1
|
Cruchaga C, Western D, Timsina J, Wang L, Wang C, Yang C, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey A, Morris J, Perrin R, Ruiz A, Marquié M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson E, Guen YL, Alvarez I, Aguilar M, Greicius M, Pastor P, Pulford D, Ibanez L, Wyss-Coray T, Sung YJ, Phillips B. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and informs causal proteins for Alzheimer's disease. RESEARCH SQUARE 2023:rs.3.rs-2814616. [PMID: 37333337 PMCID: PMC10275048 DOI: 10.21203/rs.3.rs-2814616/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The integration of quantitative trait loci (QTL) with disease genome-wide association studies (GWAS) has proven successful at prioritizing candidate genes at disease-associated loci. QTL mapping has mainly been focused on multi-tissue expression QTL or plasma protein QTL (pQTL). Here we generated the largest-to-date cerebrospinal fluid (CSF) pQTL atlas by analyzing 7,028 proteins in 3,107 samples. We identified 3,373 independent study-wide associations for 1,961 proteins, including 2,448 novel pQTLs of which 1,585 are unique to CSF, demonstrating unique genetic regulation of the CSF proteome. In addition to the established chr6p22.2-21.32 HLA region, we identified pleiotropic regions on chr3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron-specificity and neurological development. We also integrated this pQTL atlas with the latest Alzheimer's disease (AD) GWAS through PWAS, colocalization and Mendelian Randomization and identified 42 putative causal proteins for AD, 15 of which have drugs available. Finally, we developed a proteomics-based risk score for AD that outperforms genetics-based polygenic risk scores. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.
Collapse
Affiliation(s)
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Washington University School of Medicine
| | | | | | | | | | | | - Patsy Kohlfeld
- Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | | | | | - Mercè Boada
- Memory Clinic of Fundaciò ACE, Catalan Institute of Applied Neurosciences
| | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca Mútua Terrassa, Terrassa, Barcelona, Spain
| | | | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
| | | | | | | | | | | |
Collapse
|
2
|
Genome-wide genotype-serum proteome mapping provides insights into the cross-ancestry differences in cardiometabolic disease susceptibility. Nat Commun 2023; 14:896. [PMID: 36797296 PMCID: PMC9935862 DOI: 10.1038/s41467-023-36491-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Identification of protein quantitative trait loci (pQTL) helps understand the underlying mechanisms of diseases and discover promising targets for pharmacological intervention. For most important class of drug targets, genetic evidence needs to be generalizable to diverse populations. Given that the majority of the previous studies were conducted in European ancestry populations, little is known about the protein-associated genetic variants in East Asians. Based on data-independent acquisition mass spectrometry technique, we conduct genome-wide association analyses for 304 unique proteins in 2,958 Han Chinese participants. We identify 195 genetic variant-protein associations. Colocalization and Mendelian randomization analyses highlight 60 gene-protein-phenotype associations, 45 of which (75%) have not been prioritized in Europeans previously. Further cross-ancestry analyses uncover key proteins that contributed to the differences in the obesity-induced diabetes and coronary artery disease susceptibility. These findings provide novel druggable proteins as well as a unique resource for the trans-ancestry evaluation of protein-targeted drug discovery.
Collapse
|
3
|
Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
Collapse
Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| |
Collapse
|
4
|
Png G, Barysenka A, Repetto L, Navarro P, Shen X, Pietzner M, Wheeler E, Wareham NJ, Langenberg C, Tsafantakis E, Karaleftheri M, Dedoussis G, Mälarstig A, Wilson JF, Gilly A, Zeggini E. Mapping the serum proteome to neurological diseases using whole genome sequencing. Nat Commun 2021; 12:7042. [PMID: 34857772 PMCID: PMC8640022 DOI: 10.1038/s41467-021-27387-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the increasing global burden of neurological disorders, there is a lack of effective diagnostic and therapeutic biomarkers. Proteins are often dysregulated in disease and have a strong genetic component. Here, we carry out a protein quantitative trait locus analysis of 184 neurologically-relevant proteins, using whole genome sequencing data from two isolated population-based cohorts (N = 2893). In doing so, we elucidate the genetic landscape of the circulating proteome and its connection to neurological disorders. We detect 214 independently-associated variants for 107 proteins, the majority of which (76%) are cis-acting, including 114 variants that have not been previously identified. Using two-sample Mendelian randomisation, we identify causal associations between serum CD33 and Alzheimer's disease, GPNMB and Parkinson's disease, and MSR1 and schizophrenia, describing their clinical potential and highlighting drug repurposing opportunities.
Collapse
Affiliation(s)
- Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany. .,TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany.
| | - Andrei Barysenka
- grid.4567.00000 0004 0483 2525Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Linda Repetto
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Xia Shen
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK ,grid.8547.e0000 0001 0125 2443Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China ,grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Maik Pietzner
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Eleanor Wheeler
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Nicholas J. Wareham
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Claudia Langenberg
- grid.5335.00000000121885934MRC Epidemiology Unit, University of Cambridge, Cambridge, UK ,grid.484013.aComputational Medicine, Berlin Institute of Health (BIH), Charité University Medicine, Berlin, Germany
| | | | | | - George Dedoussis
- grid.15823.3d0000 0004 0622 2843Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Anders Mälarstig
- grid.4714.60000 0004 1937 0626Department of Medicine, Karolinska Institute, Solna, Sweden ,Emerging Science & Innovation, Pfizer Worldwide Research, Development and Medical, Cambridge, MA USA
| | - James F. Wilson
- grid.4305.20000 0004 1936 7988Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK ,grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Arthur Gilly
- grid.4567.00000 0004 0483 2525Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany. .,TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany.
| |
Collapse
|
5
|
Yang C, Farias FHG, Ibanez L, Suhy A, Sadler B, Fernandez MV, Wang F, Bradley JL, Eiffert B, Bahena JA, Budde JP, Li Z, Dube U, Sung YJ, Mihindukulasuriya KA, Morris JC, Fagan AM, Perrin RJ, Benitez BA, Rhinn H, Harari O, Cruchaga C. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat Neurosci 2021; 24:1302-1312. [PMID: 34239129 PMCID: PMC8521603 DOI: 10.1038/s41593-021-00886-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Understanding the tissue-specific genetic controls of protein levels is essential to uncover mechanisms of post-transcriptional gene regulation. In this study, we generated a genomic atlas of protein levels in three tissues relevant to neurological disorders (brain, cerebrospinal fluid and plasma) by profiling thousands of proteins from participants with and without Alzheimer's disease. We identified 274, 127 and 32 protein quantitative trait loci (pQTLs) for cerebrospinal fluid, plasma and brain, respectively. cis-pQTLs were more likely to be tissue shared, but trans-pQTLs tended to be tissue specific. Between 48.0% and 76.6% of pQTLs did not co-localize with expression, splicing, DNA methylation or histone acetylation QTLs. Using Mendelian randomization, we nominated proteins implicated in neurological diseases, including Alzheimer's disease, Parkinson's disease and stroke. This first multi-tissue study will be instrumental to map signals from genome-wide association studies onto functional genes, to discover pathways and to identify drug targets for neurological diseases.
Collapse
Affiliation(s)
- 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
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Fabiana H G Farias
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Laura Ibanez
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Adam Suhy
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Brooke Sadler
- Pediatrics Hematology/Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Fengxian 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
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Joseph L Bradley
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Brett Eiffert
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Jorge A Bahena
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - John P 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
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Zeran Li
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Umber Dube
- 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 Neurological Disorders, Washington University School of Medicine, 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
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Kathie A Mihindukulasuriya
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - John C Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne M Fagan
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A Benitez
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Herve Rhinn
- Department of Bioinformatics, Alector, Inc., South San Francisco, CA, USA
| | - Oscar Harari
- 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research 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 Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA.
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
6
|
Panyard DJ, Kim KM, Darst BF, Deming YK, Zhong X, Wu Y, Kang H, Carlsson CM, Johnson SC, Asthana S, Engelman CD, Lu Q. Cerebrospinal fluid metabolomics identifies 19 brain-related phenotype associations. Commun Biol 2021; 4:63. [PMID: 33437055 PMCID: PMC7803963 DOI: 10.1038/s42003-020-01583-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
The study of metabolomics and disease has enabled the discovery of new risk factors, diagnostic markers, and drug targets. For neurological and psychiatric phenotypes, the cerebrospinal fluid (CSF) is of particular importance. However, the CSF metabolome is difficult to study on a large scale due to the relative complexity of the procedure needed to collect the fluid. Here, we present a metabolome-wide association study (MWAS), which uses genetic and metabolomic data to impute metabolites into large samples with genome-wide association summary statistics. We conduct a metabolome-wide, genome-wide association analysis with 338 CSF metabolites, identifying 16 genotype-metabolite associations (metabolite quantitative trait loci, or mQTLs). We then build prediction models for all available CSF metabolites and test for associations with 27 neurological and psychiatric phenotypes, identifying 19 significant CSF metabolite-phenotype associations. Our results demonstrate the feasibility of MWAS to study omic data in scarce sample types.
Collapse
Grants
- R01 AG037639 NIA NIH HHS
- UL1 TR000427 NCATS NIH HHS
- T15 LM007359 NLM NIH HHS
- T32 LM012413 NLM NIH HHS
- RF1 AG027161 NIA NIH HHS
- T32 AG000213 NIA NIH HHS
- P2C HD047873 NICHD NIH HHS
- UL1 TR002373 NCATS NIH HHS
- P30 AG062715 NIA NIH HHS
- P50 AG033514 NIA NIH HHS
- R01 AG027161 NIA NIH HHS
- R01 AG054047 NIA NIH HHS
- P30 AG017266 NIA NIH HHS
- R21 AG067092 NIA NIH HHS
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
- U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)
- NSF | Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences (DMS)
- U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- This research is supported by National Institutes of Health (NIH) grants R01AG27161 (Wisconsin Registry for Alzheimer Prevention: Biomarkers of Preclinical AD), R01AG054047 (Genomic and Metabolomic Data Integration in a Longitudinal Cohort at Risk for Alzheimer’s Disease), R21AG067092 (Identifying Metabolomic Risk Factors in Plasma and Cerebrospinal Fluid for Alzheimer’s Disease), R01AG037639 (White Matter Degeneration: Biomarkers in Preclinical Alzheimer’s Disease), P30AG017266 (Center for Demography of Health and Aging), and P50AG033514 and P30AG062715 (Wisconsin Alzheimer’s Disease Research Center Grant), the Helen Bader Foundation, Northwestern Mutual Foundation, Extendicare Foundation, State of Wisconsin, the Clinical and Translational Science Award (CTSA) program through the NIH National Center for Advancing Translational Sciences (NCATS) grant UL1TR000427, and the University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. This research was supported in part by the Intramural Research Program of the National Institute on Aging. Computational resources were supported by a core grant to the Center for Demography and Ecology at the University of Wisconsin-Madison (P2CHD047873). Author DJP was supported by an NLM training grant to the Bio-Data Science Training Program (T32LM012413). Author BFD was supported by an NLM training grant to the Computation and Informatics in Biology and Medicine Training Program (NLM 5T15LM007359). Author YKD was supported by a training grant from the National Institute on Aging (T32AG000213). Author HK was supported by National Science Foundation (NSF) grant DMS-1811414 (Theory and Methods for Inferring Causal Effects with Mendelian Randomization).
Collapse
Affiliation(s)
- Daniel J Panyard
- Department of Population Health Sciences, University of Wisconsin-Madison, 610 Walnut Street, 707 WARF Building, Madison, WI, 53726, USA
| | - Kyeong Mo Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Burcu F Darst
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, 90033, USA
| | - Yuetiva K Deming
- Department of Population Health Sciences, University of Wisconsin-Madison, 610 Walnut Street, 707 WARF Building, Madison, WI, 53726, USA
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, 600 Highland Avenue, J5/1 Mezzanine, Madison, WI, 53792, USA
- Department of Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA
| | - Xiaoyuan Zhong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WARF Room 201, 610 Walnut Street, Madison, WI, 53726, USA
| | - Yuchang Wu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WARF Room 201, 610 Walnut Street, Madison, WI, 53726, USA
| | - Hyunseung Kang
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA
| | - Cynthia M Carlsson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, 600 Highland Avenue, J5/1 Mezzanine, Madison, WI, 53792, USA
- Department of Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA
- William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI, 53705, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, 600 Highland Avenue, J5/1 Mezzanine, Madison, WI, 53792, USA
- Department of Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA
- William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI, 53705, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin-Madison, 600 Highland Avenue, J5/1 Mezzanine, Madison, WI, 53792, USA
- Department of Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA
- William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI, 53705, USA
| | - Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin-Madison, 610 Walnut Street, 707 WARF Building, Madison, WI, 53726, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WARF Room 201, 610 Walnut Street, Madison, WI, 53726, USA.
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA.
| |
Collapse
|
7
|
Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet 2020; 22:19-37. [PMID: 32860016 DOI: 10.1038/s41576-020-0268-2] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
Proteomic analysis of cells, tissues and body fluids has generated valuable insights into the complex processes influencing human biology. Proteins represent intermediate phenotypes for disease and provide insight into how genetic and non-genetic risk factors are mechanistically linked to clinical outcomes. Associations between protein levels and DNA sequence variants that colocalize with risk alleles for common diseases can expose disease-associated pathways, revealing novel drug targets and translational biomarkers. However, genome-wide, population-scale analyses of proteomic data are only now emerging. Here, we review current findings from studies of the plasma proteome and discuss their potential for advancing biomedical translation through the interpretation of genome-wide association analyses. We highlight the challenges faced by currently available technologies and provide perspectives relevant to their future application in large-scale biobank studies.
Collapse
|
8
|
Ye J, Wen Y, Chu X, Li P, Cheng B, Cheng S, Liu L, Zhang L, Ma M, Qi X, Liang C, Kafle OP, Jia Y, Wu C, Wang S, Wang X, Ning Y, Zhang F. Association between herpes simplex virus 1 exposure and the risk of depression in UK Biobank. Clin Transl Med 2020; 10:e108. [PMID: 32564518 PMCID: PMC7403656 DOI: 10.1002/ctm2.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Herpes simplex virus-1 (HSV-1) infection is reported to be associated with depression. But limited efforts were made to investigate the relationship between HSV-1 infection and the risk of depression, especially from the genetic perspective. METHODS In UK Biobank cohort, linear and logistic regression analyses were first performed to test the association of HSV-1 seropositivity/antibody with depression, including depression status (N = 2951) and Patient Health Questionnaire (PHQ) score (N = 2839). Using individual genotypic and phenotypic data from the UK Biobank, genome-wide environmental interaction study (GWEIS) was then conducted by PLINK2.0 to evaluate gene × HSV-1 interacting effect on the risk of depression. Finally, gene set enrichment analysis was conducted to identify the biological pathways involved in the observed gene × HSV-1 interaction for depression. RESULT In UK Biobank cohort, significant associations were observed between depression status and HSV-1 (odds ratio [OR] = 1.09; 95% confidence interval [CI], 1.02-1.16; P = 2.40 × 10-2 for HSV-1 antibody and OR = 1.28; 95% CI, 1.12-1.47, P = 2.59 × 10-3 for HSV-1 seropositivity). GWEIS revealed four significant gene × HSV-1 interaction signals for PHQ score (all P < 5.0 × 10-8 ) and the leading loci was SULF2 (rs6094791, P = 8.60 × 10-9 ). Pathway analyses identified 21 pathways for PHQ score and 19 for depression status, including multiple neural development- and immune-related ones, such as KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION (false discovery rate [FDR] = 3.18 × 10-2 ) for depression and LU_AGING_BRAIN_UP (FDR = 4.21 × 10-2 ) for PHQ score. CONCLUSION Our results suggested that HSV-1 was associated with the risk of depression, which was modulated by the several genes that were related to the nerve development or immune function.
Collapse
Affiliation(s)
- Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Om Prakash Kafle
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sen Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xi Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujie Ning
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
9
|
Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z. Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biol Direct 2020; 15:10. [PMID: 32539851 PMCID: PMC7294636 DOI: 10.1186/s13062-020-00264-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/04/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes. RESULTS In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive molecular profiling across different datasets, we revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples. PRKCG expression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly, PRKCG in combination with MGMT is effective to predict survival outcomes in a more precise manner. CONCLUSIONS PRKCG bears the great potential for glioma diagnosis, prognosis and therapy, and PRKCG-like genes may represent a set of important genes associated with different molecular mechanisms in glioma tumorigenesis. Our study indicates the importance of computational integrative multi-omics data analysis and represents a data-driven scheme toward precision tumor subtyping and accurate personalized healthcare.
Collapse
Affiliation(s)
- Lin Liu
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangyu Wang
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
- Present Address: The Methodist Hospital Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Chunlei Yu
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengwei Li
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuhui Song
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Lili Hao
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Lina Ma
- China National Center for Bioinformation, Beijing, 100101, China.
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing, 100101, China.
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
10
|
Sasayama D, Hattori K, Yokota Y, Matsumura R, Teraishi T, Yoshida S, Kunugi H. Increased apolipoprotein E and decreased TNF-α in the cerebrospinal fluid of nondemented APOE-ε4 carriers. Neuropsychopharmacol Rep 2020; 40:201-205. [PMID: 32426945 PMCID: PMC7722685 DOI: 10.1002/npr2.12110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/30/2020] [Accepted: 04/10/2020] [Indexed: 01/12/2023] Open
Abstract
Aim The ε4 allele of apolipoprotein E gene (APOE) is a well‐known risk factor of late‐onset Alzheimer's disease. However, little is known why this variant confers a risk for Alzheimer's disease. The aim of this study was to examine the influence of the APOE genotype on cerebrospinal fluid (CSF) protein levels. Methods The present study performed a secondary analysis on our previously generated database to compare the CSF levels of 1128 proteins between APOE‐ε4 carriers (28 subjects) and noncarriers (104 subjects). All subjects were physically healthy Japanese individuals without dementia. Results CSF levels of apoE2, apoE3, and apoE4 were significantly higher (all nominal P < 10 × 10−5, false discovery rate < 0.001) and those of tumor necrosis factor‐α (TNF‐α) were significantly lower (nominal P = 1.39 × 10−6, false discovery rate < 0.001) in APOE‐ε4 carriers than in noncarriers. No significant correlation was observed between the CSF levels of TNF‐α and any of the apoE proteins. Conclusions Our findings indicate the possible roles of apoE and TNF‐α in the pathogenesis of APOE‐ε4‐associated Alzheimer's disease. The CSF levels of apoE2, apoE3, and apoE4 were higher in APOE‐ε4 carriers. The CSF levels of TNF‐α were significantly lower in APOE‐ε4 carriers. Our findings indicate the possible roles of apoE and TNF‐α in the pathogenesis of APOE‐ε4‐associated Alzheimer's disease.![]()
Collapse
Affiliation(s)
- Daimei Sasayama
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, National Institute of Neuroscience, Kodaira, Japan.,Department of Psychiatry, Shinshu University School of Medicine, Matsumoto, Japan.,Child and Adolescent Developmental Psychiatry, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kotaro Hattori
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, National Institute of Neuroscience, Kodaira, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yuuki Yokota
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, National Institute of Neuroscience, Kodaira, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ryo Matsumura
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Toshiya Teraishi
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, National Institute of Neuroscience, Kodaira, Japan
| | - Sumiko Yoshida
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan.,Department of Psychiatry, National Center of Neurology and Psychiatry, National Center Hospital, Kodaira, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Center of Neurology and Psychiatry, National Institute of Neuroscience, Kodaira, Japan.,Department of Psychiatry, Teikyo University School of Medicine, Itabashi-ku, Japan
| |
Collapse
|
11
|
Systemic factors as mediators of brain homeostasis, ageing and neurodegeneration. Nat Rev Neurosci 2020; 21:93-102. [PMID: 31913356 DOI: 10.1038/s41583-019-0255-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
A rapidly ageing population and a limited therapeutic toolbox urgently necessitate new approaches to treat neurodegenerative diseases. Brain ageing, the key risk factor for neurodegeneration, involves complex cellular and molecular processes that eventually result in cognitive decline. Although cell-intrinsic defects in neurons and glia may partially explain this decline, cell-extrinsic changes in the systemic environment, mediated by blood, have recently been shown to contribute to brain dysfunction with age. Here, we review the current understanding of how systemic factors mediate brain ageing, how these factors are regulated and how we can translate these findings into therapies for neurodegenerative diseases.
Collapse
|
12
|
Hillary RF, McCartney DL, Harris SE, Stevenson AJ, Seeboth A, Zhang Q, Liewald DC, Evans KL, Ritchie CW, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Marioni RE. Genome and epigenome wide studies of neurological protein biomarkers in the Lothian Birth Cohort 1936. Nat Commun 2019; 10:3160. [PMID: 31320639 PMCID: PMC6639385 DOI: 10.1038/s41467-019-11177-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023] Open
Abstract
Although plasma proteins may serve as markers of neurological disease risk, the molecular mechanisms responsible for inter-individual variation in plasma protein levels are poorly understood. Therefore, we conduct genome- and epigenome-wide association studies on the levels of 92 neurological proteins to identify genetic and epigenetic loci associated with their plasma concentrations (n = 750 healthy older adults). We identify 41 independent genome-wide significant (P < 5.4 × 10-10) loci for 33 proteins and 26 epigenome-wide significant (P < 3.9 × 10-10) sites associated with the levels of 9 proteins. Using this information, we identify biological pathways in which putative neurological biomarkers are implicated (neurological, immunological and extracellular matrix metabolic pathways). We also observe causal relationships (by Mendelian randomisation analysis) between changes in gene expression (DRAXIN, MDGA1 and KYNU), or DNA methylation profiles (MATN3, MDGA1 and NEP), and altered plasma protein levels. Together, this may help inform causal relationships between biomarkers and neurological diseases.
Collapse
Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Anne Seeboth
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - David C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Craig W Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at Austin, Austin, TX, 78712, USA.,Population Research Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK. .,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| |
Collapse
|
13
|
Abstract
Recent advance in high-throughput proteome analysis has enabled genome-wide and proteome-wide analyses of associations between single nucleotide polymorphisms and protein expression levels. Protein quantitative trait locus (pQTL) studies using cerebrospinal fluid (CSF) and DNA samples may provide valuable insights into the genetic basis and molecular mechanisms regulating protein expression in the central nervous system. In this chapter, we describe a step-by-step procedures of CSF collection and pQTL analysis, by using PLINK and R software.
Collapse
|
14
|
Angata T. Possible Influences of Endogenous and Exogenous Ligands on the Evolution of Human Siglecs. Front Immunol 2018; 9:2885. [PMID: 30564250 PMCID: PMC6288428 DOI: 10.3389/fimmu.2018.02885] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/23/2018] [Indexed: 12/25/2022] Open
Abstract
Sialic acids, a group of acidic sugars abundantly expressed in the tissues of deuterostome animals but rarely found in microbes, serve as a "signature of self" for these animals. Cognate sensors for sialic acids include Siglecs, a family of transmembrane lectins of vertebrate immune systems that recognize glycans containing sialic acids. A type of sialic acid called N-glycolylneuraminic acid (Neu5Gc) is abundant in many mammalian lineages including great apes, the closest extant relatives of modern human, but was lost in the lineage leading to modern human via the pseudogenization of the CMAH gene encoding the enzyme that converts N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. Loss of Neu5Gc appears to have influenced the evolution of human Siglecs, such as the adjustment of sialic acid binding preferences and the inactivation of at least one Siglec. In addition, various mechanistic studies using model systems and genetic association studies have revealed that some human Siglecs interact with pathogens and influence the outcome of infections, and these pathogens in turn likely influence the evolution of these Siglecs. By understanding the evolutionary forces affecting Siglecs, we shall achieve a better appreciation of Siglec functions, and by understanding Siglec functions, we can obtain deeper insight into the evolutionary processes driving Siglec evolution.
Collapse
Affiliation(s)
- Takashi Angata
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
15
|
Sasayama D, Asano S, Nogawa S, Takahashi S, Saito K, Kunugi H. A genome-wide association study on photic sneeze syndrome in a Japanese population. J Hum Genet 2018; 63:765-768. [PMID: 29559738 DOI: 10.1038/s10038-018-0441-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/25/2022]
Abstract
Photic sneeze syndrome (PSS) is characterized by a tendency to sneeze when the eye is exposed to bright light. Recent genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) associated with PSS in Caucasian populations. We performed a GWAS on PSS in Japanese individuals who responded to a web-based survey and provided saliva samples. After quality control, genotype data of 210,086 SNPs in 11,409 individuals were analyzed. The overall prevalence of PSS was 3.2%. Consistent with previous reports, SNPs at 3p12.1 were associated with PSS at genome-wide significance (p < 5.0 × 10-8). Furthermore, two novel loci at 9q34.2 and 4q35.2 reached suggestive significance (p < 5.0 × 10-6). Our data also provided evidence supporting the two additional SNPs on 2q22.3 and 9q33.2 reportedly associated with PSS. Our study reproduced previous findings in Caucasian populations and further suggested novel PSS loci in the Japanese population.
Collapse
Affiliation(s)
- Daimei Sasayama
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1, Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Psychiatry, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Shinya Asano
- Genequest Inc., 5-22-37, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Shun Nogawa
- Genequest Inc., 5-22-37, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Shoko Takahashi
- Genequest Inc., 5-22-37, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Kenji Saito
- Genequest Inc., 5-22-37, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1, Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.
| |
Collapse
|