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Sun Y, Zheng H, Wang M, Gu R, Wu X, Yang Q, Zhao H, Bi Y, Zheng J. The effect of histo-blood group ABO system transferase (BGAT) on pregnancy related outcomes:A Mendelian randomization study. Comput Struct Biotechnol J 2024; 23:2067-2075. [PMID: 38800635 PMCID: PMC11126538 DOI: 10.1016/j.csbj.2024.04.040] [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: 10/28/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Protein level of Histo-Blood Group ABO System Transferase (BGAT) has been reported to be associated with cardiometabolic diseases. But its effect on pregnancy related outcomes still remains unclear. Here we conducted a two-sample Mendelian randomization (MR) study to ascertain the putative causal roles of protein levels of BGAT in pregnancy related outcomes. Cis-acting protein quantitative trait loci (pQTLs) robustly associated with protein level of BGAT (P < 5 ×10-8) were used as instruments to proxy the BGAT protein level (N = 35,559, data from deCODE), with two additional pQTL datasets from Fenland (N = 10,708) and INTERVAL (N = 3301) used as validation exposures. Ten pregnancy related diseases and complications were selected as outcomes. We observed that a higher protein level of BGAT showed a putative causal effect on venous complications and haemorrhoids in pregnancy (VH) (odds ratio [OR]=1.19, 95% confidence interval [95% CI]=1.12-1.27, colocalization probability=91%), which was validated by using pQTLs from Fenland and INTERVAL. The Mendelian randomization results further showed effects of the BGAT protein on gestational hypertension (GH) (OR=0.97, 95% CI=0.96-0.99), despite little colocalization evidence to support it. Sensitivity analyses, including proteome-wide Mendelian randomization of the cis-acting BGAT pQTLs, showed little evidence of horizontal pleiotropy. Correctively, our study prioritised BGAT as a putative causal protein for venous complications and haemorrhoids in pregnancy. Future epidemiology and clinical studies are needed to investigate whether BGAT can be considered as a drug target to prevent adverse pregnancy outcomes.
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Affiliation(s)
- Yuqi Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haonan Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Basic Medical Science,Shanghai Jiao Tong University School of Medicine, China
| | - Manqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
| | - Rongrong Gu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Health Science and Technology,Shanghai Jiao Tong University School of Medicine, China
| | - Xueyan Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Yang
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Huiling Zhao
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
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Erdman V, Tuktarova I, Nasibullin T, Timasheva Y, Petintseva A, Korytina G. Polygenic markers of survival and longevity in the antioxidant genes PON1, PON2, MTHFR, MSRA, SOD1, NQO1, and CAT in a 20-year follow-up study in the population from the Volga-Ural region. Gene 2024; 919:148510. [PMID: 38679184 DOI: 10.1016/j.gene.2024.148510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Genetic background of healthy or pathological styles of aging and human lifespan is determined by joint gene interactions. Lucky combinations of antioxidant gene polymorphisms can result in a highly adaptive phenotype, providing a successful way to interact with external triggers. Our purpose was to identify the polygenic markers of survival and longevity in the antioxidant genes among elderly people with physiological and pathological aging. METHODS In a 20-year follow-up study of 2350 individuals aged 18-114 years residing in the Volga-Ural region of Russia, sex-adjusted association analyses of MTHFR rs1801133, MSRA rs10098474, PON1 rs662, PON2 rs7493, SOD1 rs2070424, NQO1 rs1131341 and CAT rs1001179 polymorphic loci with longevity were carried out. Survival analysis was subsequently performed using the established single genes and gene-gene combinations as cofactors. RESULTS The PON1 rs662*G allele was defined as the main longevity marker in women (OR = 1.44, p = 3E-04 in the log-additive model; HR = 0.77, p = 1.9E-04 in the Cox-survival model). The polymorphisms in the MTHFR, MSRA, PON2, SOD1, and CAT genes had an additive effect on longevity. A strong protective effect of combined MTHFR rs1801133*C, MSRA rs10098474*T, PON1 rs662*G, and PON2 rs7493*C alleles against mortality was obtained in women (HR = 0.81, p = 5E-03). The PON1 rs662*A allele had a meaningful impact on mortality for both long-lived men with cerebrovascular accidents (HR = 1.76, p = 0.027 for the PON1 rs662*AG genotype) and women with cardiovascular diseases (HR = 1.43, p = 0.002 for PON1 rs662*AA genotype). The MTHFR rs1801133*TT (HR = 1.91, p = 0.036), CAT rs1001179*TT (HR = 2.83, p = 0.031) and SOD1 rs2070424*AG (HR = 1.58, p = 0.018) genotypes were associated with the cancer mortality. CONCLUSION In our longitudinal 20-year study, we found the combinations of functional polymorphisms in antioxidant genes involved in longevity and survival in certain clinical phenotypes in the advanced age.
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Affiliation(s)
- Vera Erdman
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia.
| | - Ilsia Tuktarova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Timur Nasibullin
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Yanina Timasheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia; Bashkir State Medical University, Ufa 450008, Russia
| | - Anna Petintseva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Gulnaz Korytina
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia; Bashkir State Medical University, Ufa 450008, Russia
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3
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Kentistou KA, Kaisinger LR, Stankovic S, Vaudel M, Mendes de Oliveira E, Messina A, Walters RG, Liu X, Busch AS, Helgason H, Thompson DJ, Santoni F, Petricek KM, Zouaghi Y, Huang-Doran I, Gudbjartsson DF, Bratland E, Lin K, Gardner EJ, Zhao Y, Jia RY, Terao C, Riggan MJ, Bolla MK, Yazdanpanah M, Yazdanpanah N, Bradfield JP, Broer L, Campbell A, Chasman DI, Cousminer DL, Franceschini N, Franke LH, Girotto G, He C, Järvelin MR, Joshi PK, Kamatani Y, Karlsson R, Luan J, Lunetta KL, Mägi R, Mangino M, Medland SE, Meisinger C, Noordam R, Nutile T, Concas MP, Polašek O, Porcu E, Ring SM, Sala C, Smith AV, Tanaka T, van der Most PJ, Vitart V, Wang CA, Willemsen G, Zygmunt M, Ahearn TU, Andrulis IL, Anton-Culver H, Antoniou AC, Auer PL, Barnes CLK, Beckmann MW, Berrington de Gonzalez A, Bogdanova NV, Bojesen SE, Brenner H, Buring JE, Canzian F, Chang-Claude J, Couch FJ, Cox A, Crisponi L, Czene K, Daly MB, Demerath EW, Dennis J, Devilee P, De Vivo I, Dörk T, Dunning AM, Dwek M, Eriksson JG, Fasching PA, Fernandez-Rhodes L, Ferreli L, Fletcher O, Gago-Dominguez M, García-Closas M, García-Sáenz JA, González-Neira A, Grallert H, Guénel P, Haiman CA, Hall P, Hamann U, Hakonarson H, Hart RJ, Hickey M, Hooning MJ, Hoppe R, Hopper JL, Hottenga JJ, Hu FB, Huebner H, Hunter DJ, Jernström H, John EM, Karasik D, Khusnutdinova EK, Kristensen VN, Lacey JV, Lambrechts D, Launer LJ, Lind PA, Lindblom A, Magnusson PKE, Mannermaa A, McCarthy MI, Meitinger T, Menni C, Michailidou K, Millwood IY, Milne RL, Montgomery GW, Nevanlinna H, Nolte IM, Nyholt DR, Obi N, O'Brien KM, Offit K, Oldehinkel AJ, Ostrowski SR, Palotie A, Pedersen OB, Peters A, Pianigiani G, Plaseska-Karanfilska D, Pouta A, Pozarickij A, Radice P, Rennert G, Rosendaal FR, Ruggiero D, Saloustros E, Sandler DP, Schipf S, Schmidt CO, Schmidt MK, Small K, Spedicati B, Stampfer M, Stone J, Tamimi RM, Teras LR, Tikkanen E, Turman C, Vachon CM, Wang Q, Winqvist R, Wolk A, Zemel BS, Zheng W, van Dijk KW, Alizadeh BZ, Bandinelli S, Boerwinkle E, Boomsma DI, Ciullo M, Chenevix-Trench G, Cucca F, Esko T, Gieger C, Grant SFA, Gudnason V, Hayward C, Kolčić I, Kraft P, Lawlor DA, Martin NG, Nøhr EA, Pedersen NL, Pennell CE, Ridker PM, Robino A, Snieder H, Sovio U, Spector TD, Stöckl D, Sudlow C, Timpson NJ, Toniolo D, Uitterlinden A, Ulivi S, Völzke H, Wareham NJ, Widen E, Wilson JF, Pharoah PDP, Li L, Easton DF, Njølstad PR, Sulem P, Murabito JM, Murray A, Manousaki D, Juul A, Erikstrup C, Stefansson K, Horikoshi M, Chen Z, Farooqi IS, Pitteloud N, Johansson S, Day FR, Perry JRB, Ong KK. Understanding the genetic complexity of puberty timing across the allele frequency spectrum. Nat Genet 2024:10.1038/s41588-024-01798-4. [PMID: 38951643 DOI: 10.1038/s41588-024-01798-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 05/13/2024] [Indexed: 07/03/2024]
Abstract
Pubertal timing varies considerably and is associated with later health outcomes. We performed multi-ancestry genetic analyses on ~800,000 women, identifying 1,080 signals for age at menarche. Collectively, these explained 11% of trait variance in an independent sample. Women at the top and bottom 1% of polygenic risk exhibited ~11 and ~14-fold higher risks of delayed and precocious puberty, respectively. We identified several genes harboring rare loss-of-function variants in ~200,000 women, including variants in ZNF483, which abolished the impact of polygenic risk. Variant-to-gene mapping approaches and mouse gonadotropin-releasing hormone neuron RNA sequencing implicated 665 genes, including an uncharacterized G-protein-coupled receptor, GPR83, which amplified the signaling of MC3R, a key nutritional sensor. Shared signals with menopause timing at genes involved in DNA damage response suggest that the ovarian reserve might signal centrally to trigger puberty. We also highlight body size-dependent and independent mechanisms that potentially link reproductive timing to later life disease.
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Affiliation(s)
- Katherine A Kentistou
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Lena R Kaisinger
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Edson Mendes de Oliveira
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Andrea Messina
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alexander S Busch
- Department of General Pediatrics, University of Münster, Münster, Germany
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Federico Santoni
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Konstantin M Petricek
- Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Berlin, Germany
| | - Yassine Zouaghi
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Isabel Huang-Doran
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Eirik Bratland
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Raina Y Jia
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Marjorie J Riggan
- Department of Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Jonathan P Bradfield
- Quantinuum Research, Wayne, PA, USA
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Diana L Cousminer
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lude H Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Chunyan He
- Department of Internal Medicine, Division of Medical Oncology, University of Kentucky College of Medicine, Lexington, KY, USA
- Cancer Prevention and Control Research Program, Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu, Finland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI's and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St. Thomas' Foundation Trust, London, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, University Hospital of Augsburg, Augsburg, Germany
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Teresa Nutile
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Eleonora Porcu
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Carol A Wang
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Marek Zygmunt
- Clinic of Gynaecology and Obstetrics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Catriona L K Barnes
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Laura Crisponi
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Healthcare, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
- Yong Loo Lin School of Medicine, Department of Obstetrics and Gynecology and Human Potential Translational Research Programme, National University Singapore, Singapore City, Singapore
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | | | - Liana Ferreli
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS Santiago de Compostela, Coruña, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services Bethesda, Bethesda, MD, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy INSERM, University Paris-Saclay, UVSQ, Orsay, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roger J Hart
- Division of Obstetrics and Gynaecology, University of Western Australia, Crawley, Western Australia, Australia
| | - Martha Hickey
- Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, Victoria, Australia
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health School of Public Health, Boston, MA, USA
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Helena Jernström
- Oncology, Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine Stanford, Stanford, CA, USA
- Department of Medicine, Division of Oncology Stanford Cancer Institute, Stanford University School of Medicine Stanford, Stanford, CA, USA
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Penelope A Lind
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dale R Nyholt
- School of Biomedical Sciences, Faculty of Health, Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nadia Obi
- Institute for Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Rigshospitalet-University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aarno Palotie
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology-IBE, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Giulia Pianigiani
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', MASA, Skopje, Republic of North Macedonia
| | - Anneli Pouta
- National Institute for Health and Welfare, Helsinki, Finland
| | - Alfred Pozarickij
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paolo Radice
- Unit of Preventive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS, Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Gad Rennert
- Faculty of Medicine, Clalit National Cancer Control Center, Carmel Medical Center and Technion, Haifa, Israel
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
- IRCCS Neuromed, Isernia, Italy
| | - Emmanouil Saloustros
- Division of Oncology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Sabine Schipf
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Meir Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia Perth, Perth, Western Australia, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Emmi Tikkanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Babette S Zemel
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ko W van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam; Amsterdam Public Health (APH) Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marina Ciullo
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, Naples, Italy
- IRCCS Neuromed, Isernia, Italy
| | | | - Francesco Cucca
- Institute of Genetics and Biomedical Research, National Research Council, Sardinia, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ellen A Nøhr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics and Gynecology, Odense University Hospital, Odense, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Pennell
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Department of Maternity and Gynaecology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Doris Stöckl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- State Institute of Health, Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Cathie Sudlow
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Nic J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffele Hospital, Milano, Italy
| | - André Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Sheila Ulivi
- Institute for Maternal and Child Health-IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Adolescent Clinic, Haukeland University Hospital, Bergen, Norway
| | | | - Joanne M Murabito
- NHLBI's and Boston University's Framingham Heart Study, Framingham, MA, USA
- Boston University Chobanian and Avedisian School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA, USA
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, RILD Level 3, Royal Devon and Exeter Hospital, Exeter, UK
| | - Despoina Manousaki
- Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center, University of Montreal, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Anders Juul
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Nelly Pitteloud
- Division of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Ken K Ong
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
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4
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Kim T, Surapaneni AL, Schmidt IM, Eadon MT, Kalim S, Srivastava A, Palsson R, Stillman IE, Hodgin JB, Menon R, Otto EA, Coresh J, Grams ME, Waikar SS, Rhee EP. Plasma Proteins Associated with Chronic Histopathologic Lesions on Kidney Biopsy. J Am Soc Nephrol 2024; 35:910-922. [PMID: 38656806 DOI: 10.1681/asn.0000000000000358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Key Points
Proteomic profiling identified 35 blood proteins associated with chronic histopathologic lesions in the kidney.Testican-2 was expressed in the glomerulus, released by the kidney into circulation, and inversely associated with glomerulosclerosis severity.NELL1 was expressed in tubular epithelial cells, released by the kidney into circulation, and inversely associated with interstitial fibrosis and tubular atrophy severity.
Background
The severity of chronic histopathologic lesions on kidney biopsy is independently associated with higher risk of progressive CKD. Because kidney biopsies are invasive, identification of blood markers that report on underlying kidney histopathology has the potential to enhance CKD care.
Methods
We examined the association between 6592 plasma protein levels measured by aptamers and the severity of interstitial fibrosis and tubular atrophy (IFTA), glomerulosclerosis, arteriolar sclerosis, and arterial sclerosis among 434 participants of the Boston Kidney Biopsy Cohort. For proteins significantly associated with at least one histologic lesion, we assessed renal arteriovenous protein gradients among 21 individuals who had undergone invasive catheterization and assessed the expression of the cognate gene among 47 individuals with single-cell RNA sequencing data in the Kidney Precision Medicine Project.
Results
In models adjusted for eGFR, proteinuria, and demographic factors, we identified 35 proteins associated with one or more chronic histologic lesions, including 20 specific for IFTA, eight specific for glomerulosclerosis, and one specific for arteriolar sclerosis. In general, higher levels of these proteins were associated with more severe histologic score and lower eGFR. Exceptions included testican-2 and NELL1, which were associated with less glomerulosclerosis and IFTA, respectively, and higher eGFR; notably, both of these proteins demonstrated significantly higher levels from artery to renal vein, demonstrating net kidney release. In the Kidney Precision Medicine Project, 13 of the 35 protein hits had cognate gene expression enriched in one or more cell types in the kidney, including podocyte expression of select glomerulosclerosis markers (including testican-2) and tubular expression of several IFTA markers (including NELL1).
Conclusions
Proteomic analysis identified circulating proteins associated with chronic histopathologic lesions, some of which had concordant site-specific expression within the kidney.
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Affiliation(s)
- Taesoo Kim
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Aditya L Surapaneni
- Department of Medicine, New York University Grossman School of Medicine, New York, New York
| | - Insa M Schmidt
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sahir Kalim
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Anand Srivastava
- Division of Nephrology, University of Illinois Chicago, Chicago, Illinois
| | - Ragnar Palsson
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Isaac E Stillman
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Edgar A Otto
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Josef Coresh
- Departments of Population Health and Medicine, New York University Grossman School of Medicine, New York, New York
| | - Morgan E Grams
- Department of Medicine, New York University Grossman School of Medicine, New York, New York
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts
| | - Eugene P Rhee
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
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5
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Si S, Liu H, Xu L, Zhan S. Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome. Genome Med 2024; 16:84. [PMID: 38898508 PMCID: PMC11186236 DOI: 10.1186/s13073-024-01356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome. METHODS We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein-protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy). RESULTS Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10-1.24), IGFBP-5 (OR 0.43, 95% CI 0.29-0.62), sRAGE (OR 1.14, 95% CI 1.07-1.22), GNPTG (OR 0.90, 95% CI 0.86-0.95), and YOD1 (OR 1.39, 95% CI 1.18-1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells. CONCLUSIONS Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
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Affiliation(s)
- Shucheng Si
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Hongyan Liu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Siyan Zhan
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China.
- Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
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6
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Desai TA, Hedman ÅK, Dimitriou M, Koprulu M, Figiel S, Yin W, Johansson M, Watts EL, Atkins JR, Sokolov AV, Schiöth HB, Gunter MJ, Tsilidis KK, Martin RM, Pietzner M, Langenberg C, Mills IG, Lamb AD, Mälarstig A, Key TJ, Travis RC, Smith-Byrne K. Identifying proteomic risk factors for overall, aggressive, and early onset prostate cancer using Mendelian Randomisation and tumour spatial transcriptomics. EBioMedicine 2024; 105:105168. [PMID: 38878676 DOI: 10.1016/j.ebiom.2024.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Understanding the role of circulating proteins in prostate cancer risk can reveal key biological pathways and identify novel targets for cancer prevention. METHODS We investigated the association of 2002 genetically predicted circulating protein levels with risk of prostate cancer overall, and of aggressive and early onset disease, using cis-pQTL Mendelian randomisation (MR) and colocalisation. Findings for proteins with support from both MR, after correction for multiple-testing, and colocalisation were replicated using two independent cancer GWAS, one of European and one of African ancestry. Proteins with evidence of prostate-specific tissue expression were additionally investigated using spatial transcriptomic data in prostate tumour tissue to assess their role in tumour aggressiveness. Finally, we mapped risk proteins to drug and ongoing clinical trials targets. FINDINGS We identified 20 proteins genetically linked to prostate cancer risk (14 for overall [8 specific], 7 for aggressive [3 specific], and 8 for early onset disease [2 specific]), of which the majority replicated where data were available. Among these were proteins associated with aggressive disease, such as PPA2 [Odds Ratio (OR) per 1 SD increment = 2.13, 95% CI: 1.54-2.93], PYY [OR = 1.87, 95% CI: 1.43-2.44] and PRSS3 [OR = 0.80, 95% CI: 0.73-0.89], and those associated with early onset disease, including EHPB1 [OR = 2.89, 95% CI: 1.99-4.21], POGLUT3 [OR = 0.76, 95% CI: 0.67-0.86] and TPM3 [OR = 0.47, 95% CI: 0.34-0.64]. We confirmed an inverse association of MSMB with prostate cancer overall [OR = 0.81, 95% CI: 0.80-0.82], and also found an inverse association with both aggressive [OR = 0.84, 95% CI: 0.82-0.86] and early onset disease [OR = 0.71, 95% CI: 0.68-0.74]. Using spatial transcriptomics data, we identified MSMB as the genome-wide top-most predictive gene to distinguish benign regions from high grade cancer regions that comparatively had five-fold lower MSMB expression. Additionally, ten proteins that were associated with prostate cancer risk also mapped to existing therapeutic interventions. INTERPRETATION Our findings emphasise the importance of proteomics for improving our understanding of prostate cancer aetiology and of opportunities for novel therapeutic interventions. Additionally, we demonstrate the added benefit of in-depth functional analyses to triangulate the role of risk proteins in the clinical aggressiveness of prostate tumours. Using these integrated methods, we identify a subset of risk proteins associated with aggressive and early onset disease as priorities for investigation for the future prevention and treatment of prostate cancer. FUNDING This work was supported by Cancer Research UK (grant no. C8221/A29017).
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Affiliation(s)
- Trishna A Desai
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom.
| | - Åsa K Hedman
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marios Dimitriou
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge, United Kingdom
| | - Sandy Figiel
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Wencheng Yin
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Eleanor L Watts
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Joshua R Atkins
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience Uppsala University, 75124, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience Uppsala University, 75124, Uppsala, Sweden
| | - Marc J Gunter
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, United Kingdom; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; NIHR Bristol Biomedical Research Centre, Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, United Kingdom
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, United Kingdom; Computational Medicine, Berlin Institute of HealthHealth (BIH) at Charité - Univeritätsmedizin- Universitätsmedizin Berlin, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, United Kingdom; Computational Medicine, Berlin Institute of HealthHealth (BIH) at Charité - Univeritätsmedizin- Universitätsmedizin Berlin, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, United Kingdom
| | - Ian G Mills
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Alastair D Lamb
- University of Oxford, Nuffield Department of Surgical Sciences, Oxford, United Kingdom
| | - Anders Mälarstig
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tim J Key
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Ruth C Travis
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, United Kingdom
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7
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Rao P, Keyes MJ, Mi MY, Barber JL, Tahir UA, Deng S, Clish CB, Shen D, Farrell LA, Wilson JG, Gao Y, Yimer WK, Ekunwe L, Hall ME, Muntner PM, Guo X, Taylor KD, Tracy RP, Rich SS, Rotter JI, Xanthakis V, Vasan RS, Bouchard C, Sarzynski MA, Gerszten RE, Robbins JM. Plasma Proteomics of Exercise Blood Pressure and Incident Hypertension. JAMA Cardiol 2024:2820069. [PMID: 38865108 PMCID: PMC11170454 DOI: 10.1001/jamacardio.2024.1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/10/2024] [Indexed: 06/13/2024]
Abstract
Importance Blood pressure response during acute exercise (exercise blood pressure [EBP]) is associated with the future risk of hypertension and cardiovascular disease (CVD). Biochemical characterization of EBP could inform disease biology and identify novel biomarkers of future hypertension. Objective To identify protein markers associated with EBP and test their association with incident hypertension. Design, Setting, and Participants This study assayed 4977 plasma proteins in 681 healthy participants (from 763 assessed) of the Health, Risk Factors, Exercise Training and Genetics (HERITAGE; data collection from January 1993 to December 1997 and plasma proteomics from January 2019 to January 2020) Family Study at rest who underwent 2 cardiopulmonary exercise tests. Individuals were free of CVD at the time of recruitment. Individuals with resting SBP ≥160 mm Hg or DBP ≥100 mm Hg or taking antihypertensive drug therapy were excluded from the study. The association between resting plasma protein levels to both resting BP and EBP was evaluated. Proteins associated with EBP were analyzed for their association with incident hypertension in the Framingham Heart Study (FHS; n = 1177) and validated in the Jackson Heart Study (JHS; n = 772) and Multi-Ethnic Study of Atherosclerosis (MESA; n = 1367). Proteins associated with incident hypertension were tested for putative causal links in approximately 700 000 individuals using cis-protein quantitative loci mendelian randomization (cis-MR). Data were analyzed from January 2023 to January 2024. Exposures Plasma proteins. Main Outcomes and Measures EBP was defined as the BP response during a fixed workload (50 W) on a cycle ergometer. Hypertension was defined as BP ≥140/90 mm Hg or taking antihypertensive medication. Results Among the 681 participants in the HERITAGE Family Study, the mean (SD) age was 34 (13) years; 366 participants (54%) were female; 238 (35%) were self-reported Black and 443 (65%) were self-reported White. Proteomic profiling of EBP revealed 34 proteins that would not have otherwise been identified through profiling of resting BP alone. Transforming growth factor β receptor 3 (TGFBR3) and prostaglandin D2 synthase (PTGDS) had the strongest association with exercise systolic BP (SBP) and diastolic BP (DBP), respectively (TGFBR3: exercise SBP, β estimate, -3.39; 95% CI, -4.79 to -2.00; P = 2.33 × 10-6; PTGDS: exercise DBP β estimate, -2.50; 95% CI, -3.29 to -1.70; P = 1.18 × 10-9). In fully adjusted models, TGFBR3 was inversely associated with incident hypertension in FHS, JHS, and MESA (hazard ratio [HR]: FHS, 0.86; 95% CI, 0.75-0.97; P = .01; JHS, 0.87; 95% CI, 0.77-0.97; P = .02; MESA, 0.84; 95% CI, 0.71-0.98; P = .03; pooled cohort, 0.86; 95% CI, 0.79-0.92; P = 6 × 10-5). Using cis-MR, genetically predicted levels of TGFBR3 were associated with SBP, hypertension, and CVD events (SBP: β, -0.38; 95% CI, -0.64 to -0.11; P = .006; hypertension: odds ratio [OR], 0.99; 95% CI, 0.98-0.99; P < .001; heart failure with hypertension: OR, 0.86; 95% CI, 0.77-0.97; P = .01; CVD: OR, 0.84; 95% CI, 0.77-0.92; P = 8 × 10-5; cerebrovascular events: OR, 0.77; 95% CI, 0.70-0.85; P = 5 × 10-7). Conclusions and Relevance Plasma proteomic profiling of EBP identified a novel protein, TGFBR3, which may protect against elevated BP and long-term CVD outcomes.
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Affiliation(s)
- Prashant Rao
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michelle. J. Keyes
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael Y. Mi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jacob L. Barber
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia
| | - Usman A. Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shuliang Deng
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Clary B. Clish
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge
| | - Dongxiao Shen
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Laurie. A. Farrell
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - James G. Wilson
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Yan Gao
- Department of Data Sciences, University of Mississippi Medical Center, Jackson
| | - Wondwosen K. Yimer
- Department of Data Sciences, University of Mississippi Medical Center, Jackson
| | - Lynette Ekunwe
- Jackson Heart Study Field Center, University of Mississippi Medical Center, Jackson
| | - Michael E. Hall
- Department of Medicine, Division of Cardiology, University of Mississippi Medical Center, Jackson
| | - Paul M. Muntner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Russell P. Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Vanessa Xanthakis
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | - Mark A. Sarzynski
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge
| | - Jeremy M. Robbins
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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8
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat SM, Kentistou KA, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman BR, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman ND, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Genetic drivers and cellular selection of female mosaic X chromosome loss. Nature 2024:10.1038/s41586-024-07533-7. [PMID: 38867047 DOI: 10.1038/s41586-024-07533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of female individuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose female individuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valdislav Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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9
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Sikirzhytskaya A, Tyagin I, Sutton SS, Wyatt MD, Safro I, Shtutman M. AI-based mining of biomedical literature: Applications for drug repurposing for the treatment of dementia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597745. [PMID: 38895485 PMCID: PMC11185689 DOI: 10.1101/2024.06.06.597745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Neurodegenerative pathologies such as Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis, Multiple sclerosis, HIV-associated neurocognitive disorder, and others significantly affect individuals, their families, caregivers, and healthcare systems. While there are no cures yet, researchers worldwide are actively working on the development of novel treatments that have the potential to slow disease progression, alleviate symptoms, and ultimately improve the overall health of patients. Huge volumes of new scientific information necessitate new analytical approaches for meaningful hypothesis generation. To enable the automatic analysis of biomedical data we introduced AGATHA, an effective AI-based literature mining tool that can navigate massive scientific literature databases, such as PubMed. The overarching goal of this effort is to adapt AGATHA for drug repurposing by revealing hidden connections between FDA-approved medications and a health condition of interest. Our tool converts the abstracts of peer-reviewed papers from PubMed into multidimensional space where each gene and health condition are represented by specific metrics. We implemented advanced statistical analysis to reveal distinct clusters of scientific terms within the virtual space created using AGATHA-calculated parameters for selected health conditions and genes. Partial Least Squares Discriminant Analysis was employed for categorizing and predicting samples (122 diseases and 20889 genes) fitted to specific classes. Advanced statistics were employed to build a discrimination model and extract lists of genes specific to each disease class. Here we focus on drugs that can be repurposed for dementia treatment as an outcome of neurodegenerative diseases. Therefore, we determined dementia-associated genes statistically highly ranked in other disease classes. Additionally, we report a mechanism for detecting genes common to multiple health conditions. These sets of genes were classified based on their presence in biological pathways, aiding in selecting candidates and biological processes that are exploitable with drug repurposing. Author Summary This manuscript outlines our project involving the application of AGATHA, an AI-based literature mining tool, to discover drugs with the potential for repurposing in the context of neurocognitive disorders. The primary objective is to identify connections between approved medications and specific health conditions through advanced statistical analysis, including techniques like Partial Least Squares Discriminant Analysis (PLSDA) and unsupervised clustering. The methodology involves grouping scientific terms related to different health conditions and genes, followed by building discrimination models to extract lists of disease-specific genes. These genes are then analyzed through pathway analysis to select candidates for drug repurposing.
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10
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Wang J, Gu R, Kong X, Luan S, Luo YLL. Genome-wide association studies (GWAS) and post-GWAS analyses of impulsivity: A systematic review. Prog Neuropsychopharmacol Biol Psychiatry 2024; 132:110986. [PMID: 38430953 DOI: 10.1016/j.pnpbp.2024.110986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Impulsivity is related to a host of mental and behavioral problems. It is a complex construct with many different manifestations, most of which are heritable. The genetic compositions of these impulsivity manifestations, however, remain unclear. A number of genome-wide association studies (GWAS) and post-GWAS analyses have tried to address this issue. We conducted a systematic review of all GWAS and post-GWAS analyses of impulsivity published up to December 2023. Available data suggest that single nucleotide polymorphisms (SNPs) in more than a dozen of genes (e.g., CADM2, CTNNA2, GPM6B) are associated with different measures of impulsivity at genome-wide significant levels. Post-GWAS analyses further show that different measures of impulsivity are subject to different degrees of genetic influence, share few genetic variants, and have divergent genetic overlap with basic personality traits such as extroversion and neuroticism, cognitive ability, psychiatric disorders, substance use, and obesity. These findings shed light on controversies in the conceptualization and measurement of impulsivity, while providing new insights on the underlying mechanisms that yoke impulsivity to psychopathology.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Ruolei Gu
- Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Xiangzhen Kong
- Department of Psychology and Behavioral Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; Department of Psychiatry of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 Qingchundong Road, Hangzhou 310016, China
| | - Shenghua Luan
- Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Yu L L Luo
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China; Department of Psychology, University of Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China.
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11
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Ghosh S, Bouchard C. Considerations on efforts needed to improve our understanding of the genetics of obesity. Int J Obes (Lond) 2024:10.1038/s41366-024-01528-0. [PMID: 38849463 DOI: 10.1038/s41366-024-01528-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Affiliation(s)
- Sujoy Ghosh
- Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA.
| | - Claude Bouchard
- Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA.
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12
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Gong J, Williams DM, Scholes S, Assaad S, Bu F, Hayat S, Zaninotto P, Steptoe A. Unraveling the role of plasma proteins in dementia: insights from two cohort studies in the UK, with causal evidence from Mendelian randomization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.04.24308415. [PMID: 38883777 PMCID: PMC11177911 DOI: 10.1101/2024.06.04.24308415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Population-based proteomics offer a groundbreaking avenue to predict dementia onset. This study employed a proteome-wide, data-driven approach to investigate protein-dementia associations in 229 incident all-cause dementia (ACD) among 3,249 participants from the English Longitudinal Study of Ageing (ELSA) over a median 9.8-year follow-up, then validated in 1,506 incident ACD among 52,745 individuals from the UK Biobank (UKB) over median 13.7 years. NEFL and RPS6KB1 were robustly associated with incident ACD; MMP12 was associated with vascular dementia in ELSA. Additional markers EDA2R and KIM1 (HAVCR1) were identified from sensitivity analyses. Combining NEFL and RPS6KB1 with other factors yielded high predictive accuracy (area under the curve (AUC)=0.871) for incident ACD. Replication in the UKB confirmed associations between identified proteins with various dementia subtypes. Results from reverse Mendelian Randomization also supported the role of several proteins as early dementia biomarkers. These findings underscore proteomics' potential in identifying novel risk screening targets for dementia.
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Vacik Díaz R, Munsch G, Iglesias MJ, Pallares Robles A, Ibrahim-Kosta M, Nourse J, Khan E, Castoldi E, Saut N, Boland A, Germain M, Deleuze JF, Odeberg J, Morange PE, Danckwardt S, Tregouët DA, Goumidi L. Plasma levels of complement components C5 and C9 are associated with thrombin generation. J Thromb Haemost 2024:S1538-7836(24)00312-X. [PMID: 38838952 DOI: 10.1016/j.jtha.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/30/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND The thrombin generation assay (TGA) evaluates the potential of plasma to generate thrombin over time, providing a global picture of an individual's hemostatic balance. OBJECTIVES This study aimed to identify novel biological determinants of thrombin generation using a multiomics approach. METHODS Associations between TGA parameters and plasma levels of 377 antibodies targeting 236 candidate proteins for cardiovascular risk were tested using multiple linear regression analysis in 770 individuals with venous thrombosis from the Marseille Thrombosis Association (MARTHA) study. Proteins associated with at least 3 TGA parameters were selected for validation in an independent population of 536 healthy individuals (Etablissement Français du Sang Alpes-Méditerranée [EFS-AM]). Proteins with strongest associations in both groups underwent additional genetic analyses and in vitro experiments. RESULTS Eighteen proteins were associated (P < 1.33 × 10⁻4) with at least 3 TGA parameters in MARTHA, among which 13 demonstrated a similar pattern of associations in EFS-AM. Complement proteins C5 and C9 had the strongest associations in both groups. Ex vivo supplementation of platelet-poor plasma with purified C9 protein had a significant dose-dependent effect on TGA parameters. No effect was observed with purified C5. Several single nucleotide polymorphisms associated with C5 and C9 plasma levels were identified, with the strongest association for the C5 missense variant rs17611, which was associated with a decrease in C5 levels, endogenous thrombin potential, and peak in MARTHA. No association of this variant with TGA parameters was observed in EFS-AM. CONCLUSION This study identified complement proteins C5 and C9 as potential determinants of thrombin generation. Further studies are warranted to establish causality and elucidate the underlying mechanisms.
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Affiliation(s)
- Rocío Vacik Díaz
- Cardiovascular and Nutrition Research Center Centre de recherche en CardioVasculaire et Nutrition (C2VN), Aix-Marseille University, Institut national de la santé et de la recherche médicale 1263, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement 1260, Marseille, France; Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg, Mainz, Germany. https://twitter.com/RocioVacik
| | - Gaëlle Munsch
- Institut national de la santé et de la recherche médicale Unité Mixte de Recherche_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Maria Jesus Iglesias
- Science for Life Laboratory, Kungliga Tekniska högskolan-Royal Institute of Technology, Stockholm, Sweden
| | - Alejandro Pallares Robles
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg, Mainz, Germany
| | - Manal Ibrahim-Kosta
- Cardiovascular and Nutrition Research Center Centre de recherche en CardioVasculaire et Nutrition (C2VN), Aix-Marseille University, Institut national de la santé et de la recherche médicale 1263, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement 1260, Marseille, France; Department of Hematology, Centre Hospitalier Universitaire Timone, Marseille, France
| | - Jamie Nourse
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg, Mainz, Germany
| | - Essak Khan
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg, Mainz, Germany
| | - Elisabetta Castoldi
- Department of Biochemistry, Cell Biochemistry of Thrombosis and Haemostasis, Maastricht University, Maastricht, the Netherlands
| | - Noémie Saut
- Department of Hematology, Centre Hospitalier Universitaire Timone, Marseille, France
| | - Anne Boland
- Commissariat à l'énergie atomique et aux énergies alternatives, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Marine Germain
- Institut national de la santé et de la recherche médicale Unité Mixte de Recherche_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Jean-François Deleuze
- Commissariat à l'énergie atomique et aux énergies alternatives, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Jacob Odeberg
- Science for Life Laboratory, Kungliga Tekniska högskolan-Royal Institute of Technology, Stockholm, Sweden
| | - Pierre-Emmanuel Morange
- Cardiovascular and Nutrition Research Center Centre de recherche en CardioVasculaire et Nutrition (C2VN), Aix-Marseille University, Institut national de la santé et de la recherche médicale 1263, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement 1260, Marseille, France; Department of Hematology, Centre Hospitalier Universitaire Timone, Marseille, France
| | - Sven Danckwardt
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg, Mainz, Germany
| | - David-Alexandre Tregouët
- Institut national de la santé et de la recherche médicale Unité Mixte de Recherche_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Louisa Goumidi
- Cardiovascular and Nutrition Research Center Centre de recherche en CardioVasculaire et Nutrition (C2VN), Aix-Marseille University, Institut national de la santé et de la recherche médicale 1263, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement 1260, Marseille, France.
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Suhre K, Chen Q, Halama A, Mendez K, Dahlin A, Stephan N, Thareja G, Sarwath H, Guturu H, Dwaraka VB, Batzoglou S, Schmidt F, Lasky-Su JA. A genome-wide association study of mass spectrometry proteomics using the Seer Proteograph platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596028. [PMID: 38853852 PMCID: PMC11160678 DOI: 10.1101/2024.05.27.596028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Genome-wide association studies (GWAS) with proteomics are essential tools for drug discovery. To date, most studies have used affinity proteomics platforms, which have limited discovery to protein panels covered by the available affinity binders. Furthermore, it is not clear to which extent protein epitope changing variants interfere with the detection of protein quantitative trait loci (pQTLs). Mass spectrometry-based (MS) proteomics can overcome some of these limitations. Here we report a GWAS using the MS-based Seer Proteograph™ platform with blood samples from a discovery cohort of 1,260 American participants and a replication in 325 individuals from Asia, with diverse ethnic backgrounds. We analysed 1,980 proteins quantified in at least 80% of the samples, out of 5,753 proteins quantified across the discovery cohort. We identified 252 and replicated 90 pQTLs, where 30 of the replicated pQTLs have not been reported before. We further investigated 200 of the strongest associated cis-pQTLs previously identified using the SOMAscan and the Olink platforms and found that up to one third of the affinity proteomics pQTLs may be affected by epitope effects, while another third were confirmed by MS proteomics to be consistent with the hypothesis that genetic variants induce changes in protein expression. The present study demonstrates the complementarity of the different proteomics approaches and reports pQTLs not accessible to affinity proteomics, suggesting that many more pQTLs remain to be discovered using MS-based platforms.
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Affiliation(s)
- Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Anna Halama
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Amber Dahlin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Nisha Stephan
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
| | - Hina Sarwath
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
| | | | | | | | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144 Doha, Qatar
| | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, U.S.A
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15
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Gholami M. Novel genetic association between obesity, colorectal cancer, and inflammatory bowel disease. J Diabetes Metab Disord 2024; 23:739-744. [PMID: 38932827 PMCID: PMC11196566 DOI: 10.1007/s40200-023-01343-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/06/2023] [Indexed: 06/28/2024]
Abstract
Purpose Obesity/overweight is an important risk factor for CRC and IBD. The aim of this study was to investigate the role of common genetic factors and haplotypes associated with obesity, CRC and IBD. Methods Significant GWAS variants associated with CRC, IBD or obesity were extracted from the GWAS catalog. The common variants between CRC-IBD, CRC-obesity or IBD-obesity were identified. Finally, the haplotypic structure between these diseases was identified, and SNP function analysis, gene-gene expression, protein-protein interactions, gene survival analysis and pathway analysis were performed with the results. Results While the results showed several common variants between CRC and IBD, IBD and obesity, and CRC and obesity identified in previous GWAS, rs3184504 was the only common variant for CRC-IBD-obesity (P ≤ 5E-8). The result also identified a haplotypic block AGCAGT (r2 ≥ 0.8 and D'≥0.08) associated with the common variants of CRC-IBD-obesity. These variants are located on the SH2B3 gene, whose expression level decreases in both colon and rectal cancers (P ≤ 1E-3) and which has protein-protein interaction with inflammation- and cancer-associated genes. Conclusion The rs3184504 variant and the novel haplotype AGCAGT co-occurred in CRC, IBD, obesity, and inflammation. This novel haplotype could potentially be used in genetic panels to identify CRC/IBD susceptibility in obese patients.
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Affiliation(s)
- Morteza Gholami
- North Research Center, Pasteur Institute of Iran, Amol, Iran
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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16
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Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024; 23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, Cambridge, Massachusetts, USA.
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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17
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Yoo L, Mendoza D, Richard AJ, Stephens JM. KAT8 beyond Acetylation: A Survey of Its Epigenetic Regulation, Genetic Variability, and Implications for Human Health. Genes (Basel) 2024; 15:639. [PMID: 38790268 PMCID: PMC11121512 DOI: 10.3390/genes15050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Lysine acetyltransferase 8, also known as KAT8, is an enzyme involved in epigenetic regulation, primarily recognized for its ability to modulate histone acetylation. This review presents an overview of KAT8, emphasizing its biological functions, which impact many cellular processes and range from chromatin remodeling to genetic and epigenetic regulation. In many model systems, KAT8's acetylation of histone H4 lysine 16 (H4K16) is critical for chromatin structure modification, which influences gene expression, cell proliferation, differentiation, and apoptosis. Furthermore, this review summarizes the observed genetic variability within the KAT8 gene, underscoring the implications of various single nucleotide polymorphisms (SNPs) that affect its functional efficacy and are linked to diverse phenotypic outcomes, ranging from metabolic traits to neurological disorders. Advanced insights into the structural biology of KAT8 reveal its interaction with multiprotein assemblies, such as the male-specific lethal (MSL) and non-specific lethal (NSL) complexes, which regulate a wide range of transcriptional activities and developmental functions. Additionally, this review focuses on KAT8's roles in cellular homeostasis, stem cell identity, DNA damage repair, and immune response, highlighting its potential as a therapeutic target. The implications of KAT8 in health and disease, as evidenced by recent studies, affirm its importance in cellular physiology and human pathology.
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Affiliation(s)
- Lindsey Yoo
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David Mendoza
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Allison J. Richard
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
| | - Jacqueline M. Stephens
- Adipocyte Biology Laboratory, Pennington Biomedical, Baton Rouge, LA 70808, USA; (L.Y.); (D.M.); (A.J.R.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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18
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Feng T, Jie M, Deng K, Yang J, Jiang H. Targeted plasma proteomic analysis uncovers a high-performance biomarker panel for early diagnosis of gastric cancer. Clin Chim Acta 2024; 558:119675. [PMID: 38631604 DOI: 10.1016/j.cca.2024.119675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Gastric cancer (GC) is characterized by high morbidity, high mortality and low early diagnosis rate. Early diagnosis plays a crucial role in radically treating GC. The aim of this study was to identify plasma biomarkers for GC and early GC diagnosis. METHODS We quantified 369 protein levels with plasma samples from discovery cohort (n = 88) and validation cohort (n = 50) via high-throughput proximity extension assay (PEA) utilizing the Olink-Explore-384-Cardiometabolic panel. The multi-protein signatures were derived from LASSO and Ridge regression models. RESULTS In the discovery cohort, 13 proteins (GDF15, ITIH3, BOC, DPP7, EGFR, AMY2A, CCDC80, CD163, GPNMB, LTBP2, CTSZ, CCL18 and NECTIN2) were identified to distinguish GC (Stage I-IV) and early GC (HGIN-I) groups from control group with AUC of 0.994 and AUC of 0.998, severally. The validation cohort yielded AUC of 0.930 and AUC of 0.818 for GC and early GC, respectively. CONCLUSIONS This study identified a multi-protein signature with the potential to benefit clinical GC diagnosis, especially for Asian and early GC patients, which may contribute to the development of a less-invasive, convenient, and efficient early screening tool, promoting early diagnosis and treatment of GC and ultimately improving patient survival.
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Affiliation(s)
- Tong Feng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Minwen Jie
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Kai Deng
- Department of Gastroenterology & Hepatology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jinlin Yang
- Department of Gastroenterology & Hepatology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Hao Jiang
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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Assary E, Coleman J, Hemani G, van Der Veijer M, Howe L, Palviainen T, Grasby K, Ahlskog R, Nygaard M, Cheesman R, Lim K, Reynolds C, Ordoñana J, Colodro-Conde L, Gordon S, Madrid-Valero J, Thalamuthu A, Hottenga JJ, Mengel-From J, Armstrong NJ, Sachdev P, Lee T, Brodaty H, Trollor J, Wright M, Ames D, Catts V, Latvala A, Vuoksimaa E, Mallard T, Harden K, Tucker-Drob E, Oskarsson S, Hammond C, Christensen K, Taylor M, Lundström S, Larsson H, Karlsson R, Pedersen N, Mather K, Medland S, Boomsma D, Martin N, Plomin R, Bartels M, Lichtenstein P, Kaprio J, Eley T, Davies N, Munroe P, Keers R. Genetics of environmental sensitivity to psychiatric and neurodevelopmental phenotypes: evidence from GWAS of monozygotic twins. RESEARCH SQUARE 2024:rs.3.rs-4333635. [PMID: 38746362 PMCID: PMC11092831 DOI: 10.21203/rs.3.rs-4333635/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Individual sensitivity to environmental exposures may be genetically influenced. This genotype-by-environment interplay implies differences in phenotypic variance across genotypes. However, environmental sensitivity genetic variants have proven challenging to detect. GWAS of monozygotic twin differences is a family-based variance analysis method, which is more robust to systemic biases that impact population-based methods. We combined data from up to 21,792 monozygotic twins (10,896 pairs) from 11 studies to conduct the largest GWAS meta-analysis of monozygotic phenotypic differences in children and adolescents/adults for seven psychiatric and neurodevelopmental phenotypes: attention deficit hyperactivity disorder (ADHD) symptoms, autistic traits, anxiety and depression symptoms, psychotic-like experiences, neuroticism, and wellbeing. The SNP-heritability of variance in these phenotypes were estimated (h2: 0% to 18%), but were imprecise. We identified a total of 13 genome-wide significant associations (SNP, gene, and gene-set), including genes related to stress-reactivity for depression, growth factor-related genes for autistic traits and catecholamine uptake-related genes for psychotic-like experiences. Monozygotic twins are an important new source of evidence about the genetics of environmental sensitivity.
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Affiliation(s)
| | - Jonathan Coleman
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London
| | | | | | | | - Teemu Palviainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Karen Mather
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW)
| | | | - D Boomsma
- Vrije Universiteit Amsterdam, The Netherlands
| | | | - Robert Plomin
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London
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Zhang W, Lu T, Sladek R, Li Y, Najafabadi H, Dupuis J. SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. Bioinformatics 2024; 40:btae295. [PMID: 38688586 PMCID: PMC11105950 DOI: 10.1093/bioinformatics/btae295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
MOTIVATION Colocalization analysis is commonly used to assess whether two or more traits share the same genetic signals identified in genome-wide association studies (GWAS), and is important for prioritizing targets for functional follow-up of GWAS results. Existing colocalization methods can have suboptimal performance when there are multiple causal variants in one genomic locus. RESULTS We propose SharePro to extend the COLOC framework for colocalization analysis. SharePro integrates linkage disequilibrium (LD) modeling and colocalization assessment by grouping correlated variants into effect groups. With an efficient variational inference algorithm, posterior colocalization probabilities can be accurately estimated. In simulation studies, SharePro demonstrated increased power with a well-controlled false positive rate at a low computational cost. Compared to existing methods, SharePro provided stronger and more consistent colocalization evidence for known lipid-lowering drug target proteins and their corresponding lipid traits. Through an additional challenging case of the colocalization analysis of the circulating abundance of R-spondin 3 GWAS and estimated bone mineral density GWAS, we demonstrated the utility of SharePro in identifying biologically plausible colocalized signals. AVAILABILITY AND IMPLEMENTATION SharePro for colocalization analysis is written in Python and openly available at https://github.com/zhwm/SharePro_coloc.
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Affiliation(s)
- Wenmin Zhang
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec H1T 1C8, Canada
| | - Tianyuan Lu
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert Sladek
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Yue Li
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada
| | - Hamed Najafabadi
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Josée Dupuis
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, McGill College, QC H3A 1Y7, Canada
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21
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Lin R, Zhu Y, Chen W, Wang Z, Wang Y, Du J. Identification of Circulating Inflammatory Proteins Associated with Calcific Aortic Valve Stenosis by Multiplex Analysis. Cardiovasc Toxicol 2024; 24:499-512. [PMID: 38589550 DOI: 10.1007/s12012-024-09854-5] [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: 03/06/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
Calcific aortic valve stenosis (CAVS) is characterized by increasing inflammation and progressive calcification in the aortic valve leaflets and is a major cause of death in the aging population. This study aimed to identify the inflammatory proteins involved in CAVS and provide potential therapeutic targets. We investigated the observational and causal associations of 92 inflammatory proteins, which were measured using affinity-based proteomic assays. Firstly, the case-control cohort identified differential proteins associated with the occurrence and progression of CAVS. Subsequently, we delved into exploring the causal impacts of these associated proteins through Mendelian randomization. This involved utilizing genetic instruments derived from cis-protein quantitative loci identified in genome-wide association studies, encompassing a cohort of over 400,000 individuals. Finally, we investigated the gene transcription and protein expression levels of inflammatory proteins by single-cell and immunohistochemistry analysis. Multivariate logistic regression and spearman's correlation analysis showed that five proteins showed a significant positive correlation with disease severity. Mendelian randomization showed that elevated levels of two proteins, namely, matrix metallopeptidase-1 (MMP1) and sirtuin 2 (SIRT2), were associated with an increased risk of CAVS. Immunohistochemistry and single-cell transcriptomes showed that expression levels of MMP1 and SIRT2 at the tissue and cell levels were significantly higher in calcified valves than in non-calcified control valves. These findings indicate that MMP1 and SIRT2 are causally related to CAVS and open up the possibility for identifying novel therapeutic targets.
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Affiliation(s)
- Rui Lin
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Yuexin Zhu
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Weiyao Chen
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Zhiao Wang
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China
| | - Yuan Wang
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China.
| | - Jie Du
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Anzhen Road, Chaoyang District, Beijing, 100029, China.
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22
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Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [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: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
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Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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23
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Gagnon E, Girard A, Bourgault J, Abner E, Gill D, Thériault S, Vohl MC, Tchernof A, Esko T, Mathieu P, Arsenault BJ. Genetic assessment of efficacy and safety profiles of coagulation cascade proteins identifies Factors II and XI as actionable anticoagulant targets. EUROPEAN HEART JOURNAL OPEN 2024; 4:oeae043. [PMID: 38933427 PMCID: PMC11200102 DOI: 10.1093/ehjopen/oeae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 06/28/2024]
Abstract
Aims Anticoagulants are routinely used by millions of patients worldwide to prevent blood clots. Yet, problems with anticoagulant therapy remain, including a persistent and cumulative bleeding risk in patients undergoing prolonged anticoagulation. New safer anticoagulant targets are needed. Methods and results To prioritize anticoagulant targets with the strongest efficacy [venous thromboembolism (VTE) prevention] and safety (low bleeding risk) profiles, we performed two-sample Mendelian randomization and genetic colocalization. We leveraged three large-scale plasma protein data sets (deCODE as discovery data set and Fenland and Atherosclerosis Risk in Communities as replication data sets] and one liver gene expression data set (Institut Universitaire de Cardiologie et de Pneumologie de Québec bariatric biobank) to evaluate evidence for a causal effect of 26 coagulation cascade proteins on VTE from a new genome-wide association meta-analysis of 44 232 VTE cases and 847 152 controls, stroke subtypes, bleeding outcomes, and parental lifespan as an overall measure of efficacy/safety ratio. A 1 SD genetically predicted reduction in F2 blood levels was associated with lower risk of VTE [odds ratio (OR) = 0.44, 95% confidence interval (CI) = 0.38-0.51, P = 2.6e-28] and cardioembolic stroke risk (OR = 0.55, 95% CI = 0.39-0.76, P = 4.2e-04) but not with bleeding (OR = 1.13, 95% CI = 0.93-1.36, P = 2.2e-01). Genetically predicted F11 reduction was associated with lower risk of VTE (OR = 0.61, 95% CI = 0.58-0.64, P = 4.1e-85) and cardioembolic stroke (OR = 0.77, 95% CI = 0.69-0.86, P = 4.1e-06) but not with bleeding (OR = 1.01, 95% CI = 0.95-1.08, P = 7.5e-01). These Mendelian randomization associations were concordant across the three blood protein data sets and the hepatic gene expression data set as well as colocalization analyses. Conclusion These results provide strong genetic evidence that F2 and F11 may represent safe and efficacious therapeutic targets to prevent VTE and cardioembolic strokes without substantially increasing bleeding risk.
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Affiliation(s)
- Eloi Gagnon
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
| | - Arnaud Girard
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
| | - Jérôme Bourgault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
| | - Erik Abner
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Sébastien Thériault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Marie-Claude Vohl
- School of Nutrition, Université Laval, Quebec, QC, Canada
- Centre Nutrition, Santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Quebec, QC, Canada
| | - André Tchernof
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
- School of Nutrition, Université Laval, Quebec, QC, Canada
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Patrick Mathieu
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Benoit J Arsenault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec, Y-3106, Pavillon Marguerite D'Youville, 2725 chemin Ste-Foy, Quebec, QC, Canada, G1V 4G5
- Department of Medicine, Faculty of Medicine, 1050 Av. de la Médecine, Québec City, Quebec G1V 0A6, Canada
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24
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Sun Z, Yun Z, Lin J, Sun X, Wang Q, Duan J, Li C, Zhang X, Xu S, Wang Z, Xiong X, Yao K. Comprehensive mendelian randomization analysis of plasma proteomics to identify new therapeutic targets for the treatment of coronary heart disease and myocardial infarction. J Transl Med 2024; 22:404. [PMID: 38689297 PMCID: PMC11061979 DOI: 10.1186/s12967-024-05178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Ischemic heart disease is one of the leading causes of mortality worldwide, and thus calls for development of more effective therapeutic strategies. This study aimed to identify potential therapeutic targets for coronary heart disease (CHD) and myocardial infarction (MI) by investigating the causal relationship between plasma proteins and these conditions. METHODS A two-sample Mendelian randomization (MR) study was performed to evaluate more than 1600 plasma proteins for their causal associations with CHD and MI. The MR findings were further confirmed through Bayesian colocalization, Summary-data-based Mendelian Randomization (SMR), and Transcriptome-Wide Association Studies (TWAS) analyses. Further analyses, including enrichment analysis, single-cell analysis, MR analysis of cardiovascular risk factors, phenome-wide Mendelian Randomization (Phe-MR), and protein-protein interaction (PPI) network construction were conducted to verify the roles of selected causal proteins. RESULTS Thirteen proteins were causally associated with CHD, seven of which were also causal for MI. Among them, FES and PCSK9 were causal proteins for both diseases as determined by several analytical methods. PCSK9 was a risk factor of CHD (OR = 1.25, 95% CI: 1.13-1.38, P = 7.47E-06) and MI (OR = 1.36, 95% CI: 1.21-1.54, P = 2.30E-07), whereas FES was protective against CHD (OR = 0.68, 95% CI: 0.59-0.79, P = 6.40E-07) and MI (OR = 0.65, 95% CI: 0.54-0.77, P = 5.38E-07). Further validation through enrichment and single-cell analysis confirmed the causal effects of these proteins. Moreover, MR analysis of cardiovascular risk factors, Phe-MR, and PPI network provided insights into the potential drug development based on the proteins. CONCLUSIONS This study investigated the causal pathways associated with CHD and MI, highlighting the protective and risk roles of FES and PCSK9, respectively. FES. Specifically, the results showed that these proteins are promising therapeutic targets for future drug development.
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Affiliation(s)
- Ziyi Sun
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, 10029, China
| | - Zhangjun Yun
- Graduate School, Beijing University of Chinese Medicine, Beijing, 10029, China
- Department of Oncology and Hematology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 10070, China
| | - Jianguo Lin
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, 10070, China
| | - Xiaoning Sun
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, 10070, China
| | - Qingqing Wang
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
| | - Jinlong Duan
- Department of Andrology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
| | - Cheng Li
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, 10040, China
| | - Xiaoxiao Zhang
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, 10070, China
| | - Siyu Xu
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, 10029, China
| | - Zeqi Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 10070, China
| | - Xingjiang Xiong
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China.
| | - Kuiwu Yao
- Department of Cardiovascular, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 10053, China.
- Eye Hospital, China Academy of Chinese Medical Sciences, Beijing, 10040, China.
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25
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Smith-Byrne K, Hedman Å, Dimitriou M, Desai T, Sokolov AV, Schioth HB, Koprulu M, Pietzner M, Langenberg C, Atkins J, Penha RC, McKay J, Brennan P, Zhou S, Richards BJ, Yarmolinsky J, Martin RM, Borlido J, Mu XJ, Butterworth A, Shen X, Wilson J, Assimes TL, Hung RJ, Amos C, Purdue M, Rothman N, Chanock S, Travis RC, Johansson M, Mälarstig A. Identifying therapeutic targets for cancer among 2074 circulating proteins and risk of nine cancers. Nat Commun 2024; 15:3621. [PMID: 38684708 PMCID: PMC11059161 DOI: 10.1038/s41467-024-46834-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
Circulating proteins can reveal key pathways to cancer and identify therapeutic targets for cancer prevention. We investigate 2,074 circulating proteins and risk of nine common cancers (bladder, breast, endometrium, head and neck, lung, ovary, pancreas, kidney, and malignant non-melanoma) using cis protein Mendelian randomisation and colocalization. We conduct additional analyses to identify adverse side-effects of altering risk proteins and map cancer risk proteins to drug targets. Here we find 40 proteins associated with common cancers, such as PLAUR and risk of breast cancer [odds ratio per standard deviation increment: 2.27, 1.88-2.74], and with high-mortality cancers, such as CTRB1 and pancreatic cancer [0.79, 0.73-0.85]. We also identify potential adverse effects of protein-altering interventions to reduce cancer risk, such as hypertension. Additionally, we report 18 proteins associated with cancer risk that map to existing drugs and 15 that are not currently under clinical investigation. In sum, we identify protein-cancer links that improve our understanding of cancer aetiology. We also demonstrate that the wider consequence of any protein-altering intervention on well-being and morbidity is required to interpret any utility of proteins as potential future targets for therapeutic prevention.
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Affiliation(s)
- Karl Smith-Byrne
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK.
| | - Åsa Hedman
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Marios Dimitriou
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Trishna Desai
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Alexandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schioth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare Institute, Queen Mary University of London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare Institute, Queen Mary University of London, London, UK
| | - Joshua Atkins
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Ricardo Cortez Penha
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Brent J Richards
- Departments of Medicine (Endocrinology), Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada
| | - James Yarmolinsky
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Joana Borlido
- Cancer Immunology Discovery, Pfizer Worldwide Research and Development Medicine, Pfizer Inc, San Diego, USA
| | - Xinmeng J Mu
- Oncology Research Unit, Pfizer Worldwide Research and Development Medicine, Pfizer Inc, San Diego, USA
| | - Adam Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xia Shen
- Usher Institute, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jim Wilson
- Usher Institute, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Themistocles L Assimes
- Division of Cardiovascular Medicine and the Cardiovascular Institute, School of Medicine, Stanford University, Stanford, USA
| | - Rayjean J Hung
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Canada
| | - Christopher Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, USA
| | - Mark Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Anders Mälarstig
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
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26
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Yang N, Shi L, Xu P, Ren F, Lv S, Li C, Qi X. Identification of potential drug targets for insomnia by Mendelian randomization analysis based on plasma proteomics. Front Neurol 2024; 15:1380321. [PMID: 38725646 PMCID: PMC11079244 DOI: 10.3389/fneur.2024.1380321] [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: 02/01/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction Insomnia, a common clinical disorder, significantly impacts the physical and mental well-being of patients. Currently, available hypnotic medications are unsatisfactory due to adverse reactions and dependency, necessitating the identification of new drug targets for the treatment of insomnia. Methods In this study, we utilized 734 plasma proteins as genetic instruments obtained from genome-wide association studies to conduct a Mendelian randomization analysis, with insomnia as the outcome variable, to identify potential drug targets for insomnia. Additionally, we validated our results externally using other datasets. Sensitivity analyses entailed reverse Mendelian randomization analysis, Bayesian co-localization analysis, and phenotype scanning. Furthermore, we constructed a protein-protein interaction network to elucidate potential correlations between the identified proteins and existing targets. Results Mendelian randomization analysis indicated that elevated levels of TGFBI (OR = 1.01; 95% CI, 1.01-1.02) and PAM ((OR = 1.01; 95% CI, 1.01-1.02) in plasma are associated with an increased risk of insomnia, with external validation supporting these findings. Moreover, there was no evidence of reverse causality for these two proteins. Co-localization analysis confirmed that PAM (coloc.abf-PPH4 = 0.823) shared the same variant with insomnia, further substantiating its potential role as a therapeutic target. There are interactive relationships between the potential proteins and existing targets of insomnia. Conclusion Overall, our findings suggested that elevated plasma levels of TGFBI and PAM are connected with an increased risk of insomnia and might be promising therapeutic targets, particularly PAM. However, further exploration is necessary to fully understand the underlying mechanisms involved.
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Affiliation(s)
- Ni Yang
- Department of First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liangyuan Shi
- Qingdao Traditional Chinese Medicine Hospital (Qingdao Hiser Hospital) Qingdao Hiser Hospital Affiliated of Qingdao University, Qingdao, China
| | - Pengfei Xu
- Qingdao Traditional Chinese Medicine Hospital (Qingdao Hiser Hospital) Qingdao Hiser Hospital Affiliated of Qingdao University, Qingdao, China
| | - Fang Ren
- Department of Laboratory, Jimo District Qingdao Hospital of Traditional Chinese Medicine, Qingdao, China
| | - Shimeng Lv
- Department of First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chunlin Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xianghua Qi
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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27
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Yi H, Yang Q, Repaci C, Lee CM, Heo G, Timsina J, Gorijala P, Yang C, Budde J, Wang L, Cruchaga C, Sung YJ. TOPMed imputed genomics enhances genomic atlas of the human proteome in brain, cerebrospinal fluid, and plasma. Sci Data 2024; 11:387. [PMID: 38627416 PMCID: PMC11021418 DOI: 10.1038/s41597-024-03140-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Comprehensive expression quantitative trait loci studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein quantitative trait loci in brain, cerebrospinal fluid, and plasma. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in cerebrospinal fluid, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 loci in brain, 30 loci in cerebrospinal fluid, and 22 loci in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These resources are accessible through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer for use by the scientific community.
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Affiliation(s)
- Heng Yi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Qijun Yang
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Charlie Repaci
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheolmin Matthew Lee
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gyujin Heo
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengran Yang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University, St. Louis, MO, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA.
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28
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Ma S, Xu F, Fu Y, Zheng JS. Investigation of the influence of plasma proteome on brain structure: a Mendelian randomization study. J Genet Genomics 2024:S1673-8527(24)00073-0. [PMID: 38608937 DOI: 10.1016/j.jgg.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024]
Affiliation(s)
- Shengyi Ma
- Fudan University, Shanghai 200433, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Fengzhe Xu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Yuanqing Fu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| | - Ju-Sheng Zheng
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
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29
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Rich AL, Lin P, Gamazon ER, Zinkel SS. The broad impact of cell death genes on the human disease phenome. Cell Death Dis 2024; 15:251. [PMID: 38589365 PMCID: PMC11002008 DOI: 10.1038/s41419-024-06632-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Cell death mediated by genetically defined signaling pathways influences the health and dynamics of all tissues, however the tissue specificity of cell death pathways and the relationships between these pathways and human disease are not well understood. We analyzed the expression profiles of an array of 44 cell death genes involved in apoptosis, necroptosis, and pyroptosis cell death pathways across 49 human tissues from GTEx, to elucidate the landscape of cell death gene expression across human tissues, and the relationship between tissue-specific genetically determined expression and the human phenome. We uncovered unique cell death gene expression profiles across tissue types, suggesting there are physiologically distinct cell death programs in different tissues. Using summary statistics-based transcriptome wide association studies (TWAS) on human traits in the UK Biobank (n ~ 500,000), we evaluated 513 traits encompassing ICD-10 defined diagnoses and laboratory-derived traits. Our analysis revealed hundreds of significant (FDR < 0.05) associations between genetically regulated cell death gene expression and an array of human phenotypes encompassing both clinical diagnoses and hematologic parameters, which were independently validated in another large-scale DNA biobank (BioVU) at Vanderbilt University Medical Center (n = 94,474) with matching phenotypes. Cell death genes were highly enriched for significant associations with blood traits versus non-cell-death genes, with apoptosis-associated genes enriched for leukocyte and platelet traits. Our findings are also concordant with independently published studies (e.g. associations between BCL2L11/BIM expression and platelet & lymphocyte counts). Overall, these results suggest that cell death genes play distinct roles in their contribution to human phenotypes, and that cell death genes influence a diverse array of human traits.
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Affiliation(s)
- Abigail L Rich
- Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Phillip Lin
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Sandra S Zinkel
- Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA.
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30
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Mao R, Li J, Xiao W. Identification of prospective aging drug targets via Mendelian randomization analysis. Aging Cell 2024:e14171. [PMID: 38572516 DOI: 10.1111/acel.14171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Aging represents a multifaceted process culminating in the deterioration of biological functions. Despite the introduction of numerous anti-aging strategies, their therapeutic outcomes have often been less than optimal. Consequently, discovering new targets to mitigate aging effects is of critical importance. We applied Mendelian randomization (MR) to identify potential pharmacological targets against aging, drawing upon summary statistics from both the Decode and FinnGen cohorts, with further validation in an additional cohort. To address potential reverse causality, bidirectional MR analysis with Steiger filtering was utilized. Additionally, Bayesian co-localization and phenotype scanning were implemented to investigate previous associations between genetic variants and traits. Summary-data-based Mendelian randomization (SMR) analysis was conducted to assess the impact of genetic variants on aging via their effects on protein expression. Additionally, mediation analysis was orchestrated to uncover potential intermediaries in these associations. Finally, we probed the systemic implications of drug-target protein expression across diverse indications by MR-PheWas analysis. Utilizing a Bonferroni-corrected threshold, our MR examination identified 10 protein-aging associations. Within this cohort of proteins, MST1, LCT, GMPR2, PSMB4, ECM1, EFEMP1, and ISLR2 appear to exacerbate aging risks, while MAX, B3GNT8, and USP8 may exert protective influences. None of these proteins displayed reverse causality except EFEMP1. Bayesian co-localization inferred shared variants between aging and proteins such as B3GNT8 (rs11670143), ECM1 (rs61819393), and others listed. Mediator analysis pinpointed 1,5-anhydroglucitol as a partial intermediary in the influence LCT exhibits on telomere length. Circulating proteins play a pivotal role in influencing the aging process, making them promising candidates for therapeutic intervention. The implications of these proteins in aging warrant further investigation in future clinical research.
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Affiliation(s)
- Rui Mao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wenqin Xiao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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31
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Kalnapenkis A, Jõeloo M, Lepik K, Kukuškina V, Kals M, Alasoo K, Mägi R, Esko T, Võsa U. Genetic determinants of plasma protein levels in the Estonian population. Sci Rep 2024; 14:7694. [PMID: 38565889 PMCID: PMC10987560 DOI: 10.1038/s41598-024-57966-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184 cis and 94 trans signals for 157 protein traits, which were further fine-mapped to credible sets for 101 cis and 87 trans signals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5 cis and 14 trans associations. CNVs were associated with the levels of 11 proteins (7 cis and 5 trans), examples including a 3q12.1 deletion acting as a hub for multiple trans associations; and a CNV overlapping NAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
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Affiliation(s)
- Anette Kalnapenkis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
| | - Maarja Jõeloo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kaido Lepik
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Viktorija Kukuškina
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
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32
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Gagnon E, Arsenault BJ. Drug target Mendelian randomization supports apolipoprotein C3-lowering for lipoprotein-lipid levels reductions and cardiovascular diseases prevention. Atherosclerosis 2024; 391:117501. [PMID: 38547584 DOI: 10.1016/j.atherosclerosis.2024.117501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND AND AIMS Inhibitors of apolipoprotein C-III (apoC3) are currently approved for the reduction of triglyceride levels in patients with Familial Chylomicronemia Syndrome. We used drug target Mendelian randomization (MR) to assess the effect of genetically predicted decrease in apoC3 blood protein levels on cardiometabolic traits and diseases. METHODS We quantified lifelong reductions in apoC3 blood levels by selecting all genome wide significant and independent (r2<0.1) single nucleotide polymorphisms (SNPs) in the APOC3 gene region ±1 Mb, from three genome-wide association studies (GWAS) of apoC3 blood protein levels (deCODE, n = 35,378, Fenland, n = 10,708 and ARIC, n = 7213). We included the largest GWASes on 18 cardiometabolic traits and 9 cardiometabolic diseases as study outcomes. RESULTS A one standard deviation lowering in apoC3 blood protein levels was associated with lower triglycerides, apolipoprotein B, low-density lipoprotein cholesterol, alanine aminotransferase, and glomerular filtration rate as well as higher high-density lipoprotein cholesterol levels. ApoC3 lowering was also associated with lower risk of acute pancreatitis (odds ratio [OR] = 0.91 95% CI = 0.82 to 1.00), aortic stenosis (OR = 0.82 95% CI = 0.73 to 0.93), and coronary artery disease (OR = 0.86 95% CI = 0.80 to 0.93), and was associated with increased parental lifespan (0.06 95% CI = 0.03-0.09 years). These results were concordant across robust MR methods, the three protein datasets and upon adjustment for APOA1, APOA4 and APOA5 using a multivariable MR framework. CONCLUSIONS These results provide evidence that apoC3 lowering could result in widespread benefits for cardiometabolic health and encourage the launch of trials on apoC3 inhibition for coronary artery disease prevention.
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Affiliation(s)
- Eloi Gagnon
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada
| | - Benoit J Arsenault
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.
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33
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Pietzner M, Uluvar B, Kolnes KJ, Jeppesen PB, Frivold SV, Skattebo Ø, Johansen EI, Skålhegg BS, Wojtaszewski JFP, Kolnes AJ, Yeo GSH, O'Rahilly S, Jensen J, Langenberg C. Systemic proteome adaptions to 7-day complete caloric restriction in humans. Nat Metab 2024; 6:764-777. [PMID: 38429390 DOI: 10.1038/s42255-024-01008-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
Surviving long periods without food has shaped human evolution. In ancient and modern societies, prolonged fasting was/is practiced by billions of people globally for religious purposes, used to treat diseases such as epilepsy, and recently gained popularity as weight loss intervention, but we still have a very limited understanding of the systemic adaptions in humans to extreme caloric restriction of different durations. Here we show that a 7-day water-only fast leads to an average weight loss of 5.7 kg (±0.8 kg) among 12 volunteers (5 women, 7 men). We demonstrate nine distinct proteomic response profiles, with systemic changes evident only after 3 days of complete calorie restriction based on in-depth characterization of the temporal trajectories of ~3,000 plasma proteins measured before, daily during, and after fasting. The multi-organ response to complete caloric restriction shows distinct effects of fasting duration and weight loss and is remarkably conserved across volunteers with >1,000 significantly responding proteins. The fasting signature is strongly enriched for extracellular matrix proteins from various body sites, demonstrating profound non-metabolic adaptions, including extreme changes in the brain-specific extracellular matrix protein tenascin-R. Using proteogenomic approaches, we estimate the health consequences for 212 proteins that change during fasting across ~500 outcomes and identified putative beneficial (SWAP70 and rheumatoid arthritis or HYOU1 and heart disease), as well as adverse effects. Our results advance our understanding of prolonged fasting in humans beyond a merely energy-centric adaptions towards a systemic response that can inform targeted therapeutic modulation.
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Affiliation(s)
- Maik Pietzner
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Burulça Uluvar
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kristoffer J Kolnes
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Per B Jeppesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - S Victoria Frivold
- Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Øyvind Skattebo
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Egil I Johansen
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Bjørn S Skålhegg
- Department of Nutrition, Division for Molecular Nutrition, University of Oslo, Oslo, Norway
| | - Jørgen F P Wojtaszewski
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Kolnes
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway
| | - Giles S H Yeo
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Stephen O'Rahilly
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jørgen Jensen
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Claudia Langenberg
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
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Kresge HA, Blostein F, Goleva S, Albiñana C, Revez JA, Wray NR, Vilhjálmsson BJ, Zhu Z, McGrath JJ, Davis LK. Phenomewide Association Study of Health Outcomes Associated With the Genetic Correlates of 25 Hydroxyvitamin D Concentration and Vitamin D Binding Protein Concentration. Twin Res Hum Genet 2024; 27:69-79. [PMID: 38644690 PMCID: PMC11138239 DOI: 10.1017/thg.2024.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
While it is known that vitamin D deficiency is associated with adverse bone outcomes, it remains unclear whether low vitamin D status may increase the risk of a wider range of health outcomes. We had the opportunity to explore the association between common genetic variants associated with both 25 hydroxyvitamin D (25OHD) and the vitamin D binding protein (DBP, encoded by the GC gene) with a comprehensive range of health disorders and laboratory tests in a large academic medical center. We used summary statistics for 25OHD and DBP to generate polygenic scores (PGS) for 66,482 participants with primarily European ancestry and 13,285 participants with primarily African ancestry from the Vanderbilt University Medical Center Biobank (BioVU). We examined the predictive properties of PGS25OHD, and two scores related to DBP concentration with respect to 1322 health-related phenotypes and 315 laboratory-measured phenotypes from electronic health records. In those with European ancestry: (a) the PGS25OHD and PGSDBP scores, and individual SNPs rs4588 and rs7041 were associated with both 25OHD concentration and 1,25 dihydroxyvitamin D concentrations; (b) higher PGS25OHD was associated with decreased concentrations of triglycerides and cholesterol, and reduced risks of vitamin D deficiency, disorders of lipid metabolism, and diabetes. In general, the findings for the African ancestry group were consistent with findings from the European ancestry analyses. Our study confirms the utility of PGS and two key variants within the GC gene (rs4588 and rs7041) to predict the risk of vitamin D deficiency in clinical settings and highlights the shared biology between vitamin D-related genetic pathways a range of health outcomes.
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Affiliation(s)
- Hailey A. Kresge
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Freida Blostein
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Slavina Goleva
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus V, Denmark
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Joana A. Revez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Naomi R. Wray
- Department of Psychiatry, University of Oxford, Oxford, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Bjarni J. Vilhjálmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus V, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
| | - Zhihong Zhu
- National Centre for Register-Based Research, Aarhus University, Aarhus V, Denmark
| | - John J. McGrath
- National Centre for Register-Based Research, Aarhus University, Aarhus V, Denmark
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Lea K. Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Neurology, Pharmacology and Special Education, Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
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35
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Austin TR, Fink HA, Jalal DI, Törnqvist AE, Buzkova P, Barzilay JI, Lu T, Carbone L, Gabrielsen ME, Grahnemo L, Hveem K, Jonasson C, Kizer JR, Langhammer A, Mukamal KJ, Gerszten RE, Nethander M, Psaty BM, Robbins JA, Sun YV, Heidi Skogholt A, Åsvold BO, Valderrabano RJ, Zheng J, Brent Richards J, Coward E, Ohlsson C. Large-scale circulating proteome association study (CPAS) meta-analysis identifies circulating proteins and pathways predicting incident hip fractures. J Bone Miner Res 2024; 39:139-149. [PMID: 38477735 PMCID: PMC11070286 DOI: 10.1093/jbmr/zjad011] [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: 08/21/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 03/14/2024]
Abstract
Hip fractures are associated with significant disability, high cost, and mortality. However, the exact biological mechanisms underlying susceptibility to hip fractures remain incompletely understood. In an exploratory search of the underlying biology as reflected through the circulating proteome, we performed a comprehensive Circulating Proteome Association Study (CPAS) meta-analysis for incident hip fractures. Analyses included 6430 subjects from two prospective cohort studies (Cardiovascular Health Study and Trøndelag Health Study) with circulating proteomics data (aptamer-based 5 K SomaScan version 4.0 assay; 4979 aptamers). Associations between circulating protein levels and incident hip fractures were estimated for each cohort using age and sex-adjusted Cox regression models. Participants experienced 643 incident hip fractures. Compared with the individual studies, inverse-variance weighted meta-analyses yielded more statistically significant associations, identifying 23 aptamers associated with incident hip fractures (conservative Bonferroni correction 0.05/4979, P < 1.0 × 10-5). The aptamers most strongly associated with hip fracture risk corresponded to two proteins of the growth hormone/insulin growth factor system (GHR and IGFBP2), as well as GDF15 and EGFR. High levels of several inflammation-related proteins (CD14, CXCL12, MMP12, ITIH3) were also associated with increased hip fracture risk. Ingenuity pathway analysis identified reduced LXR/RXR activation and increased acute phase response signaling to be overrepresented among those proteins associated with increased hip fracture risk. These analyses identified several circulating proteins and pathways consistently associated with incident hip fractures. These findings underscore the usefulness of the meta-analytic approach for comprehensive CPAS in a similar manner as has previously been observed for large-scale human genetic studies. Future studies should investigate the underlying biology of these potential novel drug targets.
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Affiliation(s)
- Thomas R. Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
| | - Howard A. Fink
- Geriatric Research Education and Clinical Center, VA Health Care System, Minneapolis, MN, 56401, United States
| | - Diana I. Jalal
- Division of Nephrology, Department of Internal Medicine, Carver College of Medicine, Iowa City, IA, 52242, United States
- Iowa City VA Medical Center, Iowa City, IA, 52246, United States
| | - Anna E. Törnqvist
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, WA, 98115, United States
| | - Joshua I. Barzilay
- Division of Endocrinology, Kaiser Permanente of Georgia, Atlanta, GA, 30339, United States
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, H3G 0B1, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
| | - Laura Carbone
- Charlie Norwood VAMC, Augusta, GA, 30901, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, United States
| | - Maiken E. Gabrielsen
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Kristian Hveem
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jorge R. Kizer
- Cardiology Section, San Francisco VA Health Care System, San Francisco, CA, 94121, United States
- Department of Medicine, Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, United States
| | - Arnulf Langhammer
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, 7600, Levanger, Norway
| | - Kenneth J. Mukamal
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Robert E. Gerszten
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Bioinformatics and Data Center, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
- Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, 98195, United States
| | - John A. Robbins
- Department of Medicine, University of California, Davis, CA, 95817, United States
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, United States
| | - Anne Heidi Skogholt
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Bjørn Olav Åsvold
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, 7491, Trondheim, Norway
| | - Rodrigo J. Valderrabano
- Research Program in Men’s Health, Aging and Metabolism, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, 2130, United States
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai National Clinical Research Center for Metabolic Diseases, Shanghai Digital Medicine Innovation Center, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Bristol, BS8 2BN, United Kingdom
| | - J. Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
- Department of Twin Research, King’s College London, London, SE1 7EH, United Kingdom
| | - Eivind Coward
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Department of Drug Treatment, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
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Zhao W, Fang P, Lai C, Xu X, Wang Y, Liu H, Jiang H, Liu X, Liu J. Proteome-wide Mendelian randomization identifies therapeutic targets for ankylosing spondylitis. Front Immunol 2024; 15:1366736. [PMID: 38566994 PMCID: PMC10985162 DOI: 10.3389/fimmu.2024.1366736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background Ankylosing Spondylitis (AS) is a chronic inflammatory disorder which can lead to considerable pain and disability. Mendelian randomization (MR) has been extensively applied for repurposing licensed drugs and uncovering new therapeutic targets. Our objective is to pinpoint innovative therapeutic protein targets for AS and assess the potential adverse effects of druggable proteins. Methods We conducted a comprehensive proteome-wide MR study to assess the causal relationships between plasma proteins and the risk of AS. The plasma proteins were sourced from the UK Biobank Pharma Proteomics Project (UKB-PPP) database, encompassing GWAS data for 2,940 plasma proteins. Additionally, GWAS data for AS were extracted from the R9 version of the Finnish database, including 2,860 patients and 270,964 controls. The colocalization analysis was executed to identify shared causal variants between plasma proteins and AS. Finally, we examined the potential adverse effects of druggable proteins for AS therapy by conducting a phenome-wide association study (PheWAS) utilizing the extensive Finnish database in version R9, encompassing 2,272 phenotypes categorized into 46 groups. Results The findings revealed a positive genetic association between the predicted plasma levels of six proteins and an elevated risk of AS, while two proteins exhibited an inverse association with AS risk (P fdr < 0.05). Among these eight plasma proteins, colocalization analysis identified AIF1, TNF, FKBPL, AGER, ALDH5A1, and ACOT13 as shared variation with AS(PPH3+PPH4>0.8), suggesting that they represent potential direct targets for AS intervention. Further phenotype-wide association studies have shown some potential side effects of these six targets (P fdr < 0.05). Conclusion Our investigation examined the causal connections between six plasma proteins and AS, providing a comprehensive understanding of potential therapeutic targets.
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Affiliation(s)
- Wenlong Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Orthopedics, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Peng Fang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Chengteng Lai
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaoyu Xu
- Department of Biology, Wake Forest University, North Carolina, NC, United States
| | - Yang Wang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hao Liu
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hui Jiang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaozhou Liu
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jun Liu
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Xu X, Khunsriraksakul C, Eales JM, Rubin S, Scannali D, Saluja S, Talavera D, Markus H, Wang L, Drzal M, Maan A, Lay AC, Prestes PR, Regan J, Diwadkar AR, Denniff M, Rempega G, Ryszawy J, Król R, Dormer JP, Szulinska M, Walczak M, Antczak A, Matías-García PR, Waldenberger M, Woolf AS, Keavney B, Zukowska-Szczechowska E, Wystrychowski W, Zywiec J, Bogdanski P, Danser AHJ, Samani NJ, Guzik TJ, Morris AP, Liu DJ, Charchar FJ, Tomaszewski M. Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets. Nat Commun 2024; 15:2359. [PMID: 38504097 PMCID: PMC10950894 DOI: 10.1038/s41467-024-46132-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11, AGMAT, AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g., ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.
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Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | | | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sebastien Rubin
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Scannali
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Havell Markus
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Lida Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Maciej Drzal
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Akhlaq Maan
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Abigail C Lay
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
| | - Jeniece Regan
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Avantika R Diwadkar
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Grzegorz Rempega
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Jakub Ryszawy
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - John P Dormer
- Department of Cellular Pathology, University Hospitals of Leicester, Leicester, UK
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Marta Walczak
- Department of Internal Diseases, Metabolic Disorders and Arterial Hypertension, Poznan University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Pamela R Matías-García
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK
| | | | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - A H Jan Danser
- Department of Internal Medicine, Division of Pharmacology and Vascular Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Tomasz J Guzik
- Department of Internal Medicine, Jagiellonian University Medical College, Kraków, Poland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK.
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Han S, Yao J, Yamazaki H, Streicher SA, Rao J, Nianogo RA, Zhang Z, Huang BZ. Genetically Determined Circulating Lactase/Phlorizin Hydrolase Concentrations and Risk of Colorectal Cancer: A Two-Sample Mendelian Randomization Study. Nutrients 2024; 16:808. [PMID: 38542719 PMCID: PMC10975724 DOI: 10.3390/nu16060808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/06/2024] [Accepted: 03/10/2024] [Indexed: 04/01/2024] Open
Abstract
Previous research has found that milk is associated with a decreased risk of colorectal cancer (CRC). However, it is unclear whether the milk digestion by the enzyme lactase-phlorizin hydrolase (LPH) plays a role in CRC susceptibility. Our study aims to investigate the direct causal relationship of CRC risk with LPH levels by applying a two-sample Mendelian Randomization (MR) strategy. Genetic instruments for LPH were derived from the Fenland Study, and CRC-associated summary statistics for these instruments were extracted from the FinnGen Study, PLCO Atlas Project, and Pan-UK Biobank. Primary MR analyses focused on a cis-variant (rs4988235) for LPH levels, with results integrated via meta-analysis. MR analyses using all variants were also undertaken. This analytical approach was further extended to assess CRC subtypes (colon and rectal). Meta-analysis across the three datasets illustrated an inverse association between genetically predicted LPH levels and CRC risk (OR: 0.92 [95% CI, 0.89-0.95]). Subtype analyses revealed associations of elevated LPH levels with reduced risks for both colon (OR: 0.92 [95% CI, 0.89-0.96]) and rectal cancer (OR: 0.92 [95% CI, 0.87, 0.98]). Consistency was observed across varied analytical methods and datasets. Further exploration is warranted to unveil the underlying mechanisms and validate LPH's potential role in CRC prevention.
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Affiliation(s)
- Sihao Han
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA; (J.Y.); (J.R.); (R.A.N.); (Z.Z.)
| | - Jiemin Yao
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA; (J.Y.); (J.R.); (R.A.N.); (Z.Z.)
| | - Hajime Yamazaki
- Section of Clinical Epidemiology, Department of Community Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8303, Japan;
- Center for Innovative Research for Communities and Clinical Excellence (CiRC2LE), Fukushima Medical University, Fukushima 960-1295, Japan
| | - Samantha A. Streicher
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA;
| | - Jianyu Rao
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA; (J.Y.); (J.R.); (R.A.N.); (Z.Z.)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roch A. Nianogo
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA; (J.Y.); (J.R.); (R.A.N.); (Z.Z.)
| | - Zuofeng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA; (J.Y.); (J.R.); (R.A.N.); (Z.Z.)
| | - Brian Z. Huang
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Chen S, Huang W, Wan Q, Tang Z, Li X, Zeng F, Zheng S, Li Z, Liu X. Investigation of the acute pathogenesis of spondyloarthritis/HLA-B27-associated anterior uveitis based on genome-wide association analysis and single-cell transcriptomics. J Transl Med 2024; 22:271. [PMID: 38475831 DOI: 10.1186/s12967-024-05077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Patients with spondyloarthritis (SpA)/HLA-B27-associated acute anterior uveitis (AAU) experience recurring acute flares, which pose significant visual and financial challenges. Despite established links between SpA and HLA-B27-associated AAU, the exact mechanism involved remains unclear, and further understanding is needed for effective prevention and treatment. METHODS To investigate the acute pathogenesis of SpA/HLA-B27-associated AAU, Mendelian randomization (MR) and single-cell transcriptomic analyses were employed. The MR incorporated publicly available protein quantitative trait locus data from previous studies, along with genome-wide association study data from public databases. Causal relationships between plasma proteins and anterior uveitis were assessed using two-sample MR. Additionally, colocalization analysis was performed using Bayesian colocalization. Single-cell transcriptome analysis utilized the anterior uveitis dataset from the Gene Expression Omnibus (GEO) database. Dimensionality reduction, clustering, transcription factor analysis, pseudotime analysis, and cell communication analysis were subsequently conducted to explore the underlying mechanisms involved. RESULTS Mendelian randomization analysis revealed that circulating levels of AIF1 and VARS were significantly associated with a reduced risk of developing SpA/HLA-B27-associated AAU, with AIF1 showing a robust correlation with anterior uveitis onset. Colocalization analysis supported these findings. Single-cell transcriptome analysis showed predominant AIF1 expression in myeloid cells, which was notably lower in the HLA-B27-positive group. Pseudotime analysis revealed dendritic cell terminal positions in differentiation branches, accompanied by gradual decreases in AIF1 expression. Based on cell communication analysis, CD141+CLEC9A+ classic dendritic cells (cDCs) and the APP pathway play crucial roles in cellular communication in the Spa/HLA-B27 group. CONCLUSIONS AIF1 is essential for the pathogenesis of SpA/HLA-B27-associated AAU. Myeloid cell differentiation into DCs and decreased AIF1 levels are also pivotal in this process.
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Affiliation(s)
- Shuming Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Weidi Huang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Qiaoqian Wan
- Department of Anaesthesiology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zichun Tang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Xie Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Fang Zeng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Shuyan Zheng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Zhuo Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China.
- Hunan Provincial Key Laboratory of Critical Quality Attribute of Cell Therapy Products, Changsha, 410011, Hunan, China.
| | - Xiao Liu
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China.
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40
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Dib M, Levin MG, Zhao L, Diab A, Wang Z, Ebert C, Salman O, Azzo JD, Gan S, Zamani P, Cohen JB, Gill D, Burgess S, Zagkos L, van Empel V, Richards AM, Doughty R, Rietzschel ER, Kammerhoff K, Kvikstad E, Maranville J, Schafer P, Seiffert DA, Ramirez‐Valle F, Gordon DA, Chang C, Javaheri A, Mann DL, Cappola TP, Chirinos JA. Proteomic Associations of Adverse Outcomes in Human Heart Failure. J Am Heart Assoc 2024; 13:e031154. [PMID: 38420755 PMCID: PMC10944037 DOI: 10.1161/jaha.123.031154] [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: 10/31/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Identifying novel molecular drivers of disease progression in heart failure (HF) is a high-priority goal that may provide new therapeutic targets to improve patient outcomes. The authors investigated the relationship between plasma proteins and adverse outcomes in HF and their putative causal role using Mendelian randomization. METHODS AND RESULTS The authors measured 4776 plasma proteins among 1964 participants with HF with a reduced left ventricular ejection fraction enrolled in PHFS (Penn Heart Failure Study). Assessed were the observational relationship between plasma proteins and (1) all-cause death or (2) death or HF-related hospital admission (DHFA). The authors replicated nominally significant associations in the Washington University HF registry (N=1080). Proteins significantly associated with outcomes were the subject of 2-sample Mendelian randomization and colocalization analyses. After correction for multiple testing, 243 and 126 proteins were found to be significantly associated with death and DHFA, respectively. These included small ubiquitin-like modifier 2 (standardized hazard ratio [sHR], 1.56; P<0.0001), growth differentiation factor-15 (sHR, 1.68; P<0.0001) for death, A disintegrin and metalloproteinase with thrombospondin motifs-like protein (sHR, 1.40; P<0.0001), and pulmonary-associated surfactant protein C (sHR, 1.24; P<0.0001) for DHFA. In pathway analyses, top canonical pathways associated with death and DHFA included fibrotic, inflammatory, and coagulation pathways. Genomic analyses provided evidence of nominally significant associations between levels of 6 genetically predicted proteins with DHFA and 11 genetically predicted proteins with death. CONCLUSIONS This study implicates multiple novel proteins in HF and provides preliminary evidence of associations between genetically predicted plasma levels of 17 candidate proteins and the risk for adverse outcomes in human HF.
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Affiliation(s)
- Marie‐Joe Dib
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Michael G. Levin
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Lei Zhao
- Bristol‐Myers Squibb CompanyLawrencevilleNJUSA
| | - Ahmed Diab
- Washington University School of MedicineSt. LouisMOUSA
| | | | | | - Oday Salman
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Joe David Azzo
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Sushrima Gan
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Payman Zamani
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Jordana B. Cohen
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
- Renal‐Electrolyte and Hypertension Division, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public HealthImperial College LondonLondonUnited Kingdom
| | - Stephen Burgess
- MRC Integrative Epidemiology UnitUniversity of BristolUnited Kingdom
- Department of Public Health and Primary CareUniversity of CambridgeUnited Kingdom
| | - Loukas Zagkos
- Department of Epidemiology and Biostatistics, School of Public HealthImperial College LondonLondonUnited Kingdom
| | - Vanessa van Empel
- Department of CardiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - A. Mark Richards
- Department of CardiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Cardiovascular Research InstituteNational University of SingaporeSingapore
| | - Rob Doughty
- Christchurch Heart InstituteUniversity of OtagoChristchurchNew Zealand
| | | | | | | | | | | | | | | | | | | | - Ali Javaheri
- Washington University School of MedicineSt. LouisMOUSA
- John J. Cochran Veterans HospitalSt. LouisMOUSA
| | | | - Thomas P. Cappola
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Julio A. Chirinos
- Division of Cardiovascular MedicineHospital of the University of PennsylvaniaPhiladelphiaPAUSA
- University of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
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Gobeil É, Bourgault J, Mitchell PL, Houessou U, Gagnon E, Girard A, Paulin A, Manikpurage HD, Côté V, Couture C, Marceau S, Bossé Y, Thériault S, Mathieu P, Vohl MC, Tchernof A, Arsenault BJ. Genetic inhibition of angiopoietin-like protein-3, lipids, and cardiometabolic risk. Eur Heart J 2024; 45:707-721. [PMID: 38243829 PMCID: PMC10906986 DOI: 10.1093/eurheartj/ehad845] [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: 05/30/2023] [Revised: 10/16/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND AND AIMS RNA-based, antibody-based, and genome editing-based therapies are currently under investigation to determine if the inhibition of angiopoietin-like protein-3 (ANGPTL3) could reduce lipoprotein-lipid levels and atherosclerotic cardiovascular disease (ASCVD) risk. Mendelian randomisation (MR) was used to determine whether genetic variations influencing ANGPTL3 liver gene expression, blood levels, and protein structure could causally influence triglyceride and apolipoprotein B (apoB) levels as well as coronary artery disease (CAD), ischaemic stroke (IS), and other cardiometabolic diseases. METHODS RNA sequencing of 246 explanted liver samples and genome-wide genotyping was performed to identify single-nucleotide polymorphisms (SNPs) associated with liver expression of ANGPTL3. Genome-wide summary statistics of plasma protein levels of ANGPTL3 from the deCODE study (n = 35 359) were used. A total of 647 carriers of ANGPTL3 protein-truncating variants (PTVs) associated with lower plasma triglyceride levels were identified in the UK Biobank. Two-sample MR using SNPs that influence ANGPTL3 liver expression or ANGPTL3 plasma protein levels as exposure and cardiometabolic diseases as outcomes was performed (CAD, IS, heart failure, non-alcoholic fatty liver disease, acute pancreatitis, and type 2 diabetes). The impact of rare PTVs influencing plasma triglyceride levels on apoB levels and CAD was also investigated in the UK Biobank. RESULTS In two-sample MR studies, common genetic variants influencing ANGPTL3 hepatic or blood expression levels of ANGPTL3 had a very strong effect on plasma triglyceride levels, a more modest effect on low-density lipoprotein cholesterol, a weaker effect on apoB levels, and no effect on CAD or other cardiometabolic diseases. In the UK Biobank, the carriers of rare ANGPTL3 PTVs providing lifelong reductions in median plasma triglyceride levels [-0.37 (interquartile range 0.41) mmol/L] had slightly lower apoB levels (-0.06 ± 0.32 g/L) and similar CAD event rates compared with non-carriers (10.2% vs. 10.9% in carriers vs. non-carriers, P = .60). CONCLUSIONS PTVs influencing ANGPTL3 protein structure as well as common genetic variants influencing ANGPTL3 hepatic expression and/or blood protein levels exhibit a strong effect on circulating plasma triglyceride levels, a weak effect on circulating apoB levels, and no effect on ASCVD. Near-complete inhibition of ANGPTL3 function in patients with very elevated apoB levels may be required to reduce ASCVD risk.
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Affiliation(s)
- Émilie Gobeil
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Jérôme Bourgault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Patricia L Mitchell
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Ursula Houessou
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Eloi Gagnon
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Arnaud Girard
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Audrey Paulin
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Hasanga D Manikpurage
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Valérie Côté
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Christian Couture
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Simon Marceau
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, Canada
| | - Yohan Bossé
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, Canada
| | - Sébastien Thériault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec, Canada
| | - Patrick Mathieu
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, Canada
| | - Marie-Claude Vohl
- School of Nutrition, Université Laval, Québec, Canada
- Centre Nutrition, santé et société, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Canada
| | - André Tchernof
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- School of Nutrition, Université Laval, Québec, Canada
| | - Benoit J Arsenault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
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Yuan S, Xu F, Zhang H, Chen J, Ruan X, Li Y, Burgess S, Åkesson A, Li X, Gill D, Larsson SC. Proteomic insights into modifiable risk of venous thromboembolism and cardiovascular comorbidities. J Thromb Haemost 2024; 22:738-748. [PMID: 38029854 PMCID: PMC7615672 DOI: 10.1016/j.jtha.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Venous thromboembolism (VTE) has been associated with several modifiable factors (MFs) and cardiovascular comorbidities. However, the mechanisms are largely unknown. OBJECTIVES We aimed to decipher proteomic pathways underlying the associations of VTE with MFs and cardiovascular comorbidities. METHODS A 2-stage network Mendelian randomization analysis was conducted to explore the associations between 15 MFs, 1151 blood proteins, and VTE using data from a genome-wide meta-analysis including 81 190 cases of VTE. We used protein data from 35 559 individuals as the discovery analysis, and from 2 independent studies including 10 708 and 54 219 participants as the replication analyses. Based on the identified proteins, we assessed the druggability and examined the cardiovascular pleiotropy. RESULTS The network Mendelian randomization analyses identified 10 MF-VTE, 86 MF-protein, and 34 protein-VTE associations. These associations were overall consistent in the replication analyses. Thirty-eight pathways with directionally consistent direct and indirect effects in the MF-protein-VTE pathway were identified. Low-density lipoprotein receptor-related protein 12 (LRP12: 34.3%-58.1%) and coagulation factor (F)XI (20.6%-39.6%) mediated most of the associations between 3 obesity indicators and VTE. Likewise, coagulation FXI mediated most of the smoking-VTE association (40%; 95% CI, 20%-60%) and insomnia-VTE association (27%; 95% CI, 5%-49%). Many VTE-associated proteins were highly druggable for thrombotic conditions. Five proteins (interleukin-6 receptor subunit alpha, LRP12, prothrombin, angiopoietin-1, and low-density lipoprotein receptor-related protein 4) were associated with VTE and its cardiovascular comorbidities. CONCLUSION This study suggests that coagulation FXI, a druggable target, is an important mediator of the associations of obesity, smoking, and insomnia with VTE risk.
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Affiliation(s)
- Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Han Zhang
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Chen
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xixian Ruan
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuying Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Stephen Burgess
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Agneta Åkesson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Susanna C. Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
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White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
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Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Li H, Du S, Dai J, Jiang Y, Li Z, Fan Q, Zhang Y, You D, Zhang R, Zhao Y, Christiani DC, Shen S, Chen F. Proteome-wide Mendelian randomization identifies causal plasma proteins in lung cancer. iScience 2024; 27:108985. [PMID: 38333712 PMCID: PMC10850776 DOI: 10.1016/j.isci.2024.108985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Plasma proteins are promising biomarkers and potential drug targets in lung cancer. To evaluate the causal association between plasma proteins and lung cancer, we performed proteome-wide Mendelian randomization meta-analysis (PW-MR-meta) based on lung cancer genome-wide association studies (GWASs), protein quantitative trait loci (pQTLs) of 4,719 plasma proteins in deCODE and 4,775 in Fenland. Further, causal-protein risk score (CPRS) was developed based on causal proteins and validated in the UK Biobank. 270 plasma proteins were identified using PW-MR meta-analysis, including 39 robust causal proteins (both FDR-q < 0.05) and 78 moderate causal proteins (FDR-q < 0.05 in one and p < 0.05 in another). The CPRS had satisfactory performance in risk stratification for lung cancer (top 10% CPRS:Hazard ratio (HR) (95%CI):4.33(2.65-7.06)). The CPRS [AUC (95%CI): 65.93 (62.91-68.78)] outperformed the traditional polygenic risk score (PRS) [AUC (95%CI): 55.71(52.67-58.59)]. Our findings offer further insight into the genetic architecture of plasma proteins for lung cancer susceptibility.
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Affiliation(s)
- Hongru Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sha Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jinglan Dai
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yunke Jiang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zaiming Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qihan Fan
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yixin Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Dongfang You
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing 211166, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - David C. Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing 211166, China
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Zhang P, Zhang W, Sun W, Xu J, Hu H, Wang L, Wong L. Identification of gene biomarkers for brain diseases via multi-network topological semantics extraction and graph convolutional network. BMC Genomics 2024; 25:175. [PMID: 38350848 PMCID: PMC10865627 DOI: 10.1186/s12864-024-09967-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Brain diseases pose a significant threat to human health, and various network-based methods have been proposed for identifying gene biomarkers associated with these diseases. However, the brain is a complex system, and extracting topological semantics from different brain networks is necessary yet challenging to identify pathogenic genes for brain diseases. RESULTS In this study, we present a multi-network representation learning framework called M-GBBD for the identification of gene biomarker in brain diseases. Specifically, we collected multi-omics data to construct eleven networks from different perspectives. M-GBBD extracts the spatial distributions of features from these networks and iteratively optimizes them using Kullback-Leibler divergence to fuse the networks into a common semantic space that represents the gene network for the brain. Subsequently, a graph consisting of both gene and large-scale disease proximity networks learns representations through graph convolution techniques and predicts whether a gene is associated which brain diseases while providing associated scores. Experimental results demonstrate that M-GBBD outperforms several baseline methods. Furthermore, our analysis supported by bioinformatics revealed CAMP as a significantly associated gene with Alzheimer's disease identified by M-GBBD. CONCLUSION Collectively, M-GBBD provides valuable insights into identifying gene biomarkers for brain diseases and serves as a promising framework for brain networks representation learning.
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Affiliation(s)
- Ping Zhang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weihan Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hubei Hongshan Laboratory, Wuhan, 430074, China
| | - Weicheng Sun
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Xu
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Hu
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
- Guangxi Key Lab of Human-Machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Leon Wong
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, 518118, China.
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Boahen CK, Abee H, Ponce IR, Joosten LAB, Netea MG, Kumar V. Sex-biased genetic regulation of inflammatory proteins in the Dutch population. BMC Genomics 2024; 25:154. [PMID: 38326779 PMCID: PMC10851559 DOI: 10.1186/s12864-024-10065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Significant differences in immune responses, prevalence or susceptibility of diseases and treatment responses have been described between males and females. Despite this, sex-differentiation analysis of the genetic architecture of inflammatory proteins is largely unexplored. We performed sex-stratified meta-analysis after protein quantitative trait loci (pQTL) mapping using inflammatory biomarkers profiled using targeted proteomics (Olink inflammatory panel) of two population-based cohorts of Europeans. RESULTS Even though, around 67% of the pQTLs demonstrated shared effect between sexes, colocalization analysis identified two loci in the males (LINC01135 and ITGAV) and three loci (CNOT10, SRD5A2, and LILRB5) in the females with evidence of sex-dependent modulation by pQTL variants. Furthermore, we identified pathways with relevant functions in the sex-biased pQTL variants. We also showed through cross-validation that the sex-specific pQTLs are linked with sex-specific phenotypic traits. CONCLUSION Our study demonstrates the relevance of genetic sex-stratified analysis in the context of genetic dissection of protein abundances among individuals and reveals that, sex-specific pQTLs might mediate sex-linked phenotypes. Identification of sex-specific pQTLs associated with sex-biased diseases can help realize the promise of individualized treatment.
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Affiliation(s)
- Collins K Boahen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Hannah Abee
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Isis Ricaño Ponce
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacia, Cluj-Napoca-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, the Netherlands.
- Nitte (Deemed to Be University), Medical Sciences Complex, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangalore, 575018, India.
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Zhao H, Liu Y, Zhang X, Liao Y, Zhang H, Han X, Guo L, Fan B, Wang W, Lu C. Identifying novel proteins for suicide attempt by integrating proteomes from brain and blood with genome-wide association data. Neuropsychopharmacology 2024:10.1038/s41386-024-01807-4. [PMID: 38317018 DOI: 10.1038/s41386-024-01807-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/28/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Genome-wide association studies (GWASs) have identified risk loci for suicide attempt (SA), but deciphering how they confer risk for SA remains largely unknown. This study aims to identify the key proteins and gain insights into SA pathogenesis. We integrated data from the brain proteome (N = 376) and blood proteome (N = 35,559) and combined it with the largest SA GWAS summary statistics to date (N = 518,612). A comprehensive set of methods was employed, including Mendelian randomization (MR), Steiger filtering, Bayesian colocalization, proteome‑wide association studies (PWAS), transcript-levels, cell-type specificity, correlation, and protein-protein interaction (PPI) network analysis. Validation was performed using other protein datasets and the SA dataset from FinnGen study. We identified ten proteins (GLRX5, GMPPB, B3GALTL, FUCA2, TTLL12, ADCK1, MMAA, HIBADH, ACP1, DOC2A) associated with SA in brain proteomics. GLRX5, GMPPB, and FUCA2 showed strong colocalization evidence and were supported by PWAS and transcript-level analysis, and were predominantly expressed in glutamatergic neuronal cells. In blood proteomics, one significant protein (PEAR1) and three near-significant proteins (NDE1, EVA1C, B4GALT2) were identified, but lacked colocalization evidence. Moreover, despite the limited correlation between the same protein in brain and blood, the PPI network analysis provided new insights into the interaction between brain and blood in SA. Furthermore, GLRX5 was associated with the GSTP1, the target of Clozapine. The comprehensive analysis provides strong evidence supporting a causal association between three genetically determined brain proteins (GLRX5, GMPPB, and FUCA2) with SA. These findings offer valuable insights into SA's underlying mechanisms and potential therapeutic approaches.
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Affiliation(s)
- Hao Zhao
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
| | - Yifeng Liu
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Xuening Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuhua Liao
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Huimin Zhang
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Xue Han
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Lan Guo
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
| | - Beifang Fan
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.
| | - Wanxin Wang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China.
| | - Ciyong Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
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48
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Suhre K, Venkataraman GR, Guturu H, Halama A, Stephan N, Thareja G, Sarwath H, Motamedchaboki K, Donovan MKR, Siddiqui A, Batzoglou S, Schmidt F. Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping. Nat Commun 2024; 15:989. [PMID: 38307861 PMCID: PMC10837160 DOI: 10.1038/s41467-024-45233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technologies face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, mass spectrometry-based proteomics approach. We identify 184 protein-altering variants in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.
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Affiliation(s)
- Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | | | | | - Anna Halama
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Nisha Stephan
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | - Hina Sarwath
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | | | | | - Asim Siddiqui
- Seer, Inc., Redwood City, Redwood City, CA, 94065, USA
| | | | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
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49
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Zou X, Wang L, Wang S, Zhang Y, Ma J, Chen L, Li Y, Yao TX, Zhou H, Wu L, Tang Q, Ma S, Zhang X, Tang R, Yi Y, Liu R, Zeng Y, Zhang L. Promising therapeutic targets for ischemic stroke identified from plasma and cerebrospinal fluid proteomes: a multicenter Mendelian randomization study. Int J Surg 2024; 110:766-776. [PMID: 38016292 PMCID: PMC10871597 DOI: 10.1097/js9.0000000000000922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Ischemic stroke (IS) is more common every year, the condition is serious, and have a poor prognosis. New, efficient, and safe therapeutic targets are desperately needed as early treatment especially prevention and reperfusion is the key to lowering the occurrence of poorer prognosis. Generally circulating proteins are attractive therapeutic targets, this study aims to identify potential pharmacological targets among plasma and cerebrospinal fluid (CSF) proteins for the prevention and treatment of IS using a multicenter Mendelian randomization (MR) approach. METHODS First, the genetic instruments of 734 plasma and 151 CSF proteins were assessed for causative connections with IS from MEGASTROKE consortium by MR to identify prospective therapeutic targets. Then, for additional validation, plasma proteins from the deCODE consortium and the Fenland consortium, as well as IS GWAS data from the FinnGen cohort, the ISGC consortium and UK biobank, were employed. A thorough evaluation of the aforementioned possible pharmacological targets was carried out using meta-analysis. The robustness of MR results was then confirmed through sensitivity analysis using several techniques, such as bidirectional MR analysis, Steiger filtering, and Bayesian colocalization. Finally, methods like Protein-Protein Interaction (PPI) Networking were utilized to investigate the relationship between putative drug targets and therapeutic agents. RESULTS The authors discovered three proteins that may function as promising therapeutic targets for IS and meet the Bonferroni correction ( P <0.05/885=5.65×10 -5 ). Prekallikrein (OR=0.41, 95% CI: 0.27-0.63, P =3.61×10 -5 ), a protein found in CSF, has a 10-fold protective impact in IS, while the plasma proteins SWAP70 (OR=0.85, 95% CI: 0.80-0.91, P =1.64×10 -6 ) and MMP-12 (OR=0.92, 95% CI: 0.89-0.95, P =4.49×10 -6 ) of each SD play a protective role in IS. Prekallikrein, MMP-12, SWAP70 was replicated in the FinnGen cohort and ISGC database. MMP-12 (OR=0.93, 95% CI: 0.91-0.94, P <0.001), SWAP70 (OR=0.92, 95% CI: 0.90-0.94, P <0.001), and prekallikrein (OR=0.53, 95% CI: 0.33-0.72, P <0.001) may all be viable targets for IS, according to the combined meta-analysis results. Additionally, no evidence of reverse causality was identified, and Bayesian colocalization revealed MMP-12 (PPH 4 =0.995), SWAP70 (PPH 4 =0.987), and prekallikrein (PPH 4 =0.894) shared the same variant with IS, supporting the robustness of the aforementioned causation. Prekallikrein and MMP-12 were associated with the target protein of the current treatment of IS. Among them, Lanadelumab, a new drug whose target protein is a prekallikrein, may be a promising new drug for the treatment of IS. CONCLUSION The prekallikrein, MMP-12, and SWAP70 are causally associated with the risk of IS. Moreover, MMP-12 and prekallikrein may be treated as promising therapeutic targets for medical intervention of IS.
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Affiliation(s)
- Xuelun Zou
- Department of Neurology, Xiangya Hospital, Central South University
| | - Leiyun Wang
- Department of Pharmacy, Wuhan No.1 Hospital, Wuhan, Hubei, People’s Republic of China
| | - Sai Wang
- Department of Neurology, Xiangya Hospital, Central South University
| | - Yupeng Zhang
- Department of Neurology, Xiangya Hospital, Central South University
| | - Junyi Ma
- Department of Neurology, Xiangya Hospital, Central South University
| | - Lei Chen
- Department of Neurology, Xiangya Hospital, Central South University
| | - Ye Li
- Department of Neurology, Xiangya Hospital, Central South University
| | - Tian-Xing Yao
- Department of Neurology, Xiangya Hospital, Central South University
| | - Huifang Zhou
- Department of Neurology, Xiangya Hospital, Central South University
| | - Lianxu Wu
- Department of Neurology, Xiangya Hospital, Central South University
| | - Qiaoling Tang
- Department of Neurology, Xiangya Hospital, Central South University
| | - Siyuan Ma
- Department of Neurology, Xiangya Hospital, Central South University
| | - Xiangbin Zhang
- Department of Neurology, Xiangya Hospital, Central South University
| | - Rongmei Tang
- Department of Neurology, Xiangya Hospital, Central South University
| | - Yexiang Yi
- Department of Neurology, Xiangya Hospital, Central South University
| | - Ran Liu
- Department of Neurology, Xiangya Hospital, Central South University
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital
| | - Le Zhang
- Department of Neurology, Xiangya Hospital, Central South University
- Human Brain Disease Biological Resources Platform of Hunan Province, Xiangya Hospital
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital
- Multi-Modal Monitoring Technology for Severe Cerebrovascular Disease of Human Engineering Research Center, Xiangya Hospital
- Brain Health Center of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan
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50
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Gao M, Wu X, Jiao X, Hu Y, Wang Y, Zhuo N, Dong F, Wang Y, Wang F, Cao Y, Liu C, Li J, Shen L, Zhang H, Lu Z. Prognostic and predictive value of angiogenesis-associated serum proteins for immunotherapy in esophageal cancer. J Immunother Cancer 2024; 12:e006616. [PMID: 38302415 PMCID: PMC10836376 DOI: 10.1136/jitc-2022-006616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have significantly improved patient survival in multiple cancers. However, therapy response in esophageal cancer is limited to subgroups of patients and clinically useful predictive biomarkers are lacking. METHODS We collected a series of plasma samples from 91 patients with esophageal cancer before and after ICI treatment. The Olink Immuno-Oncology panel (92 proteins) with proximity extension assays was used to detect the dynamic changes in plasma and potential biomarkers associated with treatment outcomes. We screened all survival-related proteins and established a risk score model to better predict the prognosis and treatment response in patients with esophageal cancer immunotherapy. RESULTS We found that 47 out of 92 quantified proteins had significant changes in plasma levels during ICI treatment (p<0.050), and these changed proteins were involved in immune-related reactions, such as intercellular adhesion and T-cell activation. Notably, the baseline levels of three angiogenesis-related proteins (IL-8, TIE2, and HGF) were significantly associated with the survival outcomes of patients treated with ICIs (p<0.050). According to these prognostic proteins, we established an angiogenesis-related risk score, which could be a superior biomarker for ICI response prediction. In addition, antiangiogenic therapy combined with ICIs significantly improved overall survival compared with ICI monotherapy (p=0.044). CONCLUSIONS An angiogenesis-related risk score based on three proteins (IL-8, TIE2, and HGF) could predict ICI response and prognosis in patients with esophageal cancer, which warrants verification in the future. Our study highlights the potential application of combining ICIs and antiangiogenic therapy and supports Olink plasma protein sequencing as a liquid biopsy method for biomarker exploration.
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Affiliation(s)
- Mengting Gao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xueying Wu
- Biomedical Innovation Center, Beijing Shijitan Hospital Capital Medical University, Beijing, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital Capital Medical University, Beijing, China
| | - Xi Jiao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ying Hu
- Biomedical Innovation Center, Beijing Shijitan Hospital Capital Medical University, Beijing, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital Capital Medical University, Beijing, China
| | - Yanni Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Na Zhuo
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengxiao Dong
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yujiao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengyuan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yanshuo Cao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Chang Liu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lin Shen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Henghui Zhang
- Biomedical Innovation Center, Beijing Shijitan Hospital Capital Medical University, Beijing, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital Capital Medical University, Beijing, China
- Beijing Engineering Research Center of Immunocellular therapy, Beijing, China
| | - Zhihao Lu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
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