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Hartwell EE, Jinwala Z, Milone J, Ramirez S, Gelernter J, Kranzler HR, Kember RL. Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits. Neuropsychopharmacology 2024:10.1038/s41386-024-01922-2. [PMID: 39043921 DOI: 10.1038/s41386-024-01922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/07/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and somatic traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and somatic traits were calculated in European-ancestry (EUR; n = 5691) participants and, when discovery datasets were available, for African-ancestry (AFR; n = 4918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGSMDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGSBMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and somatic traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
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Affiliation(s)
- Emily E Hartwell
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Zeal Jinwala
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Joel Gelernter
- West Haven VA Medical Center, West Haven, CT, USA
- Yale University, New Haven, CT, USA
| | - Henry R Kranzler
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel L Kember
- Crescenz VA Medical Center, Philadelphia, PA, USA.
- University of Pennsylvania, Philadelphia, PA, USA.
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2
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Sharma A, Verhaak PF, McCoy TH, Perlis RH, Doshi-Velez F. Identifying data-driven subtypes of major depressive disorder with electronic health records. J Affect Disord 2024; 356:64-70. [PMID: 38565338 DOI: 10.1016/j.jad.2024.03.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Efforts to reduce the heterogeneity of major depressive disorder (MDD) by identifying subtypes have not yet facilitated treatment personalization or investigation of biology, so novel approaches merit consideration. METHODS We utilized electronic health records drawn from 2 academic medical centers and affiliated health systems in Massachusetts to identify data-driven subtypes of MDD, characterizing sociodemographic features, comorbid diagnoses, and treatment patterns. We applied Latent Dirichlet Allocation (LDA) to summarize diagnostic codes followed by agglomerative clustering to define patient subgroups. RESULTS Among 136,371 patients (95,034 women [70 %]; 41,337 men [30 %]; mean [SD] age, 47.0 [14.0] years), the 15 putative MDD subtypes were characterized by comorbidities and distinct patterns in medication use. There was substantial variation in rates of selective serotonin reuptake inhibitor (SSRI) use (from a low of 62 % to a high of 78 %) and selective norepinephrine reuptake inhibitor (SNRI) use (from 4 % to 21 %). LIMITATIONS Electronic health records lack reliable symptom-level data, so we cannot examine the extent to which subtypes might differ in clinical presentation or symptom dimensions. CONCLUSION These data-driven subtypes, drawing on representative clinical cohorts, merit further investigation for their utility in identifying more homogeneous patient populations for basic as well as clinical investigation.
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Affiliation(s)
- Abhishek Sharma
- Harvard John A. Paulson School of Engineering and Applied Sciences, 29 Oxford Street, Cambridge, MA 02138, United States of America
| | - Pilar F Verhaak
- Center for Quantitative Health, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States of America
| | - Thomas H McCoy
- Center for Quantitative Health, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States of America; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States of America
| | - Roy H Perlis
- Center for Quantitative Health, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States of America; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States of America.
| | - Finale Doshi-Velez
- Harvard John A. Paulson School of Engineering and Applied Sciences, 29 Oxford Street, Cambridge, MA 02138, United States of America.
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3
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Fabbri C, Lewis CM, Serretti A. Polygenic risk scores for mood and related disorders and environmental factors: Interaction effects on wellbeing in the UK biobank. Prog Neuropsychopharmacol Biol Psychiatry 2024; 132:110972. [PMID: 38367896 DOI: 10.1016/j.pnpbp.2024.110972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/15/2023] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Mood disorders have a genetic and environmental component and interactions (GxE) on the risk of psychiatric diseases have been investigated. The same GxE interactions may affect wellbeing measures, which go beyond categorical diagnoses and reflect the health-disease continuum. We evaluated GxE effects in the UK Biobank, considering as outcomes subjective wellbeing (feeling good and functioning well) and objective measures (education and income). We estimated the polygenic risk scores (PRSs) of major depressive disorder, bipolar disorder, schizophrenia, and attention deficit hyperactivity disorder. Stressful/traumatic events during adulthood or childhood were considered as E variables, as well as social support. The addition of the PRSxE interaction to PRS and E variables was tested in linear or multinomial regression models, adjusting for confounders. We included 33 k-380 k participants, depending on the variables considered. Most PRSs and E factors showed additive effects on outcomes, with effect sizes generally 3-5 times larger for E variables than PRSs. We found some interaction effects, particularly when considering recent stress, history of a long illness/disability/infirmity, and social support. Higher PRSs increased the negative effects of stress on wellbeing, but they also increased the positive effects of social support, with interaction effects particularly for the outcomes health satisfaction, loneliness, and income (p < Bonferroni corrected threshold of 1.92e-4). PRSxE terms usually added ∼0.01-0.02% variance explained to the corresponding additive model. PRSxE effects on wellbeing involve both positive and negative E factors. Despite small variance explained at the population level, preventive/therapeutic interventions that modify E factors could be beneficial at the individual level.
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Affiliation(s)
- Chiara Fabbri
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy.
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy; Department of Medicine and Surgery, Kore University of Enna, Enna, Italy
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4
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Sanchez-Ruiz JA, Coombes BJ, Pazdernik VM, Melhuish Beaupre LM, Jenkins GD, Pendegraft RS, Batzler A, Ozerdem A, McElroy SL, Gardea-Resendez MA, Cuellar-Barboza AB, Prieto ML, Frye MA, Biernacka JM. Clinical and genetic contributions to medical comorbidity in bipolar disorder: a study using electronic health records-linked biobank data. Mol Psychiatry 2024:10.1038/s41380-024-02530-8. [PMID: 38548982 DOI: 10.1038/s41380-024-02530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 06/14/2024]
Abstract
Bipolar disorder is a chronic and complex polygenic disease with high rates of comorbidity. However, the independent contribution of either diagnosis or genetic risk of bipolar disorder to the medical comorbidity profile of individuals with the disease remains unresolved. Here, we conducted a multi-step phenome-wide association study (PheWAS) of bipolar disorder using phenomes derived from the electronic health records of participants enrolled in the Mayo Clinic Biobank and the Mayo Clinic Bipolar Disorder Biobank. First, we explored the conditions associated with a diagnosis of bipolar disorder by conducting a phenotype-based PheWAS followed by LASSO-penalized regression to account for correlations within the phenome. Then, we explored the conditions associated with bipolar disorder polygenic risk score (BD-PRS) using a PRS-based PheWAS with a sequential exclusion approach to account for the possibility that diagnosis, instead of genetic risk, may drive such associations. 53,386 participants (58.7% women) with a mean age at analysis of 67.8 years (SD = 15.6) were included. A bipolar disorder diagnosis (n = 1479) was associated with higher rates of psychiatric conditions, injuries and poisonings, endocrine/metabolic and neurological conditions, viral hepatitis C, and asthma. BD-PRS was associated with psychiatric comorbidities but, in contrast, had no positive associations with general medical conditions. While our findings warrant confirmation with longitudinal-prospective studies, the limited associations between bipolar disorder genetics and medical conditions suggest that shared environmental effects or environmental consequences of diagnosis may have a greater impact on the general medical comorbidity profile of individuals with bipolar disorder than its genetic risk.
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Affiliation(s)
| | - Brandon J Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Greg D Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Aysegul Ozerdem
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Susan L McElroy
- Lindner Center of HOPE/University of Cincinnati, Cincinnati, OH, USA
| | - Manuel A Gardea-Resendez
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Alfredo B Cuellar-Barboza
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Miguel L Prieto
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry, Faculty of Medicine, Universidad de Los Andes, Santiago, Chile
- Mental Health Service, Clínica Universidad de los Andes, Santiago, Chile
| | - Mark A Frye
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Joanna M Biernacka
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
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5
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Cheng B, Bai Y, Liu L, Meng P, Cheng S, Yang X, Pan C, Wei W, Liu H, Jia Y, Wen Y, Zhang F. Mendelian randomization study of the relationship between blood and urine biomarkers and schizophrenia in the UK Biobank cohort. COMMUNICATIONS MEDICINE 2024; 4:40. [PMID: 38454150 PMCID: PMC10920902 DOI: 10.1038/s43856-024-00467-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The identification of suitable biomarkers is of crucial clinical importance for the early diagnosis of treatment-resistant schizophrenia (TRS). This study aims to comprehensively analyze the association between TRS and blood and urine biomarkers. METHODS Candidate TRS-related single nucleotide polymorphisms (SNPs) were obtained from a recent genome-wide association study. The UK Biobank cohort, comprising 376,807 subjects with blood and urine biomarker testing data, was used to calculate the polygenic risk score (PRS) for TRS. Pearson correlation analyses were performed to evaluate the correlation between TRS PRS and each of the biomarkers, using calculated TRS PRS as the instrumental variables. Bidirectional two-sample Mendelian randomization (MR) was used to assess potential causal associations between candidate biomarkers with TRS. RESULTS Here we identify a significant association between TRS PRS and phosphate (r = 0.007, P = 1.96 × 10-4). Sex subgroup analyses identify seven and three candidate biomarkers associated with TRS PRS in male and female participants, respectively. For example, total protein and phosphate for males, creatinine and phosphate for females. Bidirectional two-sample MR analyses indicate that TRS is negatively associated with cholesterol (estimate = -0.363, P = 0.008). Conversely, TRS is positively associated with total protein (estimate = 0.137, P = 0.027), mean corpuscular volume (estimate = 0.032, P = 2.25 × 10-5), and mean corpuscular hemoglobin (estimate = 0.018, P = 0.007). CONCLUSIONS Our findings provide insights into the roles of blood and urine biomarkers in the early detection and treatment of TRS.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Yunfeng Bai
- School of Public Health, Shaanxi University of Chinese Medicine, 712046, Xianyang, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Wenming Wei
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases (Xi'an Jiaotong University), National Health and Family Planning Commission, 710061, Xi'an, China.
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, 710061, Xi'an, China.
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, Xi'an, China.
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6
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Abondio P, Bruno F, Passarino G, Montesanto A, Luiselli D. Pangenomics: A new era in the field of neurodegenerative diseases. Ageing Res Rev 2024; 94:102180. [PMID: 38163518 DOI: 10.1016/j.arr.2023.102180] [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: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy.
| | - Francesco Bruno
- Academy of Cognitive Behavioral Sciences of Calabria (ASCoC), Lamezia Terme, Italy; Regional Neurogenetic Centre (CRN), Department of Primary Care, Azienda Sanitaria Provinciale Di Catanzaro, Viale A. Perugini, 88046 Lamezia Terme, CZ, Italy; Association for Neurogenetic Research (ARN), Lamezia Terme, CZ, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende 87036, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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7
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Hartwell EE, Jinwala Z, Milone J, Ramirez S, Gelernter J, Kranzler HR, Kember RL. Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and medical traits. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.22.24301615. [PMID: 38343859 PMCID: PMC10854354 DOI: 10.1101/2024.01.22.24301615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and medical traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and medical traits were calculated in European-ancestry (EUR; n=5,691) participants and, when discovery datasets were available, for African-ancestry (AFR; n=4,918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGS MDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGS BMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and medical traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
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8
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Pan C, Cheng B, Qin X, Cheng S, Liu L, Yang X, Meng P, Zhang N, He D, Cai Q, Wei W, Hui J, Wen Y, Jia Y, Liu H, Zhang F. Enhanced polygenic risk score incorporating gene-environment interaction suggests the association of major depressive disorder with cardiac and lung function. Brief Bioinform 2024; 25:bbae070. [PMID: 38436562 DOI: 10.1093/bib/bbae070] [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: 10/19/2023] [Revised: 01/18/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Depression has been linked to an increased risk of cardiovascular and respiratory diseases; however, its impact on cardiac and lung function remains unclear, especially when accounting for potential gene-environment interactions. METHODS We developed a novel polygenic and gene-environment interaction risk score (PGIRS) integrating the major genetic effect and gene-environment interaction effect of depression-associated loci. The single nucleotide polymorphisms (SNPs) demonstrating major genetic effect or environmental interaction effect were obtained from genome-wide SNP association and SNP-environment interaction analyses of depression. We then calculated the depression PGIRS for non-depressed individuals, using smoking and alcohol consumption as environmental factors. Using linear regression analysis, we assessed the associations of PGIRS and conventional polygenic risk score (PRS) with lung function (N = 42 886) and cardiac function (N = 1791) in the subjects with or without exposing to smoking and alcohol drinking. RESULTS We detected significant associations of depression PGIRS with cardiac and lung function, contrary to conventional depression PRS. Among smokers, forced vital capacity exhibited a negative association with PGIRS (β = -0.037, FDR = 1.00 × 10-8), contrasting with no significant association with PRS (β = -0.002, FDR = 0.943). In drinkers, we observed a positive association between cardiac index with PGIRS (β = 0.088, FDR = 0.010), whereas no such association was found with PRS (β = 0.040, FDR = 0.265). Notably, in individuals who both smoked and drank, forced expiratory volume in 1-second demonstrated a negative association with PGIRS (β = -0.042, FDR = 6.30 × 10-9), but not with PRS (β = -0.003, FDR = 0.857). CONCLUSIONS Our findings underscore the profound impact of depression on cardiac and lung function, highlighting the enhanced efficacy of considering gene-environment interactions in PRS-based studies.
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Affiliation(s)
- Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xiaoyue Qin
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Na Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Dan He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Qingqing Cai
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Wenming Wei
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jingni Hui
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
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9
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Choi KW. Depression Genetics as a Window Into Physical and Mental Health. Biol Psychiatry 2022; 92:918-919. [PMID: 36396244 DOI: 10.1016/j.biopsych.2022.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Karmel W Choi
- Center for Precision Psychiatry, Department of Psychiatry, and the Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, and the Department of Psychiatry, Harvard Medical School, Boston, Massachusetts.
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