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Popovics P, Jain A, Skalitzky KO, Schroeder E, Ruetten H, Cadena M, Uchtmann KS, Vezina CM, Ricke WA. Osteopontin Deficiency Ameliorates Prostatic Fibrosis and Inflammation. Int J Mol Sci 2021; 22:ijms222212461. [PMID: 34830342 PMCID: PMC8617904 DOI: 10.3390/ijms222212461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Fibrogenic and inflammatory processes in the prostate are linked to the development of lower urinary tract symptoms (LUTS) in men. Our previous studies identified that osteopontin (OPN), a pro-fibrotic cytokine, is abundant in the prostate of men with LUTS, and its secretion is stimulated by inflammatory cytokines potentially to drive fibrosis. This study investigates whether the lack of OPN ameliorates inflammation and fibrosis in the mouse prostate. We instilled uropathogenic E. coli (UTI89) or saline (control) transurethrally to C57BL/6J (WT) or Spp1tm1Blh/J (OPN-KO) mice and collected the prostates one or 8 weeks later. We found that OPN mRNA and protein expression were significantly induced by E. coli-instillation in the dorsal prostate (DP) after one week in WT mice. Deficiency in OPN expression led to decreased inflammation and fibrosis and the prevention of urinary dysfunction after 8 weeks. RNAseq analysis identified that E. coli-instilled WT mice expressed increased levels of inflammatory and fibrotic marker RNAs compared to OPN-KO mice including Col3a1, Dpt, Lum and Mmp3 which were confirmed by RNAscope. Our results indicate that OPN is induced by inflammation and prolongs the inflammatory state; genetic blockade of OPN accelerates recovery after inflammation, including a resolution of prostate fibrosis.
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Affiliation(s)
- Petra Popovics
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Asha Jain
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kegan O. Skalitzky
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Elise Schroeder
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Hannah Ruetten
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark Cadena
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kristen S. Uchtmann
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Chad M. Vezina
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William A. Ricke
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; (P.P.); (A.J.); (K.O.S.); (E.S.); (H.R.); (M.C.); (K.S.U.); (C.M.V.)
- George M. O’Brien Center of Research Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Correspondence:
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Chen SW, Chou SH, Tung YC, Hsiao FC, Ho CT, Chan YH, Wu VCC, Chou AH, Hsu ME, Lin PJ, Kao WWY, Chu PH. Expression and role of lumican in acute aortic dissection: A human and mouse study. PLoS One 2021; 16:e0255238. [PMID: 34310653 PMCID: PMC8312931 DOI: 10.1371/journal.pone.0255238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction Aortic dissection (AD) is a life-threatening emergency, and lumican (LUM) is a potential Biomarker for AD diagnosis. We investigated LUM expression patterns in patients with AD and explored the molecular functions of Lum in AD mice model. Methods LUM expression patterns were analyzed using aortic tissues of AD patients, and serum soluble LUM (s-LUM) levels were compared between patients with acute AD (AAD) and chronic AD (CAD). Lum-knockout (Lum−/−) mice were challenged with β-aminopropionitrile (BAPN) and angiotensin II (Ang II) to induce AD. The survival rate, AD incidence, and aortic aneurysm (AA) in these mice were compared with those in BAPN–Ang II–challenged wildtype (WT) mice. Tgf-β/Smad2, Mmps, Lum, and Nox expression patterns were examined. Results LUM expression was detected in the intima and media of the ascending aorta in patients with AAD. Serum s-LUM levels were significantly higher in patients with AAD than CAD. Furthermore, AD-associated mortality and thoracic aortic rupture incidence were significantly higher in the Lum−/− AD mice than in the WT AD mice. However, no significant pathologic changes in AA were observed in the Lum−/− AD mice compared with the WT AD mice. The BAPN–Ang II–challenged WT and Lum−/− AD mice had higher Tgf-β, p-Smad2, Mmp2, Mmp9, and Nox4 levels than those of non-AD mice. We also found that Lum expression was significantly higher in the BAPN-Ang II–challenged WT in comparison to the unchallenged WT mice. Conclusion LUM expression was altered in patients with AD display increased s-LUM in blood, and Lum−/− mice exhibited augmented AD pathogenesis. These findings support the notion that LUM is a biomarker signifying the pathogenesis of injured aorta seen in AAD. The presence of LUM is essential for maintenance of connective tissue integrity. Future studies should elucidate the mechanisms underlying LUM association in aortic changes.
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Affiliation(s)
- Shao-Wei Chen
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou Medical Center, Chang Gung University, Taoyuan City, Taiwan
- Center for Big Data Analytics and Statistics, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Shing-Hsien Chou
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Ying-Chang Tung
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Fu-Chih Hsiao
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Chien-Te Ho
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Yi-Hsin Chan
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - Victor Chien-Chia Wu
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
| | - An-Hsun Chou
- Department of Anesthesiology, Chang Gung Memorial Hospital, Linkou Medical Center, Chang Gung University, Taoyuan City, Taiwan
| | - Ming-En Hsu
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou Medical Center, Chang Gung University, Taoyuan City, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Linkou Medical Center, Chang Gung University, Taoyuan City, Taiwan
| | - Pyng-Jing Lin
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou Medical Center, Chang Gung University, Taoyuan City, Taiwan
| | - Winston W. Y. Kao
- Crawley Vision Research Center, Department of Ophthalmology, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Pao-Hsien Chu
- Department of Cardiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan City, Taiwan
- * E-mail:
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5
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Iglesias AI, Mishra A, Vitart V, Bykhovskaya Y, Höhn R, Springelkamp H, Cuellar-Partida G, Gharahkhani P, Bailey JNC, Willoughby CE, Li X, Yazar S, Nag A, Khawaja AP, Polašek O, Siscovick D, Mitchell P, Tham YC, Haines JL, Kearns LS, Hayward C, Shi Y, van Leeuwen EM, Taylor KD, Bonnemaijer P, Rotter JI, Martin NG, Zeller T, Mills RA, Souzeau E, Staffieri SE, Jonas JB, Schmidtmann I, Boutin T, Kang JH, Lucas SEM, Wong TY, Beutel ME, Wilson JF, Uitterlinden AG, Vithana EN, Foster PJ, Hysi PG, Hewitt AW, Khor CC, Pasquale LR, Montgomery GW, Klaver CCW, Aung T, Pfeiffer N, Mackey DA, Hammond CJ, Cheng CY, Craig JE, Rabinowitz YS, Wiggs JL, Burdon KP, van Duijn CM, MacGregor S. Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases. Nat Commun 2018; 9:1864. [PMID: 29760442 PMCID: PMC5951816 DOI: 10.1038/s41467-018-03646-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 03/02/2018] [Indexed: 12/17/2022] Open
Abstract
Central corneal thickness (CCT) is a highly heritable trait associated with complex eye diseases such as keratoconus and glaucoma. We perform a genome-wide association meta-analysis of CCT and identify 19 novel regions. In addition to adding support for known connective tissue-related pathways, pathway analyses uncover previously unreported gene sets. Remarkably, >20% of the CCT-loci are near or within Mendelian disorder genes. These included FBN1, ADAMTS2 and TGFB2 which associate with connective tissue disorders (Marfan, Ehlers-Danlos and Loeys-Dietz syndromes), and the LUM-DCN-KERA gene complex involved in myopia, corneal dystrophies and cornea plana. Using index CCT-increasing variants, we find a significant inverse correlation in effect sizes between CCT and keratoconus (r = -0.62, P = 5.30 × 10-5) but not between CCT and primary open-angle glaucoma (r = -0.17, P = 0.2). Our findings provide evidence for shared genetic influences between CCT and keratoconus, and implicate candidate genes acting in collagen and extracellular matrix regulation.
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MESH Headings
- ADAMTS Proteins/genetics
- ADAMTS Proteins/metabolism
- Asian People
- Cornea/abnormalities
- Cornea/metabolism
- Cornea/pathology
- Corneal Diseases/ethnology
- Corneal Diseases/genetics
- Corneal Diseases/metabolism
- Corneal Diseases/pathology
- Corneal Dystrophies, Hereditary/ethnology
- Corneal Dystrophies, Hereditary/genetics
- Corneal Dystrophies, Hereditary/metabolism
- Corneal Dystrophies, Hereditary/pathology
- Decorin/genetics
- Decorin/metabolism
- Ehlers-Danlos Syndrome/ethnology
- Ehlers-Danlos Syndrome/genetics
- Ehlers-Danlos Syndrome/metabolism
- Ehlers-Danlos Syndrome/pathology
- Eye Diseases, Hereditary/ethnology
- Eye Diseases, Hereditary/genetics
- Eye Diseases, Hereditary/metabolism
- Eye Diseases, Hereditary/pathology
- Fibrillin-1/genetics
- Fibrillin-1/metabolism
- Gene Expression
- Genome, Human
- Genome-Wide Association Study
- Glaucoma, Open-Angle/ethnology
- Glaucoma, Open-Angle/genetics
- Glaucoma, Open-Angle/metabolism
- Glaucoma, Open-Angle/pathology
- Humans
- Keratoconus/ethnology
- Keratoconus/genetics
- Keratoconus/metabolism
- Keratoconus/pathology
- Loeys-Dietz Syndrome/ethnology
- Loeys-Dietz Syndrome/genetics
- Loeys-Dietz Syndrome/metabolism
- Loeys-Dietz Syndrome/pathology
- Lumican/genetics
- Lumican/metabolism
- Marfan Syndrome/ethnology
- Marfan Syndrome/genetics
- Marfan Syndrome/metabolism
- Marfan Syndrome/pathology
- Mendelian Randomization Analysis
- Myopia/ethnology
- Myopia/genetics
- Myopia/metabolism
- Myopia/pathology
- Polymorphism, Single Nucleotide
- Proteoglycans/genetics
- Proteoglycans/metabolism
- Quantitative Trait Loci
- Quantitative Trait, Heritable
- Transforming Growth Factor beta2/genetics
- Transforming Growth Factor beta2/metabolism
- White People
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Affiliation(s)
- Adriana I Iglesias
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Aniket Mishra
- University of Bordeaux, Bordeaux Population Health Research Center, INSERM UMR 1219, F-33000, Bordeaux, France
| | - Veronique Vitart
- Institute of Genetics and Molecular Medicine, Medical Research Council Human Genetics Unit, University of Edinburgh, EH42XU, Edinburgh, UK
| | - Yelena Bykhovskaya
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, CA 90048, Los Angeles, CA, USA
- Cornea Genetic Eye Institute, CA 90048, Los Angeles, CA, USA
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, 55131, Mainz, Germany
- Department of Ophthalmology, Inselspital, University Hospital Bern, University of Bern, Bern, CH-3010, Switzerland
| | - Henriët Springelkamp
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Gabriel Cuellar-Partida
- Statistical Genetics, QIMR Berghofer Medical Research Institute, QLD 4029, Brisbane, Australia
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, QLD 4029, Brisbane, Australia
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, OH 44106, Cleveland, OH, USA
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Colin E Willoughby
- Biomedical Sciences Research Institute, Ulster University, BT52 1SA, Belfast, Northern Ireland, UK
- Royal Victoria Hospital, Belfast Health and Social Care Trust, BT12 6BA, Belfast, Northern Ireland, UK
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90509, CA, USA
- Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, CA, USA
| | - Seyhan Yazar
- Institute of Genetics and Molecular Medicine, Medical Research Council Human Genetics Unit, University of Edinburgh, EH42XU, Edinburgh, UK
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, WA 6009, Perth, WA, Australia
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, WC2R 2LS, London, UK
| | - Anthony P Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, CB2 0SR, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, EC1V 9EL, London, UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, HR-21000, Split, Croatia
| | - David Siscovick
- Departments of Medicine and Epidemiology and Cardiovascular Health Research Unit, University of Washington, WA 98101, Washington, USA
- The New York Academy of Medicine, NY 10029, New York, NY, USA
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, NSW 2145, Sydney, NSW, Australia
| | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, OH 44106, Cleveland, OH, USA
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lisa S Kearns
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, VIC 3002, East Melbourne, Australia
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, Medical Research Council Human Genetics Unit, University of Edinburgh, EH42XU, Edinburgh, UK
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
| | | | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90509, CA, USA
- Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, CA, USA
| | - Pieter Bonnemaijer
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90509, CA, USA
- Division of Genomic Outcomes, Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, CA, USA
| | - Nicholas G Martin
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD 4029, Brisbane, Australia
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, 20251, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, 20246, Hamburg, Germany
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, SA 5042, Adelaide, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, SA 5042, Adelaide, Australia
| | - Sandra E Staffieri
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, VIC 3002, East Melbourne, Australia
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, 68167, Mannheim, Germany
| | - Irene Schmidtmann
- Institute for Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, 55131, Mainz, Germany
| | - Thibaud Boutin
- Institute of Genetics and Molecular Medicine, Medical Research Council Human Genetics Unit, University of Edinburgh, EH42XU, Edinburgh, UK
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, MA, USA
| | - Sionne E M Lucas
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, TAS, Australia
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, 169857, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - Manfred E Beutel
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center Mainz, Mainz, 55131, Germany
| | - James F Wilson
- Institute of Genetics and Molecular Medicine, Medical Research Council Human Genetics Unit, University of Edinburgh, EH42XU, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, EH16 4UX, Edinburgh, UK
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, 2593 HW, The Hague, The Netherlands
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, EC1V 9EL, London, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, WC2R 2LS, London, UK
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, VIC 3002, East Melbourne, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, TAS, Australia
| | - Chiea Chuen Khor
- Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, MA, USA
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, MA, USA
| | - Grant W Montgomery
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, QLD 4029, Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD 4067, Brisbane, Australia
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, 169857, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, 55131, Mainz, Germany
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, WA 6009, Perth, WA, Australia
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, WC2R 2LS, London, UK
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, 168751, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, 169857, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, SA 5042, Adelaide, Australia
| | - Yaron S Rabinowitz
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, CA 90048, Los Angeles, CA, USA
- Cornea Genetic Eye Institute, CA 90048, Los Angeles, CA, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, MA 02114, MA, USA
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, TAS, Australia
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, QLD 4029, Brisbane, Australia.
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9
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Zhao Y, Chen J, Freudenberg JM, Meng Q, Rajpal DK, Yang X. Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci. Arterioscler Thromb Vasc Biol 2016; 36:928-41. [PMID: 26966275 PMCID: PMC5576868 DOI: 10.1161/atvbaha.115.306725] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/01/2016] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Recent genome-wide association studies of coronary artery disease (CAD) have revealed 58 genome-wide significant and 148 suggestive genetic loci. However, the molecular mechanisms through which they contribute to CAD and the clinical implications of these findings remain largely unknown. We aim to retrieve gene subnetworks of the 206 CAD loci and identify and prioritize candidate regulators to better understand the biological mechanisms underlying the genetic associations. APPROACH AND RESULTS We devised a new integrative genomics approach that incorporated (1) candidate genes from the top CAD loci, (2) the complete genetic association results from the 1000 genomes-based CAD genome-wide association studies from the Coronary Artery Disease Genome Wide Replication and Meta-Analysis Plus the Coronary Artery Disease consortium, (3) tissue-specific gene regulatory networks that depict the potential relationship and interactions between genes, and (4) tissue-specific gene expression patterns between CAD patients and controls. The networks and top-ranked regulators according to these data-driven criteria were further queried against literature, experimental evidence, and drug information to evaluate their disease relevance and potential as drug targets. Our analysis uncovered several potential novel regulators of CAD such as LUM and STAT3, which possess properties suitable as drug targets. We also revealed molecular relations and potential mechanisms through which the top CAD loci operate. Furthermore, we found that multiple CAD-relevant biological processes such as extracellular matrix, inflammatory and immune pathways, complement and coagulation cascades, and lipid metabolism interact in the CAD networks. CONCLUSIONS Our data-driven integrative genomics framework unraveled tissue-specific relations among the candidate genes of the CAD genome-wide association studies loci and prioritized novel network regulatory genes orchestrating biological processes relevant to CAD.
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Affiliation(s)
- Yuqi Zhao
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.)
| | - Jing Chen
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.)
| | - Johannes M Freudenberg
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.)
| | - Qingying Meng
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.)
| | - Deepak K Rajpal
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.).
| | - Xia Yang
- From the Department of Integrative Biology and Physiology, University of California, Los Angeles (Y.Z., Q.M., X.Y.); and Target Sciences Computational Biology (US), GSK, King of Prussia, PA (J.C., J.M.F., D.K.R.).
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