DOCSLIB.ORG

Identifying Novel Disease-Associated Variants and Understanding The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identifying Novel Disease-Associated Variants and Understanding The Identifying Novel Disease-variants and Understanding the Role of the STAT1-STAT4 Locus in SLE A dissertation submitted to the Graduate School of University of Cincinnati In partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Immunology Graduate Program of the College of Medicine by Zubin H. Patel B.S., Worcester Polytechnic Institute, 2009 John B. Harley, M.D., Ph.D. Committee Chair Gurjit Khurana Hershey, M.D., Ph.D Leah C. Kottyan, Ph.D. Harinder Singh, Ph.D. Matthew T. Weirauch, Ph.D. Abstract Systemic Lupus Erythematosus (SLE) or lupus is an autoimmune disorder caused by an overactive immune system with dysregulation of both innate and adaptive immune pathways. It can affect all major organ systems and may lead to inflammation of the serosal and mucosal surfaces. The pathogenesis of lupus is driven by genetic factors, environmental factors, and gene-environment interactions. Heredity accounts for a substantial proportion of SLE risk, and the role of specific genetic risk loci has been well established. Identifying the specific causal genetic variants and the underlying molecular mechanisms has been a major area of investigation. This thesis describes efforts to develop an analytical approach to identify candidate rare variants from trio analyses and a fine-mapping analysis at the STAT1-STAT4 locus, a well-replicated SLE-risk locus. For the STAT1-STAT4 locus, subsequent functional biological studies demonstrated genotype dependent gene expression, transcription factor binding, and DNA regulatory activity. Rare variants are classified as variants across the genome with an allele-frequency less than 1% in ancestral populations. Identifying these variants remains a statistical and logistical challenge due to the large number of individuals needed for a well-powered study. Currently, trio-based approaches are used to identify disease-associated rare variants. We developed a novel analytical approach to analyze high depth sequencing data from trio-studies to nominate candidate disease associated rare variants. Our approach uses multiple low-stringency filters to remove the sequencing artifacts while leaving true variation for the analysis. We tested our approach using trio data generated from three different DNA sources and increased our concordance rate from 96% to 99.999% between the three different DNA sources. We implemented our analytical approach in an analytical suite CASSI (Cincinnati Analytical Suite for Sequencing Informatics) for use by the research community at large. ii Common variants are defined as variants with a minor allele frequency greater than 1%. Many common variants are associated with lupus through GWA studies and targeted sequencing studies. One of the well-replicated lupus associations is in the STAT1-STAT4 locus. Over 25 studies have identified this association in multiple different ancestries, but a causal variant has not been identified. Using a fine-mapping analysis with complementary frequentist and Bayesian approaches, we nominate a single-nucleotide polymorphism, rs11889341, as causal. We show that this variant is shared across all ancestries in our trans-ancestral discovery and replication cohorts. We also validate the allele-dependent functionality of this variant through an expression quantitative trait loci, by identifying differential transcription factor binding, and by showing an allelic gene-regulatory element. Overall, our analytical approaches allow for the identification and functional biology validation of novel risk variants, both common and rare. Our biological experiments provide insight into a potential mechanism to explain the association between rs11889341 and lupus-risk. iii This page is intentionally left blank iv Acknowledgements The work described in this thesis would not have been possible without the support and guidance of the following individuals. I would like to thank my PhD mentor Dr. John B Harley for providing me with invaluable guidance and mentorship throughout my PhD. His efforts in securing funding for my project has allowed me to use state-of-the-art analytical and experimental technologies throughout my studies. He has challenged me to improve as a scientist and allowed me to experience some failures throughout my PhD so that I may learn and improve myself. I would like to thank Dr. Kenneth Kaufman, who has generously offered his time and expertise to help me develop as a bioinformatician. He patiently taught me about next-generation sequencing and helped me develop the CASSI story. He has always made himself available to answer my questions regarding the genetic datasets, while I was analyzing the STAT1-STAT4 locus. I would like to thank Dr. Louis Muglia for going above and beyond his role as my Senior Physician-Scientist mentor. Dr. Muglia has been an advocate for me throughout my PhD and has offered key-insights into my projects. I have always enjoyed my quarterly meetings with him, where I have been able to talk with him about not only my research, but also other my non- research life. I would like to thank Dr. Harinder Singh for serving on my thesis committee and for his mentorship throughout my PhD studies. He has challenged me during my committee meetings and made me a more sophisticated thinker. It has been a privilege to learn from a pioneer in the field of transcription factor signaling. I would like to thank Arthur Lynch, Joshua Lee, Connor Schroeder, and Avery Maddox for their help with the cloning projects. v I would like to thank Dr. David Hildeman for providing me with encouragement and critical feedback during my first couple of years in graduate schools. I would like to thank Isabel Castro for all of her help with navigating the administrative intricacies of graduate school. Isabel has always been willing to answer the numerous questions I have had regarding graduate school paperwork. I would like to thank Dr. Neeru Hershey for serving on my PhD committee and for leading the MD/PhD program at UC. On my committee Dr. Hershey has provided helpful critical feedback to improve my scientific thinking. Outside of my committee, Dr. Hershey has always been a great physician-scientist role model. She has always been receptive of my feedback. She has worked tirelessly to improve the MD/PhD program. I have reaped the benefits of her tireless work as an MD/PhD student. I would like to thank Dr. Erin Zoller for her critical feedback throughout my graduate studies. Erin has challenged me from the first day to think through the scientific method. Her constant critical feedback allowed me to develop as a scientist. I would like to thank Daniel Miller for being a great friend and a colleague. Daniel has been invaluable as a resource to help me troubleshoot my experiments and to help me improve my experiments. I would like to thank Carmy Forney for being a great friend and colleague. She provided invaluable help with the luciferase experiments. I would like to thank Xiaoming Lu for being a great friend and fellow graduate student. Xiaoming has provided me with a great deal of guidance throughout my PhD project. We have had the opportunity to collaborate on projects with each other and learn from each other’s’ experience. Xiaoming has also been a great sounding-board for my analytical and experimental ideas. I would like to thank Dr. Matthew Weirauch for his invaluable mentorship. He graciously agreed to be a co-mentor for my application to join the Multidisciplinary Training Grant. As my co- vi mentor, Matt has provided valuable feedback for experiments validating my genetic findings in the STAT1-STAT4 locus. Matt has always provided me critical feedback on my oral presentations and helped me improve as a presenter. I owe a great deal of gratitude to Dr. Leah C. Kottyan. She has always been an advocate and mentor for me. I would not have been able to get through my graduate studies without her support and mentorship. She has always been available to help me through both my analyses and experiments. She has advocated for me throughout graduate school. Through her constant mentorship, I have become a better scientist. I would like to dedicate this Thesis to my parents, Hasmukh and Madhuri Patel, and my wife Shradha Patel. I would not have had the opportunity to study in a PhD program without the efforts of my parents in immigrating to this country. My success has been on the foundation of their sacrifices. A special thanks goes to Shradha for being a supportive partner through the highs and lows of graduate school. She has been patient and understanding throughout my graduate studies. A special thanks goes to my brother Kaushal Patel, who started graduate school with me. It has been great to have someone with whom I can commiserate and celebrate the downs and ups of graduate studies. vii Table of Contents Abstract .................................................................................................................................... ii Acknowledgements ................................................................................................................. v Table of Contents ................................................................................................................... viii List of Tables and Figures ......................................................................................................xii List of Abbreviations ..............................................................................................................xv Chapter 1: Introduction ..........................................................................................................
Load more

Recommended publications
  • Download.Cse.Ucsc.Edu/ Early Age of Onset (~2.5 Years) of This PRA Form in Goldenpath/Canfam2/Database/) Using Standard Settings
    Kropatsch et al. Canine Genetics and Epidemiology (2016) 3:7 DOI 10.1186/s40575-016-0037-x RESEARCH Open Access A large deletion in RPGR causes XLPRA in Weimaraner dogs Regina Kropatsch1*, Denis A. Akkad1, Matthias Frank2, Carsten Rosenhagen3, Janine Altmüller4,5, Peter Nürnberg4,6,7, Jörg T. Epplen1,8 and Gabriele Dekomien1 Abstract Background: Progressive retinal atrophy (PRA) belongs to a group of inherited retinal disorders associated with gradual vision impairment due to degeneration of retinal photoreceptors in various dog breeds. PRA is highly heterogeneous, with autosomal dominant, recessive or X-linked modes of inheritance. In this study we used exome sequencing to investigate the molecular genetic basis of a new type of PRA, which occurred spontaneously in a litter of German short-hair Weimaraner dogs. Results: Whole exome sequencing in two PRA-affected Weimaraner dogs identified a large deletion comprising the first four exons of the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene known to be involved in human retinitis pigmentosa and canine PRA. Screening of 16 individuals in the corresponding pedigree of short-hair Weimaraners by qPCR, verified the deletion in hemizygous or heterozygous state in one male and six female dogs, respectively. The mutation was absent in 88 additional unrelated Weimaraners. The deletion was not detectable in the parents of one older female which transmitted the mutation to her offspring, indicating that the RPGR deletion represents a de novo mutation concerning only recent generations of the Weimaraner breed in Germany. Conclusion: Our results demonstrate the value of an existing DNA biobank combined with exome sequencing to identify the underlying genetic cause of a spontaneously occurring inherited disease.
    [Show full text]
  • ERAP2 Facilitates a Subpeptidome of Birdshot Uveitis-Associated HLA-A29
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.250654; this version posted August 14, 2020. 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 Title: 2 ERAP2 facilitates a subpeptidome of Birdshot Uveitis-associated 3 HLA-A29 4 5 W.J. Venema 1,2, S. Hiddingh1,2 , J.H. de Boer 1, F.H.J. Claas 3, A Mulder3 , A.I. Den Hollander4 , 6 E. Stratikos 5, S. Sarkizova 6,7, G.M.C. Janssen 8, P.A. van Veelen 8, J.J.W. Kuiper 1,2* 7 8 1. Department of Ophthalmology, University Medical Center Utrecht, University of 9 Utrecht, Utrecht, Netherlands. 10 2. Center for Translational Immunology, University Medical Center Utrecht, University of 11 Utrecht, Utrecht, Netherlands. 12 3. Department of Immunology, Leiden University Medical Center, Leiden, the 13 Netherlands 14 4. Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, 15 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The 16 Netherlands. 17 5. National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece 18 6. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. 19 7. Broad Institute of MIT and Harvard, Cambridge, MA, USA. 20 8. Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 21 the Netherlands. 22 23 * Corresponding author; email: [email protected] 24 25 ABSTRACT (words: 199): 26 27 Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects 28 HLA-A29-positive individuals.
    [Show full text]
  • Isoform-Specific Monobody Inhibitors of Small Ubiquitin-Related Modifiers Engineered Using Structure-Guided Library Design
    Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design Ryan N. Gilbretha, Khue Truongb, Ikenna Madub, Akiko Koidea, John B. Wojcika, Nan-Sheng Lia, Joseph A. Piccirillia,c, Yuan Chenb, and Shohei Koidea,1 aDepartment of Biochemistry and Molecular Biology, and cDepartment of Chemistry, University of Chicago, 929 East 57th Street, Chicago, IL 60637; and bDepartment of Molecular Medicine, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010 Edited by David Baker, University of Washington, Seattle, WA, and approved March 16, 2011 (received for review February 10, 2011) Discriminating closely related molecules remains a major challenge which SUMOylation alters protein function appears to be in the engineering of binding proteins and inhibitors. Here we through SUMO-mediated interactions with other proteins con- report the development of highly selective inhibitors of small ubi- taining a short peptide motif known as a SUMO-interacting motif quitin-related modifier (SUMO) family proteins. SUMOylation is (SIM) (4, 7, 8). involved in the regulation of diverse cellular processes. Functional There are few inhibitors of SUMO/SIM interactions, a defi- differences between two major SUMO isoforms in humans, SUMO1 ciency that limits our ability to finely dissect SUMO biology. In and SUMO2∕3, are thought to arise from distinct interactions the only reported example of such an inhibitor, a SIM-containing mediated by each isoform with other proteins containing SUMO- linear peptide was used to inhibit SUMO/SIM interactions, estab- interacting motifs (SIMs). However, the roles of such isoform- lishing their importance in coordinating DNA repair by nonho- specific interactions are largely uncharacterized due in part to the mologous end joining (9).
    [Show full text]
  • Supplementary Information
    Supplementary Information PathwayMatcher: multi-omics pathway mapping and proteoform network generation Luis Francisco Hernández Sánchez1,2,3, Bram Burger4,5, Carlos Horro4,5, Antonio Fabregat3, Stefan Johansson1,2, Pål Rasmus Njølstad1,6, Harald Barsnes4,5, Henning Hermjakob3,7, and Marc Vaudel1,2,* 1 K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway 2 Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway 3 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom 4 Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway 5 Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway 6 Department of Pediatrics, Haukeland University Hospital, Bergen, Norway 7 Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing, China * To whom correspondence should be addressed Abstract Mapping biomedical data to functional knowledge is an essential task in biomedicine and can be achieved by querying gene or protein identifiers in pathway knowledgebases. Here, we demonstrate that including fine-granularity information such as post-translational modifications greatly increases the specificity of the analysis. We present PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher), a bioinformatic application for mapping multi-omics data to pathways and show how this enables the
    [Show full text]
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Stromal Senp1 Promotes Mouse Early Folliculogenesis by Regulating BMP4
    Tan et al. Cell Biosci (2017) 7:36 DOI 10.1186/s13578-017-0163-5 Cell & Bioscience RESEARCH Open Access Stromal Senp1 promotes mouse early folliculogenesis by regulating BMP4 expression Shu Tan1†, Boya Feng2†, Mingzhu Yin1, Huanjiao Jenny Zhou1, Ge Lou3, Weidong Ji2, Yonghao Li4 and Wang Min1,2* Abstract Background: Mammalian folliculogenesis, maturation of the ovarian follicles, require both growth factors derived from oocyte and surrounding cells, including stromal cells. However, the mechanism by which stromal cells and derived factors regulate oocyte development remains unclear. Results: We observed that SENP1, a small ubiquitin-related modifer (SUMO)-specifc isopeptidase, was expressed in sm22α-positive stromal cells of mouse ovary. The sm22α-positive stromal cells tightly associated with follicle matura- tion. By using the sm22α-specifc Cre system, we show that mice with a stromal cell-specifc deletion of SENP1 exhibit attenuated stroma-follicle association, delayed oocyte growth and follicle maturation with reduced follicle number and size at early oocyte development, leading to premature ovarian failure at late stages of ovulating life. Mechanistic studies suggest that stromal SENP1 defciency induces down-regulation of BMP4 in stromal cells concomitant with decreased expression of BMP4 receptor BMPR1b and BMPR2 on oocytes. Conclusions: Our data support that protein SUMOylation-regulating enzyme SENP1 plays a critical role in early ovar- ian follicle development by regulating gene expression of BMP4 in stroma and stroma-oocyte communication. Background mechanisms, selected primordial follicles recruit a single Folliculogenesis is the maturation of the ovarian folli- layer of cuboidal granulosa cells with oocytes grow inside cle, a densely packed shell of somatic cells that contains to form primary follicles, which in turn mature into an immature oocyte.
    [Show full text]
  • An Overview on ERAP Roles in Infectious Diseases
    cells Review An Overview on ERAP Roles in Infectious Diseases 1,2, , 1, 2,3 1 Irma Saulle * y, Chiara Vicentini y, Mario Clerici and Mara Biasin 1 Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; [email protected] (C.V.); [email protected] (M.B.) 2 Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy; [email protected] 3 IRCCS Fondazione Don Carlo Gnocchi, 20157 Milan, Italy * Correspondence: [email protected]; Tel.: +39-0250319679 These authors equally contributed to this work. y Received: 13 February 2020; Accepted: 12 March 2020; Published: 14 March 2020 Abstract: Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are crucial enzymes shaping the major histocompatibility complex I (MHC I) immunopeptidome. In the ER, these enzymes cooperate in trimming the N-terminal residues from precursors peptides, so as to generate optimal-length antigens to fit into the MHC class I groove. Alteration or loss of ERAPs function significantly modify the repertoire of antigens presented by MHC I molecules, severely affecting the activation of both NK and CD8+ T cells. It is, therefore, conceivable that variations affecting the presentation of pathogen-derived antigens might result in an inadequate immune response and onset of disease. After the first evidence showing that ERAP1-deficient mice are not able to control Toxoplasma gondii infection, a number of studies have demonstrated that ERAPs are control factors for several infectious organisms. In this review we describe how susceptibility, development, and progression of some infectious diseases may be affected by different ERAPs variants, whose mechanism of action could be exploited for the setting of specific therapeutic approaches.
    [Show full text]
  • The Struggle to Find Reliable Results in Exome Sequencing Data
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE METHODS ARTICLEprovided by Frontiers - Publisher Connector published: 12 February 2014 doi: 10.3389/fgene.2014.00016 The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors Zubin H. Patel 1,2 †, Leah C. Kottyan1,3 †, Sara Lazaro1,3 , Marc S. Williams 4 , David H. Ledbetter 4 , GerardTromp 4 , Andrew Rupert 5 , Mojtaba Kohram 5 , Michael Wagner 5 , Ammar Husami 6 , Yaping Qian 6 , C. Alexander Valencia 6 , Kejian Zhang 6 , Margaret K. Hostetter 7 , John B. Harley 1,3 and Kenneth M. Kaufman1,3 * 1 Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA 2 Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA 3 Department of Veterans Affairs, Veterans Affairs Medical Center – Cincinnati, Cincinnati, OH, USA 4 Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA 5 Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA 6 Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA 7 Division of Infectious Disease, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA Edited by: Next Generation Sequencing studies generate a large quantity of genetic data in a Helena Kuivaniemi, Geisinger Health relatively cost and time efficient manner and provide an unprecedented opportunity to System, USA identify candidate causative variants that lead to disease phenotypes. A challenge to these Reviewed by: studies is the generation of sequencing artifacts by current technologies. To identify and Tatiana Foroud, Indiana University School of Medicine, USA characterize the properties that distinguish false positive variants from true variants, we Goo Jun, University of Michigan, USA sequenced a child and both parents (one trio) using DNA isolated from three sources *Correspondence: (blood, buccal cells, and saliva).
    [Show full text]
  • Biological and Prognostic Significance of Chromosome 5Q Deletions in Myeloid Malignancies Aristoteles A.N
    Review Biological and Prognostic Significance of Chromosome 5q Deletions in Myeloid Malignancies Aristoteles A.N. Giagounidis,1Ulrich Germing,2 and Carlo Aul1 Abstract The presence of del(5q), either as the sole karyotypic abnormality or as part of a more complex karyotype, has distinct clinical implications for myelodysplastic syndromes (MDS) and acute myeloid leukemia. The 5qÀ syndrome, a subtype of low-riskMDS, is characterized by an isolated 5q deletion and <5% blasts in the bone marrow and can serve as a useful model for studying the role of 5q deletions in the pathogenesis and prognosis of myeloid malignancies. Recent clinical results with lenalidomide, an oral immunomodulatory drug, have shown durable erythroid responses, including transfusion independence and complete cytogenetic remissions in patients with del(5q) MDS with or without additional chromosomal abnormalities. These results indicate that lenalidomide can overcome the pathogenic effect of 5q deletion in MDS and restore bone marrow balance. The data provide important new insights into the pathobiology of 5q chromo- somal deletions in myeloid malignancies. Cytogenetic abnormalities are detected in the bone marrow of preponderance, refractory macrocytic anemia, normal or high over 50% of patients diagnosed with primary myelodysplastic platelet counts, hypolobulated megakaryocytes, and modest syndromes (MDS) or myeloid leukemias, and up to 80% of leukopenia (11, 14, 17). The prognosis is favorable in 5qÀ patients with secondary or therapy-related MDS (1, 2). These syndrome with relatively low risk of transformation to AML abnormalities can be characterized as being balanced or (11, 18). Although the limits of 5q deletions vary among unbalanced (3, 4). Balanced cytogenetic abnormalities include patients with 5qÀ syndrome, the most frequent deletion is reciprocal translocations, inversions, and insertions (3, 5, 6).
    [Show full text]
  • SENP1-Mediated Desumoylation of USP28 Regulated HIF-1Α
    Du et al. Cancer Cell Int (2019) 19:4 https://doi.org/10.1186/s12935-018-0722-9 Cancer Cell International PRIMARY RESEARCH Open Access SENP1‑mediated deSUMOylation of USP28 regulated HIF‑1α accumulation and activation during hypoxia response Shi‑chun Du1†, Lan Zhu2†, Yu‑xing Wang3†, Jie Liu3, Die Zhang3, Yu‑lu Chen3, Qing Peng4, Wei Liu2* and Bin Liu3* Abstract Background: The ubiquitin-specifc protease 28 (USP28) is an oncogenic deubiquitinase, which plays a critical role in tumorigenesis via antagonizing the ubiquitination and degradation of tumor suppressor protein FBXW7-mediated oncogenic substrates. USP28 controls hypoxia-dependent angiogenesis and metastasis by preventing FBXW7- dependent hypoxia-inducible transcription factor-1α (HIF-1α) degradation during hypoxia. However, it remains unclear how USP28 activation and HIF-1α signaling are coordinated in response to hypoxia. Methods: The in vitro deubiquitinating activity assay was used to determine the regulation of USP28 by hypoxia. The co-immunoprecipitation and GST Pull-down assays were used to determine the interaction between USP28 and SENP1. The in vivo deSUMOylation assay was performed to determine the regulation of USP28 by SENP1. The lucif‑ erase reporter assay was used to determine the transcriptional activity of HIF-1α. Results: Here, we report that USP28 is a SUMOylated protein in normoxia with moderate deubiquitinating activity towards HIF-1α in vitro, while hypoxia and HIF-1α activate USP28 through SENP1-mediated USP28 deSUMOylation to further accumulate HIF-1α protein in cells. In agreement with this, a SUMOylation mutant USP28 showed enhanced ability to increase HIF-1α level as well as control the transcriptional activity of HIF-1α.
    [Show full text]
  • Influence of ERAP1 and ERAP2 Gene Polymorphisms on Disease
    Human Immunology 80 (2019) 325–334 Contents lists available at ScienceDirect Human Immunology journal homepage: www.elsevier.com/locate/humimm Influence of ERAP1 and ERAP2 gene polymorphisms on disease T susceptibility in different populations ⁎ Yufeng Yaoa,b, Nannan Liua, Ziyun Zhoua, Li Shia,b, a Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China b Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China ARTICLE INFO ABSTRACT Keywords: The endoplasmic reticulum aminopeptidases (ERAPs), ERAP1 and ERAP2, makes a role in shaping the HLA class ERAP1 I peptidome by trimming peptides to the optimal size in MHC-class I-mediated antigen presentation and edu- ERAP2 cating the immune system to differentiate between self-derived and foreign antigens. Association studies have Polymorphism shown that genetic variations in ERAP1 and ERAP2 genes increase susceptibility to autoimmune diseases, in- Disease association fectious diseases, and cancers. Both ERAP1 and ERAP2 genes exhibit diverse polymorphisms in different po- Population genetic background pulations, which may influence their susceptibly to the aforementioned diseases. In this article, we reviewthe distribution of ERAP1 and ERAP2 gene polymorphisms in various populations; discuss the risk or protective influence of these gene polymorphisms in autoimmune diseases, infectious diseases, and cancers; and highlight how ERAP genetic variations can influence disease associations. 1. ERAP gene introduction to CD8+ T cells [1,2]. ERAPs have been found to trim peptides to the optimal size for MHC-I binding [3,4] but can also over-trim and destroy 1.1. ERAPs play an important role in the antigen presentation process MHC-I ligands.
    [Show full text]
  • SUMO, a Small, but Powerful, Regulator of Double- Strand Break Repair Garvin, Alexander; Morris, Jo
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Birmingham Research Portal SUMO, a small, but powerful, regulator of double- strand break repair Garvin, Alexander; Morris, Jo DOI: 10.1098/rstb.2016.0281 License: Creative Commons: Attribution (CC BY) Document Version Publisher's PDF, also known as Version of record Citation for published version (Harvard): Garvin, AJ & Morris, JR 2017, 'SUMO, a small, but powerful, regulator of double-strand break repair', Royal Society of London. Proceedings B. Biological Sciences, vol. 372, no. 1731, 20160281. https://doi.org/10.1098/rstb.2016.0281 Link to publication on Research at Birmingham portal General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. •Users may freely distribute the URL that is used to identify this publication. •Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. •User may use extracts from the document in line with the concept of ‘fair dealing’ under the Copyright, Designs and Patents Act 1988 (?) •Users may not further distribute the material nor use it for the purposes of commercial gain. Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document.
    [Show full text]