1
|
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.
Collapse
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
| |
Collapse
|
2
|
Yakovlev V, Lapato DM, Rana P, Ghosh P, Frye R, Roberson-Nay R. Neuron enriched extracellular vesicles' MicroRNA expression profiles as a marker of early life alcohol consumption. Transl Psychiatry 2024; 14:176. [PMID: 38575599 PMCID: PMC10994930 DOI: 10.1038/s41398-024-02874-3] [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: 08/14/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Alcohol consumption may impact and shape brain development through perturbed biological pathways and impaired molecular functions. We investigated the relationship between alcohol consumption rates and neuron-enriched extracellular vesicles' (EVs') microRNA (miRNA) expression to better understand the impact of alcohol use on early life brain biology. Neuron-enriched EVs' miRNA expression was measured from plasma samples collected from young people using a commercially available microarray platform while alcohol consumption was measured using the Alcohol Use Disorders Identification Test. Linear regression and network analyses were used to identify significantly differentially expressed miRNAs and to characterize the implicated biological pathways, respectively. Compared to alcohol naïve controls, young people reporting high alcohol consumption exhibited significantly higher expression of three neuron-enriched EVs' miRNAs including miR-30a-5p, miR-194-5p, and miR-339-3p, although only miR-30a-5p and miR-194-5p survived multiple test correction. The miRNA-miRNA interaction network inferred by a network inference algorithm did not detect any differentially expressed miRNAs with a high cutoff on edge scores. However, when the cutoff of the algorithm was reduced, five miRNAs were identified as interacting with miR-194-5p and miR-30a-5p. These seven miRNAs were associated with 25 biological functions; miR-194-5p was the most highly connected node and was highly correlated with the other miRNAs in this cluster. Our observed association between neuron-enriched EVs' miRNAs and alcohol consumption concurs with results from experimental animal models of alcohol use and suggests that high rates of alcohol consumption during the adolescent/young adult years may impact brain functioning and development by modulating miRNA expression.
Collapse
Affiliation(s)
- Vasily Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
| | - Dana M Lapato
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Pratip Rana
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Preetam Ghosh
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Rebekah Frye
- Neuroscience Program, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
3
|
Occhipinti C, La Russa R, Iacoponi N, Lazzari J, Costantino A, Di Fazio N, Del Duca F, Maiese A, Fineschi V. miRNAs and Substances Abuse: Clinical and Forensic Pathological Implications: A Systematic Review. Int J Mol Sci 2023; 24:17122. [PMID: 38069445 PMCID: PMC10707252 DOI: 10.3390/ijms242317122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Substance addiction is a chronic and relapsing brain disorder characterized by compulsive seeking and continued substance use, despite adverse consequences. The high prevalence and social burden of addiction are indisputable; however, the available intervention is insufficient. The modulation of gene expression and aberrant adaptation of neural networks are attributed to the changes in brain functions under repeated exposure to addictive substances. Considerable studies have demonstrated that miRNAs are strong modulators of post-transcriptional gene expression in substance addiction. The emerging role of microRNA (miRNA) provides new insights into many biological and pathological processes in the central nervous system: their variable expression in different regions of the brain and tissues may play a key role in regulating the pathophysiological events of addiction. This work provides an overview of the current literature on miRNAs involved in addiction, evaluating their impaired expression and regulatory role in neuroadaptation and synaptic plasticity. Clinical implications of such modulatory capacities will be estimated. Specifically, it will evaluate the potential diagnostic role of miRNAs in the various stages of drug and substance addiction. Future perspectives about miRNAs as potential novel therapeutic targets for substance addiction and abuse will also be provided.
Collapse
Affiliation(s)
- Carla Occhipinti
- Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy; (C.O.); (N.I.); (J.L.); (A.C.)
| | - Raffaele La Russa
- Department of Clinical Medicine, Public Health, Life Sciences, and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Naomi Iacoponi
- Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy; (C.O.); (N.I.); (J.L.); (A.C.)
| | - Julia Lazzari
- Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy; (C.O.); (N.I.); (J.L.); (A.C.)
| | - Andrea Costantino
- Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy; (C.O.); (N.I.); (J.L.); (A.C.)
| | - Nicola Di Fazio
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Sapienza University of Rome, Viale Regina Elena 336, 00161 Rome, Italy; (N.D.F.); (F.D.D.); (V.F.)
| | - Fabio Del Duca
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Sapienza University of Rome, Viale Regina Elena 336, 00161 Rome, Italy; (N.D.F.); (F.D.D.); (V.F.)
| | - Aniello Maiese
- Department of Surgical Pathology, Medical, Molecular and Critical Area, Institute of Legal Medicine, University of Pisa, 56126 Pisa, Italy; (C.O.); (N.I.); (J.L.); (A.C.)
| | - Vittorio Fineschi
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Sapienza University of Rome, Viale Regina Elena 336, 00161 Rome, Italy; (N.D.F.); (F.D.D.); (V.F.)
| |
Collapse
|
4
|
Rezayof A, Ghasemzadeh Z, Sahafi OH. Addictive drugs modify neurogenesis, synaptogenesis and synaptic plasticity to impair memory formation through neurotransmitter imbalances and signaling dysfunction. Neurochem Int 2023; 169:105572. [PMID: 37423274 DOI: 10.1016/j.neuint.2023.105572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
Drug abuse changes neurophysiological functions at multiple cellular and molecular levels in the addicted brain. Well-supported scientific evidence suggests that drugs negatively affect memory formation, decision-making and inhibition, and emotional and cognitive behaviors. The mesocorticolimbic brain regions are involved in reward-related learning and habitual drug-seeking/taking behaviors to develop physiological and psychological dependence on the drugs. This review highlights the importance of specific drug-induced chemical imbalances resulting in memory impairment through various neurotransmitter receptor-mediated signaling pathways. The mesocorticolimbic modifications in the expression levels of brain-derived neurotrophic factor (BDNF) and the cAMP-response element binding protein (CREB) impair reward-related memory formation following drug abuse. The contributions of protein kinases and microRNAs (miRNAs), along with the transcriptional and epigenetic regulation have also been considered in memory impairment underlying drug addiction. Overall, we integrate the research on various types of drug-induced memory impairment in distinguished brain regions and provide a comprehensive review with clinical implications addressing the upcoming studies.
Collapse
Affiliation(s)
- Ameneh Rezayof
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Zahra Ghasemzadeh
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Oveis Hosseinzadeh Sahafi
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| |
Collapse
|
5
|
Yakovlev V, Lapato DM, Rana P, Ghosh P, Frye R, Roberson-Nay R. Neuron Enriched Exosomal MicroRNA Expression Profiles as a Marker of Early Life Alcohol Consumption. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544235. [PMID: 37333185 PMCID: PMC10274862 DOI: 10.1101/2023.06.09.544235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Alcohol consumption may impact and shape brain development through perturbed biological pathways and impaired molecular functions. We investigated the relationship between alcohol consumption rates and neuron-enriched exosomal microRNA (miRNA) expression to better understand the impact of alcohol use on early life brain biology. Methods Neuron-enriched exosomal miRNA expression was measured from plasma samples collected from young people using a commercially available microarray platform while alcohol consumption was measured using the Alcohol Use Disorders Identification Test. Linear regression and network analyses were used to identify significantly differentially expressed miRNAs and to characterize the implicated biological pathways, respectively. Results Compared to alcohol naïve controls, young people reporting high alcohol consumption exhibited significantly higher expression of four neuron-enriched exosomal miRNAs including miR-30a-5p, miR-194-5p, and miR-339-3p, although only miR-30a-5p and miR-194-5p survived multiple test correction. The miRNA-miRNA interaction network inferred by a network inference algorithm did not detect any differentially expressed miRNAs with a high cutoff on edge scores. However, when the cutoff of the algorithm was reduced, five miRNAs were identified as interacting with miR-194-5p and miR-30a-5p. These seven miRNAs were associated with 25 biological functions; miR-194-5p was the most highly connected node and was highly correlated with the other miRNAs in this cluster. Conclusions Our observed association between neuron-enriched exosomal miRNAs and alcohol consumption concurs with results from experimental animal models of alcohol use and suggests that high rates of alcohol consumption during the adolescent/young adult years may impact brain functioning and development by modulating miRNA expression.
Collapse
Affiliation(s)
- Vasily Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Preetam Ghosh
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Rebekah Frye
- Neuroscience Program, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
6
|
Gillis RF, Palmour RM. miRNA Expression Analysis of the Hippocampus in a Vervet Monkey Model of Fetal Alcohol Spectrum Disorder Reveals a Potential Role in Global mRNA Downregulation. Brain Sci 2023; 13:934. [PMID: 37371413 DOI: 10.3390/brainsci13060934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNAs (miRNAs) are short-length non-protein-coding RNA sequences that post-transcriptionally regulate gene expression in a broad range of cellular processes including neuro- development and have previously been implicated in fetal alcohol spectrum disorders (FASD). In this study, we use our vervet monkey model of FASD to follow up on a prior multivariate (developmental age × ethanol exposure) mRNA analysis (GSE173516) to explore the possibility that the global mRNA downregulation we observed in that study could be related to miRNA expression and function. We report here a predominance of upregulated and differentially expressed miRNAs. Further, the 24 most upregulated miRNAs were significantly correlated with their predicted targets (Target Scan 7.2). We then explored the relationship between these 24 miRNAs and the fold changes observed in their paired mRNA targets using two prediction platforms (Target Scan 7.2 and miRwalk 3.0). Compared to a list of non-differentially expressed miRNAs from our dataset, the 24 upregulated and differentially expressed miRNAs had a greater impact on the fold changes of their corresponding mRNA targets across both platforms. Taken together, this evidence raises the possibility that ethanol-induced upregulation of specific miRNAs might contribute functionally to the general downregulation of mRNAs observed by multiple investigators in response to prenatal alcohol exposure.
Collapse
Affiliation(s)
- Rob F Gillis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
| | - Roberta M Palmour
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0G4, Canada
- Behavioural Science Foundation, Mansion KN 0101, Saint Kitts and Nevis
| |
Collapse
|
7
|
Domi E, Barchiesi R, Barbier E. Epigenetic Dysregulation in Alcohol-Associated Behaviors: Preclinical and Clinical Evidence. Curr Top Behav Neurosci 2023. [PMID: 36717533 DOI: 10.1007/7854_2022_410] [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: 02/01/2023]
Abstract
Alcohol use disorder (AUD) is characterized by loss of control over intake and drinking despite harmful consequences. At a molecular level, AUD is associated with long-term neuroadaptations in key brain regions that are involved in reward processing and decision-making. Over the last decades, a great effort has been made to understand the neurobiological basis underlying AUD. Epigenetic mechanisms have emerged as an important mechanism in the regulation of long-term alcohol-induced gene expression changes. Here, we review the literature supporting a role for epigenetic processes in AUD. We particularly focused on the three most studied epigenetic mechanisms: DNA methylation, Histone modification and non-coding RNAs. Clinical studies indicate an association between AUD and DNA methylation both at the gene and global levels. Using behavioral paradigms that mimic some of the characteristics of AUD, preclinical studies demonstrate that changes in epigenetic mechanisms can functionally impact alcohol-associated behaviors. While many studies support a therapeutic potential for targeting epigenetic enzymes, more research is needed to fully understand their role in AUD. Identification of brain circuits underlying alcohol-associated behaviors has made major advances in recent years. However, there are very few studies that investigate how epigenetic mechanisms can affect these circuits or impact the neuronal ensembles that promote alcohol-associated behaviors. Studies that focus on the role of circuit-specific and cell-specific epigenetic changes for clinically relevant alcohol behaviors may provide new insights on the functional role of epigenetic processes in AUD.
Collapse
Affiliation(s)
- Esi Domi
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden
- School of Pharmacy, Pharmacology Unit, Center for Neuroscience, University of Camerino, Camerino, Italy
| | - Riccardo Barchiesi
- Department of Neuroscience, Waggoner Center for Alcohol and Alcohol Addiction Research, University of Texas at Austin, Austin, TX, USA
| | - Estelle Barbier
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden.
| |
Collapse
|
8
|
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.
Collapse
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,
| |
Collapse
|
9
|
Xu Y, Liu J, Ji X, Zhao G, Zhao T, Wang X, Wang L, Gao S, Hao Y, Gao Y, Gao Y, Weng X, Jia L, Chen Z. Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry ( Sapindus mukorossi Gaertn.). FRONTIERS IN PLANT SCIENCE 2023; 13:1037784. [PMID: 36699854 PMCID: PMC9869041 DOI: 10.3389/fpls.2022.1037784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/19/2022] [Indexed: 06/13/2023]
Abstract
Triterpenoid saponin are important secondary metabolites and bioactive constituents of soapberry (Sapindus mukorossi Gaertn.) and are widely used in medicine and toiletry products. However, little is known about the roles of miRNAs in the regulation of triterpenoid saponin biosynthesis in soapberry. In this study, a total of 3036 miRNAs were identified, of which 1372 miRNAs were differentially expressed at different stages of pericarp development. Important KEGG pathways, such as terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and basal transcription factors were highlighted, as well the roles of some key miRNAs, such as ath-miR5021, han-miR3630-3p, and ppe-miR858, which may play important roles in regulating triterpenoid saponin biosynthesis. In addition, 58 miRNAs might participate in saponin biosynthesis pathways by predicting the targets of those miRNAs to 53 saponin biosynthesis structural genes. And 75 miRNAs were identified to potentially play vital role in saponin accumulation by targeting transcript factor genes, bHLH, bZIP, ERF, MYB, and WRKY, respectively, which are candidate regulatory genes in the pathway of saponin biosynthesis. The results of weighted gene coexpression network analysis (WGCNA) suggested that two saponin-specific miRNA modules and 10 hub miRNAs may participate in saponin biosynthesis. Furthermore, multiple miRNA-mRNA regulatory networks potentially involved in saponin biosynthesis were generated, e.g., ath-miR5021-SmIDI2/SmGPS5/SmbAS1/SmCYP71D-3/SmUGT74G-2, han-miR3630-3p-SmCYP71A-14/SmbHLH54/SmMYB135/SmWRKY32, and ppe-miR858-SmMYB5/SmMYB32. qRT-PCR analysis validated the expression patterns of nine miRNAs and 12 corresponding target genes. This study represents the first comprehensive analysis of miRNAs in soapberry and lays the foundation for further understanding of miRNA-based regulation in triterpenoid saponin biosynthesis.
Collapse
Affiliation(s)
- Yuanyuan Xu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Jiming Liu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xiangqin Ji
- Bioinformatics Analysis Department, Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Guochun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Tianyun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xin Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Lixian Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Shilun Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yingying Hao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuhan Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuan Gao
- Planning and Design Institute of Forest Products Industry, National Forestry and Grassland Administration, Beijing, China
| | - Xuehuang Weng
- Research and Development Department, Yuanhua Forestry Biological Technology Co., Ltd., Sanming, Fujian, China
| | - Liming Jia
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Zhong Chen
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| |
Collapse
|
10
|
Wang JQ, Liu YR, Xia QR, Liang J, Wang JL, Li J. Functional roles, regulatory mechanisms and theranostics applications of ncRNAs in alcohol use disorder. Int J Biol Sci 2023; 19:1316-1335. [PMID: 36923934 PMCID: PMC10008696 DOI: 10.7150/ijbs.81518] [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: 12/04/2022] [Accepted: 02/02/2023] [Indexed: 03/14/2023] Open
Abstract
Alcohol use disorder (AUD) is one of the most prevalent neuropsychological disorders worldwide, and its pathogenesis is convoluted and poorly understood. There is considerable evidence demonstrating significant associations between multiple heritable factors and the onset and progression of AUD. In recent years, a substantial body of research conducted by emerging biotechnologies has increasingly highlighted the crucial roles of noncoding RNAs (ncRNAs) in the pathophysiology of mental diseases. As in-depth understanding of ncRNAs and their mechanisms of action, they have emerged as prospective diagnostic indicators and preclinical therapeutic targets for a variety of psychiatric illness, including AUD. Of note, dysregulated expression of ncRNAs such as circRNAs, lncRNAs and miRNAs was routinely found in AUD individuals, and besides, exogenous regulation of partial ncRNAs has also been shown to be effective in ameliorating alcohol preference and excessive alcohol consumption. However, the exact molecular mechanism still remains elusive. Herein, we systematically summarized current knowledge regarding alterations in the expression of certain ncRNAs as well as their-mediated regulatory mechanisms in individuals with AUD. And finally, we detailedly reviewed the potential theranostics applications of gene therapy agents targeting ncRNAs in AUD mice. Overall, a deeper comprehension of functional roles and biological mechanisms of ncRNAs may make significant contributions to the accurate diagnosis and effective treatment of AUD.
Collapse
Affiliation(s)
- Jie-Quan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Ya-Ru Liu
- Department of Pharmacy, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, 230022, China
| | - Qing-Rong Xia
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jun Liang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jin-Liang Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jun Li
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| |
Collapse
|
11
|
Seyednejad SA, Sartor GC. Noncoding RNA therapeutics for substance use disorder. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10807. [PMID: 36601439 PMCID: PMC9808746 DOI: 10.3389/adar.2022.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although noncoding RNAs (ncRNAs) have been shown to regulate maladaptive neuroadaptations that drive compulsive drug use, ncRNA-targeting therapeutics for substance use disorder (SUD) have yet to be clinically tested. Recent advances in RNA-based drugs have improved many therapeutic issues related to immune response, specificity, and delivery, leading to multiple successful clinical trials for other diseases. As the need for safe and effective treatments for SUD continues to grow, novel nucleic acid-based therapeutics represent an appealing approach to target ncRNA mechanisms in SUD. Here, we review ncRNA processes implicated in SUD, discuss recent therapeutic approaches for targeting ncRNAs, and highlight potential opportunities and challenges of ncRNA-targeting therapeutics for SUD.
Collapse
Affiliation(s)
- Seyed Afshin Seyednejad
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
| | - Gregory C. Sartor
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
| |
Collapse
|
12
|
Ma H, Zhang H, Yu J, Wang Z, Zeng X, Ye J, Wang C. Integrated analysis of microRNA expression profiles and function network in mice testes after low dose lead exposure from early puberty. Toxicol Appl Pharmacol 2022; 454:116260. [PMID: 36183778 DOI: 10.1016/j.taap.2022.116260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/20/2022] [Accepted: 09/24/2022] [Indexed: 10/31/2022]
Abstract
There is evidence suggesting the participation of non-coding RNAs in male reproductive dysfunction induced by lead, and the significance of microRNAs has been highlighted recently because of their essential roles in gene regulatory networks. To comprehensively understand the functions of miRNA and the regulatory networks, RNA sequencing was carried out to obtain miRNA expression profiles in mice testes exposed to low dose Pb for 90 days at the onset of puberty. In total, 44 differentially expressed miRNAs with 26 up-regulated and 18 down-regulated were identified between 200 mg/L Pb group and control group (p < 0.05). Enrichment analysis confirmed that the target genes of DE miRNAs might participate in the metabolism of testicular cells. Furthermore, a miRNA-mRNA co-expression network consisting of 19 miRNAs and 106 mRNAs and a competing endogenous RNA network of lncRNA-miRNA-mRNA including 179 genes were established. Finally, the expressions of 4 miRNAs (mmu-miR-451a, mmu-miR-133a-3p, mmu-miR-1a-3p and mmu-miR-486a-3p) and 4 mRNAs (Gramd1b, Tcf7l2, Mov10 and Srcin1) involved in regulatory networks were verified by RT-qPCR. In conclusion, our research might provide targets for the mechanism studies of miRNAs in reproductive toxicity of Pb.
Collapse
Affiliation(s)
- Haitao Ma
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Haoran Zhang
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Jun Yu
- Department of Preventive Medicine, School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning 437100, Hubei Province, China
| | - Ziqiong Wang
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xiangchao Zeng
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Jingping Ye
- Department of Pediatrics, Renmin Hospital of Wuhan University, Wuhan 430071, Hubei Province, China.
| | - Chunhong Wang
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan 430071, Hubei Province, China.
| |
Collapse
|
13
|
Mohammadi AH, Seyedmoalemi S, Moghanlou M, Akhlagh SA, Talaei Zavareh SA, Hamblin MR, Jafari A, Mirzaei H. MicroRNAs and Synaptic Plasticity: From Their Molecular Roles to Response to Therapy. Mol Neurobiol 2022; 59:5084-5102. [PMID: 35666404 DOI: 10.1007/s12035-022-02907-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 05/25/2022] [Indexed: 12/24/2022]
Abstract
Synaptic plasticity is the ability of synapses to weaken or strengthen over time, in response to changes in the activity of the neurons. It is orchestrated by a variety of genes, proteins, and external and internal factors, especially epigenetic factors. MicroRNAs (miRNAs) are well-acknowledged epigenetic modulators that regulate the translation and degradation of target genes in the nervous system. Increasing evidence has suggested that a number of miRNAs play important roles in modulating various aspects of synaptic plasticity. The deregulation of miRNAs could be associated with pathological alterations in synaptic plasticity, which could lead to different CNS-related diseases. Herein, we provide an update on the role of miRNAs in governing synaptic plasticity. In addition, we also summarize recent researches on the role of miRNAs in drug addiction, and their targets and mechanism of action. Understanding of the way in which miRNAs contribute to synaptic plasticity provides rational clues in establishing the novel biomarkers and new therapeutic strategies for the diagnosis and treatment of plasticity-related diseases and drug addiction.
Collapse
Affiliation(s)
- Amir Hossein Mohammadi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyedvahid Seyedmoalemi
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahsa Moghanlou
- Department of Psychiatry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Ameneh Jafari
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| |
Collapse
|
14
|
Zhao Y, Qin F, Han S, Li S, Zhao Y, Wang H, Tian J, Cen X. MicroRNAs in drug addiction: Current status and future perspectives. Pharmacol Ther 2022; 236:108215. [DOI: 10.1016/j.pharmthera.2022.108215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/21/2022]
|
15
|
Liu Y, Fan L, Jin L, Lu C, Li T, Zhang Z, Xie C, Li S, Zhang Y, Ren J, Lu D. Integrated bioinformatic analysis of dysregulated microRNA-mRNA co-expression network in ovarian endometriosis. Acta Obstet Gynecol Scand 2022; 101:1074-1084. [PMID: 35876135 PMCID: PMC9812100 DOI: 10.1111/aogs.14430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 07/11/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Ovarian endometriosis is a frequently occurring gynecological disease with large socioeconomic impact. Accumulating evidence has suggested that aberrant miRNA-mRNA interactions are involved in the pathogenesis and progression of ovarian endometriosis. This study aims to identify key miRNAs in ovarian endometriosis by using integrated bioinformatic analysis of a dysregulated miRNA-mRNA co-expression network. MATERIAL AND METHODS Expression profiling of miRNA and mRNA in three normal endometria and five pairs of ectopic/eutopic endometria from patients with ovarian endometriosis was determined by high-throughput sequencing techniques. The data were then integrated with the public sequencing datasets (GSE105764 and GSE105765) using a non-biased approach and a miRNA-mRNA co-expression regulatory network was constructed by in-depth bioinformatic analysis. RESULTS The constructed miRNA-mRNA network included 87 functionally DEMs, 482 target mRNAs and 1850 paired miRNA-mRNA regulatory interactions. Specifically, five miRNAs (miR-141-3p, miR-363-3p, miR-577, miR-767-5p, miR-96-5p) were gradually decreased and two miRNAs (miR-493-5p, miR-592) were gradually increased from normal endometria to eutopic endometria, and then ectopic endometria tissues. Importantly, miR-141-3p, miR-363-3p and miR-96-5p belonged to the miR-200 family, miR-106a-363 cluster and miR-183/96/182 cluster, respectively. Their target mRNAs were mainly associated with cell adhesion, locomotion and binding, which are suggested to play vital regulatory roles in the pathogenesis of ovarian endometriosis. CONCLUSIONS Integrated bioinformatic analysis of the miRNA-mRNA co-expression network defines the crucial roles of the miR-200 family, miR-106a-363 cluster and miR-183/96/182 cluster in the pathogenesis of ovarian endometriosis. Further in-depth functional studies are needed to unveil the molecular mechanisms of these miRNAs, and may provide clues for the optimization of therapeutic strategies for ovarian endometriosis.
Collapse
Affiliation(s)
- Yong Liu
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Linyuan Fan
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Lingge Jin
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Chang Lu
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Ting Li
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Zhan Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Chengmao Xie
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Shenghui Li
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Yudi Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Jian Ren
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| | - Dan Lu
- Department of Gynecology, Beijing Obstetrics and Gynecology HospitalCapital Medical University. Beijing Maternal and Child Health Care HospitalBeijingChina
| |
Collapse
|
16
|
Barney TM, Vore AS, Deak T. Acute Ethanol Challenge Differentially Regulates Expression of Growth Factors and miRNA Expression Profile of Whole Tissue of the Dorsal Hippocampus. Front Neurosci 2022; 16:884197. [PMID: 35706690 PMCID: PMC9189295 DOI: 10.3389/fnins.2022.884197] [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] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/31/2022] [Indexed: 02/02/2023] Open
Abstract
Acute ethanol exposure produces rapid alterations in neuroimmune gene expression that are both time- and cytokine-dependent. Interestingly, adolescent rats, who often consume binge-like quantities of alcohol, displayed reduced neuroimmune responses to acute ethanol challenge. However, it is not known whether growth factors, a related group of signaling factors, respond to ethanol similarly in adults and adolescents. Therefore, Experiment 1 aimed to assess the growth factor response to ethanol in both adolescents and adults. To test this, adolescent (P29-P34) and adult (P70-P80) Sprague Dawley rats of both sexes were injected with either ethanol (3.5 g/kg) or saline, and brains were harvested 3 h post-injection for assessment of growth factor, cytokine, or miRNA expression. As expected, acute ethanol challenge significantly increased IL-6 and IκBα expression in the hippocampus and amygdala, replicating our prior findings. Acute ethanol significantly decreased BDNF and increased FGF2 regardless of age condition. PDGF was unresponsive to ethanol, but showed heightened expression among adolescent males. Because recent work has focused on the PDE4 inhibitor ibudilast for treatment in alcohol use disorder, Experiment 2 tested whether ibudilast would alter ethanol-evoked gene expression changes in cytokines and growth factors in the CNS. Ibudilast (9.0 mg/kg s.c.) administration 1 h prior to ethanol had no effect on ethanol-induced changes in cytokine or growth factor changes in the hippocampus or amygdala. To further explore molecular alterations evoked by acute ethanol challenge in the adult rat hippocampus, Experiment 3 tested whether acute ethanol would change the miRNA expression profile of the dorsal hippocampus using RNASeq, which revealed a rapid suppression of 12 miRNA species 3 h after acute ethanol challenge. Of the miRNA affected by ethanol, the majority were related to inflammation or cell survival and proliferation factors, including FGF2, MAPK, NFκB, and VEGF. Overall, these findings suggest that ethanol-induced, rapid alterations in neuroimmune gene expression were (i) muted among adolescents; (ii) independent of PDE4 signaling; and (iii) accompanied by changes in several growth factors (increased FGF2, decreased BDNF). In addition, ethanol decreased expression of multiple miRNA species, suggesting a dynamic molecular profile of changes in the hippocampus within a few short hours after acute ethanol challenge. Together, these findings may provide important insight into the molecular consequences of heavy drinking in humans.
Collapse
|
17
|
Wiedmann F, Kraft M, Kallenberger S, Büscher A, Paasche A, Blochberger PL, Seeger T, Jávorszky N, Warnecke G, Arif R, Kremer J, Karck M, Frey N, Schmidt C. MicroRNAs Regulate TASK-1 and Are Linked to Myocardial Dilatation in Atrial Fibrillation. J Am Heart Assoc 2022; 11:e023472. [PMID: 35301863 PMCID: PMC9075420 DOI: 10.1161/jaha.121.023472] [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] [Indexed: 12/28/2022]
Abstract
Background Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. However, underlying molecular mechanisms are insufficiently understood. Previous studies suggested that microRNA (miRNA) dependent gene regulation plays an important role in the initiation and maintenance of AF. The 2‐pore‐domain potassium channel TASK‐1 (tandem of P domains in a weak inward rectifying K+ channel–related acid sensitive K+ channel 1) is an atrial‐specific ion channel that is upregulated in AF. Inhibition of TASK‐1 current prolongs the atrial action potential duration to similar levels as in patients with sinus rhythm. Here, we hypothesize that miRNAs might be responsible for the regulation of KCNK3 that encodes for TASK‐1. Methods and Results We selected miRNAs potentially regulating KCNK3 and studied their expression in atrial tissue samples obtained from patients with sinus rhythm, paroxysmal AF, or permanent/chronic AF. MiRNAs differentially expressed in AF were further investigated for their ability to regulate KCNK3 mRNA and TASK‐1 protein expression in human induced pluripotent stem cells, transfected with miRNA mimics or inhibitors. Thereby, we observed that miR‐34a increases TASK‐1 expression and current and further decreases the resting membrane potential of Xenopus laevis oocytes, heterologously expressing hTASK‐1. Finally, we investigated associations between miRNA expression in atrial tissues and clinical parameters of our patient cohort. A cluster containing AF stage, left ventricular end‐diastolic diameter, left ventricular end‐systolic diameter, left atrial diameter, atrial COL1A2 (collagen alpha‐2(I) chain), and TASK‐1 protein level was associated with increased expression of miR‐25, miR‐21, miR‐34a, miR‐23a, miR‐124, miR‐1, and miR‐29b as well as decreased expression of miR‐9 and miR‐485. Conclusions These results suggest an important pathophysiological involvement of miRNAs in the regulation of atrial expression of the TASK‐1 potassium channel in patients with atrial cardiomyopathy.
Collapse
Affiliation(s)
- Felix Wiedmann
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Manuel Kraft
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Stefan Kallenberger
- Digital Health Center Berlin Institute of Health (BIH) and Charité Berlin Germany.,Department of Medical Oncology National Center for Tumor DiseasesHeidelberg University Hospital Heidelberg Germany.,Health Data Science UnitMedical Faculty Heidelberg Heidelberg Germany
| | - Antonius Büscher
- Department for Cardiology II: Electrophysiology University Hospital Münster Münster Germany
| | - Amelie Paasche
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Pablo L Blochberger
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Timon Seeger
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany
| | - Natasa Jávorszky
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Gregor Warnecke
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Rawa Arif
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Jamila Kremer
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Matthias Karck
- Department of Cardiac Surgery University of Heidelberg Germany
| | - Norbert Frey
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| | - Constanze Schmidt
- Department of Cardiology Heidelberg University Hospital Heidelberg Germany.,DZHK (German Center for Cardiovascular Research) Partner Site Heidelberg/Mannheim University of Heidelberg Germany.,HCR Heidelberg Center for Heart Rhythm Disorders Heidelberg University Hospital Heidelberg Germany
| |
Collapse
|
18
|
Xia H, Akay YM, Akay M. Investigating miRNA-mRNA interactions and gene regulatory networks from VTA dopaminergic neurons following perinatal nicotine and alcohol exposure using Bayesian network analysis. IEEE J Biomed Health Inform 2022; 26:3550-3555. [PMID: 35290190 DOI: 10.1109/jbhi.2022.3158620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
MicroRNAs play an important role in gene regulation for many biological systems, including nicotine and alcohol addiction. However, the underlying mechanism behind miRNAs and mRNA interaction is not well characterized. Microarrays are commonly used to quantify the expression levels of mRNAs and/or miRNAs simultaneously. In this study, we performed a Bayesian network analysis to identify mRNA and miRNA interactions following perinatal exposure to nicotine and/or alcohol. We utilized three sets of microarray data to predict the regulation relationship between mRNA and miRNAs. Following perinatal alcohol exposure, we identified two miRNAs: miR-542-5p and miR-874-3p, that exhibited a strong mutual influence on several mRNA in gene regulatory pathways, mainly Axon guidance and Dopaminergic synapses. Finally, we confirmed our predicted addiction pathways based on the Bayesian network analysis with the widely used Kyoto Encyclopedia of Genes and Genomes (KEGG)-based database and identified comparable relevant miRNA-mRNA pairs. We believe the Bayesian network can provide insight into the complexity biological process related to addiction and can potentially be applied to other diseases.
Collapse
|
19
|
Non-coding RNA in alcohol use disorder by affecting synaptic plasticity. Exp Brain Res 2022; 240:365-379. [PMID: 35028694 DOI: 10.1007/s00221-022-06305-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022]
Abstract
Alcohol use disorder (AUD) is one of the most serious public health problems worldwide. AUD is a complex disorder, and there is ample evidence that genetic predisposition is critical to its development. Recent studies have shown that genetic predisposition leads to the onset of AUD, and alcohol metabolism can affect epigenetic inheritance, which in turn affects synaptic plasticity, alters brain function, and leads to more severe addictive behaviors. Non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), play an important role in alcohol addiction. This paper reviews the regulatory role of ncRNAs. ncRNAs are involved in enzyme and neurotransmitter reaction systems during alcohol use disorder. Alcohol consumption regulates the expression of ncRNAs that mediate epigenetic modification and synaptic plasticity, which play an important role in the development of chronic AUD. ncRNAs may be used not only as predictors of therapeutic responses but also as therapeutic targets of AUD. Chronic alcoholism is more likely to lead to neuroimmune disorders, including permanent brain dysfunction. AUD induced by long-term alcoholism greatly alters the expression of genes in the human genome, especially the expression of ncRNAs. Alcohol can cause a series of pathological changes by interfering with gene expression, such as through disordered miRNA-mRNA expression networks, epigenetic modifications, disordered metabolism, and even synaptic remodeling. ncRNAs are involved in the transition from moderate drinking to alcohol dependence.
Collapse
|
20
|
Liu Q, Deng J, Qiu Y, Gao J, Li J, Guan L, Lee H, Zhou Q, Xiao J. Non-coding RNA basis of muscle atrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1066-1078. [PMID: 34786211 PMCID: PMC8569427 DOI: 10.1016/j.omtn.2021.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Muscle atrophy is a common complication of many chronic diseases including heart failure, cancer cachexia, aging, etc. Unhealthy habits and usage of hormones such as dexamethasone can also lead to muscle atrophy. However, the underlying mechanisms of muscle atrophy are not completely understood. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), play vital roles in muscle atrophy. This review mainly discusses the regulation of ncRNAs in muscle atrophy induced by various factors such as heart failure, cancer cachexia, aging, chronic obstructive pulmonary disease (COPD), peripheral nerve injury (PNI), chronic kidney disease (CKD), unhealthy habits, and usage of hormones; highlights the findings of ncRNAs as common regulators in multiple types of muscle atrophy; and summarizes current therapies and underlying mechanisms for muscle atrophy. This review will deepen the understanding of skeletal muscle biology and provide new strategies and insights into gene therapy for muscle atrophy.
Collapse
Affiliation(s)
- Qi Liu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Jiali Deng
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Yan Qiu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Juan Gao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Jin Li
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Longfei Guan
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China
| | - Hangil Lee
- Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Qiulian Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China.,Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Rodriguez FD. Targeting Epigenetic Mechanisms to Treat Alcohol Use Disorders (AUD). Curr Pharm Des 2021; 27:3252-3272. [PMID: 33535943 PMCID: PMC8778698 DOI: 10.2174/1381612827666210203142539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND The impact of abusive alcohol consumption on human health is remarkable. According to the World Health Organization (WHO), approximately 3.3 million people die annually because of harmful alcohol consumption (the figure represents around 5.9% of global deaths). Alcohol Use Disorder (AUD) is a chronic disease where individuals exhibit compulsive alcohol drinking and present negative emotional states when they do not drink. In the most severe manifestations of AUD, the individuals lose control over intake despite a decided will to stop drinking. Given the multiple faces and the specific forms of this disease, the term AUD often appears in the plural (AUDs). Since only a few approved pharmacological treatments are available to treat AUD and they do not apply to all individuals or AUD forms, the search for compounds that may help to eliminate the burden of the disease and complement other therapeutical approaches is necessary. METHODS This work reviews recent research focused on the involvement of epigenetic mechanisms in the pathophysiology of AUD. Excessive drinking leads to chronic and compulsive consumption that eventually damages the organism. The central nervous system is a key target and is the focus of this study. The search for the genetic and epigenetic mechanisms behind the intricated dysregulation induced by ethanol will aid researchers in establishing new therapy approaches. CONCLUSION Recent findings in the field of epigenetics are essential and offer new windows for observation and research. The study of small molecules that inhibit key epienzymes involved in nucleosome architecture dynamics is necessary in order to prove their action and specificity in the laboratory and to test their effectivity and safety in clinical trials with selected patients bearing defined alterations caused by ethanol.
Collapse
Affiliation(s)
- F. David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemistry, University of Salamanca and Group GIR BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
| |
Collapse
|
23
|
Inno R, Kikas T, Lillepea K, Laan M. Coordinated Expressional Landscape of the Human Placental miRNome and Transcriptome. Front Cell Dev Biol 2021; 9:697947. [PMID: 34368147 PMCID: PMC8334369 DOI: 10.3389/fcell.2021.697947] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Placenta is a unique organ that serves its own function, and contributes to maternal gestational adaptation and fetal development. Coordination of its transcriptome to satisfy all the maternal-fetal needs across gestation is not fully understood. MicroRNAs are powerful transcriptome modulators capable to adjust rapidly the expression level and dynamics of large gene sets. This MiR-Seq based study presents a multi-omics investigation of the human placental miRNome and its synergy with the transcriptome. The analysis included 52 placentas representing three trimesters of normal pregnancy, and term cases of late-onset preeclampsia (LO-PE), gestational diabetes and affected fetal growth. Gestational-age dependent differential expression (FDR < 0.05) was detected for 319 of 417 tested miRNAs (76.5%). A shared list of target genes of dynamic miRNAs suggested their coordinated action. The most abundant miR-143-3p revealed as a marker for pregnancy progression. The data suggested critical, but distinct roles of placenta-specific imprinted C19MC and C14MC miRNA clusters. Paternally encoded primate-specific C19MC was highly transcribed during first trimester, potentially fine-tuning the early placental transcriptome in dosage-sensitive manner. Maternally encoded eutherian C14MC showed high expression until term, underlining its key contribution across gestation. A major shift in placental miRNome (16% miRNAs) was observed in LO-PE, but not in other term pregnancy complications. Notably, 13/38 upregulated miRNAs were transcribed from C19MC and only one from C14MC, whereas 11/28 downregulated miRNAs represented C14MC and none C19MC. miR-210-3p, miR-512-5p, miR-32-5p, miR-19a-3p, miR-590-3p, miR-379-5p were differentially expressed in LO-PE and cases of small-for-gestational-age newborns, supporting a shared etiology. Expression correlation analysis with the RNA-Seq data (16,567 genes) of the same samples clustered PE-linked miRNAs into five groups. Large notable clusters of miRNA–gene pairs showing directly and inversely correlated expression dynamics suggested potential functional relationships in both scenarios. The first genome-wide study of placental miR-eQTLs identified 66 placental SNVs associated with the expression of neighboring miRNAs, including PE-linked miRNAs miR-30a-5p, miR-210-3p, miR-490-3p and miR-518-5p. This study provided a rich catalog of miRNAs for further in-depth investigations of their individual and joint effect on placental transcriptome. Several highlighted miRNAs may serve as potential biomarkers for pregnancy monitoring and targets to prevent or treat gestational disorders.
Collapse
Affiliation(s)
- Rain Inno
- Human Genetics Research Group, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Triin Kikas
- Human Genetics Research Group, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Lillepea
- Human Genetics Research Group, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Human Genetics Research Group, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
24
|
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: 6] [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: 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.
Collapse
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
| |
Collapse
|
25
|
Gowen AM, Odegaard KE, Hernandez J, Chand S, Koul S, Pendyala G, Yelamanchili SV. Role of microRNAs in the pathophysiology of addiction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1637. [PMID: 33336550 PMCID: PMC8026578 DOI: 10.1002/wrna.1637] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Addiction is a chronic and relapsing brain disorder characterized by compulsive seeking despite adverse consequences. There are both heritable and epigenetic mechanisms underlying drug addiction. Emerging evidence suggests that non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs, and circular RNAs regulate synaptic plasticity and related behaviors caused by substances of abuse. These ncRNAs modify gene expression and may contribute to the behavioral phenotypes of addiction. Among the ncRNAs, the most widely researched and impactful are miRNAs. The goal in this systematic review is to provide a detailed account of recent research involving the role of miRNAs in addiction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Austin M Gowen
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Katherine E Odegaard
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jordan Hernandez
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Subhash Chand
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sneh Koul
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gurudutt Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sowmya V Yelamanchili
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| |
Collapse
|
26
|
Qin L, Zou J, Barnett A, Vetreno RP, Crews FT, Coleman LG. TRAIL Mediates Neuronal Death in AUD: A Link between Neuroinflammation and Neurodegeneration. Int J Mol Sci 2021; 22:2547. [PMID: 33806288 PMCID: PMC7961445 DOI: 10.3390/ijms22052547] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Although the cause of progressive neurodegeneration is often unclear, neuronal death can occur through several mechanisms. In conditions such as Alzheimer's or alcohol use disorder (AUD), Toll-like receptor (TLR) induction is observed with neurodegeneration. However, links between TLR activation and neurodegeneration are lacking. We report a role of apoptotic neuronal death in AUD through TLR7-mediated induction of death receptor signaling. In postmortem human cortex, a two-fold increase in apoptotic terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining in neurons was found in AUD versus controls. This occurred with the increased expression of TLR7 and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) death receptors. Binge ethanol treatment in C57BL/6 mice increased TLR7 and induced neuronal apoptosis in cortical regions that was blocked by TLR7 antagonism. Mechanistic studies in primary organotypic brain slice culture (OBSC) found that the inhibition of TLR7 and its endogenous ligand let-7b blocked ethanol-induced neuronal cell death. Both IMQ and ethanol induced the expression of TRAIL and its death receptor. In addition, TRAIL-neutralizing monoclonal antibodies blocked both imiquimod (IMQ) and ethanol induced neuronal death. These findings implicate TRAIL as a mediator of neuronal apoptosis downstream of TLR7 activation. TLR7 and neuronal apoptosis are implicated in other neurodegenerative diseases, including Alzheimer's disease. Therefore, TRAIL may represent a therapeutic target to slow neurodegeneration in multiple diseases.
Collapse
Affiliation(s)
- Liya Qin
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jian Zou
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Alexandra Barnett
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Ryan P. Vetreno
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Department of Psychiatry, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Fulton T. Crews
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Department of Psychiatry, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Department of Pharmacology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leon G. Coleman
- Bowles Center for Alcohol Studies, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Department of Pharmacology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
27
|
Differential expression of microRNAs in the hippocampi of male and female rodents after chronic alcohol administration. Biol Sex Differ 2020; 11:65. [PMID: 33228793 PMCID: PMC7684718 DOI: 10.1186/s13293-020-00342-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background Women are more vulnerable than men to the neurotoxicity and severe brain damage caused by chronic heavy alcohol use. In addition, brain damage due to chronic heavy alcohol use may be associated with sex-dependent epigenetic modifications. This study aimed to identify microRNAs (miRNAs) and their target genes that are differentially expressed in the hippocampi of male and female animal models in response to alcohol. Methods After chronic alcohol administration (3~3.5 g/kg/day) in male (control, n = 10; alcohol, n = 12) or female (control, n = 10; alcohol, n = 12) Sprague-Dawley rats for 6 weeks, we measured body weights and doublecortin (DCX; a neurogenesis marker) concentrations and analyzed up- or downregulated miRNAs using GeneChip miRNA 4.0 arrays. The differentially expressed miRNAs and their putative target genes were validated by RT-qPCR. Results Alcohol attenuated body weight gain only in the male group. On the other hand, alcohol led to increased serum AST in female rats and decreased serum total cholesterol concentrations in male rats. The expression of DCX was significantly reduced in the hippocampi of male alcohol-treated rats. Nine miRNAs were significantly up- or downregulated in male alcohol-treated rats, including upregulation of miR-125a-3p, let-7a-5p, and miR-3541, and downregulation of their target genes (Prdm5, Suv39h1, Ptprz1, Mapk9, Ing4, Wt1, Nkx3-1, Dab2ip, Rnf152, Ripk1, Lin28a, Apbb3, Nras, and Acvr1c). On the other hand, 7 miRNAs were significantly up- or downregulated in alcohol-treated female rats, including downregulation of miR-881-3p and miR-504 and upregulation of their target genes (Naa50, Clock, Cbfb, Arih1, Ube2g1, and Gng7). Conclusions These results suggest that chronic heavy alcohol use produces sex-dependent effects on neurogenesis and miRNA expression in the hippocampus and that sex differences should be considered when developing miRNA biomarkers to diagnose or treat alcoholics. Supplementary Information The online version contains supplementary material available at 10.1186/s13293-020-00342-3.
Collapse
|
28
|
Epigenetic and non-coding regulation of alcohol abuse and addiction. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:63-86. [PMID: 33461665 DOI: 10.1016/bs.irn.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alcohol use disorder is a chronic debilitated condition adversely affecting the lives of millions of individuals throughout the modern world. Individuals suffering from an alcohol use disorder diagnosis frequently have serious cooccurring conditions, which often further exacerbates problematic drinking behavior. Comprehending the biochemical processes underlying the progression and perpetuation of disease is essential for mitigating maladaptive behavior in order to restore both physiological and psychological health. The range of cellular and biological systems contributing to, and affected by, alcohol use disorder and other comorbid disorders necessitates a fundamental grasp of intricate functional relationships that govern molecular biology. Epigenetic factors are recognized as essential mediators of cellular behavior, orchestrating a symphony of gene expression changes within multicellular environments that are ultimately responsible for directing human behavior. Understanding the epigenetic and transcriptional regulatory mechanisms involved in the pathogenesis of disease is important for improving available pharmacotherapies and reducing the incidence of alcohol abuse and cooccurring conditions.
Collapse
|
29
|
Salem NA, Mahnke AH, Wells AB, Tseng AM, Yevtushok L, Zymak-Zakutnya N, Wertlecki W, Chambers CD, Miranda RC. Association between fetal sex and maternal plasma microRNA responses to prenatal alcohol exposure: evidence from a birth outcome-stratified cohort. Biol Sex Differ 2020; 11:51. [PMID: 32912312 PMCID: PMC7488011 DOI: 10.1186/s13293-020-00327-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
Most persons with fetal alcohol spectrum disorders (FASDs) remain undiagnosed or are diagnosed in later life. To address the need for earlier diagnosis, we previously assessed miRNAs in the blood plasma of pregnant women who were classified as unexposed to alcohol (UE), heavily exposed with affected infants (HEa), or heavily exposed with apparently unaffected infants (HEua). We reported that maternal miRNAs predicted FASD-related growth and psychomotor deficits in infants. Here, we assessed whether fetal sex influenced alterations in maternal circulating miRNAs following prenatal alcohol exposure (PAE). To overcome the loss of statistical power due to disaggregating maternal samples by fetal sex, we adapted a strategy of iterative bootstrap resampling with replacement to assess the stability of statistical parameter estimates. Bootstrap estimates of parametric and effect size tests identified male and female fetal sex-associated maternal miRNA responses to PAE that were not observed in the aggregated sample. Additionally, we observed, in HEa mothers of female, but not male fetuses, a network of co-secreted miRNAs whose expression was linked to miRNAs encoded on the X-chromosome. Interestingly, the number of significant miRNA correlations for the HEua group mothers with female fetuses was intermediate between HEa and UE mothers at mid-pregnancy, but more similar to UE mothers by the end of pregnancy. Collectively, these data show that fetal sex predicts maternal circulating miRNA adaptations, a critical consideration when adopting maternal miRNAs as diagnostic biomarkers. Moreover, a maternal co-secretion network, predominantly in pregnancies with female fetuses, emerged as an index of risk for adverse birth outcomes due to PAE.
Collapse
Affiliation(s)
- Nihal A Salem
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA.,Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA
| | - Amanda H Mahnke
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA.,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Alan B Wells
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA
| | - Alexander M Tseng
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA
| | - Lyubov Yevtushok
- Rivne Regional Medical Diagnostic Center, Rivne, Ukraine.,Lviv National Medical University, Lviv, Ukraine.,OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine
| | - Natalya Zymak-Zakutnya
- OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine.,Khmelnytsky Perinatal Center, Khmelnytsky, Ukraine
| | - Wladimir Wertlecki
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA.,OMNI-Net Ukraine Birth Defects Program, Rivne, Ukraine
| | - Christina D Chambers
- Clinical and Translational Research Institute, University of California San Diego, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, 9500 Gilman Drive MC 0828, La Jolla, San Diego, CA, 92093, USA.
| | - Rajesh C Miranda
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Medical Research and Education Bldg., Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, TX, 77807-3260, USA. .,Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, USA. .,Women's Health in Neuroscience Program, Texas A&M University Health Science Center, Bryan, TX, USA.
| | | |
Collapse
|
30
|
Identification and the potential involvement of miRNAs in the regulation of artemisinin biosynthesis in A. annua. Sci Rep 2020; 10:13614. [PMID: 32788629 PMCID: PMC7423619 DOI: 10.1038/s41598-020-69707-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Micro RNAs (miRNAs) play crucial regulatory roles in multiple biological processes. Recently they have garnered the attention for their strong influence on the secondary metabolite production in plants. Their role in the regulation of artemisinin (ART) biosynthesis is, however, not fully elucidated. ART is a potent anti-malarial compound recommended by WHO for the treatment of drug-resistant malaria. It is produced by Artemisia annua (A. annua). The lower in planta content of ART necessitates a deep understanding of regulatory mechanisms involved in the biosynthesis of this metabolite. In this study, using modern high throughput small RNA-sequencing by Illumina Nextseq 500 platform for identification and stem-loop RT PCR for validation, miRNAs were identified in the leaf sample of A. annua plant. Here, we report a total of 121 miRNAs from A. annua that target several important genes and transcription factors involved in the biosynthesis of ART. This study revealed the presence of some important conserved miRNA families, miR396, miR319, miR399, miR858, miR5083 and miR6111 not identified so far in A. annua. The expression patterns and correlation between miRNAs and their corresponding targets at different developmental stages of the plant using real-time PCR indicate that they may influence ART accumulation. These findings thus, open new possibilities for the rational engineering of the secondary metabolite pathways in general and ART biosynthesis in particular.
Collapse
|
31
|
Almeida L, Andreu-Fernández V, Navarro-Tapia E, Aras-López R, Serra-Delgado M, Martínez L, García-Algar O, Gómez-Roig MD. Murine Models for the Study of Fetal Alcohol Spectrum Disorders: An Overview. Front Pediatr 2020; 8:359. [PMID: 32760684 PMCID: PMC7373736 DOI: 10.3389/fped.2020.00359] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Prenatal alcohol exposure is associated to different physical, behavioral, cognitive, and neurological impairments collectively known as fetal alcohol spectrum disorder. The underlying mechanisms of ethanol toxicity are not completely understood. Experimental studies during human pregnancy to identify new diagnostic biomarkers are difficult to carry out beyond genetic or epigenetic analyses in biological matrices. Therefore, animal models are a useful tool to study the teratogenic effects of alcohol on the central nervous system and analyze the benefits of promising therapies. Animal models of alcohol spectrum disorder allow the analysis of key variables such as amount, timing and frequency of ethanol consumption to describe the harmful effects of prenatal alcohol exposure. In this review, we aim to synthetize neurodevelopmental disabilities in rodent fetal alcohol spectrum disorder phenotypes, considering facial dysmorphology and fetal growth restriction. We examine the different neurodevelopmental stages based on the most consistently implicated epigenetic mechanisms, cell types and molecular pathways, and assess the advantages and disadvantages of murine models in the study of fetal alcohol spectrum disorder, the different routes of alcohol administration, and alcohol consumption patterns applied to rodents. Finally, we analyze a wide range of phenotypic features to identify fetal alcohol spectrum disorder phenotypes in murine models, exploring facial dysmorphology, neurodevelopmental deficits, and growth restriction, as well as the methodologies used to evaluate behavioral and anatomical alterations produced by prenatal alcohol exposure in rodents.
Collapse
Affiliation(s)
- Laura Almeida
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Fundació Sant Joan de Déu, Barcelona, Spain
- BCNatal Barcelona Center for Maternal Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Barcelona, Spain
| | - Vicente Andreu-Fernández
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Nutrition and Health Deparment, Valencian International University (VIU), Valencia, Spain
- Grup de Recerca Infancia i Entorn (GRIE), Institut D'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elisabet Navarro-Tapia
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- BCNatal Barcelona Center for Maternal Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Barcelona, Spain
- Grup de Recerca Infancia i Entorn (GRIE), Institut D'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Aras-López
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Congenital Malformations Lab, Institute of Medicine and Molecular Genetic (INGEMM), Institute for Health Research of La Paz Universitary Hospital (IdiPAZ), Madrid, Spain
| | - Mariona Serra-Delgado
- BCNatal Barcelona Center for Maternal Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Barcelona, Spain
| | - Leopoldo Martínez
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Congenital Malformations Lab, Institute of Medicine and Molecular Genetic (INGEMM), Institute for Health Research of La Paz Universitary Hospital (IdiPAZ), Madrid, Spain
- Department of Pediatric Surgery, Hospital Universitario La Paz, Madrid, Spain
| | - Oscar García-Algar
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Grup de Recerca Infancia i Entorn (GRIE), Institut D'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Neonatology, Hospital Clínic-Maternitat, ICGON, IDIBAPS, BCNatal, Barcelona, Spain
| | - María Dolores Gómez-Roig
- Maternal and Child Health and Development Network II (SAMID II), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
- Fundació Sant Joan de Déu, Barcelona, Spain
- BCNatal Barcelona Center for Maternal Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Barcelona, Spain
| |
Collapse
|
32
|
Pascual M, Ureña-Peralta JR, Guerri C. The Regulatory Role of miRNAs in Ethanol-induced TLR4 Activation and Neuroinflammation. CURRENT PATHOBIOLOGY REPORTS 2020. [DOI: 10.1007/s40139-020-00208-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
33
|
Kozell LB, Lockwood D, Darakjian P, Edmunds S, Shepherdson K, Buck KJ, Hitzemann R. RNA-Seq Analysis of Genetic and Transcriptome Network Effects of Dual-Trait Selection for Ethanol Preference and Withdrawal Using SOT and NOT Genetic Models. Alcohol Clin Exp Res 2020; 44:820-830. [PMID: 32090358 PMCID: PMC7169974 DOI: 10.1111/acer.14312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Genetic factors significantly affect alcohol consumption and vulnerability to withdrawal. Furthermore, some genetic models showing predisposition to severe withdrawal are also predisposed to low ethanol (EtOH) consumption and vice versa, even when tested independently in naïve animals. METHODS Beginning with a C57BL/6J × DBA/2J F2 intercross founder population, animals were simultaneously selectively bred for both high alcohol consumption and low acute withdrawal (SOT line), or vice versa (NOT line). Using randomly chosen fourth selected generation (S4) mice (N = 18-22/sex/line), RNA-Seq was employed to assess genome-wide gene expression in ventral striatum. The MegaMUGA array was used to detect genome-wide genotypic differences. Differential gene expression and the weighted gene co-expression network analysis were implemented as described elsewhere (Genes Brain Behav 16, 2017, 462). RESULTS The new selection of the SOT and NOT lines was similar to that reported previously (Alcohol Clin Exp Res 38, 2014, 2915). One thousand eight hundred and sixteen transcripts were detected as differentially expressed between the lines. For genes more highly expressed in the SOT line, there was enrichment in genes associated with cell adhesion, synapse organization, and postsynaptic membrane. The genes with a cell adhesion annotation included 23 protocadherins, Mpdz and Dlg2. Genes with a postsynaptic membrane annotation included Gabrb3, Gphn, Grid1, Grin2b, Grin2c, and Grm3. The genes more highly expressed in the NOT line were enriched in a network module (red) with annotations associated with mitochondrial function. Several of these genes were module hub nodes, and these included Nedd8, Guk1, Elof1, Ndufa8, and Atp6v1f. CONCLUSIONS Marked effects of selection on gene expression were detected. The NOT line was characterized by higher expression of hub nodes associated with mitochondrial function. Genes more highly expressed in the SOT aligned with previous findings, for example, Colville and colleagues (Genes Brain Behav 16, 2017, 462) that both high EtOH preference and consumption are associated with effects on cell adhesion and glutamate synaptic plasticity.
Collapse
Affiliation(s)
- Laura B Kozell
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Denesa Lockwood
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Priscila Darakjian
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Stephanie Edmunds
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Karen Shepherdson
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Kari J Buck
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| | - Robert Hitzemann
- From the, Department of Behavioral Neuroscience, VA Portland Health Care System, Oregon Health & Science University, Portland, Oregon
| |
Collapse
|
34
|
Walter NAR, Zheng CL, Searles RP, McWeeney SK, Grant KA, Hitzemann R. Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46. Alcohol Clin Exp Res 2020; 44:470-478. [PMID: 31840818 PMCID: PMC7018568 DOI: 10.1111/acer.14259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/05/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genome-wide profiling to examine brain transcriptional features associated with excessive ethanol (EtOH) consumption has been applied to a variety of species including rodents, nonhuman primates (NHPs), and humans. However, these data were obtained from cross-sectional samples which are particularly vulnerable to individual variation when obtained from small outbred populations typical of human and NHP studies. In the current study, a novel within-subject design was used to examine the effects of voluntary EtOH consumption on prefrontal cortex (PFC) gene expression in a NHP model. METHODS Two cohorts of cynomolgus macaques (n = 23) underwent a schedule-induced polydipsia procedure to establish EtOH self-administration followed by 6 months of daily open access to EtOH (4% w/v) and water. Individual daily EtOH intakes ranged from an average of 0.7 to 3.7 g/kg/d. Dorsal lateral PFC area 46 (A46) brain biopsies were collected in EtOH-naïve and control monkeys; contralateral A46 biopsies were collected from the same monkeys following the 6 months of fluid consumption. Gene expression changes were assessed using RNA-Seq paired analysis, which allowed for correction of individual baseline differences in gene expression. RESULTS A total of 675 genes were significantly down-regulated following EtOH consumption; these were functionally enriched for immune response, cell adhesion, plasma membrane, and extracellular matrix. A total of 567 genes that were up-regulated following EtOH consumption were enriched in microRNA target sites and included target sites associated with Toll-like receptor pathways. The differentially expressed genes were also significantly enriched in transcription factor binding sites. CONCLUSIONS The data presented here are the first to use a longitudinal biopsy strategy to examine how chronic EtOH consumption affects gene expression in the primate PFC. Prominent effects were seen in both cell adhesion and neuroimmune pathways; the latter contained both pro- and antiinflammatory genes. The data also indicate that changes in miRNAs and transcription factors may be important epigenetic regulators of EtOH consumption.
Collapse
Affiliation(s)
- Nicole A R Walter
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon.,Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Christina L Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Robert P Searles
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon.,Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| |
Collapse
|
35
|
Dhahbi J, Nunez Lopez YO, Schneider A, Victoria B, Saccon T, Bharat K, McClatchey T, Atamna H, Scierski W, Golusinski P, Golusinski W, Masternak MM. Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half. Front Oncol 2019; 9:959. [PMID: 31616639 PMCID: PMC6775249 DOI: 10.3389/fonc.2019.00959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.
Collapse
Affiliation(s)
- Joseph Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Tatiana Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Krish Bharat
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Thaddeus McClatchey
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Hani Atamna
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Wojciech Scierski
- Department of Otorhinolaryngology and Laryngological Oncology in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Zielona Gora, Poland
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| |
Collapse
|
36
|
Identifying Interaction Clusters for MiRNA and MRNA Pairs in TCGA Network. Genes (Basel) 2019; 10:genes10090702. [PMID: 31514484 PMCID: PMC6770970 DOI: 10.3390/genes10090702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022] Open
Abstract
Existing methods often fail to recognize the conversions for the biological roles of the pairs of genes and microRNAs (miRNAs) between the tumor and normal samples. We have developed a novel cluster scoring method to identify messenger RNA (mRNA) and miRNA interaction pairs and clusters while considering tumor and normal samples jointly. Our method has identified 54 significant clusters for 15 cancer types selected from The Cancer Genome Atlas project. We also determined the shared clusters across tumor types and/or subtypes. In addition, we compared gene and miRNA overlap between lists identified in our liver hepatocellular carcinoma (LIHC) study and regulatory relationships reported from human and rat nonalcoholic fatty liver disease studies (NAFLD). Finally, we analyzed biological functions for the single significant cluster in LIHC and uncovered a significantly enriched pathway (phospholipase D signaling pathway) with six genes represented in the cluster, symbols: DGKQ, LPAR2, PDGFRB, PIK3R3, PTGFR and RAPGEF3.
Collapse
|
37
|
Ding L, Feng Z, Bai Y. Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms. BMC Med Genomics 2019; 12:117. [PMID: 31382962 PMCID: PMC6683425 DOI: 10.1186/s12920-019-0562-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Background microRNA (miRNA) is a short RNA (~ 22 nt) that regulates gene expression at the posttranscriptional level. Aberration of miRNA expressions could affect their targeting mRNAs involved in cancer-related signaling pathways. We conduct clustering analysis of miRNA and mRNA using expression data from the Cancer Genome Atlas (TCGA). We combine the Hungarian algorithm and blossom algorithm in graph theory. Data analysis is done using programming language R and Python. Methods We first quantify edge-weights of the miRNA-mRNA pairs by combining their expression correlation coefficient in tumor (T_CC) and correlation coefficient in normal (N_CC). We thereby introduce a bipartite graph partition procedure to identify cluster candidates. Specifically, we propose six weight formulas to quantify the change of miRNA-mRNA expression T_CC relative to N_CC, and apply the traditional hierarchical clustering to subjectively evaluate the different weight formulas of miRNA-mRNA pairs. Among these six different weight formulas, we choose the optimal one, which we define as the integrated mean value weights, to represent the connections between miRNA and mRNAs. Then the Hungarian algorithm and the blossom algorithm are employed on the miRNA-mRNA bipartite graph to passively determine the clusters. The combination of Hungarian and the blossom algorithms is dubbed maximum weighted merger method (MWMM). Results MWMM identifies clusters of different sizes that meet the mathematical criterion that internal connections inside a cluster are relatively denser than external connections outside the cluster and biological criterion that the intra-cluster Gene Ontology (GO) term similarities are larger than the inter-cluster GO term similarities. MWMM is developed using breast invasive carcinoma (BRCA) as training data set, but can also applies to other cancer type data sets. MWMM shows advantage in GO term similarity in most cancer types, when compared to other algorithms. Conclusions miRNAs and mRNAs that are likely to be affected by common underlying causal factors in cancer can be clustered by MWMM approach and potentially be used as candidate biomarkers for different cancer types and provide clues for targets of precision medicine in cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12920-019-0562-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lizhong Ding
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Zheyun Feng
- Department of Mathematics and Computer Science, Indiana State University, Terre Haute, IN, 47809, USA
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. .,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA.
| |
Collapse
|
38
|
Ethanol and caffeine consumption modulates the expression of miRNAs in the cerebellum and plasma of UChB rats. Life Sci 2019; 229:180-186. [DOI: 10.1016/j.lfs.2019.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022]
|
39
|
Most D, Salem NA, Tiwari GR, Blednov YA, Mayfield RD, Harris RA. Silencing synaptic MicroRNA-411 reduces voluntary alcohol consumption in mice. Addict Biol 2019; 24:604-616. [PMID: 29665166 DOI: 10.1111/adb.12625] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/09/2018] [Accepted: 03/19/2018] [Indexed: 12/12/2022]
Abstract
Chronic alcohol consumption alters the levels of microRNAs and mRNAs in the brain, but the specific microRNAs and processes that target mRNAs to affect cellular function and behavior are not known. We examined the in vivo manipulation of previously identified alcohol-responsive microRNAs as potential targets to reduce alcohol consumption. Silencing of miR-411 by infusing antagomiR-411 into the prefrontal cortex of female C57BL/6J mice reduced alcohol consumption and preference, without altering total fluid consumption, saccharin consumption, or anxiety-related behaviors. AntagomiR-411 reduced alcohol consumption when given to mice exposed to a chronic alcohol drinking paradigm but did not affect the acquisition of consumption in mice without a history of alcohol exposure, suggesting that antagomiR-411 has a neuroadaptive, alcohol-dependent effect. AntagomiR-411 decreased the levels of miR-411, as well as the association of immunoprecipitated miR-411 with Argonaute2; and, it increased levels of Faah and Ppard mRNAs. Moreover, antagomiR-411 increased the neuronal expression of glutamate receptor AMPA-2 protein, a known alcohol target and a predicted target of miR-411. These results suggest that alcohol and miR-411 function in a homeostatic manner to regulate synaptic mRNA and protein, thus reversing alcohol-related neuroadaptations and reducing chronic alcohol consumption.
Collapse
Affiliation(s)
- Dana Most
- Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at Austin Austin TX USA
- Institute for NeuroscienceUniversity of Texas at Austin Austin TX USA
| | - Nihal A. Salem
- Texas A&M Institute for Neuroscience and Department of Neuroscience and Experimental Therapeutics, College of MedicineTexas A&M University College Station TX USA
| | - Gayatri R. Tiwari
- Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at Austin Austin TX USA
| | - Yuri A. Blednov
- Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at Austin Austin TX USA
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at Austin Austin TX USA
| | - R. Adron Harris
- Waggoner Center for Alcohol and Addiction ResearchThe University of Texas at Austin Austin TX USA
- Institute for NeuroscienceUniversity of Texas at Austin Austin TX USA
| |
Collapse
|
40
|
Abstract
Innate immune signaling is an important feature in the pathology of alcohol use disorders. Alcohol abuse causes persistent innate immune activation in the brain. This is seen in postmortem human alcoholic brain specimens, as well as in primate and rodent models of alcohol consumption. Further, in vitro models of alcohol exposure in neurons and glia also demonstrate innate immune activation. The activation of the innate immune system seems to be important in the development of alcohol use pathology, as anti-immune therapies reduce pathology and ethanol self-administration in rodent models. Further, innate immune activation has been identified in each of the stages of addiction: binge/intoxication, withdrawal/negative affect, and preoccupation/craving. This suggests that innate immune activation may play a role both in the development and maintenance of alcoholic pathology. In this chapter, we discuss the known contributions of innate immune signaling in the pathology of alcohol use disorders, and present potential therapeutic interventions that may be beneficial for alcohol use disorders.
Collapse
Affiliation(s)
- Leon G Coleman
- Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Fulton T Crews
- Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
41
|
Engel GL, Taber K, Vinton E, Crocker AJ. Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2019; 15:7. [PMID: 30992041 PMCID: PMC6469124 DOI: 10.1186/s12993-019-0159-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/04/2019] [Indexed: 02/08/2023]
Abstract
Our understanding of the networks of genes and protein functions involved in Alcohol Use Disorder (AUD) remains incomplete, as do the mechanisms by which these networks lead to AUD phenotypes. The fruit fly (Drosophila melanogaster) is an efficient model for functional and mechanistic characterization of the genes involved in alcohol behavior. The fly offers many advantages as a model organism for investigating the molecular and cellular mechanisms of alcohol-related behaviors, and for understanding the underlying neural circuitry driving behaviors, such as locomotor stimulation, sedation, tolerance, and appetitive (reward) learning and memory. Fly researchers are able to use an extensive variety of tools for functional characterization of gene products. To understand how the fly can guide our understanding of AUD in the era of Big Data we will explore these tools, and review some of the gene networks identified in the fly through their use, including chromatin-remodeling, glial, cellular stress, and innate immunity genes. These networks hold great potential as translational drug targets, making it prudent to conduct further research into how these gene mechanisms are involved in alcohol behavior.
Collapse
Affiliation(s)
- Gregory L. Engel
- Department of Psychological Sciences, Castleton University, Castleton, VT 05735 USA
| | - Kreager Taber
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Elizabeth Vinton
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| | - Amanda J. Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753 USA
| |
Collapse
|
42
|
Yan S, Wang Q, Huo Z, Yang T, Yin X, Wang Z, Zhang Z, Wu H. Gene expression profiles between cystic and solid vestibular schwannoma indicate susceptible molecules and pathways in the cystic formation of vestibular schwannoma. Funct Integr Genomics 2019; 19:673-684. [PMID: 30953268 PMCID: PMC6570702 DOI: 10.1007/s10142-019-00672-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/22/2019] [Accepted: 03/06/2019] [Indexed: 12/29/2022]
Abstract
Previous research has shown that although NF2 gene mutation is the major cause of vestibular schwannoma (VS), it may not directly participate in cystic VS (CVS). To elucidate the underlying potential genetic mechanisms in the cystic formation of VS, we compared differences in gene expression between solid VS (SVS) and CVS via a bioinformatics analysis. The cDNA microarray method and miRNA sequencing were performed on 29 representative VSs (17 CVSs and 12 SVSs). A differential expression analysis was used to identify differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs). Then, miRNA-mRNA regulatory networks were constructed. Gene ontology (GO), a KEGG pathway enrichment analysis, and the protein-protein interaction (PPI) were used to analyze the co-differentially expressed DEmRNAs at the functional level. From the differential expression analyses, 1304 DEmRNAs, 55 DEmiRNAs, and hub genes including PTEN, FOXO1, FOXO3, VEGFA, and SIRT1 were identified. Histological evidence is presented to confirm the makeup of the hubs, which corresponded with the cDNA microarray. Our analysis revealed that the maps of apoptosis, cellular response to hypoxia, and the PI3K-Akt, AMPK, FOXO, and chemokine signaling pathways were significantly enriched. In addition, the TUNEL assay, immunoblotting analysis, and transmission electron microscope revealed increased degenerative changes in CVS. These findings could be the foundation for understanding the potential role of differential genes in the cystic formation of VS and be helpful in exploring the potential biomarkers for the differential diagnosis, prognosis, and development of drug targets for CVS.
Collapse
Affiliation(s)
- Shuang Yan
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Quan Wang
- Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.,Department of Otolaryngology & Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zirong Huo
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Tao Yang
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Xiaoling Yin
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Zhaoyan Wang
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Zhihua Zhang
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
| | - Hao Wu
- Department of Otorhinolaryngology, Head & Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
| |
Collapse
|
43
|
Warden AS, Azzam M, DaCosta A, Mason S, Blednov YA, Messing RO, Mayfield RD, Harris RA. Toll-like receptor 3 activation increases voluntary alcohol intake in C57BL/6J male mice. Brain Behav Immun 2019; 77:55-65. [PMID: 30550931 PMCID: PMC6399060 DOI: 10.1016/j.bbi.2018.12.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 11/21/2018] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Many genes differentially expressed in brain tissue from human alcoholics and animals that have consumed large amounts of alcohol are components of the innate immune toll-like receptor (TLR) pathway. TLRs initiate inflammatory responses via two branches: (1) MyD88-dependent or (2) TRIF-dependent. All TLRs signal through MyD88 except TLR3. Prior work demonstrated a direct role for MyD88-dependent signaling in regulation of alcohol consumption. However, the role of TLR3 as a potential regulator of excessive alcohol drinking has not previously been investigated. To test the possibility TLR3 activation regulates alcohol consumption, we injected mice with the TLR3 agonist polyinosinic:polycytidylic acid (poly(I:C)) and tested alcohol consumption in an every-other-day two-bottle choice test. Poly(I:C) produced a persistent increase in alcohol intake that developed over several days. Repeated poly(I:C) and ethanol exposure altered innate immune transcript abundance; increased levels of TRIF-dependent pathway components correlated with increased alcohol consumption. Administration of poly(I:C) before exposure to alcohol did not alter alcohol intake, suggesting that poly(I:C) and ethanol must be present together to change drinking behavior. To determine which branch of TLR signaling mediates poly(I:C)-induced changes in drinking behavior, we tested either mice lacking MyD88 or mice administered a TLR3/dsRNA complex inhibitor. MyD88 null mutants showed poly(I:C)-induced increases in alcohol intake. In contrast, mice pretreated with a TLR3/dsRNA complex inhibitor reduced their alcohol intake, suggesting poly(I:C)-induced escalations in alcohol intake are, at least partially, dependent on TLR3. Together, these results strongly suggest that TLR3-dependent signaling drives excessive alcohol drinking behavior.
Collapse
Affiliation(s)
- Anna S Warden
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA.
| | - Moatasem Azzam
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
| | - Adriana DaCosta
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
| | - Sonia Mason
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
| | - Yuri A Blednov
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert O Messing
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA; Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
44
|
Grantham EK, Farris SP. Bioinformatic and biological avenues for understanding alcohol use disorder. Alcohol 2019; 74:65-71. [PMID: 30144960 PMCID: PMC8939236 DOI: 10.1016/j.alcohol.2018.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 11/21/2022]
Abstract
Alcohol Use Disorder (AUD) is a multifarious psychiatric condition resulting from complex relationships between genetics, gene expression, neuroadaptations, and environmental influences. Understanding these complex relationships is essential to uncovering the mechanisms involved in the development and progression of AUD, with the ultimate goal of devising effective behavioral and therapeutic interventions. Technical advances in the fields of omics-based research and bioinformatics have yielded insights into gene interactions, biological networks, and cellular responses across humans and animal models. This review highlights several of the newly developed sequencing methodologies and resultant discoveries in neuroscience, as well as the importance of a multi-faceted and integrative approach for determining causal factors in AUD.
Collapse
Affiliation(s)
- Emily K Grantham
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712-1095, United States
| | - Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712-1095, United States.
| |
Collapse
|
45
|
Nunez Lopez YO, Retnakaran R, Zinman B, Pratley RE, Seyhan AA. Predicting and understanding the response to short-term intensive insulin therapy in people with early type 2 diabetes. Mol Metab 2019; 20:63-78. [PMID: 30503831 PMCID: PMC6358589 DOI: 10.1016/j.molmet.2018.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Short-term intensive insulin therapy (IIT) early in the course of type 2 diabetes acutely improves beta-cell function with long-lasting effects on glycemic control. However, conventional measures cannot determine which patients are better suited for IIT, and little is known about the molecular mechanisms determining response. Therefore, this study aimed to develop a model that could accurately predict the response to IIT and provide insight into molecular mechanisms driving such response in humans. METHODS Twenty-four patients with early type 2 diabetes were assessed at baseline and four weeks after IIT, consisting of basal detemir and premeal insulin aspart. Twelve individuals had a beneficial beta-cell response to IIT (responders) and 12 did not (nonresponders). Beta-cell function was assessed by multiple methods, including Insulin Secretion-Sensitivity Index-2. MicroRNAs (miRNAs) were profiled in plasma samples before and after IIT. The response to IIT was modeled using a machine learning algorithm and potential miRNA-mediated regulatory mechanisms assessed by differential expression, correlation, and functional network analyses (FNA). RESULTS Baseline levels of circulating miR-145-5p, miR-29c-3p, and HbA1c accurately (91.7%) predicted the response to IIT (OR = 121 [95% CI: 6.7, 2188.3]). Mechanistically, a previously described regulatory loop between miR-145-5p and miR-483-3p/5p, which controls TP53-mediated apoptosis, appears to also occur in our study population of humans with early type 2 diabetes. In addition, significant (fold change > 2, P < 0.05) longitudinal changes due to IIT in the circulating levels of miR-138-5p, miR-192-5p, miR-195-5p, miR-320b, and let-7a-5p further characterized the responder group and significantly correlated (|r| > 0.4, P < 0.05) with the changes in measures of beta-cell function and insulin sensitivity. FNA identified a network of coordinately/cooperatively regulated miRNA-targeted genes that potentially drives the IIT response through negative regulation of apoptotic processes that underlie beta cell dysfunction and concomitant positive regulation of proliferation. CONCLUSIONS Responses to IIT in people with early type 2 diabetes are associated with characteristic miRNA signatures. This study represents a first step to identify potential responders to IIT (a current limitation in the field) and provides important insight into the pathophysiologic determinants of the reversibility of beta-cell dysfunction. ClinicalTrial.gov identifier: NCT01270789.
Collapse
Affiliation(s)
- Yury O Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA
| | - Ravi Retnakaran
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bernard Zinman
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Richard E Pratley
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA.
| | - Attila A Seyhan
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL 32804, USA; The Chemical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
46
|
Oliver RJ, Mandyam CD. Regulation of Adult Neurogenesis by Non-coding RNAs: Implications for Substance Use Disorders. Front Neurosci 2018; 12:849. [PMID: 30524229 PMCID: PMC6261985 DOI: 10.3389/fnins.2018.00849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/30/2018] [Indexed: 12/25/2022] Open
Abstract
The discovery of non-coding RNAs (ncRNAs)has been one of the central findings from early genomic sequencing studies. Not only was the presence of these genes unknown previously, it was the staggering disproportionate share of the genome that was predicted to be encoded by ncRNAs that was truly significant in genomic research. Over the years the function of various classes of these ncRNAs has been revealed. One of the first and enduring regulatory programs associated with these factors was development. In the neurosciences, the discovery of adult derived populations of dividing cells within the brain was equally substantial. The brain was hypothesized to be plastic only in its neuronal connectivity, but the discovery of the generation of new neurons was a novel mechanism of neuronal and behavioral plasticity. The process of adult neurogenesis resembles early neuronal development and has been found to share many parallels in the proper stages of specified genetic programs. Adult neurogenesis has also been found to play a role in learning and memory involved in particular hippocampal-dependent behaviors. Substance use disorders (SUDs) are an example of a behavioral condition that is associated with and possibly driven by hippocampal alterations. Our laboratory has determined that hippocampal adult neurogenesis is necessary for a rodent model of methamphetamine relapse. Due to the previous research on ncRNAs in development and in other brain regions involved in SUDs, we posit that ncRNAs may play a role in adult neurogenesis associated with this disorder. This review will cover the regulatory mechanisms of various classes of ncRNAs on the coordinated genetic program associated with adult neurogenesis with a special focus on how these programs could be dysregulated in SUDs.
Collapse
Affiliation(s)
- Robert J Oliver
- VA San Diego Healthcare System, San Diego, CA, United States
| | - Chitra D Mandyam
- VA San Diego Healthcare System, San Diego, CA, United States
- Department of Anesthesiology, University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
47
|
De Oliveira PSN, Coutinho LL, Tizioto PC, Cesar ASM, de Oliveira GB, Diniz WJDS, De Lima AO, Reecy JM, Mourão GB, Zerlotini A, Regitano LCA. An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. Sci Rep 2018; 8:17072. [PMID: 30459456 PMCID: PMC6244318 DOI: 10.1038/s41598-018-35315-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA's target genes and miRNA-mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
Collapse
Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Wellison J da S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Andressa O De Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | |
Collapse
|
48
|
Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. Sci Rep 2018; 8:15913. [PMID: 30374194 PMCID: PMC6206094 DOI: 10.1038/s41598-018-34277-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Alcohol abuse can induce brain injury and neurodegeneration, and recent evidence shows the participation of immune receptors toll-like in the neuroinflammation and brain damage. We evaluated the role of miRNAs as potential modulators of the neuroinflammation associated with alcohol abuse and the influence of the TLR4 response. Using mice cerebral cortex and next-generation sequencing (NGS), we identified miRNAs that were differentially expressed in the chronic alcohol-treated versus untreated WT or TLR4-KO mice. We observed a differentially expression of miR-183 Cluster (C) (miR-96/-182/-183), miR-200a and miR-200b, which were down-regulated, while mirR-125b was up-regulated in alcohol-treated WT versus (vs.) untreated mice. These miRNAs modulate targets genes related to the voltage-gated sodium channel, neuron hyperexcitability (Nav1.3, Trpv1, Smad3 and PP1-γ), as well as genes associated with innate immune TLR4 signaling response (Il1r1, Mapk14, Sirt1, Lrp6 and Bdnf). Functional enrichment of the miR-183C and miR-200a/b family target genes, revealed neuroinflammatory pathways networks involved in TLR4 signaling and alcohol abuse. The changes in the neuroinflammatory targets genes associated with alcohol abuse were mostly abolished in the TLR4-KO mice. Our results show the relationship between alcohol intake and miRNAs expression and open up new therapeutically targets to prevent deleterious effects of alcohol on the brain.
Collapse
|
49
|
Demin KA, Meshalkina DA, Kysil EV, Antonova KA, Volgin AD, Yakovlev OA, Alekseeva PA, Firuleva MM, Lakstygal AM, de Abreu MS, Barcellos LJG, Bao W, Friend AJ, Amstislavskaya TG, Rosemberg DB, Musienko PE, Song C, Kalueff AV. Zebrafish models relevant to studying central opioid and endocannabinoid systems. Prog Neuropsychopharmacol Biol Psychiatry 2018; 86:301-312. [PMID: 29604314 DOI: 10.1016/j.pnpbp.2018.03.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/19/2022]
Abstract
The endocannabinoid and opioid systems are two interplaying neurotransmitter systems that modulate drug abuse, anxiety, pain, cognition, neurogenesis and immune activity. Although they are involved in such critical functions, our understanding of endocannabinoid and opioid physiology remains limited, necessitating further studies, novel models and new model organisms in this field. Zebrafish (Danio rerio) is rapidly emerging as one of the most effective translational models in neuroscience and biological psychiatry. Due to their high physiological and genetic homology to humans, zebrafish may be effectively used to study the endocannabinoid and opioid systems. Here, we discuss current models used to target the endocannabinoid and opioid systems in zebrafish, and their potential use in future translational research and high-throughput drug screening. Emphasizing the high degree of conservation of the endocannabinoid and opioid systems in zebrafish and mammals, we suggest zebrafish as an excellent model organism to study these systems and to search for the new drugs and therapies targeting their evolutionarily conserved mechanisms.
Collapse
Affiliation(s)
- Konstantin A Demin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Russian Research Center for Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Darya A Meshalkina
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Russian Research Center for Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Elana V Kysil
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kristina A Antonova
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey D Volgin
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Medical Military Academy, St. Petersburg, Russia
| | - Oleg A Yakovlev
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Medical Military Academy, St. Petersburg, Russia
| | - Polina A Alekseeva
- Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Maria M Firuleva
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo (UPF), Passo Fundo, RS, Brazil; Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Leonardo J G Barcellos
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil; Graduate Programs in Environmental Sciences, and Bio-Experimentation, University of Passo Fundo (UPF), Passo Fundo, Brazil; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Wandong Bao
- School of Pharmacy, Southwest University, Chongqing, China
| | - Ashton J Friend
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Tamara G Amstislavskaya
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Laboratory of Translational Biopsychiatry, Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; Neuroscience Department, Novosibirsk State University, Novosibirsk, Russia
| | - Denis B Rosemberg
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Pavel E Musienko
- Laboratory of Neuroprosthetics, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Laboratory of Motor Physiology, Pavlov Institute of Physiology RAS, St. Petersburg, Russia; Laboratory of Neurophysiology and Experimental Neurorehabilitation, St. Petersburg State Research Institute of Phthysiopulmonology, Ministry of Health, St. Petersburg, Russia; Russian Research Center of Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia
| | - Cai Song
- Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, China; Marine Medicine Research and Development Center, Shenzhen Institute of Guangdong Ocean University, Shenzhen, China
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Laboratory of Translational Biopsychiatry, Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; Neuroscience Department, Novosibirsk State University, Novosibirsk, Russia; ZENEREI Research Center, Slidell, LA, USA; Russian Research Center of Radiology and Surgical Technologies, Ministry of Health, St. Petersburg, Russia; Ural Federal University, Ekaterinburg, Russia; Aquatic Laboratory, Institute of Experimental Medicine, Almazov National Medical Research Centre, St. Petersburg, Russia.
| |
Collapse
|
50
|
Rudra P, Shi WJ, Russell P, Vestal B, Tabakoff B, Hoffman P, Kechris K, Saba L. Predictive modeling of miRNA-mediated predisposition to alcohol-related phenotypes in mouse. BMC Genomics 2018; 19:639. [PMID: 30157779 PMCID: PMC6114181 DOI: 10.1186/s12864-018-5004-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that bind messenger RNAs and promote their degradation or repress their translation. There is increasing evidence of miRNAs playing an important role in alcohol related disorders. However, the role of miRNAs as mediators of the genetic effect on alcohol phenotypes is not fully understood. We conducted a high-throughput sequencing study to measure miRNA expression levels in alcohol naïve animals in the LXS panel of recombinant inbred (RI) mouse strains. We then combined the sequencing data with genotype data, microarry gene expression data, and data on alcohol-related behavioral phenotypes such as 'Drinking in the dark', 'Sleep time', and 'Low dose activation' from the same RI panel. SNP-miRNA-gene triplets with strong association within the triplet that were also associated with one of the 4 alcohol phenotypes were selected and a Bayesian network analysis was used to aggregate results into a directed network model. RESULTS We found several triplets with strong association within the triplet that were also associated with one of the alcohol phenotypes. The Bayesian network analysis found two networks where a miRNA mediates the genetic effect on the alcohol phenotype. The miRNAs were found to influence the expression of protein-coding genes, which in turn influences the quantitative phenotypes. The pathways in which these genes are enriched have been previously associated with alcohol-related traits. CONCLUSION This work enhances association studies by identifying miRNAs that may be mediating the association between genetic markers (SNPs) and the alcohol phenotypes. It suggests a mechanism of how genetic variants are affecting traits of interest through the modification of miRNA expression.
Collapse
Affiliation(s)
- Pratyaydipta Rudra
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, 80045 CO USA
| | - Wen J. Shi
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, 80045 CO USA
| | - Pamela Russell
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, 80045 CO USA
| | - Brian Vestal
- Center for Genes, Environment and Health, National Jewish Health, Denver, 80206 CO USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, 80045 CO USA
| | - Paula Hoffman
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, 80045 CO USA
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, 80045 CO USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, 80045 CO USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, 80045 CO USA
| |
Collapse
|