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Benjamin-Zukerman T, Shimon G, Gaine ME, Dakwar A, Peled N, Aboraya M, Masri-Ismail A, Safadi-Safa R, Solomon M, Lev-Ram V, Rissman RA, Mayrhofer JE, Raffeiner A, Mol MO, Argue BMR, McCool S, Doan B, van Swieten J, Stefan E, Abel T, Ilouz R. A mutation in the PRKAR1B gene drives pathological mechanisms of neurodegeneration across species. Brain 2024:awae154. [PMID: 38743596 DOI: 10.1093/brain/awae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Protein Kinase A (PKA) neuronal function is controlled by the interaction of a regulatory (R) subunit dimer to two catalytic (C) subunits. Recently, the L50R variant in the gene encoding the RIβ subunit was identified in individuals with a novel neurodegenerative disease. However, the mechanisms driving the disease phenotype remained unknown. In this study, we generated a mouse model carrying the RIβ-L50R mutation to replicate the human disease phenotype and study its progression with age. We examined postmortem brains of affected individuals as well as live cell cultures. Employing biochemical assays, immunohistochemistry, and behavioral assessments, we investigated the impact of the mutation on PKA complex assembly, protein aggregation and neuronal degeneration. We reveal that RIβ is an aggregation-prone protein that progressively accumulates in wildtype and Alzheimer's mouse models with age, while aggregation is accelerated in the RIβ-L50R mouse model. We define RIβ-L50R as a causal mutation driving an age-dependent behavioral and disease phenotype in human and mouse models. Mechanistically, this mutation disrupts RIβ dimerization, leading to aggregation of its monomers. Intriguingly, interaction with the C-subunit protects the RIβ-L50R from self-aggregating, in a dose-dependent manner. Furthermore, cAMP signaling induces RIβ-L50R aggregation. The pathophysiological mechanism elucidated here for a newly recognized neurodegenerative disease, in which protein aggregation is the result of disrupted homodimerization, sheds light on a remarkably under-appreciated but potentially common mechanism across several neurodegenerative diseases.
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Affiliation(s)
| | - Gilat Shimon
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Marie E Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Anwar Dakwar
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Netta Peled
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Mohammad Aboraya
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Ashar Masri-Ismail
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Rania Safadi-Safa
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Meir Solomon
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Varda Lev-Ram
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert A Rissman
- Department of Physiology and Neurosciences, Alzheimer's Therapeutic Research Institute, Keck School of Medicine of University of Southern California, San Diego CA 92121, USA
| | - Johanna E Mayrhofer
- Institute of Molecular Biology, Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, 6020 Tyrol, Austria
| | - Andrea Raffeiner
- Institute of Molecular Biology, Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, 6020 Tyrol, Austria
| | - Merel O Mol
- Department of Neurology and Alzheimer Center Erasmus MC, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands
| | - Benney M R Argue
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Shaylah McCool
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - Binh Doan
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 52242, USA
| | - John van Swieten
- Department of Neurology and Alzheimer Center Erasmus MC, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands
| | - Eduard Stefan
- Institute of Molecular Biology, Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, 6020 Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, 6020 Tyrol, Austria
| | - Ted Abel
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ronit Ilouz
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
- The Leslie & Susan Goldschmied (Gonda) Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
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Alrfooh A, Casten LG, Richards JG, Wemmie JA, Magnotta VA, Fiedorowicz JG, Michaelson J, Williams AJ, Gaine ME. Investigating the relationship between DNA methylation, genetic variation, and suicide attempt in bipolar disorder. medRxiv 2024:2024.04.03.24305263. [PMID: 38633806 PMCID: PMC11023653 DOI: 10.1101/2024.04.03.24305263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Individuals with bipolar disorder are at increased risk for suicide, and this can be influenced by a range of biological, clinical, and environmental risk factors. Biological components associated with suicide include DNA modifications that lead to changes in gene expression. Common genetic variation and DNA methylation changes are some of the most frequent types of DNA findings associated with an increased risk for suicidal behavior. Importantly, the interplay between genetic predisposition and DNA methylation patterns is becoming more prevalent in genetic studies. We hypothesized that DNA methylation patterns in specific loci already genetically associated with suicide would be altered in individuals with bipolar disorder and a history of suicide attempt. To test this hypothesis, we searched the literature to identify common genetic variants (N=34) previously associated with suicidal thoughts and behaviors in individuals with bipolar disorder. We then created a customized sequencing panel that covered our chosen genomic loci. We profiled DNA methylation patterns from blood samples collected from bipolar disorder participants with suicidal behavior (N=55) and without suicidal behavior (N=51). We identified seven differentially methylated CpG sites and five differentially methylated regions between the two groups. Additionally, we found that DNA methylation changes in MIF and CACNA1C were associated with lethality or number of suicide attempts. Finally, we identified three meQTLs in SIRT1 , IMPA2 , and INPP1 . This study illustrates that DNA methylation is altered in individuals with bipolar disorder and a history of suicide attempts in regions known to harbor suicide-related variants.
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Glebov-McCloud AGP, Saide WS, Gaine ME, Strack S. Protein Kinase A in neurological disorders. J Neurodev Disord 2024; 16:9. [PMID: 38481146 PMCID: PMC10936040 DOI: 10.1186/s11689-024-09525-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Cyclic adenosine 3', 5' monophosphate (cAMP)-dependent Protein Kinase A (PKA) is a multi-functional serine/threonine kinase that regulates a wide variety of physiological processes including gene transcription, metabolism, and synaptic plasticity. Genomic sequencing studies have identified both germline and somatic variants of the catalytic and regulatory subunits of PKA in patients with metabolic and neurodevelopmental disorders. In this review we discuss the classical cAMP/PKA signaling pathway and the disease phenotypes that result from PKA variants. This review highlights distinct isoform-specific cognitive deficits that occur in both PKA catalytic and regulatory subunits, and how tissue-specific distribution of these isoforms may contribute to neurodevelopmental disorders in comparison to more generalized endocrine dysfunction.
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Affiliation(s)
- Alexander G P Glebov-McCloud
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Walter S Saide
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Marie E Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy Building, College of Pharmacy, University of Iowa, 180 S. Grand Ave, Iowa City, IA, 52242, USA
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA.
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA.
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Khan KM, Gaine ME, Daniel AR, Chilamkuri P, Rohlman DS. Organophosphorus pesticide exposure from house dust and parent-reported child behavior in Latino children from an orchard community. Neurotoxicology 2024; 102:29-36. [PMID: 38453034 DOI: 10.1016/j.neuro.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Organophosphorus pesticide (OP) exposure is known to have adverse effects on the nervous system. Children from agricultural communities are at risk of exposure to these chemicals from their indoor environments that can lead to neurological and developmental problems, including changes in behavior. OBJECTIVE The aim of this study is to evaluate whether the take-home pathway exposure is associated with behavioral and emotional problems in Latino Orchid Community children. METHOD The study was implemented over a period of two years (2008-2010) in an orchard farming community with a total of 324 parents who had children between the ages of 5-12 years old. Mothers of the children were asked to complete the Child Behavior Checklist (CBCL) and dust from their carpets was collected. Emotional and behavioral deficits were assessed based on the CBCL and house dust was assessed for OP concentrations. In this study, correlations between OPs in house dust and CBCL subscales were estimated using linear regression models with total OP concentrations classified by tertiles. This study also facilitated the comparison between the agricultural and non-agricultural families in terms of behavioral deficits and house dust concentrations of pesticides. RESULTS The data from the study shows that there was a positive association between the concentration of OP residues in house dust and internalizing behavior (β=2.06, p=0.05) whereas the association with externalizing behavior was not significant after accounting for sociocultural covariates. Significant positive associations of OP residues with somatic problems (p=0.02) and thought problems (p=0.05) were also found. CONCLUSION The data support a potential role of OP exposure in childhood development, with a specific focus on internalizing behavior. Future work focused on longitudinal studies may uncover the long-term consequences of OP exposure and behavior.
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Affiliation(s)
- Khalid M Khan
- Department of Public Health, College of Health Science, Sam Houston State University, 1901 Ave I, Huntsville, TX 77340, USA.
| | - Marie E Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, 546 CPB, 180 S Grand Ave, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa R Daniel
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, 546 CPB, 180 S Grand Ave, Iowa City, IA 52242, USA; Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA 52242, USA
| | - Pavani Chilamkuri
- Department of Public Health, College of Health Science, Sam Houston State University, 1901 Ave I, Huntsville, TX 77340, USA
| | - Diane S Rohlman
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, S143 CPHB 145 N. Riverside Drive, Iowa City, IA 52242, USA
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Mirza S, Lima CNC, Del Favero-Campbell A, Rubinstein A, Topolski N, Cabrera-Mendoza B, Kovács EHC, Blumberg HP, Richards JG, Williams AJ, Wemmie JA, Magnotta VA, Fiedorowicz JG, Gaine ME, Walss-Bass C, Quevedo J, Soares JC, Fries GR. Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder. Transl Psychiatry 2024; 14:70. [PMID: 38296944 PMCID: PMC10831084 DOI: 10.1038/s41398-024-02760-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at >700,000 positions in a discovery cohort of n = 84 adults with BD with a history of SA (BD/SA), n = 79 adults with BD without history of SA (BD/non-SA), and n = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort of n = 48 BD/SA and n = 47 BD/non-SA, fold changes at the discovery cohort's significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8-93.8%) and 82.1% (CI = 73.6-90.5%) for the combined epigenetic-clinical classifier in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.
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Affiliation(s)
- Salahudeen Mirza
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Institute of Child Development, University of Minnesota, 55455, Minneapolis, MN, USA
- Department of Psychiatry, Yale School of Medicine, 06510, New Haven, CT, USA
| | - Camila N C Lima
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Alexandra Del Favero-Campbell
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Alexandre Rubinstein
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Natasha Topolski
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | | | - Emese H C Kovács
- Department of Neuroscience and Pharmacology, The University of Iowa, 51 Newton Rd, 52242, Iowa City, IA, USA
| | - Hilary P Blumberg
- Department of Psychiatry, Yale School of Medicine, 06510, New Haven, CT, USA
| | - Jenny Gringer Richards
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Aislinn J Williams
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
| | - John A Wemmie
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
- Department of Veterans Affairs Medical Center, Iowa City, IA, USA
| | - Vincent A Magnotta
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Jess G Fiedorowicz
- University of Ottawa Brain and Mind Research Institute, Ottawa Hospital Research Institute, 501 Smyth, K1H 8L6, Ottawa, ON, Canada
| | - Marie E Gaine
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, IA, USA
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Center for Interventional Psychiatry, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Jair C Soares
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Gabriel R Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA.
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA.
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA.
- Center for Interventional Psychiatry, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, 1941 East Rd, 77054, Houston, TX, USA.
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Kim J, Vanrobaeys Y, Kelvington B, Peterson Z, Baldwin E, Gaine ME, Nickl-Jockschat T, Abel T. Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders. Mol Psychiatry 2024:10.1038/s41380-024-02411-0. [PMID: 38278994 DOI: 10.1038/s41380-024-02411-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Neurodevelopmental disorders (NDDs) are polygenic in nature and copy number variants (CNVs) are ideal candidates to study the nature of this polygenic risk. The disruption of striatal circuits is considered a central mechanism in NDDs. The 16p11.2 hemi-deletion (16p11.2 del/+) is one of the most common CNVs associated with NDD, and 16p11.2 del/+ mice show sex-specific striatum-related behavioral phenotypes. However, the critical genes among the 27 genes in the 16p11.2 region that underlie these phenotypes remain unknown. Previously, we applied a novel strategy to identify candidate genes associated with the sex-specific phenotypes of 16p11.2 del/+ mice and highlighted three genes within the deleted region: thousand and one amino acid protein kinase 2 (Taok2), seizure-related 6 homolog-like 2 (Sez6l2), and major vault protein (Mvp). Using CRISPR/Cas9, we generated mice carrying null mutations in Taok2, Sez6l2, and Mvp (3 gene hemi-deletion (3g del/+)). Hemi-deletion of these 3 genes recapitulates sex-specific behavioral alterations in striatum-dependent behavioral tasks observed in 16p11.2 del/+ mice, specifically male-specific hyperactivity and impaired motivation for reward seeking. Moreover, RNAseq analysis revealed that 3g del/+ mice exhibit gene expression changes in the striatum similar to 16p11.2 del/+ mice exclusively in males. Subsequent analysis identified translation dysregulation and/or extracellular signal-regulated kinase signaling as plausible molecular mechanisms underlying male-specific, striatum-dependent behavioral alterations. Interestingly, ribosomal profiling supported the notion of translation dysregulation in both 3g del/+ and 16p11.2 del/+ male mice. However, mice carrying a 4-gene deletion (with an additional deletion of Mapk3) exhibited fewer phenotypic similarities with 16p11.2 del/+ mice. Together, the mutation of 3 genes within the 16p11.2 region phenocopies striatal sex-specific phenotypes of 16p11.2 del/+ mice. These results support the importance of a polygenic approach to study NDDs and underscore that the effects of the large genetic deletions result from complex interactions between multiple candidate genes.
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Affiliation(s)
- Jaekyoon Kim
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa, IA, USA
| | - Benjamin Kelvington
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA
| | - Zeru Peterson
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA, USA
| | - Emily Baldwin
- The Iowa Medical Scientist Training Program, University of Iowa, Iowa, IA, USA
| | - Marie E Gaine
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa, IA, USA
| | - Thomas Nickl-Jockschat
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA.
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA, USA.
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa, IA, USA.
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA, USA.
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7
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Harmata GIS, Barsotti EJ, Casten LG, Fiedorowicz JG, Williams A, Shaffer JJ, Richards JG, Sathyaputri L, Schmitz SL, Christensen GE, Long JD, Gaine ME, Xu J, Michaelson JJ, Wemmie JA, Magnotta VA. Cerebellar morphological differences and associations with extrinsic factors in bipolar disorder type I. J Affect Disord 2023; 340:269-279. [PMID: 37562560 PMCID: PMC10529949 DOI: 10.1016/j.jad.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/18/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The neural underpinnings of bipolar disorder (BD) remain poorly understood. The cerebellum is ideally positioned to modulate emotional regulation circuitry yet has been understudied in BD. Literature suggests differences in cerebellar activity and metabolism in BD, however findings on structural differences remain contradictory. Potential reasons include combining BD subtypes, small sample sizes, and potential moderators such as genetics, adverse childhood experiences (ACEs), and pharmacotherapy. METHODS We collected 3 T MRI scans from participants with (N = 131) and without (N = 81) BD type I, as well as blood and questionnaires. We assessed differences in cerebellar volumes and explored potentially influential factors. RESULTS The cerebellar cortex was smaller bilaterally in participants with BD. Polygenic propensity score did not predict any cerebellar volumes, suggesting that non-genetic factors may have greater influence on the cerebellar volume difference we observed in BD. Proportionate cerebellar white matter volumes appeared larger with more ACEs, but this may result from reduced ICV. Time from onset and symptom burden were not associated with cerebellar volumes. Finally, taking sedatives was associated with larger cerebellar white matter and non-significantly larger cortical volume. LIMITATIONS This study was cross-sectional, limiting interpretation of possible mechanisms. Most of our participants were White, which could limit the generalizability. Additionally, we did not account for potential polypharmacy interactions. CONCLUSIONS These findings suggest that external factors, such as sedatives and childhood experiences, may influence cerebellum structure in BD and may mask underlying differences. Accounting for such variables may be critical for consistent findings in future studies.
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Affiliation(s)
- Gail I S Harmata
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Radiology, The University of Iowa, United States
| | - Ercole John Barsotti
- Department of Psychiatry, The University of Iowa, United States; Department of Epidemiology, The University of Iowa, United States
| | - Lucas G Casten
- Department of Psychiatry, The University of Iowa, United States; Interdisciplinary Graduate Program in Genetics, The University of Iowa, United States
| | - Jess G Fiedorowicz
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Psychiatry, University of Ottawa, Canada
| | - Aislinn Williams
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States
| | - Joseph J Shaffer
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Radiology, The University of Iowa, United States; Department of Biosciences, Kansas City University, United States
| | | | | | | | - Gary E Christensen
- Department of Electrical and Computer Engineering, The University of Iowa, United States; Department of Radiation Oncology, The University of Iowa, United States
| | - Jeffrey D Long
- Department of Psychiatry, The University of Iowa, United States; Department of Biostatistics, The University of Iowa, United States
| | - Marie E Gaine
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, The University of Iowa, United States
| | - Jia Xu
- Department of Radiology, The University of Iowa, United States
| | - Jake J Michaelson
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Interdisciplinary Graduate Program in Genetics, The University of Iowa, United States
| | - John A Wemmie
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Molecular Physiology and Biophysics, The University of Iowa, United States; Department of Neurosurgery, The University of Iowa, United States; Veterans Affairs Medical Center, Iowa City, United States
| | - Vincent A Magnotta
- Department of Psychiatry, The University of Iowa, United States; Iowa Neuroscience Institute, The University of Iowa, United States; Department of Radiology, The University of Iowa, United States; Department of Biomedical Engineering, The University of Iowa, United States.
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Mirza S, de Carvalho Lima CN, Del Favero-Campbell A, Rubinstein A, Topolski N, Cabrera-Mendoza B, Kovács EH, Blumberg HP, Richards JG, Williams AJ, Wemmie JA, Magnotta VA, Fiedorowicz JG, Gaine ME, Walss-Bass C, Quevedo J, Soares JC, Fries GR. Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder. medRxiv 2023:2023.07.20.23292968. [PMID: 37546994 PMCID: PMC10402220 DOI: 10.1101/2023.07.20.23292968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at > 700,000 positions in a discovery cohort of n = 84 adults with BD with a history of SA (BD/SA), n = 79 adults with BD without history of SA (BD/non-SA), and n = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort of n = 48 BD/SA and n = 47 BD/non-SA, fold-changes at the discovery cohort's significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8-93.8%) and 82.1% (CI = 73.6-90.5%) for the combined epigenetic-clinical predictor in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.
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Affiliation(s)
- Salahudeen Mirza
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Institute of Child Development, University of Minnesota, 55455 Minneapolis, Minnesota, USA
| | - Camila N. de Carvalho Lima
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Alexandra Del Favero-Campbell
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Alexandre Rubinstein
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Natasha Topolski
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
| | | | - Emese H.C. Kovács
- Department of Neuroscience and Pharmacology, The University of Iowa, 51 Newton Rd, 52242 Iowa City, Iowa, USA
| | - Hilary P. Blumberg
- Department of Psychiatry, Yale School of Medicine, 06510 New Haven, Connecticut, USA
| | - Jenny Gringer Richards
- Department of Radiology, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
| | - Aislinn J. Williams
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
| | - John A. Wemmie
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
- Department of Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - Vincent A. Magnotta
- Department of Radiology, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
| | - Jess G. Fiedorowicz
- University of Ottawa Brain and Mind Research Institute, Ottawa Hospital Research Institute. 501 Smyth, K1H 8L6, Ottawa, Ontario, Canada
| | - Marie E. Gaine
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, Iowa, USA
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
| | - Jair C. Soares
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
| | - Gabriel R. Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
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Lima CNC, Kovács EHC, Mirza S, Del Favero-Campbell A, Diaz AP, Quevedo J, Argue BMR, Richards JG, Williams A, Wemmie JA, Magnotta VA, Fiedorowicz JG, Soares JC, Gaine ME, Fries GR. Association between the epigenetic lifespan predictor GrimAge and history of suicide attempt in bipolar disorder. Neuropsychopharmacology 2023; 48:954-962. [PMID: 36878995 PMCID: PMC10156727 DOI: 10.1038/s41386-023-01557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
Bipolar disorder (BD) has been previously associated with premature mortality and aging, including acceleration of epigenetic aging. Suicide attempts (SA) are greatly elevated in BD and are associated with decreased lifespan, biological aging, and poorer clinical outcomes. We investigated the relationship between GrimAge, an epigenetic clock trained on time-to-death and associated with mortality and lifespan, and SA in two independent cohorts of BD individuals (discovery cohort - controls (n = 50), BD individuals with (n = 77, BD/SA) and without (n = 67, BD/non-SA) lifetime history of SA; replication cohort - BD/SA (n = 48) and BD/non-SA (n = 47)). An acceleration index for the GrimAge clock (GrimAgeAccel) was computed from blood DNA methylation (DNAm) and compared between groups with multiple general linear models. Differences in epigenetic aging from the discovery cohort were validated in the independent replication cohort. In the discovery cohort, controls, BD/non-SA, and BD/SA significantly differed on GrimAgeAccel (F = 5.424, p = 0.005), with the highest GrimAgeAccel in BD/SA (p = 0.004, BD/SA vs. controls). Within the BD individuals, BD/non-SA and BD/SA differed on GrimAgeAccel in both cohorts (p = 0.008) after covariate adjustment. Finally, DNAm-based surrogates revealed possible involvement of plasminogen activator inhibitor 1, leptin, and smoking pack-years in driving accelerated epigenetic aging. These findings pair with existing evidence that not only BD, but also SA, may be associated with an accelerated biological aging and provide putative biological mechanisms for morbidity and premature mortality in this population.
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Affiliation(s)
- Camila N C Lima
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Emese H C Kovács
- Department of Neuroscience and Pharmacology, The University of Iowa, 51 Newton Rd, 52242, Iowa City, IA, USA
| | - Salahudeen Mirza
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Institute of Child Development, University of Minnesota, 51 E River Rd, 55455, Minneapolis, MN, USA
| | - Alexandra Del Favero-Campbell
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Alexandre Paim Diaz
- Center for the Study and Prevention of Suicide, Department of Psychiatry, University of Rochester Medical Center, Rochester, NY, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Ave, 77030, Houston, TX, USA
| | - Benney M R Argue
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, IA, USA
| | - Jenny Gringer Richards
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Aislinn Williams
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
| | - John A Wemmie
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Vincent A Magnotta
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Jess G Fiedorowicz
- University of Ottawa Brain and Mind Research Institute, Ottawa Hospital Research Institute, 501 Smyth, K1H 8L6, Ottawa, ON, Canada
| | - Jair C Soares
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Ave, 77030, Houston, TX, USA
| | - Marie E Gaine
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
| | - Gabriel R Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA.
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA.
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Ave, 77030, Houston, TX, USA.
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin, 77030, Houston, TX, USA.
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Kim J, Vanrobaeys Y, Peterson Z, Kelvington B, Gaine ME, Nickl-Jockschat T, Abel T. Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders. bioRxiv 2023:2023.02.09.527866. [PMID: 36798381 PMCID: PMC9934710 DOI: 10.1101/2023.02.09.527866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Neurodevelopmental disorders (NDDs) are polygenic in nature and copy number variants (CNVs) are ideal candidates to study the nature of this polygenic risk. The disruption of striatal circuits is considered a central mechanism in NDDs. The 16p11.2 hemi-deletion (16p11.2 del) is one of the most common CNVs associated with NDD, and 16p11.2 del/+ mice show sex-specific striatum-related behavioral phenotypes. However, the critical genes among the 27 genes in the 16p11.2 region that underlie these phenotypes remain unknown. Previously, we applied a novel strategy to identify candidate genes associated with the sex-specific phenotypes of 16p11.2 del/+ mice and identified 3 genes of particular importance within the deleted region: thousand and one amino acid protein kinase 2 ( Taok2 ), seizure-related 6 homolog-like 2 ( Sez6l2 ), and major vault protein ( Mvp ). Using the CRISPR/Cas9 technique, we generated 3 gene hemi-deletion (3g del/+) mice carrying null mutations in Taok2, Sez6l2 , and Mvp . We assessed striatum-dependent phenotypes of these 3g del/+ mice in behavioral, molecular, and imaging studies. Hemi-deletion of Taok2, Sez6l2 , and Mvp induces sex-specific behavioral alterations in striatum-dependent behavioral tasks, specifically male-specific hyperactivity and impaired motivation for reward seeking, resembling behavioral phenotypes of 16p11.2 del/+ mice. Moreover, RNAseq analysis revealed that 3g del/+ mice exhibit gene expression changes in the striatum similar to 16p11.2 del/+ mice, but only in males. Pathway analysis identified ribosomal dysfunction and translation dysregulation as molecular mechanisms underlying male-specific, striatum-dependent behavioral alterations. Together, the mutation of 3 genes within the 16p11.2 region phenocopies striatal sex-specific phenotypes of 16p11.2 del/+ mice, unlike single gene mutation studies. These results support the importance of a polygenic approach to study NDDs and our novel strategy to identify genes of interest using gene expression patterns in brain regions, such as the striatum, which are impacted in these disorders.
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Berdaweel IA, Hart AA, Jatis AJ, Karlan N, Akhter SA, Gaine ME, Smith RM, Anderson EJ. A Genotype-Phenotype Analysis of Glutathione Peroxidase 4 in Human Atrial Myocardium and Its Association with Postoperative Atrial Fibrillation. Antioxidants (Basel) 2022; 11:antiox11040721. [PMID: 35453406 PMCID: PMC9026099 DOI: 10.3390/antiox11040721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
Heterogeneity in the incidence of postoperative atrial fibrillation (POAF) following heart surgery implies that underlying genetic and/or physiological factors impart a higher risk of this complication to certain patients. Glutathione peroxidase-4 (GPx4) is a vital selenoenzyme responsible for neutralizing lipid peroxides, mediators of oxidative stress known to contribute to postoperative arrhythmogenesis. Here, we sought to determine whether GPX4 single nucleotide variants are associated with POAF, and whether any of these variants are linked with altered GPX4 enzyme content or activity in myocardial tissue. Sequencing analysis was performed across the GPX4 coding region within chromosome 19 from a cohort of patients (N = 189) undergoing elective coronary artery bypass graft (−/+ valve) surgery. GPx4 enzyme content and activity were also analyzed in matching samples of atrial myocardium from these patients. Incidence of POAF was 25% in this cohort. Five GPX4 variants were associated with POAF risk (permutated p ≤ 0.05), and eight variants associated with altered myocardial GPx4 content and activity (p < 0.05). One of these variants (rs713041) is a well-known modifier of cardiovascular disease risk. Collectively, these findings suggest GPX4 variants are potential risk modifiers and/or predictors of POAF. Moreover, they illustrate a genotype−phenotype link with this selenoenzyme, which will inform future mechanistic studies.
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Affiliation(s)
- Islam A. Berdaweel
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
| | - Alexander A. Hart
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Andrew J. Jatis
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
| | - Nathan Karlan
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
| | - Shahab A. Akhter
- Department of Cardiovascular Sciences, Brody School of Medicine, East Carolina Heart Institute, Greenville, NC 28592, USA;
| | - Marie E. Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
| | - Ryan M. Smith
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
| | - Ethan J. Anderson
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA; (I.A.B.); (A.J.J.); (N.K.); (M.E.G.); (R.M.S.)
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA
- Correspondence: ; Tel.: +1-(319)335-8157
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Gaine ME, Bahl E, Chatterjee S, Michaelson JJ, Abel T, Lyons LC. Altered hippocampal transcriptome dynamics following sleep deprivation. Mol Brain 2021; 14:125. [PMID: 34384474 PMCID: PMC8361790 DOI: 10.1186/s13041-021-00835-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Widespread sleep deprivation is a continuing public health problem in the United States and worldwide affecting adolescents and adults. Acute sleep deprivation results in decrements in spatial memory and cognitive impairments. The hippocampus is vulnerable to acute sleep deprivation with changes in gene expression, cell signaling, and protein synthesis. Sleep deprivation also has long lasting effects on memory and performance that persist after recovery sleep, as seen in behavioral studies from invertebrates to humans. Although previous research has shown that acute sleep deprivation impacts gene expression, the extent to which sleep deprivation affects gene regulation remains unknown. Using an unbiased deep RNA sequencing approach, we investigated the effects of acute sleep deprivation on gene expression in the hippocampus. We identified 1,146 genes that were significantly dysregulated following sleep deprivation with 507 genes upregulated and 639 genes downregulated, including protein coding genes and long non-coding RNAs not previously identified as impacted by sleep deprivation. Notably, genes significantly upregulated after sleep deprivation were associated with RNA splicing and the nucleus. In contrast, downregulated genes were associated with cell adhesion, dendritic localization, the synapse, and postsynaptic membrane. Furthermore, we found through independent experiments analyzing a subset of genes that three hours of recovery sleep following acute sleep deprivation was sufficient to normalize mRNA abundance for most genes, although exceptions occurred for some genes that may affect RNA splicing or transcription. These results clearly demonstrate that sleep deprivation differentially regulates gene expression on multiple transcriptomic levels to impact hippocampal function.
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Affiliation(s)
- Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA
- Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL, USA.
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13
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Lyons LC, Chatterjee S, Vanrobaeys Y, Gaine ME, Abel T. Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq. Mol Brain 2020; 13:165. [PMID: 33272296 PMCID: PMC7713217 DOI: 10.1186/s13041-020-00702-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Sleep deprivation is a global health problem adversely affecting health as well as causing decrements in learning and performance. Sleep deprivation induces significant changes in gene transcription in many brain regions, with the hippocampus particularly susceptible to acute sleep deprivation. However, less is known about the impacts of sleep deprivation on post-transcriptional gene regulation. To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line to express HA-labeled Rpl22 in CaMKIIα neurons to selectively isolate and sequence mRNA transcripts associated with ribosomes in excitatory neurons. We found 198 differentially expressed genes in the ribosome-associated mRNA subset after sleep deprivation. In comparison with previously published data on gene expression in the hippocampus after sleep deprivation, we found that the subset of genes affected by sleep deprivation was considerably different in the translatome compared with the transcriptome, with only 49 genes regulated similarly. Interestingly, we found 478 genes differentially regulated by sleep deprivation in the transcriptome that were not significantly regulated in the translatome of excitatory neurons. Conversely, there were 149 genes differentially regulated by sleep deprivation in the translatome but not in the whole transcriptome. Pathway analysis revealed differences in the biological functions of genes exclusively regulated in the transcriptome or translatome, with protein deacetylase activity and small GTPase binding regulated in the transcriptome and unfolded protein binding, kinase inhibitor activity, neurotransmitter receptors and circadian rhythms regulated in the translatome. These results indicate that sleep deprivation induces significant changes affecting the pool of actively translated mRNAs.
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Affiliation(s)
- Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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14
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Chatterjee S, Angelakos CC, Bahl E, Hawk JD, Gaine ME, Poplawski SG, Schneider-Anthony A, Yadav M, Porcari GS, Cassel JC, Giese KP, Michaelson JJ, Lyons LC, Boutillier AL, Abel T. The CBP KIX domain regulates long-term memory and circadian activity. BMC Biol 2020; 18:155. [PMID: 33121486 PMCID: PMC7597000 DOI: 10.1186/s12915-020-00886-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Background CREB-dependent transcription necessary for long-term memory is driven by interactions with CREB-binding protein (CBP), a multi-domain protein that binds numerous transcription factors potentially affecting expression of thousands of genes. Identifying specific domain functions for multi-domain proteins is essential to understand processes such as cognitive function and circadian clocks. We investigated the function of the CBP KIX domain in hippocampal memory and gene expression using CBPKIX/KIX mice with mutations that prevent phospho-CREB (Ser133) binding. Results We found that CBPKIX/KIX mice were impaired in long-term memory, but not learning acquisition or short-term memory for the Morris water maze. Using an unbiased analysis of gene expression in the dorsal hippocampus after training in the Morris water maze or contextual fear conditioning, we discovered dysregulation of CREB, CLOCK, and BMAL1 target genes and downregulation of circadian genes in CBPKIX/KIX mice. Given our finding that the CBP KIX domain was important for transcription of circadian genes, we profiled circadian activity and phase resetting in CBPKIX/KIX mice. CBPKIX/KIX mice exhibited delayed activity peaks after light offset and longer free-running periods in constant dark. Interestingly, CBPKIX/KIX mice displayed phase delays and advances in response to photic stimulation comparable to wildtype littermates. Thus, this work delineates site-specific regulation of the circadian clock by a multi-domain protein. Conclusions These studies provide insight into the significance of the CBP KIX domain by defining targets of CBP transcriptional co-activation in memory and the role of the CBP KIX domain in vivo on circadian rhythms. Graphical abstract ![]()
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Affiliation(s)
- Snehajyoti Chatterjee
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France.,Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Christopher C Angelakos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Joshua D Hawk
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shane G Poplawski
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, USA
| | - Anne Schneider-Anthony
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France
| | - Manish Yadav
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Giulia S Porcari
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Christophe Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, Iowa, USA.,Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France. .,LNCA, CNRS UMR 7364, Strasbourg, France.
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
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15
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Reichman RD, Gaynor SC, Monson ET, Gaine ME, Parsons MG, Zandi PP, Potash JB, Willour VL. Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2020; 183:128-139. [PMID: 31854516 PMCID: PMC8380126 DOI: 10.1002/ajmg.b.32767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Glutamatergic signaling is the primary excitatory neurotransmission pathway in the brain, and its relationship to neuropsychiatric disorders is of considerable interest. Our previous attempted suicide genome-wide association study, and numerous studies investigating gene expression, genetic variation, and DNA methylation have implicated aberrant glutamatergic signaling in suicide risk. The glutamatergic pathway gene LRRTM4 was an associated gene identified in our attempted suicide genome-wide association study, with association support seen primarily in females. Recent evidence has also shown that glutamatergic signaling is partly regulated by sex-related hormones. The LRRTM gene family encodes neuronal leucine-rich transmembrane proteins that localize to and promote glutamatergic synapse development. In this study, we sequenced the coding and regulatory regions of all four LRRTM gene members plus a large intronic region of LRRTM4 in 476 bipolar disorder suicide attempters and 473 bipolar disorder nonattempters. We identified two male-specific variants, one female- and five male-specific haplotypes significantly associated with attempted suicide in LRRTM4. Furthermore, variants within significant haplotypes may be brain expression quantitative trait loci for LRRTM4 and some of these variants overlap with predicted hormone response elements. Overall, these results provide supporting evidence for a sex-specific association of genetic variation in LRRTM4 with attempted suicide.
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Affiliation(s)
- Rachel D. Reichman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Sophia C. Gaynor
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Eric T. Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Marie E. Gaine
- Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Meredith G. Parsons
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Virginia L. Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
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16
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Gaynor SC, Monson ET, Gaine ME, Chimenti MS, Reichman RD, Parsons M, Oonthonpan L, Zandi PP, Potash JB, Willour VL. Male-specific association of the 2p25 region with suicide attempt in bipolar disorder. J Psychiatr Res 2020; 121:151-158. [PMID: 31830721 PMCID: PMC8344384 DOI: 10.1016/j.jpsychires.2019.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/20/2023]
Abstract
We previously conducted a genome-wide association study (GWAS) of attempted suicide within bipolar disorder, which implicated common variation in the 2p25 region primarily in males. The top association signal from our GWAS occurred in an intergenic region of 2p25 (p = 5.07 × 10-8) and was supported by two independent studies. In the current study, to better characterize the association of the 2p25 region with attempted suicide, we sequenced the entire 350kb 2p25 region in 476 bipolar suicide attempters and 473 bipolar non-attempters using targeted next-generation sequencing. This fine-mapping project identified 4,681 variants in the 2p25 region. We performed both gene-level and individual-variant tests on our sequencing results and identified 375 variants which were nominally significant (p < 0.05) and three common variants that were significantly associated with attempted suicide in males (corrected p = 0.035, odds ratio (OR) = 2.13). These three variants are in strong linkage disequilibrium with the top variant from our GWAS. Our top five variants are also predicted expression quantitative trait loci (eQTL) for three genes in the 2p25 region based on publicly available brain expression databases. Our sequencing and eQTL data implicate these three genes - SH3YL1, ACP1, and FAM150B - and three additional pathways - androgen receptor, Wnt signaling, and glutamatergic/GABAergic signaling - in the association of the 2p25 region with suicide. The current study provides additional support for an association of the 2p25 region with attempted suicide in males and identifies several candidate genes and pathways that warrant further investigation to understand their role in suicidal behavior.
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Affiliation(s)
- Sophia C. Gaynor
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Eric T. Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Marie E. Gaine
- Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael S. Chimenti
- Bioinformatics Division, Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Rachel D. Reichman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Meredith Parsons
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Lalita Oonthonpan
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Virginia L. Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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17
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Gaine ME, Seifuddin F, Sabunciyan S, Lee RS, Benke KS, Monson ET, Zandi PP, Potash JB, Willour VL. Differentially methylated regions in bipolar disorder and suicide. Am J Med Genet B Neuropsychiatr Genet 2019; 180:496-507. [PMID: 31350827 PMCID: PMC8375453 DOI: 10.1002/ajmg.b.32754] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/24/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022]
Abstract
The addition of a methyl group to, typically, a cytosine-guanine dinucleotide (CpG) creates distinct DNA methylation patterns across the genome that can regulate gene expression. Aberrant DNA methylation of CpG sites has been associated with many psychiatric disorders including bipolar disorder (BD) and suicide. Using the SureSelectXT system, Methyl-Seq, we investigated the DNA methylation status of CpG sites throughout the genome in 50 BD individuals (23 subjects who died by suicide and 27 subjects who died from other causes) and 31 nonpsychiatric controls. We identified differentially methylated regions (DMRs) from three analyses: (a) BD subjects compared to nonpsychiatric controls (BD-NC), (b) BD subjects who died by suicide compared to nonpsychiatric controls (BDS-NC), and (c) BDS subjects compared to BD subjects who died from other causes (BDS-BDNS). One DMR from the BDS-NC analysis, located in ARHGEF38, was significantly hypomethylated (23.4%) in BDS subjects. This finding remained significant after multiple testing (PBootstrapped = 9.0 × 10-3 ), was validated using pyrosequencing, and was more significant in males. A secondary analysis utilized Ingenuity Pathway Analysis to identify enrichment in nominally significant DMRs. This identified an association with several pathways including axonal guidance signaling, calcium signaling, β-adrenergic signaling, and opioid signaling. Our comprehensive study provides further support that DNA methylation alterations influence the risk for BD and suicide. However, further investigation is required to confirm these associations and identify their functional consequences.
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Affiliation(s)
- Marie E. Gaine
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Fayaz Seifuddin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sarven Sabunciyan
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland,Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Richard S. Lee
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kelly S. Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Eric T. Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Peter P. Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Virginia L. Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
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18
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Abstract
Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i) DNA methylation; (ii) histone modifications; and (iii) non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.
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Affiliation(s)
- Marie E Gaine
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Snehajyoti Chatterjee
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Ted Abel
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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19
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Monson ET, Pirooznia M, Parla J, Kramer M, Goes FS, Gaine ME, Gaynor SC, de Klerk K, Jancic D, Karchin R, McCombie WR, Zandi PP, Potash JB, Willour VL. Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. Mol Neuropsychiatry 2017; 3:1-11. [PMID: 28879196 DOI: 10.1159/000454773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/24/2016] [Indexed: 11/19/2022]
Abstract
Suicidal behavior is a complex and devastating phenotype with a heritable component that has not been fully explained by existing common genetic variant analyses. This study represents the first large-scale DNA sequencing project designed to assess the role of rare functional genetic variation in suicidal behavior risk. To accomplish this, whole-exome sequencing data for ∼19,000 genes were generated for 387 bipolar disorder subjects with a history of suicide attempt and 631 bipolar disorder subjects with no prior suicide attempts. Rare functional variants were assessed in all exome genes as well as pathways hypothesized to contribute to suicidal behavior risk. No result survived conservative Bonferroni correction, though many suggestive findings have arisen that merit additional attention. In addition, nominal support for past associations in genes, such as BDNF, and pathways, such as the hypothalamic-pituitary-adrenal axis, was also observed. Finally, a novel pathway was identified that is driven by aldehyde dehydrogenase genes. Ultimately, this investigation explores variation left largely untouched by existing efforts in suicidal behavior, providing a wealth of novel information to add to future investigations, such as meta-analyses.
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Affiliation(s)
- Eric T Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Parla
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Melissa Kramer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Marie E Gaine
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Sophia C Gaynor
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Kelly de Klerk
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Dubravka Jancic
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Maryland, USA
| | - W Richard McCombie
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Peter P Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Virginia L Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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