Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 'S Role in Working Memory
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A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Circular RNA Hsa Circ 0005114‑Mir‑142‑3P/Mir‑590‑5P‑ Adenomatous
ONCOLOGY LETTERS 21: 58, 2021 Circular RNA hsa_circ_0005114‑miR‑142‑3p/miR‑590‑5p‑ adenomatous polyposis coli protein axis as a potential target for treatment of glioma BO WEI1*, LE WANG2* and JINGWEI ZHAO1 1Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033; 2Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, P.R. China Received September 12, 2019; Accepted October 22, 2020 DOI: 10.3892/ol.2020.12320 Abstract. Glioma is the most common type of brain tumor APC expression with a good overall survival rate. UALCAN and is associated with a high mortality rate. Despite recent analysis using TCGA data of glioblastoma multiforme and the advances in treatment options, the overall prognosis in patients GSE25632 and GSE103229 microarray datasets showed that with glioma remains poor. Studies have suggested that circular hsa‑miR‑142‑3p/hsa‑miR‑590‑5p was upregulated and APC (circ)RNAs serve important roles in the development and was downregulated. Thus, hsa‑miR‑142‑3p/hsa‑miR‑590‑5p‑ progression of glioma and may have potential as therapeutic APC‑related circ/ceRNA axes may be important in glioma, targets. However, the expression profiles of circRNAs and their and hsa_circ_0005114 interacted with both of these miRNAs. functions in glioma have rarely been studied. The present study Functional analysis showed that hsa_circ_0005114 was aimed to screen differentially expressed circRNAs (DECs) involved in insulin secretion, while APC was associated with between glioma and normal brain tissues using sequencing the Wnt signaling pathway. In conclusion, hsa_circ_0005114‑ data collected from the Gene Expression Omnibus database miR‑142‑3p/miR‑590‑5p‑APC ceRNA axes may be potential (GSE86202 and GSE92322 datasets) and explain their mecha‑ targets for the treatment of glioma. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Independent Evidence for an Association Between General Cognitive Ability and a Genetic Locus for Educational Attainment J
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Hofstra Northwell Academic Works (Hofstra Northwell School of Medicine) Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2015 Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment J. W. Trampush Hofstra Northwell School of Medicine T. Lencz Hofstra Northwell School of Medicine S. Guha Northwell Health S. Mukherjee Northwell Health P. DeRosse Northwell Health See next page for additional authors Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Psychiatry Commons Recommended Citation Trampush JW, Lencz T, Guha S, Mukherjee S, DeRosse P, John M, Andreassen O, Deary I, Glahn D, Malhotra AK, . Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment. 2015 Jan 01; 168(5):Article 927 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/927. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. Authors J. W. Trampush, T. Lencz, S. Guha, S. Mukherjee, P. DeRosse, M. John, O. A. Andreassen, I. J. Deary, D. C. Glahn, A. K. Malhotra, and +41 additional authors This article is available at Donald and Barbara Zucker School of Medicine Academic Works: https://academicworks.medicine.hofstra.edu/articles/927 HHS Public Access Author manuscript Author Manuscript Author ManuscriptAm J Med Author Manuscript Genet B Neuropsychiatr Author Manuscript Genet. -
Genetic Influence on Cognitive Development Between Childhood
Molecular Psychiatry https://doi.org/10.1038/s41380-018-0277-0 ARTICLE Genetic influence on cognitive development between childhood and adulthood 1 1 1 2 3 Josephine Mollon ● Emma E. M. Knowles ● Samuel R. Mathias ● Ruben Gur ● Juan Manuel Peralta ● 4,5,6 4,5,6 2 3 7 1,8 Daniel J. Weiner ● Elise B. Robinson ● Raquel E. Gur ● John Blangero ● Laura Almasy ● David C. Glahn Received: 17 April 2018 / Revised: 15 August 2018 / Accepted: 11 September 2018 © Springer Nature Limited 2018 Abstract Successful cognitive development between childhood and adulthood has important consequences for future mental and physical wellbeing, as well as occupational and financial success. Therefore, delineating the genetic influences underlying changes in cognitive abilities during this developmental period will provide important insights into the biological mechanisms that govern both typical and atypical maturation. Using data from the Philadelphia Neurodevelopmental Cohort (PNC), a large population-based sample of individuals aged 8 to 21 years old (n = 6634), we used an empirical relatedness matrix to establish the heritability of general and specific cognitive functions and determine if genetic factors influence 1234567890();,: 1234567890();,: cognitive maturation (i.e., Gene × Age interactions) between childhood and early adulthood. We found that neurocognitive measures across childhood and early adulthood were significantly heritable. Moreover, genetic variance on general cognitive ability, or g, increased significantly between childhood and early adulthood. Finally, we did not find evidence for decay in genetic correlation on neurocognition throughout childhood and adulthood, suggesting that the same genetic factors underlie cognition at different ages throughout this developmental period. Establishing significant Gene × Age interactions in neurocognitive functions across childhood and early adulthood is a necessary first step in identifying genes that influence cognitive development, rather than genes that influence cognition per se. -
Whole‐Exome Sequencing in 20,197 Persons for Rare Variants In
RESEARCH PAPER Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer’s disease Neha S. Raghavan1,2, Adam M. Brickman1,2,3, Howard Andrews1,2,4, Jennifer J. Manly1,2,3, Nicole Schupf1,2,3,7, Rafael Lantigua1,6, Charles J. Wolock8, Sitharthan Kamalakaran8, Slave Petrovski8,9, Giuseppe Tosto1,2,3, Badri N. Vardarajan1,2,3,5, David B. Goldstein3,6,8, Richard Mayeux1,2,3,4,7 & The Alzheimer’s Disease Sequencing Projecta 1The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 2The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 3Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 4Department of Psychiatry, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 5Department of Systems Biology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 6Department of Medicine, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 7The Department of Epidemiology, Mailman School of Public Health, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, New York 8Institute of Genomic Medicine, Columbia University, The New York Presbyterian Hospital, New York, New York 9AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 0AA, United Kingdom Correspondence Abstract Richard Mayeux, Department of Neurology, Objective 710 West 168th Street, Columbia University, : The genetic bases of Alzheimer’s disease remain uncertain. -
Whole-Exome Sequencing Associates Novel CSMD1 Gene Mutations with Familial Parkinson Disease
Whole-exome sequencing associates novel CSMD1 gene mutations with familial Parkinson disease Javier Ruiz-Martínez, ABSTRACT MD, PhD Objective: Despite the enormous advancements made in deciphering the genetic architecture of Luis J. Azcona, BBA Parkinson disease (PD), the majority of PD is idiopathic, with single gene mutations explaining only Alberto Bergareche, MD a small proportion of the cases. Jose F. Martí-Massó, MD, Methods: In this study, we clinically evaluated 2 unrelated Spanish families diagnosed with PD, in PhD which known PD genes were previously excluded, and performed whole-exome sequencing anal- Coro Paisán-Ruiz, PhD yses in affected individuals for disease gene identification. Results: Patients were diagnosed with typical PD without relevant distinctive symptoms. Two dif- Correspondence to ferent novel mutations were identified in the CSMD1 gene. The CSMD1 gene, which encodes Dr. Paisán-Ruiz: a complement control protein that is known to participate in the complement activation and [email protected] inflammation in the developing CNS, was previously shown to be associated with the risk of PD in a genome-wide association study. Conclusions: We conclude that the CSMD1 mutations identified in this study might be responsible for the PD phenotype observed in our examined patients. This, along with previous reported studies, may suggest the complement pathway as an important therapeutic target for PD and other neurodegenerative diseases. Neurol Genet 2017;3:e177; doi: 10.1212/NXG.0000000000000177 GLOSSARY AD 5 Alzheimer disease; CCP 5 complement control protein; fPD 5 familial Parkinson disease; H&Y 5 Hoehn and Yahr; INDEL 5 insertions/deletions; LOPD 5 late-onset PD; PD 5 Parkinson disease; RBD 5 REM sleep behavior disorder; RLS 5 restless legs syndrome; SNV 5 single nucleotide variant; WES 5 whole-exome sequencing. -
Circular RNA Expression Profiles in Pediatric Ependymomas Ulvi Ahmadov1, Meile M
medRxiv preprint doi: https://doi.org/10.1101/2020.08.04.20167312; this version posted August 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Circular RNA expression profiles in pediatric ependymomas Ulvi Ahmadov1, Meile M. Bendikas2, Karoline K. Ebbesen2,3, Astrid M. Sehested4, Jørgen Kjems2,3, Helle Broholm5 and Lasse S. Kristensen1# 1. Department of Biomedicine, Aarhus University, Aarhus, Denmark 2. Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark 3. Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark 4. Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark 5. Department of Pathology, Center of Diagnostic Investigation, Rigshospitalet, Copenhagen, Denmark # corresponding author Running title: CircRNAs expression profiles in pediatric ependymomas Correspondence should be addressed to: Lasse Sommer Kristensen, PhD, Department of Biomedicine, Høegh- Guldbergs Gade 10, building 1116, room 268, Aarhus University, 8000 Aarhus, Denmark. Phone: +45 28880562, E-mail: [email protected] Key words: Pediatric ependymoma, pilocytic astrocytoma, medulloblastoma, circular RNA, RNA-sequencing, NanoString nCounter 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.08.04.20167312; this version posted August 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. -
Transcriptome Alterations of Vascular Smooth Muscle Cells in Aortic Wall of Myocardial Infarction Patients
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Wongsurawat, Thidathip; Woo, Chin Cheng; Giannakakis, Antonis; Lin, Xiao Yun; Cheow, Esther Sok Hwee; Lee, Chuen Neng; Richards, Mark; Sze, Siu Kwan; Nookaew, Intawat; Sorokin, Vitaly; Kuznetsov, Vladimir Andreevich 2018 Wongsurawat, T., Woo, C. C., Giannakakis, A., Lin, X. Y., Cheow, E. S. H., Lee, C. N., et al. (2018). Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients. Data in Brief, 17, 1112‑1135. https://hdl.handle.net/10356/85590 https://doi.org/10.1016/j.dib.2018.01.108 © 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Downloaded on 09 Oct 2021 06:21:01 SGT Data in Brief 17 (2018) 1112–1135 Contents lists available at ScienceDirect Data in Brief journal homepage: www.elsevier.com/locate/dib Data Article Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients Thidathip Wongsurawat a,b, Chin Cheng Woo c, Antonis Giannakakis a, Xiao Yun Lin d, Esther Sok Hwee Cheow e, Chuen Neng Lee c,d, Mark Richards f,g, Siu Kwan Sze e, Intawat Nookaew b, Vladimir A. Kuznetsov a,h, Vitaly Sorokin c,d,⁎ a Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), -
High Expression of PPFIA1 Is Associated with Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma
High Expression of PPFIA1 Is Associated With Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma Hongdian Zhang Tianjin Cancer Institute: Tianjin Tumor Hospital Ran Jia Tianjin Cancer Institute: Tianjin Tumor Hospital Yueyang Yang Tianjin Cancer Institute: Tianjin Tumor Hospital Zhilin Sui Tianjin Cancer Institute: Tianjin Tumor Hospital Wanyi Xiao Tianjin Cancer Institute: Tianjin Tumor Hospital Xianxian Wu Tianjin Cancer Institute: Tianjin Tumor Hospital Lei Gong Tianjin Cancer Institute: Tianjin Tumor Hospital Zhentao Yu National Cancer Center Peng Tang ( [email protected] ) Tianjin Cancer Institute: Tianjin Tumor Hospital https://orcid.org/0000-0002-5403-0817 Research article Keywords: Esophageal squamous cell carcinoma, PPFIA1, Bioinformatics analysis, Immunohistochemistry, Prognosis Posted Date: May 25th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-554718/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/24 Abstract Background: PTPRF interacting protein alpha 1 (PPFIA1) is reportedly related to the occurrence and progression of several types of malignancies. However, its role in esophageal squamous cell carcinoma (ESCC) remains unknown. We aimed to investigate the expression and clinical value of PPFIA1 in ESCC. Methods: The Oncomine, Gene Expression Proling Enrichment Analysis (GEPIA), and Gene Expression Omnibus (GEO) databases were utilized to explore PPFIA1 mRNA expression in esophageal cancer. The associations of PPFIA1 expression with clinicopathological variables and prognosis were evaluated in the GSE53625 dataset and veried in quantitative real-time polymerase chain reaction (qRT-PCR)-based cDNA array and immunohistochemistry (IHC)-based tissue microarray (TMA) datasets. The interactions between PPFIA1 and other genes based on the protein-protein interaction (PPI) network was analyzed via the STRING website. -
8P23.2-Pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature
G C A T T A C G G C A T genes Article 8p23.2-pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature Ilaria Catusi 1,* , Maria Garzo 1 , Anna Paola Capra 2 , Silvana Briuglia 2 , Chiara Baldo 3 , Maria Paola Canevini 4 , Rachele Cantone 5, Flaviana Elia 6, Francesca Forzano 7, Ornella Galesi 8, Enrico Grosso 5, Michela Malacarne 3, Angela Peron 4,9,10 , Corrado Romano 11 , Monica Saccani 4 , Lidia Larizza 1 and Maria Paola Recalcati 1 1 Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy; [email protected] (M.G.); [email protected] (L.L.); [email protected] (M.P.R.) 2 Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98100 Messina, Italy; [email protected] (A.P.C.); [email protected] (S.B.) 3 UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] (C.B.); [email protected] (M.M.) 4 Child Neuropsychiatry Unit—Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy; [email protected] (M.P.C.); [email protected] (A.P.); [email protected] (M.S.) 5 Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; [email protected] (R.C.); [email protected] (E.G.) 6 Unit of Psychology, Oasi Research Institute-IRCCS, -
Multivariate Analysis Reveals Genetic Associations of the Resting Default Mode Network in Psychotic Bipolar Disorder and Schizophrenia
Multivariate analysis reveals genetic associations of the resting default mode network in psychotic bipolar disorder and schizophrenia Shashwath A. Medaa,1, Gualberto Ruañob,c, Andreas Windemuthb, Kasey O’Neila, Clifton Berwisea, Sabra M. Dunna, Leah E. Boccaccioa, Balaji Narayanana, Mohan Kocherlab, Emma Sprootena, Matcheri S. Keshavand, Carol A. Tammingae, John A. Sweeneye, Brett A. Clementzf, Vince D. Calhoung,h,i, and Godfrey D. Pearlsona,h,j aOlin Neuropsychiatry Research Center, Institute of Living at Hartford Hospital, Hartford, CT 06102; bGenomas Inc., Hartford, CT 06102; cGenetics Research Center, Hartford Hospital, Hartford, CT 06102; dDepartment of Psychiatry, Beth Israel Deaconess Hospital, Harvard Medical School, Boston, MA 02215; eDepartment of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390; fDepartment of Psychology, University of Georgia, Athens, GA 30602; gThe Mind Research Network, Albuquerque, NM 87106; Departments of hPsychiatry and jNeurobiology, Yale University, New Haven, CT 06520; and iDepartment of Electrical and Computer Engineering, The University of New Mexico, Albuquerque, NM 87106 Edited by Robert Desimone, Massachusetts Institute of Technology, Cambridge, MA, and approved April 4, 2014 (received for review July 15, 2013) The brain’s default mode network (DMN) is highly heritable and is Although risk for psychotic illnesses is driven in small part by compromised in a variety of psychiatric disorders. However, ge- highly penetrant, often private mutations such as copy number netic control over the DMN in schizophrenia (SZ) and psychotic variants, substantial risk also is likely conferred by multiple genes bipolar disorder (PBP) is largely unknown. Study subjects (n = of small effect sizes interacting together (7). According to the 1,305) underwent a resting-state functional MRI scan and were “common disease common variant” (CDCV) model, one would analyzed by a two-stage approach.