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Vannan A, Dell’Orco M, Perrone-Bizzozero NI, Neisewander JL, Wilson MA. An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case. G3 (BETHESDA, MD.) 2023; 13:jkad143. [PMID: 37433118 PMCID: PMC10542560 DOI: 10.1093/g3journal/jkad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023]
Abstract
RNA-sequencing (RNA-seq) technology has led to a surge of neuroscience research using animal models to probe the complex molecular mechanisms underlying brain function and behavior, including substance use disorders. However, findings from rodent studies often fail to be translated into clinical treatments. Here, we developed a novel pipeline for narrowing candidate genes from preclinical studies by translational potential and demonstrated its utility in 2 RNA-seq studies of rodent self-administration. This pipeline uses evolutionary conservation and preferential expression of genes across brain tissues to prioritize candidate genes, increasing the translational utility of RNA-seq in model organisms. Initially, we demonstrate the utility of our prioritization pipeline using an uncorrected P-value. However, we found no differentially expressed genes in either dataset after correcting for multiple testing with false discovery rate (FDR < 0.05 or <0.1). This is likely due to low statistical power that is common across rodent behavioral studies, and, therefore, we additionally illustrate the use of our pipeline on a third dataset with differentially expressed genes corrected for multiple testing (FDR < 0.05). We also advocate for improved RNA-seq data collection, statistical testing, and metadata reporting that will bolster the field's ability to identify reliable candidate genes and improve the translational value of bioinformatics in rodent research.
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Affiliation(s)
- Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Michela Dell’Orco
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Nora I Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico Health Science Center, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Janet L Neisewander
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287-4501, USA
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2
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Blum K, Gold MS, Cadet JL, Gondre-Lewis MC, McLaughlin T, Braverman ER, Elman I, Paul Carney B, Cortese R, Abijo T, Bagchi D, Giordano J, Dennen CA, Baron D, Thanos PK, Soni D, Makale MT, Makale M, Murphy KT, Jafari N, Sunder K, Zeine F, Ceccanti M, Bowirrat A, Badgaiyan RD. Invited Expert Opinion- Bioinformatic and Limitation Directives to Help Adopt Genetic Addiction Risk Screening and Identify Preaddictive Reward Dysregulation: Required Analytic Evidence to Induce Dopamine Homeostatsis. MEDICAL RESEARCH ARCHIVES 2023; 11:10.18103/mra.v11i8.4211. [PMID: 37885438 PMCID: PMC10601302 DOI: 10.18103/mra.v11i8.4211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Addiction, albeit some disbelievers like Mark Lewis [1], is a chronic, relapsing brain disease, resulting in unwanted loss of control over both substance and non- substance behavioral addictions leading to serious adverse consequences [2]. Addiction scientists and clinicians face an incredible challenge in combatting the current opioid and alcohol use disorder (AUD) pandemic throughout the world. Provisional data from the Centers for Disease Control and Prevention (CDC) shows that from July 2021-2022, over 100,000 individuals living in the United States (US) died from a drug overdose, and 77,237 of those deaths were related to opioid use [3]. This number is expected to rise, and according to the US Surgeon General it is highly conceivable that by 2025 approximately 165,000 Americans will die from an opioid overdose. Alcohol abuse, according to data from the World Health Organization (WHO), results in 3 million deaths worldwide every year, which represents 5.3% of all deaths globally [4].
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Affiliation(s)
- Kenneth Blum
- The Kenneth Blum Behavioral & Neurogenetic Institute, Austin, TX., USA
- Division of Addiction Research & Education, Center for Sports, Exercise & Psychiatry, Western University Health Sciences, Pomona, CA., USA
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Psychiatry, School of Medicine, University of Vermont, Burlington, VT.,USA
- Department of Psychiatry, Wright State University Boonshoft School of Medicine and Dayton VA Medical Centre, Dayton, OH, USA
- Division of Nutrigenomics Research, TranspliceGen Therapeutics, Inc., Austin, Tx., 78701, USA
- Department of Nutrigenomic Research, Victory Nutrition International, Inc., Bonita Springs, FL, USA
- Division of Personalized Medicine, Cross-Cultural Research and Educational Institute, San Clemente, CA., USA
- Sunder Foundation, Palm Springs, CA, USA
- Department of Molecular Biology and Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Mark S Gold
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO., USA
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD., USA
| | - Marjorie C. Gondre-Lewis
- Neuropsychopharmacology Laboratory, Department of Anatomy, Howard University College of Medicine, Washington, DC., USA
| | - Thomas McLaughlin
- Division of Nutrigenomics Research, TranspliceGen Therapeutics, Inc., Austin, Tx., 78701, USA
| | - Eric R Braverman
- The Kenneth Blum Behavioral & Neurogenetic Institute, Austin, TX., USA
| | - Igor Elman
- Center for Pain and the Brain (P.A.I.N Group), Department of Anesthesiology, Critical Care & Pain Medicine, Boston Children’s Hospital, Boston, MA., USA
| | - B. Paul Carney
- Division Pediatric Neurology, University of Missouri, School of Medicine, Columbia, MO., USA
| | - Rene Cortese
- Department of Child Health – Child Health Research Institute, & Department of Obstetrics, Gynecology and Women’s Health School of Medicine, University of Missouri, MO., USA
| | - Tomilowo Abijo
- Neuropsychopharmacology Laboratory, Department of Anatomy, Howard University College of Medicine, Washington, DC., USA
| | - Debasis Bagchi
- Department of Pharmaceutical Sciences, Texas Southern University College of Pharmacy and Health Sciences, Houston, TX, USA
| | - John Giordano
- Division of Personalized Mental Illness Treatment & Research, Ketamine Infusion Clinics of South Florida, Pompano Beach, Fl., USA
| | - Catherine A. Dennen
- Department of Family Medicine, Jefferson Health Northeast, Philadelphia, PA, USA
| | - David Baron
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Panayotis K Thanos
- Behavioral Neuropharmacology and Neuroimaging Laboratory on Addictions, Clinical Research Institute on Addictions, Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biosciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Psychology, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Diwanshu Soni
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA., USA
| | - Milan T. Makale
- Department of Radiation Medicine and Applied Sciences, UC San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, USA
| | - Miles Makale
- Department of Psychology, UC San Diego, Health Sciences Drive, La Jolla, CA, 92093, USA
| | | | - Nicole Jafari
- Department of Human Development, California State University at long Beach, Long Beach, CA., USA
- Division of Personalized Medicine, Cross-Cultural Research and Educational Institute, San Clemente, CA., USA
| | - Keerthy Sunder
- Department of Psychiatry, Menifee Global Medical Center, Palm Desert, CA., USA
- Sunder Foundation, Palm Springs, CA, USA
| | - Foojan Zeine
- Awareness Integration Institute, San Clemente, CA., USA
- Department of Health Science, California State University at Long Beach, Long Beach, CA., USA
| | - Mauro Ceccanti
- Società Italiana per il Trattamento dell’Alcolismo e le sue Complicanze (SITAC), ASL Roma1, Sapienza University of Rome, Rome, Italy
| | - Abdalla Bowirrat
- Department of Molecular Biology and Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Rajendra D. Badgaiyan
- Department of Psychiatry, South Texas Veteran Health Care System, Audie L. Murphy Memorial VA Hospital, Long School of Medicine, University of Texas Medical Center, San Antonio, TX., USA
- Department of Psychiatry, Mt Sinai University School of Medicine, New York, NY., USA
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3
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Mech AM, Merteroglu M, Sealy IM, Teh MT, White RJ, Havelange W, Brennan CH, Busch-Nentwich EM. Behavioral and Gene Regulatory Responses to Developmental Drug Exposures in Zebrafish. Front Psychiatry 2022; 12:795175. [PMID: 35082702 PMCID: PMC8785235 DOI: 10.3389/fpsyt.2021.795175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023] Open
Abstract
Developmental consequences of prenatal drug exposure have been reported in many human cohorts and animal studies. The long-lasting impact on the offspring-including motor and cognitive impairments, cranial and cardiac anomalies and increased prevalence of ADHD-is a socioeconomic burden worldwide. Identifying the molecular changes leading to developmental consequences could help ameliorate the deficits and limit the impact. In this study, we have used zebrafish, a well-established behavioral and genetic model with conserved drug response and reward pathways, to identify changes in behavior and cellular pathways in response to developmental exposure to amphetamine, nicotine or oxycodone. In the presence of the drug, exposed animals showed altered behavior, consistent with effects seen in mammalian systems, including impaired locomotion and altered habituation to acoustic startle. Differences in responses seen following acute and chronic exposure suggest adaptation to the presence of the drug. Transcriptomic analysis of exposed larvae revealed differential expression of numerous genes and alterations in many pathways, including those related to cell death, immunity and circadian rhythm regulation. Differential expression of circadian rhythm genes did not correlate with behavioral changes in the larvae, however, two of the circadian genes, arntl2 and per2, were also differentially expressed at later stages of development, suggesting a long-lasting impact of developmental exposures on circadian gene expression. The immediate-early genes, egr1, egr4, fosab, and junbb, which are associated with synaptic plasticity, were downregulated by all three drugs and in situ hybridization showed that the expression for all four genes was reduced across all neuroanatomical regions, including brain regions implicated in reward processing, addiction and other psychiatric conditions. We anticipate that these early changes in gene expression in response to drug exposure are likely to contribute to the consequences of prenatal exposure and their discovery might pave the way to therapeutic intervention to ameliorate the long-lasting deficits.
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Affiliation(s)
- Aleksandra M. Mech
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Munise Merteroglu
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ian M. Sealy
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, England, United Kingdom
| | - Richard J. White
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - William Havelange
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Caroline H. Brennan
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
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