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Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep 2023; 42:112856. [PMID: 37481717 PMCID: PMC10530068 DOI: 10.1016/j.celrep.2023.112856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
To identify addiction genes, we evaluate intravenous self-administration of cocaine or saline in 84 inbred and recombinant inbred mouse strains over 10 days. We integrate the behavior data with brain RNA-seq data from 41 strains. The self-administration of cocaine and that of saline are genetically distinct. We maximize power to map loci for cocaine intake by using a linear mixed model to account for this longitudinal phenotype while correcting for population structure. A total of 15 unique significant loci are identified in the genome-wide association study. A transcriptome-wide association study highlights the Trpv2 ion channel as a key locus for cocaine self-administration as well as identifying 17 additional genes, including Arhgef26, Slc18b1, and Slco5a1. We find numerous instances where alternate splice site selection or RNA editing altered transcript abundance. Our work emphasizes the importance of Trpv2, an ionotropic cannabinoid receptor, for the response to cocaine.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jared R Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Nathan LaPierre
- Department of Computer Science, UCLA, Los Angeles, CA 90095, USA
| | | | - Tadeo C Spencer
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Department of Computational Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James D Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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Fernández-Carrión R, Sorlí JV, Coltell O, Pascual EC, Ortega-Azorín C, Barragán R, Giménez-Alba IM, Alvarez-Sala A, Fitó M, Ordovas JM, Corella D. Sweet Taste Preference: Relationships with Other Tastes, Liking for Sugary Foods and Exploratory Genome-Wide Association Analysis in Subjects with Metabolic Syndrome. Biomedicines 2021; 10:biomedicines10010079. [PMID: 35052758 PMCID: PMC8772854 DOI: 10.3390/biomedicines10010079] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 12/21/2022] Open
Abstract
Taste perception and its association with nutrition and related diseases (type 2 diabetes, obesity, metabolic syndrome, cardiovascular, etc.) are emerging fields of biomedicine. There is currently great interest in investigating the environmental and genetic factors that influence sweet taste and sugary food preferences for personalized nutrition. Our aims were: (1) to carry out an integrated analysis of the influence of sweet taste preference (both in isolation and in the context of other tastes) on the preference for sugary foods and its modulation by type 2 diabetes status; (2) as well as to explore new genetic factors associated with sweet taste preference. We studied 425 elderly white European subjects with metabolic syndrome and analyzed taste preference, taste perception, sugary-foods liking, biochemical and genetic markers. We found that type 2 diabetic subjects (38%) have a small, but statistically higher preference for sweet taste (p = 0.021) than non-diabetic subjects. No statistically significant differences (p > 0.05) in preferences for the other tastes (bitter, salty, sour or umami) were detected. For taste perception, type 2 diabetic subjects have a slightly lower perception of all tastes (p = 0.026 for the combined “total taste score”), bitter taste being statistically lower (p = 0.023). We also carried out a principal component analysis (PCA), to identify latent variables related to preferences for the five tastes. We identified two factors with eigenvalues >1. Factor 2 was the one with the highest correlation with sweet taste preference. Sweet taste preference was strongly associated with a liking for sugary foods. In the exploratory SNP-based genome-wide association study (GWAS), we identified some SNPs associated with sweet taste preference, both at the suggestive and at the genome-wide level, especially a lead SNP in the PTPRN2 (Protein Tyrosine Phosphatase Receptor Type N2) gene, whose minor allele was associated with a lower sweet taste preference. The PTPRN2 gene was also a top-ranked gene obtained in the gene-based exploratory GWAS analysis. In conclusion, sweet taste preference was strongly associated with sugary food liking in this population. Our exploratory GWAS identified an interesting candidate gene related with sweet taste preference, but more studies in other populations are required for personalized nutrition.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Jose V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellon, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Carolina Ortega-Azorín
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
| | - Rocío Barragán
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Sleep Center of Excellence, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of General Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ignacio M. Giménez-Alba
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
| | - Montserrat Fitó
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Cardiovascular Risk and Nutrition Research Group (CARIN), Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jose M. Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA;
- Nutritional Genomics and Epigenomics Group, IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain; (R.F.-C.); (J.V.S.); (E.C.P.); (C.O.-A.); (R.B.); (I.M.G.-A.); (A.A.-S.)
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (O.C.); (M.F.)
- Correspondence: ; Tel.: +34-96-386-4800
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Genomic and Personalized Medicine Approaches for Substance Use Disorders (SUDs) Looking at Genome-Wide Association Studies. Biomedicines 2021; 9:biomedicines9121799. [PMID: 34944615 PMCID: PMC8698472 DOI: 10.3390/biomedicines9121799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022] Open
Abstract
Drug addiction, or substance use disorder (SUD), is a chronic, relapsing disorder in which compulsive drug-seeking and drug-taking behaviour persist despite serious negative consequences. Drug abuse represents a problem that deserves great attention from a social point of view, and focuses on the importance of genetic studies to help in understanding the genetic basis of addiction and its medical treatment. Despite the complexity of drug addiction disorders, and the high number of environmental variables playing a role in the onset, recurrence, and duration of the symptoms, several studies have highlighted the non-negligible role of genetics, as demonstrated by heritability and genome-wide association studies. A correlation between the relative risk of addiction to specific substances and heritability has been recently observed, suggesting that neurobiological mechanisms may be, at least in part, inherited. All these observations point towards a scenario where the core neurobiological factors of addiction, involving the reward system, impulsivity, compulsivity, stress, and anxiety response, are transmitted, and therefore, genes and mutations underlying their variation might be detected. In the last few years, the development of new and more efficient sequencing technologies has paved the way for large-scale studies in searching for genetic and epigenetic factors affecting drug addiction disorders and their treatments. These studies have been crucial to pinpoint single nucleotide polymorphisms (SNPs) in genes that affect the reaction to medical treatments. This is critically important to identify pharmacogenomic approaches for substance use disorder, such as OPRM1 SNPs and methadone required doses for maintenance treatment (MMT). Nevertheless, despite the promising results obtained by genome-wide association and pharmacogenomic studies, specific studies related to population genetics diversity are lacking, undermining the overall applicability of the preliminary findings, and thus potentially affecting the portability and the accuracy of the genetic studies. In this review, focusing on cannabis, cocaine and heroin use, we report the state-of-the-art genomics and pharmacogenomics of SUDs, and the possible future perspectives related to medical treatment response in people that ask for assistance in solving drug-related problems.
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Kang T, Ye J, Qin P, Li H, Yao Z, Liu Y, Ling Y, Zhang Y, Yu T, Cao H, Li Y, Wang J, Fang F. Knockdown of Ptprn-2 delays the onset of puberty in female rats. Theriogenology 2021; 176:137-148. [PMID: 34607132 DOI: 10.1016/j.theriogenology.2021.09.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022]
Abstract
In the present study, we evaluated how Ptprn-2 (encoding tyrosine phosphatase, receptor type, N2 polypeptide protein) affects the onset of puberty in female rats. We evaluated the expression of Ptprn-2 mRNA and protein in the hypothalamus-pituitary-ovary axis of female rats using real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunofluorescence at infancy, prepuberty, puberty, peripuberty, and adulthood. We evaluated the effects of Ptprn-2 gene knockdown on different aspects of reproduction-related biology in female rats, including the expression levels of puberty-related genes in vivo and in vitro, the time to onset of puberty, the concentration of serum reproductive hormones, the morphology of ovaries, and the ultrastructure of pituitary gonadotropin cells. Our results demonstrated that PTPRN-2 was primarily distributed in the arcuate nucleus (ARC), periventricular nucleus (PeN), adenohypophysis, and the ovarian follicular theca, stroma, and granulosa cells of female rats at various stages. Ptprn-2 mRNA levels significantly varied between peripuberty and puberty (P < 0.05) in the hypothalamus and pituitary gland. In hypothalamic cells, Ptprn-2 knockdown decreased the expression of Ptprn-2 and Rfrp-3 mRNA (P < 0.05) and increased the levels of Gnrh and Kiss-1 mRNA (P < 0.05). Ptprn-2 knockdown in the hypothalamus resulted in delayed vaginal opening compared to the control group (n = 12, P < 0.01), and Ptprn-2, Gnrh, and Kiss-1 mRNA levels (P < 0.05) all decreased, while the expression of Igf-1 (P < 0.05) and Rfrp-3 mRNA (P < 0.01) increased. The concentrations of FSH and P4 in the serum of Ptprn-2 knockdown rats were lower than in control animals (P < 0.05). Large transverse perimeters and longitudinal perimeters (P < 0.05) were found in the ovaries of Ptprn-2 knockdown rats. There were fewer large secretory particles from gonadotropin cells in adenohypophysis tissue of the Ptprn-2 knockdown group compared to the control group. This indicates that Ptprn-2 knockdown can regulate levels of Gnrh, Kiss-1, and Rfrp-3 mRNA in the hypothalamus, regulate the concentration of serum FSH and P4, and alter the morphology of ovarian and gonadotropin cells, delaying the onset of puberty in female rats.
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Affiliation(s)
- Tiezhu Kang
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Jing Ye
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Ping Qin
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hailing Li
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Zhiqiu Yao
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Ya Liu
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Yinghui Ling
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Tong Yu
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hongguo Cao
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Yunsheng Li
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Juhua Wang
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Fugui Fang
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Anhui Provincial Key Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, 130 Changjiang West Road, Hefei, Anhui, 230036, China; Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China.
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Campuzano-Cortina C, Feijoó-Fonnegra LM, Manzur-Pineda K, Palacio-Muñoz M, Rendón-Fonnegra J, Montoya L, Berrouet MC, Restrepo D. Comorbidity between depressive symptoms and substance use in-patients hospitalized for non-psychiatric diseases. REVISTA COLOMBIANA DE PSIQUIATRIA (ENGLISH ED.) 2021; 50:130-137. [PMID: 34099249 DOI: 10.1016/j.rcpeng.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/31/2019] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Epidemiological studies have shown a high prevalence and concurrence between depression and substance use. This is known as "dual diagnosis" and is associated with a worse prognosis for patients. OBJECTIVE To establish the comorbidity between depressive symptoms and substance abuse in patients admitted with acute or chronic diseases to a public hospital. METHODS A descriptive, cross-sectional study of prevalence which included 296 patients aged 18-65, to whom the PHQ-9 and ASSIST 3.0 scales were applied to determine the prevalence of depressive symptoms and substance abuse. Other clinical and sociodemographic variables were also taken into account. RESULTS 50.7% were women with a median age of 41 and an interquartile range of 27 years. Moderate-to-severe depressive symptoms were found in 27.4% of the patients. Alcohol was the substance with the highest consumption in the previous 3 months with 53.7%, followed by cigarettes (47.6%), marijuana (26.7%) and cocaine (14.5%). A significant association was found between severe depressive symptoms PHQ-9 ≥ 20 and problematic use of alcohol, marijuana and cocaine (ASSIST score >26); alcohol (RP 27.30, 95% CI [2.37-314.16], P = 0.01); marijuana (RP 15.00, 95% CI [3.46-64.96], P = 0.001) and cocaine (RP 10.65, 95% CI [2.23-51.10], P = 0.01). DISCUSSION A high prevalence of depressive symptoms and substance use was found in patients hospitalised for non-psychiatric medical conditions, which worsens the prognosis of the underlying medical condition. CONCLUSIONS To provide better hospital care for patients, we need to give visibility to the problem of dual pathology. This could be achieved by conducting more related research in these clinical scenarios.
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Affiliation(s)
| | | | | | | | | | - Laura Montoya
- Médica psiquiatra, docente de pre y posgrado, Universidad CES, psiquiatra Hospital General de Medellín, Medellín, Colombia
| | - Marie Claire Berrouet
- Médica toxicóloga, Hospital General de Medellín, docente de pre y posgrado de Toxicología, Universidad CES, Medellín, Colombia
| | - Diana Restrepo
- Docente de Psiquiatría pre y posgrado, Universidad CES, Medellín, Colombia.
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Molecular Evolution, Neurodevelopmental Roles and Clinical Significance of HECT-Type UBE3 E3 Ubiquitin Ligases. Cells 2020; 9:cells9112455. [PMID: 33182779 PMCID: PMC7697756 DOI: 10.3390/cells9112455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination belongs to the best characterized pathways of protein degradation in the cell; however, our current knowledge on its physiological consequences is just the tip of an iceberg. The divergence of enzymatic executors of ubiquitination led to some 600–700 E3 ubiquitin ligases embedded in the human genome. Notably, mutations in around 13% of these genes are causative of severe neurological diseases. Despite this, molecular and cellular context of ubiquitination remains poorly characterized, especially in the developing brain. In this review article, we summarize recent findings on brain-expressed HECT-type E3 UBE3 ligases and their murine orthologues, comprising Angelman syndrome UBE3A, Kaufman oculocerebrofacial syndrome UBE3B and autism spectrum disorder-associated UBE3C. We summarize evolutionary emergence of three UBE3 genes, the biochemistry of UBE3 enzymes, their biology and clinical relevance in brain disorders. Particularly, we highlight that uninterrupted action of UBE3 ligases is a sine qua non for cortical circuit assembly and higher cognitive functions of the neocortex.
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Linthorst J, Meert W, Hestand MS, Korlach J, Vermeesch JR, Reinders MJT, Holstege H. Extreme enrichment of VNTR-associated polymorphicity in human subtelomeres: genes with most VNTRs are predominantly expressed in the brain. Transl Psychiatry 2020; 10:369. [PMID: 33139705 PMCID: PMC7608644 DOI: 10.1038/s41398-020-01060-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/27/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The human genome harbors numerous structural variants (SVs) which, due to their repetitive nature, are currently underexplored in short-read whole-genome sequencing approaches. Using single-molecule, real-time (SMRT) long-read sequencing technology in combination with FALCON-Unzip, we generated a de novo assembly of the diploid genome of a 115-year-old Dutch cognitively healthy woman. We combined this assembly with two previously published haploid assemblies (CHM1 and CHM13) and the GRCh38 reference genome to create a compendium of SVs that occur across five independent human haplotypes using the graph-based multi-genome aligner REVEAL. Across these five haplotypes, we detected 31,680 euchromatic SVs (>50 bp). Of these, ~62% were comprised of repetitive sequences with 'variable number tandem repeats' (VNTRs), ~10% were mobile elements (Alu, L1, and SVA), while the remaining variants were inversions and indels. We observed that VNTRs with GC-content >60% and repeat patterns longer than 15 bp were 21-fold enriched in the subtelomeric regions (within 5 Mb of the ends of chromosome arms). VNTR lengths can expand to exceed a critical length which is associated with impaired gene transcription. The genes that contained most VNTRs, of which PTPRN2 and DLGAP2 are the most prominent examples, were found to be predominantly expressed in the brain and associated with a wide variety of neurological disorders. Repeat-induced variation represents a sizeable fraction of the genetic variation in human genomes and should be included in investigations of genetic factors associated with phenotypic traits, specifically those associated with neurological disorders. We make available the long and short-read sequence data of the supercentenarian genome, and a compendium of SVs as identified across 5 human haplotypes.
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Affiliation(s)
- Jasper Linthorst
- grid.484519.5Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Wim Meert
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Matthew S. Hestand
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jonas Korlach
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | | | - Marcel J. T. Reinders
- grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Henne Holstege
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands. .,Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands. .,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.
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Campuzano-Cortina C, Feijoó-Fonnegra LM, Manzur-Pineda K, Palacio-Muñoz M, Rendón-Fonnegra J, Montoya L, Berrouet MC, Restrepo D. Comorbidity between depressive symptoms and substance use in-patients hospitalized for non-psychiatric diseases. ACTA ACUST UNITED AC 2020; 50:130-137. [PMID: 33735051 DOI: 10.1016/j.rcp.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/04/2019] [Accepted: 07/31/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Epidemiological studies have shown a high prevalence and concurrence between depression and substance use. This is known as "dual diagnosis" and is associated with a worse prognosis for patients. OBJECTIVE To establish the comorbidity between depressive symptoms and substance abuse in patients admitted with acute or chronic diseases to a public hospital. METHODS A descriptive, cross-sectional study of prevalence which included 296 patients aged 18 to 65, to whom the PHQ-9 and ASSIST 3.0 scales were applied to determine the prevalence of depressive symptoms and substance abuse. Other clinical and sociodemographic variables were also taken into account. RESULTS 50.7% were women with a median age of 41 and an interquartile range of 27 years. Moderate-to-severe depressive symptoms were found in 27.4% of the patients. Alcohol was the substance with the highest consumption in the previous 3 months with 53.7%, followed by cigarettes (47.6%), marijuana (26.7%) and cocaine (14.5%). A significant association was found between severe depressive symptoms PHQ-9 ≥20 and problematic use of alcohol, marijuana and cocaine (ASSIST score>26); alcohol (RP 27.30, 95% CI [2.37-314.16], P=0.01); marijuana (RP 15.00, 95% CI [3.46-64.96], P=0.001) and cocaine (RP 10.65, 95% CI [2.23-51.10], P=0.01). DISCUSSION A high prevalence of depressive symptoms and substance use was found in patients hospitalized for non-psychiatric medical conditions, which worsens the prognosis of the underlying medical condition. CONCLUSIONS To provide better hospital care for patients, we need to give visibility to the problem of dual pathology. This could be achieved by conducting more related research in these clinical scenarios.
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Affiliation(s)
| | | | | | | | | | - Laura Montoya
- Médica psiquiatra, docente de pre y posgrado, Universidad CES, psiquiatra Hospital General de Medellín, Medellín, Colombia
| | - Marie Claire Berrouet
- Médica toxicóloga, Hospital General de Medellín, docente de pre y posgrado de Toxicología, Universidad CES, Medellín, Colombia
| | - Diana Restrepo
- Docente de Psiquiatría pre y posgrado, Universidad CES, Medellín, Colombia.
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Lan T, Yang B, Zhang X, Wang T, Lu Q. Statistical Methods and Software for Substance Use and Dependence Genetic Research. Curr Genomics 2019; 20:172-183. [PMID: 31929725 PMCID: PMC6935956 DOI: 10.2174/1389202920666190617094930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Substantial substance use disorders and related health conditions emerged dur-ing the mid-20th century and continue to represent a remarkable 21st century global burden of disease. This burden is largely driven by the substance-dependence process, which is a complex process and is influenced by both genetic and environmental factors. During the past few decades, a great deal of pro-gress has been made in identifying genetic variants associated with Substance Use and Dependence (SUD) through linkage, candidate gene association, genome-wide association and sequencing studies. METHODS Various statistical methods and software have been employed in different types of SUD ge-netic studies, facilitating the identification of new SUD-related variants. CONCLUSION In this article, we review statistical methods and software that are currently available for SUD genetic studies, and discuss their strengths and limitations.
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Affiliation(s)
| | | | | | - Tong Wang
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
| | - Qing Lu
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
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10
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Alblooshi H, Al Safar H, Fisher HF, Cordell HJ, El Kashef A, Al Ghaferi H, Shawky M, Reece S, Hulse GK, Tay GK. A case-control genome wide association study of substance use disorder (SUD) identifies novel variants on chromosome 7p14.1 in patients from the United Arab Emirates (UAE). Am J Med Genet B Neuropsychiatr Genet 2019; 180:68-79. [PMID: 30556296 DOI: 10.1002/ajmg.b.32708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/17/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022]
Abstract
Genome wide association studies (GWASs) have provided insights into the molecular basis of the disorder in different population. This study presents the first GWAS of substance use disorder (SUD) in patients from the United Arab Emirates (UAE). The aim was to identify genetic association(s) that may provide insights into the molecular basis of the disorder. The GWAS discovery cohort consisted of 512 (250 cases and 262 controls) male participants from the UAE. Controls with no prior history of SUD were available from the Emirates family registry. The replication cohort consisted of 520 (415 cases and 105 controls) Australian male Caucasian participants. The GWAS discovery samples were genotyped for 4.6 million single nucleotide polymorphism (SNP). The replication cohort was genotyped using TaqMan assay. The GWAS association analysis identified three potential SNPs rs118129027 (p-value = 6.24 × 10-8 ), rs74477937 (p-value = 8.56 × 10-8 ) and rs78707086 (p-value = 8.55 × 10-8 ) on ch7p14.1, that did not meet the GWAS significance threshold but were highly suggestive. In the replication cohort, the association of the three top SNPs did not reach statistical significance. In a meta-analysis of the discovery and the replication cohorts, there were no strengthen evidence for association of the three SNPs. The top identified rs118129027 overlaps with a regulatory factor (enhancer) region that targets three neighboring genes LOC105375237, LOC105375240, and YAE1D1. The YAE1D1, which represents a potential locus that is involved in regulating translation initiation pathway. Novel associations that require further confirmation were identified, suggesting a new insight to the genetic basis of SUD.
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Affiliation(s)
- Hiba Alblooshi
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia.,School of Human Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Habiba Al Safar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Holly F Fisher
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Ahmed El Kashef
- National Rehabilitation Center, Abu Dhabi, United Arab Emirates
| | | | - Mansour Shawky
- National Rehabilitation Center, Abu Dhabi, United Arab Emirates
| | - Stuart Reece
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gary K Hulse
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia.,School of Medical Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Guan K Tay
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Crawley, Western Australia, Australia.,Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,School of Medical Science, Edith Cowan University, Joondalup, Western Australia, Australia
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11
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Weng X, Liu F, Zhang H, Kan M, Wang T, Dong M, Liu Y. Genome-wide DNA methylation profiling in infants born to gestational diabetes mellitus. Diabetes Res Clin Pract 2018; 142:10-18. [PMID: 29596946 DOI: 10.1016/j.diabres.2018.03.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 01/17/2023]
Abstract
BACKGROUND Offspring exposed to gestational diabetes mellitus (GDM) are at a high risk for metabolic diseases. The mechanisms behind the association between offspring exposed to GDM in utero and an increased risk of health consequences later in life remain unclear. The aim of this study was to clarify the changes in methylation levels in the foetuses of women with GDM and to explore the possible mechanisms linking maternal GDM with a high risk of metabolic diseases in offspring later in life. METHODS A genome-wide comparative methylome analysis on the umbilical cord blood of infants born to 30 women with GDM and 33 women with normal pregnancy was performed using Infinium HumanMethylation 450 BeadChip assays. A quantitative methylation analysis of 18 CpG dinucleotides was verified in the validation umbilical cord blood samples from 102 newborns exposed to GDM and 103 newborns who experienced normal pregnancy by MassARRAY EpiTYPER. RESULTS A total of 4485 differentially methylated sites (DMSs), including 2150 hypermethylated sites and 2335 hypomethylated sites, with a mean β-value difference of >0.05, were identified by the 450k array. Good agreement was observed between the massarray validation data and the 450k array data (R2 > 0.99; P < 0.0001). Thirty-seven CpGs (representing 20 genes) with a β-value difference of > 0.15 between the GDM and healthy groups were identified and showed potential as clinical biomarkers for GDM. "hsa04940: Type I diabetes mellitus" was the most significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, with a P-value = 3.20E-07 and 1.36E-02 in the hypermethylated and hypomethylated genepathway enrichment analyses, respectively. In the Gene Ontology (GO) pathway analyses, immune MHC (major histocompatibility complex)-related pathways and neuron development-related pathways were significantly enriched. CONCLUSIONS Our results suggest that GDM has epigenetic effects on genes that are preferentially involved in the Type I diabetes mellitus pathway, immune MHC-related pathways and neuron development-related pathways, with consequences on fetal growth and development, and provide supportive evidence that DNA methylation is involved in fetal metabolic programming.
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Affiliation(s)
- Xiaoling Weng
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China; Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, PR China
| | - Fatao Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Hong Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China
| | - Mengyuan Kan
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Ting Wang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, PR China
| | - Yun Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, PR China; Key Laboratory of Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China.
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12
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Yang BZ, Han S, Kranzler HR, Palmer AA, Gelernter J. Sex-specific linkage scans in opioid dependence. Am J Med Genet B Neuropsychiatr Genet 2017; 174:261-268. [PMID: 27762075 PMCID: PMC5695218 DOI: 10.1002/ajmg.b.32507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/03/2016] [Indexed: 02/01/2023]
Abstract
Sex influences risk for opioid dependence (OD). We hypothesized that sex might interact with genetic loci that influence the risk for OD. Therefore we performed an analysis to identify sex-specific genomic susceptibility regions for OD using linkage. Over 6,000 single nucleotide polymorphism (SNP) markers were genotyped for 1,758 African- and European-American (AA and EA) individuals from 739 families, ascertained via affected sib-pairs with OD and/or cocaine dependence. Autosomewide non-parametric linkage scans, stratified by sex and population, were performed. We identified one significant linkage region, segregating with OD in EA men, at 71.1 cM on chromosome 4 (LOD = 3.29; point-wise P = 0.00005; empirical autosome-wide P = 0.042), which significantly differed from the linkage signal at the same location in EA women (empirical P = 0.002). Three suggestive linkage signals were identified at 181.3 cM on chromosome 7 (LOD = 2.18), 104 cM on chromosome 11 (LOD = 1.85), and 60.9 cM on chromosome 16 (LOD = 1.93) in EA women. In AA men, four suggestive linkage signals were detected at 201.1 cM on chromosome 3 (LOD = 2.32), 152.9 cM on chromosome 6 (LOD = 1.86), 16.8 cM on chromosome 7 (LOD = 1.95), and 36.1 cM on chromosome 17 (LOD = 1.99). The significant region, mapping to 4q12-4q13.1, harbors several OD candidate genes with interconnected functionality, including VEGFR, CLOCK, PDCL2, NMU, NRSF, and IGFBP7. In conclusion, these results provide an evidence for the existence of sex-specific and population-specific differences in OD. Furthermore, these results provide positional information that will facilitate the use of targeted next-generation sequencing to search for genes that contribute to sex-specific differences in OD. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT
| | - Shizhong Han
- Department of Psychiatry, University of Iowa, Iowa City, IA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine and VISN 4 MIRECC, Crescenz VAMC, Philadelphia, PA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT,VA CT Healthcare Center, West Haven, CT
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13
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Ramírez-Franco JJ, Munoz-Cuevas FJ, Luján R, Jurado S. Excitatory and Inhibitory Neurons in the Hippocampus Exhibit Molecularly Distinct Large Dense Core Vesicles. Front Cell Neurosci 2016; 10:202. [PMID: 27630542 PMCID: PMC5005380 DOI: 10.3389/fncel.2016.00202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 12/21/2022] Open
Abstract
Hippocampal interneurons comprise a diverse family of inhibitory neurons that are critical for detailed information processing. Along with gamma-aminobutyric acid (GABA), interneurons secrete a myriad of neuroactive substances via secretory vesicles but the molecular composition and regulatory mechanisms remain largely unknown. In this study, we have carried out an immunohistofluorescence analysis to describe the molecular content of vesicles in distinct populations of hippocampal neurons. Our results indicate that phogrin, an integral protein of secretory vesicles in neuroendocrine cells, is highly enriched in parvalbumin-positive interneurons. Consistently, immunoelectron microscopy revealed phogrin staining in axon terminals of symmetrical synapses establishing inhibitory contacts with cell bodies of CA1 pyramidal neurons. Furthermore, phogrin is highly expressed in CA3 and dentate gyrus (DG) interneurons which are both positive for PV and neuropeptide Y. Surprisingly, chromogranin B a canonical large dense core vesicle marker, is excluded from inhibitory cells in the hippocampus but highly expressed in excitatory CA3 pyramidal neurons and DG granule cells. Our results provide the first evidence of phogrin expression in hippocampal interneurons and suggest the existence of molecularly distinct populations of secretory vesicles in different types of inhibitory neurons.
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Affiliation(s)
| | | | - Rafael Luján
- Synaptic Structure Laboratory, Departamento de Ciencias Médicas, Facultad de Medicina, Instituto de Investigación en Discapacidades Neurológicas, Universidad Castilla-La ManchaAlbacete, Spain
| | - Sandra Jurado
- Department of Pharmacology, University of Maryland School of MedicineBaltimore, MD, USA
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14
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Carey CE, Agrawal A, Bucholz KK, Hartz SM, Lynskey MT, Nelson EC, Bierut LJ, Bogdan R. Associations between Polygenic Risk for Psychiatric Disorders and Substance Involvement. Front Genet 2016; 7:149. [PMID: 27574527 PMCID: PMC4983546 DOI: 10.3389/fgene.2016.00149] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022] Open
Abstract
Despite evidence of substantial comorbidity between psychiatric disorders and substance involvement, the extent to which common genetic factors contribute to their co-occurrence remains understudied. In the current study, we tested for associations between polygenic risk for psychiatric disorders and substance involvement (i.e., ranging from ever-use to severe dependence) among 2573 non-Hispanic European–American participants from the Study of Addiction: Genetics and Environment. Polygenic risk scores (PRS) for cross-disorder psychopathology (CROSS) were generated based on the Psychiatric Genomics Consortium’s Cross-Disorder meta-analysis and then tested for associations with a factor representing general liability to alcohol, cannabis, cocaine, nicotine, and opioid involvement (GENSUB). Follow-up analyses evaluated specific associations between each of the five psychiatric disorders which comprised CROSS—attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (AUT), bipolar disorder (BIP), major depressive disorder (MDD), and schizophrenia (SCZ)—and involvement with each component substance included in GENSUB. CROSS PRS explained 1.10% of variance in GENSUB in our sample (p < 0.001). After correction for multiple testing in our follow-up analyses of polygenic risk for each individual disorder predicting involvement with each component substance, associations remained between: (A) MDD PRS and non-problem cannabis use, (B) MDD PRS and severe cocaine dependence, (C) SCZ PRS and non-problem cannabis use and severe cannabis dependence, and (D) SCZ PRS and severe cocaine dependence. These results suggest that shared covariance from common genetic variation contributes to psychiatric and substance involvement comorbidity.
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Affiliation(s)
- Caitlin E Carey
- Department of Psychological and Brain Sciences, Washington University in St. Louis St. Louis, MO, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine St. Louis, MO, USA
| | - Kathleen K Bucholz
- Department of Psychiatry, Washington University School of Medicine St. Louis, MO, USA
| | - Sarah M Hartz
- Department of Psychiatry, Washington University School of Medicine St. Louis, MO, USA
| | | | - Elliot C Nelson
- Department of Psychiatry, Washington University School of Medicine St. Louis, MO, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine St. Louis, MO, USA
| | - Ryan Bogdan
- Department of Psychological and Brain Sciences, Washington University in St. Louis St. Louis, MO, USA
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15
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Do C, Lang C, Lin J, Darbary H, Krupska I, Gaba A, Petukhova L, Vonsattel JP, Gallagher M, Goland R, Clynes R, Dwork A, Kral J, Monk C, Christiano A, Tycko B. Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. Am J Hum Genet 2016; 98:934-955. [PMID: 27153397 DOI: 10.1016/j.ajhg.2016.03.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022] Open
Abstract
Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-Seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A(∗)-ILF2, associated with immune phenotypes, MYT1L, PTPRN2, CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites were over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to macaques, indicated that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; and variation in CTCF and TF binding sites is an underlying mechanism, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supra- and sub-threshold GWAS peaks in immunological and neurological disorders.
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16
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Palmer RHC, Brick L, Nugent NR, Bidwell LC, McGeary JE, Knopik VS, Keller MC. Examining the role of common genetic variants on alcohol, tobacco, cannabis and illicit drug dependence: genetics of vulnerability to drug dependence. Addiction 2015; 110:530-7. [PMID: 25424661 PMCID: PMC4329043 DOI: 10.1111/add.12815] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/09/2014] [Accepted: 11/14/2014] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS Twin and family studies suggest that genetic influences are shared across substances of abuse. However, despite evidence of heritability, genome-wide association and candidate gene studies have indicated numerous markers of limited effects, suggesting that much of the heritability remains missing. We estimated (1) the aggregate effect of common single nucleotide polymorphisms (SNPs) on multiple indicators of comorbid drug problems that are typically employed across community and population-based samples, and (2) the genetic covariance across these measures. PARTICIPANTS A total of 2596 unrelated subjects from the Study of Addiction: Genetics and Environment provided information on alcohol, tobacco, cocaine, cannabis and other illicit substance dependence. Phenotypic measures included: (1) a factor score based on DSM-IV drug dependence diagnoses (DD), (2) a factor score based on problem use (PU; i.e. 1+ DSM-IV symptoms) and (3) dependence vulnerability (DV; a ratio of DSM-IV symptoms to the number of substances used). FINDINGS Univariate and bivariate genome-wide complex trait analyses of this selected sample indicated that common SNPs explained 25-36% of the variance across measures, with DD and DV having the largest effects [h(2) SNP (standard error) = 0.36 (0.13) and 0.33 (0.13), respectively; PU = 0.25 (0.13)]. Genetic effects were shared across the three phenotypic measures of comorbid drug problems [rDD-PU = 0.92 (0.08), rDD-DV = 0.97 (0.08) and rPU-DV = 0.96 (0.07)]. CONCLUSION At least 20% of the variance in the generalized vulnerability to substance dependence is attributable to common single nucleotide polymorphisms. The additive effect of common single nucleotide polymorphisms is shared across important indicators of comorbid drug problems.
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Affiliation(s)
- Rohan H C Palmer
- Division of Behavioral Genetics, Department of Psychiatry, Rhode Island Hospital, Providence, RI, USA; Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
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17
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Sadler B, Haller G, Agrawal A, Culverhouse R, Bucholz K, Brooks A, Tischfield J, Johnson EO, Edenberg H, Schuckit M, Saccone N, Bierut L, Goate A. Variants near CHRNB3-CHRNA6 are associated with DSM-5 cocaine use disorder: evidence for pleiotropy. Sci Rep 2014; 4:4497. [PMID: 24675634 PMCID: PMC4894386 DOI: 10.1038/srep04497] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/26/2014] [Indexed: 12/16/2022] Open
Abstract
In the U.S.A., cocaine is the second most abused illicit drug. Variants within the CHRNB3-A6 gene cluster have been associated with cigarette consumption in several GWAS. These receptors represent intriguing candidates for the study of cocaine dependence because nicotinic receptors are thought to be involved in generalized addiction pathways. Using genotypic data from a GWAS of the Study of Addiction: Genetics and Environment (SAGE) dataset, we tested for association of CHRNB3-A6 SNPs with DSM-5 cocaine use disorder. Multiple SNPs in the region were significantly associated with increased risk of cocaine use disorder. Inclusion of the most significant SNP as a covariate in a linear regression model provided evidence for an additional independent signal within this locus for cocaine use disorder. These results suggest that the CHRNB3-A6 locus contains multiple variants affecting risk for vulnerability to cocaine and nicotine dependence as well as bipolar disorder, suggesting that they have pleiotropic effects.
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Affiliation(s)
- Brooke Sadler
- 1] School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA [2] Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Gabe Haller
- 1] Department of Psychiatry, Washington University, St. Louis, MO, USA [2] Department of Genetics, Washington University, St. Louis, MO, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Rob Culverhouse
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathleen Bucholz
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Andy Brooks
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - Jay Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - Eric O Johnson
- Division of Health, Social and Economic Research, Research Triangle Institute International, Research Triangle Park, NC
| | - Howard Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Marc Schuckit
- Department of Psychiatry, University of California-San Diego, La Jolla, CA
| | - Nancy Saccone
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - Laura Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Alison Goate
- 1] Department of Psychiatry, Washington University, St. Louis, MO, USA [2] Department of Genetics, Washington University, St. Louis, MO, USA
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18
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Jiang Y, Li N, Zhang H. Identifying Genetic Variants for Addiction via Propensity Score Adjusted Generalized Kendall's Tau. J Am Stat Assoc 2014; 109:905-930. [PMID: 25382885 PMCID: PMC4219655 DOI: 10.1080/01621459.2014.901223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 12/01/2013] [Indexed: 12/18/2022]
Abstract
Identifying replicable genetic variants for addiction has been extremely challenging. Besides the common difficulties with genome-wide association studies (GWAS), environmental factors are known to be critical to addiction, and comorbidity is widely observed. Despite the importance of environmental factors and comorbidity for addiction study, few GWAS analyses adequately considered them due to the limitations of the existing statistical methods. Although parametric methods have been developed to adjust for covariates in association analysis, difficulties arise when the traits are multivariate because there is no ready-to-use model for them. Recent nonparametric development includes U-statistics to measure the phenotype-genotype association weighted by a similarity score of covariates. However, it is not clear how to optimize the similarity score. Therefore, we propose a semiparametric method to measure the association adjusted by covariates. In our approach, the nonparametric U-statistic is adjusted by parametric estimates of propensity scores using the idea of inverse probability weighting. The new measurement is shown to be asymptotically unbiased under our null hypothesis while the previous non-weighted and weighted ones are not. Simulation results show that our test improves power as opposed to the non-weighted and two other weighted U-statistic methods, and it is particularly powerful for detecting gene-environment interactions. Finally, we apply our proposed test to the Study of Addiction: Genetics and Environment (SAGE) to identify genetic variants for addiction. Novel genetic variants are found from our analysis, which warrant further investigation in the future.
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Affiliation(s)
- Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon 97331-4606
| | - Ni Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, China
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19
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Kiraly DD, Nemirovsky NE, LaRese TP, Tomek SE, Yahn SL, Olive MF, Eipper BA, Mains RE. Constitutive knockout of kalirin-7 leads to increased rates of cocaine self-administration. Mol Pharmacol 2013; 84:582-90. [PMID: 23894151 PMCID: PMC3781382 DOI: 10.1124/mol.113.087106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/26/2013] [Indexed: 01/01/2023] Open
Abstract
Kalirin-7 (Kal7) is a Rho-guanine nucleotide exchange factor that is localized in neuronal postsynaptic densities. Kal7 interacts with the NR2B subunit of the NMDA receptor and regulates aspects of dendritic spine dynamics both in vitro and in vivo. Chronic treatment with cocaine increases dendritic spine density in the nucleus accumbens (NAc) of rodents and primates. Kal7 mRNA and protein are upregulated in the NAc following cocaine treatment, and the presence of Kal7 is necessary for the normal proliferation of dendritic spines following cocaine use. Mice that constitutively lack Kal7 [Kalirin-7 knockout mice (Kal7(KO))] demonstrate increased locomotor sensitization to cocaine and a decreased place preference for cocaine. Here, using an intravenous cocaine self-administration paradigm, Kal7(KO) mice exhibit increased administration of cocaine at lower doses as compared with wild-type (Wt) mice. Analyses of mRNA transcript levels from the NAc of mice that self-administered saline or cocaine reveal that larger splice variants of the Kalrn gene are increased by cocaine more dramatically in Kal7(KO) mice than in Wt mice. Additionally, transcripts encoding the NR2B subunit of the NMDA receptor increased in Wt mice that self-administered cocaine but were unchanged in similarly experienced Kal7(KO) mice. These findings suggest that Kal7 participates in the reinforcing effects of cocaine, and that Kal7 and cocaine interact to alter the expression of genes related to critical glutamatergic signaling pathways in the NAc.
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Affiliation(s)
- Drew D Kiraly
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut (D.D.K., T.P.L., B.A.E., R.E.M.); and Department of Psychology, Program in Behavioral Neuroscience (N.E.N., S.E.T., S.L.Y., M.F.O.) and Interdisciplinary Graduate Program in Neuroscience (M.F.O.), Arizona State University, Tempe, Arizona
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20
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Hendriks WJAJ, Pulido R. Protein tyrosine phosphatase variants in human hereditary disorders and disease susceptibilities. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1673-96. [PMID: 23707412 DOI: 10.1016/j.bbadis.2013.05.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/18/2022]
Abstract
Reversible tyrosine phosphorylation of proteins is a key regulatory mechanism to steer normal development and physiological functioning of multicellular organisms. Phosphotyrosine dephosphorylation is exerted by members of the super-family of protein tyrosine phosphatase (PTP) enzymes and many play such essential roles that a wide variety of hereditary disorders and disease susceptibilities in man are caused by PTP alleles. More than two decades of PTP research has resulted in a collection of PTP genetic variants with corresponding consequences at the molecular, cellular and physiological level. Here we present a comprehensive overview of these PTP gene variants that have been linked to disease states in man. Although the findings have direct bearing for disease diagnostics and for research on disease etiology, more work is necessary to translate this into therapies that alleviate the burden of these hereditary disorders and disease susceptibilities in man.
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Affiliation(s)
- Wiljan J A J Hendriks
- Department of Cell Biology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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21
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Yang BZ, Zhang H, Ge W, Weder N, Douglas-Palumberi H, Perepletchikova F, Gelernter J, Kaufman J. Child abuse and epigenetic mechanisms of disease risk. Am J Prev Med 2013; 44:101-7. [PMID: 23332324 PMCID: PMC3758252 DOI: 10.1016/j.amepre.2012.10.012] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 07/24/2012] [Accepted: 10/05/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND Child abuse is highly prevalent and associated with increased risk for a range of health problems, including cancer, cardiovascular disease, diabetes, psychiatric disorders, and other health problems. Little is currently known about the mechanism by which early adversity confers risk for health problems later in life. PURPOSE To determine if there are epigenetic differences associated with child maltreatment that may help explain association between adverse childhood experiences and later health problems. METHODS As part of a study examining genetic and environmental factors associated with depression, saliva DNA specimens were collected on 96 maltreated children removed from their parents due to abuse or neglect and 96 demographically matched control children between 2003 and 2010. In 2011, the Illumina 450K BeadChip was used on stored DNA specimens and analyzed to examine whole-genome methylation differences between maltreated and control children. RESULTS After controlling for multiple comparisons, maltreated and control children had significantly different methylation values at 2868 CpG sites (p<5.0 × 10(-7), all sites; average methylation difference per site=17%; range=1%-62%). The gene set contained numerous markers of diseases and biological processes related to the health problems associated with early childhood adversity. CONCLUSIONS Although replication is required, this study suggests that epigenetic mechanisms may be associated with risk for health problems later in life in maltreated children. This study lays the groundwork for future studies examining health and methylation measures to further characterize the role of epigenetic mechanisms in conferring risk for medical problems in individuals with histories of early adversity.
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Affiliation(s)
- Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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22
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O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O’Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338:1619-22. [PMID: 23160955 PMCID: PMC3528801 DOI: 10.1126/science.1227764] [Citation(s) in RCA: 935] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing. We estimate that recurrent disruptive mutations in six genes-CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1-may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes (CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a β-catenin-chromatin-remodeling network to ASD etiology.
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Affiliation(s)
- Brian J. O’Roak
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jarrett D. Egertson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Gemma Carvill
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katy Ankenman
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph B. Hiatt
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily H. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Roie Levy
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diana R. O’Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Heather C. Mefford
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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Han S, Yang BZ, Kranzler HR, Oslin D, Anton R, Farrer LA, Gelernter J. Linkage analysis followed by association show NRG1 associated with cannabis dependence in African Americans. Biol Psychiatry 2012; 72:637-44. [PMID: 22520967 PMCID: PMC3699339 DOI: 10.1016/j.biopsych.2012.02.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/14/2012] [Accepted: 02/21/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND A genetic contribution to cannabis dependence (CaD) has been established but susceptibility genes for CaD remain largely unknown. METHODS We employed a multistage design to identify genetic variants underlying CaD. We first performed a genome-wide linkage scan for CaD in 384 African American (AA) and 354 European American families ascertained for genetic studies of cocaine and opioid dependence. We then conducted association analysis under the linkage peak, first using data from a genome-wide association study from the Study of Addiction: Genetics and Environment, followed by replication studies of prioritized single nucleotide polymorphisms (SNPs) in independent samples. RESULTS We identified the strongest linkage evidence with CaD (logarithm of odds = 2.9) on chromosome 8p21.1 in AAs. In the association analysis of the Study of Addiction: Genetics and Environment sample under the linkage peak, we identified one SNP (rs17664708) associated with CaD in both AAs (odds ratio [OR] = 2.93, p = .0022) and European Americans (OR = 1.38, p = .02). This SNP, located at NRG1, a susceptibility gene for schizophrenia, was prioritized for further study. We replicated the association of rs17664708 with CaD in an independent AAs sample (OR = 2.81, p = .0068). The joint analysis of the two AA samples demonstrated highly significant association between rs17664708 and CaD with adjustment for either global (p = .00044) or local ancestry (p = .00075). CONCLUSIONS Our study shows that NRG1 is probably a susceptibility gene for CaD, based on convergent evidence of linkage and replicated associations in two independent AA samples.
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Affiliation(s)
- Shizhong Han
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut and VA CT Healthcare Center, West Haven, Connecticut. USA
| | - Bao-Zhu Yang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut and VA CT Healthcare Center, West Haven, Connecticut. USA
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- VISN 4 MIRECC, Philadelphia VAMC, Philadelphia, Pennsylvania, USA
| | - David Oslin
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- VISN 4 MIRECC, Philadelphia VAMC, Philadelphia, Pennsylvania, USA
| | - Raymond Anton
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Genetics & Genomics, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut and VA CT Healthcare Center, West Haven, Connecticut. USA
- Departments of Genetics and of Neurobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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Hart AB, Engelhardt BE, Wardle MC, Sokoloff G, Stephens M, de Wit H, Palmer AA. Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS One 2012; 7:e42646. [PMID: 22952603 PMCID: PMC3429486 DOI: 10.1371/journal.pone.0042646] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/11/2012] [Indexed: 12/11/2022] Open
Abstract
Both the subjective response to d-amphetamine and the risk for amphetamine addiction are known to be heritable traits. Because subjective responses to drugs may predict drug addiction, identifying alleles that influence acute response may also provide insight into the genetic risk factors for drug abuse. We performed a Genome Wide Association Study (GWAS) for the subjective responses to amphetamine in 381 non-drug abusing healthy volunteers. Responses to amphetamine were measured using a double-blind, placebo-controlled, within-subjects design. We used sparse factor analysis to reduce the dimensionality of the data to ten factors. We identified several putative associations; the strongest was between a positive subjective drug-response factor and a SNP (rs3784943) in the 8(th) intron of cadherin 13 (CDH13; P = 4.58×10(-8)), a gene previously associated with a number of psychiatric traits including methamphetamine dependence. Additionally, we observed a putative association between a factor representing the degree of positive affect at baseline and a SNP (rs472402) in the 1(st) intron of steroid-5-alpha-reductase-α-polypeptide-1 (SRD5A1; P = 2.53×10(-7)), a gene whose protein product catalyzes the rate-limiting step in synthesis of the neurosteroid allopregnanolone. This SNP belongs to an LD-block that has been previously associated with the expression of SRD5A1 and differences in SRD5A1 enzymatic activity. The purpose of this study was to begin to explore the genetic basis of subjective responses to stimulant drugs using a GWAS approach in a modestly sized sample. Our approach provides a case study for analysis of high-dimensional intermediate pharmacogenomic phenotypes, which may be more tractable than clinical diagnoses.
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Affiliation(s)
- Amy B. Hart
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Barbara E. Engelhardt
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Computer Science, University of Chicago, Chicago, Illinois, United States of America
| | - Margaret C. Wardle
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
| | - Greta Sokoloff
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Harriet de Wit
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
| | - Abraham A. Palmer
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
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25
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Davies W. Functional themes from psychiatric genome-wide screens. Front Genet 2011; 2:89. [PMID: 22303383 PMCID: PMC3268640 DOI: 10.3389/fgene.2011.00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 11/28/2011] [Indexed: 12/24/2022] Open
Abstract
Technological advances and a greater degree of inter-laboratory co-operation mean that genome-wide analyses can now be used to identify genetic variants that are robustly associated with the risk of developing psychiatric and neurological disorders. In contrast to the candidate gene approach, such screens may identify variants within genes which have a hitherto unappreciated role in disorder pathogenesis, and whose brain function is obscure. In this Perspective, I discuss how the behavioral functions of such genes may be investigated using model systems, drawing attention to the potential caveats and limitations with such approaches. The power of focused cross-species studies needs to be effectively exploited to enable useful insights into the molecular pathogenesis of common and disabling disorders, and ultimately to provide better clinical outcomes for patients.
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Affiliation(s)
- William Davies
- Behavioural Genetics Group, Schools of Medicine and Psychology, Cardiff UniversityCardiff, UK
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff UniversityCardiff, UK
- Neuroscience and Mental Health Research Institute, Cardiff UniversityCardiff, UK
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