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Rancelis T, Domarkiene I, Ambrozaityte L, Utkus A. Implementing Core Genes and an Omnigenic Model for Behaviour Traits Prediction in Genomics. Genes (Basel) 2023; 14:1630. [PMID: 37628681 PMCID: PMC10454355 DOI: 10.3390/genes14081630] [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: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
A high number of genome variants are associated with complex traits, mainly due to genome-wide association studies (GWAS). Using polygenic risk scores (PRSs) is a widely accepted method for calculating an individual's complex trait prognosis using such data. Unlike monogenic traits, the practical implementation of complex traits by applying this method still falls behind. Calculating PRSs from all GWAS data has limited practical usability in behaviour traits due to statistical noise and the small effect size from a high number of genome variants involved. From a behaviour traits perspective, complex traits are explored using the concept of core genes from an omnigenic model, aiming to employ a simplified calculation version. Simplification may reduce the accuracy compared to a complete PRS encompassing all trait-associated variants. Integrating genome data with datasets from various disciplines, such as IT and psychology, could lead to better complex trait prediction. This review elucidates the significance of clear biological pathways in understanding behaviour traits. Specifically, it highlights the essential role of genes related to hormones, enzymes, and neurotransmitters as robust core genes in shaping these traits. Significant variations in core genes are prominently observed in behaviour traits such as stress response, impulsivity, and substance use.
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Affiliation(s)
- Tautvydas Rancelis
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu Str. 2, LT-08661 Vilnius, Lithuania; (I.D.); (L.A.); (A.U.)
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [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: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Characterizing the polygenic overlaps of bipolar disorder subtypes with schizophrenia and major depressive disorder. J Affect Disord 2022; 309:242-251. [PMID: 35487438 DOI: 10.1016/j.jad.2022.04.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Large-scale studies have shown that bipolar I disorder (BD-I) and bipolar II disorder (BD-II) have differences in genetic association with schizophrenia (SCZ) and major depressive disorder (MDD). However, the underlying shared genetic architectures between BD subtypes and both SCZ and MDD remain largely unknown. METHODS We applied univariate and bivariate causal mixture models (MiXeR) to estimate the polygenicity and polygenic overlaps on large GWASs summary statistics of BD-I (n = 25,060), BD-II (n = 6781), SCZ (n = 69,369) and MDD (n = 170,756). Then, conjunctional false discovery rate approach was used to identify specific shared genetic loci between BD subtypes and both SCZ and MDD. RESULTS Univariate MiXeR revealed that BD-II was substantially more polygenic (22.37 K causal variants) as compared to BD-I, SCZ and MDD (7.87-12.43 K causal variants). Bivariate MiXeR revealed substantial polygenic overlaps between BD-I and SCZ (Dice-coefficient = 0.83) and between BD-I and MDD (Dice-coefficient = 0.76), which are beyond the genetic correlation (rg = 0.71 and 0.36). Conjunctional FDR analysis identified 236 distinct shared loci between BD-I and BD-II (2 loci), BD-I and SCZ (227 loci), BD-I and MDD (19 loci), BD-II and SCZ (1 locus), and BD-II and MDD (3 loci). Most of these shared loci have concordant effect directions among BD subtypes, SCZ and MDD. LIMITATIONS The bivariate MiXeR model was not applied for the BD-II because of insufficient power and inadequate model fit. CONCLUSIONS These findings provide evidence for extensive polygenic effects across BD subtypes, SCZ and MDD, which further our understanding of the potential genetic basis for the comorbid symptoms across these disorders.
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Kanarik M, Grimm O, Mota NR, Reif A, Harro J. ADHD co-morbidities: A review of implication of gene × environment effects with dopamine-related genes. Neurosci Biobehav Rev 2022; 139:104757. [PMID: 35777579 DOI: 10.1016/j.neubiorev.2022.104757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/07/2023]
Abstract
ADHD is a major burden in adulthood, where co-morbid conditions such as depression, substance use disorder and obesity often dominate the clinical picture. ADHD has substantial shared heritability with other mental disorders, contributing to comorbidity. However, environmental risk factors exist but their interaction with genetic makeup, especially in relation to comorbid disorders, remains elusive. This review for the first time summarizes present knowledge on gene x environment (GxE) interactions regarding the dopamine system. Hitherto, mainly candidate (GxE) studies were performed, focusing on the genes DRD4, DAT1 and MAOA. Some evidence suggest that the variable number tandem repeats in DRD4 and MAOA may mediate GxE interactions in ADHD generally, and comorbid conditions specifically. Nevertheless, even for these genes, common variants are bound to suggest risk only in the context of gender and specific environments. For other polymorphisms, evidence is contradictory and less convincing. Particularly lacking are longitudinal studies testing the interaction of well-defined environmental with polygenic risk scores reflecting the dopamine system in its entirety.
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Affiliation(s)
- Margus Kanarik
- Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Ravila 14A Chemicum, 50411 Tartu, Estonia
| | - Oliver Grimm
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Nina Roth Mota
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Jaanus Harro
- Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Ravila 14A Chemicum, 50411 Tartu, Estonia; Psychiatry Clinic, North Estonia Medical Centre, Paldiski Road 52, 10614 Tallinn, Estonia.
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Serretti A. Precision medicine in mood disorders. PCN REPORTS : PSYCHIATRY AND CLINICAL NEUROSCIENCES 2022; 1:e1. [PMID: 38868801 PMCID: PMC11114272 DOI: 10.1002/pcn5.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/09/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2024]
Abstract
The choice of the most appropriate psychoactive medication for each of our patients is always a challenge. We can use more than 100 psychoactive drugs in the treatment of mood disorders, which can be prescribed either alone or in combination. Response and tolerability problems are common, and much trial and error is often needed before achieving a satisfactory outcome. Precision medicine is therefore needed for tailoring treatment to optimize outcome. Pharmacological, clinical, and demographic factors are important and informative, but biological factors may further inform and refine prediction. Twenty years after the first reports of gene variants modulating antidepressant response, we are now confronted with the prospect of routine clinical pharmacogenetic applications in the treatment of depression. The scientific community is divided into two camps: those who are enthusiastic and those who are skeptical. Although it appears clear that the benefit of existing tools is still not completely defined, at least in the case of central nervous system gene variants, this is not the case for metabolic gene variants, which is generally accepted. Cumulative scores encompassing many variants across the entire genome will soon predict psychiatric disorder liability and outcome. At present, precision medicine in mood disorders may be implemented using clinical and pharmacokinetic factors. In the near future, a genome-wide composite genetic score in conjunction with clinical factors within each patient is the most promising approach for developing a more effective way to target treatment for patients suffering from mood disorders.
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Affiliation(s)
- Alessandro Serretti
- Department of Biomedical and NeuroMotor SciencesUniversity of BolognaBolognaItaly
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Mills MC, Tropf FC, Brazel DM, van Zuydam N, Vaez A, Pers TH, Snieder H, Perry JRB, Ong KK, den Hoed M, Barban N, Day FR. Identification of 371 genetic variants for age at first sex and birth linked to externalising behaviour. Nat Hum Behav 2021; 5:1717-1730. [PMID: 34211149 PMCID: PMC7612120 DOI: 10.1038/s41562-021-01135-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
Age at first sexual intercourse and age at first birth have implications for health and evolutionary fitness. In this genome-wide association study (age at first sexual intercourse, N = 387,338; age at first birth, N = 542,901), we identify 371 single-nucleotide polymorphisms, 11 sex-specific, with a 5-6% polygenic score prediction. Heritability of age at first birth shifted from 9% [CI = 4-14%] for women born in 1940 to 22% [CI = 19-25%] for those born in 1965. Signals are driven by the genetics of reproductive biology and externalising behaviour, with key genes related to follicle stimulating hormone (FSHB), implantation (ESR1), infertility and spermatid differentiation. Our findings suggest that polycystic ovarian syndrome may lead to later age at first birth, linking with infertility. Late age at first birth is associated with parental longevity and reduced incidence of type 2 diabetes and cardiovascular disease. Higher childhood socioeconomic circumstances and those in the highest polygenic score decile (90%+) experience markedly later reproductive onset. Results are relevant for improving teenage and late-life health, understanding longevity and guiding experimentation into mechanisms of infertility.
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Affiliation(s)
- Melinda C Mills
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom.
- Nuffield College, University of Oxford, Oxford, United Kingdom.
| | - Felix C Tropf
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom
- Nuffield College, University of Oxford, Oxford, United Kingdom
- École Nationale de la Statistique et de L'administration Économique (ENSAE), Paris, France
- Center for Research in Economics and Statistics (CREST), Paris, France
| | - David M Brazel
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom
- Nuffield College, University of Oxford, Oxford, United Kingdom
| | - Natalie van Zuydam
- The Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tune H Pers
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Marcel den Hoed
- The Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Nicola Barban
- Department of Statistical Sciences, University of Bologna, Bologna, Italy
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom.
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Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses. Genome Med 2021; 13:94. [PMID: 34034819 PMCID: PMC8145796 DOI: 10.1186/s13073-021-00907-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/11/2021] [Indexed: 01/26/2023] Open
Abstract
Background The interleukin (IL)-1 pathway is primarily associated with innate immunological defense and plays a major role in the induction and regulation of inflammation. Both common and rare genetic variation in this pathway underlies various inflammation-mediated diseases, but the role of rare variants relative to common variants in immune response variability in healthy individuals remains unclear. Methods We performed molecular inversion probe sequencing on 48 IL-1 pathway-related genes in 463 healthy individuals from the Human Functional Genomics Project. We functionally grouped common and rare variants, over gene, subpathway, and inflammatory levels and performed the Sequence Kernel Association Test to test for association with in vitro stimulation-induced cytokine responses; specifically, IL-1β and IL-6 cytokine measurements upon stimulations that represent an array of microbial infections: lipopolysaccharide (LPS), phytohaemagglutinin (PHA), Candida albicans (C. albicans), and Staphylococcus aureus (S. aureus). Results We identified a burden of NCF4 rare variants with PHA-induced IL-6 cytokine and showed that the respective carriers are in the 1% lowest IL-6 producers. Collapsing rare variants in IL-1 subpathway genes produces a bidirectional association with LPS-induced IL-1β cytokine levels, which is reflected by a significant Spearman correlation. On the inflammatory level, we identified a burden of rare variants in genes encoding for proteins with an anti-inflammatory function with S. aureus-induced IL-6 cytokine. In contrast to these rare variant findings which were based on different types of stimuli, common variant associations were exclusively identified with C. albicans-induced cytokine over various levels of grouping, from the gene, to subpathway, to inflammatory level. Conclusions In conclusion, this study shows that functionally grouping common and rare genetic variants enables the elucidation IL-1-mediated biological mechanisms, specifically, for IL-1β and IL-6 cytokine responses induced by various stimuli. The framework used in this study may allow for the analysis of rare and common genetic variants in a wider variety of (non-immune) complex phenotypes and therefore has the potential to contribute to better understanding of unresolved, complex traits and diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00907-w.
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Nawar N, Paul A, Mahmood HN, Faisal MI, Hosen MI, Shekhar HU. Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference. Bioinformation 2021; 17:424-438. [PMID: 34092963 PMCID: PMC8131579 DOI: 10.6026/97320630017424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Partner and Localizer of BRCA2 or PALB2 is a typical tumor suppressor protein, that responds to DNA double stranded breaks through homologous recombination repair. Heterozygous mutations in PALB2 are known to contribute to the susceptibility of breast and ovarian cancer. However, there is no comprehensive study characterizing the structural and functional impacts of SNPs located in the PALB2 gene. Therefore, it is of interest to document a comprehensive analysis of coding and non-coding SNPs located at the PALB2 loci using in silico tools. The data for 1455 non-synonymous SNPs (nsSNPs) located in the PALB2 loci were retrieved from the dbSNP database. Comprehensive characterization of the SNPs using a combination of in silico tools such as SIFT, PROVEAN, PolyPhen, PANTHER, PhD-SNP, Pmut, MutPred 2.0 and SNAP-2, identified 28 functionally important SNPs. Among these, 16 nsSNPs were further selected for structural analysis using conservation profile and protein stability. The most deleterious nsSNPs were documented within the WD40 domain of PALB2. A general outline of the structural consequences of each variant was developed using the HOPE project data. These 16 mutant structures were further modelled using SWISS Model and three most damaging mutant models (rs78179744, rs180177123 and rs45525135) were identified. The non-coding SNPs in the 3' UTR region of the PALB2 gene were analyzed for altered miRNA target sites. The comprehensive characterization of the coding and non-coding SNPs in the PALB2 locus has provided a list of damaging SNPs with potential disease association. Further validation through genetic association study will reveal their clinical significance.
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Affiliation(s)
- Noshin Nawar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Anik Paul
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Hamida Nooreen Mahmood
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Ismail Faisal
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
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Picard M, Sandi C. The social nature of mitochondria: Implications for human health. Neurosci Biobehav Rev 2020; 120:595-610. [PMID: 32651001 DOI: 10.1016/j.neubiorev.2020.04.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 12/15/2022]
Abstract
Sociality has profound evolutionary roots and is observed from unicellular organisms to multicellular animals. In line with the view that social principles apply across levels of biological complexity, a growing body of data highlights the remarkable social nature of mitochondria - life-sustaining endosymbiotic organelles with their own genome that populate the cell cytoplasm. Here, we draw from organizing principles of behavior in social organisms to reveal that similar to individuals among social networks, mitochondria communicate with each other and with the cell nucleus, exhibit group formation and interdependence, synchronize their behaviors, and functionally specialize to accomplish specific functions within the organism. Mitochondria are social organelles. The extension of social principles across levels of biological complexity is a theoretical shift that emphasizes the role of communication and interdependence in cell biology, physiology, and neuroscience. With the help of emerging computational methods capable of capturing complex dynamic behavioral patterns, the implementation of social concepts in mitochondrial biology may facilitate cross-talk across disciplines towards increasingly holistic and accurate models of human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA.
| | - Carmen Sandi
- Laboratory of Behavioral Genetics, Brain Mind Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland
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Giurgescu C, Nowak AL, Gillespie S, Nolan TS, Anderson CM, Ford JL, Hood DB, Williams KP. Neighborhood Environment and DNA Methylation: Implications for Cardiovascular Disease Risk. J Urban Health 2019; 96:23-34. [PMID: 30635842 PMCID: PMC6430282 DOI: 10.1007/s11524-018-00341-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Exposure to chronic stress such as living in disadvantaged neighborhoods has been related to cardiovascular disease (CVD). Chronic stress may increase the risk for CVD by increasing levels of systemic inflammation (e.g., higher levels of pro-inflammatory cytokines). Differential DNA methylation of inflammation-related candidate genes is also related to higher risk for CVD. Thus, the purpose of this review was to examine the association of neighborhood disadvantage with DNA methylation. A search of literature was conducted using Scopus, CINAHL, PubMed, Medline, and Embase databases. The keywords neighborhood, neighborhood disorder, neighborhood crime, neighborhood violence, neighborhood safety, built environment, and housing vacancy were combined with the keywords DNA methylation and epigenetics. Five studies were included in this review (n = 3 adult blood samples and n = 2 fetal blood samples). Four of the five studies reported an association of neighborhood socioeconomic status, social environment, and crime with either global or gene-specific DNA methylation. Only two studies examined the association of neighborhood disadvantage with inflammation-related candidate genes. One of these studies found a significant association of neighborhood socioeconomic disadvantage and social environment with DNA methylation in inflammation-related candidate genes. Thus, data are limited on the association between neighborhood disadvantage and DNA methylation of inflammation-related candidate genes, as well as genes in other potential mechanistic pathways including psychosocial stress, toxin response, and adiposity. Future studies should examine these associations and the potential epigenetic mechanisms by which neighborhood disadvantage increases the risk for CVD.
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Affiliation(s)
- Carmen Giurgescu
- College of Nursing, The Ohio State University, Columbus, OH, USA.
| | | | | | - Timiya S Nolan
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Cindy M Anderson
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Jodi L Ford
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Daryl B Hood
- College of Public Health, The Ohio State University, Columbus, OH, USA
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Gianfrancesco O, Bubb VJ, Quinn JP. Treating the "E" in "G × E": Trauma-Informed Approaches and Psychological Therapy Interventions in Psychosis. Front Psychiatry 2019; 10:9. [PMID: 30761022 PMCID: PMC6363686 DOI: 10.3389/fpsyt.2019.00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Despite advances in genetic research, causal variants affecting risk for schizophrenia remain poorly characterized, and the top 108 loci identified through genome-wide association studies (GWAS) explain only 3.4% of variance in risk profiles. Such work is defining the highly complex nature of this condition, with omnigenic models of schizophrenia suggesting that gene regulatory networks are sufficiently interconnected such that altered expression of any "peripheral" gene in a relevant cell type has the capacity to indirectly modulate the expression of "core" schizophrenia-associated genes. This wealth of associated genes with small effect sizes makes identifying new druggable targets difficult, and current pharmacological treatments for schizophrenia can involve serious side effects. However, the fact that the majority of schizophrenia genome-wide associated variants fall within non-coding DNA is suggestive of their potential to modulate gene regulation. This would be consistent with risks that can be mediated in a "gene × environment" (G × E) manner. Stress and trauma can alter the regulation of key brain-related pathways over the lifetime of an individual, including modulation of brain development, and neurochemistry in the adult. Recent studies demonstrate a significant overlap between psychotic symptoms and trauma, ranging from prior trauma contributing to psychosis, as well as trauma in response to the experience of psychosis itself or in response to treatment. Given the known effects of trauma on both CNS gene expression and severity of psychosis symptoms, it may be that pharmacological treatment alone risks leaving individuals with a highly stressful and unresolved environmental component that continues to act in a "G × E" manner, with the likelihood that this would negatively impact recovery and relapse risk. This review aims to cover the recent advances elucidating the complex genetic architecture of schizophrenia, as well as the long-term effects of early life trauma on brain function and future mental health risk. Further, the evidence demonstrating the role of ongoing responses to trauma or heightened stress sensitivity, and their impact on the course of illness and recovery, is presented. Finally, the need for trauma-informed approaches and psychological therapy-based interventions is discussed, and a brief overview of the evidence to determine their utility is presented.
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Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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