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Huggett SB, Selveraj S, McGeary JE, Ikeda A, Yuan E, Loeffel LB, Rohan HCP. Bulk and Single-cell Transcriptomic Brain Data Identify Overlapping Processes and Cell-types with Human AUD and Mammalian Models of Alcohol Use. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601528. [PMID: 39005451 PMCID: PMC11245012 DOI: 10.1101/2024.07.02.601528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
This study explores the neurobiological underpinnings of alcohol use disorder (AUD) by integrating bulk and single-cell transcriptomic data from humans, primates, and mice across three brain regions associated with addiction (i.e., prefrontal cortex (PFC), nucleus accumbens (NAc), and central amygdala (CeA)). We compared AUD RNA expression and cell-type abundance from 92 human brain to data from 53 primates and 90 mice engaged in diverse alcohol use paradigms. The findings revealed significant and reproducible correlations between human AUD and mammalian models of alcohol use that vary by tissue, species, and behavioral paradigm. The strongest correlations occurred between primate and mouse models of binge drinking (i.e., high drinking in the dark). Certain primate models demonstrated that the brain RNA correlations with human alcohol use disorder (AUD) were approximately 40% as strong as the correlations observed within human samples themselves. By integrating single-cell transcriptomic data, this study observed decreased oligodendrocyte proportions in the PFC and NAc of human AUD with similar trends in animal models. Gene co-expression network analyses revealed conserved systems associated with human AUD and animal models of heavy/binge alcohol consumption. Gene co-expression networks were enriched for pathways related to inflammation, myelination, and synaptic plasticity and the genes within them accounted for ~20% of the heritability in human alcohol consumption. Identified hub genes were associated with relevant traits (e.g., impulsivity, motivation) in humans and mice. This study sheds light on conserved biological entities underlying AUD and chronic alcohol use, providing insights into the cellular, genetic, and neuromolecular basis across species.
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Affiliation(s)
- Spencer B Huggett
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA, USA
| | - Sharmila Selveraj
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA, USA
| | - John E McGeary
- Department of Psychiatry, Alpert Medical School of Brown University, Providence RI, USA
- Providence VA Medical Center, Providence, RI, USA
| | - Ami Ikeda
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA, USA
| | - Emerald Yuan
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA, USA
| | - Lauren B Loeffel
- VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - H C Palmer Rohan
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA, USA
- Providence VA Medical Center, Providence, RI, USA
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Zeisler ZR, Heslin KA, Stoll FM, Hof PR, Clem RL, Rudebeck PH. Comparative basolateral amygdala connectomics reveals dissociable single-neuron projection patterns to frontal cortex in macaques and mice. Curr Biol 2024:S0960-9822(24)00764-4. [PMID: 38964318 DOI: 10.1016/j.cub.2024.06.012] [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: 03/08/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Basolateral amygdala (BLA) is a key hub for affect in the brain,1,2,3 and dysfunction within this area contributes to a host of psychiatric disorders.4,5 BLA is extensively and reciprocally interconnected with frontal cortex,6,7,8,9 and some aspects of its function are evolutionarily conserved across rodents, anthropoid primates, and humans.10 Neuron density in BLA is substantially lower in primates compared to murine rodents,11 and frontal cortex (FC) is dramatically expanded in primates, particularly the more anterior granular and dysgranular areas.12,13,14 Yet, how these anatomical differences influence the projection patterns of single BLA neurons to frontal cortex across rodents and primates is unknown. Using a barcoded connectomic approach, we assessed the single BLA neuron connections to frontal cortex in mice and macaques. We found that BLA neurons are more likely to project to multiple distinct parts of FC in mice than in macaques. Further, while single BLA neuron projections to nucleus accumbens were similarly organized in mice and macaques, BLA-FC connections differed substantially. Notably, BLA connections to subcallosal anterior cingulate cortex (scACC) in macaques were least likely to branch to other medial frontal cortex areas compared to perigenual ACC (pgACC). This pattern of connections was reversed in the mouse homologues of these areas, infralimbic and prelimbic cortex (IL and PL), mirroring functional differences between rodents and non-human primates. Taken together, these results indicate that BLA connections to FC are not linearly scaled from mice to macaques and instead the organization of single-neuron BLA connections is distinct between these species.
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Affiliation(s)
- Zachary R Zeisler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kelsey A Heslin
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Frederic M Stoll
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, 787 11(th) Avenue, New York, NY 10019, USA
| | - Roger L Clem
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Peter H Rudebeck
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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3
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Zeisler ZR, Heslin KA, Stoll FM, Hof PR, Clem RL, Rudebeck PH. Comparative basolateral amygdala connectomics reveals dissociable single-neuron projection patterns to frontal cortex in macaques and mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.571711. [PMID: 38187599 PMCID: PMC10769239 DOI: 10.1101/2023.12.18.571711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The basolateral amygdala (BLA) projects to the frontal cortex (FC) in both rodents and primates, but the comparative organization of single-neuron BLA-FC projections is unknown. Using a barcoded connectomic approach, we found that BLA neurons are more likely to project to multiple distinct parts of FC in mice than in macaques. Further, while single BLA neuron projections to nucleus accumbens are similarly organized in mice and macaques, BLA-FC connections differ.
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Affiliation(s)
- Zachary R Zeisler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kelsey A Heslin
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Frederic M Stoll
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Roger L Clem
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Peter H Rudebeck
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Lipschultz Center for Cognitive Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Baker EJ, Moore S, Gonzales SW, Grant KA. Long-term drinking stability in the open-access self-administration monkey model. Alcohol 2023; 113:41-48. [PMID: 37516372 PMCID: PMC10818025 DOI: 10.1016/j.alcohol.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/14/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023]
Abstract
The Non-Human Primate (NHP) model for the study of Alcohol Use Disorders (AUD) as developed in our laboratories is critical to our understanding of the pathophysiology of voluntary, chronic, ethanol consumption. Previous work in this model established categories of ethanol consumption that parallel reported categories of human consumption across a spectrum spanning low drinking, binge drinking, heavy drinking, and very heavy drinking, albeit at generally higher daily intakes across categories than documented in people. Original categories assigned to ethanol consumption patterns were established using a limited cohort of rhesus macaques. This study revisits the validity of categorical drinking using an additional 28 monkeys. In addition to finding categorical representations consistent with the original 2014 report, our findings demonstrate that drinking categories remain stable across the observed 12 months of nearly consistent access to ethanol (22 h/day), termed "open access". Animals occupying the two ends of the spectrum, "low" and "very heavy" drinkers, exhibit the largest stability. The findings also indicate a slight escalatory drift over time, with very heavy drinking animals experiencing fatigue near the end of open access.
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Affiliation(s)
- Erich J Baker
- Department of Computer Science, Baylor University, Waco, TX, USA.
| | - Sharon Moore
- Department of Computer Science, Baylor University, Waco, TX, USA
| | - Steven W Gonzales
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
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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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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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Kisby BR, Farris SP, McManus MM, Varodayan FP, Roberto M, Harris RA, Ponomarev I. Alcohol Dependence in Rats Is Associated with Global Changes in Gene Expression in the Central Amygdala. Brain Sci 2021; 11:brainsci11091149. [PMID: 34573170 PMCID: PMC8468792 DOI: 10.3390/brainsci11091149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/06/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
Alcohol dependence is associated with adverse consequences of alcohol (ethanol) use and is evident in most severe cases of alcohol use disorder (AUD). The central nucleus of the amygdala (CeA) plays a critical role in the development of alcohol dependence and escalation of alcohol consumption in dependent subjects. Molecular mechanisms underlying the CeA-driven behavioral changes are not well understood. Here, we examined the effects of alcohol on global gene expression in the CeA using a chronic intermittent ethanol (CIE) vapor model in rats and RNA sequencing (RNA-Seq). The CIE procedure resulted in robust changes in CeA gene expression during intoxication, as the number of differentially expressed genes (DEGs) was significantly greater than those expected by chance. Over-representation analysis of cell types, functional groups and molecular pathways revealed biological categories potentially important for the development of alcohol dependence in our model. Genes specific for astrocytes, myelinating oligodendrocytes, and endothelial cells were over-represented in the DEG category, suggesting that these cell types were particularly affected by the CIE procedure. The majority of the over-represented functional groups and molecular pathways were directly related to the functions of glial and endothelial cells, including extracellular matrix (ECM) organization, myelination, and the regulation of innate immune response. A coordinated regulation of several ECM metalloproteinases (e.g., Mmp2; Mmp14), their substrates (e.g., multiple collagen genes and myelin basic protein; Mbp), and a metalloproteinase inhibitor, Reck, suggests a specific mechanism for ECM re-organization in response to chronic alcohol, which may modulate neuronal activity and result in behavioral changes, such as an escalation of alcohol drinking. Our results highlight the importance of glial and endothelial cells in the effects of chronic alcohol exposure on the CeA, and demonstrate further insight into the molecular mechanisms of alcohol dependence in rats. These molecular targets may be used in future studies to develop therapeutics to treat AUD.
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Affiliation(s)
- Brent R. Kisby
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (B.R.K.); (M.M.M.)
| | - Sean P. Farris
- Department of Neuroscience, University of Texas at Austin, Austin, TX 78715, USA; (S.P.F.); (R.A.H.)
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
| | - Michelle M. McManus
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (B.R.K.); (M.M.M.)
| | - Florence P. Varodayan
- Department of Psychology, Binghamton University-SUNY, Binghamton, NY 13902, USA;
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - Marisa Roberto
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - R. Adron Harris
- Department of Neuroscience, University of Texas at Austin, Austin, TX 78715, USA; (S.P.F.); (R.A.H.)
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78741, USA
| | - Igor Ponomarev
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (B.R.K.); (M.M.M.)
- Correspondence:
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