143 results on '"Ferraro, TN"'
Search Results
2. Case-control association analysis of polymorphisms in the δ-opioid receptor, OPRD1, with cocaine and opioid addicted populations.
- Author
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Crist RC, Ambrose-Lanci LM, Vaswani M, Clarke TK, Zeng A, Yuan C, Ferraro TN, Hakonarson H, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, Doyle GA, Lohoff FW, Berrettini WH, Crist, R C, Ambrose-Lanci, L M, Vaswani, M, and Clarke, T K
- Abstract
Background: Addiction susceptibility and treatment responsiveness are greatly influenced by genetic factors. Sequence variation in genes involved in the mechanisms of drug action have the potential to influence addiction risk and treatment outcome. The opioid receptor system is involved in mediating the rewarding effects of cocaine and opioids. The μ-opioid receptor (MOR) has traditionally been considered the primary target for opioid addiction. The MOR, however, interacts with and is regulated by many known MOR interacting proteins (MORIPs), including the δ-opioid receptor (DOR).Methods: The present study evaluated the contribution of OPRD1, the gene encoding the DOR, to the risk of addiction to opioids and cocaine. The association of OPRD1 polymorphisms with both opioid addiction (OA) and cocaine addiction (CA) was analyzed in African American (OA n=336, CA n=503) and European American (OA n=1007, CA n=336) populations.Results: The primary finding of this study is an association of rs678849 with cocaine addiction in African Americans (allelic p=0.0086). For replication purposes, this SNP was analyzed in a larger independent population of cocaine addicted African Americans and controls and the association was confirmed (allelic p=4.53 × 10(-5); n=993). By performing a meta-analysis on the expanded populations, the statistical evidence for an association was substantially increased (allelic p=8.5 × 10(-7)) (p-values non-FDR corrected).Conclusion: The present study suggests that polymorphisms in OPRD1 are relevant for cocaine addiction in the African American population and provides additional support for a broad role for OPRD1 variants in drug dependence. [ABSTRACT FROM AUTHOR]- Published
- 2013
- Full Text
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3. Galantamine-Memantine Combination in the Treatment of Parkinson's Disease Dementia.
- Author
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Frost ED, Shi SX, Byroju VV, Pitton Rissardo J, Donlon J, Vigilante N, Murray BP, Walker IM, McGarry A, Ferraro TN, Hanafy KA, Echeverria V, Mitrev L, Kling MA, Krishnaiah B, Lovejoy DB, Rahman S, Stone TW, and Koola MM
- Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder that affects over 1% of population over age 60. It is defined by motor and nonmotor symptoms including a spectrum of cognitive impairments known as Parkinson's disease dementia (PDD). Currently, the only US Food and Drug Administration-approved treatment for PDD is rivastigmine, which inhibits acetylcholinesterase and butyrylcholinesterase increasing the level of acetylcholine in the brain. Due to its limited efficacy and side effect profile, rivastigmine is often not prescribed, leaving patients with no treatment options. PD has several derangements in neurotransmitter pathways (dopaminergic neurons in the nigrostriatal pathway, kynurenine pathway (KP), acetylcholine, α7 nicotinic receptor, and N-methyl-D-aspartate (NMDA) receptors) and rivastigmine is only partially effective as it only targets one pathway. Kynurenic acid (KYNA), a metabolite of tryptophan metabolism, affects the pathophysiology of PDD in multiple ways. Both galantamine (α7 nicotinic receptor) and memantine (antagonist of the NMDA subtype of the glutamate receptor) are KYNA modulators. When used in combination, they target multiple pathways. While randomized controlled trials (RCTs) with each drug alone for PD have failed, the combination of galantamine and memantine has demonstrated a synergistic effect on cognitive enhancement in animal models. It has therapeutic potential that has not been adequately assessed, warranting future randomized controlled trials. In this review, we summarize the KYNA-centric model for PD pathophysiology and discuss how this treatment combination is promising in improving cognitive function in patients with PDD through its action on KYNA.
- Published
- 2024
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4. Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes.
- Author
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Chen S, Abou-Khalil BW, Afawi Z, Ali QZ, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Arslan M, Auce P, Bahlo M, Baker MD, Balagura G, Balestrini S, Banks E, Barba C, Barboza K, Bartolomei F, Bass N, Baum LW, Baumgartner TH, Baykan B, Bebek N, Becker F, Bennett CA, Beydoun A, Bianchini C, Bisulli F, Blackwood D, Blatt I, Borggräfe I, Bosselmann C, Braatz V, Brand H, Brockmann K, Buono RJ, Busch RM, Caglayan SH, Canafoglia L, Canavati C, Castellotti B, Cavalleri GL, Cerrato F, Chassoux F, Cherian C, Cherny SS, Cheung CL, Chou IJ, Chung SK, Churchhouse C, Ciullo V, Clark PO, Cole AJ, Cosico M, Cossette P, Cotsapas C, Cusick C, Daly MJ, Davis LK, Jonghe P, Delanty N, Dennig D, Depondt C, Derambure P, Devinsky O, Di Vito L, Dickerson F, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Ellis CA, Epstein L, Evans M, Faucon A, Feng YA, Ferguson L, Ferraro TN, Da Silva IF, Ferri L, Feucht M, Fields MC, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, French JA, Freri E, Fu JM, Gabriel S, Gagliardi M, Gambardella A, Gauthier L, Giangregorio T, Gili T, Glauser TA, Goldberg E, Goldman A, Goldstein DB, Granata T, Grant R, Greenberg DA, Guerrini R, Gundogdu-Eken A, Gupta N, Haas K, Hakonarson H, Haryanyan G, Häusler M, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne H, Hirose S, Hirsch E, Ho CJ, Hoeper O, Howrigan DP, Hucks D, Hung PC, Iacomino M, Inoue Y, Inuzuka LM, Ishii A, Jehi L, Johnson MR, Johnstone M, Kälviäinen R, Kanaan M, Kara B, Kariuki SM, Kegele J, Kesim Y, Khoueiry-Zgheib N, Khoury J, King C, Klein KM, Kluger G, Knake S, Kok F, Korczyn AD, Korinthenberg R, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurlemann G, Kuzniecky RI, Kwan P, La Vega-Talbott M, Labate A, Lacey A, Lal D, Laššuthová P, Lauxmann S, Lawthom C, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GH, Liao C, Licchetta L, Lin CH, Lin KL, Linnankivi T, Lo W, Lowenstein DH, Lowther C, Lubbers L, Lui CHT, Macedo-Souza LI, Madeleyn R, Madia F, Magri S, Maillard L, Marcuse L, Marques P, Marson AG, Matthews AG, May P, Mayer T, McArdle W, McCarroll SM, McGoldrick P, McGraw CM, McIntosh A, McQuillan A, Meador KJ, Mei D, Michel V, Millichap JJ, Minardi R, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neaves S, Neubauer BA, Newton CRJC, Noebels JL, Northstone K, Novod S, O'Brien TJ, Owusu-Agyei S, Özkara Ç, Palotie A, Papacostas SS, Parrini E, Pato C, Pato M, Pendziwiat M, Pennell PB, Petrovski S, Pickrell WO, Pinsky R, Pinto D, Pippucci T, Piras F, Piras F, Poduri A, Pondrelli F, Posthuma D, Powell RHW, Privitera M, Rademacher A, Ragona F, Ramirez-Hamouz B, Rau S, Raynes HR, Rees MI, Regan BM, Reif A, Reinthaler E, Rheims S, Ring SM, Riva A, Rojas E, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Salman B, Salmon A, Salpietro V, Sammarra I, Scala M, Schachter S, Schaller A, Schankin CJ, Scheffer IE, Schneider N, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sedláčková L, Shain C, Sham PC, Shiedley BR, Siena SA, Sills GJ, Sisodiya SM, Smoller JW, Solomonson M, Spalletta G, Sparks KR, Sperling MR, Stamberger H, Steinhoff BJ, Stephani U, Štěrbová K, Stewart WC, Stipa C, Striano P, Strzelczyk A, Surges R, Suzuki T, Talarico M, Talkowski ME, Taneja RS, Tanteles GA, Timonen O, Timpson NJ, Tinuper P, Todaro M, Topaloglu P, Tsai MH, Tumiene B, Turkdogan D, Uğur-İşeri S, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vari MS, Vetro A, Vlčková M, von Brauchitsch S, von Spiczak S, Wagner RG, Watts N, Weber YG, Weckhuysen S, Widdess-Walsh P, Wiebe S, Wolf SM, Wolff M, Wolking S, Wong I, von Wrede R, Wu D, Yamakawa K, Yapıcı Z, Yis U, Yolken R, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zimprich F, Zizovic M, Zsurka G, Neale BM, and Berkovic SF
- Abstract
Identifying genetic risk factors for highly heterogeneous disorders like epilepsy remains challenging. Here, we present the largest whole-exome sequencing study of epilepsy to date, with >54,000 human exomes, comprising 20,979 deeply phenotyped patients from multiple genetic ancestry groups with diverse epilepsy subtypes and 33,444 controls, to investigate rare variants that confer disease risk. These analyses implicate seven individual genes, three gene sets, and four copy number variants at exome-wide significance. Genes encoding ion channels show strong association with multiple epilepsy subtypes, including epileptic encephalopathies, generalized and focal epilepsies, while most other gene discoveries are subtype-specific, highlighting distinct genetic contributions to different epilepsies. Combining results from rare single nucleotide/short indel-, copy number-, and common variants, we offer an expanded view of the genetic architecture of epilepsy, with growing evidence of convergence among different genetic risk loci on the same genes. Top candidate genes are enriched for roles in synaptic transmission and neuronal excitability, particularly postnatally and in the neocortex. We also identify shared rare variant risk between epilepsy and other neurodevelopmental disorders. Our data can be accessed via an interactive browser, hopefully facilitating diagnostic efforts and accelerating the development of follow-up studies., Competing Interests: Competing Interests B.M.N is a member of the scientific advisory board at Deep Genomics and Neumora. No other authors have competing interests to declare
- Published
- 2024
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5. Analysis of single-cell transcriptome data from a mouse model implicates protein synthesis dysfunction in schizophrenia.
- Author
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Weller AE, Ferraro TN, Doyle GA, Reiner BC, Berrettini WH, and Crist RC
- Subjects
- Animals, Mice, Disease Models, Animal, Protein Biosynthesis genetics, Mice, Knockout, Histone-Lysine N-Methyltransferase genetics, Histone-Lysine N-Methyltransferase metabolism, Corpus Striatum metabolism, Schizophrenia genetics, Schizophrenia metabolism, Schizophrenia pathology, Single-Cell Analysis, Transcriptome, Prefrontal Cortex metabolism
- Abstract
Background: Schizophrenia is a mental disorder that causes considerable morbidity, whose risk largely results from genetic factors. Setd1a is a gene implicated in schizophrenia., Objective: To study the gene expression changes found in heterozygous Setd1a
± knockout mice in order to gain useful insight into schizophrenia pathogenesis., Methods: We mined a single-cell RNA sequencing (scRNAseq) dataset from the prefrontal cortex (PFC) and striatum of Setd1a± mice and identified cell type-specific differentially expressed genes (DEGs) and differential transcript usage (DTU). DEGs and genes containing DTU found in each cell type were used to identify affected biological pathways using Ingenuity Pathway Analysis (IPA)., Results: We identified 273 unique DEGs across all cell types in PFC and 675 unique gene peaks containing DTU. In striatum, we identified 327 unique DEGs across all cell types and 8 unique gene peaks containing DTU. Key IPA findings from the analysis of DEGs found in PFC and striatum implicate processes involved in protein synthesis, mitochondrial function, cell metabolism, and inflammation. IPA analysis of genes containing DTU in PFC points to protein synthesis, as well as cellular activities involving intracellular signaling and neurotransmission. One canonical pathway, 'EIF2 Signaling', which is involved in the regulation of protein synthesis, was detected in PFC DEGs, striatum DEGs, and PFC genes containing DTU, drawing attention to its importance in schizophrenia pathophysiology., Conclusion: Processes involving protein synthesis in general and the 'EIF2 Signaling' pathway in particular could be targets for the development of new research strategies and biomarkers in schizophrenia., (© 2024. The Author(s) under exclusive licence to The Genetics Society of Korea.)- Published
- 2024
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6. An exploratory metabolomic comparison of participants with fast or absent functional progression from 2CARE, a randomized, double-blind clinical trial in Huntington's disease.
- Author
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McGarry A, Hunter K, Gaughan J, Auinger P, Ferraro TN, Pradhan B, Ferrucci L, Egan JM, and Moaddel R
- Subjects
- Humans, Cross-Sectional Studies, Polyamines, Arginine, Glucose, Disease Progression, Huntington Disease metabolism
- Abstract
Huntington's disease (HD) is increasingly recognized for diverse pathology outside of the nervous system. To describe the biology of HD in relation to functional progression, we previously analyzed the plasma and CSF metabolome in a cross-sectional study of participants who had various degrees of functional impairment. Here, we carried out an exploratory study in plasma from HD individuals over a 3-year time frame to assess whether differences exist between those with fast or absent clinical progression. There were more differences in circulating metabolite levels for fast progressors compared to absent progressors (111 vs 20, nominal p < 0.05). All metabolite changes in faster progressors were decreases, whereas some metabolite concentrations increased in absent progressors. Many of the metabolite levels that decreased in the fast progressors were higher at Screening compared to absent progressors but ended up lower by Year 3. Changes in faster progression suggest greater oxidative stress and inflammation (kynurenine, diacylglycerides, cysteine), disturbances in nitric oxide and urea metabolism (arginine, citrulline, ornithine, GABR), lower polyamines (putrescine and spermine), elevated glucose, and deficient AMPK signaling. Metabolomic differences between fast and absent progressors suggest the possibility of predicting functional decline in HD, and possibly delaying it with interventions to augment arginine, polyamines, and glucose regulation., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
- Published
- 2024
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7. Postmortem toxicology findings from the Camden Opioid Research Initiative.
- Author
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Kusic DM, Heil J, Zajic S, Brangan A, Dairo O, Heil S, Feigin G, Kacinko S, Buono RJ, Ferraro TN, Rafeq R, Haroz R, Baston K, Bodofsky E, Sabia M, Salzman M, Resch A, Madzo J, Scheinfeldt LB, Issa JJ, and Jelinek J
- Subjects
- Humans, United States, Analgesics, Opioid adverse effects, Pandemics, Fentanyl adverse effects, Naloxone therapeutic use, Opioid-Related Disorders epidemiology, Opioid-Related Disorders drug therapy, Drug Overdose epidemiology
- Abstract
The United States continues to be impacted by decades of an opioid misuse epidemic, worsened by the COVID-19 pandemic and by the growing prevalence of highly potent synthetic opioids (HPSO) such as fentanyl. In instances of a toxicity event, first-response administration of reversal medications such as naloxone can be insufficient to fully counteract the effects of HPSO, particularly when there is co-occurring substance use. In an effort to characterize and study this multi-faceted problem, the Camden Opioid Research Initiative (CORI) has been formed. The CORI study has collected and analyzed post-mortem toxicology data from 42 cases of decedents who expired from opioid-related toxicity in the South New Jersey region to characterize substance use profiles. Co-occurring substance use, whether by intent or through possible contamination of the illicit opioid supply, is pervasive among deaths due to opioid toxicity, and evidence of medication-assisted treatment is scarce. Nearly all (98%) of the toxicology cases show the presence of the HPSO, fentanyl, and very few (7%) results detected evidence of medication-assisted treatment for opioid use disorder, such as buprenorphine or methadone, at the time of death. The opioid toxicity reversal drug, naloxone, was detected in 19% of cases, but 100% of cases expressed one or more stimulants, and sedatives including xylazine were detected in 48% of cases. These results showing complex substance use profiles indicate that efforts at mitigating the opioid misuse epidemic must address the complications presented by co-occurring stimulant and other substance use, and reduce barriers to and stigmas of seeking effective medication-assisted treatments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Kusic et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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8. Decoding brain memory formation by single-cell RNA sequencing.
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Sardoo AM, Zhang S, Ferraro TN, Keck TM, and Chen Y
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- Mice, Animals, Humans, Sequence Analysis, RNA methods, RNA, Small Nuclear, Brain, Gene Expression Profiling methods, Single-Cell Analysis methods, Computational Biology methods
- Abstract
To understand how distinct memories are formed and stored in the brain is an important and fundamental question in neuroscience and computational biology. A population of neurons, termed engram cells, represents the physiological manifestation of a specific memory trace and is characterized by dynamic changes in gene expression, which in turn alters the synaptic connectivity and excitability of these cells. Recent applications of single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) are promising approaches for delineating the dynamic expression profiles in these subsets of neurons, and thus understanding memory-specific genes, their combinatorial patterns and regulatory networks. The aim of this article is to review and discuss the experimental and computational procedures of sc/snRNA-seq, new studies of molecular mechanisms of memory aided by sc/snRNA-seq in human brain diseases and related mouse models, and computational challenges in understanding the regulatory mechanisms underlying long-term memory formation., (© The Author(s) 2022. Published by Oxford University Press.)
- Published
- 2022
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9. Single nucleus transcriptomic analysis of rat nucleus accumbens reveals cell type-specific patterns of gene expression associated with volitional morphine intake.
- Author
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Reiner BC, Zhang Y, Stein LM, Perea ED, Arauco-Shapiro G, Ben Nathan J, Ragnini K, Hayes MR, Ferraro TN, Berrettini WH, Schmidt HD, and Crist RC
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- Analgesics, Opioid pharmacology, Animals, Humans, Male, Neurons metabolism, Phosphoric Diester Hydrolases metabolism, Rats, Transcriptome, Morphine pharmacology, Nucleus Accumbens metabolism
- Abstract
Opioid exposure is known to cause transcriptomic changes in the nucleus accumbens (NAc). However, no studies to date have investigated cell type-specific transcriptomic changes associated with volitional opioid taking. Here, we use single nucleus RNA sequencing (snRNAseq) to comprehensively characterize cell type-specific alterations of the NAc transcriptome in rats self-administering morphine. One cohort of male Brown Norway rats was injected with acute morphine (10 mg/kg, i.p.) or saline. A second cohort of rats was allowed to self-administer intravenous morphine (1.0 mg/kg/infusion) for 10 consecutive days. Each morphine-experienced rat was paired with a yoked saline control rat. snRNAseq libraries were generated from NAc punches and used to identify cell type-specific gene expression changes associated with volitional morphine taking. We identified 1106 differentially expressed genes (DEGs) in the acute morphine group, compared to 2453 DEGs in the morphine self-administration group, across 27 distinct cell clusters. Importantly, we identified 1329 DEGs that were specific to morphine self-administration. DEGs were identified in novel clusters of astrocytes, oligodendrocytes, and D1R- and D2R-expressing medium spiny neurons in the NAc. Cell type-specific DEGs included Rgs9, Celf5, Oprm1, and Pde10a. Upregulation of Rgs9 and Celf5 in D2R-expressing neurons was validated by RNAscope. Approximately 85% of all oligodendrocyte DEGs, nearly all of which were associated with morphine taking, were identified in two subtypes. Bioinformatic analyses identified cell type-specific upstream regulatory mechanisms of the observed transcriptome alterations and downstream signaling pathways, including both novel and previously identified molecular pathways. These findings show that volitional morphine taking is associated with distinct cell type-specific transcriptomic changes in the rat NAc and highlight specific striatal cell populations and novel molecular substrates that could be targeted to reduce compulsive opioid taking., (© 2022. The Author(s).)
- Published
- 2022
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10. Patient Perceptions and Potential Utility of Pharmacogenetic Testing in Chronic Pain Management and Opioid Use Disorder in the Camden Opioid Research Initiative.
- Author
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Kusic D, Heil J, Zajic S, Brangan A, Dairo O, Smith G, Morales-Scheihing D, Buono RJ, Ferraro TN, Haroz R, Salzman M, Baston K, Bodofsky E, Sabia M, Resch A, and Scheinfeldt LB
- Abstract
Pharmacogenetics (PGx) has the potential to improve opioid medication management. Here, we present patient perception data, pharmacogenetic data and medication management trends in patients with chronic pain (arm 1) and opioid use disorder (arm 2) treated at Cooper University Health Care in Camden City, NJ. Our results demonstrate that the majority of patients in both arms of the study (55% and 65%, respectively) are open to pharmacogenetic testing, and most (66% and 69%, respectively) believe that genetic testing has the potential to improve their medical care. Our results further support the potential for CYP2D6 PGx testing to inform chronic pain medication management for poor metabolizers (PMs) and ultrarapid metabolizers (UMs). Future efforts to implement PGx testing in chronic pain management, however, must address patient concerns about genetic test result access and genetic discrimination.
- Published
- 2022
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11. Single Nucleus Transcriptome Data from Alzheimer's Disease Mouse Models Yield New Insight into Pathophysiology.
- Author
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Weller AE, Ferraro TN, Doyle GA, Reiner BC, Crist RC, and Berrettini WH
- Subjects
- Animals, Mice, Transcriptome, Mice, Transgenic, Mice, Inbred C57BL, Disease Models, Animal, Mice, Knockout, Membrane Glycoproteins genetics, Receptors, Immunologic genetics, Nerve Tissue Proteins genetics, Alzheimer Disease pathology
- Abstract
Background: 5XFAD humanized mutant mice and Trem2 knockout (T2KO) mice are two mouse models relevant to the study of Alzheimer's disease (AD)-related pathology., Objective: To determine hippocampal transcriptomic and polyadenylation site usage alterations caused by genetic mutations engineered in 5XFAD and T2KO mice., Methods: Employing a publicly available single-nucleus RNA sequencing dataset, we used Seurat and Sierra analytic programs to identify differentially expressed genes (DEGs) and differential transcript usage (DTU), respectively, in hippocampal cell types from each of the two mouse models. We analyzed cell type-specific DEGs further using Ingenuity Pathway Analysis (IPA)., Results: We identified several DEGs in both neuronal and glial cell subtypes in comparisons of wild type (WT) versus 5XFAD and WT versus T2KO mice, including Ttr, Fth1, Pcsk1n, Malat1, Rpl37, Rtn1, Sepw1, Uba52, Mbp, Arl6ip5, Gm26917, Vwa1, and Pgrmc1. We also observed DTU in common between the two comparisons in neuronal and glial subtypes, specifically in the genes Prnp, Rbm4b, Pnisr, Opcml, Cpne7, Adgrb1, Gabarapl2, Ubb, Ndfip1, Car11, and Stmn4. IPA identified three statistically significant canonical pathways that appeared in multiple cell types and that overlapped between 5XFAD and T2KO comparisons to WT, including 'FXR/RXR Activation', 'LXR/RXR Activation', and 'Acute Phase Response Signaling'., Conclusion: DEG, DTU, and IPA findings, derived from two different mouse models of AD, highlight the importance of energy imbalance and inflammatory processes in specific hippocampal cell types, including subtypes of neurons and glial cells, in the development of AD-related pathology. Additional studies are needed to further characterize these findings.
- Published
- 2022
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12. Consensus clustering of single-cell RNA-seq data by enhancing network affinity.
- Author
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Cui Y, Zhang S, Liang Y, Wang X, Ferraro TN, and Chen Y
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- Databases, Genetic, Reproducibility of Results, Web Browser, Algorithms, Cluster Analysis, Computational Biology methods, RNA-Seq, Single-Cell Analysis methods
- Abstract
Elucidation of cell subpopulations at high resolution is a key and challenging goal of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data analysis. Although unsupervised clustering methods have been proposed for de novo identification of cell populations, their performance and robustness suffer from the high variability, low capture efficiency and high dropout rates which are characteristic of scRNA-seq experiments. Here, we present a novel unsupervised method for Single-cell Clustering by Enhancing Network Affinity (SCENA), which mainly employed three strategies: selecting multiple gene sets, enhancing local affinity among cells and clustering of consensus matrices. Large-scale validations on 13 real scRNA-seq datasets show that SCENA has high accuracy in detecting cell populations and is robust against dropout noise. When we applied SCENA to large-scale scRNA-seq data of mouse brain cells, known cell types were successfully detected, and novel cell types of interneurons were identified with differential expression of gamma-aminobutyric acid receptor subunits and transporters. SCENA is equipped with CPU + GPU (Central Processing Units + Graphics Processing Units) heterogeneous parallel computing to achieve high running speed. The high performance and running speed of SCENA combine into a new and efficient platform for biological discoveries in clustering analysis of large and diverse scRNA-seq datasets., (© The Author(s) 2021. Published by Oxford University Press.)
- Published
- 2021
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13. Genetics and prescription opioid use (GaPO): study design for consenting a cohort from an existing biobank to identify clinical and genetic factors influencing prescription opioid use and abuse.
- Author
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Troiani V, Crist RC, Doyle GA, Ferraro TN, Beiler D, Ranck S, McBryan K, Jarvis MA, Barbour JS, Han JJ, Ness RJ, Berrettini WH, and Robishaw JD
- Subjects
- Analgesics, Opioid adverse effects, Electronic Health Records, Genome-Wide Association Study, Humans, Prospective Studies, Analgesics, Opioid administration & dosage, Biological Specimen Banks, Opioid-Related Disorders genetics
- Abstract
Background: Prescription opioids (POs) are commonly used to treat moderate to severe chronic pain in the health system setting. Although they improve quality of life for many patients, more work is needed to identify both the clinical and genetic factors that put certain individuals at high risk for developing opioid use disorder (OUD) following use of POs for pain relief. With a greater understanding of important risk factors, physicians will be better able to identify patients at highest risk for developing OUD for whom non-opioid alternative therapies and treatments should be considered., Methods: We are conducting a prospective observational study that aims to identify the clinical and genetic factors most stongly associated with OUD. The study design leverages an existing biobank that includes whole exome sequencing and array genotyping. The biobank is maintained within an integrated health system, allowing for the large-scale capture and integration of genetic and non-genetic data. Participants are enrolled into the health system biobank via informed consent and then into a second study that focuses on opioid medication use. Data capture includes validated self-report surveys measuring addiction severity, depression, anxiety, and nicotine use, as well as additional clinical, prescription, and brain imaging data extracted from electronic health records., Discussion: We will harness this multimodal data capture to establish meaningful patient phenotypes in order to understand the genetic and non-genetic contributions to OUD., (© 2021. The Author(s).)
- Published
- 2021
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14. Genetic Variation in PADI6-PADI4 on 1p36.13 Is Associated with Common Forms of Human Generalized Epilepsy.
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Buono RJ, Bradfield JP, Wei Z, Sperling MR, Dlugos DJ, Privitera MD, French JA, Lo W, Cossette P, Schachter SC, Basehore H, Lohoff FW, Grant SFA, Ferraro TN, and Hakonarson H
- Subjects
- Black or African American genetics, Case-Control Studies, Chromosomes, Human, Pair 1, Epilepsies, Partial genetics, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, White People genetics, Epilepsy, Generalized genetics, Polymorphism, Single Nucleotide, Protein-Arginine Deiminase Type 4 genetics, Protein-Arginine Deiminase Type 6 genetics
- Abstract
We performed a genome-wide association study (GWAS) to identify genetic variation associated with common forms of idiopathic generalized epilepsy (GE) and focal epilepsy (FE). Using a cohort of 2220 patients and 14,448 controls, we searched for single nucleotide polymorphisms (SNPs) associated with GE, FE and both forms combined. We did not find any SNPs that reached genome-wide statistical significance ( p ≤ 5 × 10
-8 ) when comparing all cases to all controls, and few SNPs of interest comparing FE cases to controls. However, we document multiple linked SNPs in the PADI6 - PADI4 genes that reach genome-wide significance and are associated with disease when comparing GE cases alone to controls. PADI genes encode enzymes that deiminate arginine to citrulline in molecular pathways related to epigenetic regulation of histones and autoantibody formation. Although epilepsy genetics and treatment are focused strongly on ion channel and neurotransmitter mechanisms, these results suggest that epigenetic control of gene expression and the formation of autoantibodies may also play roles in epileptogenesis.- Published
- 2021
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15. Effectiveness of a Team-Based Learning exercise in the learning outcomes of a medical pharmacology course: insight from struggling students.
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Carrasco GA, Behling KC, Gentile M, Fischer BD, and Ferraro TN
- Subjects
- Educational Measurement, Humans, Learning, Education, Medical methods, Pharmacology education, Students, Medical
- Abstract
We have previously reported that multiple Team-Based Learning (TBL™) exercises in a 4-week pre-clinical medical school course improved final exam performance and significantly reduced the number of course failures. Here, we conducted a long-term study, with eight cohorts of first-year medical students, to determine whether the implementation of a single TBL individual readiness assessment test (iRAT) exercise in a 4-week medical school pharmacology course produces similar effects in overall course performance. We implemented a single TBL iRAT exercise that covered the subjects addressed during one week of the medical pharmacology course, with the four most recent cohorts of students matriculating at Cooper Medical School of Rowan University (n = 403). The first four cohorts matriculating at CMSRU did not participate in the TBL exercises (n = 266). Correlation of individual student TBL iRAT and final examination scores in the medical pharmacology course was compared to a second, unrelated first-year course (physiology) to control for variation in student performance between cohorts. We found that there was a significant moderate correlation between final examination and TBL iRAT scores (r = 0.49, p < 0.01, n = 403). Interestingly this moderate correlation was seen in students performing in the lower 25
th percentile on the course final examination (r = 0.41, p < 0.01, n = 101) and negligible in students performing in the upper 25th percentile (r = 0.11, n = 101, p > 0.05). Implementation of the single TBL exercise also significantly reduced variance or range of student final examination performance compared to the group of the first four cohorts. These results suggest that implementation of a single TBL exercise, which covers only one week of content delivered in a 1-month medical pharmacology course, benefits first-year medical students by reducing the disparity in knowledge acquisition among them and providing a means to identify students who may struggle with course content., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)- Published
- 2021
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16. Investigation of long interspersed element-1 retrotransposons as potential risk factors for idiopathic temporal lobe epilepsy.
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Doyle GA, Reiner BC, Crist RC, Rao AM, Ojeah NS, Arauco-Shapiro G, Levinson RN, Shah LD, Sperling MR, Ferraro TN, Buono RJ, and Berrettini WH
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- Adult, Calcium metabolism, Computational Biology, Electroencephalography, Epilepsy, Temporal Lobe epidemiology, Female, Humans, Kv Channel-Interacting Proteins genetics, Magnetic Resonance Imaging, Male, Middle Aged, Neurons pathology, Reference Values, Risk Factors, Temporal Lobe chemistry, DNA Transposable Elements genetics, Epilepsy, Temporal Lobe genetics, Long Interspersed Nucleotide Elements genetics
- Abstract
Objective: To determine if long interspersed element-1 (L1) retrotransposons convey risk for idiopathic temporal lobe epilepsy (TLE)., Methods: Surgically resected temporal cortex from individuals with TLE (N = 33) and postmortem temporal cortex from individuals with no known neurological disease (N = 33) were analyzed for L1 content by Restriction Enzyme Based Enriched L1Hs sequencing (REBELseq). Expression of three KCNIP4 splice variants was assessed by droplet digital PCR (ddPCR). Protein ANalysis THrough Evolutionary Relationships (PANTHER) was used to determine ontologies and pathways for lists of genes harboring L1 insertions., Results: We identified novel L1 insertions specific to individuals with TLE, and others specific to controls. Although there were no statistically significant differences between cases and controls in the numbers of known and novel L1 insertions, PANTHER analyses of intragenic L1 insertions showed statistically significant enrichments for epilepsy-relevant gene ontologies in both cases and controls. Gene ontologies "neuron projection development" and "calcium ion transmembrane transport" were among those found only in individuals with TLE. We confirmed novel L1 insertions in several genes associated with seizures/epilepsy, including a de novo somatic L1 retrotransposition in KCNIP4 that occurred after neural crest formation in one patient. However, ddPCR results suggest this de novo L1 did not alter KCNIP4 mRNA expression., Significance: Given current data from this small cohort, we conclude that L1 elements, either rare heritable germline insertions or de novo somatic retrotranspositions, may contribute only minimally to overall genetic risk for idiopathic TLE. We suggest that further studies in additional patients and additional brain regions are warranted., (© 2021 International League Against Epilepsy.)
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- 2021
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17. Author Correction: Cross-sectional analysis of plasma and CSF metabolomic markers in Huntington's disease for participants of varying functional disability: a pilot study.
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McGarry A, Gaughan J, Hackmyer C, Lovett J, Khadeer M, Shaikh H, Pradhan B, Ferraro TN, Wainer IW, and Moaddel R
- Published
- 2021
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18. The Genomics of Opioid Addiction Longitudinal Study (GOALS): study design for a prospective evaluation of genetic and non-genetic factors for development of and recovery from opioid use disorder.
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Heil J, Zajic S, Albertson E, Brangan A, Jones I, Roberts W, Sabia M, Bodofsky E, Resch A, Rafeq R, Haroz R, Buono R, Ferraro TN, Scheinfeldt L, Salzman M, and Baston K
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- Humans, Longitudinal Studies, Prospective Studies, Male, Female, Adult, Risk Factors, Research Design, Opioid-Related Disorders genetics, Genomics
- Abstract
Background: The opioid use disorder and overdose crisis in the United States affects public health as well as social and economic welfare. While several genetic and non-genetic risk factors for opioid use disorder have been identified, many of the genetic associations have not been independently replicated, and it is not well understood how these factors interact. This study is designed to evaluate relationships among these factors prospectively to develop future interventions to help prevent or treat opioid use disorder., Methods: The Genomics of Opioid Addiction Longitudinal Study (GOALS) is a prospective observational study assessing the interplay of genetic and non-genetic by collecting comprehensive genetic and non-genetic information on 400 participants receiving medication for opioid use disorder. Participants will be assessed at four time points over 1 year. A saliva sample will be collected for large-scale genetic data analyses. Non-genetic assessments include validated surveys measuring addiction severity, depression, anxiety, and adverse childhood experiences, as well as treatment outcomes such as urine toxicology results, visit frequency, and number of pre and post-treatment overdoses extracted from electronic medical records., Discussion: We will use these complex data to investigate the relative contributions of genetic and non-genetic risk factors to opioid use disorder and related treatment outcomes.
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- 2021
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19. Cross-sectional analysis of plasma and CSF metabolomic markers in Huntington's disease for participants of varying functional disability: a pilot study.
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McGarry A, Gaughan J, Hackmyer C, Lovett J, Khadeer M, Shaikh H, Pradhan B, Ferraro TN, Wainer IW, and Moaddel R
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- Adult, Arginine blood, Arginine cerebrospinal fluid, Creatine blood, Creatine cerebrospinal fluid, Cross-Sectional Studies, Female, Glycine blood, Glycine cerebrospinal fluid, Humans, Huntington Disease metabolism, Male, Middle Aged, Pilot Projects, Treatment Outcome, Young Adult, Biomarkers blood, Biomarkers cerebrospinal fluid, Disability Evaluation, Huntington Disease blood, Huntington Disease cerebrospinal fluid, Metabolomics
- Abstract
Huntington's Disease (HD) is a progressive, fatal neurodegenerative condition. While generally considered for its devastating neurological phenotype, disturbances in other organ systems and metabolic pathways outside the brain have attracted attention for possible relevance to HD pathology, potential as therapeutic targets, or use as biomarkers of progression. In addition, it is not established how metabolic changes in the HD brain correlate to progression across the full spectrum of early to late-stage disease. In this pilot study, we sought to explore the metabolic profile across manifest HD from early to advanced clinical staging through metabolomic analysis by mass spectrometry in plasma and cerebrospinal fluid (CSF). With disease progression, we observed nominally significant increases in plasma arginine, citrulline, and glycine, with decreases in total and D-serine, cholesterol esters, diacylglycerides, triacylglycerides, phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins. In CSF, worsening disease was associated with nominally significant increases in NAD
+ , arginine, saturated long chain free fatty acids, diacylglycerides, triacylglycerides, and sphingomyelins. Notably, diacylglycerides and triacylglyceride species associated with clinical progression were different between plasma and CSF, suggesting different metabolic preferences for these compartments. Increasing NAD+ levels strongly correlating with disease progression was an unexpected finding. Our data suggest that defects in the urea cycle, glycine, and serine metabolism may be underrecognized in the progression HD pathology, and merit further study for possible therapeutic relevance.- Published
- 2020
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20. Assessment of Probable Opioid Use Disorder Using Electronic Health Record Documentation.
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Palumbo SA, Adamson KM, Krishnamurthy S, Manoharan S, Beiler D, Seiwell A, Young C, Metpally R, Crist RC, Doyle GA, Ferraro TN, Li M, Berrettini WH, Robishaw JD, and Troiani V
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- Adult, Aged, Cross-Sectional Studies, Documentation methods, Female, Humans, Male, Middle Aged, Opioid-Related Disorders physiopathology, Prevalence, Retrospective Studies, Documentation statistics & numerical data, Electronic Health Records statistics & numerical data, Opioid-Related Disorders diagnosis
- Abstract
Importance: Electronic health records are a potentially valuable source of information for identifying patients with opioid use disorder (OUD)., Objective: To evaluate whether proxy measures from electronic health record data can be used reliably to identify patients with probable OUD based on Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition) (DSM-5) criteria., Design, Setting, and Participants: This retrospective cross-sectional study analyzed individuals within the Geisinger health system who were prescribed opioids between December 31, 2000, and May 31, 2017, using a mixed-methods approach. The cohort was identified from 16 253 patients enrolled in a contract-based, Geisinger-specific medication monitoring program (GMMP) for opioid use, including patients who maintained or violated contract terms, as well as a demographically matched control group of 16 253 patients who were prescribed opioids but not enrolled in the GMMP. Substance use diagnoses and psychiatric comorbidities were assessed using automated electronic health record summaries. A manual medical record review procedure using DSM-5 criteria for OUD was completed for a subset of patients. The analysis was conducted beginning from June 5, 2017, until May 29, 2020., Main Outcomes and Measures: The primary outcome was the prevalence of OUD as defined by proxy measures for DSM-5 criteria for OUD as well as the prevalence of comorbidities among patients prescribed opioids within an integrated health system., Results: Among the 16 253 patients enrolled in the GMMP (9309 women [57%]; mean [SD] age, 52 [14] years), OUD diagnoses as defined by diagnostic codes were present at a much lower rate than expected (291 [2%]), indicating the necessity for alternative diagnostic strategies. The DSM-5 criteria for OUD can be assessed using manual medical record review; a manual review of 200 patients in the GMMP and 200 control patients identifed a larger percentage of patients with probable moderate to severe OUD (GMMP, 145 of 200 [73%]; and control, 27 of 200 [14%]) compared with the prevalence of OUD assessed using diagnostic codes., Conclusions and Relevance: These results suggest that patients with OUD may be identified using information available in the electronic health record, even when diagnostic codes do not reflect this diagnosis. Furthermore, the study demonstrates the utility of coding for DSM-5 criteria from medical records to generate a quantitative DSM-5 score that is associated with OUD severity.
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- 2020
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21. Epidemiological study of Trichosporon asahii infections over the past 23 years.
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Li H, Guo M, Wang C, Li Y, Fernandez AM, Ferraro TN, Yang R, and Chen Y
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- Animals, Global Health, Humans, Retrospective Studies, Trichosporon, Trichosporonosis epidemiology, Trichosporonosis microbiology
- Abstract
Trichosporon is a yeast-like basidiomycete, a conditional pathogenic fungus that is rare in the clinic but often causes fatal infections in immunocompromised individuals. Trichosporon asahii is the most common pathogenic fungus in this genus and the occurrence of infections has dramatically increased in recent years. Here, we report a systematic literature review detailing 140 cases of T. asahii infection reported during the past 23 years. Statistical analysis shows that T. asahii infections were most frequently reported within immunodeficient or immunocompromised patients commonly with blood diseases. Antibiotic use, invasive medical equipment and chemotherapy were the leading risk factors for acquiring infection. In vitro susceptibility, clinical information and prognosis analysis showed that voriconazole is the primary drug of choice in the treatment of T. asahii infection. Combination treatment with voriconazole and amphotericin B did not show superiority over either drug alone. Finally, we found that the types of infections prevalent in China are significantly different from those in other countries. These results provide detailed information and relevant clinical treatment strategies for the diagnosis and treatment of T. asahii infection.
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- 2020
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22. The Molecular Genetic Interaction Between Circadian Rhythms and Susceptibility to Seizures and Epilepsy.
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Re CJ, Batterman AI, Gerstner JR, Buono RJ, and Ferraro TN
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Seizure patterns observed in patients with epilepsy suggest that circadian rhythms and sleep/wake mechanisms play some role in the disease. This review addresses key topics in the relationship between circadian rhythms and seizures in epilepsy. We present basic information on circadian biology, but focus on research studying the influence of both the time of day and the sleep/wake cycle as independent but related factors on the expression of seizures in epilepsy. We review studies investigating how seizures and epilepsy disrupt expression of core clock genes, and how disruption of clock mechanisms impacts seizures and the development of epilepsy. We focus on the overlap between mechanisms of circadian-associated changes in SCN neuronal excitability and mechanisms of epileptogenesis as a means of identifying key pathways and molecules that could represent new targets or strategies for epilepsy therapy. Finally, we review the concept of chronotherapy and provide a perspective regarding its application to patients with epilepsy based on their individual characteristics (i.e., being a "morning person" or a "night owl"). We conclude that better understanding of the relationship between circadian rhythms, neuronal excitability, and seizures will allow both the identification of new therapeutic targets for treating epilepsy as well as more effective treatment regimens using currently available pharmacological and non-pharmacological strategies., (Copyright © 2020 Re, Batterman, Gerstner, Buono and Ferraro.)
- Published
- 2020
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23. The imperative of clinical and molecular research on neonatal opioid withdrawal syndrome.
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Metpally RP, Krishnamurthy S, Moran KM, Weller AE, Crist RC, Reiner BC, Doyle GA, Ferraro TN, Radhakrishna U, Bahado-Singh R, Troiani V, and Berrettini WH
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- Analgesics, Opioid therapeutic use, Humans, Infant, Infant, Newborn, Methadone therapeutic use, Opioid-Related Disorders metabolism, Opioid-Related Disorders physiopathology, Substance Withdrawal Syndrome metabolism, Substance Withdrawal Syndrome physiopathology, Neonatal Abstinence Syndrome metabolism, Neonatal Abstinence Syndrome physiopathology
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- 2019
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24. Cognitive and behavioral effects of brief seizures in mice.
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Batterman AI, DeChiara J, Islam A, Brenner MB, Fischer BD, Buono RJ, Keck TM, and Ferraro TN
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- Animals, Cognition Disorders etiology, Cognition Disorders psychology, Electroshock adverse effects, Male, Mice, Mice, Inbred C57BL, Quality of Life psychology, Seizures etiology, Cognition physiology, Exploratory Behavior physiology, Motor Activity physiology, Recognition, Psychology physiology, Seizures psychology
- Abstract
Comorbidities associated with epilepsy greatly reduce patients' quality of life. Since antiepilepsy drugs show limited success in ameliorating cognitive and behavioral symptoms, there is a need to better understand the mechanisms underlying epilepsy-related cognitive and behavioral impairments. Most prior research addressing this problem has focused on chronic epilepsy, wherein many factors can simultaneously impact cognition and behavior. The purpose of the present study was to develop a testing paradigm using mice that can provide new insight into how short-term biological changes underlying acute seizures impact cognition and behavior. In Experiment 1, naïve C57BL/6J mice were subjected to either three brief, generalized electroconvulsive seizure (ECS) or three sham treatments equally spaced over the course of 30 min. Over the next 2 h, mice were tested in a novel object recognition paradigm. Follow-up studies examined locomotor activity immediately before and after (Experiment 2), immediately after (Experiment 3), and 45 min after (Experiment 4) a set of three ECS or sham treatments. Whereas results demonstrated that there was no statistically significant difference in recognition memory acquisition between ECS and sham-treated mice, measures of anxiety-like behavior were increased and novel object interest was decreased in ECS-treated mice compared with that in sham. Interestingly, ECS also produced a delayed inhibitory effect on locomotion, decreasing open-field activity 45-min posttreatment compared to sham. We conclude that a small cluster of brief seizures can have acute, behaviorally relevant effects in mice, and that greater emphasis should be placed on events that take place before chronic epilepsy is established in order to better understand epilepsy-related cognitive and behavioral impairments. Future research would benefit from using the paradigms defined above to study the effects of individual seizures on mouse cognition and behavior., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
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25. Deletion of the vesicular monoamine transporter 1 (vmat1/slc18a1) gene affects dopamine signaling.
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Lohoff FW, Carr GV, Brookshire B, Ferraro TN, and Lucki I
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- Amphetamine metabolism, Amphetamine pharmacology, Animals, Dopamine genetics, Dopamine Plasma Membrane Transport Proteins metabolism, Frontal Lobe metabolism, Male, Mental Disorders genetics, Mental Disorders metabolism, Mice, Mice, Knockout, Signal Transduction, Synaptic Transmission physiology, Tyrosine 3-Monooxygenase metabolism, Dopamine metabolism, Vesicular Monoamine Transport Proteins genetics, Vesicular Monoamine Transport Proteins metabolism
- Abstract
The vesicular monoamine transporter is involved in presynaptic catecholamine storage and neurotransmission. Two isoforms of the transporter exist, VMAT1 and VMAT2, and both are expressed in the brain, though VMAT2 expression is more robust and has been more widely studied. In this study we investigated the role of VMAT1 KO on markers of dopaminergic function and neurotransmission, and dopamine-related behaviors. Null-mutant VMAT1 mice were studied behaviorally using the tail suspension test, elevated zero maze and locomotor activity assessments. Tissue monoamines were measured both ex vivo and by using in vivo microdialysis. Protein expression of tyrosine hydroxylase and D2 dopamine receptors was measured using western blot analysis. Results show that VMAT1 KO mice have decreased dopamine levels in the frontal cortex, increased postsynaptic D2 expression, and lower frontal cortex tyrosine hydroxylase expression compared to WT mice. VMAT1 KO mice also show an exaggerated behavioral locomotor response to acute amphetamine treatment. We conclude that dopaminergic signaling is robustly altered in the frontal cortex of VMAT1 null-mutant mice and suggest that VMAT1 may be relevant to the pathogenesis and/or treatment of psychiatric illnesses including schizophrenia and bipolar disease., (Copyright © 2019. Published by Elsevier B.V.)
- Published
- 2019
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26. Analysis of shared heritability in common disorders of the brain.
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Anttila V, Bulik-Sullivan B, Finucane HK, Walters RK, Bras J, Duncan L, Escott-Price V, Falcone GJ, Gormley P, Malik R, Patsopoulos NA, Ripke S, Wei Z, Yu D, Lee PH, Turley P, Grenier-Boley B, Chouraki V, Kamatani Y, Berr C, Letenneur L, Hannequin D, Amouyel P, Boland A, Deleuze JF, Duron E, Vardarajan BN, Reitz C, Goate AM, Huentelman MJ, Kamboh MI, Larson EB, Rogaeva E, St George-Hyslop P, Hakonarson H, Kukull WA, Farrer LA, Barnes LL, Beach TG, Demirci FY, Head E, Hulette CM, Jicha GA, Kauwe JSK, Kaye JA, Leverenz JB, Levey AI, Lieberman AP, Pankratz VS, Poon WW, Quinn JF, Saykin AJ, Schneider LS, Smith AG, Sonnen JA, Stern RA, Van Deerlin VM, Van Eldik LJ, Harold D, Russo G, Rubinsztein DC, Bayer A, Tsolaki M, Proitsi P, Fox NC, Hampel H, Owen MJ, Mead S, Passmore P, Morgan K, Nöthen MM, Rossor M, Lupton MK, Hoffmann P, Kornhuber J, Lawlor B, McQuillin A, Al-Chalabi A, Bis JC, Ruiz A, Boada M, Seshadri S, Beiser A, Rice K, van der Lee SJ, De Jager PL, Geschwind DH, Riemenschneider M, Riedel-Heller S, Rotter JI, Ransmayr G, Hyman BT, Cruchaga C, Alegret M, Winsvold B, Palta P, Farh KH, Cuenca-Leon E, Furlotte N, Kurth T, Ligthart L, Terwindt GM, Freilinger T, Ran C, Gordon SD, Borck G, Adams HHH, Lehtimäki T, Wedenoja J, Buring JE, Schürks M, Hrafnsdottir M, Hottenga JJ, Penninx B, Artto V, Kaunisto M, Vepsäläinen S, Martin NG, Montgomery GW, Kurki MI, Hämäläinen E, Huang H, Huang J, Sandor C, Webber C, Muller-Myhsok B, Schreiber S, Salomaa V, Loehrer E, Göbel H, Macaya A, Pozo-Rosich P, Hansen T, Werge T, Kaprio J, Metspalu A, Kubisch C, Ferrari MD, Belin AC, van den Maagdenberg AMJM, Zwart JA, Boomsma D, Eriksson N, Olesen J, Chasman DI, Nyholt DR, Avbersek A, Baum L, Berkovic S, Bradfield J, Buono RJ, Catarino CB, Cossette P, De Jonghe P, Depondt C, Dlugos D, Ferraro TN, French J, Hjalgrim H, Jamnadas-Khoda J, Kälviäinen R, Kunz WS, Lerche H, Leu C, Lindhout D, Lo W, Lowenstein D, McCormack M, Møller RS, Molloy A, Ng PW, Oliver K, Privitera M, Radtke R, Ruppert AK, Sander T, Schachter S, Schankin C, Scheffer I, Schoch S, Sisodiya SM, Smith P, Sperling M, Striano P, Surges R, Thomas GN, Visscher F, Whelan CD, Zara F, Heinzen EL, Marson A, Becker F, Stroink H, Zimprich F, Gasser T, Gibbs R, Heutink P, Martinez M, Morris HR, Sharma M, Ryten M, Mok KY, Pulit S, Bevan S, Holliday E, Attia J, Battey T, Boncoraglio G, Thijs V, Chen WM, Mitchell B, Rothwell P, Sharma P, Sudlow C, Vicente A, Markus H, Kourkoulis C, Pera J, Raffeld M, Silliman S, Boraska Perica V, Thornton LM, Huckins LM, William Rayner N, Lewis CM, Gratacos M, Rybakowski F, Keski-Rahkonen A, Raevuori A, Hudson JI, Reichborn-Kjennerud T, Monteleone P, Karwautz A, Mannik K, Baker JH, O'Toole JK, Trace SE, Davis OSP, Helder SG, Ehrlich S, Herpertz-Dahlmann B, Danner UN, van Elburg AA, Clementi M, Forzan M, Docampo E, Lissowska J, Hauser J, Tortorella A, Maj M, Gonidakis F, Tziouvas K, Papezova H, Yilmaz Z, Wagner G, Cohen-Woods S, Herms S, Julià A, Rabionet R, Dick DM, Ripatti S, Andreassen OA, Espeseth T, Lundervold AJ, Steen VM, Pinto D, Scherer SW, Aschauer H, Schosser A, Alfredsson L, Padyukov L, Halmi KA, Mitchell J, Strober M, Bergen AW, Kaye W, Szatkiewicz JP, Cormand B, Ramos-Quiroga JA, Sánchez-Mora C, Ribasés M, Casas M, Hervas A, Arranz MJ, Haavik J, Zayats T, Johansson S, Williams N, Dempfle A, Rothenberger A, Kuntsi J, Oades RD, Banaschewski T, Franke B, Buitelaar JK, Arias Vasquez A, Doyle AE, Reif A, Lesch KP, Freitag C, Rivero O, Palmason H, Romanos M, Langley K, Rietschel M, Witt SH, Dalsgaard S, Børglum AD, Waldman I, Wilmot B, Molly N, Bau CHD, Crosbie J, Schachar R, Loo SK, McGough JJ, Grevet EH, Medland SE, Robinson E, Weiss LA, Bacchelli E, Bailey A, Bal V, Battaglia A, Betancur C, Bolton P, Cantor R, Celestino-Soper P, Dawson G, De Rubeis S, Duque F, Green A, Klauck SM, Leboyer M, Levitt P, Maestrini E, Mane S, De-Luca DM, Parr J, Regan R, Reichenberg A, Sandin S, Vorstman J, Wassink T, Wijsman E, Cook E, Santangelo S, Delorme R, Rogé B, Magalhaes T, Arking D, Schulze TG, Thompson RC, Strohmaier J, Matthews K, Melle I, Morris D, Blackwood D, McIntosh A, Bergen SE, Schalling M, Jamain S, Maaser A, Fischer SB, Reinbold CS, Fullerton JM, Guzman-Parra J, Mayoral F, Schofield PR, Cichon S, Mühleisen TW, Degenhardt F, Schumacher J, Bauer M, Mitchell PB, Gershon ES, Rice J, Potash JB, Zandi PP, Craddock N, Ferrier IN, Alda M, Rouleau GA, Turecki G, Ophoff R, Pato C, Anjorin A, Stahl E, Leber M, Czerski PM, Cruceanu C, Jones IR, Posthuma D, Andlauer TFM, Forstner AJ, Streit F, Baune BT, Air T, Sinnamon G, Wray NR, MacIntyre DJ, Porteous D, Homuth G, Rivera M, Grove J, Middeldorp CM, Hickie I, Pergadia M, Mehta D, Smit JH, Jansen R, de Geus E, Dunn E, Li QS, Nauck M, Schoevers RA, Beekman AT, Knowles JA, Viktorin A, Arnold P, Barr CL, Bedoya-Berrio G, Bienvenu OJ, Brentani H, Burton C, Camarena B, Cappi C, Cath D, Cavallini M, Cusi D, Darrow S, Denys D, Derks EM, Dietrich A, Fernandez T, Figee M, Freimer N, Gerber G, Grados M, Greenberg E, Hanna GL, Hartmann A, Hirschtritt ME, Hoekstra PJ, Huang A, Huyser C, Illmann C, Jenike M, Kuperman S, Leventhal B, Lochner C, Lyon GJ, Macciardi F, Madruga-Garrido M, Malaty IA, Maras A, McGrath L, Miguel EC, Mir P, Nestadt G, Nicolini H, Okun MS, Pakstis A, Paschou P, Piacentini J, Pittenger C, Plessen K, Ramensky V, Ramos EM, Reus V, Richter MA, Riddle MA, Robertson MM, Roessner V, Rosário M, Samuels JF, Sandor P, Stein DJ, Tsetsos F, Van Nieuwerburgh F, Weatherall S, Wendland JR, Wolanczyk T, Worbe Y, Zai G, Goes FS, McLaughlin N, Nestadt PS, Grabe HJ, Depienne C, Konkashbaev A, Lanzagorta N, Valencia-Duarte A, Bramon E, Buccola N, Cahn W, Cairns M, Chong SA, Cohen D, Crespo-Facorro B, Crowley J, Davidson M, DeLisi L, Dinan T, Donohoe G, Drapeau E, Duan J, Haan L, Hougaard D, Karachanak-Yankova S, Khrunin A, Klovins J, Kučinskas V, Lee Chee Keong J, Limborska S, Loughland C, Lönnqvist J, Maher B, Mattheisen M, McDonald C, Murphy KC, Nenadic I, van Os J, Pantelis C, Pato M, Petryshen T, Quested D, Roussos P, Sanders AR, Schall U, Schwab SG, Sim K, So HC, Stögmann E, Subramaniam M, Toncheva D, Waddington J, Walters J, Weiser M, Cheng W, Cloninger R, Curtis D, Gejman PV, Henskens F, Mattingsdal M, Oh SY, Scott R, Webb B, Breen G, Churchhouse C, Bulik CM, Daly M, Dichgans M, Faraone SV, Guerreiro R, Holmans P, Kendler KS, Koeleman B, Mathews CA, Price A, Scharf J, Sklar P, Williams J, Wood NW, Cotsapas C, Palotie A, Smoller JW, Sullivan P, Rosand J, Corvin A, Neale BM, Schott JM, Anney R, Elia J, Grigoroiu-Serbanescu M, Edenberg HJ, and Murray R
- Subjects
- Brain Diseases classification, Brain Diseases diagnosis, Genetic Variation, Genome-Wide Association Study, Humans, Mental Disorders classification, Mental Disorders diagnosis, Phenotype, Quantitative Trait, Heritable, Risk Factors, Brain Diseases genetics, Mental Disorders genetics
- Abstract
Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2018
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27. Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia.
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Doyle GA, Crist RC, Karatas ET, Hammond MJ, Ewing AD, Ferraro TN, Hahn CG, and Berrettini WH
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- Aged, Cell Nucleus metabolism, Computational Biology, Female, Gene Frequency, Gene Ontology, Genotyping Techniques, Humans, Male, Neurons metabolism, Sequence Analysis, DNA, Long Interspersed Nucleotide Elements, Prefrontal Cortex metabolism, Schizophrenia genetics, Schizophrenia metabolism
- Abstract
Whereas some rare genetic variants convey high risk for schizophrenia (SZ), common alleles conveying even moderate risk remain elusive. Long interspersed element-1s (L1) are mobile retrotransposons comprising ~17% of the human genome. L1 retrotransposition can cause somatic mosaicism during neurodevelopment by insertional mutagenesis. We hypothesized that, compared to controls, patients diagnosed with schizophrenia (PDS) may have increased numbers of deleterious L1 insertions, perhaps occurring de novo, in brain-expressed genes of dorsolateral prefrontal cortex (DLPFC) neurons. Neuronal and non-neuronal nuclei were separated by fluorescence-activated cell sorting from postmortem DLPFC of 36 PDS and 26 age-matched controls. Genomic sequences flanking the 3'-side of L1s were amplified from neuronal DNA, and neuronal L1 libraries were sequenced. Aligned sequences were analyzed for L1 insertions using custom bioinformatics programs. Ontology and pathway analyses were done on lists of genes putatively disrupted by L1s in PDS and controls. Cellular or population allele frequencies of L1s were assessed by droplet digital PCR or Taqman genotyping. We observed a statistically significant increase in the proportion of intragenic novel L1s in DLPFC of PDS. We found over-representation of L1 insertions within the gene ontologies 'cell projection' and 'postsynaptic membrane' in the gene lists derived from PDS samples, but not from controls. Cellular allele frequencies of examined L1 insertions indicated heterozygosity in genomes of DLPFC cells. An L1 within ERI1 exoribonuclease family member 3 (ERI3) was found to associate with SZ. These results extend prior work documenting increased L1 genetic burden in the brains of PDS and also identify unique genes that may provide new insight into the pathophysiology of schizophrenia.
- Published
- 2017
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28. The relevance of inter- and intrastrain differences in mice and rats and their implications for models of seizures and epilepsy.
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Löscher W, Ferland RJ, and Ferraro TN
- Subjects
- Animals, Male, Mice, Rats, Species Specificity, Disease Models, Animal, Epilepsy genetics, Seizures genetics
- Abstract
It is becoming increasingly clear that the genetic background of mice and rats, even in inbred strains, can have a profound influence on measures of seizure susceptibility and epilepsy. These differences can be capitalized upon through genetic mapping studies to reveal genes important for seizures and epilepsy. However, strain background and particularly mixed genetic backgrounds of transgenic animals need careful consideration in both the selection of strains and in the interpretation of results and conclusions. For instance, mice with targeted deletions of genes involved in epilepsy can have profoundly disparate phenotypes depending on the background strain. In this review, we discuss findings related to how this genetic heterogeneity has and can be utilized in the epilepsy field to reveal novel insights into seizures and epilepsy. Moreover, we discuss how caution is needed in regards to rodent strain or even animal vendor choice, and how this can significantly influence seizure and epilepsy parameters in unexpected ways. This is particularly critical in decisions regarding the strain of choice used in generating mice with targeted deletions of genes. Finally, we discuss the role of environment (at vendor and/or laboratory) and epigenetic factors for inter- and intrastrain differences and how such differences can affect the expression of seizures and the animals' performance in behavioral tests that often accompany acute and chronic seizure testing., (Copyright © 2017 Elsevier Inc. All rights reserved.)
- Published
- 2017
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29. Reading LINEs within the cocaine addicted brain.
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Doyle GA, Doucet-O'Hare TT, Hammond MJ, Crist RC, Ewing AD, Ferraro TN, Mash DC, Kazazian HH Jr, and Berrettini WH
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- Adult, Animals, Autopsy, Female, Humans, Male, Mice, Mutation, Polymerase Chain Reaction, Cocaine-Related Disorders genetics, Cocaine-Related Disorders metabolism, Long Interspersed Nucleotide Elements genetics, Prefrontal Cortex metabolism
- Abstract
Introduction: Long interspersed element (LINE)-1 (L1) is a type of retrotransposon capable of mobilizing into new genomic locations. Often studied in Mendelian diseases or cancer, L1s may also cause somatic mutation in the developing central nervous system. Recent reports showed L1 transcription was activated in brains of cocaine-treated mice, and L1 retrotransposition was increased in cocaine-treated neuronal cell cultures. We hypothesized that the predisposition to cocaine addiction may result from inherited L1s or somatic L1 mobilization in the brain., Methods: Postmortem medial prefrontal cortex (mPFC) tissue from 30 CA and 30 control individuals was studied. An Alexafluor488-labeled NeuN antibody and fluorescence activated nuclei sorting were used to separate neuronal from non-neuronal cell nuclei. L1s and their 3' flanking sequences were amplified from neuronal and non-neuronal genomic DNA (gDNA) using L1-seq. L1 DNA libraries from the neuronal gDNA were sequenced on an Illumina HiSeq2000. Sequences aligned to the hg19 human genome build were analyzed for L1 insertions using custom "L1-seq" bioinformatics programs., Results: Previously uncataloged L1 insertions, some validated by PCR, were detected in neurons from both CA and control brain samples. Steady-state L1 mRNA levels in CA and control mPFC were also assessed. Gene ontology and pathway analyses were used to assess relationships between genes putatively disrupted by novel L1s in CA and control individuals. L1 insertions in CA samples were enriched in gene ontologies and pathways previously associated with CA., Conclusions: We conclude that neurons in the mPFC harbor L1 insertions that have the potential to influence predisposition to CA.
- Published
- 2017
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30. Barriers to the use of genetic information for the development of new epilepsy treatments.
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Ferraro TN
- Subjects
- Genetic Heterogeneity, Humans, Epilepsy genetics, Epilepsy therapy, Genetic Therapy standards, Genetic Therapy trends
- Abstract
Genetic analysis is providing new information on the biological basis of epilepsy at a rapid pace; this article identifies factors acting as major barriers to use of these data for therapy development. Disease heterogeneity is a primary obstacle since so many genes can cause or predispose to epilepsy and the clinical presentation of epilepsy is so diverse, thus making it difficult to define the most therapeutically relevant targets. Further, many epilepsy genes affect brain development, an observation that represents a barrier unto itself given the challenge of reversing or preventing genetically mediated alterations of brain pathway formation. Finally, the lack of appropriate models for testing new therapies is also recognized as a fundamental limitation. Overcoming these barriers will be aided by full characterization of the genetic landscape of epilepsy, elucidation of key pathway points for therapeutic intervention and creation of unique experimental models to validate results.
- Published
- 2016
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31. Analysis of candidate genes for morphine preference quantitative trait locus Mop2.
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Doyle GA, Schwebel CL, Ruiz SE, Chou AD, Lai AT, Wang MJ, Smith GG, Buono RJ, Berrettini WH, and Ferraro TN
- Subjects
- Analgesics, Non-Narcotic administration & dosage, Animals, Brain physiology, Choice Behavior drug effects, Choice Behavior physiology, Drinking Behavior drug effects, Drinking Behavior physiology, Gene Expression physiology, Mice, Inbred C57BL, Mice, Inbred DBA, Quinine administration & dosage, RGS Proteins metabolism, Species Specificity, Drug-Seeking Behavior physiology, Morphine administration & dosage, Narcotics administration & dosage, Quantitative Trait Loci
- Abstract
Compared to DBA/2J (D2), C57BL/6J (B6) inbred mice exhibit strong morphine preference when tested using a two-bottle choice drinking paradigm. A morphine preference quantitative trait locus (QTL), Mop2, was originally mapped to proximal chromosome (Chr) 10 using a B6xD2 F2 intercross population, confirmed with reciprocal congenic strains and fine mapped with recombinant congenic strains. These efforts identified a ∼ 10-Million base pair (Mbp) interval, underlying Mop2, containing 35 genes. To further reduce the interval, mice from the D2.B6-Mop2-P1 congenic strain were backcrossed to parental D2 mice and two new recombinant strains of interest were generated: D2.B6-Mop2-P1.pD.dB and D2.B6-Mop2-P1.pD.dD. Results obtained from testing these strains in the two-bottle choice drinking paradigm suggest that the gene(s) responsible for the Mop2 QTL is one or more of 22 remaining within the newly defined interval (∼ 7.6 Mbp) which includes Oprm1 and several other genes related to opioid pharmacology. Real-time qRT-PCR analysis of Oprm1 and opioid-related genes Rgs17, Ppp1r14c, Vip, and Iyd revealed both between-strain and within-strain expression differences in comparisons of saline- and morphine-treated B6 and D2 mice. Analysis of Rgs17 protein levels also revealed both between-strain and within-strain differences in comparisons of saline- and morphine-treated B6 and D2 mice. Results suggest that the Mop2 QTL represents the combined influence of multiple genetic variants on morphine preference in these two strains. Relative contributions of each variant remain to be determined., (Copyright © 2014 IBRO. All rights reserved.)
- Published
- 2014
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32. BMAL1 controls the diurnal rhythm and set point for electrical seizure threshold in mice.
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Gerstner JR, Smith GG, Lenz O, Perron IJ, Buono RJ, and Ferraro TN
- Abstract
The epilepsies are a heterogeneous group of neurological diseases defined by the occurrence of unprovoked seizures which, in many cases, are correlated with diurnal rhythms. In order to gain insight into the biological mechanisms controlling this phenomenon, we characterized time-of-day effects on electrical seizure threshold in mice. Male C57BL/6J wild-type mice were maintained on a 14/10 h light/dark cycle, from birth until 6 weeks of age for seizure testing. Seizure thresholds were measured using a step-wise paradigm involving a single daily electrical stimulus. Results showed that the current required to elicit both generalized and maximal seizures was significantly higher in mice tested during the dark phase of the diurnal cycle compared to mice tested during the light phase. This rhythm was absent in BMAL1 knockout (KO) mice. BMAL1 KO also exhibited significantly reduced seizure thresholds at all times tested, compared to C57BL/6J mice. Results document a significant influence of time-of-day on electrical seizure threshold in mice and suggest that this effect is under the control of genes that are known to regulate circadian behaviors. Furthermore, low seizure thresholds in BMAL1 KO mice suggest that BMAL1 itself is directly involved in controlling neuronal excitability.
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- 2014
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33. The relationship between genes affecting the development of epilepsy and approaches to epilepsy therapy.
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Ferraro TN
- Subjects
- Humans, Epilepsy genetics, Epilepsy therapy, Genetic Predisposition to Disease genetics
- Abstract
The epilepsies are a clinically heterogeneous group of common brain diseases which are refractory to pharmacotherapy in up to one-third of patients. The discovery of DNA variants that cause or predispose to epilepsy has the potential to lead to new treatments that are based on the protein products or functional pathways of implicated genes. Overlap of gene classes involved in several broad phenotypic categories of epilepsy provides a means to prioritize various genetic leads for therapy development. In cases of epilepsy that are influenced strongly by single genetic defects, treatments may be personalized based upon the structural nature of the DNA alteration rather than on the function of the defective gene(s) or pathway(s). However, since most cases of epilepsy may be polygenic, the extent to which this approach may be widely applicable is unclear, thus creating a need for development of new target-based medications as well as further refinement of currently effective therapies.
- Published
- 2014
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34. Functional genetic variants in the vesicular monoamine transporter 1 modulate emotion processing.
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Lohoff FW, Hodge R, Narasimhan S, Nall A, Ferraro TN, Mickey BJ, Heitzeg MM, Langenecker SA, Zubieta JK, Bogdan R, Nikolova YS, Drabant E, Hariri AR, Bevilacqua L, Goldman D, and Doyle GA
- Subjects
- Adolescent, Affective Symptoms pathology, Animals, Biogenic Monoamines metabolism, Brain blood supply, Brain metabolism, Brain pathology, Case-Control Studies, Cell Line, Transformed, Chlorocebus aethiops, Female, Genetic Association Studies, Genotype, Humans, Image Processing, Computer-Assisted, Male, Transfection, Vesicular Monoamine Transport Proteins metabolism, Young Adult, Affective Symptoms genetics, Emotions physiology, Polymorphism, Genetic genetics, Vesicular Monoamine Transport Proteins genetics
- Abstract
Emotional behavior is in part heritable and often disrupted in psychopathology. Identification of specific genetic variants that drive this heritability may provide important new insight into molecular and neurobiological mechanisms involved in emotionality. Our results demonstrate that the presynaptic vesicular monoamine transporter 1 (VMAT1) Thr136Ile (rs1390938) polymorphism is functional in vitro, with the Ile allele leading to increased monoamine transport into presynaptic vesicles. Moreover, we show that the Thr136Ile variant predicts differential responses in emotional brain circuits consistent with its effects in vitro. Lastly, deep sequencing of bipolar disorder (BPD) patients and controls identified several rare novel VMAT1 variants. The variant Phe84Ser was only present in individuals with BPD and leads to marked increase monoamine transport in vitro. Taken together, our data show that VMAT1 polymorphisms influence monoamine signaling, the functional response of emotional brain circuits and risk for psychopathology.
- Published
- 2014
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35. Quantitative trait loci analysis reveals candidate genes implicated in regulating functional deficit and CNS vascular permeability in CD8 T cell-initiated blood-brain barrier disruption.
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Johnson HL, Hanson LM, Chen Y, Bieber AJ, Buono RJ, Ferraro TN, Pirko I, and Johnson AJ
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- Animals, Astrocytes pathology, Blood-Brain Barrier immunology, Capillary Permeability immunology, Chi-Square Distribution, Mice, Mice, Inbred C57BL, Motor Activity, Quantitative Trait, Heritable, Syndrome, Blood-Brain Barrier pathology, Blood-Brain Barrier physiopathology, CD8-Positive T-Lymphocytes immunology, Capillary Permeability genetics, Genetic Association Studies, Quantitative Trait Loci genetics
- Abstract
Background: Blood-brain barrier (BBB) disruption is an integral feature of numerous neurological disorders. However, there is a relative lack of knowledge regarding the underlying molecular mechanisms of immune-mediated BBB disruption. We have previously shown that CD8 T cells and perforin play critical roles in initiating altered permeability of the BBB in the peptide-induced fatal syndrome (PIFS) model developed by our laboratory. Additionally, despite having indistinguishable CD8 T cell responses, C57BL/6J (B6) mice are highly susceptible to PIFS, exhibiting functional motor deficits, increased astrocyte activation, and severe CNS vascular permeability, while 129S1/SvImJ (129S1) mice remain resistant. Therefore, to investigate the potential role of genetic factors, we performed a comprehensive genetic analysis of (B6 x 129S1) F2 progeny to define quantitative trait loci (QTL) linked to the phenotypic characteristics stated above that mediate CD8 T cell-initiated BBB disruption., Results: Using single nucleotide polymorphism (SNP) markers and a 95% confidence interval, we identified one QTL (PIFS1) on chromosome 12 linked to deficits in motor function (SNP markers rs6292954, rs13481303, rs3655057, and rs13481324, LOD score = 3.3). In addition we identified a second QTL (PIFS2) on chromosome 17 linked to changes in CNS vascular permeability (SNP markers rs6196216 and rs3672065, LOD score = 3.7)., Conclusions: The QTL critical intervals discovered have allowed for compilation of a list of candidate genes implicated in regulating functional deficit and CNS vascular permeability. These genes encode for factors that may be potential targets for therapeutic approaches to treat disorders characterized by CD8 T cell-mediated BBB disruption.
- Published
- 2013
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36. Further evidence for association of polymorphisms in the CNR1 gene with cocaine addiction: confirmation in an independent sample and meta-analysis.
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Clarke TK, Bloch PJ, Ambrose-Lanci LM, Ferraro TN, Berrettini WH, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, and Lohoff FW
- Subjects
- Adolescent, Case-Control Studies, Chi-Square Distribution, Cocaine adverse effects, Cocaine pharmacology, Diagnostic and Statistical Manual of Mental Disorders, Dopamine metabolism, Dopamine physiology, Female, Gene Frequency, Genome-Wide Association Study, Haplotypes, Humans, Linkage Disequilibrium, Male, Reward, United States epidemiology, Black or African American genetics, Cocaine-Related Disorders genetics, Genetic Predisposition to Disease genetics, Polymorphism, Single Nucleotide genetics, Receptor, Cannabinoid, CB1 genetics
- Abstract
Genetic research on cocaine dependence (CD) may help clarify our understanding of the disorder as well as provide insights for effective treatment. As endocannabinoid signaling and dopamine neurotransmission have been shown to be involved in drug reward, genes related to these systems are plausible candidates for susceptibility to CD. The cannabinoid receptor 1 protein regulates both the endocannabinoid and dopaminergic neurobiological systems, and polymorphisms in the cannabinoid receptor gene, CNR1, have been associated previously with substance dependence. In this study, we attempt to replicate findings associating CNR1 with CD in African Americans. Cocaine-addicted individuals (n=860) and unaffected controls (n=334) of African descent were genotyped for two single nucleotide polymorphisms (SNPs) in CNR1 (rs6454674, rs806368). We observed a significant difference in genotype frequencies between cases and controls for both SNPs (P≤0.042). A meta-analysis was also performed combining our data with that of Zuo et al. who also studied these polymorphisms in African American cocaine addicts (total n=1253 cases versus 543 controls). When our data were combined, rs6454674 increased in significance to P=0.027; however, rs806368 was no longer significant. This study confirms the association between rs6454674 and CD. However, because there is considerable co-morbidity of CD with other drugs of abuse, additional studies are necessary to determine whether polymorphisms in CNR1 induce a general susceptibility to substance dependence or are specific to cocaine addiction. Furthermore, as this population consists of American individuals of African descent, the possibility of population stratification should not be excluded., (© 2011 The Authors, Addiction Biology © 2011 Society for the Study of Addiction.)
- Published
- 2013
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37. Case-control association study of WLS variants in opioid and cocaine addicted populations.
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Crist RC, Ambrose-Lanci LM, Zeng A, Yuan C, Kampman KM, Pettinati HM, Oslin DW, O'Brien CP, Ferraro TN, Doyle GA, Lohoff FW, and Berrettini WH
- Subjects
- Black or African American genetics, Black or African American psychology, Case-Control Studies, Female, Genetic Association Studies, Genotype, Humans, Male, Polymorphism, Single Nucleotide genetics, White People genetics, White People psychology, Cocaine-Related Disorders genetics, Genetic Predisposition to Disease genetics, Intracellular Signaling Peptides and Proteins genetics, Opioid-Related Disorders genetics, Receptors, G-Protein-Coupled genetics
- Abstract
The opioid receptor family is involved in the development and maintenance of drug addiction. The mu-opioid receptor (MOR) mediates the rewarding effects of multiple drugs, including opiates and cocaine. A number of proteins interact with MOR, potentially modulating MOR function and altering the physiological consequences of drug use. These mu-opioid receptor interacting proteins (MORIPs) are potential therapeutic targets for the treatment of addiction. The Wntless (WLS) protein was recently identified as a MORIP in a yeast two-hybrid screen. In this study, we conducted a case-control association analysis of 16 WLS genetic variants in opioid and cocaine addicted individuals of both African-American (opioid n=336, cocaine n=908) and European-American (opioid n=335, cocaine n=336) ancestry. Of the analyzed SNPs, three were nominally associated with opioid addiction and four were nominally associated with cocaine addiction. None of these associations were significant following multiple testing correction. These data suggest that the common variants of WLS analyzed in this study are not associated with opioid or cocaine addiction. However, this study does not exclude the possibilities that rare variants in WLS may affect susceptibility to drug addiction, or that common variants with small effect size may fall below the detection level of our analysis., (Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2013
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38. MOR is not enough: identification of novel mu-opioid receptor interacting proteins using traditional and modified membrane yeast two-hybrid screens.
- Author
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Petko J, Justice-Bitner S, Jin J, Wong V, Kittanakom S, Ferraro TN, Stagljar I, and Levenson R
- Subjects
- Analgesics, Opioid pharmacology, Animals, Brain drug effects, Brain metabolism, Cell Line, Female, HEK293 Cells, Humans, Immunoprecipitation methods, Mice, Mice, Inbred C57BL, Morphine pharmacology, Nuclear Proteins metabolism, Receptors, Opioid, delta metabolism, Receptors, Opioid, kappa metabolism, Signal Transduction drug effects, Two-Hybrid System Techniques, Ubiquitin-Protein Ligases metabolism, Ubiquitination drug effects, Seven in Absentia Proteins, Analgesics, Opioid metabolism, Receptors, Opioid, mu metabolism, Yeasts metabolism
- Abstract
The mu-opioid receptor (MOR) is the G-protein coupled receptor primarily responsible for mediating the analgesic and rewarding properties of opioid agonist drugs such as morphine, fentanyl, and heroin. We have utilized a combination of traditional and modified membrane yeast two-hybrid screening methods to identify a cohort of novel MOR interacting proteins (MORIPs). The interaction between the MOR and a subset of MORIPs was validated in pulldown, co-immunoprecipitation, and co-localization studies using HEK293 cells stably expressing the MOR as well as rodent brain. Additionally, a subset of MORIPs was found capable of interaction with the delta and kappa opioid receptors, suggesting that they may represent general opioid receptor interacting proteins (ORIPS). Expression of several MORIPs was altered in specific mouse brain regions after chronic treatment with morphine, suggesting that these proteins may play a role in response to opioid agonist drugs. Based on the known function of these newly identified MORIPs, the interactions forming the MOR signalplex are hypothesized to be important for MOR signaling and intracellular trafficking. Understanding the molecular complexity of MOR/MORIP interactions provides a conceptual framework for defining the cellular mechanisms of MOR signaling in brain and may be critical for determining the physiological basis of opioid tolerance and addiction.
- Published
- 2013
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39. Low frequency genetic variants in the μ-opioid receptor (OPRM1) affect risk for addiction to heroin and cocaine.
- Author
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Clarke TK, Crist RC, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, Ferraro TN, Lohoff FW, and Berrettini WH
- Subjects
- Adult, Black People, Case-Control Studies, Cocaine-Related Disorders ethnology, Cohort Studies, Female, Genetic Association Studies, Genetic Predisposition to Disease, Heroin Dependence ethnology, Humans, Male, Polymorphism, Single Nucleotide, Risk, White People, Black or African American, Cocaine-Related Disorders genetics, Heroin Dependence genetics, Receptors, Opioid, mu genetics
- Abstract
The μ-opioid receptor (MOR) binds exogenous and endogenous opioids and is known to mediate the rewarding effects of drugs of abuse. Numerous genetic studies have sought to identify common genetic variation in the gene encoding MOR (OPRM1) that affects risk for drug addiction. The purpose of this study was to examine the contribution of rare coding variants in OPRM1 to the risk for addiction. Rare and low frequency variants were selected using the National Heart Lung and Blood Institute - Exome Sequencing Project (NHLBI-ESP) database, which has screened the exomes of over 6500 individuals. Two SNPs (rs62638690 and rs17174794) were selected for genotyping in 1377 European American individuals addicted to heroin and/or cocaine. Two different SNPs (rs1799971 and rs17174801) were genotyped in 1238 African American individuals addicted to heroin and/or cocaine. Using the minor allele frequencies from the NHLBI-ESP dataset as a comparison group, case-control association analyses were performed. Results revealed an association between rs62638690 and cocaine and heroin addiction in European Americans (p=0.02; 95% C.I. 0.47 [0.24-0.92]). This study suggests a potential role for rare OPRM1 variants in addiction disorders and highlights an area worthy of future study., (Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2013
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40. Quantitative trait locus on distal chromosome 1 regulates the occurrence of spontaneous spike-wave discharges in DBA/2 mice.
- Author
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Bessaïh T, de Yebenes EG, Kirkland K, Higley MJ, Buono RJ, Ferraro TN, and Contreras D
- Subjects
- Animals, Animals, Congenic genetics, Brain physiopathology, Electroencephalography, Epilepsy, Absence physiopathology, Genetic Predisposition to Disease genetics, Male, Mice, Mice, Inbred C57BL, Mice, Inbred DBA, Chromosome Mapping, Epilepsy, Absence genetics, Quantitative Trait Loci genetics
- Abstract
Purpose: Most common forms of human epilepsy result from a complex combination of polygenetic and environmental factors. Quantitative trait locus (QTL) mapping is a first step toward the nonbiased discovery of epilepsy-related candidate genes. QTL studies of susceptibility to induced seizures in mouse strains have consistently converged on a distal region of chromosome 1 as a major phenotypic determinant; however, its influence on spontaneous epilepsy remains unclear. In the present study we characterized the influence of allelic variations within this QTL, termed Szs1, on the occurrence of spontaneous spike-wave discharges (SWDs) characteristic of absence seizures in DBA/2 (D2) mice., Methods: We analyzed SWD occurrence and patterns in freely behaving D2, C57BL/6 (B6) and the congenic strains D2.B6-Szs1 and B6.D2-Szs1., Key Findings: We showed that congenic manipulation of the Szs1 locus drastically reduced the number and the duration of SWDs in D2.B6-Szs1 mice, which are homozygous for Szs1 from B6 strain on a D2 strain background. However, it failed to induce the full expression of SWDs in the reverse congenic animals B6.D2-Szs1., Significance: Our results demonstrate that the occurrence of SWDs in D2 animals is under polygenic control and, therefore, the D2 and B6 strains might be a useful model to dissect the genetic determinants of polygenic SWDs characteristic of typical absence seizures. Furthermore, we point to the existence of epistatic interactions between at least one modifier gene within Szs1 and genes within unlinked QTLs in regulating the occurrence of spontaneous nonconvulsive forms of epilepsies., (Wiley Periodicals, Inc. © 2012 International League Against Epilepsy.)
- Published
- 2012
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41. Association study of the β-arrestin 2 gene (ARRB2) with opioid and cocaine dependence in a European-American population.
- Author
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Ambrose-Lanci LM, Vaswani M, Clarke TK, Zeng A, Lohoff FW, Ferraro TN, and Berrettini WH
- Subjects
- Humans, Polymorphism, Single Nucleotide, beta-Arrestin 2, beta-Arrestins, Arrestins genetics, Cocaine-Related Disorders genetics, Opioid-Related Disorders genetics, White People
- Abstract
The rewarding properties of drugs of abuse are mediated by the mu-opioid receptor (MOR). Genetic variations in MOR and MOR interacting proteins (MORIPs) involved in MOR signaling may increase the risk for drug dependence. The MORIP β-arrestin plays an important role in the regulation of MOR trafficking, thereby highlighting it as a candidate gene for addiction phenotypes. In this case-control association study, DNA samples from cocaine-dependent (n=336) and opioid-dependent (n=335) patients and controls (n=656) were genotyped for seven single nucleotide polymorphisms (rs11868227, rs3786047, rs4522461, rs1045280, rs2271167, rs2036657, and rs4790694) across ARRB2, the gene encoding the β-arrestin 2 protein. No significant differences were observed in genotype or allele frequency between drug-dependent and control individuals for any of the single nucleotide polymorphisms analyzed. Haplotype analysis was similarly negative. Further studies are needed to determine whether variations in ARRB2 (or other MORIPs) are relevant to cocaine or opioid dependence in different ethnic populations or whether they confer a risk that is specific to dependence on other drugs of abuse.
- Published
- 2012
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42. Genetic association analyses of PDYN polymorphisms with heroin and cocaine addiction.
- Author
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Clarke TK, Ambrose-Lanci L, Ferraro TN, Berrettini WH, Kampman KM, Dackis CA, Pettinati HM, O'Brien CP, Oslin DW, and Lohoff FW
- Subjects
- Adolescent, Adult, Black or African American genetics, Alleles, Behavior, Addictive genetics, Female, Gene Frequency, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Humans, Linkage Disequilibrium, Male, Middle Aged, Sex Factors, White People genetics, Cocaine-Related Disorders genetics, Enkephalins genetics, Heroin Dependence genetics, Polymorphism, Single Nucleotide, Protein Precursors genetics
- Abstract
Genetic factors are believed to account for 30-50% of the risk for cocaine and heroin addiction. Dynorphin peptides, derived from the prodynorphin (PDYN) precursor, bind to opioid receptors, preferentially the kappa-opioid receptor, and may mediate the aversive effects of drugs of abuse. Dynorphin peptides produce place aversion in animals and produce dysphoria in humans. Cocaine and heroin have both been shown to increase expression of PDYN in brain regions relevant for drug reward and use. Polymorphisms in PDYN are therefore hypothesized to increase risk for addiction to drugs of abuse. In this study, 3 polymorphisms in PDYN (rs1022563, rs910080 and rs1997794) were genotyped in opioid-addicted [248 African Americans (AAs) and 1040 European Americans (EAs)], cocaine-addicted (1248 AAs and 336 EAs) and control individuals (674 AAs and 656 EAs). Sex-specific analyses were also performed as a previous study identified PDYN polymorphisms to be more significantly associated with female opioid addicts. We found rs1022563 to be significantly associated with opioid addiction in EAs [P = 0.03, odds ratio (OR) = 1.31; false discovery rate (FDR) corrected q-value]; however, when we performed female-specific association analyses, the OR increased from 1.31 to 1.51. Increased ORs were observed for rs910080 and rs199774 in female opioid addicts also in EAs. No statistically significant associations were observed with cocaine or opioid addiction in AAs. These data show that polymorphisms in PDYN are associated with opioid addiction in EAs and provide further evidence that these risk variants may be more relevant in females., (© 2012 The Authors. Genes, Brain and Behavior © 2012 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.)
- Published
- 2012
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43. Discovery of epilepsy susceptibility genes: implications for therapy development and pharmacogenomics.
- Author
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Ferraro TN
- Subjects
- Anticonvulsants therapeutic use, Genetic Predisposition to Disease, Genetic Therapy, Humans, Molecular Targeted Therapy, NAV1.2 Voltage-Gated Sodium Channel genetics, Polymorphism, Genetic, Epilepsy genetics, Epilepsy therapy, NAV1.1 Voltage-Gated Sodium Channel genetics
- Published
- 2012
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44. Opiate agonist-induced re-distribution of Wntless, a mu-opioid receptor interacting protein, in rat striatal neurons.
- Author
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Reyes BA, Vakharia K, Ferraro TN, Levenson R, Berrettini WH, and Van Bockstaele EJ
- Subjects
- Analysis of Variance, Animals, Immunohistochemistry methods, Male, Microscopy, Immunoelectron methods, Neurons metabolism, Neurons ultrastructure, Protein Transport drug effects, Rats, Rats, Sprague-Dawley, Synapses drug effects, Synapses metabolism, Synapses ultrastructure, Analgesics, Opioid pharmacology, Corpus Striatum cytology, Enkephalin, Ala(2)-MePhe(4)-Gly(5)- pharmacology, Intracellular Signaling Peptides and Proteins metabolism, Morphine pharmacology, Neurons drug effects, Receptors, G-Protein-Coupled metabolism
- Abstract
Wntless (WLS), a mu-opioid receptor (MOR) interacting protein, mediates Wnt protein secretion that is critical for neuronal development. We investigated whether MOR agonists induce re-distribution of WLS within rat striatal neurons. Adult male rats received either saline, morphine or [d-Ala2, N-Me-Phe4, Gly-ol5]-enkephalin (DAMGO) directly into the lateral ventricles. Following thirty minutes, brains were extracted and tissue sections were processed for immunogold silver detection of WLS. In saline-treated rats, WLS was distributed along the plasma membrane and within the cytoplasmic compartment of striatal dendrites as previously described. The ratio of cytoplasmic to total dendritic WLS labeling was 0.70±0.03 in saline-treated striatal tissue. Morphine treatment decreased this ratio to 0.48±0.03 indicating a shift of WLS from the intracellular compartment to the plasma membrane. However, following DAMGO treatment, the ratio was 0.85±0.05 indicating a greater distribution of WLS intracellularly. The difference in the re-distribution of the WLS following different agonist exposure may be related to DAMGO's well known ability to induce internalization of MOR in contrast to morphine, which is less effective in producing receptor internalization. Furthermore, these data are consistent with our hypothesis that MOR agonists promote dimerization of WLS and MOR, thereby preventing WLS from mediating Wnt secretion. In summary, our findings indicate differential agonist-induced trafficking of WLS in striatal neurons following distinct agonist exposure. Adaptations in WLS trafficking may represent a novel pharmacological target in the treatment of opiate addiction and/or pain., (Copyright © 2011 Elsevier Inc. All rights reserved.)
- Published
- 2012
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45. Quantitative trait loci for electrical seizure threshold mapped in C57BLKS/J and C57BL/10SnJ mice.
- Author
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Ferraro TN, Smith GG, Ballard D, Zhao H, Schwebel CL, Gupta A, Rappaport EF, Ruiz SE, Lohoff FW, Doyle GA, Berrettini WH, and Buono RJ
- Subjects
- Animals, Brain Chemistry genetics, Disease Models, Animal, Electric Stimulation adverse effects, Electric Stimulation methods, Epilepsy physiopathology, Female, Male, Mice, Mice, Inbred C57BL, Mice, Mutant Strains, Chromosome Mapping methods, Epilepsy genetics, Genetic Predisposition to Disease genetics, Quantitative Trait Loci genetics
- Abstract
We mapped the quantitative trait loci (QTL) that contribute to the robust difference in maximal electroshock seizure threshold (MEST) between C57BLKS/J (BKS) and C57BL10S/J (B10S) mice. BKS, B10S, BKS × B10S F1 and BKS × B10S F2 intercross mice were tested for MEST at 8-9 weeks of age. Results of F2 testing showed that, in this cross, MEST is a continuously distributed trait determined by polygenic inheritance. Mice from the extremes of the trait distribution were genotyped using microarray technology. MEST correlated significantly with body weight and sex; however, because of the high correlation between these factors, the QTL mapping was conditioned on sex alone. A sequential series of statistical analyses was used to map QTLs including single-point, multipoint and multilocus methods. Two QTLs reached genome-wide levels of significance based upon an empirically determined permutation threshold: chromosome 6 (LOD = 6.0 at ∼69 cM) and chromosome 8 (LOD = 5.7 at ∼27 cM). Two additional QTLs were retained in a multilocus regression model: chromosome 3 (LOD = 2.1 at ∼68 cM) and chromosome 5 (LOD = 2.7 at ∼73 cM). Together the four QTLs explain one third of the total phenotypic variance in the mapping population. Lack of overlap between the major MEST QTLs mapped here in BKS and B10S mice and those mapped previously in C57BL/6J and DBA/2J mice (strains that are closely related to BKS and B10S) suggest that BKS and B10S represent a new polygenic mouse model for investigating susceptibility to seizures., (© 2010 The Authors. Genes, Brain and Behavior © 2010 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.)
- Published
- 2011
- Full Text
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46. Genetic dissection of intermale aggressive behavior in BALB/cJ and A/J mice.
- Author
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Dow HC, Kreibich AS, Kaercher KA, Sankoorikal GM, Pauley ED, Lohoff FW, Ferraro TN, Li H, and Brodkin ES
- Subjects
- Animals, Chromosome Mapping, Chromosomes, Mammalian genetics, Chromosomes, Mammalian physiology, Crosses, Genetic, Genetic Linkage, Genome-Wide Association Study, Genotype, Haplotypes, Male, Mice, Mice, Inbred A, Mice, Inbred BALB C, Phenotype, Species Specificity, Aggression physiology, Aggression psychology
- Abstract
Aggressive behaviors are disabling, treatment refractory, and sometimes lethal symptoms of several neuropsychiatric disorders. However, currently available treatments for patients are inadequate, and the underlying genetics and neurobiology of aggression is only beginning to be elucidated. Inbred mouse strains are useful for identifying genomic regions, and ultimately the relevant gene variants (alleles) in these regions, that affect mammalian aggressive behaviors, which, in turn, may help to identify neurobiological pathways that mediate aggression. The BALB/cJ inbred mouse strain exhibits relatively high levels of intermale aggressive behaviors and shows multiple brain and behavioral phenotypes relevant to neuropsychiatric syndromes associated with aggression. The A/J strain shows very low levels of aggression. We hypothesized that a cross between BALB/cJ and A/J inbred strains would reveal genomic loci that influence the tendency to initiate intermale aggressive behavior. To identify such loci, we conducted a genomewide scan in an F2 population of 660 male mice bred from BALB/cJ and A/J inbred mouse strains. Three significant loci on chromosomes 5, 10 and 15 that influence aggression were identified. The chromosome 5 and 15 loci are completely novel, and the chromosome 10 locus overlaps an aggression locus mapped in our previous study that used NZB/B1NJ and A/J as progenitor strains. Haplotype analysis of BALB/cJ, NZB/B1NJ and A/J strains showed three positional candidate genes in the chromosome 10 locus. Future studies involving fine genetic mapping of these loci as well as additional candidate gene analysis may lead to an improved biological understanding of mammalian aggressive behaviors., (© 2010 The Authors. Genes, Brain and Behavior © 2010 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.)
- Published
- 2011
- Full Text
- View/download PDF
47. Association study of polymorphisms in the autosomal mitochondrial complex I subunit gene, NADH dehydrogenase (ubiquinone) flavoprotein 2, and bipolar disorder.
- Author
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Doyle GA, Dahl JP, Bloch PJ, Weller AE, Lohoff FW, Ferraro TN, and Berrettini WH
- Subjects
- Haplotypes genetics, Humans, Linkage Disequilibrium genetics, Protein Subunits genetics, Bipolar Disorder enzymology, Bipolar Disorder genetics, Electron Transport Complex I genetics, Genetic Association Studies, Genetic Predisposition to Disease, NADH Dehydrogenase genetics, Polymorphism, Single Nucleotide genetics
- Published
- 2011
- Full Text
- View/download PDF
48. In vitro and ex vivo analysis of CHRNA3 and CHRNA5 haplotype expression.
- Author
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Doyle GA, Wang MJ, Chou AD, Oleynick JU, Arnold SE, Buono RJ, Ferraro TN, and Berrettini WH
- Subjects
- 5' Untranslated Regions genetics, Autopsy, Binding Sites genetics, Brain metabolism, Cell Line, Tumor, Electrophoretic Mobility Shift Assay, Gene Expression Regulation, Gene Frequency, Genetic Predisposition to Disease genetics, Genotype, HeLa Cells, Humans, Luciferases genetics, Luciferases metabolism, Mutation, Promoter Regions, Genetic genetics, Protein Binding, Risk Factors, Sp1 Transcription Factor metabolism, Tobacco Use Disorder genetics, White People genetics, Haplotypes genetics, Nerve Tissue Proteins genetics, Polymorphism, Single Nucleotide, Receptors, Nicotinic genetics
- Abstract
Genome-wide association studies implicate variations in CHRNA5 and CHRNA3 as being associated with nicotine addiction (NA). Multiple common haplotypes ("risk", "mixed" and "protective") exist in Europeans; however, high linkage disequilibrium between variations in CHRNA5 and CHRNA3 makes assigning causative allele(s) for NA difficult through genotyping experiments alone. We investigated whether CHRNA5 or CHRNA3 promoter haplotypes, associated previously with NA, might influence allelic expression levels. For in vitro analyses, promoter haplotypes were sub-cloned into a luciferase reporter vector. When assessed in BE(2)-C cells, luciferase expression was equivalent among CHRNA3 haplotypes, but the combination of deletion at rs3841324 and variation at rs503464 decreased CHRNA5 promoter-derived luciferase activity, possibly due to loss of an SP-1 and other site(s). Variation within the CHRNA5 5'UTR at rs55853698 and rs55781567 also altered luciferase expression in BE(2)-C cells. Allelic expression imbalance (AEI) from the "risk" or "protective" haplotypes was assessed in post-mortem brain tissue from individuals heterozygous at coding polymorphisms in CHRNA3 (rs1051730) or CHRNA5 (rs16969968). In most cases, equivalent allelic expression was observed; however, one individual showed CHRNA5 AEI that favored the "protective" allele and that was concordant with heterozygosity at polymorphisms ∼13.5 kb upstream of the CHRNA5 transcription start site. Putative enhancer activity from these distal promoter elements was assessed using heterologous promoter constructs. We observed no differences in promoter activity from the two distal promoter haplotypes examined, but found that the distal promoter region strongly repressed transcription. We conclude that CHRNA5 promoter variants may affect relative risk for NA in some heterozygous individuals.
- Published
- 2011
- Full Text
- View/download PDF
49. Association analysis between polymorphisms in the myo-inositol monophosphatase 2 (IMPA2) gene and bipolar disorder.
- Author
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Bloch PJ, Weller AE, Doyle GA, Ferraro TN, Berrettini WH, Hodge R, and Lohoff FW
- Subjects
- Adult, Bipolar Disorder diagnosis, Female, Genetic Markers genetics, Haplotypes genetics, Humans, Male, Bipolar Disorder enzymology, Bipolar Disorder genetics, Genome-Wide Association Study methods, Phosphoric Monoester Hydrolases genetics, Polymorphism, Single Nucleotide genetics
- Abstract
Linkage studies in bipolar disorder (BPD) suggest that a susceptibility locus exists on chromosome 18p11. The myo-inositol monophosphatase 2 gene (IMPA2) maps to this genomic region. Myo-inositol monophosphatase dephosphorylates inositol monophosphate, regenerating free inositol. Lithium, a common treatment for BPD, has been shown to inhibit IMPA2 activity and decrease levels of inositol. It is hypothesized that lithium conveys its therapeutic effect for BPD patients partially through inositol regulation. Hence, dysfunction of inositol caused by IMPA2 irregularity may contribute to the pathophysiology of BPD. In this study, we hypothesize that genetic variations in the IMPA2 gene contributes to increased susceptibility to BPD. We tested this hypothesis by genotyping 9 SNPs (rs1787984; rs585247; rs3974759; rs650727; rs589247; rs669838; rs636173; rs3786285; rs613993) in BPD patients (n=556) and controls (n=735). Genotype and allele frequencies were compared between groups using Chi square contingency analysis. Linkage disequilibrium (LD) between markers was calculated and estimated haplotype frequencies were compared between groups. Single marker analysis revealed several associations between IMPA2 variations and BPD, which were subsequently rendered non-significant after correction for multiple testing. Although our study did not show strong support for an association between the tested IMPA2 polymorphisms and susceptibility to BPD, additional larger studies are necessary to comprehensively investigate a role of the IMPA2 gene in the pathophysiology of BPD., (Copyright © 2010 Elsevier Inc. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
50. Confirmation of multiple seizure susceptibility QTLs on chromosome 15 in C57BL/6J and DBA/2J inbred mice.
- Author
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Ferraro TN, Smith GG, Schwebel CL, Doyle GA, Ruiz SE, Oleynick JU, Lohoff FW, Berrettini WH, and Buono RJ
- Subjects
- Animals, Female, Genotype, Male, Mice, Mice, Inbred C57BL, Mice, Inbred DBA, Chromosomes, Mammalian genetics, Genetic Predisposition to Disease genetics, Quantitative Trait Loci genetics, Seizures genetics
- Abstract
To confirm seizure susceptibility (SZS) quantitative trait loci (QTLs) on chromosome (chr) 15 identified previously using C57BL/6J (B6) and DBA/2J (D2) mice and to refine their genomic map position, we studied a set of three congenic strains in which overlapping segments of chr 15 from D2 were transferred onto the B6 background. We measured thresholds for generalized electroshock seizure (GEST) and maximal electroshock seizure (MEST) in congenic strains and B6-like littermates and also tested their responses to kainic acid (KA) and pentylenetetrazol (PTZ). Results document that MEST is significantly lower in strains 15M and 15D, which harbor medial and distal (telomeric) segments of chr 15 (respectively) from D2, compared with strain 15P, which harbors the proximal (acromeric) segment of chr 15 from D2, and with control littermates. Congenic strains 15P and 15M exhibited greater KA SZS compared with strain 15D and B6-like controls. All congenic strains were similar to controls with regard to PTZ SZS. Taken together, results suggest there are multiple SZS QTLs on chr 15 and that two QTLs harbor gene variants that affect MEST and KA SZS independently. The MEST QTL is refined to a 19 Mb region flanked by rs13482630 and D15Mit159. This interval contains 350 genes, 183 of which reside in areas where the polymorphism rate between B6 and D2 is high. The KA QTL interval spans a 65 Mb region flanked by markers D15Mit13 and rs31271969. It harbors 83 genes in highly polymorphic areas, 310 genes in all. Complete dissection of these loci will lead to identification of genetic variants that influence SZS in mice and provide a better understanding of seizure biology.
- Published
- 2010
- Full Text
- View/download PDF
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