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Schizophrenia Bioinformatics

Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Olympia Gianfrancesco, Daniel Griffiths, Paul Myers, David A Collier, Vivien J Bubb, John P Quinn
Genome-wide association studies (GWAS) have identified a region at chromosome 1p21.3, containing the microRNA MIR137, to be among the most significant associations for schizophrenia. However, the mechanism by which genetic variation at this locus increases risk of schizophrenia is unknown. Identifying key regulatory regions around MIR137 is crucial to understanding the potential role of this gene in the aetiology of psychiatric disorders. Through alignment of vertebrate genomes, we identified seven non-coding regions at the MIR137 locus with conservation comparable to exons (>70 %)...
October 2016: Journal of Molecular Neuroscience: MN
Mamneet Manghera, Jennifer Ferguson-Parry, Rongtuan Lin, Renée N Douville
UNLABELLED: Thousands of endogenous retroviruses (ERV), viral fossils of ancient germ line infections, reside within the human genome. Evidence of ERV activity has been observed widely in both health and disease. While this is most often cited as a bystander effect of cell culture or disease states, it is unclear which signals control ERV transcription. Bioinformatic analysis suggests that the viral promoter of endogenous retrovirus K (ERVK) is responsive to inflammatory transcription factors...
October 15, 2016: Journal of Virology
Xiang Zhan, Santhosh Girirajan, Ni Zhao, Michael C Wu, Debashis Ghosh
MOTIVATION: Copy number variants (CNVs) have been implicated in a variety of neurodevelopmental disorders, including autism spectrum disorders, intellectual disability and schizophrenia. Recent advances in high-throughput genomic technologies have enabled rapid discovery of many genetic variants including CNVs. As a result, there is increasing interest in studying the role of CNVs in the etiology of many complex diseases. Despite the availability of an unprecedented wealth of CNV data, methods for testing association between CNVs and disease-related traits are still under-developed due to the low prevalence and complicated multi-scale features of CNVs...
August 6, 2016: Bioinformatics
Yoshifumi Ashikawa, Yuhei Nishimura, Shiko Okabe, Shota Sasagawa, Soichiro Murakami, Mizuki Yuge, Koki Kawaguchi, Reiko Kawase, Toshio Tanaka
Oligodendrocytes are major myelin-producing cells and play essential roles in the function of a healthy nervous system. However, they are also one of the most vulnerable neural cell types in the central nervous system (CNS), and myelin abnormalities in the CNS are found in a wide variety of neurological disorders, including multiple sclerosis, adrenoleukodystrophy, and schizophrenia. There is an urgent need to identify small molecular weight compounds that can stimulate myelination. In this study, we performed comparative transcriptome analysis to identify pharmacodynamic effects common to miconazole and clobetasol, which have been shown to stimulate myelination by mouse oligodendrocyte progenitor cells (OPCs)...
2016: Frontiers in Pharmacology
Fanglin Guan, Tianxiao Zhang, Lu Li, Dongke Fu, Huali Lin, Gang Chen, Teng Chen
Schizophrenia is a devastating psychiatric condition with high heritability. Replicating the specific genetic variants that increase susceptibility to schizophrenia in different populations is critical to better understand schizophrenia. CNNM2 and NT5C2 are genes recently identified as susceptibility genes for schizophrenia in Europeans, but the exact mechanism by which these genes confer risk for schizophrenia remains unknown. In this study, we examined the potential for genetic susceptibility to schizophrenia of a three-gene cluster region, AS3MT-CNNM2-NT5C2...
October 2016: Schizophrenia Research
T Bernard Bigdeli, Donghyung Lee, Bradley Todd Webb, Brien P Riley, Vladimir I Vladimirov, Ayman H Fanous, Kenneth S Kendler, Silviu-Alin Bacanu
MOTIVATION: For genetic studies, statistically significant variants explain far less trait variance than 'sub-threshold' association signals. To dimension follow-up studies, researchers need to accurately estimate 'true' effect sizes at each SNP, e.g. the true mean of odds ratios (ORs)/regression coefficients (RRs) or Z-score noncentralities. Naïve estimates of effect sizes incur winner's curse biases, which are reduced only by laborious winner's curse adjustments (WCAs). Given that Z-scores estimates can be theoretically translated on other scales, we propose a simple method to compute WCA for Z-scores, i...
September 1, 2016: Bioinformatics
Luciana Tovo-Rodrigues, Mariana Recamonde-Mendoza, Vanessa Rodrigues Paixão-Côrtes, Estela M Bruxel, Jaqueline B Schuch, Deise C Friedrich, Luis A Rohde, Mara H Hutz
Although new candidate genes for Autism Spectrum Disorder (ASD), Schizophrenia (SCZ), Attention-Deficit/Hyperactivity Disorder (ADHD), and Bipolar Disorder (BD) emerged from genome-wide association studies (GWAS), their underlying molecular mechanisms remain poorly understood. Evidences of the involvement of intrinsically disordered proteins in diseases have grown in the last decade. These proteins lack tridimensional structure under physiological conditions and are involved in important cellular functions such as signaling, recognition and regulation...
September 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
T K Alshammari, M A Alshammari, M N Nenov, E Hoxha, M Cambiaghi, A Marcinno, T F James, P Singh, D Labate, J Li, H Y Meltzer, B Sacchetti, F Tempia, F Laezza
Cognitive processing is highly dependent on the functional integrity of gamma-amino-butyric acid (GABA) interneurons in the brain. These cells regulate excitability and synaptic plasticity of principal neurons balancing the excitatory/inhibitory tone of cortical networks. Reduced function of parvalbumin (PV) interneurons and disruption of GABAergic synapses in the cortical circuitry result in desynchronized network activity associated with cognitive impairment across many psychiatric disorders, including schizophrenia...
2016: Translational Psychiatry
Jin Liu, Xiang Wan, Shuangge Ma, Can Yang
MOTIVATION: Researchers worldwide have generated a huge volume of genomic data, including thousands of genome-wide association studies (GWAS) and massive amounts of gene expression data from different tissues. How to perform a joint analysis of these data to gain new biological insights has become a critical step in understanding the etiology of complex diseases. Due to the polygenic architecture of complex diseases, the identification of risk genes remains challenging. Motivated by the shared risk genes found in complex diseases and tissue-specific gene expression patterns, we propose as an Empirical Bayes approach to integrating Pleiotropy and Tissue-Specific information (EPS) for prioritizing risk genes...
June 15, 2016: Bioinformatics
Fernando S Goes, Mehdi Pirooznia, Jennifer S Parla, Melissa Kramer, Elena Ghiban, Senem Mavruk, Yun-Ching Chen, Eric T Monson, Virginia L Willour, Rachel Karchin, Matthew Flickinger, Adam E Locke, Shawn E Levy, Laura J Scott, Michael Boehnke, Eli Stahl, Jennifer L Moran, Christina M Hultman, Mikael Landén, Shaun M Purcell, Pamela Sklar, Peter P Zandi, W Richard McCombie, James B Potash
IMPORTANCE: Complex disorders, such as bipolar disorder (BD), likely result from the influence of both common and rare susceptibility alleles. While common variation has been widely studied, rare variant discovery has only recently become feasible with next-generation sequencing. OBJECTIVE: To utilize a combined family-based and case-control approach to exome sequencing in BD using multiplex families as an initial discovery strategy, followed by association testing in a large case-control meta-analysis...
June 1, 2016: JAMA Psychiatry
Zhihui Xie, Jing Li, Jonathan Baker, Kathie L Eagleson, Marcelo P Coba, Pat Levitt
BACKGROUND: Atypical synapse development and plasticity are implicated in many neurodevelopmental disorders (NDDs). NDD-associated, high-confidence risk genes have been identified, yet little is known about functional relationships at the level of protein-protein interactions, which are the dominant molecular bases responsible for mediating circuit development. METHODS: Proteomics in three independent developing neocortical synaptosomal preparations identified putative interacting proteins of the ligand-activated MET receptor tyrosine kinase, an autism risk gene that mediates synapse development...
February 26, 2016: Biological Psychiatry
Jaqueline Bohrer Schuch, Vanessa Rodrigues Paixão-Côrtes, Deise C Friedrich, Luciana Tovo-Rodrigues
Several autism spectrum disorders (ASD) exome studies suggest that coding single nucleotide variants (SNVs) play an important role on ASD etiology. Usually, the pathogenic effect of missense mutations is estimated through predictors that lose accuracy for those SNVs placed in intrinsically disordered regions of protein. Here, we used bioinformatics tools to investigate the effect of mutations described in ASD published exome studies (549 mutations) in protein disorder, considering post-translational modification, PEST and Molecular Recognition Features (MoRFs) motifs...
April 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Hao Yu, Lifang Wang, Luxian Lv, Cuicui Ma, Bo Du, Tianlan Lu, Chao Jin, Hao Yan, Yongfeng Yang, Wenqiang Li, Yanyan Ruan, Hongyan Zhang, Hongxing Zhang, Weifeng Mi, Bryan Mowry, Wenbin Ma, Keqing Li, Dai Zhang, Weihua Yue
BACKGROUND: Antipsychotic-induced weight gain (AIWG) is a serious concern in therapy with antipsychotic medications. To identify single nucleotide polymorphisms (SNPs) associated with AIWG, we conducted a genome-wide association study (GWAS) for antipsychotic treatment. METHODS: The discovery cohort consisted of 534 patients with schizophrenia, who underwent 8-week treatment with antipsychotics and were genotyped using the Illumina Human 610-Quad BeadChip. The independent replication cohort consisted of 547 patients with schizophrenia, treated with similar antipsychotics, and genotyped using the Sequenom MassARRAY platform...
May 2016: Schizophrenia Bulletin
Sinaya Vaisburd, Zeev Shemer, Adva Yeheskel, Eliezer Giladi, Illana Gozes
Mutated disrupted in schizophrenia 1 (DISC1), a microtubule regulating protein, leads to schizophrenia and other psychiatric illnesses. It is hypothesized that microtubule stabilization may provide neuroprotection in schizophrenia. The NAP (NAPVSIPQ) sequence of activity-dependent neuroprotective protein (ADNP) contains the SxIP motif, microtubule end binding (EB) protein target, which is critical for microtubule dynamics leading to synaptic plasticity and neuroprotection. Bioinformatics prediction for FDA approved drugs mimicking SxIP-like motif which displace NAP-EB binding identified Risperidone...
2015: Scientific Reports
Qiongshi Lu, Xinwei Yao, Yiming Hu, Hongyu Zhao
MOTIVATION: Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks...
February 15, 2016: Bioinformatics
Qi Liao, Yunliang Wang, Jia Cheng, Dongjun Dai, Xingyu Zhou, Yuzheng Zhang, Jinfeng Li, Honglei Yin, Shugui Gao, Shiwei Duan
Schizophrenia (SCZ) is one of the most complex mental illnesses affecting ~1% of the population worldwide. SCZ pathogenesis is considered to be a result of genetic as well as epigenetic alterations. Previous studies have aimed to identify the causative genes of SCZ. However, DNA methylation of long non-coding RNAs (lncRNAs) involved in SCZ has not been fully elucidated. In the present study, a comprehensive genome-wide analysis of DNA methylation was conducted using samples from two male patients with paranoid and undifferentiated SCZ, respectively...
November 2015: Molecular Medicine Reports
Ping Wang, Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Zheng Zhang, Wenjun Guo, Herbert M Lachman, Deyou Zheng
BACKGROUND: Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. METHODS: To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation...
2015: Molecular Autism
Maria Suntsova, Andrew Garazha, Alena Ivanova, Dmitry Kaminsky, Alex Zhavoronkov, Anton Buzdin
Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV...
October 2015: Cellular and Molecular Life Sciences: CMLS
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