to new insights into experimental hematology. Exp Hematol 2014; 42:630-6. [PMID: 24746874 DOI: 10.1016/j.exphem.2014.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 03/30/2014] [Accepted: 04/05/2014] [Indexed: 11/22/2022]
Abstract
Despite significant improvements in our knowledge of the mechanisms of normal and pathological hematopoiesis, our current understanding is most likely an oversimplification of the complexity of regulatory networks at play. Thus, considerable efforts have been made to catalogue the total sum of germline alterations in individual genomes affecting human hematopoiesis. These efforts ultimately led to the discovery of a large number of new genes not previously implicated in blood formation. Although identification of novel genes is important in revealing the profiles of genetic variations associated with normal hematopoiesis, further functional studies are necessary to improve our understanding of the mechanism(s) involved in these processes. In this review, we summarize the knowledge gained from genome-wide association studies to elucidate the relationship between genetics and blood cell traits. We discuss the most important recent advances, with an emphasis on functional follow-up studies that have been particularly useful in providing an insight into novel regulatory processes that influence blood cell formation and function. We also discuss potential future directions and challenges in the field.
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Affiliation(s)
- Ana Cvejic
- Department of Haematology, University of Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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Stratmann B, Xu T, Meisinger C, Menart B, Roden M, Herder C, Grallert H, Peters A, Koenig W, Illig T, Wichmann HE, Wang-Sattler R, Rathmann W, Tschoepe D. PLA1A2 platelet polymorphism predicts mortality in prediabetic subjects of the population based KORA S4-Cohort. Cardiovasc Diabetol 2014; 13:90. [PMID: 24886443 PMCID: PMC4022397 DOI: 10.1186/1475-2840-13-90] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/28/2014] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE The genetic polymorphism concerning the ß3-subunit of platelet integrin receptor glycoprotein IIIa is held responsible for enhanced binding of adhesive proteins resulting in increased thrombogenic potential. Whether it is associated with mortality, HbA1c or platelet volume is tested prospectively in an epidemiological cohort. RESEARCH DESIGN AND METHODS Population-based Cooperative Health Research in the Region of Augsburg (KORA) S4-Survey (N = 4,028) was investigated for prognostic value of PLA1A2-polymorphism regarding all-cause mortality, correlation with HbA1c, and mean platelet volume. Multivariate analysis was performed to investigate association between genotype and key variables. RESULTS Prevalence of thrombogenic allele variant PLA2 was 15.0%. Multivariate analysis revealed no association between PLA1A2 polymorphism and mortality in the KORA-cohort. HbA1c was a prognostic marker of mortality in non-diabetic persons resulting in J-shaped risk curve with dip at HbA1c = 5.5% (37 mmol/mol), confirming previous findings regarding aged KORA-S4 participants (55-75 years). PLA1A2 was significantly associated with elevated HbA1c levels in diabetic patients (N = 209) and reduced mean platelet volume in general population. In non-diabetic participants (N = 3,819), carriers of PLA2 allele variant presenting with HbA1c > 5.5% (37 mmol/mol) showed higher relative risk of mortality with increasing HbA1c. CONCLUSION PLA1A2 polymorphism is associated with mortality in participants with HbA1c ranging from 5.5% (37 mmol/mol) to 6.5% (48 mmol/mol). Maintenance of euglycemic control and antiplatelet therapy are therefore regarded as effective primary prevention in this group.
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Affiliation(s)
- Bernd Stratmann
- Heart and Diabetes Center NRW, Ruhr University Bochum, Georgstr. 11, D-32545 Bad Oeynhausen, Germany
| | - Tao Xu
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
| | - Barbara Menart
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Duesseldorf, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Duesseldorf, Germany
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Duesseldorf, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
| | - Wolfgang Koenig
- Department Internal Medicine II, University Clinic Ulm, Ulm, Germany
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Heinz-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center of Environmental Health, Neuherberg, Germany
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Duesseldorf, Germany
| | - Diethelm Tschoepe
- Heart and Diabetes Center NRW, Ruhr University Bochum, Georgstr. 11, D-32545 Bad Oeynhausen, Germany
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Schramm K, Marzi C, Schurmann C, Carstensen M, Reinmaa E, Biffar R, Eckstein G, Gieger C, Grabe HJ, Homuth G, Kastenmüller G, Mägi R, Metspalu A, Mihailov E, Peters A, Petersmann A, Roden M, Strauch K, Suhre K, Teumer A, Völker U, Völzke H, Wang-Sattler R, Waldenberger M, Meitinger T, Illig T, Herder C, Grallert H, Prokisch H. Mapping the genetic architecture of gene regulation in whole blood. PLoS One 2014; 9:e93844. [PMID: 24740359 PMCID: PMC3989189 DOI: 10.1371/journal.pone.0093844] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/07/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND We aimed to assess whether whole blood expression quantitative trait loci (eQTLs) with effects in cis and trans are robust and can be used to identify regulatory pathways affecting disease susceptibility. MATERIALS AND METHODS We performed whole-genome eQTL analyses in 890 participants of the KORA F4 study and in two independent replication samples (SHIP-TREND, N = 976 and EGCUT, N = 842) using linear regression models and Bonferroni correction. RESULTS In the KORA F4 study, 4,116 cis-eQTLs (defined as SNP-probe pairs where the SNP is located within a 500 kb window around the transcription unit) and 94 trans-eQTLs reached genome-wide significance and overall 91% (92% of cis-, 84% of trans-eQTLs) were confirmed in at least one of the two replication studies. Different study designs including distinct laboratory reagents (PAXgene™ vs. Tempus™ tubes) did not affect reproducibility (separate overall replication overlap: 78% and 82%). Immune response pathways were enriched in cis- and trans-eQTLs and significant cis-eQTLs were partly coexistent in other tissues (cross-tissue similarity 40-70%). Furthermore, four chromosomal regions displayed simultaneous impact on multiple gene expression levels in trans, and 746 eQTL-SNPs have been previously reported to have clinical relevance. We demonstrated cross-associations between eQTL-SNPs, gene expression levels in trans, and clinical phenotypes as well as a link between eQTLs and human metabolic traits via modification of gene regulation in cis. CONCLUSIONS Our data suggest that whole blood is a robust tissue for eQTL analysis and may be used both for biomarker studies and to enhance our understanding of molecular mechanisms underlying gene-disease associations.
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Affiliation(s)
- Katharina Schramm
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, München, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Maren Carstensen
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), partner site Düsseldorf, Germany
| | - Eva Reinmaa
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Reiner Biffar
- Department of Prosthetic Dentistry, Gerostomatology and Dental Materials, University Medicine Greifswald, Greifswald, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, University Medicine of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Gabriele Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Annette Peters
- Institute of Human Genetics, Technical University Munich, München, Germany
| | - Astrid Petersmann
- Institute of Clinical Chemistry and Laboratory Medicine, Greifswald, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), partner site Düsseldorf, Germany
- Division of Endocrinology and Diabetology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität Munich, Neuherberg, Germany
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, München, Germany
- Munich Heart Alliance, München, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), partner site Düsseldorf, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, München, Germany
- * E-mail:
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Chami N, Lettre G. Lessons and Implications from Genome-Wide Association Studies (GWAS) Findings of Blood Cell Phenotypes. Genes (Basel) 2014; 5:51-64. [PMID: 24705286 PMCID: PMC3978511 DOI: 10.3390/genes5010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/03/2014] [Accepted: 01/20/2014] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified reproducible genetic associations with hundreds of human diseases and traits. The vast majority of these associated single nucleotide polymorphisms (SNPs) are non-coding, highlighting the challenge in moving from genetic findings to mechanistic and functional insights. Nevertheless, large-scale (epi)genomic studies and bioinformatic analyses strongly suggest that GWAS hits are not randomly distributed in the genome but rather pinpoint specific biological pathways important for disease development or phenotypic variation. In this review, we focus on GWAS discoveries for the three main blood cell types: red blood cells, white blood cells and platelets. We summarize the knowledge gained from GWAS of these phenotypes and discuss their possible clinical implications for common (e.g., anemia) and rare (e.g., myeloproliferative neoplasms) human blood-related diseases. Finally, we argue that blood phenotypes are ideal to study the genetics of complex human traits because they are fully amenable to experimental testing.
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Affiliation(s)
- Nathalie Chami
- Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada.
| | - Guillaume Lettre
- Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada.
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41
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Shameer K, Denny JC, Ding K, Jouni H, Crosslin DR, de Andrade M, Chute CG, Peissig P, Pacheco JA, Li R, Bastarache L, Kho AN, Ritchie MD, Masys DR, Chisholm RL, Larson EB, McCarty CA, Roden DM, Jarvik GP, Kullo IJ. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Hum Genet 2014; 133:95-109. [PMID: 24026423 PMCID: PMC3880605 DOI: 10.1007/s00439-013-1355-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/22/2013] [Indexed: 12/21/2022]
Abstract
Platelets are enucleated cell fragments derived from megakaryocytes that play key roles in hemostasis and in the pathogenesis of atherothrombosis and cancer. Platelet traits are highly heritable and identification of genetic variants associated with platelet traits and assessing their pleiotropic effects may help to understand the role of underlying biological pathways. We conducted an electronic medical record (EMR)-based study to identify common variants that influence inter-individual variation in the number of circulating platelets (PLT) and mean platelet volume (MPV), by performing a genome-wide association study (GWAS). We characterized genetic variants associated with MPV and PLT using functional, pathway and disease enrichment analyses; we assessed pleiotropic effects of such variants by performing a phenome-wide association study (PheWAS) with a wide range of EMR-derived phenotypes. A total of 13,582 participants in the electronic MEdical Records and GEnomic network had data for PLT and 6,291 participants had data for MPV. We identified five chromosomal regions associated with PLT and eight associated with MPV at genome-wide significance (P < 5E-8). In addition, we replicated 20 SNPs [out of 56 SNPs (α: 0.05/56 = 9E-4)] influencing PLT and 22 SNPs [out of 29 SNPs (α: 0.05/29 = 2E-3)] influencing MPV in a published meta-analysis of GWAS of PLT and MPV. While our GWAS did not find any new associations, our functional analyses revealed that genes in these regions influence thrombopoiesis and encode kinases, membrane proteins, proteins involved in cellular trafficking, transcription factors, proteasome complex subunits, proteins of signal transduction pathways, proteins involved in megakaryocyte development, and platelet production and hemostasis. PheWAS using a single-SNP Bonferroni correction for 1,368 diagnoses (0.05/1368 = 3.6E-5) revealed that several variants in these genes have pleiotropic associations with myocardial infarction, autoimmune, and hematologic disorders. We conclude that multiple genetic loci influence interindividual variation in platelet traits and also have significant pleiotropic effects; the related genes are in multiple functional pathways including those relevant to thrombopoiesis.
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Affiliation(s)
- Khader Shameer
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Joshua C. Denny
- Departments of Medicine and Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
| | - Keyue Ding
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Hayan Jouni
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - David R. Crosslin
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Christopher G. Chute
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Peggy Peissig
- Biomedical Informatics Research Center, Marshfield Clinic, Marshfield, WI, 54449, USA
| | - Jennifer A. Pacheco
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rongling Li
- Office of Population Genomics, National Human Genome Research Institute, 5635 Fishers Lane, Suite 3058, MSC 9307, Bethesda, MD, 20892, USA
| | - Lisa Bastarache
- Departments of Medicine and Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
| | - Abel N. Kho
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Pennsylvania State University, Eberly College of Science, The Huck Institutes of the Life Sciences, 512 Wartik Laboratory, University Park, PA 16802 USA
| | - Daniel R. Masys
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Room 416 Eskind Medical Library, Nashville, TN, 37232, USA
| | - Rex L. Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric B. Larson
- Group Health Research Institute, 1730 Minor Avenue, Suite 1600, Seattle, WA, 98101, USA
| | | | - Dan M. Roden
- Department of Pharmacology, Vanderbilt University School of Medicine, 1285 Medical Research Building IV, Nashville, TN, 37232, USA
| | - Gail P. Jarvik
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle WA 98195, USA
| | - Iftikhar J. Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
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Mutsaers HAM, Engelke UFH, Wilmer MJG, Wetzels JFM, Wevers RA, van den Heuvel LP, Hoenderop JG, Masereeuw R. Optimized metabolomic approach to identify uremic solutes in plasma of stage 3-4 chronic kidney disease patients. PLoS One 2013; 8:e71199. [PMID: 23936492 PMCID: PMC3732267 DOI: 10.1371/journal.pone.0071199] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/28/2013] [Indexed: 11/18/2022] Open
Abstract
Background Chronic kidney disease (CKD) is characterized by the progressive accumulation of various potential toxic solutes. Furthermore, uremic plasma is a complex mixture hampering accurate determination of uremic toxin levels and the identification of novel uremic solutes. Methods In this study, we applied 1H-nuclear magnetic resonance (NMR) spectroscopy, following three distinct deproteinization strategies, to determine differences in the plasma metabolic status of stage 3–4 CKD patients and healthy controls. Moreover, the human renal proximal tubule cell line (ciPTEC) was used to study the influence of newly indentified uremic solutes on renal phenotype and functionality. Results Protein removal via ultrafiltration and acetonitrile precipitation are complementary techniques and both are required to obtain a clear metabolome profile. This new approach, revealed that a total of 14 metabolites were elevated in uremic plasma. In addition to confirming the retention of several previously identified uremic toxins, including p-cresyl sulphate, two novel uremic retentions solutes were detected, namely dimethyl sulphone (DMSO2) and 2-hydroxyisobutyric acid (2-HIBA). Our results show that these metabolites accumulate in non-dialysis CKD patients from 9±7 µM (control) to 51±29 µM and from 7 (0–9) µM (control) to 32±15 µM, respectively. Furthermore, exposure of ciPTEC to clinically relevant concentrations of both solutes resulted in an increased protein expression of the mesenchymal marker vimentin with more than 10% (p<0.05). Moreover, the loss of epithelial characteristics significantly correlated with a loss of glucuronidation activity (Pearson r = −0.63; p<0.05). In addition, both solutes did not affect cell viability nor mitochondrial activity. Conclusions This study demonstrates the importance of sample preparation techniques in the identification of uremic retention solutes using 1H-NMR spectroscopy, and provide insight into the negative impact of DMSO2 and 2-HIBA on ciPTEC, which could aid in understanding the progressive nature of renal disease.
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Affiliation(s)
- Henricus A. M. Mutsaers
- Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Physiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Udo F. H. Engelke
- Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Martijn J. G. Wilmer
- Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jack F. M. Wetzels
- Department of Nephrology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lambertus P. van den Heuvel
- Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Pediatrics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Pediatrics, Catholic University Leuven, Leuven, Belgium
| | - Joost G. Hoenderop
- Department of Physiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rosalinde Masereeuw
- Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
- * E-mail:
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Zhang Z, Hong Y, Gao J, Xiao S, Ma J, Zhang W, Ren J, Huang L. Genome-wide association study reveals constant and specific loci for hematological traits at three time stages in a White Duroc × Erhualian F2 resource population. PLoS One 2013; 8:e63665. [PMID: 23691082 PMCID: PMC3656948 DOI: 10.1371/journal.pone.0063665] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
Hematological traits are important indicators of immune function and have been commonly examined as biomarkers of disease and disease severity in humans. Pig is an ideal biomedical model for human diseases due to its high degree of similarity with human physiological characteristics. Here, we conducted genome-wide association studies (GWAS) for 18 hematological traits at three growth stages (days 18, 46 and 240) in a White Duroc × Erhualian F2 intercross. In total, we identified 38 genome-wide significant regions containing 185 genome-wide significant SNPs by single-marker GWAS or LONG-GWAS. The significant regions are distributed on pig chromosomes (SSC) 1, 4, 5, 7, 8, 10, 11, 12, 13, 17 and 18, and most of significant SNPs reside on SSC7 and SSC8. Of the 38 significant regions, 7 show constant effects on hematological traits across the whole life stages, and 6 regions have time-specific effects on the measured traits at early or late stages. The most prominent locus is the genomic region between 32.36 and 84.49 Mb on SSC8 that is associated with multiple erythroid traits. The KIT gene in this region appears to be a promising candidate gene. The findings improve our understanding of the genetic architecture of hematological traits in pigs. Further investigations are warranted to characterize the responsible gene(s) and causal variant(s) especially for the major loci on SSC7 and SSC8.
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Affiliation(s)
- Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China
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Wang Q, Ma C, Kemmner W. Wdr66 is a novel marker for risk stratification and involved in epithelial-mesenchymal transition of esophageal squamous cell carcinoma. BMC Cancer 2013; 13:137. [PMID: 23514407 PMCID: PMC3610187 DOI: 10.1186/1471-2407-13-137] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 03/11/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND We attempted to identify novel biomarkers and therapeutic targets for esophageal squamous cell carcinoma by gene expression profiling of frozen esophageal squamous carcinoma specimens and examined the functional relevance of a newly discovered marker gene, WDR66. METHODS Laser capture microdissection technique was applied to collect the cells from well-defined tumor areas in collaboration with an experienced pathologist. Whole human gene expression profiling of frozen esophageal squamous carcinoma specimens (n = 10) and normal esophageal squamous tissue (n = 18) was performed using microarray technology. A gene encoding WDR66, WD repeat-containing protein 66 was significantly highly expressed in esophageal squamous carcinoma specimens. Microarray results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in a second and independent cohort (n = 71) consisting of esophageal squamous cell carcinoma (n = 25), normal esophagus (n = 11), esophageal adenocarcinoma (n = 13), gastric adenocarcinoma (n = 15) and colorectal cancers (n = 7). In order to understand WDR66's functional relevance siRNA-mediated knockdown was performed in a human esophageal squamous cell carcinoma cell line, KYSE520 and the effects of this treatment were then checked by another microarray analysis. RESULTS High WDR66 expression was significantly associated with poor overall survival (P = 0.031) of patients suffering from esophageal squamous carcinomas. Multivariate Cox regression analysis revealed that WDR66 expression remained an independent prognostic factor (P = 0.042). WDR66 knockdown by RNA interference resulted particularly in changes of the expression of membrane components. Expression of vimentin was down regulated in WDR66 knockdown cells while that of the tight junction protein occludin was markedly up regulated. Furthermore, siRNA-mediated knockdown of WDR66 resulted in suppression of cell growth and reduced cell motility. CONCLUSIONS WDR66 might be a useful biomarker for risk stratification of esophageal squamous carcinomas. WDR66 expression is likely to play an important role in esophageal squamous cell carcinoma growth and invasion as a positive modulator of epithelial-mesenchymal transition. Furthermore, due to its high expression and possible functional relevance, WDR66 might be a novel drug target for the treatment of squamous carcinoma.
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Affiliation(s)
- Qing Wang
- Experimental Clinical Research Center at the Max-Delbrueck-Center for Molecular Medicine, Charité Campus Buch, Lindenbergerweg 80, Berlin, 13125, Germany
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45
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Sankaran VG, Orkin SH. Genome-wide association studies of hematologic phenotypes: a window into human hematopoiesis. Curr Opin Genet Dev 2013; 23:339-44. [PMID: 23477921 PMCID: PMC4711360 DOI: 10.1016/j.gde.2013.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/11/2013] [Indexed: 01/20/2023]
Abstract
The study of human hematopoiesis is often limited by the inability to manipulate this process in vivo and differences that exist between humans and commonly employed model organisms. However, human genetics provides a way to gain insight into natural variation in a variety of hematologic phenotypes and creates an opportunity to better understand hematopoiesis. In this review, we discuss how genome-wide association studies are revealing common genetic variation that is associated with hematologic traits and diseases. We discuss how the resulting insight from these studies promises to increase our understanding of human hematopoiesis and outline the challenges that lay ahead in this field.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, United States.
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Li J, Glessner JT, Zhang H, Hou C, Wei Z, Bradfield JP, Mentch FD, Guo Y, Kim C, Xia Q, Chiavacci RM, Thomas KA, Qiu H, Grant SFA, Furth SL, Hakonarson H, Sleiman PMA. GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. Hum Mol Genet 2012; 22:1457-64. [PMID: 23263863 DOI: 10.1093/hmg/dds534] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Hematological traits are important clinical indicators, the genetic determinants of which have not been fully investigated. Common measures of hematological traits include red blood cell (RBC) count, hemoglobin concentration (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), MCH concentration (MCHC), mean corpuscular volume (MCV), platelet count (PLT) and white blood cell (WBC) count. We carried out a genome-wide association study of the eight common hematological traits among 7943 African-American children and 6234 Caucasian children. In African Americans, we report five novel associations of HBE1 variants with HCT and MCHC, the alpha-globin gene cluster variants with RBC and MCHC, and a variant at the ARHGEF3 locus with PLT, as well as replication of four previously reported loci at genome-wide significance. In Caucasians, we report a novel association of variants at the COPZ1 locus with PLT as well as replication of four previously reported loci at genome-wide significance. Extended analysis of an association observed between MCH and the alpha-globin gene cluster variants demonstrated independent effects and epistatic interaction at the locus, impacting the risk of iron deficiency anemia in African Americans with specific genotype states. In summary, we extend the understanding of genetic variants underlying hematological traits based on analyses in African-American children.
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Affiliation(s)
- Jin Li
- Center for Applied Genomics, Abramson Research Center and Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Abstract
PURPOSE OF REVIEW This review summarizes our current knowledge of common gene variants (polymorphisms) that have small individual effects on platelet function in humans, but can cumulatively lead to hyperreactive platelets and increase risk for negative outcomes in thrombotic disorders. RECENT FINDINGS Candidate gene association and genome-wide association studies (GWAS) have identified loci that include single nucleotide polymorphisms, which exert a cumulative effect on platelet function by modifying basic platelet parameters, such as mean platelet volume (MPV) or platelet count, by altering the expression or activity of key platelet receptors, or by influencing downstream effector pathways utilized by these receptors. SUMMARY Variation in MPV between normal individuals is responsible for roughly a two-fold range in platelet protein content, including key surface receptors and reactive granule constituents, the association of ADRA2, GP1BA, GP6, ITGA2 and P2Y12 variants with platelet reactivity, initially identified by candidate gene analyses, has now been validated by genome-wide approaches in much larger individual cohorts, and GWAS have identified novel gene variants, most notably PEAR1, that participate in variation in platelet reactivity among normal individuals, all of which contribute to a genetic basis for differences in platelet reactivty among normal individuals.
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48
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Auer P, Johnsen J, Johnson A, Logsdon B, Lange L, Nalls M, Zhang G, Franceschini N, Fox K, Lange E, Rich S, O’Donnell C, Jackson R, Wallace R, Chen Z, Graubert T, Wilson J, Tang H, Lettre G, Reiner A, Ganesh S, Li Y. Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet 2012; 91:794-808. [PMID: 23103231 DOI: 10.1016/j.ajhg.2012.08.031] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/12/2012] [Accepted: 08/27/2012] [Indexed: 01/07/2023] Open
Abstract
Researchers have successfully applied exome sequencing to discover causal variants in selected individuals with familial, highly penetrant disorders. We demonstrate the utility of exome sequencing followed by imputation for discovering low-frequency variants associated with complex quantitative traits. We performed exome sequencing in a reference panel of 761 African Americans and then imputed newly discovered variants into a larger sample of more than 13,000 African Americans for association testing with the blood cell traits hemoglobin, hematocrit, white blood count, and platelet count. First, we illustrate the feasibility of our approach by demonstrating genome-wide-significant associations for variants that are not covered by conventional genotyping arrays; for example, one such association is that between higher platelet count and an MPL c.117G>T (p.Lys39Asn) variant encoding a p.Lys39Asn amino acid substitution of the thrombopoietin receptor gene (p = 1.5 × 10(-11)). Second, we identified an association between missense variants of LCT and higher white blood count (p = 4 × 10(-13)). Third, we identified low-frequency coding variants that might account for allelic heterogeneity at several known blood cell-associated loci: MPL c.754T>C (p.Tyr252His) was associated with higher platelet count; CD36 c.975T>G (p.Tyr325(∗)) was associated with lower platelet count; and several missense variants at the α-globin gene locus were associated with lower hemoglobin. By identifying low-frequency missense variants associated with blood cell traits not previously reported by genome-wide association studies, we establish that exome sequencing followed by imputation is a powerful approach to dissecting complex, genetically heterogeneous traits in large population-based studies.
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49
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Qayyum R, Snively BM, Ziv E, Nalls MA, Liu Y, Tang W, Yanek LR, Lange L, Evans MK, Ganesh S, Austin MA, Lettre G, Becker DM, Zonderman AB, Singleton AB, Harris TB, Mohler ER, Logsdon BA, Kooperberg C, Folsom AR, Wilson JG, Becker LC, Reiner AP. A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans. PLoS Genet 2012; 8:e1002491. [PMID: 22423221 PMCID: PMC3299192 DOI: 10.1371/journal.pgen.1002491] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 12/05/2011] [Indexed: 12/24/2022] Open
Abstract
Several genetic variants associated with platelet count and mean platelet volume (MPV) were recently reported in people of European ancestry. In this meta-analysis of 7 genome-wide association studies (GWAS) enrolling African Americans, our aim was to identify novel genetic variants associated with platelet count and MPV. For all cohorts, GWAS analysis was performed using additive models after adjusting for age, sex, and population stratification. For both platelet phenotypes, meta-analyses were conducted using inverse-variance weighted fixed-effect models. Platelet aggregation assays in whole blood were performed in the participants of the GeneSTAR cohort. Genetic variants in ten independent regions were associated with platelet count (N = 16,388) with p<5×10(-8) of which 5 have not been associated with platelet count in previous GWAS. The novel genetic variants associated with platelet count were in the following regions (the most significant SNP, closest gene, and p-value): 6p22 (rs12526480, LRRC16A, p = 9.1×10(-9)), 7q11 (rs13236689, CD36, p = 2.8×10(-9)), 10q21 (rs7896518, JMJD1C, p = 2.3×10(-12)), 11q13 (rs477895, BAD, p = 4.9×10(-8)), and 20q13 (rs151361, SLMO2, p = 9.4×10(-9)). Three of these loci (10q21, 11q13, and 20q13) were replicated in European Americans (N = 14,909) and one (11q13) in Hispanic Americans (N = 3,462). For MPV (N = 4,531), genetic variants in 3 regions were significant at p<5×10(-8), two of which were also associated with platelet count. Previously reported regions that were also significant in this study were 6p21, 6q23, 7q22, 12q24, and 19p13 for platelet count and 7q22, 17q11, and 19p13 for MPV. The most significant SNP in 1 region was also associated with ADP-induced maximal platelet aggregation in whole blood (12q24). Thus through a meta-analysis of GWAS enrolling African Americans, we have identified 5 novel regions associated with platelet count of which 3 were replicated in other ethnic groups. In addition, we also found one region associated with platelet aggregation that may play a potential role in atherothrombosis.
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Affiliation(s)
- Rehan Qayyum
- GeneSTAR Research Program, Division of General
Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United
States of America
| | - Beverly M. Snively
- Department of Biostatistical Sciences, Wake
Forest School of Medicine, Winston-Salem, North Carolina, United States of
America
| | - Elad Ziv
- Department of Medicine, University of
California San Francisco, San Francisco, California, United States of
America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National
Institute on Aging, National Institutes of Health, Bethesda, Maryland, United
States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention,
Division of Public Health Sciences, Wake Forest University School of Medicine,
Winston-Salem, North Carolina, United States of America
| | - Weihong Tang
- Division of Epidemiology and Community Health,
University of Minnesota School of Public Health, Minneapolis, Minnesota, United
States of America
| | - Lisa R. Yanek
- GeneSTAR Research Program, Division of General
Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United
States of America
| | - Leslie Lange
- Department of Genetics, School of Medicine,
The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,
United States of America
| | - Michele K. Evans
- Health Disparities Research Section, Clinical
Research Branch, National Institute on Aging, National Institutes of Health,
Baltimore, Maryland, United States of America
| | - Santhi Ganesh
- Division of Cardiology, University of Michigan
Health System, Ann Arbor, Michigan, United States of America
| | - Melissa A. Austin
- Department of Epidemiology, University of
Washington, Seattle, Washington, United States of America
- Division of Public Health Sciences, Fred
Hutchinson Cancer Research Center, Seattle, Washington, United States of
America
| | | | - Diane M. Becker
- GeneSTAR Research Program, Division of General
Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United
States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition,
National Institute on Aging, National Institutes of Health, Baltimore, Maryland,
United States of America
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National
Institute on Aging, National Institutes of Health, Bethesda, Maryland, United
States of America
| | - Tamara B. Harris
- Laboratory for Epidemiology, Demography, and
Biometry, National Institute on Aging, National Institutes of Health, Baltimore,
Maryland, United States of America
| | - Emile R. Mohler
- Department of Medicine, University of
Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of
America
| | - Benjamin A. Logsdon
- Program in Biostatistics and Biomathematics,
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center,
Seattle, Washington, United States of America
| | - Charles Kooperberg
- Program in Biostatistics and Biomathematics,
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center,
Seattle, Washington, United States of America
| | - Aaron R. Folsom
- Division of Epidemiology and Community Health,
University of Minnesota School of Public Health, Minneapolis, Minnesota, United
States of America
| | - James G. Wilson
- Department of Medicine, University of
Mississippi Medical Center, Jackson, Mississippi, United States of
America
| | - Lewis C. Becker
- GeneSTAR Research Program, Division of General
Internal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United
States of America
| | - Alexander P. Reiner
- Department of Epidemiology, University of
Washington, Seattle, Washington, United States of America
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50
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Jeff JM, Brown-Gentry K, Crawford DC. Replication and characterisation of genetic variants in the fibrinogen gene cluster with plasma fibrinogen levels and haematological traits in the Third National Health and Nutrition Examination Survey. Thromb Haemost 2012; 107:458-67. [PMID: 22273812 PMCID: PMC3989929 DOI: 10.1160/th11-07-0497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 12/05/2011] [Indexed: 01/04/2023]
Abstract
Previous genetic association studies of the fibrinogen gene cluster have identified associations with plasma fibrinogen levels. These studies are typically limited to plasma fibrinogen measured among European-descent populations. We sought to replicate previous well-known associations with fibrinogen variants and plasma fibrinogen. We then sought to identify and characterise novel associations with fibrinogen variants with plasma fibrinogen and several haematological traits in three racial/ethnic populations. We genotyped 25 single nucleotide polymorphisms (SNPs) in the fibrinogen gene cluster in 2,631 non-Hispanic whites, 2,108 non-Hispanic blacks, and 2,073 Mexican-Americans from the Third National Health and Nutrition Examination Survey (NHANES). We performed single SNP tests of association for plasma fibrinogen, mean platelet volume, platelet distribution width, platelet count, white blood cell count, and serum triglycerides. Five previously identified associations with plasma fibrinogen replicated in our study in non-Hispanic whites and blacks. We identified two novel associations between genetic variants and decreased plasma fibrinogen: rs2227395 (p=0.0007; non-Hispanic whites) and rs2070022 (p=0.001; Mexican-Americans). Several fibrinogen SNPs were also associated with haematological traits: rs6050 with decreased platelet distribution width in non-Hispanic whites; rs6050 and rs2066879 with decreased and increased platelet distribution width, respectively, in non-Hispanic whites;rs2227409 with increased mean platelet volume, rs2070017 with decreased platelet count, and rs6063 with increased platelet distribution width in non-Hispanic blacks; and rs4220 and rs2227395 with decreased white blood cell count, rs2227409 with increased platelet distribution width, rs2066860 and rs1800792 with increased and decreased triclyceride levels, respectively, and rs1800792 with decreased platelet counts in Mexican-Americans. We successfully replicated and identified novel associations with fibrinogen variants and plasma fibrinogen. These data confirm the importance of the fibrinogen gene cluster for plasma fibrinogen levels as well as suggest this gene cluster may have pleiotropic effects on haematological traits.
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Affiliation(s)
- Janina M. Jeff
- Center for Human Genetics Research, University, Nashville, TN 37232
| | | | - Dana C. Crawford
- Center for Human Genetics Research, University, Nashville, TN 37232
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232
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