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Ho MF, Zhang C, Cohan JS, Tuncturk M, Heider RM, Coombes BJ, Biernacka J, Moon I, Skime M, Ho AM, Ngo Q, Skillon C, Croarkin PE, Oesterle TS, Karpyak VM, Li H, Weinshilboum RM. IL17RB genetic variants are associated with acamprosate treatment response in patients with alcohol use disorder: A proteomics-informed genomics study. Brain Behav Immun 2024; 120:304-314. [PMID: 38852760 PMCID: PMC11269006 DOI: 10.1016/j.bbi.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024] Open
Abstract
Acamprosate is a Food and Drug Administration (FDA) approved medication for the treatment of alcohol use disorder (AUD). However, only a subset of patients achieves optimal treatment outcomes. Currently, no biological measures are utilized to predict response to acamprosate treatment. We applied our established pharmaco-omics informed genomics strategy to identify potential biomarkers associated with acamprosate treatment response. Specifically, our previous open-label acamprosate clinical trial recruited 442 patients with AUD who were treated with acamprosate for three months. We first performed proteomics using baseline plasma samples to identify potential biomarkers associated with acamprosate treatment outcomes. Next, we applied our established "proteomics-informed genome-wide association study (GWAS)" research strategy, and identified 12 proteins, including interleukin-17 receptor B (IL17RB), associated with acamprosate treatment response. A GWAS for IL17RB concentrations identified several genome-wide significant signals. Specifically, the top hit single nucleotide polymorphism (SNP) rs6801605 with a minor allele frequency of 38% in the European American population mapped 4 kilobase (Kb) upstream of IL17RB, and intron 1 of the choline dehydrogenase (CHDH) gene on chromosome 3 (p: 4.8E-20). The variant genotype (AA) for the SNP rs6801605 was associated with lower IL17RB protein expression. In addition, we identified a series of genetic variants in IL17RB that were associated with acamprosate treatment outcomes. Furthermore, the variantgenotypes for all of those IL17RB SNPs were protective for alcohol relapse. Finally, we demonstrated that the basal level of mRNA expression of IL17RB was inversely correlated with those of nuclear factor-κB (NF-κB) subunits, and a significantly higher expression of NF-κB subunits was observed in AUD patients who relapsed to alcohol use. In summary, this study illustrates that IL17RB genetic variants might contribute to acamprosate treatment outcomes. This series of studies represents an important step toward generating functional hypotheses that could be tested to gain insight into mechanisms underlying acamprosate treatment response phenotypes. (The ClinicalTrials.gov Identifier: NCT00662571).
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Affiliation(s)
- Ming-Fen Ho
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA.
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - James S Cohan
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Mustafa Tuncturk
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Robin M Heider
- Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - Brandon J Coombes
- Division of Computational Biology, Quantitative Health Sciences, Rochester, MN, USA
| | - Joanna Biernacka
- Division of Computational Biology, Quantitative Health Sciences, Rochester, MN, USA
| | - Irene Moon
- Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
| | - Michelle Skime
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Ada M Ho
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Quyen Ngo
- Hazelden Betty Ford Foundation, Center City, MN, USA
| | | | - Paul E Croarkin
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Tyler S Oesterle
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Victor M Karpyak
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, USA
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Allard RL, Mayfield J, Barchiesi R, Salem NA, Mayfield RD. Toll-like receptor 7: A novel neuroimmune target to reduce excessive alcohol consumption. Neurobiol Stress 2024; 31:100639. [PMID: 38765062 PMCID: PMC11101708 DOI: 10.1016/j.ynstr.2024.100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Toll-like receptors (TLRs) are a family of innate immune receptors that recognize molecular patterns in foreign pathogens and intrinsic danger/damage signals from cells. TLR7 is a nucleic acid sensing endosomal TLR that is activated by single-stranded RNAs from microbes or by small noncoding RNAs that act as endogenous ligands. TLR7 signals through the MyD88 adaptor protein and activates the transcription factor interferon regulatory factor 7 (IRF7). TLR7 is found throughout the brain and is highly expressed in microglia, the main immune cells of the brain that have also been implicated in alcohol drinking in mice. Upregulation of TLR7 mRNA and protein has been identified in postmortem hippocampus and cortex from AUD subjects that correlated positively with lifetime consumption of alcohol. Similarly, Tlr7 and downstream signaling genes were upregulated in rat hippocampal and cortical slice cultures after chronic alcohol exposure and in these regions after chronic binge-like alcohol treatment in mice. In addition, repeated administration of the synthetic TLR7 agonists imiquimod (R837) or resiquimod (R848) increased voluntary alcohol drinking in different rodent models and produced sustained upregulation of IRF7 in the brain. These findings suggest that chronic TLR7 activation may drive excessive alcohol drinking. In the brain, this could occur through increased levels of endogenous TLR7 activators, like microRNAs and Y RNAs. This review explores chronic TLR7 activation as a pathway of dysregulated neuroimmune signaling in AUD and the endogenous small RNA ligands in the brain that could perpetuate innate immune responses and escalate alcohol drinking.
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Affiliation(s)
- Ruth L. Allard
- Waggoner Center for Alcohol and Addiction Research and The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jody Mayfield
- Waggoner Center for Alcohol and Addiction Research and The University of Texas at Austin, Austin, TX, 78712, USA
| | - Riccardo Barchiesi
- Waggoner Center for Alcohol and Addiction Research and The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nihal A. Salem
- Waggoner Center for Alcohol and Addiction Research and The University of Texas at Austin, Austin, TX, 78712, USA
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research and The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
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3
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Hitzemann R, Gao L, Fei SS, Ray K, Vigh-Conrad KA, Phillips TJ, Searles R, Cervera-Juanes RP, Khadka R, Carlson TL, Gonzales SW, Newman N, Grant KA. Effects of repeated alcohol abstinence on within-subject prefrontal cortical gene expression in rhesus macaques. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2024; 4:12528. [PMID: 38737578 PMCID: PMC11082748 DOI: 10.3389/adar.2024.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Male rhesus monkeys (n = 24) had a biopsy of prefrontal cortical area 46 prior to chronic ethanol self-administration (n = 17) or caloric control (n = 7). Fourteen months of daily self-administration (water vs. 4% alcohol, 22 h access/day termed "open-access") was followed by two cycles of prolonged abstinence (5 weeks) each followed by 3 months of open-access alcohol and a final abstinence followed by necropsy. At necropsy, a biopsy of Area 46, contralateral to the original biopsy, was obtained. Gene expression data (RNA-Seq) were collected comparing biopsy/necropsy samples. Monkeys were categorized by drinking status during the final post-abstinent drinking phase as light (LD), binge (BD), heavy (HD) and very heavy (VHD drinkers). Comparing pre-ethanol to post-abstinent biopsies, four animals that converted from HD to VHD status had significant ontology enrichments in downregulated genes (necropsy minus biopsy n = 286) that included immune response (FDR < 9 × 10-7) and plasma membrane changes (FDR < 1 × 10-7). Genes in the immune response category included IL16 and 18, CCR1, B2M, TLR3, 6 and 7, SP2 and CX3CR1. Upregulated genes (N = 388) were particularly enriched in genes associated with the negative regulation of MAP kinase activity (FDR < 3 × 10-5), including DUSP 1, 4, 5, 6 and 18, SPRY 2, 3, and 4, SPRED2, BMP4 and RGS2. Overall, these data illustrate the power of the NHP model and the within-subject design of genomic changes due to alcohol and suggest new targets for treating severe escalated drinking following repeated alcohol abstinence attempts.
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Affiliation(s)
- Robert Hitzemann
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Lina Gao
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Suzanne S. Fei
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Karina Ray
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Katinka A. Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Tamara J. Phillips
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Robert Searles
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Integrated Genomics Laboratory, Oregon Health and Science University, Portland, OR, United States
| | - Rita P. Cervera-Juanes
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Rupak Khadka
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Timothy L. Carlson
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Steven W. Gonzales
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Natali Newman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Kathleen A. Grant
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
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4
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Plasil SL, Farris SP, Blednov Y, Mayfield RD, Mangieri RA, Nwokeji UJ, Aziz HC, Lambeth PS, Harris RA, Homanics GE. Mutation of novel ethanol-responsive lncRNA Gm41261 impacts ethanol-related behavioral responses in mice. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12886. [PMID: 38373108 PMCID: PMC10876150 DOI: 10.1111/gbb.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/26/2024] [Indexed: 02/21/2024]
Abstract
Chronic alcohol exposure results in widespread dysregulation of gene expression that contributes to the pathogenesis of Alcohol Use Disorder (AUD). Long noncoding RNAs are key regulators of the transcriptome that we hypothesize coordinate alcohol-induced transcriptome dysregulation and contribute to AUD. Based on RNA-Sequencing data of human prefrontal cortex, basolateral amygdala and nucleus accumbens of AUD versus non-AUD brain, the human LINC01265 and its predicted murine homolog Gm41261 (i.e., TX2) were selected for functional interrogation. We tested the hypothesis that TX2 contributes to ethanol drinking and behavioral responses to ethanol. CRISPR/Cas9 mutagenesis was used to create a TX2 mutant mouse line in which 306 base-pairs were deleted from the locus. RNA analysis revealed that an abnormal TX2 transcript was produced at an unchanged level in mutant animals. Behaviorally, mutant mice had reduced ethanol, gaboxadol and zolpidem-induced loss of the righting response and reduced tolerance to ethanol in both sexes. In addition, a male-specific reduction in two-bottle choice every-other-day ethanol drinking was observed. Male TX2 mutants exhibited evidence of enhanced GABA release and altered GABAA receptor subunit composition in neurons of the nucleus accumbens shell. In C57BL6/J mice, TX2 within the cortex was cytoplasmic and largely present in Rbfox3+ neurons and IBA1+ microglia, but not in Olig2+ oligodendrocytes or in the majority of GFAP+ astrocytes. These data support the hypothesis that TX2 mutagenesis and dysregulation impacts ethanol drinking behavior and ethanol-induced behavioral responses in mice, likely through alterations in the GABAergic system.
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Affiliation(s)
- S. L. Plasil
- Department of Pharmacology and Chemical BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - S. P. Farris
- Department of Anesthesiology and Perioperative MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Biomedical InformaticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
| | - Y. Blednov
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
| | - R. D. Mayfield
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
- Department of NeuroscienceThe University of Texas at AustinAustinTexasUSA
| | - R. A. Mangieri
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
- Division of Pharmacology and Toxicology, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - U. J. Nwokeji
- Department of Pharmacology and Chemical BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - H. C. Aziz
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
- Division of Pharmacology and Toxicology, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - P. S. Lambeth
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
- Department of NeuroscienceThe University of Texas at AustinAustinTexasUSA
| | - R. A. Harris
- The Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at AustinAustinTexasUSA
| | - G. E. Homanics
- Department of Pharmacology and Chemical BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Anesthesiology and Perioperative MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of NeurobiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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5
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Melbourne JK, Wooden JI, Carlson ER, Anasooya Shaji C, Nixon K. Neuroimmune Activation and Microglia Reactivity in Female Rats Following Alcohol Dependence. Int J Mol Sci 2024; 25:1603. [PMID: 38338883 PMCID: PMC10855949 DOI: 10.3390/ijms25031603] [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: 11/22/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 02/12/2024] Open
Abstract
The rates of alcohol use disorder among women are growing, yet little is known about how the female brain is affected by alcohol. The neuroimmune system, and specifically microglia, have been implicated in mediating alcohol neurotoxicity, but most preclinical studies have focused on males. Further, few studies have considered changes to the microglial phenotype when examining the effects of ethanol on brain structure and function. Therefore, we quantified microglial reactivity in female rats using a binge model of alcohol dependence, assessed through morphological and phenotypic marker expression, coupled with regional cytokine levels. In a time- and region-dependent manner, alcohol altered the microglial number and morphology, including the soma and process area, and the overall complexity within the corticolimbic regions examined, but no significant increases in the proinflammatory markers MHCII or CD68 were observed. The majority of cytokine and growth factor levels examined were similarly unchanged. However, the expression of the proinflammatory cytokine TNFα was increased, and the anti-inflammatory IL-10, decreased. Thus, female rats showed subtle differences in neuroimmune reactivity compared to past work in males, consistent with reports of enhanced neuroimmune responses in females across the literature. These data suggest that specific neuroimmune reactions in females may impact their susceptibility to alcohol neurotoxicity and other neurodegenerative events with microglial contributions.
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Affiliation(s)
| | | | | | | | - Kimberly Nixon
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA; (J.K.M.)
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6
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Hitzemann R, Ozburn AR, Lockwood D, Phillips TJ. Modeling Brain Gene Expression in Alcohol Use Disorder with Genetic Animal Models. Curr Top Behav Neurosci 2023. [PMID: 37982929 DOI: 10.1007/7854_2023_455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Animal genetic models have and will continue to provide important new information about the behavioral and physiological adaptations associated with alcohol use disorder (AUD). This chapter focuses on two models, ethanol preference and drinking in the dark (DID), their usefulness in interrogating brain gene expression data and the relevance of the data obtained to interpret AUD-related GWAS and TWAS studies. Both the animal and human data point to the importance for AUD of changes in synaptic transmission (particularly glutamate and GABA transmission), of changes in the extracellular matrix (specifically including collagens, cadherins and protocadherins) and of changes in neuroimmune processes. The implementation of new technologies (e.g., cell type-specific gene expression) is expected to further enhance the value of genetic animal models in understanding AUD.
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Affiliation(s)
- Robert Hitzemann
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA.
| | - Angela R Ozburn
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Denesa Lockwood
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Tamara J Phillips
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, USA
- Veterans Affairs Portland Health Care System, Portland, OR, USA
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7
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Li R, Reiter JL, Chen AB, Chen SX, Foroud T, Edenberg HJ, Lai D, Liu Y. RNA alternative splicing impacts the risk for alcohol use disorder. Mol Psychiatry 2023; 28:2922-2933. [PMID: 37217680 PMCID: PMC10615768 DOI: 10.1038/s41380-023-02111-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Alcohol use disorder (AUD) is a complex genetic disorder characterized by problems arising from excessive alcohol consumption. Identifying functional genetic variations that contribute to risk for AUD is a major goal. Alternative splicing of RNA mediates the flow of genetic information from DNA to gene expression and expands proteome diversity. We asked whether alternative splicing could be a risk factor for AUD. Herein, we used a Mendelian randomization (MR)-based approach to identify skipped exons (the predominant splicing event in brain) that contribute to AUD risk. Genotypes and RNA-seq data from the CommonMind Consortium were used as the training dataset to develop predictive models linking individual genotypes to exon skipping in the prefrontal cortex. We applied these models to data from the Collaborative Studies on Genetics of Alcoholism to examine the association between the imputed cis-regulated splicing outcome and the AUD-related traits. We identified 27 exon skipping events that were predicted to affect AUD risk; six of these were replicated in the Australian Twin-family Study of Alcohol Use Disorder. Their host genes are DRC1, ELOVL7, LINC00665, NSUN4, SRRM2 and TBC1D5. The genes downstream of these splicing events are enriched in neuroimmune pathways. The MR-inferred impacts of the ELOVL7 skipped exon on AUD risk was further supported in four additional large-scale genome-wide association studies. Additionally, this exon contributed to changes of gray matter volumes in multiple brain regions, including the visual cortex known to be involved in AUD. In conclusion, this study provides strong evidence that RNA alternative splicing impacts the susceptibility to AUD and adds new information on AUD-relevant genes and pathways. Our framework is also applicable to other types of splicing events and to other complex genetic disorders.
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Affiliation(s)
- Rudong Li
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill L Reiter
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Andy B Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Steven X Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Medina AM, Hagenauer MH, Krolewski DM, Hughes E, Forrester LCT, Walsh DM, Waselus M, Richardson E, Turner CA, Sequeira PA, Cartagena PM, Thompson RC, Vawter MP, Bunney BG, Myers RM, Barchas JD, Lee FS, Schatzberg AF, Bunney WE, Akil H, Watson SJ. Neurotransmission-related gene expression in the frontal pole is altered in subjects with bipolar disorder and schizophrenia. Transl Psychiatry 2023; 13:118. [PMID: 37031222 PMCID: PMC10082811 DOI: 10.1038/s41398-023-02418-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/10/2023] Open
Abstract
The frontal pole (Brodmann area 10, BA10) is the largest cytoarchitectonic region of the human cortex, performing complex integrative functions. BA10 undergoes intensive adolescent grey matter pruning prior to the age of onset for bipolar disorder (BP) and schizophrenia (SCHIZ), and its dysfunction is likely to underly aspects of their shared symptomology. In this study, we investigated the role of BA10 neurotransmission-related gene expression in BP and SCHIZ. We performed qPCR to measure the expression of 115 neurotransmission-related targets in control, BP, and SCHIZ postmortem samples (n = 72). We chose this method for its high sensitivity to detect low-level expression. We then strengthened our findings by performing a meta-analysis of publicly released BA10 microarray data (n = 101) and identified sources of convergence with our qPCR results. To improve interpretation, we leveraged the unusually large database of clinical metadata accompanying our samples to explore the relationship between BA10 gene expression, therapeutics, substances of abuse, and symptom profiles, and validated these findings with publicly available datasets. Using these convergent sources of evidence, we identified 20 neurotransmission-related genes that were differentially expressed in BP and SCHIZ in BA10. These results included a large diagnosis-related decrease in two important therapeutic targets with low levels of expression, HTR2B and DRD4, as well as other findings related to dopaminergic, GABAergic and astrocytic function. We also observed that therapeutics may produce a differential expression that opposes diagnosis effects. In contrast, substances of abuse showed similar effects on BA10 gene expression as BP and SCHIZ, potentially amplifying diagnosis-related dysregulation.
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Affiliation(s)
- Adriana M Medina
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | - David M Krolewski
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Evan Hughes
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Maria Waselus
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Evelyn Richardson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Cortney A Turner
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Robert C Thompson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | | | | | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Stanley J Watson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
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9
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Huggett SB, Ikeda AS, Yuan Q, Benca-Bachman CE, Palmer RHC. Genome- and transcriptome-wide splicing associations with alcohol use disorder. Sci Rep 2023; 13:3950. [PMID: 36894673 PMCID: PMC9998611 DOI: 10.1038/s41598-023-30926-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Genetic mechanisms of alternative mRNA splicing have been shown in the brain for a variety of neuropsychiatric traits, but not substance use disorders. Our study utilized RNA-sequencing data on alcohol use disorder (AUD) in four brain regions (n = 56; ages 40-73; 100% 'Caucasian'; PFC, NAc, BLA and CEA) and genome-wide association data on AUD (n = 435,563, ages 22-90; 100% European-American). Polygenic scores of AUD were associated with AUD-related alternative mRNA splicing in the brain. We identified 714 differentially spliced genes between AUD vs controls, which included both putative addiction genes and novel gene targets. We found 6463 splicing quantitative trait loci (sQTLs) that linked to the AUD differentially spliced genes. sQTLs were enriched in loose chromatin genomic regions and downstream gene targets. Additionally, the heritability of AUD was enriched for DNA variants in and around differentially spliced genes associated with AUD. Our study also performed splicing transcriptome-wide association studies (TWASs) of AUD and other drug use traits that unveiled specific genes for follow-up and splicing correlations across SUDs. Finally, we showed that differentially spliced genes between AUD vs control were also associated with primate models of chronic alcohol consumption in similar brain regions. Our study found substantial genetic contributions of alternative mRNA splicing in AUD.
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Affiliation(s)
- Spencer B Huggett
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Ami S Ikeda
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Qingyue Yuan
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Chelsie E Benca-Bachman
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Rohan H C Palmer
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA.
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10
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Johnson EC, Kapoor M, Hatoum AS, Zhou H, Polimanti R, Wendt FR, Walters RK, Lai D, Kember RL, Hartz S, Meyers JL, Peterson RE, Ripke S, Bigdeli TB, Fanous AH, Pato CN, Pato MT, Goate AM, Kranzler HR, O'Donovan MC, Walters JTR, Gelernter J, Edenberg HJ, Agrawal A. Investigation of convergent and divergent genetic influences underlying schizophrenia and alcohol use disorder. Psychol Med 2023; 53:1196-1204. [PMID: 34231451 PMCID: PMC8738774 DOI: 10.1017/s003329172100266x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Alcohol use disorder (AUD) and schizophrenia (SCZ) frequently co-occur, and large-scale genome-wide association studies (GWAS) have identified significant genetic correlations between these disorders. METHODS We used the largest published GWAS for AUD (total cases = 77 822) and SCZ (total cases = 46 827) to identify genetic variants that influence both disorders (with either the same or opposite direction of effect) and those that are disorder specific. RESULTS We identified 55 independent genome-wide significant single nucleotide polymorphisms with the same direction of effect on AUD and SCZ, 8 with robust effects in opposite directions, and 98 with disorder-specific effects. We also found evidence for 12 genes whose pleiotropic associations with AUD and SCZ are consistent with mediation via gene expression in the prefrontal cortex. The genetic covariance between AUD and SCZ was concentrated in genomic regions functional in brain tissues (p = 0.001). CONCLUSIONS Our findings provide further evidence that SCZ shares meaningful genetic overlap with AUD.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander S Hatoum
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Hang Zhou
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Frank R Wendt
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Sarah Hartz
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Henri Begleiter Neurodynamics Laboratory, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Ayman H Fanous
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA, USA
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - James T R Walters
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - Joel Gelernter
- Department of Psychiatry, Division of Human Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
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11
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Kong W, Huang S, Chen Z, Li X, Liu S, Zhang Z, Yang Y, Wang Z, Zhu X, Ni X, Lu H, Zhang M, Li Z, Wen Y, Shang D. Proteomics and weighted gene correlated network analysis reveal glutamatergic synapse signaling in diazepam treatment of alcohol withdrawal. Front Pharmacol 2023; 13:1111758. [PMID: 36712652 PMCID: PMC9873974 DOI: 10.3389/fphar.2022.1111758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Alcohol use disorder (AUD) is characterized by chronic excessive alcohol consumption, often alternating with periods of abstinence known as alcohol withdrawal syndrome (AWS). Diazepam is the preferred benzodiazepine for treatment of alcohol withdrawal syndrome under most circumstances, but the specific mechanism underlying the treatment needs further research. Methods: We constructed an animal model of two-bottle choices and chronic intermittent ethanol exposure. LC-MS/MS proteomic analysis based on the label-free and intensity-based quantification approach was used to detect the protein profile of the whole brain. Weighted gene correlated network analysis was applied for scale-free network topology analysis. We established a protein-protein interaction network based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software and identified hub proteins by CytoHubba and MCODE plugins of Cytoscape. The online tool Targetscan identified miRNA-mRNA pair interactions. Results: Seven hub proteins (Dlg3, Dlg4, Shank3, Grin2b, Camk2b, Camk2a and Syngap1) were implicated in alcohol withdrawal syndrome or diazepam treatment. In enrichment analysis, glutamatergic synapses were considered the most important pathway related to alcohol use disorder. Decreased glutamatergic synapses were observed in the late stage of withdrawal, as a protective mechanism that attenuated withdrawal-induced excitotoxicity. Diazepam treatment during withdrawal increased glutamatergic synapses, alleviating withdrawal-induced synapse inhibition. Conclusion: Glutamatergic synapses are considered the most important pathway related to alcohol use disorder that may be a potential molecular target for new interventional strategies.
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Affiliation(s)
- Wan Kong
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shanqing Huang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zikai Chen
- Department of Administration, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaolin Li
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shujing Liu
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zi Zhang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ye Yang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhanzhang Wang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiuqing Zhu
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaojia Ni
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haoyang Lu
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ming Zhang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zezhi Li
- Department of Adult Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China,*Correspondence: Zezhi Li, ; Yuguan Wen, ; Dewei Shang,
| | - Yuguan Wen
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China,*Correspondence: Zezhi Li, ; Yuguan Wen, ; Dewei Shang,
| | - Dewei Shang
- Department of Pharmacy, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China,*Correspondence: Zezhi Li, ; Yuguan Wen, ; Dewei Shang,
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12
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Bogdan R, Hatoum AS, Johnson EC, Agrawal A. The Genetically Informed Neurobiology of Addiction (GINA) model. Nat Rev Neurosci 2023; 24:40-57. [PMID: 36446900 PMCID: PMC10041646 DOI: 10.1038/s41583-022-00656-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
Addictions are heritable and unfold dynamically across the lifespan. One prominent neurobiological theory proposes that substance-induced changes in neural circuitry promote the progression of addiction. Genome-wide association studies have begun to characterize the polygenic architecture undergirding addiction liability and revealed that genetic loci associated with risk can be divided into those associated with a general broad-spectrum liability to addiction and those associated with drug-specific addiction risk. In this Perspective, we integrate these genomic findings with our current understanding of the neurobiology of addiction to propose a new Genetically Informed Neurobiology of Addiction (GINA) model.
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Affiliation(s)
- Ryan Bogdan
- Department of Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA.
| | - Alexander S Hatoum
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
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13
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Li Z, Vidjro OE, Guo G, Du Y, Zhou Y, Xie Q, Li J, Gao K, Zhou L, Ma T. NLRP3 deficiency decreases alcohol intake controlling anxiety-like behavior via modification of glutamatergic transmission in corticostriatal circuits. J Neuroinflammation 2022; 19:308. [PMID: 36539796 PMCID: PMC9764485 DOI: 10.1186/s12974-022-02666-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Alcohol use disorders result from repeated binge and chronic alcohol consumption followed by negative effects, such as anxiety, upon cessation. This process is associated with the activation of NLRP3 inflammasome-mediated responses. However, whether and how inhibition of the NLRP3 inflammasome alters alcohol intake and anxiety behavior remains unclear. METHODS A combination of drinking-in-the-dark and gavage was established in NLRP3-knockout and control mice. Behavior was assessed by open-field and elevated plus maze tests. Binge alcohol drinking was measured at 2 h and 4 h. A 2 h/4 h/24 h voluntary drinking was determined by a two-bottle choice paradigm. Western blotting and ELISA were applied to examine the levels of the NLRP3 inflammasome and- inflammatory factors, such as IL-1β and TNF-α. Nissl staining was used to measure neuronal injury. The electrophysiological method was used to determine glutamatergic transmission in corticostriatal circuits. In vivo optogenetic LTP and LTD were applied to control the function of corticostriatal circuits on the behavior of mice. MCC950 was used to antagonize the NLRP3 inflammasome. RESULTS The binge alcohol intake was decreased in NLRP3 KO mice compared to the control mice. During alcohol withdrawal, NLRP3 deficiency attenuated anxiety-like behavior and neuronal injury in the mPFC and striatum. Moreover, we discovered that glutamatergic transmission to striatal neurons was reduced in NLRP3 KO mice. Importantly, in vivo optogenetic induction of long-term potentiation (LTP) of corticostriatal circuits reversed the effects of NLRP3 deficiency on glutamatergic transmission and anxiety behavior. We also demonstrated that optogenetic induction of LTD decreased anxiety-like behavior and caused a reduction in glutamatergic transmission. Interestingly, NLRP3 deficiency or inhibition (MCC950 injection) attenuated the anxiety-like behavior, but it did not prevent DID + gavage paradigm-induced a persistent enhancement of drinking in a two-bottle choice at 2 and 4 days into withdrawal. CONCLUSION Our results demonstrate that NLRP3 deficiency decreases binge alcohol intake and anxiety-like behavior through downregulation of glutamatergic transmission in corticostriatal circuits, which may provide an anti-inflammatory target for treating alcohol use disorders.
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Affiliation(s)
- Ziyi Li
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Olivia Ewi Vidjro
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Gengni Guo
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China ,grid.89957.3a0000 0000 9255 8984Grade 2020 in Pharmacy, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu China
| | - Yanfeng Du
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Yao Zhou
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Qian Xie
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Jiaxin Li
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Keqiang Gao
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
| | - Li Zhou
- grid.459791.70000 0004 1757 7869Department of Anesthesiology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei Lane, Mochou Road, Nanjing, 210004 Jiangsu China ,grid.89957.3a0000 0000 9255 8984Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, Jiangsu China
| | - Tengfei Ma
- grid.89957.3a0000 0000 9255 8984Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, 101 Longmian Street, Nanjing, 211166 Jiangsu China
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14
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Plasil SL, Collins VJ, Baratta AM, Farris SP, Homanics GE. Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10831. [PMID: 36908580 PMCID: PMC10004261 DOI: 10.3389/adar.2022.10831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular mechanisms regulating the development and progression of alcohol use disorder (AUD) are largely unknown. While noncoding RNAs have previously been implicated as playing key roles in AUD, long-noncoding RNA (lncRNA) remains understudied in relation to AUD. In this study, we first identified ethanol-responsive lncRNAs in the mouse hippocampus that are transcriptional network hub genes. Microarray analysis of lncRNA, miRNA, circular RNA, and protein coding gene expression in the hippocampus from chronic intermittent ethanol vapor- or air- (control) exposed mice was used to identify ethanol-responsive competing endogenous RNA (ceRNA) networks. Highly interconnected lncRNAs (genes that had the strongest overall correlation to all other dysregulated genes identified) were ranked. The top four lncRNAs were novel, previously uncharacterized genes named Gm42575, 4930413E15Rik, Gm15767, and Gm33447, hereafter referred to as Pitt1, Pitt2, Pitt3, and Pitt4, respectively. We subsequently tested the hypothesis that CRISPR/Cas9 mutagenesis of the putative promoter and first exon of these lncRNAs in C57BL/6J mice would alter ethanol drinking behavior. The Drinking in the Dark (DID) assay was used to examine binge-like drinking behavior, and the Every-Other-Day Two-Bottle Choice (EOD-2BC) assay was used to examine intermittent ethanol consumption and preference. No significant differences between control and mutant mice were observed in the DID assay. Female-specific reductions in ethanol consumption were observed in the EOD-2BC assay for Pitt1, Pitt3, and Pitt4 mutant mice compared to controls. Male-specific alterations in ethanol preference were observed for Pitt1 and Pitt2. Female-specific increases in ethanol preference were observed for Pitt3 and Pitt4. Total fluid consumption was reduced in Pitt1 and Pitt2 mutants at 15% v/v ethanol and in Pitt3 and Pitt4 at 20% v/v ethanol in females only. We conclude that all lncRNAs targeted altered ethanol drinking behavior, and that lncRNAs Pitt1, Pitt3, and Pitt4 influenced ethanol consumption in a sex-specific manner. Further research is necessary to elucidate the biological mechanisms for these effects. These findings add to the literature implicating noncoding RNAs in AUD and suggest lncRNAs also play an important regulatory role in the disease.
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Affiliation(s)
- SL Plasil
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - VJ Collins
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - AM Baratta
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - SP Farris
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - GE Homanics
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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15
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Toikumo S, Xu H, Gelernter J, Kember RL, Kranzler HR. Integrating human brain proteomic data with genome-wide association study findings identifies novel brain proteins in substance use traits. Neuropsychopharmacology 2022; 47:2292-2299. [PMID: 35941285 PMCID: PMC9630289 DOI: 10.1038/s41386-022-01406-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 11/09/2022]
Abstract
Despite the identification of a growing number of genetic risk loci for substance use traits (SUTs), the impact of these loci on protein abundance and the potential utility of relevant proteins as therapeutic targets are unknown. We conducted a proteome-wide association study (PWAS) in which we integrated human brain proteomes from discovery (Banner; N = 152) and validation (ROSMAP; N = 376) datasets with genome-wide association study (GWAS) summary statistics for 4 SUTs. The 4 samples comprised GWAS of European-ancestry individuals for smoking initiation [Smk] (N = 1,232,091), alcohol use disorder [AUD] (N = 313,959), cannabis use disorder [CUD] (N = 384,032), and opioid use disorder [OUD] (N = 302,585). We conducted transcriptome-wide association studies (TWAS) with human brain transcriptomic data to examine the overlap of genetic effects at the proteomic and transcriptomic levels and characterize significant genes through conditional, colocalization, and fine-mapping analyses. We identified 27 genes (Smk = 21, AUD = 3, CUD = 2, OUD = 1) that were significantly associated with cis-regulated brain protein abundance. Of these, 7 showed evidence for causality (Smk: NT5C2, GMPPB, NQO1, RHOT2, SRR and ACTR1B; and AUD: CTNND1). Cis-regulated transcript levels for 8 genes (Smk = 6, CUD = 1, OUD = 1) were associated with SUTs, indicating that genetic loci could confer risk for these SUTs by modulating both gene expression and proteomic abundance. Functional studies of the high-confidence risk proteins identified here are needed to determine whether they are modifiable targets and useful in developing medications and biomarkers for these SUTs.
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Affiliation(s)
- Sylvanus Toikumo
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Heng Xu
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA.
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA.
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16
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Narendra S, Klengel C, Hamzeh B, Patel D, Otten J, Lardenoije R, Newman EL, Miczek KA, Klengel T, Ressler KJ, Suh J. Genome-wide transcriptomics of the amygdala reveals similar oligodendrocyte-related responses to acute and chronic alcohol drinking in female mice. Transl Psychiatry 2022; 12:476. [PMID: 36371333 PMCID: PMC9653459 DOI: 10.1038/s41398-022-02231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
Repeated excessive alcohol consumption is a risk factor for alcohol use disorder (AUD). Although AUD has been more common in men than women, women develop more severe behavioral and physical impairments. However, relatively few new therapeutics targeting development of AUD, particularly in women, have been validated. To gain a better understanding of molecular mechanisms underlying alcohol intake, we conducted a genome-wide RNA-sequencing analysis in female mice exposed to different modes (acute vs chronic) of ethanol drinking. We focused on transcriptional profiles in the amygdala including the central and basolateral subnuclei, brain areas previously implicated in alcohol drinking and seeking. Surprisingly, we found that both drinking modes triggered similar changes in gene expression and canonical pathways, including upregulation of ribosome-related/translational pathways and myelination pathways, and downregulation of chromatin binding and histone modification. In addition, analyses of hub genes and upstream regulatory pathways revealed that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and the oligodendrocyte-related transcription factor, Sox17. Furthermore, a viral vector-assisted knockdown of Sox17 gene expression in the amygdala prevented a gradual increase in alcohol consumption during repeated accesses. Overall, these results suggest that the expression of oligodendrocyte-related genes in the amygdala is sensitive to voluntary alcohol drinking in female mice. These findings suggest potential molecular targets for future therapeutic approaches to prevent the development of AUD, due to repeated excessive alcohol consumption, particularly in women.
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Affiliation(s)
- Sharvari Narendra
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
- Department of Bioinformatics, Northeastern University, Boston, MA, 02115, USA
| | - Claudia Klengel
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
| | - Bilal Hamzeh
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
| | - Drasti Patel
- Department of Bioinformatics, Northeastern University, Boston, MA, 02115, USA
| | - Joy Otten
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Roy Lardenoije
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Emily L Newman
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
| | - Klaus A Miczek
- Psychology and Neuroscience Departments, Tufts University, Medford, MA, 02155, USA
| | - Torsten Klengel
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Kerry J Ressler
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA.
| | - Junghyup Suh
- Division of Depression and Anxiety Disorders, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA.
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17
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Gerstner N, Krontira AC, Cruceanu C, Roeh S, Pütz B, Sauer S, Rex-Haffner M, Schmidt MV, Binder EB, Knauer-Arloth J. DiffBrainNet: Differential analyses add new insights into the response to glucocorticoids at the level of genes, networks and brain regions. Neurobiol Stress 2022; 21:100496. [DOI: 10.1016/j.ynstr.2022.100496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/25/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022] Open
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18
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Chang XW, Sun Y, Muhai JN, Li YY, Chen Y, Lu L, Chang SH, Shi J. Common and distinguishing genetic factors for substance use behavior and disorder: an integrated analysis of genomic and transcriptomic studies from both human and animal studies. Addiction 2022; 117:2515-2529. [PMID: 35491750 DOI: 10.1111/add.15908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Genomic and transcriptomic findings greatly broaden the biological knowledge regarding substance use. However, systematic convergence and comparison evidence of genome-wide findings is lacking for substance use. Here, we combined all the genome-wide findings from both substance use behavior and disorder (SUBD) and identified common and distinguishing genetic factors for different SUBDs. METHODS Systemic literature search for genome-wide association (GWAS) and RNA-seq studies of alcohol/nicotine/drug use behavior (partially meets or not reported diagnostic criteria) and alcohol use behavior and disorder (AUBD), nicotine use behavior and disorder (NUBD) and drug use behavior and disorder (DUBD) was performed using PubMed and the GWAS catalog. Drug use was focused upon cannabis, opioid, cocaine and methamphetamine use. GWAS studies required case-control or case/cohort samples. RNA-seq studies were based on brain tissues. The genes which contained significant single nucleotide polymorphism (P ≤ 1 × 10-6 ) in GWAS and reported as significant in RNA-seq studies were extracted. Pathway enrichment was performed by using Metascape. Gene interaction networks were identified by using the Protein Interaction Network Analysis database. RESULTS Total SUBD-related 2910 genes were extracted from 75 GWAS studies (2 773 889 participants) and 17 RNA-seq studies. By overlapping the genes and pathways of AUBD, NUBD and DUBD, four shared genes (CACNB2, GRIN2B, PLXDC2 and PKNOX2), four shared pathways [two Gene Ontology (GO) terms of 'modulation of chemical synaptic transmission', 'regulation of trans-synaptic signaling', two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of 'dopaminergic synapse', 'cocaine addiction'] were identified (significantly higher than random, P < 1 × 10-5 ). The top shared KEGG pathways (Benjamini-Hochberg-corrected P-value < 0.05) in the pairwise comparison of AUBD versus DUBD, NUBD versus DUBD, AUBD versus NUBD were 'Epstein-Barr virus infection', 'protein processing in endoplasmic reticulum' and 'neuroactive ligand-receptor interaction', respectively. We also identified substance-specific genetic factors: i.e. ADH1B and ALDH2 were unique for AUBD, while CHRNA3 and CHRNA4 were unique for NUBD. CONCLUSIONS This systematic review identifies the shared and unique genes and pathways for alcohol, nicotine and drug use behaviors and disorders at the genome-wide level and highlights critical biological processes for the common and distinguishing vulnerability of substance use behaviors and disorders.
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Affiliation(s)
- Xiang-Wen Chang
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Yan Sun
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Jia-Na Muhai
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Yang-Yang Li
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Yun Chen
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,National Institute on Drug Dependence, Peking University, Beijing, China
| | - Lin Lu
- National Institute on Drug Dependence, Peking University, Beijing, China.,Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Su-Hua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jie Shi
- National Institute on Drug Dependence, Peking University, Beijing, China.,Beijing Key Laboratory of Drug Dependence Research, Peking University, Beijing, China.,The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China.,The Key Laboratory for Neuroscience of the Ministry of Education and Health, Peking University, Beijing, China
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19
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De la Rosa-Cáceres A, Narvaez-Camargo M, Blanc-Molina A, Romero-Pérez N, Dacosta-Sánchez D, González-Ponce BM, Parrado-González A, Torres-Rosado L, Mancheño-Velasco C, Lozano-Rojas ÓM. Bridge Nodes between Personality Traits and Alcohol-Use Disorder Criteria: The Relevance of Externalizing Traits of Risk Taking, Callousness, and Irresponsibility. J Clin Med 2022; 11:jcm11123468. [PMID: 35743541 PMCID: PMC9225009 DOI: 10.3390/jcm11123468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Personality disorders show strong comorbidities with alcohol-use disorder (AUD), and several personality traits have been found to be more frequent in people with AUD. This study analyzes which personality facets of those proposed in the Alternative Model of Personality Disorder (AMPD) of DSM-5 are associated with the diagnostic criteria of AUD. Methods: The sample was composed of 742 participants randomly selected from the Spanish population, and 243 patients attending mental health services. All participants were of legal age and signed an informed consent form. The instruments were administered to the community sample in an online format, and a psychologist conducted individual face-to-face interviews with the patients. AMPD facets were assessed through the Personality Inventory of DSM-5 Short-Form, and the AUD criteria through the Substance Dependence Severity Scale. A network analysis was applied to identify the personality facets mostly associated with the AUD criteria. Results: The network analysis showed the existence of three communities, grouping the AUD criteria, externalizing spectrum facets, and internalizing spectrum facets, respectively. Risk taking, callousness, and irresponsibility facets showed the strongest association with the AUD criteria, bridging externalizing personality traits with AUD criteria. Conclusions: The facets of risk taking, callousness, and irresponsibility should be accurately assessed in patients with AUD to differentiate between a possible primary personality disorder and a syndrome induced by alcohol addiction.
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Affiliation(s)
- Ana De la Rosa-Cáceres
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Marta Narvaez-Camargo
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Andrea Blanc-Molina
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Nehemías Romero-Pérez
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Daniel Dacosta-Sánchez
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Bella María González-Ponce
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Alberto Parrado-González
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Lidia Torres-Rosado
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Cinta Mancheño-Velasco
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
| | - Óscar Martín Lozano-Rojas
- Departamento de Psicología Clínica y Experimental, University of Huelva, 21071 Huelva, Spain; (A.D.l.R.-C.); (M.N.-C.); (A.B.-M.); (N.R.-P.); (D.D.-S.); (B.M.G.-P.); (A.P.-G.); (L.T.-R.); (C.M.-V.)
- Research Center for Natural Resources, Health and Environment, University of Huelva, 21071 Huelva, Spain
- Correspondence:
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20
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Kim HB, Lu Y, Oh SC, Morris J, Miyashiro K, Kim J, Eberwine J, Sul JY. Astrocyte ethanol exposure reveals persistent and defined calcium response subtypes and associated gene signatures. J Biol Chem 2022; 298:102147. [PMID: 35716779 PMCID: PMC9293641 DOI: 10.1016/j.jbc.2022.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/26/2022] Open
Abstract
Astrocytes play a critical role in brain function, but their contribution during ethanol (EtOH) consumption remains largely understudied. In light of recent findings on the heterogeneity of astrocyte physiology and gene expression, an approach with the ability to identify subtypes and capture this heterogeneity is necessary. Here, we combined measurements of calcium signaling and gene expression to define EtOH-induced astrocyte subtypes. In the absence of a demonstrated EtOH receptor, EtOH is believed to have effects on the function of many receptors and downstream biological cascades that underlie calcium responsiveness. This mechanism of EtOH-induced calcium signaling is unknown and this study provides the first step in understanding the characteristics of cells displaying these observed responses. To characterize underlying astrocyte subtypes, we assessed the correlation between calcium signaling and astrocyte gene expression signature in response to EtOH. We found that various EtOH doses increased intracellular calcium levels in a subset of astrocytes, distinguishing three cellular response types and one nonresponsive subtype as categorized by response waveform properties. Furthermore, single-cell RNA-seq analysis of astrocytes from the different response types identified type-enriched discriminatory gene expression signatures. Combining single-cell calcium responses and gene expression analysis identified specific astrocyte subgroups among astrocyte populations defined by their response to EtOH. This result provides a basis for identifying the relationship between astrocyte susceptibility to EtOH and corresponding measurable markers of calcium signaling and gene expression, which will be useful to investigate potential subgroup-specific influences of astrocytes on the physiology and pathology of EtOH exposure in the brain.
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Affiliation(s)
- Hyun-Bum Kim
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seonkyung C Oh
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacqueline Morris
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Miyashiro
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jai-Yoon Sul
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; PENN Program in Single Cell Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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21
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Zillich L, Poisel E, Frank J, Foo JC, Friske MM, Streit F, Sirignano L, Heilmann-Heimbach S, Heimbach A, Hoffmann P, Degenhardt F, Hansson AC, Bakalkin G, Nöthen MM, Rietschel M, Spanagel R, Witt SH. Multi-omics signatures of alcohol use disorder in the dorsal and ventral striatum. Transl Psychiatry 2022; 12:190. [PMID: 35523767 PMCID: PMC9076849 DOI: 10.1038/s41398-022-01959-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Alcohol Use Disorder (AUD) is a major contributor to global mortality and morbidity. Postmortem human brain tissue enables the investigation of molecular mechanisms of AUD in the neurocircuitry of addiction. We aimed to identify differentially expressed (DE) genes in the ventral and dorsal striatum between individuals with AUD and controls, and to integrate the results with findings from genome- and epigenome-wide association studies (GWAS/EWAS) to identify functionally relevant molecular mechanisms of AUD. DNA-methylation and gene expression (RNA-seq) data was generated from postmortem brain samples of 48 individuals with AUD and 51 controls from the ventral striatum (VS) and the dorsal striatal regions caudate nucleus (CN) and putamen (PUT). We identified DE genes using DESeq2, performed gene-set enrichment analysis (GSEA), and tested enrichment of DE genes in results of GWASs using MAGMA. Weighted correlation network analysis (WGCNA) was performed for DNA-methylation and gene expression data and gene overlap was tested. Differential gene expression was observed in the dorsal (FDR < 0.05), but not the ventral striatum of AUD cases. In the VS, DE genes at FDR < 0.25 were overrepresented in a recent GWAS of problematic alcohol use. The ARHGEF15 gene was upregulated in all three brain regions. GSEA in CN and VS pointed towards cell-structure associated GO-terms and in PUT towards immune pathways. The WGCNA modules most strongly associated with AUD showed strong enrichment for immune response and inflammation pathways. Our integrated analysis of multi-omics data sets provides further evidence for the importance of immune- and inflammation-related processes in AUD.
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Affiliation(s)
- Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eric Poisel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jerome C Foo
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marion M Friske
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Department of Biomedicine, University of Basel, Basel, 4003, Switzerland
| | - Franziska Degenhardt
- Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anita C Hansson
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rainer Spanagel
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Innovative Psychiatric and Psychotherapeutic Research, Biobank, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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22
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Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, Chen H. GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships. G3 (BETHESDA, MD.) 2022; 12:jkac059. [PMID: 35285473 PMCID: PMC9073678 DOI: 10.1093/g3journal/jkac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022]
Abstract
Interpreting and integrating results from omics studies typically requires a comprehensive and time consuming survey of extant literature. GeneCup is a literature mining web service that retrieves sentences containing user-provided gene symbols and keywords from PubMed abstracts. The keywords are organized into an ontology and can be extended to include results from human genome-wide association studies. We provide a drug addiction keyword ontology that contains over 300 keywords as an example. The literature search is conducted by querying the PubMed server using a programming interface, which is followed by retrieving abstracts from a local copy of the PubMed archive. The main results presented to the user are sentences where gene symbol and keywords co-occur. These sentences are presented through an interactive graphical interface or as tables. All results are linked to the original abstract in PubMed. In addition, a convolutional neural network is employed to distinguish sentences describing systemic stress from those describing cellular stress. The automated and comprehensive search strategy provided by GeneCup facilitates the integration of new discoveries from omic studies with existing literature. GeneCup is free and open source software. The source code of GeneCup and the link to a running instance is available at https://github.com/hakangunturkun/GeneCup.
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Affiliation(s)
- Mustafa H Gunturkun
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Efraim Flashner
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Megan K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science, Memphis, TN 38103, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science, Memphis, TN 38103, USA
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23
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Ramos‐Mucci L, Sarmiento P, Little D, Snelling S. Research perspectives-Pipelines to human tendon transcriptomics. J Orthop Res 2022; 40:993-1005. [PMID: 35239195 PMCID: PMC9007907 DOI: 10.1002/jor.25315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023]
Abstract
Tendon transcriptomics is a rapidly growing field in musculoskeletal biology. The ultimate aim of many current tendon transcriptomic studies is characterization of in vitro, ex vivo, or in vivo, healthy, and diseased tendon microenvironments to identify the underlying pathways driving human tendon pathology. The transcriptome interfaces between genomic, proteomic, and metabolomic signatures of the tendon cellular niche and the response of this niche to stimuli. Some of the greatest bottlenecks in tendon transcriptomics relate to the availability and quality of human tendon tissue, hence animal tissues are frequently used even though human tissue is most translationally relevant. Here, we review the variability associated with human donor and procurement factors, such as whether the tendon is cadaveric or a clinical remnant, and how these variables affect the quality and relevance of the transcriptomes obtained. Moreover, age, sex, and health demographic variables impact the human tendon transcriptome. Tendons present tissue-specific challenges for cell, nuclei, and RNA extraction that include a dense extracellular matrix, low cellularity, and therefore low RNA yield of variable quality. Consideration of these factors is particularly important for single-cell and single-nuclei resolution transcriptomics due to the necessity for unbiased and representative cell or nuclei populations. Different cell, nuclei, and RNA extraction methods, library preparation, and quality control methods are used by the tendon research community and attention should be paid to these when designing and reporting studies. We discuss the different components and challenges of human tendon transcriptomics, and propose pipelines, quality control, and reporting guidelines for future work in the field.
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Affiliation(s)
- Lorenzo Ramos‐Mucci
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal ScienceUniversity of OxfordOxfordUK
| | - Paula Sarmiento
- Department of Biomedical EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Dianne Little
- Department of Biomedical EngineeringPurdue UniversityWest LafayetteIndianaUSA,Department of Basic Medical SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Sarah Snelling
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal ScienceUniversity of OxfordOxfordUK
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24
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Chen YP, Ferguson LB, Salem NA, Zheng G, Mayfield RD, Eslami M. RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST). Bioinformatics 2022; 38:397-403. [PMID: 34570193 PMCID: PMC8723147 DOI: 10.1093/bioinformatics/btab673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Transcriptomics is a common approach to identify changes in gene expression induced by a disease state. Standard transcriptomic analyses consider differentially expressed genes (DEGs) as indicative of disease states so only a few genes would be treated as signals when the effect size is small, such as in brain tissue. For tissue with small effect sizes, if the DEGs do not belong to a pathway known to be involved in the disease, there would be little left in the transcriptome for researchers to follow up with. RESULTS We developed RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST), a new approach to identify hidden signals in transcriptomic data by linking differential expression and co-expression networks using machine learning. We applied our approach to RNA-seq data of post-mortem brains that compared the Alcohol Use Disorder (AUD) group with the control group. Many of the candidate genes are not differentially expressed so would likely be ignored by standard transcriptomic analysis pipelines. Through multiple validation strategies, we concluded that these RNASSIST-identified genes likely play a significant role in AUD. AVAILABILITY AND IMPLEMENTATION The RNASSIST algorithm is available at https://github.com/netrias/rnassist and both the software and the data used in RNASSIST are available at https://figshare.com/articles/software/RNAssist_Software_and_Data/16617250. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Laura B Ferguson
- Department of Neuroscience, The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nihal A Salem
- Department of Neuroscience, The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - R Dayne Mayfield
- Department of Neuroscience, The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA
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25
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Vornholt E, Drake J, Mamdani M, McMichael G, Taylor ZN, Bacanu S, Miles MF, Vladimirov VI. Identifying a novel biological mechanism for alcohol addiction associated with circRNA networks acting as potential miRNA sponges. Addict Biol 2021; 26:e13071. [PMID: 34164896 PMCID: PMC8590811 DOI: 10.1111/adb.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/21/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022]
Abstract
Our lab and others have shown that chronic alcohol use leads to gene and miRNA expression changes across the mesocorticolimbic (MCL) system. Circular RNAs (circRNAs) are noncoding RNAs that form closed-loop structures and are reported to alter gene expression through miRNA sequestration, thus providing a potentially novel neurobiological mechanism for the development of alcohol dependence (AD). Genome-wide expression of circRNA was assessed in the nucleus accumbens (NAc) from 32 AD-matched cases/controls. Significant circRNAs (unadj. p ≤ 0.05) were identified via regression and clustered in circRNA networks via weighted gene co-expression network analysis (WGCNA). CircRNA interactions with previously generated mRNA and miRNA were detected via correlation and bioinformatic analyses. Significant circRNAs (N = 542) clustered in nine significant AD modules (FWER p ≤ 0.05), within which we identified 137 circRNA hubs. We detected 23 significant circRNA-miRNA-mRNA interactions (FDR ≤ 0.10). Among these, circRNA-406742 and miR-1200 significantly interact with the highest number of mRNA, including genes associated with neuronal functioning and alcohol addiction (HRAS, PRKCB, HOMER1, and PCLO). Finally, we integrate genotypic information that revealed 96 significant circRNA expression quantitative trait loci (eQTLs) (unadj. p ≤ 0.002) that showed significant enrichment within recent alcohol use disorder (AUD) and smoking genome-wide association study (GWAS). To our knowledge, this is the first study to examine the role of circRNA in the neuropathology of AD. We show that circRNAs impact mRNA expression by interacting with miRNA in the NAc of AD subjects. More importantly, we provide indirect evidence for the clinical importance of circRNA in the development of AUD by detecting a significant enrichment of our circRNA eQTLs among GWAS of substance abuse.
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Affiliation(s)
- Eric Vornholt
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Integrative Life Sciences Doctoral ProgramVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - John Drake
- Department of Psychiatry and Behavioral SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Gowon McMichael
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Zachary N. Taylor
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Silviu‐Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- VCU‐Alcohol Research CenterVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Pharmacology and ToxicologyVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of NeurologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Center for Biomarker Research and Precision MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Physiology & BiophysicsVirginia Commonwealth UniversityRichmondVirginiaUSA
- School of PharmacyVirginia Commonwealth UniversityRichmondVirginiaUSA
- Lieber Institute for Brain DevelopmentJohns Hopkins UniversityBaltimoreMarylandUSA
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26
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Lim Y, Beane-Ebel JE, Tanaka Y, Ning B, Husted CR, Henderson DC, Xiang Y, Park IH, Farrer LA, Zhang H. Exploration of alcohol use disorder-associated brain miRNA-mRNA regulatory networks. Transl Psychiatry 2021; 11:504. [PMID: 34601489 PMCID: PMC8487426 DOI: 10.1038/s41398-021-01635-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Transcriptomic changes in specific brain regions can influence the risk of alcohol use disorder (AUD), but the underlying mechanism is not fully understood. We investigated AUD-associated miRNA-mRNA regulatory networks in multiple brain regions by analyzing transcriptomic changes in two sets of postmortem brain tissue samples and ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons. miRNA and mRNA transcriptomes were profiled in 192 tissue samples (Set 1) from eight brain regions (amygdala, caudate nucleus, cerebellum, hippocampus, nucleus accumbens, prefrontal cortex, putamen, and ventral tegmental area) of 12 AUD and 12 control European Australians. Nineteen differentially expressed miRNAs (fold-change>2.0 & P < 0.05) and 97 differentially expressed mRNAs (fold-change>2.0 & P < 0.001) were identified in one or multiple brain regions of AUD subjects. AUD-associated miRNA-mRNA regulatory networks in each brain region were constructed using differentially expressed and negatively correlated miRNA-mRNA pairs. AUD-relevant pathways (including CREB Signaling, IL-8 Signaling, and Axonal Guidance Signaling) were potentially regulated by AUD-associated brain miRNA-mRNA pairs. Moreover, miRNA and mRNA transcriptomes were mapped in additional 96 tissue samples (Set 2) from six of the above eight brain regions of eight AUD and eight control European Australians. Some of the AUD-associated miRNA-mRNA regulatory networks were confirmed. In addition, miRNA and mRNA transcriptomes were analyzed in hESC-derived cortical interneurons with or without ethanol exposure, and ethanol-influenced miRNA-mRNA regulatory networks were constructed. This study provided evidence that alcohol could induce concerted miRNA and mRNA expression changes in reward-related or alcohol-responsive brain regions. We concluded that altered brain miRNA-mRNA regulatory networks might contribute to AUD development.
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Affiliation(s)
- Yolpanhchana Lim
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- The Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, MA, USA
| | - Jennifer E Beane-Ebel
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Center, University of Montreal, Montreal, QC, H1T 2M4, Canada
| | - Boting Ning
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Christopher R Husted
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David C Henderson
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Yangfei Xiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - In-Hyun Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lindsay A Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston, MA, USA
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA.
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, MA, USA.
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Abstract
Substance use disorders (SUDs) are prevalent and result in an array of negative consequences. They are influenced by genetic factors (h2 = ~50%). Recent years have brought substantial progress in our understanding of the genetic etiology of SUDs and related traits. The present review covers the current state of the field for SUD genetics, including the epidemiology and genetic epidemiology of SUDs, findings from the first-generation of SUD genome-wide association studies (GWAS), cautions about translating GWAS findings to clinical settings, and suggested prioritizations for the next wave of SUD genetics efforts. Recent advances in SUD genetics have been facilitated by the assembly of large GWAS samples, and the development of state-of-the-art methods modeling the aggregate effect of genome-wide variation. These advances have confirmed that SUDs are highly polygenic with many variants across the genome conferring risk, the vast majority of which are of small effect. Downstream analyses have enabled finer resolution of the genetic architecture of SUDs and revealed insights into their genetic relationship with other psychiatric disorders. Recent efforts have also prioritized a closer examination of GWAS findings that have suggested non-uniform genetic influences across measures of substance use (e.g. consumption) and problematic use (e.g. SUD). Additional highlights from recent SUD GWAS include the robust confirmation of loci in alcohol metabolizing genes (e.g. ADH1B and ALDH2) affecting alcohol-related traits, and loci within the CHRNA5-CHRNA3-CHRNB4 gene cluster influencing nicotine-related traits. Similar successes are expected for cannabis, opioid, and cocaine use disorders as sample sizes approach those assembled for alcohol and nicotine.
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Affiliation(s)
- Joseph D. Deak
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Emma C. Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
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Kapoor M, Chao MJ, Johnson EC, Novikova G, Lai D, Meyers JL, Schulman J, Nurnberger JI, Porjesz B, Liu Y, Foroud T, Edenberg HJ, Marcora E, Agrawal A, Goate A. Multi-omics integration analysis identifies novel genes for alcoholism with potential overlap with neurodegenerative diseases. Nat Commun 2021; 12:5071. [PMID: 34417470 PMCID: PMC8379159 DOI: 10.1038/s41467-021-25392-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/03/2021] [Indexed: 11/27/2022] Open
Abstract
Identification of causal variants and genes underlying genome-wide association study (GWAS) loci is essential to understand the biology of alcohol use disorder (AUD) and drinks per week (DPW). Multi-omics integration approaches have shown potential for fine mapping complex loci to obtain biological insights to disease mechanisms. In this study, we use multi-omics approaches, to fine-map AUD and DPW associations at single SNP resolution to demonstrate that rs56030824 on chromosome 11 significantly reduces SPI1 mRNA expression in myeloid cells and lowers risk for AUD and DPW. Our analysis also identifies MAPT as a candidate causal gene specifically associated with DPW. Genes prioritized in this study show overlap with causal genes associated with neurodegenerative disorders. Multi-omics integration analyses highlight, genetic similarities and differences between alcohol intake and disordered drinking, suggesting molecular heterogeneity that might inform future targeted functional and cross-species studies.
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Affiliation(s)
- Manav Kapoor
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Michael J Chao
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Gloriia Novikova
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Jessica Schulman
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernice Porjesz
- Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edoardo Marcora
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison Goate
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models. Genes (Basel) 2021; 12:1101. [PMID: 34356117 PMCID: PMC8304351 DOI: 10.3390/genes12071101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.
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Affiliation(s)
- Yanning Zuo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Don Wei
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carissa Zhu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Ormina Naveed
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Weizhe Hong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
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30
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10-Dehydrogingerdione ameliorates renal endoplasmic reticulum/oxidative stress and apoptosis in alcoholic nephropathy induced in experimental rats. Life Sci 2021; 279:119673. [PMID: 34081991 DOI: 10.1016/j.lfs.2021.119673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Chronic alcoholism induces kidney injury (KI), leading to increased mortality in alcoholic hepatitis patients. Endoplasmic reticulum stress (ER) represents the main initiator of kidney diseases and alcoholic nephropathy. AIMS We used alcoholic nephropathy rat model followed by 10-dehydrogingerdione (10-DHGD) intake as potential modulator. This is to focus on ER/oxidative stress/inflammatory and apoptotic pathways involvement. MAIN METHOD Alcoholic nephropathy was induced by alcohol administration (3.7 g/kg/body weight) orally and daily for 45 days. 10-DHGD (10 mg/kg/day) was administered either alone or along with alcohol. KEY FINDINGS Our results demonstrated significant increase in kidney function parameters like f creatinine, urea, uric acid, and blood urea nitrogen (BUN) levels. Renal ER/oxidative stress markers such as cytochrome P450 family two subfamily E member 1 (CYP2E1), C/EBP homologous protein (CHOP), and endoplasmic glucose-regulated protein 78 (GRP-78) demonstrated also significant increase. Inflammatory mediators like nuclear factor-kappa B (NF-kB), tumor necrosis factor-α (TNF-α), and transforming growth factor-β (TGF-β along with apoptotic marker caspase-3 behaved similarly. Antioxidant molecules like reduced glutathione (GSH), superoxide dismutase (SOD), and catalase demonstrated marked decrease. SIGNIFICANCE 10-DHGD administration resulted in significant modulation represented by an enhancement in the kidney functions and the histopathological patterns in a conclusion of its potential to ameliorate the pathological changes (kidney injury) induced by alcohol intake.
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31
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Cabrera-Mendoza B, Martínez-Magaña JJ, Monroy-Jaramillo N, Genis-Mendoza AD, Fresno C, Fries GR, Walss-Bass C, López Armenta M, García-Dolores F, Díaz-Otañez CE, Flores G, Vázquez-Roque RA, Nicolini H. Candidate pharmacological treatments for substance use disorder and suicide identified by gene co-expression network-based drug repositioning. Am J Med Genet B Neuropsychiatr Genet 2021; 186:193-206. [PMID: 33403748 DOI: 10.1002/ajmg.b.32830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 10/30/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
Patients with substance use disorders (SUD) are at high risk to die by suicide. So far, the neurobiology of the suicide-SUD association has not been elucidated. This study aimed to identify potential pharmacological targets among hub genes from brain gene co-expression networks of individuals with SUD in a suicidal and non-suicidal context. Post-mortem samples from the prefrontal cortex of 79 individuals were analyzed. Individuals were classified into the following groups: suicides with SUD (n = 28), suicides without SUD (n = 23), nonsuicides with SUD (n = 9), nonsuicides without SUD (n = 19). Gene expression profiles were evaluated with the Illumina HumanHT-12 v4 array. Co-expression networks were constructed in WGCNA using the differentially expressed genes found in the comparisons: (a) suicides with and without SUD and (b) nonsuicides with and without SUD. Hub genes were selected for drug-gene interaction testing in the DGIdb database. Among drugs interacting with hub genes in suicides we found MAOA inhibitors and dextromethorphan. In the nonsuicide individuals, we found interactions with eglumegad and antipsychotics (olanzapine, clozapine, loxapine). Modafinil was found to interact with genes in both suicides and nonsuicides. These drugs represent possible candidate treatments for patients with SUD with and without suicidal behavior and their study in each context is encouraged.
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Affiliation(s)
- Brenda Cabrera-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,PECEM, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - José Jaime Martínez-Magaña
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Multidisciplinary Academic Division of Comalcalco, Juárez Autonomous University of Tabasco, Comalcalco, Tabasco, Mexico
| | - Nancy Monroy-Jaramillo
- Department of Genetics, National Institute of Neurology and Neurosurgery, Mexico City, Mexico
| | - Alma Delia Genis-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Cristóbal Fresno
- Department of Technological Development, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Gabriel Rodrigo Fries
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Consuelo Walss-Bass
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | | | | | - Gonzalo Flores
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Rubén Antonio Vázquez-Roque
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
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Hade AC, Philips MA, Reimann E, Jagomäe T, Eskla KL, Traks T, Prans E, Kõks S, Vasar E, Väli M. Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. Brain Sci 2021; 11:435. [PMID: 33805312 PMCID: PMC8066746 DOI: 10.3390/brainsci11040435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The Mediodorsal (MD) thalamus that represents a fundamental subcortical relay has been underrepresented in the studies focusing on the molecular changes in the brains of subjects with alcohol use disorder (AUD). In the current study, MD thalamic regions from AUD subjects and controls were analyzed with Affymetrix Clariom S human microarray. Long-term alcohol use induced a significant (FDR ≤ 0.05) upregulation of 2802 transcripts and downregulation of 1893 genes in the MD thalamus of AUD subjects. A significant upregulation of GRIN1 (glutamate receptor NMDA type 1) and FTO (alpha-ketoglutarate dependent dioxygenase) was confirmed in western blot analysis. Immunohistochemical staining revealed similar heterogenous distribution of GRIN1 in the thalamic nuclei of both AUD and control subjects. The most prevalent functional categories of upregulated genes were related to glutamatergic and GABAergic neurotransmission, cellular metabolism, and neurodevelopment. The prevalent gene cluster among down-regulated genes was immune system mediators. Forty-two differentially expressed genes, including FTO, ADH1B, DRD2, CADM2, TCF4, GCKR, DPP6, MAPT and CHRH1, have been shown to have strong associations (FDR p < 10-8) with AUD or/and alcohol use phenotypes in recent GWA studies. Despite a small number of subjects, we were able to detect robust molecular changes in the mediodorsal thalamus caused by alcohol emphasizing the importance of deeper brain structures such as diencephalon, in the development of AUD-related dysregulation of neurocircuitry.
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Affiliation(s)
- Andreas-Christian Hade
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia;
| | - Toomas Jagomäe
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Tanel Traks
- Department of Dermatology and Venerology, Institute of Clinical Medicine, University of Tartu, 51010 Tartu, Estonia;
| | - Ele Prans
- Department of Anaesthesiology and Intensive Care, Tartu University Hospital, 50406 Tartu, Estonia;
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Marika Väli
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
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Warden AS, Triplett TA, Lyu A, Grantham EK, Azzam MM, DaCosta A, Mason S, Blednov YA, Ehrlich LI, Mayfield RD, Harris RA. Microglia depletion and alcohol: Transcriptome and behavioral profiles. Addict Biol 2021; 26:e12889. [PMID: 32176824 DOI: 10.1111/adb.12889] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/13/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022]
Abstract
Alcohol abuse induces changes in microglia morphology and immune function, but whether microglia initiate or simply amplify the harmful effects of alcohol exposure is still a matter of debate. Here, we determine microglia function in acute and voluntary drinking behaviors using a colony-stimulating factor 1 receptor inhibitor (PLX5622). We show that microglia depletion does not alter the sedative or hypnotic effects of acute intoxication. Microglia depletion also does not change the escalation or maintenance of chronic voluntary alcohol consumption. Transcriptomic analysis revealed that although many immune genes have been implicated in alcohol abuse, downregulation of microglia genes does not necessitate changes in alcohol intake. Instead, microglia depletion and chronic alcohol result in compensatory upregulation of alcohol-responsive, reactive astrocyte genes, indicating astrocytes may play a role in regulation of these alcohol behaviors. Taken together, our behavioral and transcriptional data indicate that microglia are not the primary effector cell responsible for regulation of acute and voluntary alcohol behaviors. Because microglia depletion did not regulate acute or voluntary alcohol behaviors, we hypothesized that these doses were insufficient to activate microglia and recruit them to an effector phenotype. Therefore, we used a model of repeated immune activation using polyinosinic:polycytidylic acid (poly(I:C)) to activate microglia. Microglia depletion blocked poly(I:C)-induced escalations in alcohol intake, indicating microglia regulate drinking behaviors with sufficient immune activation. By testing the functional role of microglia in alcohol behaviors, we provide insight into when microglia are causal and when they are consequential for the transition from alcohol use to dependence.
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Affiliation(s)
- Anna S. Warden
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
- Institute for Neuroscience University of Texas at Austin Austin TX USA
| | - Todd A. Triplett
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology The University of Texas at Austin Austin TX USA
- Department of Oncology University of Texas Dell Medical School, LiveSTRONG Cancer Institutes Austin TX USA
| | - Aram Lyu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology The University of Texas at Austin Austin TX USA
| | - Emily K. Grantham
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
- Institute for Neuroscience University of Texas at Austin Austin TX USA
| | - Moatasem M. Azzam
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
| | - Adriana DaCosta
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
| | - Sonia Mason
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
| | - Yuri A. Blednov
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
| | - Lauren I.R. Ehrlich
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology The University of Texas at Austin Austin TX USA
- Department of Oncology University of Texas Dell Medical School, LiveSTRONG Cancer Institutes Austin TX USA
| | - R. Dayne Mayfield
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
- Institute for Neuroscience University of Texas at Austin Austin TX USA
| | - R. Adron Harris
- Waggoner Center for Alcoholism and Addiction Research University of Texas at Austin Austin TX USA
- Institute for Neuroscience University of Texas at Austin Austin TX USA
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34
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De Carvalho LM, Wiers CE, Sun H, Wang G, Volkow ND. Increased transcription of TSPO, HDAC2, and HDAC6 in the amygdala of males with alcohol use disorder. Brain Behav 2021; 11:e01961. [PMID: 33216461 PMCID: PMC7882159 DOI: 10.1002/brb3.1961] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Repeated exposure to high doses of alcohol triggers neuroinflammatory processes that contribute to craving and mood dysfunction in alcohol use disorder (AUD). The upregulation of the translocator protein (TSPO) is considered a biomarker of neuroinflammation, and TSPO ligands have been used as neuroimaging biomarkers of neuroinflammation. Epigenetic mechanisms are also implicated in neuroinflammatory responses to alcohol, and elevated expression of HDAC2 and HDAC6 has been reported in the brain of animals exposed to chronic alcohol. METHODS The present study examined the transcriptional regulation of TSPO, HDAC2, and HDAC6 in human postmortem brain tissue from males previously diagnosed with AUD (n = 11) compared to age-matched nondependent males (n = 13) in four brain regions relevant to AUD: prefrontal cortex (PFC), nucleus accumbens (NAc), hippocampus (HPP), and amygdala (AMY). RESULTS Translocator protein mRNA levels in AMY and PFC and HDAC2 and HDAC6 mRNA levels in AMY were upregulated in AUD compared to controls. In AMY, TSPO mRNA levels were positively associated with HDAC2 and HDAC6 mRNA levels, suggesting a possible regulation of TSPO by HDAC2 and HDAC6 in this brain region. In contrast, there were no group differences for TSPO, HDAC2, and HDAC6 in NAc and HPP. CONCLUSION Our study is the first to find upregulated TSPO mRNA levels in AMY and PFC in postmortem brains from AUD consistent with neuroinflammation, and in the amygdala, they implicate epigenetic regulation of TSPO by HDAC2 and HDAC6.
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Affiliation(s)
- Luana Martins De Carvalho
- National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
- Center for Alcohol Research in Epigenetics, Department of PsychiatryUniversity of Illinois at ChicagoChicagoILUSA
| | - Corinde E. Wiers
- National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
- Department of PsychiatryPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Hui Sun
- National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
| | - Gene‐Jack Wang
- National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
| | - Nora D. Volkow
- National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
- National Institute on Drug AbuseNational Institutes of HealthRockvilleMDUSA
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Cortical astrocytes regulate ethanol consumption and intoxication in mice. Neuropsychopharmacology 2021; 46:500-508. [PMID: 32464636 PMCID: PMC8027025 DOI: 10.1038/s41386-020-0721-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Astrocytes are fundamental building blocks of the central nervous system. Their dysfunction has been implicated in many psychiatric disorders, including alcohol use disorder, yet our understanding of their functional role in ethanol intoxication and consumption is very limited. Astrocytes regulate behavior through multiple intracellular signaling pathways, including G-protein coupled-receptor (GPCR)-mediated calcium signals. To test the hypothesis that GPCR-induced calcium signaling is also involved in the behavioral effects of ethanol, we expressed astrocyte-specific excitatory DREADDs in the prefrontal cortex (PFC) of mice. Activating Gq-GPCR signaling in PFC astrocytes increased drinking in ethanol-naïve mice, but not in mice with a history of ethanol drinking. In contrast, reducing calcium signaling with an astrocyte-specific calcium extruder reduced ethanol intake. Cortical astrocyte calcium signaling also altered the acute stimulatory and sedative-hypnotic effects of ethanol. Astrocyte-specific Gq-DREADD activation increased both the locomotor-activating effects of low dose ethanol and the sedative-hypnotic effects of a high dose, while reduced astrocyte calcium signaling diminished sensitivity to the hypnotic effects. In addition, we found that adenosine A1 receptors were required for astrocyte calcium activation to increase ethanol sedation. These results support integral roles for PFC astrocytes in the behavioral actions of ethanol that are due, at least in part, to adenosine receptor activation.
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García-Baos A, Alegre-Zurano L, Cantacorps L, Martín-Sánchez A, Valverde O. Role of cannabinoids in alcohol-induced neuroinflammation. Prog Neuropsychopharmacol Biol Psychiatry 2021; 104:110054. [PMID: 32758518 DOI: 10.1016/j.pnpbp.2020.110054] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
Alcohol is a psychoactive substance highly used worldwide, whose harmful use might cause a broad range of mental and behavioural disorders. Underlying brain impact, the neuroinflammatory response induced by alcohol is recognised as a key contributing factor in the progression of other neuropathological processes, such as neurodegeneration. These sequels are determined by multiple factors, including age of exposure. Strikingly, it seems that the endocannabinoid system modulation could regulate the alcohol-induced neuroinflammation. Although direct CB1 activation can worsen alcohol consequences, targeting other components of the expanded endocannabinoid system may counterbalance the pro-inflammatory response. Indeed, specific modulations of the expanded endocannabinoid system have been proved to exert anti-inflammatory effects, primarily through the CB2 and PPARγ signalling. Among them, some endo- and exogeneous cannabinoids can block certain pro-inflammatory mediators, such as NF-κB, thereby neutralizing the neuroinflammatory intracellular cascades. Furthermore, a number of cannabinoids are able to activate complementary anti-inflammatory pathways, which are necessary for the transition from chronically overactivated microglia to a regenerative microglial phenotype. Thus, cannabinoid modulation provides cooperative anti-inflammatory mechanisms that may be advantageous to resolve a pathological neuroinflammation in an alcohol-dependent context.
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Affiliation(s)
- Alba García-Baos
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laia Alegre-Zurano
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lídia Cantacorps
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Martín-Sánchez
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Neuroscience Research Programme, IMIM-Hospital del Mar Research Institute, Barcelona, Spain
| | - Olga Valverde
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Neuroscience Research Programme, IMIM-Hospital del Mar Research Institute, Barcelona, Spain.
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Alcohol use disorder causes global changes in splicing in the human brain. Transl Psychiatry 2021; 11:2. [PMID: 33414398 PMCID: PMC7790816 DOI: 10.1038/s41398-020-01163-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/11/2023] Open
Abstract
Alcohol use disorder (AUD) is a widespread disease leading to the deterioration of cognitive and other functions. Mechanisms by which alcohol affects the brain are not fully elucidated. Splicing constitutes a nuclear process of RNA maturation, which results in the formation of the transcriptome. We tested the hypothesis as to whether AUD impairs splicing in the superior frontal cortex (SFC), nucleus accumbens (NA), basolateral amygdala (BLA), and central nucleus of the amygdala (CNA). To evaluate splicing, bam files from STAR alignments were indexed with samtools for use by rMATS software. Computational analysis of affected pathways was performed using Gene Ontology Consortium, Gene Set Enrichment Analysis, and LncRNA Ontology databases. Surprisingly, AUD was associated with limited changes in the transcriptome: expression of 23 genes was altered in SFC, 14 in NA, 102 in BLA, and 57 in CNA. However, strikingly, mis-splicing in AUD was profound: 1421 mis-splicing events were detected in SFC, 394 in NA, 1317 in BLA, and 469 in CNA. To determine the mechanism of mis-splicing, we analyzed the elements of the spliceosome: small nuclear RNAs (snRNAs) and splicing factors. While snRNAs were not affected by alcohol, expression of splicing factor heat shock protein family A (Hsp70) member 6 (HSPA6) was drastically increased in SFC, BLA, and CNA. Also, AUD was accompanied by aberrant expression of long noncoding RNAs (lncRNAs) related to splicing. In summary, alcohol is associated with genome-wide changes in splicing in multiple human brain regions, likely due to dysregulation of splicing factor(s) and/or altered expression of splicing-related lncRNAs.
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Warden AS, Wolfe SA, Khom S, Varodayan FP, Patel RR, Steinman MQ, Bajo M, Montgomery SE, Vlkolinsky R, Nadav T, Polis I, Roberts AJ, Mayfield RD, Harris RA, Roberto M. Microglia Control Escalation of Drinking in Alcohol-Dependent Mice: Genomic and Synaptic Drivers. Biol Psychiatry 2020; 88:910-921. [PMID: 32680583 PMCID: PMC7674270 DOI: 10.1016/j.biopsych.2020.05.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Microglia, the primary immune cells of the brain, are implicated in alcohol use disorder. However, it is not known if microglial activation contributes to the transition from alcohol use to alcohol use disorder or is a consequence of alcohol intake. METHODS We investigated the role of microglia in a mouse model of alcohol dependence using a colony stimulating factor 1 receptor inhibitor (PLX5622) to deplete microglia and a chronic intermittent ethanol vapor two-bottle choice drinking procedure. Additionally, we examined anxiety-like behavior during withdrawal. We then analyzed synaptic neuroadaptations in the central nucleus of the amygdala (CeA) and gene expression changes in the medial prefrontal cortex and CeA from the same animals used for behavioral studies. RESULTS PLX5622 prevented escalations in voluntary alcohol intake and decreased anxiety-like behavior associated with alcohol dependence. PLX5622 also reversed expression changes in inflammatory-related genes and glutamatergic and GABAergic (gamma-aminobutyric acidergic) genes in the medial prefrontal cortex and CeA. At the cellular level in these animals, microglia depletion reduced inhibitory GABAA and excitatory glutamate receptor-mediated synaptic transmission in the CeA, supporting the hypothesis that microglia regulate dependence-induced changes in neuronal function. CONCLUSIONS Our multifaceted approach is the first to link microglia to the molecular, cellular, and behavioral changes associated with the development of alcohol dependence, suggesting that microglia may also be critical for the development and progression of alcohol use disorder.
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Affiliation(s)
- Anna S Warden
- Waggoner Center for Alcoholism and Addiction Research, University of Texas at Austin, Austin, Texas; Institute for Neuroscience, University of Texas at Austin, Austin, Texas
| | - Sarah A Wolfe
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Sophia Khom
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Florence P Varodayan
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Reesha R Patel
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Michael Q Steinman
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Michal Bajo
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Sarah E Montgomery
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Roman Vlkolinsky
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Tali Nadav
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Ilham Polis
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Amanda J Roberts
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California
| | - R Dayne Mayfield
- Waggoner Center for Alcoholism and Addiction Research, University of Texas at Austin, Austin, Texas; Institute for Neuroscience, University of Texas at Austin, Austin, Texas
| | - R Adron Harris
- Waggoner Center for Alcoholism and Addiction Research, University of Texas at Austin, Austin, Texas; Institute for Neuroscience, University of Texas at Austin, Austin, Texas
| | - Marisa Roberto
- Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, California.
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Portis SM, Haass-Koffler CL. New Microglial Mechanisms Revealed in Alcohol Use Disorder: How Does That Translate? Biol Psychiatry 2020; 88:893-895. [PMID: 33213701 PMCID: PMC7909747 DOI: 10.1016/j.biopsych.2020.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Samantha M. Portis
- Center for Alcohol and Addiction Studies, Brown University, Providence, RI, USA,Department of Behavioral and Social Sciences, School of Public Health, Brown University, Providence, RI, USA
| | - Carolina L. Haass-Koffler
- Center for Alcohol and Addiction Studies, Brown University, Providence, RI, USA,Department of Behavioral and Social Sciences, School of Public Health, Brown University, Providence, RI, USA,Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA,Corresponding Author: Carolina L. Haass-Koffler, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Center for Alcohol and Addiction Studies, Brown University, 121 S Main Street, Providence, RI 02903, Cell: 415-519-1385,
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Drake J, McMichael GO, Vornholt ES, Cresswell K, Williamson V, Chatzinakos C, Mamdani M, Hariharan S, Kendler KS, Kalsi G, Riley BP, Dozmorov M, Miles MF, Bacanu S, Vladimirov VI. Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence. Alcohol Clin Exp Res 2020; 44:2468-2480. [PMID: 33067813 PMCID: PMC7756309 DOI: 10.1111/acer.14479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Long noncoding RNA (lncRNA) have been implicated in the etiology of alcohol use. Since lncRNA provide another layer of complexity to the transcriptome, assessing their expression in the brain is the first critical step toward understanding lncRNA functions in alcohol use and addiction. Thus, we sought to profile lncRNA expression in the nucleus accumbens (NAc) in a large postmortem alcohol brain sample. METHODS LncRNA and protein-coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL). RESULTS At Bonferroni adj. p-value ≤ 0.05, we identified 19 lncRNA and 5 PCG significant modules, which were enriched for neuronal and immune-related processes. In these modules, we further identified 86 and 315 PCG and lncRNA hubs, respectively. At false discovery rate (FDR) of 10%, the correlation analyses between the lncRNA and PCG hubs revealed 3,125 positive and 1,860 negative correlations. Integration of hubs with genotype data identified 243 eQTLs affecting the expression of 39 and 204 PCG and lncRNA hubs, respectively. CONCLUSIONS Our study identified lncRNA and gene networks significantly associated with AD in the NAc, coordinated lncRNA and mRNA coexpression changes, highlighting potentially regulatory functions for the lncRNA, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
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Affiliation(s)
- John Drake
- From the Center for Integrative Life Sciences Education (JD)Virginia Commonwealth UniversityRichmondVirginia
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Eric Sean Vornholt
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Kellen Cresswell
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Vernell Williamson
- Department of Pathology(VW)Virginia Commonwealth UniversityRichmondVirginia
| | - Chris Chatzinakos
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Siddharth Hariharan
- Summer Research Fellowship(SH)School of MedicineVirginia Commonwealth UniversityRichmondVirginia
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry(GK)Institute of PsychiatryLondonUK
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Mikhail Dozmorov
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Pharmacology and Toxicology(MFM)Virginia Commonwealth UniversityRichmondVirginia
| | - Silviu‐Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Center for Biomarker Research and Personalized Medicine(VIV)Virginia Commonwealth UniversityRichmondVirginia
- Lieber Institute for Brain Development(VIV)Johns Hopkins UniversityBaltimoreMaryland
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Hippocampal metabolite concentrations in schizophrenia vary in association with rare gene variants in the TRIO gene. Schizophr Res 2020; 224:167-169. [PMID: 33183947 DOI: 10.1016/j.schres.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/23/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
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Casanova Ferrer F, Pascual M, Hidalgo MR, Malmierca-Merlo P, Guerri C, García-García F. Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. Genes (Basel) 2020; 11:E1106. [PMID: 32967293 PMCID: PMC7564639 DOI: 10.3390/genes11091106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
The abuse of alcohol, one of the most popular psychoactive substances, can cause several pathological and psychological consequences, including alcohol use disorder (AUD). An impaired ability to stop or control alcohol intake despite adverse health or social consequences characterize AUD. While AUDs predominantly occur in men, growing evidence suggests the existence of distinct cognitive and biological consequences of alcohol dependence in women. The molecular and physiological mechanisms participating in these differential effects remain unknown. Transcriptomic technology permits the detection of the biological mechanisms responsible for such sex-based differences, which supports the subsequent development of novel personalized therapeutics to treat AUD. We conducted a systematic review and meta-analysis of transcriptomics studies regarding alcohol dependence in humans with representation from both sexes. For each study, we processed and analyzed transcriptomic data to obtain a functional profile of pathways and biological functions and then integrated the resulting data by meta-analysis to characterize any sex-based transcriptomic differences associated with AUD. Global results of the transcriptomic analysis revealed the association of decreased tissue regeneration, embryo malformations, altered intracellular transport, and increased rate of RNA and protein replacement with female AUD patients. Meanwhile, our analysis indicated that increased inflammatory response and blood pressure and a reduction in DNA repair capabilities are associated with male AUD patients. In summary, our functional meta-analysis of transcriptomic studies provides evidence for differential biological mechanisms of AUD patients of differing sex.
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Affiliation(s)
- Franc Casanova Ferrer
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Hospital Clinico Research Foundation, INCLIVA, 46010 Valencia, Spain
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain;
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center (CIPF), 46012 Valencia, Spain;
| | - Marta R. Hidalgo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
| | - Pablo Malmierca-Merlo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Atos Research Innovation (ARI), 28037 Madrid, Spain
| | - Consuelo Guerri
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center (CIPF), 46012 Valencia, Spain;
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Spanish National Bioinformatics Institute, ELIXIR-Spain (INB, ELIXIR-ES), 46012 Valencia, Spain
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Huggett SB, Stallings MC. Genetic Architecture and Molecular Neuropathology of Human Cocaine Addiction. J Neurosci 2020; 40:5300-5313. [PMID: 32457073 PMCID: PMC7329314 DOI: 10.1523/jneurosci.2879-19.2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/12/2023] Open
Abstract
We integrated genomic and bioinformatic analyses, using data from the largest genome-wide association study of cocaine dependence (CD; n = 6546; 82.37% with CD; 57.39% male) and the largest postmortem gene-expression sample of individuals with cocaine use disorder (CUD; n = 36; 51.35% with CUD; 100% male). Our genome-wide analyses identified one novel gene (NDUFB9) associated with the genetic predisposition to CD in African-Americans. The genetic architecture of CD was similar across ancestries. Individual genes associated with CD demonstrated modest overlap across European-Americans and African-Americans, but the genetic liability for CD converged on many similar tissue types (brain, heart, blood, liver) across ancestries. In a separate sample, we investigated the neuronal gene expression associated with CUD by using RNA sequencing of dorsal-lateral prefrontal cortex neurons. We identified 133 genes differentially expressed between CUD case patients and cocaine-free control subjects, including previously implicated candidates for cocaine use/addiction (FOSB, ARC, KCNJ9/GIRK3, NR4A2, JUNB, and MECP2). Differential expression analyses significantly correlated across European-Americans and African-Americans. While genes significantly associated with CD via genome-wide methods were not differentially expressed, two of these genes (NDUFB9 and C1qL2) were part of a robust gene coexpression network associated with CUD involved in neurotransmission (GABA, acetylcholine, serotonin, and dopamine) and drug addiction. We then used a "guilt-by-association" approach to unravel the biological relevance of NDUFB9 and C1qL2 in the context of CD. In sum, our study furthers the understanding of the genetic architecture and molecular neuropathology of human cocaine addiction and provides a framework for translating biological meaning into otherwise obscure genome-wide associations.SIGNIFICANCE STATEMENT Our study further clarifies the genetic and neurobiological contributions to cocaine addiction, provides a rapid approach for generating testable hypotheses for specific candidates identified by genome-wide research, and investigates the cross-ancestral biological contributions to cocaine use disorder/dependence for individuals of European-American and African-American ancestries.
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Affiliation(s)
- Spencer B Huggett
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado 80309-0345
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309-0447
| | - Michael C Stallings
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado 80309-0345
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado 80309-0447
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Johnson EC, Chang Y, Agrawal A. An update on the role of common genetic variation underlying substance use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:35-46. [PMID: 33457110 PMCID: PMC7810203 DOI: 10.1007/s40142-020-00184-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF THE REVIEW Sample size increases have resulted in novel and replicable loci for substance use disorders (SUDs). We summarize some of the latest insights into SUD genetics and discuss some next steps in addiction genetics. RECENT FINDINGS Genome-wide association studies have substantiated the role of previously known variants (e.g., rs1229984 in ADH1B for alcohol) and identified several novel loci for alcohol, tobacco, cannabis, opioid and cocaine use disorders. SUDs are genetically correlated with psychiatric outcomes, while liability to substance use is inconsistently associated with these outcomes and more closely associated with lifestyle factors. Specific variant associations appear to differ somewhat across populations, although similar genes and systems are implicated. SUMMARY The next decade of human genetic studies of addiction should focus on expanding to non-European populations, consider pleiotropy across SUD and with other psychiatric disorders, and leverage human and cross-species functional data to elucidate the biological mechanisms underlying SUDs.
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Affiliation(s)
- Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
| | - Yoonhoo Chang
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO
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Gupta I, Dandavate R, Gupta P, Agrawal V, Kapoor M. Recent advances in genetic studies of alcohol use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:27-34. [PMID: 33344068 PMCID: PMC7748121 DOI: 10.1007/s40142-020-00185-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Alcohol use disorder (AUD) is a complex genetic disorder with very high heritability. This polygenic disorder not only results in increased morbidity and mortality, it is also a substantial social and economic burden on families and the nation. For past three decades, several genetic studies were conducted to identify genes and pathways associated with AUD. This review aims to summarize past efforts and recent advances in genetic association studies of AUD and related traits. RECENT FINDINGS Initial genetic association studies achieved a limted success and suffered from low power due to small sample sizes. AUD is a polygenic trait and data from several thousands individuals was required to identify the genetic factors of small effect sizes. The scenario changed recently with technological advances and significant reduction in cost of the genome wide association analyses (GWAS). This enabled researchers to generate genomic data on mega biobanks and cohorts with access to extensive clinical and non-clinical phenotypes. Public access to data from biobanks and collaborative efforts of researchers lead to identification of several novel loci associated with AUDs and related traits. Efforts are now underway to identify the causal variants under the GWAS loci to identify target genes and biological mechanisms underpining AUDs. Many GWAS variants occur in promoter or enhancer regions of the genes and are involved in regulation of gene expression of causal genes. This, large amounts of "omics" data from projects such as "ENCODE", RoadMap and GTEx is also helping researchers to integrate "multi-omics" data to interpret functional significance of GWAS variants. SUMMARY With current review, we aim to present the recent advances in genetic and molecular studies of AUDs. Recent successes in genetic studies of AUDs will definetely motivate researchers and lead to better therapeutic interventions for this complex disorder.
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Affiliation(s)
| | - Rohan Dandavate
- Indian Institute of Science Education and Research, Bhopal, India
| | - Pallavi Gupta
- Indian Institute of Science Education and Research, Bhopal, India
| | - Viplav Agrawal
- Indian Institute of Science Education and Research, Bhopal, India
| | - Manav Kapoor
- Icahn School of Medicine at Mount Sinai, New york, USA
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Brenner E, Tiwari GR, Kapoor M, Liu Y, Brock A, Mayfield RD. Single cell transcriptome profiling of the human alcohol-dependent brain. Hum Mol Genet 2020; 29:1144-1153. [PMID: 32142123 PMCID: PMC7206851 DOI: 10.1093/hmg/ddaa038] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Alcoholism remains a prevalent health concern throughout the world. Previous studies have identified transcriptomic patterns in the brain associated with alcohol dependence in both humans and animal models. But none of these studies have systematically investigated expression within the unique cell types present in the brain. We utilized single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of over 16 000 nuclei isolated from the prefrontal cortex of alcoholic and control individuals. Each nucleus was assigned to one of seven major cell types by unsupervised clustering. Cell type enrichment patterns varied greatly among neuroinflammatory-related genes, which are known to play roles in alcohol dependence and neurodegeneration. Differential expression analysis identified cell type-specific genes with altered expression in alcoholics. The largest number of differentially expressed genes (DEGs), including both protein-coding and non-coding, were detected in astrocytes, oligodendrocytes and microglia. To our knowledge, this is the first single cell transcriptome analysis of alcohol-associated gene expression in any species and the first such analysis in humans for any addictive substance. These findings greatly advance the understanding of transcriptomic changes in the brain of alcohol-dependent individuals.
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Affiliation(s)
- Eric Brenner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Gayatri R Tiwari
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA
- Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
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Farris SP, Tiwari GR, Ponomareva O, Lopez MF, Mayfield RD, Becker HC. Transcriptome Analysis of Alcohol Drinking in Non-Dependent and Dependent Mice Following Repeated Cycles of Forced Swim Stress Exposure. Brain Sci 2020; 10:brainsci10050275. [PMID: 32370184 PMCID: PMC7288165 DOI: 10.3390/brainsci10050275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/01/2023] Open
Abstract
Chronic stress is a known contributing factor to the development of drug and alcohol addiction. Animal models have previously shown that repeated forced swim stress promotes escalated alcohol consumption in dependent animals. To investigate the underlying molecular adaptations associated with stress and chronic alcohol exposure, RNA-sequencing and bioinformatics analyses were conducted on the prefrontal cortex (CTX) of male C57BL/6J mice that were behaviorally tested for either non-dependent alcohol consumption (CTL), chronic intermittent ethanol (CIE) vapor dependent alcohol consumption, repeated bouts of forced swim stress alone (FSS), and chronic intermittent ethanol with forced swim stress (CIE + FSS). Brain tissue from each group was collected at 0-h, 72-h, and 168-h following the final test to determine long-lasting molecular changes associated with maladaptive behavior. Our results demonstrate unique temporal patterns and persistent changes in coordinately regulated gene expression systems with respect to the tested behavioral group. For example, increased expression of genes involved in “transmitter-gated ion channel activity” was only determined for CIE + FSS. Overall, our results provide a summary of transcriptomic adaptations across time within the CTX that are relevant to understanding the neurobiology of chronic alcohol exposure and stress.
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Affiliation(s)
- Sean P. Farris
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
| | - Gayatri R. Tiwari
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (G.R.T.); (O.P.); (R.D.M.)
| | - Olga Ponomareva
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (G.R.T.); (O.P.); (R.D.M.)
| | - Marcelo F. Lopez
- Charleston Alcohol Research Center, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC 28425, USA;
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (G.R.T.); (O.P.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Howard C. Becker
- Charleston Alcohol Research Center, Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC 28425, USA;
- Department of Neuroscience, Medical University of South, Charleston, SC 29425, USA
- Department of Veterans Affairs Medical Center, Charleston, SC 20401, USA
- Correspondence:
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Convergent Evidence for Predispositional Effects of Brain Gray Matter Volume on Alcohol Consumption. Biol Psychiatry 2020; 87:645-655. [PMID: 31699293 PMCID: PMC7412715 DOI: 10.1016/j.biopsych.2019.08.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Alcohol use has been reliably associated with smaller subcortical and cortical regional gray matter volumes (GMVs). Whether these associations reflect shared predisposing risk factors or causal consequences of alcohol use remains poorly understood. METHODS Data came from 3 neuroimaging samples (N = 2423), spanning childhood or adolescence to middle age, with prospective or family-based data. First, we identified replicable GMV correlates of alcohol use. Next, we used family-based and longitudinal data to test whether these associations may plausibly reflect a predispositional liability for alcohol use or a causal consequence of alcohol use. Finally, we used heritability, gene-set enrichment, and transcriptome-wide association study approaches to evaluate whether genome-wide association study-defined genomic risk for alcohol consumption is enriched for genes that are preferentially expressed in regions that were identified in our neuroimaging analyses. RESULTS Smaller right dorsolateral prefrontal cortex (DLPFC) (i.e., middle and superior frontal gyri) and insula GMVs were associated with increased alcohol use across samples. Family-based and prospective longitudinal data suggest that these associations are genetically conferred and that DLPFC GMV prospectively predicts future use and initiation. Genomic risk for alcohol use was enriched in gene sets that were preferentially expressed in the DLPFC and was associated with replicable differential gene expression in the DLPFC. CONCLUSIONS These data suggest that smaller DLPFC and insula GMV plausibly represent genetically conferred predispositional risk factors for, as opposed to consequences of, alcohol use. DLPFC and insula GMV represent promising biomarkers for alcohol-consumption liability and related psychiatric and behavioral phenotypes.
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Dai Y, Hu R, Pei G, Zhang H, Zhao Z, Jia P. Diverse types of genomic evidence converge on alcohol use disorder risk genes. J Med Genet 2020; 57:733-743. [PMID: 32170004 DOI: 10.1136/jmedgenet-2019-106490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/08/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most common forms of substance use disorders with a strong contribution of genetic (50%-60%) and environmental factors. Genome-wide association studies (GWAS) have identified a number of AUD-associated variants, including those in alcohol metabolism genes. These genetic variants may modulate gene expression, making individuals more susceptible to AUD. A long-term alcohol consumption can also change the transcriptome patterns of subjects via epigenetic modulations. METHODS To explore the interactive effect of genetic and epigenetic factors on AUD, we conducted a secondary analysis by integrating GWAS, CNV, brain transcriptome and DNA methylation data to unravel novel AUD-associated genes/variants. We applied the mega-analysis of OR (MegaOR) method to prioritise AUD candidate genes (AUDgenes). RESULTS We identified a consensus set of 206 AUDgenes based on the multi-omics data. We demonstrated that these AUDgenes tend to interact with each other more frequent than chance expectation. Functional annotation analysis indicated that these AUDgenes were involved in substance dependence, synaptic transmission, glial cell proliferation and enriched in neuronal and liver cells. We obtained a multidimensional evidence that AUD is a polygenic disorder influenced by both genetic and epigenetic factors as well as the interaction of them. CONCLUSION We characterised multidimensional evidence of genetic, epigenetic and transcriptomic data in AUD. We found that 206 AUD associated genes were highly expressed in liver, brain cerebellum, frontal cortex, hippocampus and pituitary. Our studies provides important insights into the molecular mechanism of AUD and potential target genes for AUD treatment.
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Affiliation(s)
- Yulin Dai
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ruifeng Hu
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Guangsheng Pei
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, Massachusetts, USA.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Zhongming Zhao
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peilin Jia
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
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Lai D, Wetherill L, Kapoor M, Johnson EC, Schwandt M, Ramchandani VA, Goldman D, Joslyn G, Rao X, Liu Y, Farris S, Mayfield RD, Dick D, Hesselbrock V, Kramer J, McCutcheon VV, Nurnberger J, Tischfield J, Goate A, Edenberg HJ, Porjesz B, Agrawal A, Foroud T, Schuckit M. Genome-wide association studies of the self-rating of effects of ethanol (SRE). Addict Biol 2020; 25:e12800. [PMID: 31270906 PMCID: PMC6940552 DOI: 10.1111/adb.12800] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/06/2019] [Accepted: 05/27/2019] [Indexed: 12/22/2022]
Abstract
The level of response (LR) to alcohol as measured with the Self-Report of the Effects of Alcohol Retrospective Questionnaire (SRE) evaluates the number of standard drinks usually required for up to four effects. The need for a higher number of drinks for effects is genetically influenced and predicts higher risks for heavy drinking and alcohol problems. We conducted genome-wide association study (GWAS) in the African-American (COGA-AA, N = 1527 from 309 families) and European-American (COGA-EA, N = 4723 from 956 families) subsamples of the Collaborative Studies on the Genetics of Alcoholism (COGA) for two SRE scores: SRE-T (average of first five times of drinking, the period of heaviest drinking, and the most recent 3 months of consumption) and SRE-5 (the first five times of drinking). We then meta-analyzed the two COGA subsamples (COGA-AA + EA). Both SRE-T and SRE-5 were modestly heritable (h2 : 21%-31%) and genetically correlated with alcohol dependence (AD) and DSM-IV AD criterion count (rg : 0.35-0.76). Genome-wide significant associations were observed (SRE-T: chromosomes 6, rs140154945, COGA-EA P = 3.30E-08 and 11, rs10647170, COGA-AA+EA P = 3.53E-09; SRE-5: chromosome13, rs4770359, COGA-AA P = 2.92E-08). Chromosome 11 was replicated in an EA dataset from the National Institute on Alcohol Abuse and Alcoholism intramural program. In silico functional analyses and RNA expression analyses suggest that the chromosome 6 locus is an eQTL for KIF25. Polygenic risk scores derived using the COGA SRE-T and SRE-5 GWAS predicted 0.47% to 2.48% of variances in AD and DSM-IV AD criterion count in independent datasets. This study highlights the genetic contribution of alcohol response phenotypes to the etiology of alcohol use disorders.
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at
Mt. Sinai, New York, NY
| | - Emma C. Johnson
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - Melanie Schwandt
- Office of the Clinical Director, National Institute on
Alcohol Abuse & Alcoholism, Bethesda, MD
| | - Vijay A. Ramchandani
- Section on Human Psychopharmacology, Division of
Intramural Clinical and Biological Research, National Institute on Alcohol Abuse and
Alcoholism, Bethesda, MD
| | - David Goldman
- Office of the Clinical Director, National Institute on
Alcohol Abuse & Alcoholism, Bethesda, MD
| | - Geoff Joslyn
- Ernest Gallo Clinic and Research Center, Emeryville,
CA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Sean Farris
- Waggoner Center for Alcohol and Addiction Research, The
University of Texas at Austin, Austin, TX
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The
University of Texas at Austin, Austin, TX
| | - Danielle Dick
- Department of Psychology, Virginia Commonwealth
University, Richmond, VA
| | | | - John Kramer
- Department of Psychiatry, Roy Carver College of
Medicine, University of Iowa, Iowa City, IA
| | - Vivia V. McCutcheon
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - John Nurnberger
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
- Department of Psychiatry, Indiana University School of
Medicine, Indianapolis, IN
| | - Jay Tischfield
- Department of Genetics and the Human Genetics Institute
of New Jersey, Rutgers University, Piscataway, NJ
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at
Mt. Sinai, New York, NY
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
- Department of Biochemistry and Molecular Biology,
Indiana University School of Medicine, Indianapolis, IN
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Lab, Department of
Psychiatry, State University of New York, Downstate Medical Center, Brooklyn,
NY
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana
University School of Medicine, Indianapolis, IN
| | - Marc Schuckit
- Department of Psychiatry, University of California, San
Diego Medical School, San Diego, CA
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