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Xu L, Zhou Y, Ren X, Xu C, Ren R, Yan X, Li X, Yang H, Xu X, Guo X, Sheng G, Hua Y, Yuan Z, Wang S, Gu W, Sun D, Gao F. Expanding the Phenotypic and Genotypic Spectrum of ARFGEF1-Related Neurodevelopmental Disorder. Front Mol Neurosci 2022; 15:862096. [PMID: 35782386 PMCID: PMC9248374 DOI: 10.3389/fnmol.2022.862096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Mono-allelic loss-of-function variants in ARFGEF1 have recently caused a developmental delay, intellectual disability, and epilepsy, with varying clinical expressivity. However, given the clinical heterogeneity and low-penetrance mutations of ARFGEF1-related neurodevelopmental disorder, the robustness of the gene-disease association requires additional evidence. In this study, five novel heterozygous ARFGEF1 variants were identified in five unrelated pediatric patients with neurodevelopmental disorders, including one missense change (c.3539T>G), two canonical splice site variants (c.917-1G>T, c.2850+2T>A), and two frameshift (c.2923_c.2924delCT, c.4951delG) mutations resulting in truncation of ARFGEF1. The pathogenic/likely pathogenic variants presented here will be highly beneficial to patients undergoing genetic testing in the future by providing an expanded reference list of disease-causing variants.
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Affiliation(s)
- Lu Xu
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Youfeng Zhou
- Department of Pediatrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoyan Ren
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenlu Xu
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
| | - Rongna Ren
- Department of Pediatrics and Neurosurgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Xuke Yan
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuelian Li
- Department of Pediatric Neurology, Anhui Provincial Children's Hospital, Hefei, China
| | - Huimin Yang
- Department of Pediatric, Inner Mongolia Maternal and Child Health Care Hospital, Hohhot, China
| | - Xuebin Xu
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotong Guo
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxia Sheng
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Hua
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhefeng Yuan
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shugang Wang
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
| | - Weiyue Gu
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
- *Correspondence: Weiyue Gu
| | - Dan Sun
- Department of Pediatric Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Dan Sun
| | - Feng Gao
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Feng Gao
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Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity. Genet Med 2021; 23:1901-1911. [PMID: 34113008 DOI: 10.1038/s41436-021-01218-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE ADP ribosylation factor guanine nucleotide exchange factors (ARFGEFs) are a family of proteins implicated in cellular trafficking between the Golgi apparatus and the plasma membrane through vesicle formation. Among them is ARFGEF1/BIG1, a protein involved in axon elongation, neurite development, and polarization processes. ARFGEF1 has been previously suggested as a candidate gene for different types of epilepsies, although its implication in human disease has not been well characterized. METHODS International data sharing, in silico predictions, and in vitro assays with minigene study, western blot analyses, and RNA sequencing. RESULTS We identified 13 individuals with heterozygous likely pathogenic variants in ARFGEF1. These individuals displayed congruent clinical features of developmental delay, behavioral problems, abnormal findings on brain magnetic resonance image (MRI), and epilepsy for almost half of them. While nearly half of the cohort carried de novo variants, at least 40% of variants were inherited from mildly affected parents who were clinically re-evaluated by reverse phenotyping. Our in silico predictions and in vitro assays support the contention that ARFGEF1-related conditions are caused by haploinsufficiency, and are transmitted in an autosomal dominant fashion with variable expressivity. CONCLUSION We provide evidence that loss-of-function variants in ARFGEF1 are implicated in sporadic and familial cases of developmental delay with or without epilepsy.
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Teoh J, Subramanian N, Pero ME, Bartolini F, Amador A, Kanber A, Williams D, Petri S, Yang M, Allen AS, Beal J, Haut SR, Frankel WN. Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABA A receptors. Neurobiol Dis 2019; 134:104632. [PMID: 31678406 DOI: 10.1016/j.nbd.2019.104632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/23/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022] Open
Abstract
ARFGEF1 encodes a guanine exchange factor involved in intracellular vesicle trafficking, and is a candidate gene for childhood genetic epilepsies. To model ARFGEF1 haploinsufficiency observed in a recent Lennox Gastaut Syndrome patient, we studied a frameshift mutation (Arfgef1fs) in mice. Arfgef1fs/+ pups exhibit signs of developmental delay, and Arfgef1fs/+ adults have a significantly decreased threshold to induced seizures but do not experience spontaneous seizures. Histologically, the Arfgef1fs/+ brain exhibits a disruption in the apical lining of the dentate gyrus and altered spine morphology of deep layer neurons. In primary hippocampal neuron culture, dendritic surface and synaptic but not total GABAA receptors (GABAAR) are reduced in Arfgef1fs/+ neurons with an accompanying decrease in the number of GABAAR-containing recycling endosomes in cell body. Arfgef1fs/+ neurons also display differences in the relative ratio of Arf6+:Rab11+:TrfR+ recycling endosomes. Although the GABAAR-containing early endosomes in Arfgef1fs/+ neurons are comparable to wildtype, Arfgef1fs/+ neurons show an increase in the number of GABAAR-containing lysosomes in dendrite and cell body. Together, the altered endosome composition and decreased neuronal surface GABAAR results suggests a mechanism whereby impaired neuronal inhibition leads to seizure susceptibility.
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Affiliation(s)
- JiaJie Teoh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America.
| | - Narayan Subramanian
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Maria Elena Pero
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, United States of America; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Bartolini
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Ariadna Amador
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Ayla Kanber
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Damian Williams
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Sabrina Petri
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Mu Yang
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, United States of America
| | - Jules Beal
- The Saul R. Korey Department of Neurology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Sheryl R Haut
- The Saul R. Korey Department of Neurology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Wayne N Frankel
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, United States of America; Department of Genetic and Development, Columbia University Irving Medical Center, New York, NY, United States of America
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Bakhtiarizadeh MR, Salehi A, Rivera RM. Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. PLoS One 2018; 13:e0193316. [PMID: 29470549 PMCID: PMC5823453 DOI: 10.1371/journal.pone.0193316] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/08/2018] [Indexed: 12/30/2022] Open
Abstract
RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information. Our methods take into account sequencing errors, mapping bias, as well as biological replication to reduce the probability of obtaining a false-positive result. We conducted a detailed characterization of sequence and structural features related to novel candidate sites and found 1,600 novel canonical A-to-I editing sites in the nine bovine tissues analyzed. Results show that these sites 1) occur frequently in clusters and short interspersed nuclear elements (SINE) repeats, 2) have a preference for guanines depletion/enrichment in the flanking 5′/3′ nucleotide, 3) occur less often in coding sequences than other regions of the genome, and 4) have low evolutionary conservation. Further, we found that a positive correlation exists between expression of ADAR family members and tissue-specific RNA editing. Most of the genes with predicted A-to-I editing in each tissue were significantly enriched in biological terms relevant to the function of the corresponding tissue. Lastly, the results highlight the importance of the RNA editome in nervous system regulation. The present study extends the list of RNA editing sites in bovine and provides pipelines that may be used to investigate the editome in other organisms.
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Affiliation(s)
| | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Rocío Melissa Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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Mahfouz A, Huisman SMH, Lelieveldt BPF, Reinders MJT. Brain transcriptome atlases: a computational perspective. Brain Struct Funct 2017; 222:1557-1580. [PMID: 27909802 PMCID: PMC5406417 DOI: 10.1007/s00429-016-1338-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/15/2016] [Indexed: 01/31/2023]
Abstract
The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases allow researchers to probe the molecular mechanisms which define neuronal identities, neuroanatomy, and patterns of connectivity. Despite the immense effort put into generating such atlases, to answer fundamental questions in neuroscience, an even greater effort is needed to develop methods to probe the resulting high-dimensional multivariate data. We provide a comprehensive overview of the various computational methods used to analyze brain transcriptome atlases.
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Affiliation(s)
- Ahmed Mahfouz
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands.
| | - Sjoerd M H Huisman
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
| | - Boudewijn P F Lelieveldt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands
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Wang Z, Zhang Y, Fang J, Yu F, Heng D, Fan Y, Xu J, Peng B, Liu W, Han S, He X. Decreased Methylation Level of H3K27me3 Increases Seizure Susceptibility. Mol Neurobiol 2016; 54:7343-7352. [PMID: 27815838 DOI: 10.1007/s12035-016-0197-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023]
Abstract
Epigenetic modifications including histone modifications are associated with seizure development and epileptogenesis; however, its underlying mechanism remains to be elucidated. Dipeptidyl peptidase 4 (DPP4) and IL6 are identified as febrile seizure (FS)-related genes using gene microarray analysis in hyperthermia prone (HP) rats. This purpose of the study focused on exploring whether epigenetic modifications marker histone H3 lysine 27 trimethylation (H3K27me3)-regulated DPP4 and IL6 expression further affected seizures development. Herein, we reported broad between-group differences in the global levels of H3K27me3 with increased seizure severity in vivo. Using chromatin immunoprecipitation (ChIP), we identified markedly decreased H3K27me3 enrichment at their promoters of DPP4 and IL6 in vivo. We further showed that hyperthermia significantly decreased protein levels of H3K27me3, increased mRNA levels of DPP4 and IL6 by decreasing H3K27me3 enrichment at their promoters of DPP4 and IL6 in vitro. Importantly, H3K27me3 loss via enhancer of zeste homolog 2 (EZH2) knockdown promoted expression of DPP4 and IL6 via the same mechanism in vitro. EZH2 knockdown also increased neuronal firing frequency in vitro and FS susceptibility in vivo companied with upregulation expression of DPP4 and IL6. Taken together, our study provided the first evidence that hyperthermia-induced decreased of H3K27me3 promoted seizure susceptibility via regulating the expression pattern of DPP4 and IL6. These findings suggested that the methylation level of H3K27me3 might be a key regulator of seizure susceptibility.
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Affiliation(s)
- Zhongcheng Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China
| | - Yusong Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China
| | - Jian Fang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China
| | - Fang Yu
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China
| | - Duanhe Heng
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China
| | - Yuanteng Fan
- Department of Neurology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jian Xu
- Weifang Maternity and Child Hospital, Weifang, China
| | - Biwen Peng
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wanhong Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Song Han
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China.
| | - Xiaohua He
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Donghu Road No. 185, Wuchang, Wuhan, 430071, China.
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Breen MS, Beliakova-Bethell N, Mujica-Parodi LR, Carlson JM, Ensign WY, Woelk CH, Rana BK. Acute psychological stress induces short-term variable immune response. Brain Behav Immun 2016; 53:172-182. [PMID: 26476140 DOI: 10.1016/j.bbi.2015.10.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/01/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022] Open
Abstract
In spite of advances in understanding the cross-talk between the peripheral immune system and the brain, the molecular mechanisms underlying the rapid adaptation of the immune system to an acute psychological stressor remain largely unknown. Conventional approaches to classify molecular factors mediating these responses have targeted relatively few biological measurements or explored cross-sectional study designs, and therefore have restricted characterization of stress-immune interactions. This exploratory study analyzed transcriptional profiles and flow cytometric data of peripheral blood leukocytes with physiological (endocrine, autonomic) measurements collected throughout the sequence of events leading up to, during, and after short-term exposure to physical danger in humans. Immediate immunomodulation to acute psychological stress was defined as a short-term selective up-regulation of natural killer (NK) cell-associated cytotoxic and IL-12 mediated signaling genes that correlated with increased cortisol, catecholamines and NK cells into the periphery. In parallel, we observed down-regulation of innate immune toll-like receptor genes and genes of the MyD88-dependent signaling pathway. Correcting gene expression for an influx of NK cells revealed a molecular signature specific to the adrenal cortex. Subsequently, focusing analyses on discrete groups of coordinately expressed genes (modules) throughout the time-series revealed immune stress responses in modules associated to immune/defense response, response to wounding, cytokine production, TCR signaling and NK cell cytotoxicity which differed between males and females. These results offer a spring-board for future research towards improved treatment of stress-related disease including the impact of stress on cardiovascular and autoimmune disorders, and identifies an immune mechanism by which vulnerabilities to these diseases may be gender-specific.
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Affiliation(s)
- Michael S Breen
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK.
| | | | - Lilianne R Mujica-Parodi
- Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794-5281, USA
| | - Joshua M Carlson
- Department of Psychology, Northern Michigan University, Marquette, MI 49855, USA
| | - Wayne Y Ensign
- Space and Naval Warfare Systems Center - Pacific, Applied Sciences Division, San Diego, CA 92152, USA
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Brinda K Rana
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; VA San Diego Center for Stress and Mental Health, La Jolla, CA 92093, USA.
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Oliver KL, Lukic V, Thorne NP, Berkovic SF, Scheffer IE, Bahlo M. Harnessing gene expression networks to prioritize candidate epileptic encephalopathy genes. PLoS One 2014; 9:e102079. [PMID: 25014031 PMCID: PMC4090166 DOI: 10.1371/journal.pone.0102079] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/14/2014] [Indexed: 01/11/2023] Open
Abstract
We apply a novel gene expression network analysis to a cohort of 182 recently reported candidate Epileptic Encephalopathy genes to identify those most likely to be true Epileptic Encephalopathy genes. These candidate genes were identified as having single variants of likely pathogenic significance discovered in a large-scale massively parallel sequencing study. Candidate Epileptic Encephalopathy genes were prioritized according to their co-expression with 29 known Epileptic Encephalopathy genes. We utilized developing brain and adult brain gene expression data from the Allen Human Brain Atlas (AHBA) and compared this to data from Celsius: a large, heterogeneous gene expression data warehouse. We show replicable prioritization results using these three independent gene expression resources, two of which are brain-specific, with small sample size, and the third derived from a heterogeneous collection of tissues with large sample size. Of the nineteen genes that we predicted with the highest likelihood to be true Epileptic Encephalopathy genes, two (GNAO1 and GRIN2B) have recently been independently reported and confirmed. We compare our results to those produced by an established in silico prioritization approach called Endeavour, and finally present gene expression networks for the known and candidate Epileptic Encephalopathy genes. This highlights sub-networks of gene expression, particularly in the network derived from the adult AHBA gene expression dataset. These networks give clues to the likely biological interactions between Epileptic Encephalopathy genes, potentially highlighting underlying mechanisms and avenues for therapeutic targets.
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Affiliation(s)
- Karen L. Oliver
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Vesna Lukic
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Natalie P. Thorne
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Samuel F. Berkovic
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Ingrid E. Scheffer
- Epilepsy Research Center, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
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Abstract
This community page describes the database and associated Web application that comprise the Allen Human Brain Atlas, an open online resource that integrates genomic and anatomic human brain data.
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Sadeque A, Serão NV, Southey BR, Delfino KR, Rodriguez-Zas SL. Identification and characterization of alternative exon usage linked glioblastoma multiforme survival. BMC Med Genomics 2012. [PMID: 23206951 PMCID: PMC3548711 DOI: 10.1186/1755-8794-5-59] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Alternative exon usage (AEU) is an important component of gene regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identified associations between gene expression and the brain cancer glioblastoma multiforme (GBM). The few consistent gene expression biomarkers of GBM that have been reported may be due to the limited consideration of AEU and the analytical approaches used. The objectives of this study were to develop a model that accounts for the variations in expression present between the exons within a gene and to identify AEU biomarkers of GBM survival. Methods The expression of exons corresponding to 25,403 genes was related to the survival of 250 individuals diagnosed with GBM in a training data set. Genes exhibiting AEU in the training data set were confirmed in an independent validation data set of 78 patients. A hierarchical mixed model that allows the consideration of covariation between exons within a gene and of the effect of the epidemiological characteristics of the patients was developed to identify associations between exon expression and patient survival. This general model describes all three possible scenarios: multi-exon genes with and without AEU, and single-exon genes. Results AEU associated with GBM survival was identified on 2477 genes (P-value < 5.0E-04 or FDR-adjusted P-value < 0.05). G-protein coupled receptor 98 (Gpr98) and epidermal growth factor (Egf) were among the genes exhibiting AEU with 30 and 9 exons associated with GBM survival, respectively. Pathways enriched among the AEU genes included focal adhesion, ECM-receptor interaction, ABC transporters and pathways in cancer. In addition, 24 multi-exon genes without AEU and 8 single-exon genes were associated with GBM survival (FDR-adjusted P-value < 0.05). Conclusions The inferred patterns of AEU were consistent with in silico AS models. The hierarchical model used offered a flexible and simple way to interpret and identify associations between survival that accommodates multi-exon genes with or without AEU and single exon genes. Our results indicate that differential expression of AEU could be used as biomarker for GBM and potentially other cancers.
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Affiliation(s)
- Ahmed Sadeque
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Kwong AKY, Fung CW, Chan SY, Wong VCN. Identification of SCN1A and PCDH19 mutations in Chinese children with Dravet syndrome. PLoS One 2012; 7:e41802. [PMID: 22848613 PMCID: PMC3405017 DOI: 10.1371/journal.pone.0041802] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/25/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dravet syndrome is a severe form of epilepsy. Majority of patients have a mutation in SCN1A gene, which encodes a voltage-gated sodium channel. A recent study has demonstrated that 16% of SCN1A-negative patients have a mutation in PCDH19, the gene encoding protocadherin-19. Mutations in other genes account for only a very small proportion of families. TSPYL4 is a novel candidate gene within the locus 6q16.3-q22.31 identified by linkage study. OBJECTIVE The present study examined the mutations in epileptic Chinese children with emphasis on Dravet syndrome. METHODS A hundred children with severe epilepsy were divided into Dravet syndrome and non-Dravet syndrome groups and screened for SCN1A mutations by direct sequencing. SCN1A-negative Dravet syndrome patients and patients with phenotypes resembling Dravet syndrome were checked for PCDH19 and TSPYL4 mutations. RESULTS Eighteen patients (9 males, 9 females) were diagnosed to have Dravet syndrome. Among them, 83% (15/18) had SCN1A mutations including truncating (7), splice site (2) and missense mutations (6). The truncating/splice site mutations were associated with moderate to severe degree of intellectual disability (p<0.05). During the progression of disease, 73% (11/15) had features fitting into the diagnostic criteria of autism spectrum disorder and 53% (8/15) had history of vaccination-induced seizures. A novel PCDH19 p.D377N mutation was identified in one SCN1A-negative female patient with Dravet syndrome and a known PCDH19 p.N340S mutation in a female non-Dravet syndrome patient. The former also inherited a TSPYL4 p.G60R variant. CONCLUSION A high percentage of SCN1A mutations was identified in our Chinese cohort of Dravet syndrome patients but none in the rest of patients. We demonstrated that truncating/splice site mutations were linked to moderate to severe intellectual disability in these patients. A de novo PCDH19 missense mutation together with an inherited TSPYL4 missense variant were identified in a patient with Dravet syndrome.
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Affiliation(s)
- Anna Ka-Yee Kwong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cheuk-Wing Fung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Siu-Yuen Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Virginia Chun-Nei Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Piro RM, Di Cunto F. Computational approaches to disease-gene prediction: rationale, classification and successes. FEBS J 2012; 279:678-96. [PMID: 22221742 DOI: 10.1111/j.1742-4658.2012.08471.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The identification of genes involved in human hereditary diseases often requires the time-consuming and expensive examination of a great number of possible candidate genes, since genome-wide techniques such as linkage analysis and association studies frequently select many hundreds of 'positional' candidates. Even considering the positive impact of next-generation sequencing technologies, the prioritization of candidate genes may be an important step for disease-gene identification. In this paper we develop a basic classification scheme for computational approaches to disease-gene prediction and apply it to exhaustively review bioinformatics tools that have been developed for this purpose, focusing on conceptual aspects rather than technical detail and performance. Finally, we discuss some past successes obtained by computational approaches to illustrate their beneficial contribution to medical research.
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Affiliation(s)
- Rosario M Piro
- Department of Theoretical Bioinformatics, German Cancer Research Center, (DKFZ), Heidelberg, Germany.
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