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Li PP, Zhou YY, Gao L, Lv JN, Xu SS, Zhao YW, Xu D, Huang R, Zhang X, Li P, Fu X, He Z. The de novo missense mutation F224S in GABRB2, identified in epileptic encephalopathy and developmental delay, impairs GABA AR function. Neuroscience 2024; 553:172-184. [PMID: 38964454 DOI: 10.1016/j.neuroscience.2024.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Genetic variants in genes encoding subunits of the γ-aminobutyric acid-A receptor (GABAAR) have been found to cause neurodevelopmental disorders and epileptic encephalopathy. In a patient with epilepsy and developmental delay, a de novo heterozygous missense mutation c.671 T > C (p.F224S) was discovered in the GABRB2 gene, which encodes the β2 subunit of GABAAR. Based on previous studies on GABRB2 variants, this new GABRB2 variant (F224S) would be pathogenic. To confirm and investigate the effects of this GABRB2 mutation on GABAAR channel function, we conducted transient expression experiments using GABAAR subunits in HEK293T cells. The GABAARs containing mutant β2 (F224S) subunit showed poor trafficking to the cell membrane, while the expression and distribution of the normal α1 and γ2 subunits were unaffected. Furthermore, the peak current amplitude of the GABAAR containing the β2 (F224S) subunit was significantly smaller compared to the wild type GABAAR. We propose that GABRB2 variant F224S is pathogenic and GABAARs containing this β2 mutant reduce response to GABA under physiological conditions, which could potentially disrupt the excitation/inhibition balance in the brain, leading to epilepsy.
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Affiliation(s)
- Ping-Ping Li
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yue-Yuan Zhou
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Li Gao
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jia-Nan Lv
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Shi-Shi Xu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yan-Wen Zhao
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Di Xu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Ruoke Huang
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Xiong Zhang
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Peijun Li
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117 Jinan, Shandong, China
| | - Xiaoqin Fu
- Department of Geriatrics and Neurology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117 Jinan, Shandong, China
| | - Zhiyong He
- Department of Pediatric Rehabilitation, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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2
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Mitra S, Bp K, C R S, Saikumar NV, Philip P, Narayanan M. Alzheimer's disease rewires gene coexpression networks coupling different brain regions. NPJ Syst Biol Appl 2024; 10:50. [PMID: 38724582 PMCID: PMC11082197 DOI: 10.1038/s41540-024-00376-y] [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: 10/21/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Connectome studies have shown how Alzheimer's disease (AD) disrupts functional and structural connectivity among brain regions. But the molecular basis of such disruptions is less studied, with most genomic/transcriptomic studies performing within-brain-region analyses. To inspect how AD rewires the correlation structure among genes in different brain regions, we performed an Inter-brain-region Differential Correlation (Inter-DC) analysis of RNA-seq data from Mount Sinai Brain Bank on four brain regions (frontal pole, superior temporal gyrus, parahippocampal gyrus and inferior frontal gyrus, comprising 264 AD and 372 control human post-mortem samples). An Inter-DC network was assembled from all pairs of genes across two brain regions that gained (or lost) correlation strength in the AD group relative to controls at FDR 1%. The differentially correlated (DC) genes in this network complemented known differentially expressed genes in AD, and likely reflects cell-intrinsic changes since we adjusted for cell compositional effects. Each brain region used a distinctive set of DC genes when coupling with other regions, with parahippocampal gyrus showing the most rewiring, consistent with its known vulnerability to AD. The Inter-DC network revealed master dysregulation hubs in AD (at genes ZKSCAN1, SLC5A3, RCC1, IL17RB, PLK4, etc.), inter-region gene modules enriched for known AD pathways (synaptic signaling, endocytosis, etc.), and candidate signaling molecules that could mediate region-region communication. The Inter-DC network generated in this study is a valuable resource of gene pairs, pathways and signaling molecules whose inter-brain-region functional coupling is disrupted in AD, thereby offering a new perspective of AD etiology.
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Affiliation(s)
- Sanga Mitra
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Kailash Bp
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Srivatsan C R
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Naga Venkata Saikumar
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Philge Philip
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India
| | - Manikandan Narayanan
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India.
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India.
- Sudha Gopalakrishnan Brain Centre, IIT Madras, Chennai, India.
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Liao K, Xiang Y, Huang F, Huang M, Xu W, Lin Y, Liao P, Wang Z, Yang L, Tian X, Chen D, Wang Z, Liu S, Zhuang Z. Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum. iScience 2024; 27:109009. [PMID: 38333704 PMCID: PMC10850779 DOI: 10.1016/j.isci.2024.109009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The avian optic tectum (OT) has been studied for its diverse functions, yet a comprehensive molecular landscape at the cellular level has been lacking. In this study, we applied spatial transcriptome sequencing and single-nucleus RNA sequencing (snRNA-seq) to explore the cellular organization and molecular characteristics of the avian OT from two species: Columba livia and Taeniopygia guttata. We identified precise layer structures and provided comprehensive layer-specific signatures of avian OT. Furthermore, we elucidated diverse functions in different layers, with the stratum griseum periventriculare (SGP) potentially playing a key role in advanced functions of OT, like fear response and associative learning. We characterized detailed neuronal subtypes and identified a population of FOXG1+ excitatory neurons, resembling those found in the mouse neocortex, potentially involved in neocortex-related functions and expansion of avian OT. These findings could contribute to our understanding of the architecture of OT, shedding light on visual perception and multifunctional association.
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Affiliation(s)
- Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Ya Xiang
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Fubaoqian Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI Research, Hangzhou 310030, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenbo Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Youning Lin
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Pingfang Liao
- BGI Research, Hangzhou 310030, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zishi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lin Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinmao Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Duoyuan Chen
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Zhenkun Zhuang
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
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Miao B, Xing X, Bazylianska V, Madden P, Moszczynska A, Zhang B. Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats. Commun Biol 2023; 6:991. [PMID: 37758941 PMCID: PMC10533900 DOI: 10.1038/s42003-023-05355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Psychostimulant methamphetamine (METH) is neurotoxic to the brain and, therefore, its misuse leads to neurological and psychiatric disorders. The gene regulatory network (GRN) response to neurotoxic METH binge remains unclear in most brain regions. Here we examined the effects of binge METH on the GRN in the nucleus accumbens, dentate gyrus, Ammon's horn, and subventricular zone in male rats. At 24 h after METH, ~16% of genes displayed altered expression and over a quarter of previously open chromatin regions - parts of the genome where genes are typically active - showed shifts in their accessibility. Intriguingly, most changes were unique to each area studied, and independent regulation between transcriptome and chromatin accessibility was observed. Unexpectedly, METH differentially impacted gene activity and chromatin accessibility within the dentate gyrus and Ammon's horn. Around 70% of the affected chromatin-accessible regions in the rat brain have conserved DNA sequences in the human genome. These regions frequently act as enhancers, ramping up the activity of nearby genes, and contain mutations linked to various neurological conditions. By sketching out the gene regulatory networks associated with binge METH in specific brain regions, our study offers fresh insights into how METH can trigger profound, region-specific molecular shifts.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Viktoriia Bazylianska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Hu X, Zhao M, Yang X, Wang D, Wu Q. Association between the SLC6A11 rs2304725 and GABRG2 rs211037 polymorphisms and drug-resistant epilepsy: a meta-analysis. Front Physiol 2023; 14:1191927. [PMID: 37275237 PMCID: PMC10235491 DOI: 10.3389/fphys.2023.1191927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Background: Previous studies have shown that SLC6A11 and GABRG2 are linked to drug-resistant epilepsy (DRE), although there have been conflicting results in the literature. In this study, we systematically assessed the relationship between DRE and these two genes. Methods: We systematically searched the PubMed, Embase, Cochrane Library, Web of Science, Google Scholar, Wanfang Data, CNKI, and VIP databases. To clarify whether heterogeneity existed between studies, tools such as the Q-test and I 2 statistic were selected. According to study heterogeneity, we chose fixed- or random-effects models for analysis. We then used the chi-squared ratio to evaluate any bias of the experimental data. Results: In total, 11 trials and 3,813 patients were selected. To investigate the relationship with DRE, we performed model tests on the two genes separately. The results showed that SLC6A11 rs2304725 had no significant correlation with DRE risk in the allele, dominant, recessive, and additive models in a pooled population. However, for the over-dominant model, DRE was correlated with rs2304725 (OR = 1.08, 95% CI: 0.92-1.27, p = 0.33) in a pooled population. Similarly, rs211037 was weakly significantly correlated with DRE for the dominant, recessive, over-dominant, and additive models in a pooled population. The subgroup analysis results showed that rs211037 expressed a genetic risk of DRE in allele (OR = 1.01, 95% CI: 0.76-1.35, p = 0.94), dominant (OR = 1.08, 95% CI: 0.77-1.50, p = 0.65), and additive models (OR = 1.14, 95% CI: 0.62-2.09, p = 0.67) in an Asian population. Conclusion: In this meta-analysis, our results showed that SLC6A11 rs2304725 and GABRG2 rs211037 are not significantly correlated with DRE. However, in the over-dominant model, rs2304725 was significantly correlated with DRE. Likewise, rs211037 conveyed a genetic risk for DRE in an Asian population in the allele, dominant, and additive models.
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Affiliation(s)
- Xuemei Hu
- Clinical Medical College of Jining Medical University, Jining, Shandong, China
- Department of Emergency, Jining No. 1 People’s Hospital, Jining, Shandong, China
| | - Mingyang Zhao
- Clinical Medical College of Jining Medical University, Jining, Shandong, China
- Department of Emergency, Jining No. 1 People’s Hospital, Jining, Shandong, China
| | - Xue Yang
- Department of Emergency, Jining No. 1 People’s Hospital, Jining, Shandong, China
| | - Dongsen Wang
- Clinical Medical College of Jining Medical University, Jining, Shandong, China
- Department of Emergency, Jining No. 1 People’s Hospital, Jining, Shandong, China
| | - Qingjian Wu
- Department of Emergency, Jining No. 1 People’s Hospital, Jining, Shandong, China
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Holtby AR, Hall TJ, McGivney BA, Han H, Murphy KJ, MacHugh DE, Katz LM, Hill EW. Integrative genomics analysis highlights functionally relevant genes for equine behaviour. Anim Genet 2023. [DOI: 10.1111/age.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/29/2023]
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Ullah S, Ali N, Ahmad S, Sha SWA, Ali S, Almarshad F. The likelihood approach for potential role of "GABRG2 (C588T, C315T) gene polymorphisms" on the poor response to carbamazepine therapy in Pakhtun population of Pakistan. Medicine (Baltimore) 2022; 101:e30948. [PMID: 36221407 PMCID: PMC9542555 DOI: 10.1097/md.0000000000030948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Gamma-aminobutyric acid A receptor, gamma 2 gene (GABRG2) encode the GABAA receptor which is responsible for fast neuronal inhibition. Polymorphisms in GABGR2 gene affect the clinical response of anti-epileptic drugs (AEDs). Therefore, we carried out an updated study to find the association GABRG2 gene polymorphisms with carbamazepine (CBZ) non-responsive therapy in the Pakhtun population. METHODS A clinical prospective cohort study was conducted in 79 CBZ treated patients upon consent after the approval of Khyber Medical University Advanced Study and Research Board. Blood sample were taken at optimal dose of CBZ at base line, third and sixth months of the treatment. Blood level of CBZ was measure through reverse phase high performance liquid chromatography (HPLC). Restriction fragment length polymorphisms techniques were used to genotype GABRG2 gene in these patients. CBZ responses were evaluated on three and six months of study by measuring the decrease in frequency of seizure per week. RESULTS The average maximum dose of CBZ was 455 ± 133 mg/day at baseline, 479 ± 142 mg/day at third month and 495 ± 133 mg/day at sixth month of the treatment. CBZ level was found within therapeutic range (4-12 mg/L) without any significant (P > .5) variations among the CC, CT and TT genotypes of GABRG2 (C588T and C315T) gene. But the poor clinical response during CBZ treatment was linked (P < .05) with CT and TT genotypes of GABRG2 (C588T and C315T) gene in Pakhtun Population. CONCLUSION A poor response to CBZ was found in variant genotypes (CT and TT) of GABRG2 (C588T and C315T) gene in Pakhtun Population.
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Affiliation(s)
- Shakir Ullah
- Department of Pharmacology Institute of Basic Medical Science, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan
- * Correspondence: Shakir Ullah, Institute of Basic Medical Sciences/Institute of Pharmaceutical Sciences, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan (e-mail: )
| | - Niaz Ali
- Department of Pharmacology Institute of Basic Medical Science, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sajjad Ahmad
- Department of Pharmacology Institute of Basic Medical Science, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Syed Wadood Ali Sha
- Department of Pharmacy (Pharmacology), University of Malakand, Chakdara, Pakistan
| | - Saad Ali
- Department of Neurology, Govt. Lady Reading Hospital Peshawar, Khyber Pakhtunkhwa, Pakistan
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Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, Pardo-Manuel de Villena F, Ferris MT, Gygi SP, Churchill GA. Regulation of protein abundance in genetically diverse mouse populations. CELL GENOMICS 2021; 1:100003. [PMID: 36212994 PMCID: PMC9536773 DOI: 10.1016/j.xgen.2021.100003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
Genetically diverse mouse populations are powerful tools for characterizing the regulation of the proteome and its relationship to whole-organism phenotypes. We used mass spectrometry to profile and quantify the abundance of 6,798 proteins in liver tissue from mice of both sexes across 58 Collaborative Cross (CC) inbred strains. We previously collected liver proteomics data from the related Diversity Outbred (DO) mice and their founder strains. We show concordance across the proteomics datasets despite being generated from separate experiments, allowing comparative analysis. We map protein abundance quantitative trait loci (pQTLs), identifying 1,087 local and 285 distal in the CC mice and 1,706 local and 414 distal in the DO mice. We find that regulatory effects on individual proteins are conserved across the mouse populations, in particular for local genetic variation and sex differences. In comparison, proteins that form complexes are often co-regulated, displaying varying genetic architectures, and overall show lower heritability and map fewer pQTLs. We have made this resource publicly available to enable quantitative analyses of the regulation of the proteome.
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Affiliation(s)
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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Abstract
Pathogenic variants in epilepsy genes result in a spectrum of clinical severity. One source of phenotypic heterogeneity is modifier genes that affect expressivity of a primary pathogenic variant. Mouse epilepsy models also display varying degrees of clinical severity on different genetic backgrounds. Mice with heterozygous deletion of Scn1a (Scn1a+/−) model Dravet syndrome, a severe epilepsy most often caused by SCN1A haploinsufficiency. Scn1a+/− mice recapitulate features of Dravet syndrome, including spontaneous seizures, sudden death, and cognitive/behavioral deficits. Scn1a+/− mice maintained on the 129S6/SvEvTac (129) strain have normal lifespan and no spontaneous seizures. In contrast, admixture with C57BL/6J (B6) results in epilepsy and premature lethality. We previously mapped Dravet Survival Modifier loci (Dsm1-Dsm5) responsible for strain-dependent differences in survival. Gabra2, encoding the GABAA α2 subunit, was nominated as a candidate modifier at Dsm1. Direct measurement of GABAA receptors found lower abundance of α2-containing receptors in hippocampal synapses of B6 mice relative to 129. We also identified a B6-specific single nucleotide deletion within Gabra2 that lowers mRNA and protein by nearly 50%. Repair of this deletion reestablished normal levels of Gabra2 expression. In this study, we used B6 mice with a repaired Gabra2 allele to evaluate Gabra2 as a genetic modifier of severity in Scn1a+/− mice. Gabra2 repair restored transcript and protein expression, increased abundance of α2-containing GABAA receptors in hippocampal synapses, and rescued epilepsy phenotypes of Scn1a+/− mice. These findings validate Gabra2 as a genetic modifier of Dravet syndrome, and support enhancing function of α2-containing GABAA receptors as treatment strategy for Dravet syndrome.
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Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland. Hum Genet 2021; 140:1011-1029. [PMID: 33710394 PMCID: PMC8197721 DOI: 10.1007/s00439-021-02268-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.
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Association between GABRG2 rs211037 polymorphism and febrile seizures: a meta-analysis. ACTA EPILEPTOLOGICA 2021. [DOI: 10.1186/s42494-021-00038-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Emerging evidence has implied that the GABRG2 gene play a role in the mechanism of febrile seizure (FS), however, the relationship between GABRG2 rs211037 polymorphism and the risk of FS remains controversial. This meta-analysis was conducted to investigate the relationship of GABRG2 rs211037 polymorphism with the susceptibility to FS.
Methods
MEDLINE, Embase, Cochrane Library and CNKI databases were searched (until April 6, 2019) for eligible studies on the relationship between GABRG2 rs211037 polymorphism and FS. We calculated the odds ratios (ORs) by a fixed or random model with the STATA 15.0 software. Subgroup analyses for the ethnicity, the source of the control, and age and sex matching of controls were conducted.
Results
A total of 8 studies consisting of 775 FS patients and 5162 controls were included in this study. Based on the overall data, he GABRG2 rs211037 polymorphism was not significantly associated with the risk of FS (TT + CT vs CC: OR = 0.95, 95%CI 0.64–1.41, P = 0.80). Notably, the GABRG2 rs211037 variant was significantly associated with decreased risk of FS in Asian populations (TT vs CT + CC: OR = 0.63, 95%CI 0.45–0.88, P = 0.006), but increased risk in Caucasian populations (CT vs CC: OR = 1.56, 95%CI 1.14–2.15, P = 0.006). Significant associations were also detected when healthy controls out of the whole controls were employed for comparison (TT vs CT + CC: OR = 0.59, 95% CI 0.45–0.77, P < 0.001) and when data from studies with age- and sex-matched controls were used (TT + CT vs CC: OR = 0.60, 95% CI 0.43–0.86, P = 0.001).
Conclusion
The GABRG2 rs211037 polymorphism may decrease the risk of FS in Asian populations, while increasing the risk in Caucasian populations. Further well-designed studies with large sample sizes are essential to verify the conclusions in other ethnicities.
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A high-resolution in vivo atlas of the human brain's benzodiazepine binding site of GABA A receptors. Neuroimage 2021; 232:117878. [PMID: 33610745 PMCID: PMC8256681 DOI: 10.1016/j.neuroimage.2021.117878] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/15/2020] [Accepted: 02/12/2021] [Indexed: 12/29/2022] Open
Abstract
Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the human brain and plays a key role in several brain functions and neuropsychiatric disorders such as anxiety, epilepsy, and depression. For decades, several in vivo and ex vivo techniques have been used to highlight the mechanisms of the GABA system, however, no studies have currently combined the techniques to create a high-resolution multimodal view of the GABA system. Here, we present a quantitative high-resolution in vivo atlas of the human brain benzodiazepine receptor sites (BZR) located on postsynaptic ionotropic GABAA receptors (GABAA Rs), generated on the basis of in vivo [11C]flumazenil Positron Emission Tomography (PET) data. Next, based on ex vivo autoradiography data, we transform the PET-generated atlas from binding values into BZR protein density. Finally, we examine the brain regional association between BZR protein density and ex vivo mRNA expression for the 19 subunits in the GABAA R, including an estimation of the minimally required expression of mRNA levels for each subunit to translate into BZR protein. This represents the first publicly available quantitative high-resolution in vivo atlas of the spatial distribution of BZR densities in the healthy human brain. The atlas provides a unique neuroscientific tool as well as novel insights into the association between mRNA expression for individual subunits in the GABAA R and the BZR density at each location in the brain.
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13
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Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Fürth D, Williams RW, Ascoli GA, Dumitriu D. Highlights from the Era of Open Source Web-Based Tools. J Neurosci 2021; 41:927-936. [PMID: 33472826 PMCID: PMC7880282 DOI: 10.1523/jneurosci.1657-20.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022] Open
Abstract
High digital connectivity and a focus on reproducibility are contributing to an open science revolution in neuroscience. Repositories and platforms have emerged across the whole spectrum of subdisciplines, paving the way for a paradigm shift in the way we share, analyze, and reuse vast amounts of data collected across many laboratories. Here, we describe how open access web-based tools are changing the landscape and culture of neuroscience, highlighting six free resources that span subdisciplines from behavior to whole-brain mapping, circuits, neurons, and gene variants.
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Affiliation(s)
- Kristin R Anderson
- Departments of Pediatrics and Psychiatry, Columbia University, New York, New York 10032
- Division of Developmental Psychobiology, New York State Psychiatric Institute, New York, New York 10032
- The Sackler Institute for Developmental Psychobiology, Columbia University, New York, New York 10032
- Columbia Population Research Center, Columbia University, New York, New York 10027
- Zuckerman Institute, Columbia University, New York, New York 10027
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Sara Memar
- Robarts Research Institute, BrainsCAN, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 3K7, Canada
| | - Bengt Ljungquist
- Center for Neural Informatics, Structures, and Plasticity, Krasnow Institute for Advanced Study; and Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia 22030
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, and Plasticity, Krasnow Institute for Advanced Study; and Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia 22030
| | - Dani Dumitriu
- Departments of Pediatrics and Psychiatry, Columbia University, New York, New York 10032
- Division of Developmental Psychobiology, New York State Psychiatric Institute, New York, New York 10032
- The Sackler Institute for Developmental Psychobiology, Columbia University, New York, New York 10032
- Columbia Population Research Center, Columbia University, New York, New York 10027
- Zuckerman Institute, Columbia University, New York, New York 10027
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14
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Sigmon JS, Blanchard MW, Baric RS, Bell TA, Brennan J, Brockmann GA, Burks AW, Calabrese JM, Caron KM, Cheney RE, Ciavatta D, Conlon F, Darr DB, Faber J, Franklin C, Gershon TR, Gralinski L, Gu B, Gaines CH, Hagan RS, Heimsath EG, Heise MT, Hock P, Ideraabdullah F, Jennette JC, Kafri T, Kashfeen A, Kulis M, Kumar V, Linnertz C, Livraghi-Butrico A, Lloyd KCK, Lutz C, Lynch RM, Magnuson T, Matsushima GK, McMullan R, Miller DR, Mohlke KL, Moy SS, Murphy CEY, Najarian M, O'Brien L, Palmer AA, Philpot BD, Randell SH, Reinholdt L, Ren Y, Rockwood S, Rogala AR, Saraswatula A, Sassetti CM, Schisler JC, Schoenrock SA, Shaw GD, Shorter JR, Smith CM, St Pierre CL, Tarantino LM, Threadgill DW, Valdar W, Vilen BJ, Wardwell K, Whitmire JK, Williams L, Zylka MJ, Ferris MT, McMillan L, Manuel de Villena FP. Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research. Genetics 2020; 216:905-930. [PMID: 33067325 PMCID: PMC7768238 DOI: 10.1534/genetics.120.303596] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.
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Affiliation(s)
- John Sebastian Sigmon
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Matthew W Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jennifer Brennan
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - A Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Richard E Cheney
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dominic Ciavatta
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Frank Conlon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James Faber
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Craig Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211
| | - Timothy R Gershon
- Department of Neurology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lisa Gralinski
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Bin Gu
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christiann H Gaines
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert S Hagan
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ernest G Heimsath
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Tal Kafri
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Anwica Kashfeen
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mike Kulis
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Colton Linnertz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alessandra Livraghi-Butrico
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - K C Kent Lloyd
- Department of Surgery, University of California Davis, Davis, California 95616
- School of Medicine, University of California Davis, California 95616
- Mouse Biology Program, University of California Davis, California 95616
| | | | - Rachel M Lynch
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Glenn K Matsushima
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel McMullan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Caroline E Y Murphy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maya Najarian
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lori O'Brien
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Yuyu Ren
- University of California San Diego, La Jolla, California 92093
| | | | - Allison R Rogala
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Avani Saraswatula
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Jonathan C Schisler
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R Shorter
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | | | - Lisa M Tarantino
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David W Threadgill
- University of California San Diego, La Jolla, California 92093
- Department of Biochemistry and Biophysics, Texas A&M University, Texas 77843
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Barbara J Vilen
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Jason K Whitmire
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lucy Williams
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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15
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Korneev KV, Sviriaeva EN, Mitkin NA, Gorbacheva AM, Uvarova AN, Ustiugova AS, Polanovsky OL, Kulakovskiy IV, Afanasyeva MA, Schwartz AM, Kuprash DV. Minor C allele of the SNP rs7873784 associated with rheumatoid arthritis and type-2 diabetes mellitus binds PU.1 and enhances TLR4 expression. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165626. [PMID: 31785408 DOI: 10.1016/j.bbadis.2019.165626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/08/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022]
Abstract
Toll-like receptor 4 (TLR4) is an innate immunity receptor predominantly expressed on myeloid cells and involved in the development of various diseases, many of them with complex genetics. Here we present data on functionality of single nucleotide polymorphism rs7873784 located in the 3'-untranslated region (3'-UTR) of TLR4 gene and associated with various pathologies involving chronic inflammation. We demonstrate that TLR4 3'-UTR strongly enhanced the activity of TLR4 promoter in U937 human monocytic cell line while minor rs7873784(C) allele created a binding site for transcription factor PU.1 (encoded by SPI1 gene), a known regulator of TLR4 expression. Increased binding of PU.1 further augmented the TLR4 transcription while PU.1 knockdown or complete disruption of the PU.1 binding site abrogated the effect. We hypothesize that additional functional PU.1 site may increase TLR4 expression in individuals carrying minor C variant of rs7873784 and modulate the development of certain pathologies, such as rheumatoid arthritis and type-2 diabetes mellitus.
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Affiliation(s)
- Kirill V Korneev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina N Sviriaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nikita A Mitkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alisa M Gorbacheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Aksinya N Uvarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alina S Ustiugova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Oleg L Polanovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Marina A Afanasyeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anton M Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry V Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia.
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16
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Nomura T, Hawkins NA, Kearney JA, George AL, Contractor A. Potentiating α 2 subunit containing perisomatic GABA A receptors protects against seizures in a mouse model of Dravet syndrome. J Physiol 2019; 597:4293-4307. [PMID: 31045243 DOI: 10.1113/jp277651] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/15/2019] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Dravet syndrome mice (Scn1a+/- ) demonstrate a marked strain dependence for the severity of seizures which is correlated with GABAA receptor α2 subunit expression. The α2 /α3 subunit selective positive allosteric modulator (PAM) AZD7325 potentiates inhibitory postsynaptic currents (IPSCs) specifically in perisomatic synapses. AZD7325 demonstrates stronger effects on IPSCs in the seizure resistant mouse strain, consistent with higher α2 subunit expression. AZD7325 demonstrates seizure protective effects in Scn1a+/- mice without apparent sedative effects in vivo. ABSTRACT GABAA receptor potentiators are commonly used for the treatment of epilepsy, but it is not clear whether targeting distinct GABAA receptor subtypes will have disproportionate benefits over adverse effects. Here we demonstrate that the α2 /α3 selective positive allosteric modulator (PAM) AZD7325 preferentially potentiates hippocampal inhibitory responses at synapses proximal to the soma of CA1 neurons. The effect of AZD7325 on synaptic responses was more prominent in mice on the 129S6/SvEvTac background strain, which have been demonstrated to be seizure resistant in the model of Dravet syndrome (Scn1a+/- ), and in which the α2 GABAA receptor subunits are expressed at higher levels relative to in the seizure prone C57BL/6J background strain. Consistent with this, treatment of Scn1a+/- mice with AZD7325 elevated the temperature threshold for hyperthermia-induced seizures without apparent sedative effects. Our results in a model system indicate that selectively targeting α2 is a potential therapeutic option for Dravet syndrome.
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Affiliation(s)
- Toshihiro Nomura
- Department of Physiology, Northwestern University, Chicago, IL, 60611, USA
| | - Nicole A Hawkins
- Department of Pharmacology Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Kearney
- Department of Pharmacology Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Alfred L George
- Department of Pharmacology Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Anis Contractor
- Department of Physiology, Northwestern University, Chicago, IL, 60611, USA.,Department of Neurobiology Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL, 60611, USA
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17
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Sequeira A, Shen K, Gottlieb A, Limon A. Human brain transcriptome analysis finds region- and subject-specific expression signatures of GABA AR subunits. Commun Biol 2019; 2:153. [PMID: 31069263 PMCID: PMC6494906 DOI: 10.1038/s42003-019-0413-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/03/2019] [Indexed: 11/19/2022] Open
Abstract
Altered expression of GABA receptors (GABAARs) has been implicated in neurological and psychiatric disorders, but limited information about region-specific GABAAR subunit expression in healthy human brains, heteromeric assembly of major isoforms, and their collective organization across healthy individuals, are major roadblocks to understanding their role in non-physiological states. Here, by using microarray and RNA-Seq datasets-from single cell nuclei to global brain expression-from the Allen Institute, we find that transcriptional expression of GABAAR subunits is anatomically organized according to their neurodevelopmental origin. The data show a combination of complementary and mutually-exclusive expression patterns that delineate major isoforms, and which is highly stereotypical across brains from control donors. We summarize the region-specific signature of GABAR subunits per subject and its variability in a control population sample that can be used as a reference for remodeling changes during homeostatic rearrangements of GABAAR subunits after physiological, pharmacological or pathological challenges.
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Affiliation(s)
- Adolfo Sequeira
- Department of Psychiatry and Human Behavior, School of Medicine, University of California Irvine, Irvine, CA USA
| | - Kevin Shen
- Department of Neurology, Mitchel Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch, Galveston, TX USA
| | - Assaf Gottlieb
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX USA
| | - Agenor Limon
- Department of Neurology, Mitchel Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch, Galveston, TX USA
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18
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Mulligan MK, Abreo T, Neuner SM, Parks C, Watkins CE, Houseal MT, Shapaker TM, Hook M, Tan H, Wang X, Ingels J, Peng J, Lu L, Kaczorowski CC, Bryant CD, Homanics GE, Williams RW. Identification of a Functional Non-coding Variant in the GABA A Receptor α2 Subunit of the C57BL/6J Mouse Reference Genome: Major Implications for Neuroscience Research. Front Genet 2019; 10:188. [PMID: 30984232 PMCID: PMC6449455 DOI: 10.3389/fgene.2019.00188] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
GABA type-A (GABA-A) receptors containing the α2 subunit (GABRA2) are expressed in most brain regions and are critical in modulating inhibitory synaptic function. Genetic variation at the GABRA2 locus has been implicated in epilepsy, affective and psychiatric disorders, alcoholism and drug abuse. Gabra2 expression varies as a function of genotype and is modulated by sequence variants in several brain structures and populations, including F2 crosses originating from C57BL/6J (B6J) and the BXD recombinant inbred family derived from B6J and DBA/2J. Here we demonstrate a global reduction of GABRA2 brain protein and mRNA in the B6J strain relative to other inbred strains, and identify and validate the causal mutation in B6J. The mutation is a single base pair deletion located in an intron adjacent to a splice acceptor site that only occurs in the B6J reference genome. The deletion became fixed in B6J between 1976 and 1991 and is now pervasive in many engineered lines, BXD strains generated after 1991, the Collaborative Cross, and the majority of consomic lines. Repair of the deletion using CRISPR-Cas9-mediated gene editing on a B6J genetic background completely restored brain levels of GABRA2 protein and mRNA. Comparison of transcript expression in hippocampus, cortex, and striatum between B6J and repaired genotypes revealed alterations in GABA-A receptor subunit expression, especially in striatum. These results suggest that naturally occurring variation in GABRA2 levels between B6J and other substrains or inbred strains may also explain strain differences in anxiety-like or alcohol and drug response traits related to striatal function. Characterization of the B6J private mutation in the Gabra2 gene is of critical importance to molecular genetic studies in neurobiological research because this strain is widely used to generate genetically engineered mice and murine genetic populations, and is the most widely utilized strain for evaluation of anxiety-like, depression-like, pain, epilepsy, and drug response traits that may be partly modulated by GABRA2 function.
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Affiliation(s)
- Megan K Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Timothy Abreo
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Sarah M Neuner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States.,The Jackson Laboratory, Bar Harbor, ME, United States
| | - Cory Parks
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Christine E Watkins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - M Trevor Houseal
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Thomas M Shapaker
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Michael Hook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Haiyan Tan
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Xusheng Wang
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Jesse Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | | | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, United States
| | - Gregg E Homanics
- Departments of Anesthesiology and Perioperative Medicine, Neurobiology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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19
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Wu X, Xie S, Wang L, Fan P, Ge S, Xie XQ, Wu W. A computational strategy for finding novel targets and therapeutic compounds for opioid dependence. PLoS One 2018; 13:e0207027. [PMID: 30403753 PMCID: PMC6221321 DOI: 10.1371/journal.pone.0207027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022] Open
Abstract
Opioids are widely used for treating different types of pains, but overuse and abuse of prescription opioids have led to opioid epidemic in the United States. Besides analgesic effects, chronic use of opioid can also cause tolerance, dependence, and even addiction. Effective treatment of opioid addiction remains a big challenge today. Studies on addictive effects of opioids focus on striatum, a main component in the brain responsible for drug dependence and addiction. Some transcription regulators have been associated with opioid addiction, but relationship between analgesic effects of opioids and dependence behaviors mediated by them at the molecular level has not been thoroughly investigated. In this paper, we developed a new computational strategy that identifies novel targets and potential therapeutic molecular compounds for opioid dependence and addiction. We employed several statistical and machine learning techniques and identified differentially expressed genes over time which were associated with dependence-related behaviors after exposure to either morphine or heroin, as well as potential transcription regulators that regulate these genes, using time course gene expression data from mouse striatum. Moreover, our findings revealed that some of these dependence-associated genes and transcription regulators are known to play key roles in opioid-mediated analgesia and tolerance, suggesting that an intricate relationship between opioid-induce pain-related pathways and dependence may develop at an early stage during opioid exposure. Finally, we determined small compounds that can potentially target the dependence-associated genes and transcription regulators. These compounds may facilitate development of effective therapy for opioid dependence and addiction. We also built a database (http://daportals.org) for all opioid-induced dependence-associated genes and transcription regulators that we discovered, as well as the small compounds that target those genes and transcription regulators.
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Affiliation(s)
- Xiaojun Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Siwei Xie
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peihao Fan
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Songwei Ge
- School of Information, Renmin University of China, Beijing, China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wei Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Farris SP, Riley BP, Williams RW, Mulligan MK, Miles MF, Lopez MF, Hitzemann R, Iancu OD, Colville A, Walter NAR, Darakjian P, Oberbeck DL, Daunais JB, Zheng CL, Searles RP, McWeeney SK, Grant KA, Mayfield RD. Cross-species molecular dissection across alcohol behavioral domains. Alcohol 2018; 72:19-31. [PMID: 30213503 PMCID: PMC6309876 DOI: 10.1016/j.alcohol.2017.11.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/14/2022]
Abstract
This review summarizes the proceedings of a symposium presented at the "Alcoholism and Stress: A Framework for Future Treatment Strategies" conference held in Volterra, Italy on May 9-12, 2017. Psychiatric diseases, including alcohol-use disorders (AUDs), are influenced through complex interactions of genes, neurobiological pathways, and environmental influences. A better understanding of the common neurobiological mechanisms underlying an AUD necessitates an integrative approach, involving a systematic assessment of diverse species and phenotype measures. As part of the World Congress on Stress and Alcoholism, this symposium provided a detailed account of current strategies to identify mechanisms underlying the development and progression of AUDs. Dr. Sean Farris discussed the integration and organization of transcriptome and postmortem human brain data to identify brain regional- and cell type-specific differences related to excessive alcohol consumption that are conserved across species. Dr. Brien Riley presented the results of a genome-wide association study of DSM-IV alcohol dependence; although replication of genetic associations with alcohol phenotypes in humans remains challenging, model organism studies show that COL6A3, KLF12, and RYR3 affect behavioral responses to ethanol, and provide substantial evidence for their role in human alcohol-related traits. Dr. Rob Williams expanded upon the systematic characterization of extensive genetic-genomic resources for quantifying and clarifying phenotypes across species that are relevant to precision medicine in human disease. The symposium concluded with Dr. Robert Hitzemann's description of transcriptome studies in a mouse model selectively bred for high alcohol ("binge-like") consumption and a non-human primate model of long-term alcohol consumption. Together, the different components of this session provided an overview of systems-based approaches that are pioneering the experimental prioritization and validation of novel genes and gene networks linked with a range of behavioral phenotypes associated with stress and AUDs.
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Affiliation(s)
- Sean P Farris
- University of Texas at Austin, Austin, TX, United States
| | - Brien P Riley
- Virginia Commonwealth University, Richmond, VA, United States
| | - Robert W Williams
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Megan K Mulligan
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Michael F Miles
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marcelo F Lopez
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Robert Hitzemann
- Oregon Health and Science University, Portland, OR, United States
| | - Ovidiu D Iancu
- Oregon Health and Science University, Portland, OR, United States
| | | | | | | | | | - James B Daunais
- Wake Forest School of Medicine, Winston-Salem, NC, United States
| | | | - Robert P Searles
- Oregon Health and Science University, Portland, OR, United States
| | | | - Kathleen A Grant
- Oregon Health and Science University, Portland, OR, United States
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21
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Yuan JT, Gatti DM, Philip VM, Kasparek S, Kreuzman AM, Mansky B, Sharif K, Taterra D, Taylor WM, Thomas M, Ward JO, Holmes A, Chesler EJ, Parker CC. Genome-wide association for testis weight in the diversity outbred mouse population. Mamm Genome 2018; 29:310-324. [PMID: 29691636 DOI: 10.1007/s00335-018-9745-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
Testis weight is a genetically mediated trait associated with reproductive efficiency across numerous species. We sought to evaluate the genetically diverse, highly recombinant Diversity Outbred (DO) mouse population as a tool to identify and map quantitative trait loci (QTLs) associated with testis weight. Testis weights were recorded for 502 male DO mice and the mice were genotyped on the GIGAMuga array at ~ 143,000 SNPs. We performed a genome-wide association analysis and identified one significant and two suggestive QTLs associated with testis weight. Using bioinformatic approaches, we developed a list of candidate genes and identified those with known roles in testicular size and development. Candidates of particular interest include the RNA demethylase gene Alkbh5, the cyclin-dependent kinase inhibitor gene Cdkn2c, the dynein axonemal heavy chain gene Dnah11, the phospholipase D gene Pld6, the trans-acting transcription factor gene Sp4, and the spermatogenesis-associated gene Spata6, each of which has a human ortholog. Our results demonstrate the utility of DO mice in high-resolution genetic mapping of complex traits, enabling us to identify developmentally important genes in adult mice. Understanding how genetic variation in these genes influence testis weight could aid in the understanding of mechanisms of mammalian reproductive function.
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Affiliation(s)
- Joshua T Yuan
- Department of Computer Science, Program in Molecular Biology & Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Daniel M Gatti
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Steven Kasparek
- Department of Psychology, Middlebury College, Middlebury, VT, 05753, USA
| | - Andrew M Kreuzman
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Benjamin Mansky
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Kayvon Sharif
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Dominik Taterra
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Walter M Taylor
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Mary Thomas
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Jeremy O Ward
- Department of Biology, Program in Molecular Biology & Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcoholism and Alcohol Abuse (NIAAA), US National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elissa J Chesler
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Clarissa C Parker
- Department of Psychology, Middlebury College, Middlebury, VT, 05753, USA. .,Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA.
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Butilă AT, Zazgyva A, Sin AI, Szabo ER, Tilinca MC. GABRG2 C588T gene polymorphisms might be a predictive genetic marker of febrile seizures and generalized recurrent seizures: a case-control study in a Romanian pediatric population. Arch Med Sci 2018; 14:157-166. [PMID: 29379546 PMCID: PMC5778423 DOI: 10.5114/aoms.2016.63739] [Citation(s) in RCA: 17] [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: 06/10/2016] [Accepted: 08/14/2016] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION This case-control study aimed to assess two single nucleotide polymorphisms of the gene encoding the GABRG2 protein - GABRG2 (3145 G>A) and GABRG2 rs 211037 Asn196Asn (C588T) - in a cohort of pediatric patients from Romania, and evaluate their possible impact on drug-resistant forms of generalized epilepsy and recurrent febrile seizures. MATERIAL AND METHODS One hundred and fourteen children with idiopathic generalized epilepsy (group 1) or febrile seizures (group 2) were compared to 153 controls. Peripheral blood samples were assessed using polymerase chain reaction-restriction fragment length polymorphism analysis, with results interpreted based on the disappearance of a restriction site in the C allele (122 bp) compared to the T allele (100 bp + 22 bp). RESULTS A significant association was found with the TT homozygous genotype and T allele for both febrile seizures and epilepsy for the C588T locus, while GABRG2 G>A 3145 showed no significant association with any type of seizure. The TT homozygous genotype of GABRG2 Asn196Asn polymorphism was more frequent in patients with a history of febrile seizures (p = 0.0001), without a significant association identified for GABRG2-G>A 3145. Composite analysis showed associations with epilepsy for CC-AG (p = 0.02) and CT-AG (p = 0.007) with the CC-AA combination as reference. CONCLUSIONS C588T polymorphism of the GABRG2 gene might be a predictive genetic marker in triggering febrile convulsions. GABRG2 rs211037 TT homozygotes and T allele variants have an increased risk for developing febrile seizures. Recurrent crises and repeated episodes of seizures are more frequent in the GABRG2 Asn196Asn TT genotype polymorphism, with a 45 and 8 times higher risk of developing idiopathic generalized epilepsy and recurrent febrile seizures, respectively.
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Affiliation(s)
- Anamaria Todoran Butilă
- Department of Genetics, University of Medicine and Pharmacy of Târgu-Mureş, Târgu-Mureş, Romania
| | - Ancuta Zazgyva
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy of Târgu-Mureş, Târgu-Mureş, Romania
| | - Anca Ileana Sin
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy of Târgu-Mureş, Târgu-Mureş, Romania
| | - Elisabeta Racoș Szabo
- Department of Psychiatry, University of Medicine and Pharmacy of Târgu-Mureş, Târgu-Mureş, Romania
| | - Mariana Cornelia Tilinca
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy of Târgu-Mureş, Târgu-Mureş, Romania
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Yao Z, Luo J, Hu K, Lin J, Huang H, Wang Q, Zhang P, Xiong Z, He C, Huang Z, Liu B, Yang Y. ZKSCAN1 gene and its related circular RNA (circZKSCAN1) both inhibit hepatocellular carcinoma cell growth, migration, and invasion but through different signaling pathways. Mol Oncol 2017; 11:422-437. [PMID: 28211215 PMCID: PMC5527481 DOI: 10.1002/1878-0261.12045] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 12/21/2022] Open
Abstract
There is increasing evidence that circular RNA (circRNA) are involved in cancer development, but the regulation and function of human circRNA remain largely unknown. In this study, we demonstrated that ZKSCAN1, a zinc finger family gene, is expressed in both linear and circular (circZKSCAN1) forms of RNA in human hepatocellular carcinoma (HCC) tissues and cell lines. Here, we analyzed a cohort of 102 patients and found that expression of both ZKSCAN1mRNA and circZKSCAN1 was significantly lower (P < 0.05) in the HCC samples compared with that in matched adjacent nontumorous tissues by reverse transcription PCR (RT-PCR). The low expression level of ZKSCAN1 was only associated with tumor size (P = 0.032), while the cirZKSCAN1 levels varied in patients with different tumor numbers (P < 0.01), cirrhosis (P = 0.031), vascular invasion (P = 0.002), or microscopic vascular invasion (P = 0.002), as well as with the tumor grade (P < 0.001). Silencing both ZKSCAN1mRNA and circZKSCAN1 promoted cell proliferation, migration, and invasion. In contrast, overexpression of both forms of RNA repressed HCC progression in vivo and in vitro. Silencing or overexpression of both forms of RNA did not interfere with each other. RNA-seq revealed a very different molecular basis for the observed effects; ZKSCAN1mRNA mainly regulated cellular metabolism, while circZKSCAN1 mediated several cancer-related signaling pathways, suggesting a nonredundant role for ZKSCAN1mRNA and circRNA. In conclusion, our results revealed two post-translational products (ZKSCAN1mRNA and circZKSCAN1) that cooperated closely with one another to inhibit growth, migration, and invasion of HCC. cirZKSCAN1 might be a useful marker for the diagnosis of HCC.
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Affiliation(s)
- Zhicheng Yao
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jingyan Luo
- R&D Unit 602Forevergen Biosciences CenterGuangzhouGuangdongChina
| | - Kunpeng Hu
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jizong Lin
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - He Huang
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Qiangliang Wang
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Peng Zhang
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhiyong Xiong
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Chonghua He
- R&D Unit 602Forevergen Biosciences CenterGuangzhouGuangdongChina
| | - Zejian Huang
- Department of Hepatobiliary SurgerySun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Bo Liu
- Department of General SurgeryThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yang Yang
- Department of Liver TransplantationThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
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24
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Analyses of differentially expressed genes after exposure to acute stress, acute ethanol, or a combination of both in mice. Alcohol 2017; 58:139-151. [PMID: 28027852 DOI: 10.1016/j.alcohol.2016.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 12/31/2022]
Abstract
Alcohol abuse is a complex disorder, which is confounded by other factors, including stress. In the present study, we examined gene expression in the hippocampus of BXD recombinant inbred mice after exposure to ethanol (NOE), stress (RSS), and the combination of both (RSE). Mice were given an intraperitoneal (i.p.) injection of 1.8 g/kg ethanol or saline, and subsets of both groups were exposed to acute restraint stress for 15 min or controls. Gene expression in the hippocampus was examined using microarray analysis. Genes that were significantly (p < 0.05, q < 0.1) differentially expressed were further evaluated. Bioinformatic analyses were predominantly performed using tools available at GeneNetwork.org, and included gene ontology, presence of cis-regulation or polymorphisms, phenotype correlations, and principal component analyses. Comparisons of differential gene expression between groups showed little overlap. Gene Ontology demonstrated distinct biological processes in each group with the combined exposure (RSE) being unique from either the ethanol (NOE) or stress (RSS) group, suggesting that the interaction between these variables is mediated through diverse molecular pathways. This supports the hypothesis that exposure to stress alters ethanol-induced gene expression changes and that exposure to alcohol alters stress-induced gene expression changes. Behavior was profiled in all groups following treatment, and many of the differentially expressed genes are correlated with behavioral variation within experimental groups. Interestingly, in each group several genes were correlated with the same phenotype, suggesting that these genes are the potential origins of significant genetic networks. The distinct sets of differentially expressed genes within each group provide the basis for identifying molecular networks that may aid in understanding the complex interactions between stress and ethanol, and potentially provide relevant therapeutic targets. Using Ptp4a1, a candidate gene underlying the quantitative trait locus for several of these phenotypes, and network analyses, we show that a large group of differentially expressed genes in the NOE group are highly interrelated, some of which have previously been linked to alcohol addiction or alcohol-related phenotypes.
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25
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Chintalapudi SR, Jablonski MM. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene. Methods Mol Biol 2017; 1488:391-417. [PMID: 27933535 DOI: 10.1007/978-1-4939-6427-7_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA
| | - Monica M Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Anatomy and Neurobiology, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA. .,Department of Pharmaceutical Sciences, Hamilton Eye Institute, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 710, Memphis, TN, 38163, USA.
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Chintalapudi SR, Wang X, Li H, Lau YHC, Williams RW, Jablonski MM. Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas. Mol Vis 2016; 22:1318-1331. [PMID: 27881906 PMCID: PMC5108462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
PURPOSE Photoreceptor degenerative diseases are among the leading causes of vision loss. Although the causative genetic mutations are often known, mechanisms leading to photoreceptor degeneration remain poorly defined. We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 expression in the retina. METHODS Quantitative trait locus (QTL) mapping was used to map the genomic region that regulates Hspa5 in the cross between C57BL/6J X DBA/2J mice (BXD) genetic reference panel. The stepwise refinement of candidate genes was based on expression QTL mapping, gene expression correlation analyses (direct and partial), and analysis of regional sequence variants. The subcellular localization of candidate proteins and HSPA5 in mouse and human retinas was evaluated by immunohistochemistry. Differences in the localization of extracellular HSPA5 were assessed between healthy human donor and atrophic age-related macular degeneration (AMD) donor eyes. RESULTS In the eyes of healthy mice, extracellular HSPA5 was confined to the area around the cone photoreceptor outer segments. Mapping variation in Hspa5 mRNA expression levels in the retina revealed a statistically significant trans-acting expression QTL (eQTL) on Chromosome 2 (Chr 2) and a suggestive locus on Chr 15. Sulf2 on Chr 2 was the strongest candidate gene based on partial correlation analysis, Pearson correlation with Hspa5, expression levels in the retina, a missense variant in exon 14, and its reported function in the extracellular matrix and interphotoreceptor matrix. SULF2 is localized to the rod and cone photoreceptors in both human and mouse retinas. In human retinas with no pathology, extracellular HSPA5 was localized around many cones within the macular area. In contrast, fewer HSPA5-immunopositive cones were observed in the retinas from AMD donors. CONCLUSIONS We identified Sulf2 as a candidate gene modulating the Hspa5 expression in the retina. The preferential loss of HSPA5 in the interphotoreceptor matrix around cone photoreceptors in atrophic AMD retinas opens up new avenues for exploring the changes in interphotoreceptor matrix (IPM) that are associated with macular disease.
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Affiliation(s)
- Sumana R. Chintalapudi
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN
| | - XiaoFei Wang
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN
| | - Huiling Li
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Ophthalmology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yin H. Chan Lau
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN,Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, TN
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Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq. PLoS Genet 2016; 12:e1006398. [PMID: 27768696 PMCID: PMC5074504 DOI: 10.1371/journal.pgen.1006398] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022] Open
Abstract
A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy. SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome, an infant-onset epileptic encephalopathy. Dravet syndrome patients experience multiple seizures types that are often refractory to treatment, developmental delays, and elevated risk for SUDEP. The same sodium channel mutation can produce epilepsy phenotypes of varying clinical severity. This suggests that other factors, including genetic, modify the primary mutation and change disease severity. Mouse models provide a useful tool in studying the genetic basis of epilepsy. The mouse strain background can alter phenotype severity, supporting a contribution of genetic modifiers in epilepsy. The Scn1a+/- mouse model has a strain-dependent epilepsy phenotype. Scn1a+/- mice on the 129S6/SvEvTac (129) strain have a normal phenotype and lifespan, while [129xC57BL/6J]F1-Scn1a+/- mice experience spontaneous seizures, hyperthermia-induced seizures and high rates of premature death. We hypothesize the phenotypic differences are due to strain-specific genetic modifiers that influence expressivity of the Scn1a+/- phenotype. Low resolution mapping of Scn1a+/- identified several Dravet syndrome modifier (Dsm) loci responsible for the strain-dependent difference in survival. One locus of interest, Dsm1 located on chromosome 5, was fine mapped to a 9 Mb region using interval specific congenics. RNA-Seq was then utilized to identify candidate modifier genes within this narrowed region. Three genes with significant total gene expression differences between 129S6/SvEvTac and [129xC57BL/6J]F1 were identified, including the GABAA receptor subunit, Gabra2. Further analysis of Gabra2 demonstrated allele-specific expression. Pharmological manipulation by clobazam, a common anticonvulsant with preferential affinity for the GABRA2 receptor, revealed dose-dependent protection against hyperthermia-induced seizures in Scn1a+/- mice. These findings support Gabra2 as a genetic modifier of the Scn1a+/- mouse model of Dravet syndrome. Epilepsy is a neurological disorder affecting approximately 3 million Americans and 1% of the worldwide population. Approximately 70% of patients diagnosed with epilepsy have a genetic basis for their disease. The same genetic mutation can result in epilepsy with varying clinical severity in some individuals. This suggests that additional factors modify the effect of the primary mutation, resulting in the differences observed. Mouse models of epilepsy also exhibit variable severity depending on the inbred strain background. This is a useful model system that enables us to determine other genetic factors that influence phenotype presentation. This study investigates a mouse model of Dravet syndrome. Similar to Dravet syndrome patients, the mice experience a variety of seizure types and have increased risk for premature death. Interestingly, the Dravet syndrome phenotype is completely masked on one mouse strain background. Through a series of genetic and pharmacological techniques we were able to identify a gene that is likely responsible for the strain-dependent phenotype difference of Dravet mice. Identifying genes that modify diseases can help predict patient outcomes and suggest new therapies for the treatment of epilepsy.
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28
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Ralvenius WT, Acuña MA, Benke D, Matthey A, Daali Y, Rudolph U, Desmeules J, Zeilhofer HU, Besson M. The clobazam metabolite N-desmethyl clobazam is an α2 preferring benzodiazepine with an improved therapeutic window for antihyperalgesia. Neuropharmacology 2016; 109:366-375. [PMID: 27392635 PMCID: PMC4981430 DOI: 10.1016/j.neuropharm.2016.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/27/2016] [Accepted: 07/04/2016] [Indexed: 12/14/2022]
Abstract
Data from genetically modified mice suggest that benzodiazepine (BDZ)-site agonists with improved selectivity for α2-subtype GABAA receptors (α2GABAAR) are potentially useful for the treatment of neuropathic pain. Subtype-selective compounds available for preclinical tests in rodents support this concept but have not been approved for human use, hindering proof-of-concept studies in patients. We recently proposed that N-desmethyl clobazam (NDMC), the main metabolite of the licensed BDZ clobazam (CBZ), is responsible for most of the antihyperalgesia observed in mice after CBZ administration. In order to assess a potentially favorable pharmacological profile of NDMC, we analyzed differences in the GABAAR subtype specificity of CBZ, NDMC and diazepam (DZP) in recombinant receptors. DZP and CBZ potentiated sedating α1GABAARs and antihyperalgesic α2GABAARs with similar efficacies, whereas NDMC preferred α2GABAARs over α1GABAARs across a wide concentration range. In vivo, DZP and NDMC reduced neuropathic pain at doses between 3 and 30 mg/kg. At these doses, DZP had strong locomotor sedating effects while NDMC caused no or only weak sedation. Sedative effects of NDMC became apparent when the action of NDMC was restricted to α1GABAARs. However, when GABAAR point-mutated mice were studied that allow the analysis of antihyperalgesia and sedation in isolation, we found that, compared to DZP, NDMC had a significantly improved therapeutic window, consistent with its more favorable α2/α1 in vitro activity ratio. Given that NDMC should share the safety profile of its parent compound CBZ, it should be well-suited for proof-of-concept studies in human volunteers or patients.
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Affiliation(s)
- William T Ralvenius
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mario A Acuña
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Dietmar Benke
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Alain Matthey
- Division of Clinical Pharmacology and Toxicology, Multidisciplinary Pain Center, Department of Anesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals, University of Geneva, 4 rue Gabrielle-Perret-Gentil, CH-1211 Geneva, Switzerland
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Multidisciplinary Pain Center, Department of Anesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals, University of Geneva, 4 rue Gabrielle-Perret-Gentil, CH-1211 Geneva, Switzerland
| | - Uwe Rudolph
- Laboratory of Genetic Neuropharmacology, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA; Department of Psychiatry, Harvard Medical School, 401 Park Drive, Boston, MA 02215, USA
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Multidisciplinary Pain Center, Department of Anesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals, University of Geneva, 4 rue Gabrielle-Perret-Gentil, CH-1211 Geneva, Switzerland
| | - Hanns Ulrich Zeilhofer
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 10, CH-8093 Zürich, Switzerland; Drug Discovery Network Zurich (DDNZ), CH-8057 Zurich, Switzerland.
| | - Marie Besson
- Division of Clinical Pharmacology and Toxicology, Multidisciplinary Pain Center, Department of Anesthesiology, Pharmacology and Intensive Care, Geneva University Hospitals, University of Geneva, 4 rue Gabrielle-Perret-Gentil, CH-1211 Geneva, Switzerland
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Yeo S, Hodgkinson CA, Zhou Z, Jung J, Leung M, Yuan Q, Goldman D. The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits. BMC Genomics 2016; 17:620. [PMID: 27515598 PMCID: PMC4982227 DOI: 10.1186/s12864-016-2922-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/07/2016] [Indexed: 12/16/2022] Open
Abstract
Background Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL’s for complex phenotypes. Results We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Conclusions Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2922-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seungeun Yeo
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Zhifeng Zhou
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Jeesun Jung
- Laboratory of Epidemiology and Biometry, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Ming Leung
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Qiaoping Yuan
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - David Goldman
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA.
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Dixit AB, Banerjee J, Ansari A, Tripathi M, Chandra SP. Mutations in GABRG2 receptor gene are not a major factor in the pathogenesis of mesial temporal lobe epilepsy in Indian population. Ann Indian Acad Neurol 2016; 19:236-41. [PMID: 27293336 PMCID: PMC4888688 DOI: 10.4103/0972-2327.182304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM This study is focused on GABRG2 gene sequence variations in patients with mesial temporal lobe epilepsy (mTLE). The GABAAreceptor is a heteropentameric receptor and alpha-1 beta-2 gamma-2 subunits combination is most abundant and present in almost all regions of the brain. The gamma-2 subunit (GABRG2) gene mutations have been reported in different epilepsy pathologies. In the present study we have looked for GABRG2 gene sequence variations in patients with mTLE. MATERIALS AND METHODS Twenty patients (12 females and eight males, age 4.6-38 years) with MTLE were recruited for this investigation. Patients were recommended for epilepsy surgery after all clinical investigations as per the epilepsy protocol. Ethnically matched glioma or meningioma patients were considered as nonepileptic controls. During temporal lobectomy of amygdalohippocampectomy, hippocampal brain tissue samples were resected guided by intraoperative electrocorticography (ECoG) activity. All 11 exons of GABRG2 gene with their flanking intronic regions were amplified by polymerase chain reaction (PCR) and screened by DNA sequencing analysis for sequence variations. STATISTICAL ANALYSIS USED Comparison of allele frequencies between patient and control groups was determined using a c(2) test. RESULTS AND CONCLUSIONS Total five DNA sequence variations were identified, three in exonic regions (c.643A > G, rs211035), (c.T > A, rs424740), and (c.C > T, rs418210) and two in intronic regions (c.751 + 41A > G, rs211034) and (c.751 + 52G > A, rs 34281163). Allele frequencies of variants identified in this study did not differ between patients and normal controls. Thus, we conclude that GABRG2 gene may not be playing significant role in the development of epilepsy or as a susceptibility gene in patients with MTLE in Indian population.
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Affiliation(s)
- Aparna Banerjee Dixit
- Center for Excellence in Epilepsy, A joint National Brain Research Centre-All Institute of Medical Sciences Collaboration, National Brain Research Centre, Manesar, Haryana, India
| | - Jyotirmoy Banerjee
- Center for Excellence in Epilepsy, A joint National Brain Research Centre-All Institute of Medical Sciences Collaboration, National Brain Research Centre, Manesar, Haryana, India
| | - Abuzar Ansari
- Department of Neurosurgery, All Institute of Medical Sciences, New Delhi, India
| | - Manjari Tripathi
- Department of Neurology, All Institute of Medical Sciences, New Delhi, India
| | - Sarat P Chandra
- Department of Neurosurgery, All Institute of Medical Sciences, New Delhi, India
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Loos M, Li KW, van der Schors R, Gouwenberg Y, van der Loo R, Williams RW, Smit AB, Spijker S. Impact of genetic variation on synaptic protein levels in genetically diverse mice. Proteomics 2016; 16:1123-30. [DOI: 10.1002/pmic.201500154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 12/07/2015] [Accepted: 01/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Maarten Loos
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
- Sylics (Synaptologics BV); Amsterdam The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Roel van der Schors
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Yvonne Gouwenberg
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Rolinka van der Loo
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics; University of Tennessee Health Science Center; Memphis TN USA
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology; Center for Neurogenomics and Cognitive Research; Neuroscience Campus Amsterdam; VU University Amsterdam; Amsterdam The Netherlands
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Bubier JA, Wilcox TD, Jay JJ, Langston MA, Baker EJ, Chesler EJ. Cross-Species Integrative Functional Genomics in GeneWeaver Reveals a Role for Pafah1b1 in Altered Response to Alcohol. Front Behav Neurosci 2016; 10:1. [PMID: 26834590 PMCID: PMC4720795 DOI: 10.3389/fnbeh.2016.00001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/04/2016] [Indexed: 12/12/2022] Open
Abstract
Identifying the biological substrates of complex neurobehavioral traits such as alcohol dependency pose a tremendous challenge given the diverse model systems and phenotypic assessments used. To address this problem we have developed a platform for integrated analysis of high-throughput or genome-wide functional genomics studies. A wealth of such data exists, but it is often found in disparate, non-computable forms. Our interactive web-based software system, Gene Weaver (http://www.geneweaver.org), couples curated results from genomic studies to graph-theoretical tools for combinatorial analysis. Using this system we identified a gene underlying multiple alcohol-related phenotypes in four species. A search of over 60,000 gene sets in GeneWeaver's database revealed alcohol-related experimental results including genes identified in mouse genetic mapping studies, alcohol selected Drosophila lines, Rattus differential expression, and human alcoholic brains. We identified highly connected genes and compared these to genes currently annotated to alcohol-related behaviors and processes. The most highly connected gene not annotated to alcohol was Pafah1b1. Experimental validation using a Pafah1b1 conditional knock-out mouse confirmed that this gene is associated with an increased preference for alcohol and an altered thermoregulatory response to alcohol. Although this gene has not been previously implicated in alcohol-related behaviors, its function in various neural mechanisms makes a role in alcohol-related phenomena plausible. By making diverse cross-species functional genomics data readily computable, we were able to identify and confirm a novel alcohol-related gene that may have implications for alcohol use disorders and other effects of alcohol.
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Affiliation(s)
| | | | - Jeremy J Jay
- The Jackson LaboratoryBar Harbor, ME, USA; Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, North Carolina Research CampusKannapolis, NC, USA
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee Knoxville, TN, USA
| | - Erich J Baker
- School of Engineering and Department of Computer Science, Baylor University Waco, TX, USA
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Chintalapudi SR, Morales-Tirado VM, Williams RW, Jablonski MM. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells. FEBS J 2016; 283:678-93. [PMID: 26663874 DOI: 10.1111/febs.13620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
Abstract
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.
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Affiliation(s)
- Sumana R Chintalapudi
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vanessa M Morales-Tirado
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, Memphis, TN, USA
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Contribution of GABRG2 Polymorphisms to Risk of Epilepsy and Febrile Seizure: a Multicenter Cohort Study and Meta-analysis. Mol Neurobiol 2015; 53:5457-67. [DOI: 10.1007/s12035-015-9457-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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Zhao W, Zhao T, Chen Y, Zhao F, Gu Q, Williams RW, Bhattacharya SK, Lu L, Sun Y. A Murine Hypertrophic Cardiomyopathy Model: The DBA/2J Strain. PLoS One 2015; 10:e0133132. [PMID: 26241864 PMCID: PMC4524617 DOI: 10.1371/journal.pone.0133132] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 06/07/2015] [Indexed: 12/12/2022] Open
Abstract
Familial hypertrophic cardiomyopathy (HCM) is attributed to mutations in genes that encode for the sarcomere proteins, especially Mybpc3 and Myh7. Genotype-phenotype correlation studies show significant variability in HCM phenotypes among affected individuals with identical causal mutations. Morphological changes and clinical expression of HCM are the result of interactions with modifier genes. With the exceptions of angiotensin converting enzyme, these modifiers have not been identified. Although mouse models have been used to investigate the genetics of many complex diseases, natural murine models for HCM are still lacking. In this study we show that the DBA/2J (D2) strain of mouse has sequence variants in Mybpc3 and Myh7, relative to widely used C57BL/6J (B6) reference strain and the key features of human HCM. Four-month-old of male D2 mice exhibit hallmarks of HCM including increased heart weight and cardiomyocyte size relative to B6 mice, as well as elevated markers for cardiac hypertrophy including β-myosin heavy chain (MHC), atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and skeletal muscle alpha actin (α1-actin). Furthermore, cardiac interstitial fibrosis, another feature of HCM, is also evident in the D2 strain, and is accompanied by up-regulation of type I collagen and α-smooth muscle actin (SMA)-markers of fibrosis. Of great interest, blood pressure and cardiac function are within the normal range in the D2 strain, demonstrating that cardiac hypertrophy and fibrosis are not secondary to hypertension, myocardial infarction, or heart failure. Because D2 and B6 strains have been used to generate a large family of recombinant inbred strains, the BXD cohort, the D2 model can be effectively exploited for in-depth genetic analysis of HCM susceptibility and modifier screens.
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MESH Headings
- Actins/blood
- Animals
- Biomarkers
- Blood Pressure
- Cardiomyopathy, Hypertrophic, Familial/blood
- Cardiomyopathy, Hypertrophic, Familial/diagnostic imaging
- Cardiomyopathy, Hypertrophic, Familial/genetics
- Cardiomyopathy, Hypertrophic, Familial/pathology
- Carrier Proteins/genetics
- Disease Models, Animal
- Fibrosis
- Gene Expression Profiling
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred DBA/genetics
- Myocardium/metabolism
- Myocardium/pathology
- Myocytes, Cardiac/pathology
- Myofibroblasts/pathology
- Myosin Heavy Chains/blood
- Myosin Heavy Chains/genetics
- Natriuretic Peptides/blood
- Phenotype
- RNA, Messenger/biosynthesis
- Ultrasonography
- Ventricular Dysfunction, Left/etiology
- Ventricular Dysfunction, Left/physiopathology
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Affiliation(s)
- Wenyuan Zhao
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
| | - Tieqiang Zhao
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
| | - Yuanjian Chen
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
| | - Fengbo Zhao
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Syamal K. Bhattacharya
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Jiangsu Key Laboratory of Neuroregenertion, Nantong University, Nantong, Jiangsu, China
- * E-mail: (YS); (LL)
| | - Yao Sun
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee HealthScience Center, Memphis, Tennessee, United States of America
- * E-mail: (YS); (LL)
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Mueller TM, Remedies CE, Haroutunian V, Meador-Woodruff JH. Abnormal subcellular localization of GABAA receptor subunits in schizophrenia brain. Transl Psychiatry 2015; 5:e612. [PMID: 26241350 PMCID: PMC4564557 DOI: 10.1038/tp.2015.102] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/27/2015] [Accepted: 06/01/2015] [Indexed: 12/21/2022] Open
Abstract
Inhibitory neurotransmission is primarily mediated by γ-aminobutyric acid (GABA) activating synaptic GABA type A receptors (GABA(A)R). In schizophrenia, presynaptic GABAergic signaling deficits are among the most replicated findings; however, postsynaptic GABAergic deficits are less well characterized. Our lab has previously demonstrated that although there is no difference in total protein expression of the α1-6, β1-3 or γ2 GABA(A)R subunits in the superior temporal gyrus (STG) in schizophrenia, the α1, β1 and β2 GABA(A)R subunits are abnormally N-glycosylated. N-glycosylation is a posttranslational modification that has important functional roles in protein folding, multimer assembly and forward trafficking. To investigate the impact that altered N-glycosylation has on the assembly and trafficking of GABA(A)Rs in schizophrenia, this study used western blot analysis to measure the expression of α1, α2, β1, β2 and γ2 GABA(A)R subunits in subcellular fractions enriched for endoplasmic reticulum (ER) and synapses (SYN) from STG of schizophrenia (N = 16) and comparison (N = 14) subjects and found evidence of abnormal localization of the β1 and β2 GABA(A)R subunits and subunit isoforms in schizophrenia. The β2 subunit is expressed as three isoforms at 52 kDa (β2(52 kDa)), 50 kDa (β2(50 kDa)) and 48 kDa (β2(48 kDa)). In the ER, we found increased total β2 GABA(A)R subunit (β2(ALL)) expression driven by increased β2(50 kDa), a decreased ratio of β(248 kDa):β2(ALL) and an increased ratio of β2(50 kDa):β2(48 kDa). Decreased ratios of β1:β2(ALL) and β1:β2(50 kDa) in both the ER and SYN fractions and an increased ratio of β2(52 kDa):β(248 kDa) at the synapse were also identified in schizophrenia. Taken together, these findings provide evidence that alterations of N-glycosylation may contribute to GABAergic signaling deficits in schizophrenia by disrupting the assembly and trafficking of GABA(A)Rs.
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Affiliation(s)
- T M Mueller
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA,Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, 1719 6th Avenue South, CIRC 593A, Birmingham, AL 35294-0021, USA. E-mail:
| | - C E Remedies
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA,Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL, USA
| | - V Haroutunian
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - J H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
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Steenbergen L, Sellaro R, Stock AK, Verkuil B, Beste C, Colzato LS. RETRACTED: Transcutaneous vagus nerve stimulation (tVNS) enhances response selection during action cascading processes. Eur Neuropsychopharmacol 2015; 25:773-8. [PMID: 25869158 DOI: 10.1016/j.euroneuro.2015.03.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/12/2015] [Accepted: 03/22/2015] [Indexed: 12/18/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This retraction comes after a thorough and time-consuming analysis of the published article and the data it reports, following an investigation from the University of Leiden. On date 15th November 2021 European Neuropsychopharmacology received advice from University of Leiden, containing allegations of misconduct concerning the data reported in this article. Due to the nature of the concerns raised about this paper, the Editor-in-Chief examined all documents provided, all aspects of the peer review and editorial process and requested the view of each of the authors. The Editor-in-Chief wishes to acknowledge the co-operation of all parties. The Editor-in-Chief considers that there is a legitimate cause for concern regarding deletion of participants from datasets. The Editor-in-Chief commends the authors for their willingness in participating in this dialogue. However, given the concerns raised, the suggestion of the University of Leiden, and the view expressed by some of the authors, Retraction of this paper is inevitable. The Editor-in-Chief and the entire editorial board will use this case as a reminder to be as diligent as possible in the peer review process and to support transparency and openness in data sharing.
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Affiliation(s)
- Laura Steenbergen
- Institute for Psychological Research and Leiden Institute for Brain and Cognition, Leiden University, Leiden, The Netherlands.
| | - Roberta Sellaro
- Institute for Psychological Research and Leiden Institute for Brain and Cognition, Leiden University, Leiden, The Netherlands
| | - Ann-Kathrin Stock
- Cognitive Neurophysiology, Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany
| | - Bart Verkuil
- Institute for Psychological Research and Leiden Institute for Brain and Cognition, Leiden University, Leiden, The Netherlands
| | - Christian Beste
- Cognitive Neurophysiology, Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany
| | - Lorenza S Colzato
- Institute for Psychological Research and Leiden Institute for Brain and Cognition, Leiden University, Leiden, The Netherlands
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Lambert MP, Ancey PB, Esposti DD, Cros MP, Sklias A, Scoazec JY, Durantel D, Hernandez-Vargas H, Herceg Z. Aberrant DNA methylation of imprinted loci in hepatocellular carcinoma and after in vitro exposure to common risk factors. Clin Epigenetics 2015; 7:15. [PMID: 25755686 PMCID: PMC4353474 DOI: 10.1186/s13148-015-0053-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/06/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is among the most frequent human malignancies and a major cause of cancer-related death worldwide. It is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be one of the molecular mechanisms leading to hepatocarcinogenesis. Previous studies from our group revealed that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression. Imprinted genes are mono-allelically expressed in a parent-of-origin-dependent manner and have been suggested to be more susceptible to deregulation in cancer. To test this notion, we performed a targeted analysis of DNA methylation in known imprinted genes, using HCC samples and in vitro models of carcinogenic exposure. RESULTS Analysis of HCC DNA methylation in two independent datasets showed that differentially methylated loci are significantly enriched in imprinted genes. Most of the promoters of imprinted genes were found hypomethylated in HCC tumors compared to surrounding tissues, contrasting with the frequent promoter hypermethylation observed in tumors. We next investigated the status of methylation of the imprinting control region (ICR) of different imprinted clusters and found that the 15q11-13 ICR was significantly hypomethylated in tumors relative to their surrounding tissues. In addition, expression of imprinted genes within this cluster was frequently deregulated in a gene-specific manner, suggesting distinct mechanisms of regulation in this region. Finally, primary human hepatocytes and hepatocyte-like HepaRG cells displayed higher methylation variability in certain imprinted loci after natural hepatitis B virus (HBV) infection and after lipid accumulation, respectively. CONCLUSION The methylation status of a large panel of imprinted genes was found deregulated in HCC, suggesting a major role of this mechanism during hepatocarcinogenesis. In vitro models support the hypothesis of imprinted gene methylation as a potential marker of environmental exposures.
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Affiliation(s)
- Marie-Pierre Lambert
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
- />Current address: Epissage alternatif et progression tumorale, Centre de Recherche en Cancérologie de Lyon (CRCL), 28 rue Laennec, 69008 Lyon, France
| | - Pierre-Benoit Ancey
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Davide Degli Esposti
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Marie-Pierre Cros
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Athena Sklias
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Jean-Yves Scoazec
- />Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - David Durantel
- />INSERM U871, Molecular physiopathology and new treatments of viral hepatitis, Centre de recherche en cancérologie (CRCL), 151 Cours Albert-Thomas, 69008 Lyon, France
| | - Hector Hernandez-Vargas
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
| | - Zdenko Herceg
- />Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008 Lyon, France
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Ashbrook DG, Williams RW, Lu L, Stein JL, Hibar DP, Nichols TE, Medland SE, Thompson PM, Hager R. Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. BMC Genomics 2014; 15:850. [PMID: 25280473 PMCID: PMC4192369 DOI: 10.1186/1471-2164-15-850] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 09/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variation in hippocampal volume has been linked to significant differences in memory, behavior, and cognition among individuals. To identify genetic variants underlying such differences and associated disease phenotypes, multinational consortia such as ENIGMA have used large magnetic resonance imaging (MRI) data sets in human GWAS studies. In addition, mapping studies in mouse model systems have identified genetic variants for brain structure variation with great power. A key challenge is to understand how genetically based differences in brain structure lead to the propensity to develop specific neurological disorders. RESULTS We combine the largest human GWAS of brain structure with the largest mammalian model system, the BXD recombinant inbred mouse population, to identify novel genetic targets influencing brain structure variation that are linked to increased risk for neurological disorders. We first use a novel cross-species, comparative analysis using mouse and human genetic data to identify a candidate gene, MGST3, associated with adult hippocampus size in both systems. We then establish the coregulation and function of this gene in a comprehensive systems-analysis. CONCLUSIONS We find that MGST3 is associated with hippocampus size and is linked to a group of neurodegenerative disorders, such as Alzheimer's.
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Affiliation(s)
- David G Ashbrook
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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Abstract
Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. The mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Liang and Wilusz used extensive mutagenesis of expression plasmids to show that miniature introns containing the splice sites along with short (∼30- to 40-nt) inverted repeats are sufficient to allow the intervening exons to circularize in cells. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3′ end processing signal is required, suggesting that circularization may occur post-transcriptionally. Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the precursor messenger RNA (pre-mRNA) splicing machinery “backsplices” and covalently joins, for example, the two ends of a single exon. However, the mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Using extensive mutagenesis of expression plasmids, we show that miniature introns containing the splice sites along with short (∼30- to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening exons to circularize in cells. The intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other. More than simple thermodynamics is clearly at play, however, as not all repeats support circularization, and increasing the stability of the hairpin between the repeats can sometimes inhibit circular RNA biogenesis. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3′ end processing signal is required, suggesting that circularization may occur post-transcriptionally. These results suggest detailed and generalizable models that explain how the splicing machinery determines whether to produce a circular noncoding RNA or a linear mRNA.
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Affiliation(s)
- Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Effects of L-theanine on posttraumatic stress disorder induced changes in rat brain gene expression. ScientificWorldJournal 2014; 2014:419032. [PMID: 25165739 PMCID: PMC4137547 DOI: 10.1155/2014/419032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/11/2014] [Accepted: 05/13/2014] [Indexed: 01/02/2023] Open
Abstract
Posttraumatic stress disorder (PTSD) is characterized by the occurrence of a traumatic event that is beyond the normal range of human experience. The future of PTSD treatment may specifically target the molecular mechanisms of PTSD. In the US, approximately 20% of adults report taking herbal products to treat medical illnesses. L-theanine is the amino acid in green tea primarily responsible for relaxation effects. No studies have evaluated the potential therapeutic properties of herbal medications on gene expression in PTSD. We evaluated gene expression in PTSD-induced changes in the amygdala and hippocampus of Sprague-Dawley rats. The rats were assigned to PTSD-stressed and nonstressed groups that received either saline, midazolam, L-theanine, or L-theanine + midazolam. Amygdala and hippocampus tissue samples were analyzed for changes in gene expression. One-way ANOVA was used to detect significant difference between groups in the amygdala and hippocampus. Of 88 genes examined, 17 had a large effect size greater than 0.138. Of these, 3 genes in the hippocampus and 5 genes in the amygdala were considered significant (P < 0.05) between the groups. RT-PCR analysis revealed significant changes between groups in several genes implicated in a variety of disorders ranging from PTSD, anxiety, mood disorders, and substance dependence.
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Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics. Genetics 2014; 197:1377-93. [PMID: 24923803 DOI: 10.1534/genetics.114.166165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits.
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Fritschy JM, Panzanelli P. GABAAreceptors and plasticity of inhibitory neurotransmission in the central nervous system. Eur J Neurosci 2014; 39:1845-65. [DOI: 10.1111/ejn.12534] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Jean-Marc Fritschy
- Institute of Pharmacology and Toxicology; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Neuroscience Center Zurich; University of Zurich and ETH; Zurich Switzerland
| | - Patrizia Panzanelli
- Department of Neuroscience Rita Levi Montalcini; University of Turin; Turin Italy
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Abstract
Transcriptome studies have revealed a surprisingly high level of variation among individuals in expression of key genes in the CNS under both normal and experimental conditions. Ten-fold variation is common, yet the specific causes and consequences of this variation are largely unknown. By combining classic gene mapping methods-family linkage studies and genomewide association-with high-throughput genomics, it is now possible to define quantitative trait loci (QTLs), single-gene variants, and even single SNPs and indels that control gene expression in different brain regions and cells. This review considers some of the major technical and conceptual challenges in analyzing variation in expression in the CNS with a focus on mRNAs, rather than noncoding RNAs or proteins. At one level of analysis, this work has been highly successful, and we finally have techniques that can be used to track down small numbers of loci that control expression in the CNS. But at a higher level of analysis, we still do not understand the genetic architecture of gene expression in brain, the consequences of expression QTLs on protein levels or on cell function, or the combined impact of expression differences on behavior and disease risk. These important gaps are likely to be bridged over the next several decades using (1) much larger sample sizes, (2) more powerful RNA sequencing and proteomic methods, and (3) novel statistical and computational models to predict genome-to-phenome relations.
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Affiliation(s)
- Ashutosh K Pandey
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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Chesler EJ. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research. Mamm Genome 2013; 25:3-11. [PMID: 24272351 PMCID: PMC3916706 DOI: 10.1007/s00335-013-9492-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.
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Affiliation(s)
- Elissa J Chesler
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA,
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Mulligan MK, Dubose C, Yue J, Miles MF, Lu L, Hamre KM. Expression, covariation, and genetic regulation of miRNA Biogenesis genes in brain supports their role in addiction, psychiatric disorders, and disease. Front Genet 2013; 4:126. [PMID: 23847651 PMCID: PMC3701868 DOI: 10.3389/fgene.2013.00126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 06/14/2013] [Indexed: 11/16/2022] Open
Abstract
The role of miRNA and miRNA biogenesis genes in the adult brain is just beginning to be explored. In this study we have performed a comprehensive analysis of the expression, genetic regulation, and co-expression of major components of the miRNA biogenesis pathway using human and mouse data sets and resources available on the GeneNetwork web site (genenetwork.org). We found a wide range of variation in expression in both species for key components of the pathway—Drosha, Pasha, and Dicer. Across species, tissues, and expression platforms all three genes are generally well-correlated. No single genetic locus exerts a strong and consistent influence on the expression of these key genes across murine brain regions. However, in mouse striatum, many members of the miRNA pathway are correlated—including Dicer, Drosha, Pasha, Ars2 (Srrt), Eif2c1 (Ago1), Eif2c2 (Ago2), Zcchc11, and Snip1. The expression of these genes may be partly influenced by a locus on Chromosome 9 (105.67–106.32 Mb). We explored ~1500 brain phenotypes available for the C57BL/6J × DBA/2J (BXD) genetic mouse population in order to identify miRNA biogenesis genes correlated with traits related to addiction and psychiatric disorders. We found a significant association between expression of Dicer and Drosha in several brain regions and the response to many drugs of abuse, including ethanol, cocaine, and methamphetamine. Expression of Dicer, Drosha, and Pasha in most of the brain regions explored is strongly correlated with the expression of key members of the dopamine system. Drosha, Pasha, and Dicer expression is also correlated with the expression of behavioral traits measuring depression and sensorimotor gating, impulsivity, and anxiety, respectively. Our study provides a global survey of the expression and regulation of key miRNA biogenesis genes in brain and provides preliminary support for the involvement of these genes and their product miRNAs in addiction and psychiatric disease processes.
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Affiliation(s)
- Megan K Mulligan
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center Memphis, TN, USA
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GABRG2 rs211037 polymorphism and epilepsy: A systematic review and meta-analysis. Seizure 2013; 22:53-8. [DOI: 10.1016/j.seizure.2012.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022] Open
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Williams RW, Mulligan MK. Genetic and molecular network analysis of behavior. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23195314 DOI: 10.1016/b978-0-12-398323-7.00006-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This chapter provides an introduction into the genetic control and analysis of behavioral variation using powerful online resources. We introduce you to the new field of systems genetics using "case studies" drawn from the world of behavioral genetics that exploit populations of genetically diverse lines of mice. These lines differ very widely in patterns of gene and protein expression in the brain and in patterns of behavior. In this chapter, we address the following set of related questions: (1) Can we combine massive genomic data sets with large aggregates of precise quantitative data on behavior? (2) Can we map causal relations between gene variants and behavioral differences? (3) Can we simultaneously use these highly coherent data sets to understand more about the underlying molecular and cellular basis of behavior?
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Affiliation(s)
- Robert W Williams
- Department of Anatomy and Neurobiology, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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