Arf6-Driven Cell Invasion Is Intrinsically Linked to TRAK1-Mediated Mitochondrial Anterograde Trafficking to Avoid Oxidative Catastrophe
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
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. -
Systems Analysis Implicates WAVE2&Nbsp
JACC: BASIC TO TRANSLATIONAL SCIENCE VOL.5,NO.4,2020 ª 2020 THE AUTHORS. PUBLISHED BY ELSEVIER ON BEHALF OF THE AMERICAN COLLEGE OF CARDIOLOGY FOUNDATION. THIS IS AN OPEN ACCESS ARTICLE UNDER THE CC BY-NC-ND LICENSE (http://creativecommons.org/licenses/by-nc-nd/4.0/). PRECLINICAL RESEARCH Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects a b b b Jonathan J. Edwards, MD, Andrew D. Rouillard, PHD, Nicolas F. Fernandez, PHD, Zichen Wang, PHD, b c d d Alexander Lachmann, PHD, Sunita S. Shankaran, PHD, Brent W. Bisgrove, PHD, Bradley Demarest, MS, e f g h Nahid Turan, PHD, Deepak Srivastava, MD, Daniel Bernstein, MD, John Deanfield, MD, h i j k Alessandro Giardini, MD, PHD, George Porter, MD, PHD, Richard Kim, MD, Amy E. Roberts, MD, k l m m,n Jane W. Newburger, MD, MPH, Elizabeth Goldmuntz, MD, Martina Brueckner, MD, Richard P. Lifton, MD, PHD, o,p,q r,s t d Christine E. Seidman, MD, Wendy K. Chung, MD, PHD, Martin Tristani-Firouzi, MD, H. Joseph Yost, PHD, b u,v Avi Ma’ayan, PHD, Bruce D. Gelb, MD VISUAL ABSTRACT Edwards, J.J. et al. J Am Coll Cardiol Basic Trans Science. 2020;5(4):376–86. ISSN 2452-302X https://doi.org/10.1016/j.jacbts.2020.01.012 JACC: BASIC TO TRANSLATIONALSCIENCEVOL.5,NO.4,2020 Edwards et al. 377 APRIL 2020:376– 86 WAVE2 Complex in LVOTO HIGHLIGHTS ABBREVIATIONS AND ACRONYMS Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. -
TRAK1 (NM 014965) Human Recombinant Protein – TP304282 | Origene
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP304282 TRAK1 (NM_014965) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human trafficking protein, kinesin binding 1 (TRAK1), transcript variant 2 Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 77.1 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_055780 Locus ID: 22906 UniProt ID: Q9UPV9, B7ZAE5 RefSeq Size: 4623 Cytogenetics: 3p22.1 RefSeq ORF: 2064 Synonyms: EIEE68; MILT1; OIP106 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 TRAK1 (NM_014965) Human Recombinant Protein – TP304282 Summary: Involved in the regulation of endosome-to-lysosome trafficking, including endocytic trafficking of EGF-EGFR complexes and GABA-A receptors (PubMed:18675823). Involved in mitochondrial motility. When O-glycosylated, abolishes mitochondrial motility. Crucial for recruiting OGT to the mitochondrial surface of neuronal processes (PubMed:24995978). TRAK1 and RHOT form an essential protein complex that links KIF5 to mitochondria for light chain-independent, anterograde transport of mitochondria (By similarity).[UniProtKB/Swiss-Prot Function] Protein Families: Transcription Factors Product images: Coomassie blue staining of purified TRAK1 protein (Cat# TP304282). -
Mitoxplorer, a Visual Data Mining Platform To
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, Cecilia Garcia-Perez, José Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, et al. To cite this version: Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dy- namics and mutations. Nucleic Acids Research, Oxford University Press, 2020, 10.1093/nar/gkz1128. hal-02394433 HAL Id: hal-02394433 https://hal-amu.archives-ouvertes.fr/hal-02394433 Submitted on 4 Dec 2019 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. Distributed under a Creative Commons Attribution| 4.0 International License Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz1128 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim1,†, Prasanna Koti1,†, Adrien Bonnard2, Fabio Marchiano3, Milena Durrbaum¨ 1, Cecilia Garcia-Perez4, Jose Villaveces1, Salma Gamal1, Giovanni Cardone1, Fabiana Perocchi4, Zuzana Storchova1,5 and Bianca H. -
A Curated Database of Experimentally Identified Interaction Proteins Of
International Journal of Molecular Sciences Article OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT Junfeng Ma 1,* , Chunyan Hou 2, Yaoxiang Li 1 , Shufu Chen 3 and Ci Wu 1 1 Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA; [email protected] (Y.L.); [email protected] (C.W.) 2 Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; [email protected] 3 School of Engineering, Pennsylvania State University Behrend, Erie, PA 16563, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-202-6873802 Abstract: Interactions between proteins are essential to any cellular process and constitute the basis for molecular networks that determine the functional state of a cell. With the technical advances in recent years, an astonishingly high number of protein–protein interactions has been revealed. However, the interactome of O-linked N-acetylglucosamine transferase (OGT), the sole enzyme adding the O-linked β-N-acetylglucosamine (O-GlcNAc) onto its target proteins, has been largely undefined. To that end, we collated OGT interaction proteins experimentally identified in the past several decades. Rigorous curation of datasets from public repositories and O-GlcNAc-focused publications led to the identification of up to 929 high-stringency OGT interactors from multiple species studied (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Citation: Ma, J.; Hou, C.; Li, Y.; Chen, S.; Wu, C. OGT Protein Interaction Arabidopsis thaliana, and others). Among them, 784 human proteins were found to be interactors Network (OGT-PIN): A Curated of human OGT. -
Bioinformatics Analysis of Potential Key Genes and Mechanisms in Type 2 Diabetes Mellitus Basavaraj Vastrad1, Chanabasayya Vastrad*2
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.28.437386; this version posted March 29, 2021. 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. Bioinformatics analysis of potential key genes and mechanisms in type 2 diabetes mellitus 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, Karnataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2021.03.28.437386; this version posted March 29, 2021. 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 Type 2 diabetes mellitus (T2DM) is etiologically related to metabolic disorder. The aim of our study was to screen out candidate genes of T2DM and to elucidate the underlying molecular mechanisms by bioinformatics methods. Expression profiling by high throughput sequencing data of GSE154126 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between T2DM and normal control were identified. And then, functional enrichment analyses of gene ontology (GO) and REACTOME pathway analysis was performed. Protein–protein interaction (PPI) network and module analyses were performed based on the DEGs. Additionally, potential miRNAs of hub genes were predicted by miRNet database . Transcription factors (TFs) of hub genes were detected by NetworkAnalyst database. Further, validations were performed by receiver operating characteristic curve (ROC) analysis and real-time polymerase chain reaction (RT-PCR). -
Gene Ontology Functional Annotations and Pleiotropy
Network based analysis of genetic disease associations Sarah Gilman Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2013 Sarah Gilman All Rights Reserved ABSTRACT Network based analysis of genetic disease associations Sarah Gilman Despite extensive efforts and many promising early findings, genome-wide association studies have explained only a small fraction of the genetic factors contributing to common human diseases. There are many theories about where this “missing heritability” might lie, but increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying selection, and therefore may be particularly pertinent for neuropsychiatric disorders and other diseases with greatly reduced fecundity. Recently, several researchers have made great progress towards uncovering the genetics behind autism and schizophrenia. By sequencing families, they have found hundreds of de novo variants occurring only in affected individuals, both large structural copy number variants and single nucleotide variants. Despite studying large cohorts there has been little recurrence among the genes implicated suggesting that many hundreds of genes may underlie these complex phenotypes. The question -
Eutherian Adaptation from a TRAK-Like Protein, Conserved Gene Promoter Elements, and Localization in the Human Intestine Amanda L
Lumsden et al. BMC Evolutionary Biology (2016) 16:214 DOI 10.1186/s12862-016-0780-3 RESEARCH ARTICLE Open Access Huntingtin-associated protein 1: Eutherian adaptation from a TRAK-like protein, conserved gene promoter elements, and localization in the human intestine Amanda L. Lumsden1*, Richard L. Young2,3, Nektaria Pezos2,3 and Damien J. Keating1,2* Abstract Background: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved “HAP1_N” domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a “Milt/TRAK” domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response. We have investigated HAP1 function by examining its evolution, and upstream gene promoter sequences. We performed phylogenetic analyses of the HAP1_N domain family of proteins, incorporating HAP1 orthologues (identified by genomic synteny) from 5 vertebrate classes, and also searched the Dictyostelium proteome for a common ancestor. Computational analyses of mammalian HAP1 gene promoters were performed to identify phylogenetically conserved regulatory motifs. Results: We found that as recently as marsupials, HAP1 contained a Milt/TRAK domain and was more similar to TRAK1 and TRAK2 than to eutherian HAP1. The Milt/TRAK domain likely arose post multicellularity, as it was absent in the Dictyostelium proteome. It was lost from HAP1 in the eutherian lineage, and also from T27A3.1 in C. -
Expanding the Genetic Heterogeneity of Intellectual Disability Shams
Expanding the genetic heterogeneity of intellectual disability Shams Anazi*1, Sateesh Maddirevula*1, Yasmine T Asi2, Saud Alsahli1, Amal Alhashem3, Hanan E. Shamseldin1, Fatema AlZahrani1, Nisha Patel1, Niema Ibrahim1, Firdous M. Abdulwahab1, Mais Hashem1, Nadia Alhashmi4, Fathiya Al Murshedi4, Ahmad Alshaer12, Ahmed Rumayyan5,6, Saeed Al Tala7, Wesam Kurdi9, Abdulaziz Alsaman17, Ali Alasmari17, Mohammed M Saleh17, Hisham Alkuraya10, Mustafa A Salih11, Hesham Aldhalaan12, Tawfeg Ben-Omran13, Fatima Al Musafri13, Rehab Ali13, Jehan Suleiman14, Brahim Tabarki3, Ayman W El-Hattab15, Caleb Bupp18, Majid Alfadhel19, Nada Al-Tassan1,16, Dorota Monies1,16, Stefan Arold20, Mohamed Abouelhoda1,16, Tammaryn Lashley2, Eissa Faqeih17, Fowzan S Alkuraya1,3,16,21,18 *These authors have contributed equally 1Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. 2Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK. 3Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. 4Department of Genetics, College of Medicine, Sultan Qaboos University, Sultanate of Oman. 5King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia. 6Neurology Division, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia. 7Armed Forces Hospital Khamis Mushayt, Department of Pediatrics and Genetic Unit, Riyadh, Saudi Arabia. 9Department of Obstetrics and Gynecology, King Faisal Specialist Hospital, Riyadh, Saudi Arabia 10Department of Ophthalmology, Specialized Medical Center Hospital, Riyadh, Saudi Arabia. 11Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia. 12Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. 13Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Qatar. -
Genome Wide High Density SNP-Based Linkage Analysis of Childhood Absence Epilepsy Identifies a Susceptibility Locus on Chromosome 3P23-P14
Epilepsy Research (2009) 87, 247—255 journal homepage: www.elsevier.com/locate/epilepsyres Genome wide high density SNP-based linkage analysis of childhood absence epilepsy identifies a susceptibility locus on chromosome 3p23-p14 Barry A. Chioza a,1, Jean Aicardi b,2, Harald Aschauer c,3, Oebele Brouwer d,4, Petra Callenbach d,4, Athanasios Covanis e,5, Joseph M. Dooley f,6, Olivier Dulac g,7, Martina Durner h,8, Orvar Eeg-Olofsson i,9, Martha Feucht j,10, Mogens Laue Friis k,11, Renzo Guerrini l,12, Marianne Juel Kjeldsen m,13, Rima Nabbout g,7, Lina Nashef n,14, Thomas Sander o,p,15, Auli Sirén q,16, Elaine Wirrell r,17, Paul McKeigue s,18, Robert Robinson t,19, R. Mark Gardiner a,20, Kate V. Everett a,∗ Available online 17 October 2009 ∗ Corresponding author. Tel.: +44 2079052114; fax: +44 2074046191. E-mail addresses: [email protected] (B.A. Chioza), [email protected] (J. Aicardi), [email protected] (H. Aschauer), [email protected] (O. Brouwer), [email protected] (P. Callenbach), [email protected] (A. Covanis), [email protected] (J.M. Dooley), [email protected] (O. Dulac), [email protected] (M. Durner), [email protected] (O. Eeg-Olofsson), [email protected] (M. Feucht), [email protected] (M.L. Friis), [email protected] (R. Guerrini), [email protected] (M.J. Kjeldsen), [email protected] (R. Nabbout), [email protected] (L. -
Several Fusion Genes Identified in a Spermatic Cord Leiomyoma With
CANCER GENOMICS & PROTEOMICS 18 : 531-542 (2021) doi:10.21873/cgp.20278 Several Fusion Genes Identified in a Spermatic Cord Leiomyoma With Rearrangements of Chromosome Arms 3p and 21q IOANNIS PANAGOPOULOS 1, LUDMILA GORUNOVA 1, KRISTIN ANDERSEN 1, INGVILD LOBMAIER 2 and SVERRE HEIM 1,3 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 2Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 3Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway Abstract. Background/Aim: Benign smooth-muscle tumors, Leiomyomas are benign smooth -muscle tumors . They have leiomyomas, occur in nearly every organ but are most been described in nearly every organ but are most common common in the uterus. Whereas much is known about the in the uterus (fibroids) (1-5). genetics of uterine leiomyomas, little genetic information Much is known about the genetics , and hence the exists about leiomyomas of other organs. Here, we report pathogenesis, of uterine leiomyomas (6-9). In brief, most and discuss the genetic findings in a para-testicular uterine leiomyomas are cytogenetically characterized by the leiomyoma. Materials and Methods: Cytogenetic, array presence of one or more of the following cytogenetic comparative genomic hybridization (aCGH) RNA aberrations: t(12;14)(q15;q23–24) ; del(7)(q21.2q31.2) ; sequencing, reverse-transcription polymerase chain reaction rearrangements involving 6p21, 10q 22, and 1p ; trisomy 12 ; (RT- PCR), and Sanger sequencing analyses were performed deletions of 3q ; and changes of the X chromosome (10, 11). on a leiomyoma of the spermatic cord removed from a 61- These chromosomal aberrations rearrange and deregulate year-old man.