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Identification of a Novel CHN1 P.(Phe213val) Variant in a Large Han Chinese Family with Congenital Duane Retraction Syndrome
www.nature.com/scientificreports OPEN Identifcation of a novel CHN1 p.(Phe213Val) variant in a large Han Chinese family with congenital Duane retraction syndrome Tai‑Cheng Zhou1,3, Wen‑Hua Duan1,3, Xiao‑Lin Fu2,3, Qin Zhu1, Li‑Yun Guo1, Yuan Zhou1, Zhi‑Juan Hua1, Xue‑Jiao Li1, Dong‑Mei Yang1, Jie‑Ying Zhang1, Jie Yin1, Xiao‑Fan Zhang1, Guang‑Long Zhou1 & Min Hu1* Duane retraction syndrome (DRS) is a neuromuscular dysfunction of the eyes. Although many causative genes of DRS have been identifed in Europe and the United States, few reports have been published in regard to Chinese DRS. The aim of the present study was to explore the genetic defect of DRS in a Chinese family. Exome sequencing was used to identify the disease‑causing gene for the two afected family members. Ophthalmic and physical examinations, as well as genetic screenings for variants in chimerin 1 (CHN1), were performed for all family members. Functional analyses of a CHN1 variant in 293T cells included a Rac‑GTP activation assay, α2‑chimaerin translocation assay, and co‑immunoprecipitation assay. Genetic analysis revealed a NM_001822.7: c.637T > G variant in the CHN1 gene, which resulted in the substitution of a highly conserved C1 domain with valine at codon 213 (NP_001813.1: p.(Phe213Val)) (ClinVar Accession Number: SCV001335305). In-silico analysis revealed that the p.(Phe213Val) substitution afected the protein stability and connections among the amino acids of CHN1 in terms of its tertiary protein structure. Functional studies indicated that the p.(Phe213Val) substitution reduced Rac‑GTP activity and enhanced membrane translocation in response to phorbol‑myristoyl acetate (PMA). -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Neuronal and Glial DNA Methylation and Gene Expression Changes in Early Epileptogenesis
RESEARCH ARTICLE Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis 1,2☯ 3☯ 3 4,5 Toni C. BergerID *, Magnus D. Vigeland , Hanne S. Hjorthaug , Lars Etholm , Cecilie G. Nome2, Erik Taubøll1,2, Kjell Heuser1,2³, Kaja K. Selmer3,4,6³ 1 Department of Neurology, Oslo University Hospital, Oslo, Norway, 2 University of Oslo, Oslo, Norway, 3 Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway, 4 National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway, 5 Department of Neurology, Section for Neurophysiology, Oslo University Hospital, Oslo, Norway, 6 Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, Oslo, Norway a1111111111 ☯ These authors contributed equally to this work. a1111111111 ³ KH and KKS also contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 Abstract Background and aims OPEN ACCESS Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons Citation: Berger TC, Vigeland MD, Hjorthaug HS, Etholm L, Nome CG, Taubøll E, et al. (2019) and glia, also referred to as epileptogenesis. No curative treatment options, apart from sur- Neuronal and glial DNA methylation and gene gery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epilep- expression changes in early epileptogenesis. PLoS togenesis and may serve as a novel therapeutic target. To our knowledge, this is the first ONE 14(12): e0226575. https://doi.org/10.1371/ study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in journal.pone.0226575 neurons and glia. Editor: Giuseppe Biagini, University of Modena and Reggio Emilia, ITALY Methods Received: July 18, 2019 We used the intracortical kainic acid injection model to elicit status epilepticus. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 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. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India 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/10.1101/2020.12.21.20248688; this version posted December 24, 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. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Systematic Analysis of Brain Lactate and Ph Levels in 65 Animal Models Related To
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.02.428362; this version posted February 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Full title: Systematic analysis of brain lactate and pH levels in 65 animal models related to 2 neuropsychiatric conditions 3 Short title: Brain lactate and pH in neuropsychiatric disorder models 4 Authors: Hideo Hagihara1,2, Hirotaka Shoji1,2, International Brain pH Project Consortium2, 5 and Tsuyoshi Miyakawa1,2* 6 Affiliations: 7 1 Division of Systems Medical Science, Institute for Comprehensive Medical Science, 8 Fujita Health University, Toyoake, Aichi 470-1192, Japan 9 2A full list of the authors in the International Brain pH Project Consortium is provided 10 at the end of the paper along with their affiliations and contributions. 11 *Corresponding Author: Tsuyoshi Miyakawa ([email protected]) 12 Keywords: lactate, pH, brain, neuropsychiatric disorders, animal models, working memory 13 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.02.428362; this version posted February 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 14 Abstract 15 Altered brain energy metabolism associated with increase in lactate levels and the 16 resultant decrease in pH have been increasingly implicated in multiple neuropsychiatric 17 disorders, such as schizophrenia, bipolar disorder, autism spectrum disorder and 18 neurodegenerative disorders. -
Supplementary Materials
Supplementary material. S1. Images from automatic imaging reader Cytation™ 1. A, A’, A’’ present the same field of view. Cells migrating from the upper compartment of the inserts are stained with DID (red color), Cell nuclei are stained with DAPI (blue color). A’ and A’’ demonstrate the method of analysis (A’ – nuclei numbering, A’’ – migrating cells numbering), scale bar – 300 µm. ASC BM-MSC Y BM-MSC A mean SEM mean SEM mean SEM CXCL6 2.240 0.727 4.158 0.677 2.149 1.816 CXCL16 4.277 0.248 0.763 0.405 1.130 0.346 CXCL12 -2.855 0.483 -4.528 0.226 -3.616 0.318 SMAD3 -0.511 0.191 -1.522 0.188 -1.332 0.215 TGFB2 3.742 0.533 1.238 0.210 0.990 0.568 COL14A 1.532 0.357 -0.397 0.736 -1.522 0.469 MHX 1.397 0.414 1.145 0.412 0.642 0.613 SCX 2.984 0.301 2.062 0.320 2.031 0.249 RUNX2 3.290 0.359 2.319 0.388 2.546 0.529 PPRAG 1.720 0.303 2.926 0.423 2.912 0.215 Supplementary material S3. The table provides the mean Δct and SEM values for all genes and all groups analyzed in this study (n=8 in each group). Supplementary material S2. The table provides the list of genes which displayed significantly different expression between hASCs and hBM-MSCs A based on microarray nr Exp p-value Exp Fold Change ID Symbol Entrez Gene Name 1 2.84E-05 16.896 16960355 TM4SF1 transmembrane 4 L six family member 1 2 9.10E-09 12.238 16684080 IFI6 interferon alpha inducible protein 6 3 3.93E-08 11.851 16667702 VCAM1 vascular cell adhesion molecule 1 4 1.54E-05 9.944 16840113 CXCL16 C-X-C motif chemokine ligand 16 5 2.01E-06 9.123 16852463 RAB27B RAB27B, member RAS oncogene -
Identification of RNA Bound to the TDP-43 Ribonucleoprotein Complex in the Adult Mouse Brain
Identification of RNA bound to the TDP-43 ribonucleoprotein complex in the adult mouse brain Running Title: Identification of RNA bound to TDP-43 Ramesh K. Narayanan1, Marie Mangelsdorf1, Ajay Panwar1, Tim J. Butler1, Peter G. Noakes1,2, Robyn H. Wallace1,3* 1Queensland Brain Institute, 2School of Biomedical Sciences, 3School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia *Corresponding author: [email protected] Objectives. Cytoplasmic inclusions containing TDP-43 are a pathological hallmark of several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. TDP-43 is an RNA binding protein involved in gene regulation through control of RNA transcription, splicing and transport. However, the function of TDP-43 in the nervous system is largely unknown and its role in the pathogenesis of ALS is unclear. The aim of this study was to identify genes in the central nervous system that are regulated by TDP-43. Methods. RNA-immunoprecipitation with anti-TDP-43 antibody, followed by microarray analysis (RIP- chip), was used to isolate and identify RNA bound to TDP-43 protein from mouse brain. Results. This analysis produced a list of 1,839 potential TDP-43 gene targets, many of which overlap with previous studies and whose functions include RNA processing and synaptic function. Immunohistochemistry demonstrated that the TDP-43 protein could be found at the presynaptic membrane of axon terminals in the neuromuscular junction in mice. Conclusions. The finding that TDP-43 binds to RNA that codes for genes related to synaptic function, together with the localisation of TDP-43 protein at axon terminals, suggest a role for TDP-43 in the transport of synaptic mRNAs into distal processes. -
Human CHN1 / Chimerin 1 Protein
Human CHN1 / Chimerin 1 Protein Catalog Number: 14914-HNCB General Information SDS-PAGE: Gene Name Synonym: ARHGAP2; CHN; DURS2; NC; RHOGAP2; 0610007I19Rik; 0710001E19Rik; 1700112L09Rik; 2900046J01Rik; AI413815; ARHGAP2 Protein Construction: A DNA sequence encoding the human CHN1 (NP_001813.1) (Ala2- Phe459) was fused with two additional amino acids (Gly&Pro) at the N- terminus. Source: Human Expression Host: Baculovirus-Insect Cells QC Testing Purity: > 90 % as determined by SDS-PAGE Protein Description Endotoxin: CHN1, also known as chimerin 1, is a TPase-activating protein for ras- < 1.0 EU per μg of the protein as determined by the LAL method related p21-rac and a phorbol ester receptor. It is predominantly expressed in neurons, and plays an important role in neuronal signal-transduction Stability: mechanisms. CHN1 is involved in the assembly of neuronal locomotor circuits as a direct effector of EPHA4 in axon guidance. The CHN1 gene Samples are stable for up to twelve months from date of receipt at -70 ℃ provides instructions for making two very similar proteins called α1- chimaerin and α2-chimaerin. These proteins play an important role in the Predicted N terminal: Gly early development of the nervous system. In particular, they help regulate Molecular Mass: complex chemical signaling pathways during the formation and development of nerve cells (neurons). These proteins help guide the The recombinant human CHN1 consists of 460 amino acids and has a growth of axons and dendrites, which are specialized extensions of calculated molecular mass of 53.2 kDa. The recombinant protein migrates neurons that transmit and receive nerve impulses throughout the nervous as an approximately 45 kDa band in SDS-PAGE under reducing conditions. -
Identification of Genetic Modifiers in Hereditary Spastic Paraplegias Due to SPAST/SPG4 Mutations Livia Parodi
Identification of genetic modifiers in Hereditary Spastic Paraplegias due to SPAST/SPG4 mutations Livia Parodi To cite this version: Livia Parodi. Identification of genetic modifiers in Hereditary Spastic Paraplegias due to SPAST/SPG4 mutations. Human health and pathology. Sorbonne Université, 2019. English. NNT : 2019SORUS317. tel-03141229 HAL Id: tel-03141229 https://tel.archives-ouvertes.fr/tel-03141229 Submitted on 15 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sorbonne Université Institut du Cerveau et de la Moelle Épinière École Doctorale Cerveau-Cognition-Comportement Thèse de doctorat en Neurosciences Identification of genetic modifiers in Hereditary Spastic Paraplegias due to SPAST/SPG4 mutations Soutenue le 9 octobre 2019 par Livia Parodi Membres du jury : Pr Bruno Stankoff Président Pr Lesley Jones Rapporteur Dr Susanne de Bot Rapporteur Pr Christel Depienne Examinateur Pr Cyril Goizet Examinateur Pr Alexandra Durr Directeur de thèse Table of contents Abbreviations _________________________________________________________ -
In Silico Search for Modifier Genes Associated with Pancreatic and Liver Disease in Cystic Fibrosis
RESEARCH ARTICLE In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis Pascal Trouve 1*, Emmanuelle GeÂnin1, Claude FeÂrec1,2,3,4 1 Inserm, UMR1078, Brest, France, 2 Universite de Bretagne Occidentale, Faculte de MeÂdecine et des sciences de la santeÂ, Brest, France, 3 C.H.U. Brest, HoÃpital Morvan, Laboratoire de GeÂneÂtique MoleÂculaire, Brest, France, 4 Etablissement FrancËais du Sang - Bretagne, Brest, France a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white popula- tion, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between OPEN ACCESS genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Citation: Trouve P, GeÂnin E, FeÂrec C (2017) In Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis. admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the PLoS ONE 12(3): e0173822. https://doi.org/ environment as well as modifier genes. Our objective was to highlight new modifier genes 10.1371/journal.pone.0173822 with potential implications in the lung, pancreatic and liver outcomes of the disease. For this Editor: Francisco X. Real, Centro Nacional de purpose we performed a system biology approach which combined, database mining, litera- Investigaciones Oncologicas, SPAIN ture mining, gene expression study and network analysis as well as pathway enrichment Received: September 26, 2016 analysis and protein-protein interactions. -
The Zebrafish Homologue of Mammalian Chimerin Rac-Gaps Is Implicated in Epiboly Progression During Development
The zebrafish homologue of mammalian chimerin Rac-GAPs is implicated in epiboly progression during development Federico Coluccio Leskow*, Beth A. Holloway†, HongBin Wang*, Mary C. Mullins†, and Marcelo G. Kazanietz*‡ Departments of *Pharmacology and †Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160 Edited by Brigid L. M. Hogan, Duke University Medical Center, Durham, NC, and approved February 1, 2006 (received for review September 30, 2005) In this paper, we report an in vivo model for the chimerins, a family Because chimerins have been found to be down-regulated in various of Rac GTPase-activating proteins (Rac-GAPs) that are uniquely types of cancers (7, 9), a tumor suppressor role for these Rac-GAPs regulated by the lipid second messenger diacylglycerol and have has been postulated. been implicated in the control of actin dynamics, migration, and The lack of in vivo models and limited information available in proliferation. We cloned the zebrafish homologue of mammalian lower organisms has represented a serious limitation in our under- ␣2-chimerin (chn1) and determined that it possesses Rac-GAP standing of the functional properties of chimerin Rac-GAPs. In this activity and a C1 domain with phorbol ester͞diacylglycerol-binding paper, we report the identification of the product of the zebrafish capability. chn1 morpholino knockdown embryos exhibit severe ␣-chimerin gene (chn1) and its functional characterization. To gain abnormalities, including the development of round somites, lack of further understanding on the role of chimerins in vivo,weused yolk extension, and a kinked posterior notochord. These zebrafish morpholino antisense oligonucleotides to knock down chn1 in morphants show Rac hyperactivation and progress faster through zebrafish.