1
|
Merikangas AK, Shelly M, Knighton A, Kotler N, Tanenbaum N, Almasy L. What genes are differentially expressed in individuals with schizophrenia? A systematic review. Mol Psychiatry 2022; 27:1373-1383. [PMID: 35091668 PMCID: PMC9095490 DOI: 10.1038/s41380-021-01420-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 11/15/2022]
Abstract
Schizophrenia is a severe, complex mental disorder characterized by a combination of positive symptoms, negative symptoms, and impaired cognitive function. Schizophrenia is highly heritable (~80%) with multifactorial etiology and complex polygenic genetic architecture. Despite the large number of genetic variants associated with schizophrenia, few causal variants have been established. Gaining insight into the mechanistic influences of these genetic variants may facilitate our ability to apply these findings to prevention and treatment. Though there have been more than 300 studies of gene expression in schizophrenia over the past 15 years, none of the studies have yielded consistent evidence for specific genes that contribute to schizophrenia risk. The aim of this work is to conduct a systematic review and synthesis of case-control studies of genome-wide gene expression in schizophrenia. Comprehensive literature searches were completed in PubMed, EmBase, and Web of Science, and after a systematic review of the studies, data were extracted from those that met the following inclusion criteria: human case-control studies comparing the genome-wide transcriptome of individuals diagnosed with schizophrenia to healthy controls published between January 1, 2000 and June 30, 2020 in the English language. Genes differentially expressed in cases were extracted from these studies, and overlapping genes were compared to previous research findings from the genome-wide association, structural variation, and tissue-expression studies. The transcriptome-wide analysis identified different genes than those previously reported in genome-wide association, exome sequencing, and structural variation studies of schizophrenia. Only one gene, GBP2, was replicated in five studies. Previous work has shown that this gene may play a role in immune function in the etiology of schizophrenia, which in turn could have implications for risk profiling, prevention, and treatment. This review highlights the methodological inconsistencies that impede valid meta-analyses and synthesis across studies. Standardization of the use of covariates, gene nomenclature, and methods for reporting results could enhance our understanding of the potential mechanisms through which genes exert their influence on the etiology of schizophrenia. Although these results are promising, collaborative efforts with harmonization of methodology will facilitate the identification of the role of genes underlying schizophrenia.
Collapse
Affiliation(s)
- Alison K. Merikangas
- grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Matthew Shelly
- grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.268256.d0000 0000 8510 1943Department of Biology, College of Science and Engineering, Wilkes University, Wilkes-Barre, PA USA
| | - Alexys Knighton
- grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Nicholas Kotler
- grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Nicole Tanenbaum
- grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Laura Almasy
- grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| |
Collapse
|
3
|
Vachon J, Pagé-Larivière F, Sirard MA, Rodriguez MJ, Levallois P, Campagna C. Availability, Quality, and Relevance of Toxicogenomics Data for Human Health Risk Assessment: A Scoping Review of the Literature on Trihalomethanes. Toxicol Sci 2018. [DOI: 10.1093/toxsci/kfy050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Julien Vachon
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
| | - Florence Pagé-Larivière
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Marc-André Sirard
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Manuel J Rodriguez
- École Supérieure d’Aménagement du Territoire et de Développement Régional, Université Laval, Québec, Québec, Canada G1V 0A6
- Chaire de Recherche CRSNG en Eau Potable, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Patrick Levallois
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Québec, Canada G1S 4L8
| | - Céline Campagna
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
| |
Collapse
|
5
|
Vachon J, Campagna C, Rodriguez MJ, Sirard MA, Levallois P. Barriers to the use of toxicogenomics data in human health risk assessment: A survey of Canadian risk assessors. Regul Toxicol Pharmacol 2017; 85:119-123. [PMID: 28137640 DOI: 10.1016/j.yrtph.2017.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/24/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Regulatory agencies worldwide need to modernize human health risk assessment (HHRA) to meet challenges of the 21st century. Toxicogenomics is at the core of this improvement. Today, however, the use of toxicogenomics data in HHRA is very limited. The purpose of this survey was to identify barriers to the application of toxicogenomics data in HHRA by human health risk assessors. An online survey targeting Canadian risk assessors gathered information on their knowledge and perception of toxicogenomics, their current and future inclusion of toxicogenomics data in HHRA, and barriers to the use of such data. Twenty-nine (29) participants completed a questionnaire after 2 months of solicitation. The results show that the application of toxicogenomics data in Canada is marginal, with 85% of respondents reporting that they never or rarely used such data. Knowledge of toxicogenomics by Canadian risk assessors is also limited: about two-thirds of respondents (68%) were not at all or only slightly familiar with the concept. Lack of guidelines for toxicogenomics data interpretation, data quality assessment and on their use in HHRA, were found to be major barriers. In conclusion, there is a need for interventions aimed at facilitating the use of toxicogenomics data in HHRA, when available.
Collapse
Affiliation(s)
- Julien Vachon
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada; Axe Santé des populations et pratiques optimales en santé, Centre de recherche du Centre hospitalier universitaire de Québec, Québec, QC, Canada.
| | - Céline Campagna
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada.
| | - Manuel J Rodriguez
- École supérieure d'aménagement du territoire et de développement régional, Faculté d'aménagement, d'architecture, d'art et de design, Université Laval, Québec, QC, Canada; Chaire de recherche industrielle CRSNG, Gestion et surveillance de la qualité de l'eau potable, Université Laval, Québec, QC, Canada.
| | - Marc-André Sirard
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en reproduction, développement et santé intergénérationnelle, Centre de recherche du Centre hospitalier de Québec, Québec, QC, Canada.
| | - Patrick Levallois
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada; Axe Santé des populations et pratiques optimales en santé, Centre de recherche du Centre hospitalier universitaire de Québec, Québec, QC, Canada.
| |
Collapse
|
6
|
Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. The Next Generation of Risk Assessment Multi-Year Study-Highlights of Findings, Applications to Risk Assessment, and Future Directions. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1671-1682. [PMID: 27091369 PMCID: PMC5089888 DOI: 10.1289/ehp233] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/30/2015] [Accepted: 03/29/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Next Generation (NexGen) of Risk Assessment effort is a multi-year collaboration among several organizations evaluating new, potentially more efficient molecular, computational, and systems biology approaches to risk assessment. This article summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. OBJECTIVE Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures. METHODS New data and methods were applied and evaluated for use in hazard identification and dose-response assessment. Biomarkers of exposure and effect, and risk characterization were also examined. Consideration was given to various decision contexts with increasing regulatory and public health impacts. Data types included transcriptomics, genomics, and proteomics. Methods included molecular epidemiology and clinical studies, bioinformatic knowledge mining, pathway and network analyses, short-duration in vivo and in vitro bioassays, and quantitative structure activity relationship modeling. DISCUSSION NexGen has advanced our ability to apply new science by more rapidly identifying chemicals and exposures of potential concern, helping characterize mechanisms of action that influence conclusions about causality, exposure-response relationships, susceptibility and cumulative risk, and by elucidating new biomarkers of exposure and effects. Additionally, NexGen has fostered extensive discussion among risk scientists and managers and improved confidence in interpreting and applying new data streams. CONCLUSIONS While considerable uncertainties remain, thoughtful application of new knowledge to risk assessment appears reasonable for augmenting major scope assessments, forming the basis for or augmenting limited scope assessments, and for prioritization and screening of very data limited chemicals. Citation: Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. 2016. The Next Generation of Risk Assessment multiyear study-highlights of findings, applications to risk assessment, and future directions. Environ Health Perspect 124:1671-1682; http://dx.doi.org/10.1289/EHP233.
Collapse
Affiliation(s)
- Ila Cote
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
- Address correspondence to I. Cote, U.S. Environmental Protection Agency, Region 8, Room 8152, 1595 Wynkoop St., Denver, CO 80202-1129 USA. Telephone: (202) 288-9539. E-mail:
| | | | - Gerald T. Ankley
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Stanley Barone
- Office of Chemical Safety and Pollution Prevention, U.S. EPA, Washington, District of Columbia, USA
| | - Linda S. Birnbaum
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Frederic Y. Bois
- Unité Modèles pour l’Écotoxicologie et la Toxicologie, Institut National de l’Environnement Industriel et des Risques, Verneuil en Halatte, France
| | - Lyle D. Burgoon
- U.S. Army Engineer Research and Development Center, Research Triangle Park, North Carolina, USA
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | | | | | - Michael DeVito
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Robert B. Devlin
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Stephen W. Edwards
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | | | - Dale Hattis
- George Perkins Marsh Institute, Clark University, Worcester, Massachusetts, USA
| | | | - Derek Knight
- European Chemicals Agency, Annankatu, Helsinki, Finland
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada
| | - Jason Lambert
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Elizabeth Anne Maull
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Donna Mendrick
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Chirag Jagdish Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward J. Perkins
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, USA
| | - Gerald Poje
- Grant Consulting Group, Washington, District of Columbia, USA
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Paul A. Schulte
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Kristina A. Thayer
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
| | - Raymond R. Tice
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - John J. Vandenberg
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
| | - Daniel L. Villeneuve
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Scott Wesselkamper
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Maurice Whelan
- Systems Toxicology Unit, European Commission Joint Research Centre, Ispra, Italy
| | - Christine Whittaker
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Ronald White
- Center for Effective Government, Washington, District of Columbia, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Carole Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Lauren Zeise
- Office of Environmental Health Hazard Assessment, California EPA, Oakland, California, USA
| | - Jay Zhao
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Robert S. DeWoskin
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
| |
Collapse
|
7
|
Bourdon-Lacombe JA, Moffat ID, Deveau M, Husain M, Auerbach S, Krewski D, Thomas RS, Bushel PR, Williams A, Yauk CL. Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals. Regul Toxicol Pharmacol 2015; 72:292-309. [PMID: 25944780 DOI: 10.1016/j.yrtph.2015.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 01/14/2023]
Abstract
Toxicogenomics promises to be an important part of future human health risk assessment of environmental chemicals. The application of gene expression profiles (e.g., for hazard identification, chemical prioritization, chemical grouping, mode of action discovery, and quantitative analysis of response) is growing in the literature, but their use in formal risk assessment by regulatory agencies is relatively infrequent. Although additional validations for specific applications are required, gene expression data can be of immediate use for increasing confidence in chemical evaluations. We believe that a primary reason for the current lack of integration is the limited practical guidance available for risk assessment specialists with limited experience in genomics. The present manuscript provides basic information on gene expression profiling, along with guidance on evaluating the quality of genomic experiments and data, and interpretation of results presented in the form of heat maps, pathway analyses and other common approaches. Moreover, potential ways to integrate information from gene expression experiments into current risk assessment are presented using published studies as examples. The primary objective of this work is to facilitate integration of gene expression data into human health risk assessments of environmental chemicals.
Collapse
Affiliation(s)
| | - Ivy D Moffat
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada.
| | - Michelle Deveau
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada
| | - Mainul Husain
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Scott Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, ON, Canada
| | - Russell S Thomas
- National Centre for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| |
Collapse
|