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Hridoy HM, Haidar MN, Khatun C, Sarker A, Hossain MP, Aziz MA, Hossain MT. In silico based analysis to explore genetic linkage between atherosclerosis and its potential risk factors. Biochem Biophys Rep 2023; 36:101574. [PMID: 38024867 PMCID: PMC10652116 DOI: 10.1016/j.bbrep.2023.101574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Atherosclerosis (ATH) is a chronic cardiovascular disease characterized by plaque formation in arteries, and it is a major cause of illness and death. Although therapeutic advances have significantly improved the prognosis of ATH, missing therapeutic targets pose a significant residual threat. This research used a systems biology approach to identify the molecular biomarkers involved in the onset and progression of ATH, analysing microarray gene expression datasets from ATH and tissues impacted by risk factors such as high cholesterol, adipose tissue, smoking, obesity, sedentary lifestyle, stress, alcohol consumption, hypertension, hyperlipidaemia, high fat, diabetes to find the differentially expressed genes (DEGs). Bioinformatic analyses of Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on differentially expressed genes, revealing metabolic and signaling pathways (the chemokine signaling pathway, cytokine-cytokine receptor interaction, the cytosolic DNA-sensing pathway, the peroxisome proliferator-activated receptors signaling pathway, and the nuclear factor-kappa B signaling pathway), ten hubs proteins (CCL5, CCR1, TLR1, CCR2, FCGR2A, IL1B, CD163, AIF1, CXCL-1 and TNF), five transcription factors (YY1, FOXL1, FOXC1, SRF, and GATA2), and five miRNAs (mir-27a-3p, mir-124-3p, mir-16-5p, mir-129-2-3p, mir-1-3p). These findings identify potential biomarkers that may increase knowledge of the mechanisms underlying ATH and their connection to risk factors, aiding in the development of new therapies.
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Affiliation(s)
- Hossain Mohammad Hridoy
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nasim Haidar
- Department of Electrical and Electronic Engineering, Rangpur Engineering College, Rangpur, Bangladesh
| | - Chadni Khatun
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Arnob Sarker
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Pervez Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Abdul Aziz
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Tofazzal Hossain
- Bioinformatics and Structural Biology Lab, Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
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2
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Xiong D, Yang J, Li D, Wang J. Exploration of Key Immune-Related Transcriptomes Associated with Doxorubicin-Induced Cardiotoxicity in Patients with Breast Cancer. Cardiovasc Toxicol 2023; 23:329-348. [PMID: 37684436 PMCID: PMC10514147 DOI: 10.1007/s12012-023-09806-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Based on a few studies, heart failure patients with breast cancer were assessed to find potential biomarkers for doxorubicin-induced cardiotoxicity. However, key immune-related transcriptional markers linked to doxorubicin-induced cardiotoxicity in breast cancer patients have not been thoroughly investigated. We used GSE40447, GSE76314, and TCGA BRCA cohorts to perform this study. Then, we performed various bioinformatics approaches to identify the key immune-related transcriptional markers and their association with doxorubicin-induced cardiotoxicity in patients with breast cancer. We found 255 upregulated genes and 286 downregulated genes in patients with doxorubicin-induced heart failure in breast cancer. We discovered that in patients with breast cancer comorbidity doxorubicin-induced cardiotoxicity, the 58 immunological genes are elevated (such as CPA3, VSIG4, GATA2, RFX2, IL3RA, and LRP1), and the 60 genes are significantly suppressed (such as MS4A1, FCRL1, CD200, FCRLA, FCRL2, and CD79A). Furthermore, we revealed that the immune-related differentially expressed genes (DEGs) are substantially associated with the enrichment of KEGG pathways, including B-cell receptor signaling pathway, primary immunodeficiency, chemokine signaling pathway, hematopoietic cell lineage, cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, MAPK signaling pathway, focal adhesion, dilated cardiomyopathy, cell adhesion molecule, etc. Moreover, we discovered that the doxorubicin-induced immune-related genes are crucially involved in the protein-protein interaction and gene clusters. The immune-related genes, including IFIT5, XCL1, SPIB, BTLA, MS4A1, CD19, TCL1A, CD83, CD200, FCRLA, CD79A, BIRC3, and IGF2R are significantly associated with a poor survival prognosis of breast cancer patients and showed diagnostic efficacy in patients with breast cancer and heart failure. Molecular docking revealed that the survival-associated genes interact with the doxorubicin with appreciable binding affinity. Finally, we validated the expression level of immune-related genes in breast cancer patients-derived cardiomyocytes with doxorubicin-induced cardiotoxicity and found that the level of RAD9A, HSPA1B, GATA2, IGF2R, CD200, ERCC8, and BCL11A genes are consistently dysregulated. Our findings offered a basis for understanding the mechanism and pathogenesis of the cardiotoxicity caused by doxorubicin in breast cancer patients and predicted the interaction of immune-related potential biomarkers with doxorubicin.
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Affiliation(s)
- Daiqin Xiong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Jianhua Yang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Dongfeng Li
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Jie Wang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
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3
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Boshev M, Stankovic S, Panov S, Josifovska S, Georgiev A, Poposka L, Pejkov H. Association of the Polymorphism rs3918242 of the Matrix Metalloproteinase-9 Gene with Coronary Artery Disease in a Younger Population. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2023; 44:31-39. [PMID: 37453108 DOI: 10.2478/prilozi-2023-0022] [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] [Indexed: 07/18/2023]
Abstract
Coronary artery disease (CAD) is a complex disease resulting from the interaction of numerous so-called traditional risk factors and comorbid conditions on the one side (such as dyslipidemia, smoking, obesity, diabetes, hypertension) and genetic factors on the other. The evidence of a genetic contribution to the development of CAD, especially in the last 2 decades is consistent. It is important that a number of established gene polymorphisms in the younger CAD population are in the genes involved in the inflammatory response and tissue maintenance and remodeling processes. The aim of this study is to investigate the association of the rs3918242 polymorphism of the matrix metal-loproteinase 9 (MMP9) gene with the coronary artery disease in the younger population. In this observational genetic-association study of cases and controls, the demographic, clinical, laboratory and genetic data of the younger population in a group of selected 70 CAD patients aged up to 45 years were analyzed, of which 35 patients have negative and 35 have positive coronary angiography finding, and 43 are men and 27 are women. The analysis of the genotypic and allelic frequency determined an association of the polymorphism and the occurrence of the positive coronary angiographic findings in the population of patients under the age of 45. The carriers of the heterozygous genotype CT have almost 5 times higher probability of having a positive coronary angiography finding compared to the carriers of the reference homozygous genotype CC (p=0.012). Thus, this parameter could be used for clinical risk assessment for the development of CAD.
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Affiliation(s)
- Marjan Boshev
- 1University Clinic of Cardiology, Skopje, RN Macedonia
- 4Medical Faculty, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Svetlana Stankovic
- 2University Clinic of Hematology, Skopje, RN Macedonia
- 4Medical Faculty, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Sasho Panov
- 3Laboratory for Molecular Biology, Faculty of Natural Sciences and Mathematics, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Slavica Josifovska
- 3Laboratory for Molecular Biology, Faculty of Natural Sciences and Mathematics, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Antonio Georgiev
- 1University Clinic of Cardiology, Skopje, RN Macedonia
- 4Medical Faculty, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Lidija Poposka
- 1University Clinic of Cardiology, Skopje, RN Macedonia
- 4Medical Faculty, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
| | - Hristo Pejkov
- 1University Clinic of Cardiology, Skopje, RN Macedonia
- 4Medical Faculty, University "Ss. Cyril and Methodius" in Skopje, RN Macedonia
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4
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Man HSJ, Subramaniam N, Downs T, Sukumar AN, Saha AD, Nair R, Chen L, Teitelbaum D, Turgeon PJ, Ku KH, Tran E, de Perrot M, Marsden PA. Long noncoding RNA GATA2-AS1 augments endothelial Hypoxia Inducible Factor 1-α induction and regulates hypoxic signaling. J Biol Chem 2023; 299:103029. [PMID: 36806681 PMCID: PMC10148162 DOI: 10.1016/j.jbc.2023.103029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Vascular endothelial cells form the inner cellular lining of blood vessels and have myriad physiologic functions including angiogenesis and response to hypoxia. We recently identified a set of endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs) in differentiated human primary cell types and described the role of the STEEL lncRNA in angiogenic patterning. We sought to further understand the role of EC-enriched lncRNAs in physiologic adaptation of the vascular endothelium. In this work, we describe an abundant, cytoplasmic, and EC-enriched lncRNA, GATA2-AS1, that is divergently transcribed from the EC-enriched developmental regulator, GATA2. While GATA2-AS1 is largely co-expressed with GATA2 in ECs, GATA2-AS1 and GATA2 appear to be complementary rather than synergistic as they have mostly distinct target genes. Common single nucleotide variants (SNVs) in GATA2-AS1 exons are associated with early onset coronary artery disease (CAD) and decreased expression of GATA2-AS1 in endothelial cell lines. In most cells, HIF1-α is central to the transcriptional response to hypoxia, while in ECs, both HIF1-α and HIF2-α are required to coordinate an acute and chronic response respectively. In this setting, GATA2-AS1 contributes to the "HIF switch" and augments HIF1-α induction in acute hypoxia to regulate HIF1-α/ HIF2-α balance. In hypoxia, GATA2-AS1 orchestrates HIF1-α-dependent induction of the glycolytic pathway, and HIF1-α-independent maintenance of mitochondrial biogenesis. Similarly, GATA2-AS1 coordinates both metabolism and "tip/stalk" cell signaling to regulate angiogenesis in hypoxic ECs. Furthermore, we find that GATA2-AS1 expression patterns are perturbed in atherosclerotic disease. Together, these results define a role for GATA2-AS1 in the EC-specific response to hypoxia.
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Affiliation(s)
- H S Jeffrey Man
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Respirology, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Noeline Subramaniam
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tiana Downs
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aravin N Sukumar
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Aninda D Saha
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ranju Nair
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Chen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Teitelbaum
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kyung Ha Ku
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eileen Tran
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marc de Perrot
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Division of Thoracic Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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5
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Kotmayer L, Romero‐Moya D, Marin‐Bejar O, Kozyra E, Català A, Bigas A, Wlodarski MW, Bödör C, Giorgetti A. GATA2 deficiency and MDS/AML: Experimental strategies for disease modelling and future therapeutic prospects. Br J Haematol 2022; 199:482-495. [PMID: 35753998 PMCID: PMC9796058 DOI: 10.1111/bjh.18330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 12/30/2022]
Abstract
The importance of predisposition to leukaemia in clinical practice is being increasingly recognized. This is emphasized by the establishment of a novel WHO disease category in 2016 called "myeloid neoplasms with germline predisposition". A major syndrome within this group is GATA2 deficiency, a heterogeneous immunodeficiency syndrome with a very high lifetime risk to develop myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). GATA2 deficiency has been identified as the most common hereditary cause of MDS in adolescents with monosomy 7. Allogenic haematopoietic stem cell transplantation is the only curative option; however, chances of survival decrease with progression of immunodeficiency and MDS evolution. Penetrance and expressivity within families carrying GATA2 mutations is often variable, suggesting that co-operating extrinsic events are required to trigger the disease. Predictive tools are lacking, and intrafamilial heterogeneity is poorly understood; hence there is a clear unmet medical need. On behalf of the ERAPerMed GATA2 HuMo consortium, in this review we describe the genetic, clinical, and biological aspects of familial GATA2-related MDS, highlighting the importance of developing robust disease preclinical models to improve early detection and clinical decision-making of GATA2 carriers.
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Affiliation(s)
- Lili Kotmayer
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Damia Romero‐Moya
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Oskar Marin‐Bejar
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain
| | - Emilia Kozyra
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Albert Català
- Department of Hematology and OncologyInstitut de Recerca Sant Joan de DéuHospital Sant Joan de DeuBarcelonaSpain,Biomedical Network Research Centre on Rare DiseasesInstituto de Salud Carlos IIIMadridSpain
| | - Anna Bigas
- Cancer Research ProgramInstitut Hospital del Mar d'Investigacions Mèdiques, CIBERONC, Hospital del MarBarcelonaSpain,Josep Carreras Research Institute (IJC), BadalonaBarcelonaSpain
| | - Marcin W. Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of MedicineUniversity of FreiburgFreiburgGermany,Department of HematologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Csaba Bödör
- HCEMM‐SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Alessandra Giorgetti
- Regenerative Medicine ProgramInstitut d'Investigació Biomèdica de Bellvitge (IDIBELL)BarcelonaSpain,Fondazione Pisana Per la Scienza ONLUS (FPS)San Giuliano TermeItaly,Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health SciencesBarcelona UniversityBarcelonaSpain
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6
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Elwazir MY, Hussein MH, Toraih EA, Al Ageeli E, Esmaeel SE, Fawzy MS, Faisal S. Association of Angio-LncRNAs MIAT rs1061540/MALAT1 rs3200401 Molecular Variants with Gensini Score in Coronary Artery Disease Patients Undergoing Angiography. Biomolecules 2022; 12:biom12010137. [PMID: 35053285 PMCID: PMC8773982 DOI: 10.3390/biom12010137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as essential biomolecules with variable diagnostic and/or prognostic utility in several diseases, including coronary artery disease (CAD). We aimed for the first time to investigate the potential association of five angiogenesis-related lncRNAs (PUNISHER, SENCR, MIAT, MALAT1, and GATA6-AS) variants with CAD susceptibility and/or severity. TaqMan Real-Time genotyping for PUNISHER rs12318065A/C, SENCR rs12420823C/T, MIAT rs1061540C/T, MALAT1 rs3200401T/C, and GATA6-AS1 rs73390820A/G were run on the extracted genomic DNA from 100 unrelated patients with stable CAD undergoing diagnostic coronary angiography and from 100 controls. After adjusting covariates, the studied variants showed no association with disease susceptibility; however, MIAT*T/T genotype was associated with a more severe Gensini score. In contrast, MALAT1*T/C heterozygosity was associated with a lower score. The lipid profile, and to a lesser extent smoking status, male sex, weight, hypertension, and MALAT1 (T > C) (negative correlation), explained the variance between patients/control groups via a principal component analysis. Incorporating the principal components into a logistic regression model to predict CAD yielded a 0.92 AUC. In conclusion: MIAT rs1061540 and MALAT1 rs3200401 variants were associated with CAD severity and Gensini score in the present sample of the Egyptian population. Further large multi-center and functional analyses are needed to confirm the results and identify the underlying molecular mechanisms.
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Affiliation(s)
- Mohamed Y. Elwazir
- Department of Cardiology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Mohammad H. Hussein
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia;
| | - Safya E. Esmaeel
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Salwa Faisal
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
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7
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Veninga A, De Simone I, Heemskerk JWM, Cate HT, van der Meijden PEJ. Clonal hematopoietic mutations linked to platelet traits and the risk of thrombosis or bleeding. Haematologica 2020; 105:2020-2031. [PMID: 32554558 PMCID: PMC7395290 DOI: 10.3324/haematol.2019.235994] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
Platelets are key elements in thrombosis, particularly in atherosclerosis-associated arterial thrombosis (atherothrombosis), and hemostasis. Megakaryocytes in the bone marrow, differentiated from hematopoietic stem cells are generally considered as a uniform source of platelets. However, recent insights into the causes of malignancies, including essential thrombocytosis, indicate that not only inherited but also somatic mutations in hematopoietic cells are linked to quantitative or qualitative platelet abnormalities. In particular cases, these form the basis of thrombo-hemorrhagic complications regularly observed in patient groups. This has led to the concept of clonal hematopoiesis of indeterminate potential (CHIP), defined as somatic mutations caused by clonal expansion of mutant hematopoietic cells without evident disease. This concept also provides clues regarding the importance of platelet function in relation to cardiovascular disease. In this summative review, we present an overview of genes associated with clonal hematopoiesis and altered platelet production and/or functionality, like mutations in JAK2 We consider how reported CHIP genes can influence the risk of cardiovascular disease, by exploring the consequences for platelet function related to (athero)thrombosis, or the risk of bleeding. More insight into the functional consequences of the CHIP mutations may favor personalized risk assessment, not only with regard to malignancies but also in relation to thrombotic vascular disease.
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Affiliation(s)
- Alicia Veninga
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Ilaria De Simone
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht
| | - Hugo Ten Cate
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht.,Thrombosis Expertise Center, Heart and Vascular Center, Maastricht University Medical Center, Maastricht.,Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Paola E J van der Meijden
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht .,Thrombosis Expertise Center, Heart and Vascular Center, Maastricht University Medical Center, Maastricht
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8
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Haidar MN, Islam MB, Chowdhury UN, Rahman MR, Huq F, Quinn JMW, Moni MA. Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. IET Syst Biol 2020; 14:75-84. [PMID: 32196466 PMCID: PMC8687405 DOI: 10.1049/iet-syb.2019.0074] [Citation(s) in RCA: 8] [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: 07/11/2019] [Revised: 09/23/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiomyopathy (CMP) is a group of myocardial diseases that progressively impair cardiac function. The mechanisms underlying CMP development are poorly understood, but lifestyle factors are clearly implicated as risk factors. This study aimed to identify molecular biomarkers involved in inflammatory CMP development and progression using a systems biology approach. The authors analysed microarray gene expression datasets from CMP and tissues affected by risk factors including smoking, ageing factors, high body fat, clinical depression status, insulin resistance, high dietary red meat intake, chronic alcohol consumption, obesity, high-calorie diet and high-fat diet. The authors identified differentially expressed genes (DEGs) from each dataset and compared those from CMP and risk factor datasets to identify common DEGs. Gene set enrichment analyses identified metabolic and signalling pathways, including MAPK, RAS signalling and cardiomyopathy pathways. Protein-protein interaction (PPI) network analysis identified protein subnetworks and ten hub proteins (CDK2, ATM, CDT1, NCOR2, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E and HIST1H4L). Five transcription factors (FOXC1, GATA2, FOXL1, YY1, CREB1) and five miRNAs were also identified in CMP. Thus the authors' approach reveals candidate biomarkers that may enhance understanding of mechanisms underlying CMP and their link to risk factors. Such biomarkers may also be useful to develop new therapeutics for CMP.
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Affiliation(s)
- Md Nasim Haidar
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh
| | - Fazlul Huq
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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9
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Angelidis G, Valotassiou V, Kollia P, Skoularigis J, Tsougos I, Georgoulias P. Novel approaches for the management of coronary artery disease. Herz 2020; 46:89-90. [PMID: 32006079 DOI: 10.1007/s00059-019-04885-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 11/27/2019] [Accepted: 12/09/2019] [Indexed: 11/29/2022]
Affiliation(s)
- G Angelidis
- Nuclear Medicine Laboratory, University Hospital of Larissa, Larissa, Greece.
| | - V Valotassiou
- Nuclear Medicine Laboratory, University Hospital of Larissa, Larissa, Greece
| | - P Kollia
- Faculty of Biology, National & Kapodistrian University of Athens, Athens, Greece
| | - J Skoularigis
- Department of Cardiology, University Hospital of Larissa, Larissa, Greece
| | - I Tsougos
- Nuclear Medicine Laboratory, University Hospital of Larissa, Larissa, Greece
| | - P Georgoulias
- Nuclear Medicine Laboratory, University Hospital of Larissa, Larissa, Greece
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10
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Wang Y, Tang M. Integrative analysis of mRNAs, miRNAs and lncRNAs in urban particulate matter SRM 1648a-treated EA.hy926 human endothelial cells. CHEMOSPHERE 2019; 233:711-723. [PMID: 31200131 DOI: 10.1016/j.chemosphere.2019.05.294] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Considering the unique physiochemical properties of concentrated ambient particles (CAPs), it is extremely important to be aware of their toxic effect. A number of studies have investigated the vascular toxicity of CAPs, while potential mechanisms are still not clearly defined. Differentially expressed mRNAs, miRNAs and lncRNAs were analyzed in EA.hy926 endothelial cells after incubation with 2.5 and 10 μg/cm2 urban particulate matter SRM 1648a for 24 h. As a result, the microarray profile showed that 97 mRNA, 18 miRNA, and 356 lncRNA transcripts are dysregulated in 2.5 μg/cm2 group. And the expression of 440 mRNAs, 40 miRNAs, and 1283 lncRNAs significantly changes in 10 μg/cm2 group. Through the miRNA-mRNA-transcription factor (TF) network, hsa-miR-128-3p, miR-18-5p and miR-376a-3p, miR-4306 as well, are key miRNAs in SRM 1648a-induced endothelial damage. Withal, lncRNA-mRNA-TF analysis hinted the importance of lncRNA T018951 and T200627. Subsequently, competing endogenous RNA (CeRNA) network was constructed for the comprehensive analysis of the regulation dogma between mRNAs and non-coding RNAs. It suggested that 35 GO terms and 1 KEGG pathway are significantly enriched in 2.5 μg/cm2 group. Meanwhile, 185 terms and 18 pathways are important in 10 μg/cm2 group. Pathway analysis revealed that Gap junction, Ras and MAPK signaling pathways are most significant in endothelial cell lesion. In conclusion, integrative analysis of mRNA and non-coding RNA in human endothelial cells suggests that a vast majority of non-coding RNAs regulate vascular toxicity in response to SRM 1648a. Moreover, it highlights the need for comprehensive analysis of latent mechanisms through a combination of signaling pathways with epigenetics studies.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Meng Tang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China.
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11
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Whitcomb J, Gharibeh L, Nemer M. From embryogenesis to adulthood: Critical role for GATA factors in heart development and function. IUBMB Life 2019; 72:53-67. [PMID: 31520462 DOI: 10.1002/iub.2163] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/25/2019] [Indexed: 12/21/2022]
Abstract
Cardiac development is governed by a complex network of transcription factors (TFs) that regulate cell fates in a spatiotemporal manner. Among these, the GATA family of zinc finger TFs plays prominent roles in regulating the development of the myocardium, endocardium, and outflow tract. This family comprises six members three of which, GATA4, 5, and 6, are predominantly expressed in cardiac cells where they activate specific downstream gene targets via interactions with one another and with other TFs and signaling molecules. Their critical function in heart formation is evidenced by the phenotypes of animal models lacking these factors and by the broad spectrum of human congenital heart diseases associated with mutations in their genes. Similarly, in the postnatal heart, these proteins play significant and nonredundant roles in cardiac function, regulating adaptive stress responses including cardiomyocyte hypertrophy and survival, as well as endothelial homeostasis and angiogenesis. As such, decreased expression of either GATA4, 5, or 6 results in impaired cardiovascular homeostasis and increased risk of premature and serious cardiovascular events such as hypertension, arrhythmia, aortopathy, and heart failure. Although a great deal of progress has been made in understanding GATA-dependent regulatory processes in the heart, the molecular mechanisms underlying the specificity of GATA factors and their upstream regulation remain incompletely understood. The knowledge and tools developed since their discovery 25 years ago should accelerate progress toward further elucidation of their mechanisms of action in health and disease. This in turn will greatly improve diagnosis and care for the millions of individuals affected by congenital and acquired cardiac disease worldwide.
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Affiliation(s)
- Jamieson Whitcomb
- Molecular Genetics and Cardiac Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Lara Gharibeh
- Molecular Genetics and Cardiac Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mona Nemer
- Molecular Genetics and Cardiac Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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12
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Izadpanah P, Khabbzi E, Erfanian S, Jafaripour S, Shojaie M. Case-control study on the association between the GATA2 gene and premature myocardial infarction in the Iranian population. Herz 2019; 46:71-75. [PMID: 31468074 DOI: 10.1007/s00059-019-04841-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
In recent decades, due to the high prevalence of coronary artery disease (CAD) and myocardial infarction (MI), numerous studies have attempted to elucidate genetic contributing factors in these complex disorders. A very interesting gene in this regard is GATA-binding protein 2 (GATA2), an important regulator of various gene expressions in vascular endothelial cells. Accordingly, the association of different GATA2 polymorphisms with CAD and MI has already been evaluated. Rs2713604 is a genetic marker whose association with CAD has not been reproduced in previous studies. Considering the importance of replicating the initial association, the present case-control study aimed to examine the association of this intronic variant with premature MI in a sample of the Iranian population. In this study, 193 participants from Jahrom Hospital (Jahrom, Iran) were consecutively recruited during a 1.5-year period, and, following blood sampling, genomic DNA was extracted. We then proceeded to genotype rs2713604 using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and statistically analyzed the data. After adjustment for hyperlipidemia, hypertension, and type 2 diabetes mellitus, the results of the multivariate regression analysis showed no significant association between rs2713604 and premature MI. Interestingly, the risk allele (A-allele) of rs2713604 displayed a slightly higher frequency among controls compared to cases.
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Affiliation(s)
- Peyman Izadpanah
- Cardiology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Khabbzi
- School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Saiedeh Erfanian
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran. .,Department of Advanced Medical Sciences and Technologies, School of Medicine, Jahrom University of Medical Sciences, Motahhari Street, 74148-46199, Jahrom, Iran.
| | - Simin Jafaripour
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Vakil abad Blv., 99191-91778, Mashhad, Iran.
| | - Mohammad Shojaie
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
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13
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Mendes-de-Almeida DP, Andrade FG, Borges G, Dos Santos-Bueno FV, Vieira IF, da Rocha LKMDS, Mendes-da-Cruz DA, Zancopé-Oliveira RM, Calado RT, Pombo-de-Oliveira MS. GATA2 mutation in long stand Mycobacterium kansasii infection, myelodysplasia and MonoMAC syndrome: a case-report. BMC MEDICAL GENETICS 2019; 20:64. [PMID: 31035956 PMCID: PMC6489290 DOI: 10.1186/s12881-019-0799-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/03/2019] [Indexed: 11/26/2022]
Abstract
Background GATA2 is a transcription factor that is a critical regulator of gene expression in hematopoietic cells. GATA2 deficiency presents with multi-lineage cytopenia, mycobacterial, fungal and viral infections. Patients with GATA2 mutation have a high risk of developing myelodysplastic syndrome or acute myeloid leukemia. Case presentation We described a 43 years-old white male with 20-year follow-up of autoimmune and thrombotic phenomena, hypothyroidism, disseminated refractory Mycobacterium kansasii infection and MonoMAC syndrome. GATA2 c.1061 C > T; p.T354 M mutation was identified after he progressed from myelodysplastic pancytopenia to refractory anemia with excess blasts type II. His relatives were also investigated and he underwent unsuccessful haematopoietic stem cell transplantation. We discuss the clinical features, genetic diagnosis and treatment of this immunodeficiency disorder. Conclusions This case illustrates the challenge how a multidisciplinary disease should be handle. Once usual causes of immunodeficiency were excluded, clinicians should considerGATA2 deficiency in patients with myelodysplasia and long-standing Mycobacterium kansasii infection. Electronic supplementary material The online version of this article (10.1186/s12881-019-0799-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Palheiro Mendes-de-Almeida
- Division of Hematology, Evandro Chagas National Institute of Infectology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Pediatric Hematology-Oncology Program, 6thfloor, Research Center, Instituto Nacional de Câncer-INCa, Rua André Cavalcanti, 37, Rio de Janeiro, Zip code: 20231- 050, Brazil
| | - Francianne Gomes Andrade
- Pediatric Hematology-Oncology Program, 6thfloor, Research Center, Instituto Nacional de Câncer-INCa, Rua André Cavalcanti, 37, Rio de Janeiro, Zip code: 20231- 050, Brazil
| | - Gustavo Borges
- Department of Internal Medicine, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, Brazil
| | - Filipe V Dos Santos-Bueno
- Pediatric Hematology-Oncology Program, 6thfloor, Research Center, Instituto Nacional de Câncer-INCa, Rua André Cavalcanti, 37, Rio de Janeiro, Zip code: 20231- 050, Brazil
| | - Iracema F Vieira
- Infectious Diseases Department, Hospital dos Servidores do Estado, Rio de Janeiro, Brazil
| | | | - Daniella A Mendes-da-Cruz
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Rosely M Zancopé-Oliveira
- Laboratory of Mycology, Evandro Chagas National Institute of Infectology, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rodrigo T Calado
- Department of Internal Medicine, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, 6thfloor, Research Center, Instituto Nacional de Câncer-INCa, Rua André Cavalcanti, 37, Rio de Janeiro, Zip code: 20231- 050, Brazil.
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14
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Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. SCIENCE ADVANCES 2019; 5:eaav3262. [PMID: 30944857 PMCID: PMC6436936 DOI: 10.1126/sciadv.aav3262] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/30/2019] [Indexed: 05/20/2023]
Abstract
Transcriptional regulation is pivotal to the specification of distinct cell types during embryonic development. However, it still lacks a systematic way to identify key transcription factors (TFs) orchestrating the temporal and tissue specificity of gene expression. Here, we integrated epigenomic and transcriptomic data to reveal key regulators from two cells to postnatal day 0 in mouse embryogenesis. We predicted three-dimensional chromatin interactions in 12 tissues across eight developmental stages, which facilitates linking TFs to their target genes for constructing transcriptional regulatory networks. To identify driver TFs, we developed a new algorithm, dubbed Taiji, to assess the global influence of each TF and systematically uncovered TFs critical for lineage-specific and stage-dependent tissue specification. We have also identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress. Furthermore, lacking stage-specific TF combinations suggests a distributed timing strategy to orchestrate the coordination between tissues during embryonic development.
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Affiliation(s)
- Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Ying Zhao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Corresponding author.
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15
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Wang Y, Wu T, Zou L, Xiong L, Zhang T, Kong L, Xue Y, Tang M. Genome-wide identification and functional analysis of long non-coding RNAs in human endothelial cell line after incubation with PM2.5. CHEMOSPHERE 2019; 216:396-403. [PMID: 30384309 DOI: 10.1016/j.chemosphere.2018.10.101] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/06/2018] [Accepted: 10/16/2018] [Indexed: 06/08/2023]
Abstract
Epidemiological studies and experimental research have illustrated that PM2.5 has an association with cardiovascular adverse events. However, the underlying mechanisms are still unknown. Long non-coding RNAs (lncRNAs) have been proposed to take part in diverse diseases. To comprehensively gain insight into the molecular toxicity of PM2.5, expression patterns are analyzed in EA.hy926 cell line through RNAs microarray. A total of 356 lncRNA transcripts are dysregulated in 2.5 μg/cm2 group, and there are 1283 lncRNAs differentially expressed in 10 μg/cm2 group. From functional analysis, several lncRNAs may be implicated in the bio-pathways of phagosome, TNF signaling pathway, chemokine signaling pathway and gap junction. Moreover, certain lncRNAs participate in the toxicity of PM2.5 through cis- and/or trans-regulation of their co-expressed genes. Therefore, lncRNAs may be used as new candidate biomarkers and potentially preventive targets in cardiotoxicity of PM2.5. Our study indicates that not limited to transcriptional regulation, post-transcriptional regulation plays a pivotal role in PM2.5-caused toxicity.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Tianshu Wu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Lingyue Zou
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Lilin Xiong
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Department of Environmental Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, Jiangsu, 210003, China
| | - Ting Zhang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Lu Kong
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yuying Xue
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Meng Tang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing, Jiangsu, 210009, China; Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, 210009, China.
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16
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Geng X, Cha B, Mahamud MR, Srinivasan RS. Intraluminal valves: development, function and disease. Dis Model Mech 2018; 10:1273-1287. [PMID: 29125824 PMCID: PMC5719258 DOI: 10.1242/dmm.030825] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The circulatory system consists of the heart, blood vessels and lymphatic vessels, which function in parallel to provide nutrients and remove waste from the body. Vascular function depends on valves, which regulate unidirectional fluid flow against gravitational and pressure gradients. Severe valve disorders can cause mortality and some are associated with severe morbidity. Although cardiac valve defects can be treated by valve replacement surgery, no treatment is currently available for valve disorders of the veins and lymphatics. Thus, a better understanding of valves, their development and the progression of valve disease is warranted. In the past decade, molecules that are important for vascular function in humans have been identified, with mouse studies also providing new insights into valve formation and function. Intriguing similarities have recently emerged between the different types of valves concerning their molecular identity, architecture and development. Shear stress generated by fluid flow has also been shown to regulate endothelial cell identity in valves. Here, we review our current understanding of valve development with an emphasis on its mechanobiology and significance to human health, and highlight unanswered questions and translational opportunities.
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Affiliation(s)
- Xin Geng
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Boksik Cha
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Md Riaj Mahamud
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - R Sathish Srinivasan
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA .,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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17
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Lyu G, Zhang C, Ling T, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, Li C, Nie Y, Tao W. Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease. BMC Genomics 2018; 19:428. [PMID: 29866040 PMCID: PMC5987557 DOI: 10.1186/s12864-018-4814-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epigenomic differences between a pair of twins discordant for a form of congenital heart disease, double outlet right ventricle (DORV). RESULTS A monoamniotic monozygotic (MZ) twin pair discordant for DORV were subjected to genome-wide sequencing and methylation analysis. We identified few genomic differences but 1566 differentially methylated regions (DMRs) between the MZ twins. Twenty percent (312/1566) of the DMRs are located within 2 kb upstream of transcription start sites (TSS), containing 121 binding sites of transcription factors. Particularly, ZIC3 and NR2F2 are found to have hypermethylated promoters in both the diseased twin and additional patients suffering from DORV. CONCLUSIONS The results showed a high correlation between hypermethylated promoters at ZIC3 and NR2F2 and down-regulated gene expression levels of these two genes in patients with DORV compared to normal controls, providing new insight into the potential mechanism of this rare form of CHD.
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Affiliation(s)
- Guoliang Lyu
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Chao Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Te Ling
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Rui Liu
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Le Zong
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiting Guan
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoke Huang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lei Sun
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lijun Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yu Nie
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
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18
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Genetics of Atherosclerosis. Coron Artery Dis 2018. [DOI: 10.1016/b978-0-12-811908-2.00007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Cheng M, An S, Li J. CDKN2B - AS may indirectly regulate coronary artery disease-associated genes via targeting miR - 92a. Gene 2017; 629:101-107. [DOI: 10.1016/j.gene.2017.07.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/20/2017] [Accepted: 07/27/2017] [Indexed: 12/27/2022]
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20
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Hamadou WS, Mani R, Besbes S, Bourdon V, Youssef YB, Eisinger F, Mari V, Gesta P, Dreyfus H, Bonadona V, Dugast C, Zattara H, Faivre L, Noguchi T, Khélif A, Sobol H, Soua Z. GATA2 gene analysis in several forms of hematological malignancies including familial aggregations. Ann Hematol 2017; 96:1635-1639. [DOI: 10.1007/s00277-017-3076-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/14/2017] [Indexed: 12/26/2022]
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21
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The critical role of SENP1-mediated GATA2 deSUMOylation in promoting endothelial activation in graft arteriosclerosis. Nat Commun 2017; 8:15426. [PMID: 28569748 PMCID: PMC5461500 DOI: 10.1038/ncomms15426] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
Data from clinical research and our previous study have suggested the potential involvement of SENP1, the major protease of post-translational SUMOylation, in cardiovascular disorders. Here, we investigate the role of SENP1-mediated SUMOylation in graft arteriosclerosis (GA), the major cause of allograft failure. We observe an endothelial-specific induction of SENP1 and GATA2 in clinical graft rejection specimens that show endothelial activation-mediated vascular remodelling. In mouse aorta transplantation GA models, endothelial-specific SENP1 knockout grafts demonstrate limited neointima formation with attenuated leukocyte recruitment, resulting from diminished induction of adhesion molecules in the graft endothelium due to increased GATA2 SUMOylation. Mechanistically, inflammation-induced SENP1 promotes the deSUMOylation of GATA2 and IκBα in endothelial cells, resulting in increased GATA2 stability, promoter-binding capability and NF-κB activity, which leads to augmented endothelial activation and inflammation. Therefore, upon inflammation, endothelial SENP1-mediated SUMOylation drives GA by regulating the synergistic effect of GATA2 and NF-κB and consequent endothelial dysfunction.
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22
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Kumar GR, Spurthi KM, Kumar GK, Aiyengar TM, Chiranjeevi P, Nivas S, Anuradha C, Swathi B, Sahu SK, Ali A, Rani HS. Genetic polymorphisms of eNOS (-786T/C, Intron 4b/4a & 894G/T) and its association with asymptomatic first degree relatives of coronary heart disease patients. Nitric Oxide 2016; 60:40-49. [DOI: 10.1016/j.niox.2016.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/23/2016] [Accepted: 09/04/2016] [Indexed: 10/21/2022]
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23
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Kraus WE, Granger CB, Sketch MH, Donahue MP, Ginsburg GS, Hauser ER, Haynes C, Newby LK, Hurdle M, Dowdy ZE, Shah SH. A Guide for a Cardiovascular Genomics Biorepository: the CATHGEN Experience. J Cardiovasc Transl Res 2015; 8:449-57. [PMID: 26271459 DOI: 10.1007/s12265-015-9648-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/03/2015] [Indexed: 02/06/2023]
Abstract
The CATHeterization GENetics (CATHGEN) biorepository was assembled in four phases. First, project start-up began in 2000. Second, between 2001 and 2010, we collected clinical data and biological samples from 9334 individuals undergoing cardiac catheterization. Samples were matched at the individual level to clinical data collected at the time of catheterization and stored in the Duke Databank for Cardiovascular Diseases (DDCD). Clinical data included the following: subject demographics (birth date, race, gender, etc.); cardiometabolic history including symptoms; coronary anatomy and cardiac function at catheterization; and fasting chemistry data. Third, as part of the DDCD regular follow-up protocol, yearly evaluations included interim information: vital status (verified via National Death Index search and supplemented by Social Security Death Index search), myocardial infarction (MI), stroke, rehospitalization, coronary revascularization procedures, medication use, and lifestyle habits including smoking. Fourth, samples were used to generate molecular data. CATHGEN offers the opportunity to discover biomarkers and explore mechanisms of cardiovascular disease.
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Affiliation(s)
- William E Kraus
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA. .,Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA.
| | - Christopher B Granger
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.,Duke Clinical Research Institute, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Michael H Sketch
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Mark P Donahue
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, 27710, USA
| | - Elizabeth R Hauser
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.,Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA
| | - Carol Haynes
- Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA
| | - L Kristin Newby
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.,Duke Clinical Research Institute, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Melissa Hurdle
- Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA
| | - Z Elaine Dowdy
- Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA
| | - Svati H Shah
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.,Duke Molecular Physiology Institute, School of Medicine, Duke University, 300 N. Duke Street, Durham, NC, 27710, USA
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Kazenwadel J, Betterman KL, Chong CE, Stokes PH, Lee YK, Secker GA, Agalarov Y, Demir CS, Lawrence DM, Sutton DL, Tabruyn SP, Miura N, Salminen M, Petrova TV, Matthews JM, Hahn CN, Scott HS, Harvey NL. GATA2 is required for lymphatic vessel valve development and maintenance. J Clin Invest 2015. [PMID: 26214525 DOI: 10.1172/jci78888] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heterozygous germline mutations in the zinc finger transcription factor GATA2 have recently been shown to underlie a range of clinical phenotypes, including Emberger syndrome, a disorder characterized by lymphedema and predisposition to myelodysplastic syndrome/acute myeloid leukemia (MDS/AML). Despite well-defined roles in hematopoiesis, the functions of GATA2 in the lymphatic vasculature and the mechanisms by which GATA2 mutations result in lymphedema have not been characterized. Here, we have provided a molecular explanation for lymphedema predisposition in a subset of patients with germline GATA2 mutations. Specifically, we demonstrated that Emberger-associated GATA2 missense mutations result in complete loss of GATA2 function, with respect to the capacity to regulate the transcription of genes that are important for lymphatic vessel valve development. We identified a putative enhancer element upstream of the key lymphatic transcriptional regulator PROX1 that is bound by GATA2, and the transcription factors FOXC2 and NFATC1. Emberger GATA2 missense mutants had a profoundly reduced capacity to bind this element. Conditional Gata2 deletion in mice revealed that GATA2 is required for both development and maintenance of lymphovenous and lymphatic vessel valves. Together, our data unveil essential roles for GATA2 in the lymphatic vasculature and explain why a select catalogue of human GATA2 mutations results in lymphedema.
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25
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Gupta V, Khan AA, Sasi BK, Mahapatra NR. Molecular mechanism of monoamine oxidase A gene regulation under inflammation and ischemia-like conditions: key roles of the transcription factors GATA2, Sp1 and TBP. J Neurochem 2015; 134:21-38. [PMID: 25810277 DOI: 10.1111/jnc.13099] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
Monoamine oxidase A (MAOA) plays important roles in the pathogenesis of several neurological and cardiovascular disorders. The mechanism of transcriptional regulation of MAOA under basal and pathological conditions, however, remains incompletely understood. Here, we report systematic identification and characterization of cis elements and transcription factors that govern the expression of MAOA gene. Extensive computational analysis of MAOA promoter, followed by 5'-promoter deletion/reporter assays, revealed that the -71/-40 bp domain was sufficient for its basal transcription. Gel-shift and chromatin immunoprecipitation assays provided evidence of interactions of the transcription factors GATA-binding protein 2 (GATA2), Sp1 and TATA-binding protein (TBP) with this proximal promoter region. Consistently, over-expression of GATA2, Sp1 and TBP augmented MAOA promoter activity in a coordinated manner. In corroboration, siRNA-mediated down-regulation of GATA2/Sp1/TBP repressed the endogenous MAOA expression as well as transfected MAOA promoter activity. Tumor necrosis factor-α and forskolin activated MAOA transcription that was reversed by Sp1 siRNA; in support, tumor necrosis factor-α- and forskolin-induced activities were enhanced by ectopic over-expression of Sp1. On the other hand, MAOA transcription was diminished upon exposure of neuroblasts or cardiac myoblasts to ischemia-like conditions because of reduced binding of GATA2/Sp1/TBP with MAOA promoter. In conclusion, this study revealed previously unknown roles of GATA2, Sp1 and TBP in modulating MAOA expression under basal as well as pathophysiological conditions such as inflammation and ischemia, thus providing new insights into the molecular basis of aberrant MAOA expression in neuronal/cardiovascular disease states. Dysregulation of monoamine oxidase A (MAOA) have been implicated in several behavioral and neuronal disease states. Here, we identified three crucial transcription factors (GATA2, Sp1 and TBP) that regulate MAOA gene expression in a coordinated manner. Aberrant MAOA expression under pathophysiological conditions including inflammation and ischemia is mediated by altered binding of GATA2/Sp1/TBP with MAOA proximal promoter. Thus, these findings provide new insights into pathogenesis of several common diseases. GATA2, GATA-binding protein 2; Sp1, specificity protein 1; TBP, TATA-binding protein.
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Affiliation(s)
- Vinayak Gupta
- Cardiovascular Genetics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Abrar A Khan
- Cardiovascular Genetics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Binu K Sasi
- Cardiovascular Genetics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Nitish R Mahapatra
- Cardiovascular Genetics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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26
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G RK, K MS, G KK, Kurapati M, M S, T MA, P C, G SR, S N, P K, K SS, H SR. Evaluation of Hs-CRP levels and interleukin 18 (-137G/C) promoter polymorphism in risk prediction of coronary artery disease in first degree relatives. PLoS One 2015; 10:e0120359. [PMID: 25822970 PMCID: PMC4379155 DOI: 10.1371/journal.pone.0120359] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/20/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Coronary Artery Disease (CAD) is clearly a multifactorial disease that develops from childhood and ultimately leads to death. Several reports revealed having a First Degree Relatives (FDRS) with premature CAD is a significant autonomous risk factor for CAD development. C - reactive protein (CRP) is a member of the pentraxin family and is the most widely studied proinflammatory biomarker. IL-18 is a pleiotrophic and proinflammatory cytokine which is produced mainly by macrophages and plays an important role in the inflammatory cascade. METHODS AND RESULTS Hs-CRP levels were estimated by ELISA and Genotyping of IL-18 gene variant located on promoter -137 (G/C) by Allele specific PCR in blood samples of 300 CAD patients and 300 controls and 100 FDRS. Promoter Binding sites and Protein interacting partners were identified by Alibaba 2.1 and Genemania online tools respectively. Hs-CRP levels were significantly high in CAD patients followed by FDRS when compared to controls. In IL-18 -137 (G/C) polymorphism homozygous GG is significantly associated with occurrence of CAD and Hs-CRP levels were significantly higher in GG genotype subjects when compared to GC and CC. IL-18 was found to be interacting with 100 protein interactants. CONCLUSION Our results indicate that Hs-CRP levels and IL-18-137(G/C) polymorphism may help to identify risk of future events of CAD in asymptomatic healthy FDRS.
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Affiliation(s)
- Rajesh Kumar G
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Mrudula Spurthi K
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Kishore Kumar G
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | | | - Saraswati M
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Mohini Aiyengar T
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Chiranjeevi P
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Srilatha Reddy G
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Nivas S
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Kaushik P
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
| | - Sanjib Sahu K
- Durgabai Deshmukh Hospital and Research Center, Vidyanagar, Hyderabad 500007, Telangana, India
| | - Surekha Rani H
- Department of Genetics, Osmania University, Hyderabad 500007, Telangana, India
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Parizadeh SA, Jamialahmadi K, Rooki H, Mirhafez SR, Moohebati M, Hosseini N, Zaim-Kohan H, Mohiti-Ardakani J, Masoudi A, Ferns GA, Ghayour-Mobarhan M. Lack of an association between a functional polymorphism in the neuropeptide Y gene promoter and the presence of coronary artery disease in an Iranian population. ANNALS OF NUTRITION AND METABOLISM 2014; 65:333-40. [PMID: 25427865 DOI: 10.1159/000367854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS Several genetic factors have been identified that may contribute to the risk of coronary artery disease (CAD). Variants of the neuropeptide Y (NPY) gene, whose products play an important role in regulating several physiological functions, have been associated with the risk of CAD in some populations. The purpose of this study was to investigate the relationship between the NPY gene rs16147 polymorphism and the presence of CAD in an Iranian population. METHODS DNA samples of 922 subjects, including 433 with angiographically defined CAD (CAD+), 196 without angiographically defined significant CAD (CAD-) and 293 controls, were genotyped using polymerase chain reaction based on the amplification-refractory mutation system. Logistic regression analyses were performed to assess the association of rs16147 genotypes with the presence of significant CAD. RESULTS Although logistic regression analysis indicated that the NPY polymorphism rs16147 was nominally associated with an increased risk of CAD (p < 0.05), after adjustment for confounding factors, there was no evidence for any significantly increased or decreased risk of CAD with this polymorphism. However, in stratified analyses, the C allele was significantly associated with a reduced risk of CAD in males and subjects who were <50 years of age. CONCLUSIONS This study suggests that the rs16147 polymorphism in the NPY gene may not be a potential contributor to the risk of CAD in an Iranian population.
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Affiliation(s)
- Seyed Alireza Parizadeh
- Biochemistry of Nutrition Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Galimudi RK, Spurthi MK, Padala C, Kumar KG, Mudigonda S, Reddy SG, Aiyengar MT, Sahu SK, Rani SH. Interleukin 6(-174G/C) variant and its circulating levels in coronary artery disease patients and their first degree relatives. Inflammation 2014; 37:314-21. [PMID: 24072607 DOI: 10.1007/s10753-013-9742-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interleukin-6 (IL-6) a pleiotropic cytokine is a central mediator of inflammation in the pathogenesis of coronary artery disease (CAD). Our aim is to evaluate the serum levels of IL-6 and C-reactive protein (CRP) and to analyze the IL-6 polymorphism in CAD patients and to identify the first-degree relatives (FDRs) at risk of the disease in comparison with healthy controls. Estimation of IL-6 levels by enzyme-linked immunosorbent assay (ELISA) and CRP by latex reagent kit method, and genotyping of IL6 gene variants -174 (G>C) was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 600 subjects. IL-6 and CRP levels were significantly high in patients followed by FDRs compared to controls. The frequency of the IL-6 genotype was significantly different between cases, FDRs and controls and association of serum IL-6 levels with genotype found to be significant in CC genotype compared to GC and GG at p < 0.01 in CAD patients and FDRs, while there is no significant difference observed in controls. The study shows the importance of inflammation in the pathogenesis of CAD and predicts the risk of future coronary events in healthy asymptomatic FDRs.
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29
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Effect of interactions between genetic polymorphisms and cigarette smoking on plasma triglyceride levels in elderly Koreans: the Hallym Aging Study. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0234-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese. Eur J Hum Genet 2014; 23:374-80. [PMID: 24916648 DOI: 10.1038/ejhg.2014.110] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 05/01/2014] [Accepted: 05/08/2014] [Indexed: 12/18/2022] Open
Abstract
Despite considerable progress in preventive and therapeutic strategies, myocardial infarction (MI) is one of the leading causes of death throughout the world. A total of 55 susceptibility genes have been identified mostly in European genome-wide association studies (GWAS). Nevertheless, large-scale GWAS from other population could possibly find additional susceptibility loci. To identify as many MI susceptibility loci as possible, we performed a large-scale genomic analysis in Japanese population. To identify MI susceptibility loci in Japanese, we conducted a GWAS using 1666 cases and 3198 controls using the Illumina Human610-Quad BeadChip and HumanHap550v3 Genotyping BeadChip. We performed replication studies using a total of 11,412 cases and 28,397 controls in the Japanese population. Our study identified two novel susceptibility loci for MI: PLCL2 on chromosome 3p24.3 (rs4618210:A>G, P = 2.60 × 10(-9), odds ratio (OR) = 0.91) and AP3D1-DOT1L-SF3A2 on chromosome 19p13.3 (rs3803915:A>C, P = 3.84 × 10(-9), OR = 0.89). Besides, a total of 14 previously reported MI susceptibility loci were replicated in our study. In particular, we validated a strong association on chromosome 12q24 (rs3782886:A>G: P = 1.14 × 10(-14), OR = 1.46). Following pathway analysis using 265 genes related to MI or coronary artery disease, we found that these loci might be involved in the pathogenesis of MI via the promotion of atherosclerosis. In the present large-scale genomic analysis, we identified PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for MI in the Japanese population. Our findings will add novel findings for MI susceptibility loci.
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31
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Muiya NP, Wakil S, Al-Najai M, Tahir AI, Baz B, Andres E, Al-Boudari O, Al-Tassan N, Al-Shahid M, Meyer BF, Dzimiri N. A study of the role of GATA2 gene polymorphism in coronary artery disease risk traits. Gene 2014; 544:152-8. [PMID: 24786211 DOI: 10.1016/j.gene.2014.04.064] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/17/2014] [Accepted: 04/27/2014] [Indexed: 11/26/2022]
Abstract
The GATA2 is a multi-catalytic transcription factor believed to play an important role in regulating inflammatory processes, largely contributory to cardiovascular-related events. However, its role in coronary artery disease (CAD) risk traits remains poorly understood. In a preliminary study using Affymetrix 250K, we established a link on chromosome (chr) 3, which harbors the GATA2 gene, to early onset of CAD in two families with heterozygous familial hyperlipidemia (HFH), suggesting a role for the gene in metabolic-related CAD in the general population. We then sequenced the gene in the families and an additional 200 individuals in the general population, followed by an association study for 8 SNPs on CAD metabolic risk traits in a total of 4557 individuals (2386 CAD cases versus 2171 angiographed controls) by the Applied Biosystems real-time PCR system. The rs1573949_C [1.15(1.00-1.32); p=0.049] was associated with MI, rs7431368_AA [5.2(1.05-26.60); p=0.43] conferred risk for harboring low high density lipoprotein, and obesity was linked to rs10934857_AA [5.69(1.04-30.98); p=0.045] following Bonferroni corrections and multivariate adjustments for confounders. Furthermore, a haplotype CCCGGGTC (χ(2)=4.23; p=0.04) constructed from the eight studied SNPs and its 6-mer derivative CGGGTC (χ(2)=5.05; p=0.025) were associated with CAD. Obesity was associated with the 6-mer CATAAA (χ(2)=3.66; p=0.049), and hypercholesterolemia was linked to the 8-mer CCTGGACC (χ(2)=6.02; p=0.014), but most significantly so with its 5-mer derivative, CTGGA (χ(2)=6.75; p=0.009). On the other hand, high low density lipoprotein was linked to TGG (χ(2)=4.48; p=0.034). Our study points to an association of GATA2 at both SNP and haplotype levels with important metabolic risk traits for atherosclerosis.
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Affiliation(s)
- Nzioka P Muiya
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Salma Wakil
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Mohammed Al-Najai
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Asma I Tahir
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Batoul Baz
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Editha Andres
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Olyan Al-Boudari
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Nada Al-Tassan
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Maie Al-Shahid
- King Faisal Heart Institute, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Brian F Meyer
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Nduna Dzimiri
- Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh 11211, Saudi Arabia.
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Mitochondrial genetic background modulates bioenergetics and susceptibility to acute cardiac volume overload. Biochem J 2013; 455:157-67. [PMID: 23924350 DOI: 10.1042/bj20130029] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dysfunctional bioenergetics has emerged as a key feature in many chronic pathologies such as diabetes and cardiovascular disease. This has led to the mitochondrial paradigm in which it has been proposed that mtDNA sequence variation contributes to disease susceptibility. In the present study we show a novel animal model of mtDNA polymorphisms, the MNX (mitochondrial-nuclear exchange) mouse, in which the mtDNA from the C3H/HeN mouse has been inserted on to the C57/BL6 nuclear background and vice versa to test this concept. Our data show a major contribution of the C57/BL6 mtDNA to the susceptibility to the pathological stress of cardiac volume overload which is independent of the nuclear background. Mitochondria harbouring the C57/BL6J mtDNA generate more ROS (reactive oxygen species) and have a higher mitochondrial membrane potential relative to those with C3H/HeN mtDNA, independent of nuclear background. We propose this is the primary mechanism associated with increased bioenergetic dysfunction in response to volume overload. In summary, these studies support the 'mitochondrial paradigm' for the development of disease susceptibility, and show that the mtDNA modulates cellular bioenergetics, mitochondrial ROS generation and susceptibility to cardiac stress.
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Common dysfunctional variants in ABCG2 are a major cause of early-onset gout. Sci Rep 2013; 3:2014. [PMID: 23774753 PMCID: PMC3684804 DOI: 10.1038/srep02014] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/30/2013] [Indexed: 01/26/2023] Open
Abstract
Gout is a common disease which mostly occurs after middle age, but more people nowadays develop it before the age of thirty. We investigated whether common dysfunction of ABCG2, a high-capacity urate transporter which regulates serum uric acid levels, causes early-onset gout. 705 Japanese male gout cases with onset age data and 1,887 male controls were genotyped, and the ABCG2 functions which are estimated by its genotype combination were determined. The onset age was 6.5 years earlier with severe ABCG2 dysfunction than with normal ABCG2 function (P = 6.14 × 10(-3)). Patients with mild to severe ABCG2 dysfunction accounted for 88.2% of early-onset cases (twenties or younger). Severe ABCG2 dysfunction particularly increased the risk of early-onset gout (odds ratio 22.2, P = 4.66 × 10(-6)). Our finding that common dysfunction of ABCG2 is a major cause of early-onset gout will serve to improve earlier prevention and therapy for high-risk individuals.
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Dungan JR, Hauser ER, Qin X, Kraus WE. The genetic basis for survivorship in coronary artery disease. Front Genet 2013; 4:191. [PMID: 24143143 PMCID: PMC3784965 DOI: 10.3389/fgene.2013.00191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 09/06/2013] [Indexed: 01/14/2023] Open
Abstract
Survivorship is a trait characterized by endurance and virility in the face of hardship. It is largely considered a psychosocial attribute developed during fatal conditions, rather than a biological trait for robustness in the context of complex, age-dependent diseases like coronary artery disease (CAD). The purpose of this paper is to present the novel phenotype, survivorship in CAD as an observed survival advantage concurrent with clinically significant CAD. We present a model for characterizing survivorship in CAD and its relationships with overlapping time- and clinically-related phenotypes. We offer an optimal measurement interval for investigating survivorship in CAD. We hypothesize genetic contributions to this construct and review the literature for evidence of genetic contribution to overlapping phenotypes in support of our hypothesis. We also present preliminary evidence of genetic effects on survival in people with clinically significant CAD from a primary case-control study of symptomatic coronary disease. Identifying gene variants that confer improved survival in the context of clinically appreciable CAD may improve our understanding of cardioprotective mechanisms acting at the gene level and potentially impact patients clinically in the future. Further, characterizing other survival-variant genetic effects may improve signal-to-noise ratio in detecting gene associations for CAD.
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Abstract
Key components of atherosclerotic plaque known to drive disease progression are macrophages and cholesterol. It has been widely understood, and bolstered by recent evidence, that the efflux of cholesterol from macrophage foam cells quells disease progression or even to promote regression. Following macrophage cholesterol efflux, cholesterol loaded onto HDL must be removed from the plaque environment. Here, we focus on recent evidence that the lymphatic vasculature is critical for the removal of cholesterol, likely as a component of HDL, from tissues including skin and the artery wall. We discuss the possibility that progression of atherosclerosis might in part be linked to sluggish removal of cholesterol from the plaque.
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Affiliation(s)
- Catherine Martel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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36
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Johnson KD, Hsu AP, Ryu MJ, Wang J, Gao X, Boyer ME, Liu Y, Lee Y, Calvo KR, Keles S, Zhang J, Holland SM, Bresnick EH. Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity. J Clin Invest 2012; 122:3692-704. [PMID: 22996659 DOI: 10.1172/jci61623] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 07/19/2012] [Indexed: 11/17/2022] Open
Abstract
Haploinsufficiency for GATA2 causes human immunodeficiency syndromes characterized by mycobacterial infection, myelodysplasia, lymphedema, or aplastic anemia that progress to myeloid leukemia. GATA2 encodes a master regulator of hematopoiesis that is also linked to endothelial biology. Though the disease-causing mutations commonly occur in the GATA-2 DNA binding domain, we identified a patient with mycobacterial infection and myelodysplasia who had an uncharacterized heterozygous deletion in a GATA2 cis-element consisting of an E-box and a GATA motif. Targeted deletion of the equivalent murine element to yield homozygous mutant mice revealed embryonic lethality later than occurred with global Gata2 knockout, hematopoietic stem/progenitor cell depletion, and impaired vascular integrity. Heterozygous mutant mice were viable, but embryos exhibited deficits in definitive, but not primitive, hematopoietic stem/progenitor activity and reduced expression of Gata2 and its target genes. Mechanistic analysis revealed disruption of the endothelial cell transcriptome and loss of vascular integrity. Thus, the composite element disrupted in a human immunodeficiency is essential for establishment of the murine hematopoietic stem/progenitor cell compartment in the fetal liver and for essential vascular processes.
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Affiliation(s)
- Kirby D Johnson
- Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, USA
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Abstract
Sample tracking errors have been and always will be a part of the practical implementation of large experiments. It has recently been proposed that expression quantitative trait loci (eQTLs) and their associated effects could be used to identify sample mix-ups and this approach has been applied to a number of large population genomics studies to illustrate the prevalence of the problem. We had adopted a similar approach, termed ‘BADGER’, in the METABRIC project. METABRIC is a large breast cancer study that may have been the first in which eQTL-based detection of mismatches was used during the study, rather than after the event, to aid quality assurance. We report here on the particular issues associated with large cancer studies performed using historical samples, which complicate the interpretation of such approaches. In particular we identify the complications of using tumour samples, of considering cellularity and RNA quality, of distinct subgroups existing in the study population (including family structures), and of choosing eQTLs to use. We also present some results regarding the design of experiments given consideration of these matters. The eQTL-based approach to identifying sample tracking errors is seen to be of value to these studies, but requiring care in its implementation.
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Grossman TR, Gamliel A, Wessells RJ, Taghli-Lamallem O, Jepsen K, Ocorr K, Korenberg JR, Peterson KL, Rosenfeld MG, Bodmer R, Bier E. Over-expression of DSCAM and COL6A2 cooperatively generates congenital heart defects. PLoS Genet 2011; 7:e1002344. [PMID: 22072978 PMCID: PMC3207880 DOI: 10.1371/journal.pgen.1002344] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/29/2011] [Indexed: 11/19/2022] Open
Abstract
A significant current challenge in human genetics is the identification of interacting genetic loci mediating complex polygenic disorders. One of the best characterized polygenic diseases is Down syndrome (DS), which results from an extra copy of part or all of chromosome 21. A short interval near the distal tip of chromosome 21 contributes to congenital heart defects (CHD), and a variety of indirect genetic evidence suggests that multiple candidate genes in this region may contribute to this phenotype. We devised a tiered genetic approach to identify interacting CHD candidate genes. We first used the well vetted Drosophila heart as an assay to identify interacting CHD candidate genes by expressing them alone and in all possible pairwise combinations and testing for effects on rhythmicity or heart failure following stress. This comprehensive analysis identified DSCAM and COL6A2 as the most strongly interacting pair of genes. We then over-expressed these two genes alone or in combination in the mouse heart. While over-expression of either gene alone did not affect viability and had little or no effect on heart physiology or morphology, co-expression of the two genes resulted in ≈50% mortality and severe physiological and morphological defects, including atrial septal defects and cardiac hypertrophy. Cooperative interactions between DSCAM and COL6A2 were also observed in the H9C2 cardiac cell line and transcriptional analysis of this interaction points to genes involved in adhesion and cardiac hypertrophy. Our success in defining a cooperative interaction between DSCAM and COL6A2 suggests that the multi-tiered genetic approach we have taken involving human mapping data, comprehensive combinatorial screening in Drosophila, and validation in vivo in mice and in mammalian cells lines should be applicable to identifying specific loci mediating a broad variety of other polygenic disorders.
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Affiliation(s)
- Tamar R. Grossman
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Amir Gamliel
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Ouarda Taghli-Lamallem
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Kristen Jepsen
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Karen Ocorr
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Julie R. Korenberg
- The Brain Institute, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Kirk L. Peterson
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Rolf Bodmer
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
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Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development 2011; 138:4555-64. [PMID: 21937602 PMCID: PMC3177320 DOI: 10.1242/dev.066779] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2011] [Indexed: 12/20/2022]
Abstract
Zinc-finger nucleases (ZFNs) allow targeted gene inactivation in a wide range of model organisms. However, construction of target-specific ZFNs is technically challenging. Here, we evaluate a straightforward modular assembly-based approach for ZFN construction and gene inactivation in zebrafish. From an archive of 27 different zinc-finger modules, we assembled more than 70 different zinc-finger cassettes and evaluated their specificity using a bacterial one-hybrid assay. In parallel, we constructed ZFNs from these cassettes and tested their ability to induce lesions in zebrafish embryos. We found that the majority of zinc-finger proteins assembled from these modules have favorable specificities and nearly one-third of modular ZFNs generated lesions at their targets in the zebrafish genome. To facilitate the application of ZFNs within the zebrafish community we constructed a public database of sites in the zebrafish genome that can be targeted using this archive. Importantly, we generated new germline mutations in eight different genes, confirming that this is a viable platform for heritable gene inactivation in vertebrates. Characterization of one of these mutants, gata2a, revealed an unexpected role for this transcription factor in vascular development. This work provides a resource to allow targeted germline gene inactivation in zebrafish and highlights the benefit of a definitive reverse genetic strategy to reveal gene function.
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Affiliation(s)
- Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tom Smith
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joseph McNulty
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Abirami Lakshmanan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Arndt F. Siekmann
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Buffardi
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiangdong Meng
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jimann Shin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Arun Padmanabhan
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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40
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Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A 2011; 108:13641-6. [PMID: 21808000 DOI: 10.1073/pnas.1108440108] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Vascular endothelial dysfunction underlies the genesis and progression of numerous diseases. Although the GATA transcription factor GATA-2 is expressed in endothelial cells and is implicated in coronary heart disease, it has been studied predominantly as a master regulator of hematopoiesis. Because many questions regarding GATA-2 function in the vascular biology realm remain unanswered, we used ChIP sequencing and loss-of-function strategies to define the GATA-2-instigated genetic network in human endothelial cells. In contrast to erythroid cells, GATA-2 occupied a unique target gene ensemble consisting of genes encoding key determinants of endothelial cell identity and inflammation. GATA-2-occupied sites characteristically contained motifs that bind activator protein-1 (AP-1), a pivotal regulator of inflammatory genes. GATA-2 frequently occupied the same chromatin sites as c-JUN and c-FOS, heterodimeric components of AP-1. Although all three components were required for maximal AP-1 target gene expression, GATA-2 was not required for AP-1 chromatin occupancy. GATA-2 conferred maximal phosphorylation of chromatin-bound c-JUN at Ser-73, which stimulates AP-1-dependent transactivation, in a chromosomal context-dependent manner. This work establishes a link between a GATA factor and inflammatory genes, mechanistic insights underlying GATA-2-AP-1 cooperativity and a rigorous genetic framework for understanding GATA-2 function in normal and pathophysiological vascular states.
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41
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Krzywanski DM, Moellering DR, Fetterman JL, Dunham-Snary KJ, Sammy MJ, Ballinger SW. The mitochondrial paradigm for cardiovascular disease susceptibility and cellular function: a complementary concept to Mendelian genetics. J Transl Med 2011; 91:1122-35. [PMID: 21647091 PMCID: PMC3654682 DOI: 10.1038/labinvest.2011.95] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While there is general agreement that cardiovascular disease (CVD) development is influenced by a combination of genetic, environmental, and behavioral contributors, the actual mechanistic basis of how these factors initiate or promote CVD development in some individuals while others with identical risk profiles do not, is not clearly understood. This review considers the potential role for mitochondrial genetics and function in determining CVD susceptibility from the standpoint that the original features that molded cellular function were based upon mitochondrial-nuclear relationships established millions of years ago and were likely refined during prehistoric environmental selection events that today, are largely absent. Consequently, contemporary risk factors that influence our susceptibility to a variety of age-related diseases, including CVD were probably not part of the dynamics that defined the processes of mitochondrial-nuclear interaction, and thus, cell function. In this regard, the selective conditions that contributed to cellular functionality and evolution should be given more consideration when interpreting and designing experimental data and strategies. Finally, future studies that probe beyond epidemiologic associations are required. These studies will serve as the initial steps for addressing the provocative concept that contemporary human disease susceptibility is the result of selection events for mitochondrial function that increased chances for prehistoric human survival and reproductive success.
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Affiliation(s)
- David M Krzywanski
- Division of Molecular and Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
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42
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Minear MA, Crosslin DR, Sutton BS, Connelly JJ, Nelson SC, Gadson-Watson S, Wang T, Seo D, Vance JM, Sketch MH, Haynes C, Goldschmidt-Clermont PJ, Shah SH, Kraus WE, Hauser ER, Gregory SG. Polymorphic variants in tenascin-C (TNC) are associated with atherosclerosis and coronary artery disease. Hum Genet 2011; 129:641-54. [PMID: 21298289 PMCID: PMC3576662 DOI: 10.1007/s00439-011-0959-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 01/23/2011] [Indexed: 01/01/2023]
Abstract
Tenascin-C (TNC) is an extracellular matrix protein implicated in biological processes important for atherosclerotic plaque development and progression, including smooth muscle cell migration and proliferation. Previously, we observed differential expression of TNC in atherosclerotic aortas compared with healthy aortas. The goal of this study was to investigate whether common genetic variation within TNC is associated with risk of atherosclerosis and coronary artery disease (CAD) in three independent datasets. We genotyped 35 single nucleotide polymorphisms (SNPs), including 21 haplotype tagging SNPs, in two of these datasets: human aorta tissue samples (n = 205) and the CATHGEN cardiovascular study (n = 1,325). Eleven of these 35 SNPs were then genotyped in a third dataset, the GENECARD family study of early-onset CAD (n = 879 families). Three SNPs representing a block of linkage disequilibrium, rs3789875, rs12347433, and rs4552883, were significantly associated with atherosclerosis in multiple datasets and demonstrated consistent, but suggestive, genetic effects in all analyses. In combined analysis rs3789875 and rs12347433 were statistically significant after Bonferroni correction for 35 comparisons, p = 2 × 10(-6) and 5 × 10(-6), respectively. The SNP rs12347433 is a synonymous coding SNP and may be biologically relevant to the mechanism by which tenascin-C influences the pathophysiology of CAD and atherosclerosis. This is the first report of genetic association between polymorphisms in TNC and atherosclerosis or CAD.
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Affiliation(s)
- Mollie A. Minear
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA
| | - David R. Crosslin
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Beth S. Sutton
- School of Pharmacy, Campbell University, Morrisvillie, NC, USA
| | - Jessica J. Connelly
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Sarah C. Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Shera Gadson-Watson
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA
| | - Tianyuan Wang
- Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
| | - David Seo
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Michael H. Sketch
- Department of Medicine, Duke University Medical Center, Duhram, NC, USA
| | - Carol Haynes
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA
| | | | - Svati H. Shah
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Duhram, NC, USA
| | - William E. Kraus
- Department of Medicine, Duke University Medical Center, Duhram, NC, USA
| | - Elizabeth R. Hauser
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Duhram, NC, USA
| | - Simon G. Gregory
- Center for Human Genetics, Duke University Medical Center, 905 S. La Salle Street DUMC 3445, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Duhram, NC, USA
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43
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The role of the GATA2 transcription factor in normal and malignant hematopoiesis. Crit Rev Oncol Hematol 2011; 82:1-17. [PMID: 21605981 DOI: 10.1016/j.critrevonc.2011.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/18/2011] [Accepted: 04/21/2011] [Indexed: 11/23/2022] Open
Abstract
Hematopoiesis involves an elaborate regulatory network of transcription factors that coordinates the expression of multiple downstream genes, and maintains homeostasis within the hematopoietic system through the accurate orchestration of cellular proliferation, differentiation and survival. As a result, defects in the expression levels or the activity of these transcription factors are intimately linked to hematopoietic disorders, including leukemia. The GATA family of nuclear regulatory proteins serves as a prototype for the action of lineage-restricted transcription factors. GATA1 and GATA2 are expressed principally in hematopoietic lineages, and have essential roles in the development of multiple hematopoietic cells, including erythrocytes and megakaryocytes. Moreover, GATA2 is crucial for the proliferation and maintenance of hematopoietic stem cells and multipotential progenitors. In this review, we summarize the current knowledge regarding the biological properties and functions of the GATA2 transcription factor in normal and malignant hematopoiesis.
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44
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Seo D, Goldschmidt-Clermont P, Goldschidt-Clermont P, Velazquez O, Beecham G. Genomics of premature atherosclerotic vascular disease. Curr Atheroscler Rep 2010; 12:187-93. [PMID: 20425258 DOI: 10.1007/s11883-010-0104-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Atherosclerotic vascular disease is a systemic process with a common pathophysiology but with different disease manifestations depending on the vascular site. Over the past two decades, significant efforts have gone toward determining the genomic factors contributing to atherosclerotic vascular disease. Substantial information has been generated regarding the genomics of atherosclerotic coronary heart disease, and recently, several genomic analyses have looked at the cerebrovascular and peripheral vascular beds. This article reviews genomic investigations of atherosclerotic vascular disease in the coronary, cerebrovascular, and peripheral arteries. In this review, we have tried to restrict the discussion to studies of premature atherosclerosis, particularly those using non-biased genomic techniques.
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Affiliation(s)
- David Seo
- University of Miami Miller School of Medicine, 1501 NW 10th Ave, 809 Biomedical Research Building, Miami, FL 33136, USA.
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45
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van der Pouw Kraan TCTM, Schirmer SH, Fledderus JO, Moerland PD, Baggen JM, Leyen TA, van der Laan AM, Piek JJ, van Royen N, Horrevoets AJG. Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients. BMC Genomics 2010; 11:388. [PMID: 20565948 PMCID: PMC2901320 DOI: 10.1186/1471-2164-11-388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 06/21/2010] [Indexed: 11/12/2022] Open
Abstract
Background Circulating CD34+ progenitor cells have the potential to differentiate into a variety of cells, including endothelial cells. Knowledge is still scarce about the transcriptional programs used by CD34+ cells from peripheral blood, and how these are affected in coronary artery disease (CAD) patients. Results We performed a whole genome transcriptome analysis of CD34+ cells, CD4+ T cells, CD14+ monocytes, and macrophages from 12 patients with CAD and 11 matched controls. CD34+ cells, compared to other mononuclear cells from the same individuals, showed high levels of KRAB box transcription factors, known to be involved in gene silencing. This correlated with high expression levels in CD34+ cells for the progenitor markers HOXA5 and HOXA9, which are known to control expression of KRAB factor genes. The comparison of expression profiles of CD34+ cells from CAD patients and controls revealed a less naïve phenotype in patients' CD34+ cells, with increased expression of genes from the Mitogen Activated Kinase network and a lowered expression of a panel of histone genes, reaching levels comparable to that in more differentiated circulating cells. Furthermore, we observed a reduced expression of several genes involved in CXCR4-signaling and migration to SDF1/CXCL12. Conclusions The altered gene expression profile of CD34+ cells in CAD patients was related to activation/differentiation by a retinoic acid-induced differentiation program. These results suggest that circulating CD34+ cells in CAD patients are programmed by retinoic acid, leading to a reduced capacity to migrate to ischemic tissues.
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Affiliation(s)
- Tineke C T M van der Pouw Kraan
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Van der Boechorststraat, 1081BT Amsterdam, The Netherlands.
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46
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Kurzawski M, Białecka M, Sławek J, Kłodowska-Duda G, Droździk M. Association study of GATA-2 transcription factor gene (GATA2) polymorphism and Parkinson's disease. Parkinsonism Relat Disord 2010; 16:284-7. [DOI: 10.1016/j.parkreldis.2009.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 09/29/2009] [Accepted: 10/12/2009] [Indexed: 10/20/2022]
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47
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Zhang L, Connelly JJ, Peppel K, Brian L, Shah SH, Nelson S, Crosslin DR, Wang T, Allen A, Kraus WE, Gregory SG, Hauser ER, Freedman NJ. Aging-related atherosclerosis is exacerbated by arterial expression of tumor necrosis factor receptor-1: evidence from mouse models and human association studies. Hum Mol Genet 2010; 19:2754-66. [PMID: 20421368 DOI: 10.1093/hmg/ddq172] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aging is believed to be among the most important contributors to atherosclerosis, through mechanisms that remain largely obscure. Serum levels of tumor necrosis factor (TNF) rise with aging and have been correlated with the incidence of myocardial infarction. We therefore sought to determine whether genetic variation in the TNF receptor-1 gene (TNFR1) contributes to aging-related atherosclerosis in humans and whether Tnfr1 expression aggravates aging-related atherosclerosis in mice. With 1330 subjects from a coronary angiography database, we performed a case-control association study of coronary artery disease (CAD) with 16 TNFR1 single-nucleotide polymorphisms (SNPs). Two TNFR1 SNPs significantly associated with CAD in subjects >55 years old, and this association was supported by analysis of a set of 759 independent CAD cases. In multiple linear regression analysis, accounting for TNFR1 SNP rs4149573 significantly altered the relationship between aging and CAD index among 1811 subjects from the coronary angiography database. To confirm that TNFR1 contributes to aging-dependent atherosclerosis, we grafted carotid arteries from 18- and 2-month-old wild-type (WT) and Tnfr1(-/-) mice into congenic apolipoprotein E-deficient (Apoe(-/-)) mice and harvested grafts from 1 to 7 weeks post-operatively. Aged WT arteries developed accelerated atherosclerosis associated with enhanced TNFR1 expression, enhanced macrophage recruitment, reduced smooth muscle cell proliferation and collagen content, augmented apoptosis and plaque hemorrhage. In contrast, aged Tnfr1(-/-) arteries developed atherosclerosis that was indistinguishable from that in young Tnfr1(-/-) arteries and significantly less than that observed in aged WT arteries. We conclude that TNFR1 polymorphisms associate with aging-related CAD in humans, and TNFR1 contributes to aging-dependent atherosclerosis in mice.
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Affiliation(s)
- Lisheng Zhang
- Department of Medicine (Cardiology), Duke University Medical Center, Durham, NC, USA
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48
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Dandona S, Chen L, Fan M, Alam MA, Assogba O, Belanger M, Williams K, Wells GA, Tang WHW, Ellis SG, Hazen SL, McPherson R, Roberts R, Stewart AFR. The transcription factor GATA-2 does not associate with angiographic coronary artery disease in the Ottawa Heart Genomics and Cleveland Clinic GeneBank Studies. Hum Genet 2009; 127:101-5. [PMID: 19885677 DOI: 10.1007/s00439-009-0761-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 10/23/2009] [Indexed: 11/30/2022]
Abstract
The transcription factor GATA2 was reported to associate with coronary artery disease (CAD) in the family-based Genecard sample (Connelly et al. in PLoS Genet 2:e139, 2006). We asked whether GATA2 associates with sporadic cases of CAD in the Ottawa Heart Genomics Study (OHGS) and Cleveland Clinic (CC) populations. We genotyped the lead single nucleotide polymorphism (SNP) from Genecard, rs2713604 which is located in intron 5-6 of GATA2 in 600 CAD cases and 625 controls, as well as a tag SNP rs1573949 (r (2) = 0.87 in Caucasians of European ancestry in Utah from HapMap) in 1,136 cases and 1,162 controls in the OHGS1 population. A further 1,838 CAD cases and 913 controls derived from an independent sample combining genotypes from CC and OHGS2 populations were genotyped for rs1573949. Neither of the genotyped SNPs associates with CAD in the OHGS1 or CC/OHGS2 populations. Our data suggest that GATA2 does not contribute to the development of angiographic CAD among sporadic cases.
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Affiliation(s)
- Sonny Dandona
- The John & Jennifer Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
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Horne BD, Hauser ER, Wang L, Muhlestein JB, Anderson JL, Carlquist JF, Shah SH, Kraus WE. Validation study of genetic associations with coronary artery disease on chromosome 3q13-21 and potential effect modification by smoking. Ann Hum Genet 2009; 73:551-8. [PMID: 19706030 DOI: 10.1111/j.1469-1809.2009.00540.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The CATHGEN study reported associations of chromosome 3q13-21 genes (KALRN, MYLK, CDGAP, and GATA2) with early-onset coronary artery disease (CAD). This study attempted to independently validate those associations. Eleven single nucleotide polymorphisms (SNPs) were examined (rs10934490, rs16834817, rs6810298, rs9289231, rs12637456, rs1444768, rs1444754, rs4234218, rs2335052, rs3803, rs2713604) in patients (N = 1618) from the Intermountain Heart Collaborative Study (IHCS). Given the higher smoking prevalence in CATHGEN than IHCS (41% vs. 11% in controls, 74% vs. 29% in cases), smoking stratification and genotype-smoking interactions were evaluated. Suggestive association was found for GATA2 (rs2713604, p = 0.057, OR = 1.2). Among smokers, associations were found in CDGAP (rs10934490, p = 0.019, OR = 1.6) and KALRN (rs12637456, p = 0.011, OR = 2.0) and suggestive association was found in MYLK (rs16834871, p = 0.051, OR = 1.8, adjusting for gender). No SNP association was found among non-smokers, but smoking/SNP interactions were detected for CDGAP (rs10934491, p = 0.017) and KALRN (rs12637456, p = 0.010). Similar differences in SNP effects by smoking status were observed on re-analysis of CATHGEN. CAD associations were suggestive for GATA2 and among smokers significant post hoc associations were found in KALRN, MYLK, and CDGAP. Genetic risk conferred by some of these genes may be modified by smoking. Future CAD association studies of these and other genes should evaluate effect modification by smoking.
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Affiliation(s)
- Benjamin D Horne
- Cardiovascular Department, Intermountain Medical Center, Salt Lake City, UT, USA
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50
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Wang T, Furey TS, Connelly JJ, Ji S, Nelson S, Heber S, Gregory SG, Hauser ER. A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. Hum Genomics 2009; 3:221-35. [PMID: 19403457 PMCID: PMC2742312 DOI: 10.1186/1479-7364-3-3-221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factors are key mediators of human complex disease processes. Identifying the target genes of transcription factors will increase our understanding of the biological network leading to disease risk. The prediction of transcription factor binding sites (TFBSs) is one method to identify these target genes; however, current prediction methods need improvement. We chose the transcription factor upstream stimulatory factor l (USF1) to evaluate the performance of our novel TFBS prediction method because of its known genetic association with coronary artery disease (CAD) and the recent availability of USF1 chromatin immunoprecipitation microarray (ChIP-chip) results. The specific goals of our study were to develop a novel and accurate genome-scale method for predicting USF1 binding sites and associated target genes to aid in the study of CAD. Previously published USF1 ChIP-chip data for 1 per cent of the genome were used to develop and evaluate several kernel logistic regression prediction models. A combination of genomic features (phylogenetic conservation, regulatory potential, presence of a CpG island and DNaseI hypersensitivity), as well as position weight matrix (PWM) scores, were used as variables for these models. Our most accurate predictor achieved an area under the receiver operator characteristic curve of 0.827 during cross-validation experiments, significantly outperforming standard PWM-based prediction methods. When applied to the whole human genome, we predicted 24,010 USF1 binding sites within 5 kilobases upstream of the transcription start site of 9,721 genes. These predictions included 16 of 20 genes with strong evidence of USF1 regulation. Finally, in the spirit of genomic convergence, we integrated independent experimental CAD data with these USF1 binding site prediction results to develop a prioritised set of candidate genes for future CAD studies. We have shown that our novel prediction method, which employs genomic features related to the presence of regulatory elements, enables more accurate and efficient prediction of USF1 binding sites. This method can be extended to other transcription factors identified in human disease studies to help further our understanding of the biology of complex disease.
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Affiliation(s)
- Tianyuan Wang
- Department of Medicine and Center for Human Genetics, Duke University Medical Center, Durham, NC 27710, USA
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