DOCSLIB.ORG

Characterisation of Gene and Pathway Expression in Stabilised Blood from Children with Coeliac Disease

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterisation of Gene and Pathway Expression in Stabilised Blood from Children with Coeliac Disease Coeliac disease BMJ Open Gastroenterol: first published as 10.1136/bmjgast-2020-000536 on 15 December 2020. Downloaded from Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease Hanna Gustafsson Bragde ,1,2 Ulf Jansson,3 Mats Fredrikson,2 Ewa Grodzinsky,2 Jan Söderman1,2 To cite: Bragde HG, ABSTRACT Summary box Jansson U, Fredrikson M, Introduction A coeliac disease (CD) diagnosis is et al. Characterisation of likely in children with levels of tissue transglutaminase What is already known about this subject? gene and pathway expression autoantibodies (anti- TG2) >10 times the upper reference in stabilised blood from Paediatric coeliac disease (CD) diagnosis still re- value, whereas children with lower anti- TG2 levels need ► children with coeliac quires sampling and evaluation of small intestinal an intestinal biopsy to confirm or rule out CD.A blood disease. BMJ Open Gastro biopsies in many cases. sample is easier to obtain than an intestinal biopsy 2020;7:e000536. doi:10.1136/ Gene expression in small intestinal biopsies differs sample, and stabilised blood is suitable for routine ► bmjgast-2020-000536 between patients with active CD and patients with Universitets Bibliotek. Protected by copyright. diagnostics because transcript levels are preserved at non- CD. ► Additional material is sampling. Therefore, we investigated gene expression Blood is generally a more accessible sampling ma- published online only. To view in stabilised whole blood to explore the possibility of ► terial compared with small intestinal biopsies. please visit the journal online gene expression- based diagnostics for the diagnosis and (http:// dx. doi. org/ 10. 1136/ Stabilised blood is suitable for routine gene follow- up of CD. ► bmjgast- 2020- 000536). expression- based diagnostics because transcript Design We performed RNA sequencing of stabilised levels are preserved at sampling. whole blood from active CD cases (n=10), non- CD cases Received 4 September 2020 (n=10), and treated CD cases on a gluten- free diet (n=10) What are the new findings? Revised 5 November 2020 to identify diagnostic CD biomarkers and pathways Accepted 21 November 2020 ► Stabilised whole blood is not a suitable sample for involved in CD pathogenesis. clinical diagnostics of CD based on single genes. Results No single gene was differentially expressed ► Pathways of potential interest in CD have been between the sample groups. However, by using gene set identified. enrichment analysis (GSEA), significantly differentially expressed pathways were identified in active CD, and How might it impact on clinical practice in the these pathways involved the inflammatory response, foreseeable future? negative regulation of viral replication, translation, as well ► The results provide a potential starting point for the as cell proliferation, differentiation, migration, and survival. development of pathway- focused gene expression The results indicate that there are differences in pathway panels for CD. http://bmjopengastro.bmj.com/ regulation in CD, which could be used for diagnostic ► These findings add to the knowledge of CD purposes. Comparison between GSEA results based pathogenesis. on stabilised blood with GSEA results based on small intestinal biopsies revealed that type I interferon response, © Author(s) (or their defence response to virus, and negative regulation of viral symptomatic children with high levels (>10 employer(s)) 2020. Re- use replication were identified as pathways common to both times the upper reference value, URV) of permitted under CC BY- NC. No tissues. tissue transglutaminase autoantibodies (anti- commercial re- use. See rights Conclusions Stabilised whole blood is not a suitable 1 and permissions. Published TG2) if additional requirements are met. In sample for clinical diagnostics of CD based on single symptomatic children with anti- TG2 levels by BMJ. genes. However, diagnostics based on a pathway- focused 1 that are 1–10 times the URV, an intestinal on December 21, 2020 at Linkopings Laboratory Medicine, Region gene expression panel may be feasible, but requires Jönköping County, Jönköping, further investigation. biopsy is needed to confirm or rule out CD Sweden as a diagnosis. If the biopsy sample is Marsh 2 Department of Biomedical and grade 0 or 1, the diagnosis is unclear and Clinical Sciences, Linköping INTRODUCTION 1 University, Linköping, Sweden further investigations are recommended. 3Department of Paediatrics, Small intestinal biopsies have long been an In symptomatic IgA- competent patients with Region Jönköping County, essential part of coeliac disease (CD) diag- anti- TG2 <1 times the URV, a CD diagnosis Jönköping, Sweden nostics, but based on the recommendations is less likely, but not ruled out.1 Additional from the European Society for Paediatric biomarkers would aid in diagnosing CD; we Correspondence to Dr Hanna Gustafsson Bragde; Gastroenterology, Hepatology, and Nutri- previously investigated gene expression in hanna. gustafsson. bragde@ tion in 2012, the intestinal biopsy may small intestinal biopsies by RNA sequencing rjl. se be excluded from the diagnostic flow for and found differences in gene expression Bragde HG, et al. BMJ Open Gastro 2020;7:e000536. doi:10.1136/bmjgast-2020-000536 1 Open access BMJ Open Gastroenterol: first published as 10.1136/bmjgast-2020-000536 on 15 December 2020. Downloaded from in active CD cases versus non- CD cases that were detect- Study groups able also in CD cases with no or low-grade intestinal inju- Two study groups (table 1) were defined based on subjects ries (Marsh 0–1).2 However, blood is a more accessible on a gluten- containing diet: (1) group CDM3 with a CD sampling material than small intestinal biopsies that can diagnosis (histopathologic assessment Marsh 3B–3C and be sampled repeatedly to both diagnose and follow- up anti- TG2 >7 U/mL), (2) group M0 cleared from CD with patients with CD. RNA sequencing of CD4+ T cells (Marsh 0 and anti- TG2 ≤7 U/mL). A third study group and whole genome microarray transcriptome analysis of (table 1) was defined based on CD subjects at follow-up peripheral blood mononuclear cells from mainly adult on a GFD: (3) Group CDM0 (Marsh 0 and anti- TG2 CD cases have identified genes and pathways of interest ≤7 U/mL). Whole blood RNA samples were sequenced in CD.3–5 Because stabilised whole blood preserves tran- from all study subjects in all groups. Additionally, RNA script levels during collection, transport, and storage,6 samples from small intestinal biopsies from subjects in the use of stabilised whole blood would facilitate the groups M0 and CDM3 were sequenced. These subjects incorporation of gene expression-based diagnostics in were included as subgroups in a previous study involving clinical practice. We performed RNA sequencing of stabi- RNA sequencing of small intestinal biopsies.2 Based on lised whole blood from paediatric patients with active the previous analysis, one subject in group M0 was more CD, non- CD, and treated CD on a gluten- free diet (GFD) similar to Marsh 3 subjects, and therefore, that subject to identify potential CD diagnostic biomarkers and path- was excluded from all analyses. ways involved in CD pathogenesis. Sample collection and processing Sera were collected using blood tubes containing polymer METHODS gel and clot activator (Becton, Dickinson and Company, Universitets Bibliotek. Protected by copyright. Study subjects Franklin Lakes, New Jersey, USA). Serum levels of anti- Children and adolescents (<18 years of age) were TG2 and IgG antibodies against deamidated gliadin referred to Ryhov County Hospital in Jönköping, were determined using EliA-kits from Thermo Fisher Sweden with suspected CD or were followed-up after Scientific (Waltham, Massachusetts, USA) according to a period on a GFD to verify mucosal recovery. The Bragde et al.7 A cut- off of 7 U/mL was used. patients included in this study were enrolled during Blood for RNA isolation was collected in Tempus Blood the years 2009–2014, where biopsy samplings on GFD RNA tubes (Life Technologies, Carlsbad, California, were still performed as a part of the standard diagnostic USA), kept overnight at 4°C, and then stored at −20°C process for CD at the hospital. Most patients were until RNA isolation. Total RNA from stabilised blood was referred for small intestinal biopsy due to elevated anti- purified using the Tempus Spin RNA Isolation Reagent TG2 regardless of symptoms. Some children with anti- kit (Life Technologies) according to the manufactur- TG2 levels below the URV on a gluten- containing diet er’s instructions. RNA concentrations were determined (with or without selective IgA deficiency) were referred using the Qubit 2.0 Fluorometer and the Qubit RNA for biopsy to exclude CD. The patients provided written BR Assay Kit (Thermo Fisher Scientific). RNA integrity consent before blood and duodenal biopsy specimens was assessed using the Agilent 2100 Bioanalyzer with the were collected. Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa http://bmjopengastro.bmj.com/ Table 1 Descriptive statistics of the study groups No. of Age at biopsy Gender Marsh grade cases (years)* M/F (span) Anti- TG2*† (U/mL) Anti- DG*‡ (U/mL) HLA- DQ2.5cis§ M0 9 8.4 (2.2–17) 4/5 M0 0.29 (<0.10–1.3) 0.57 (<0.40–1.6) 67%, 22%, 11% CDM0 10 8.8 (3.0–17) 2/8 M0 2.3 (0.10–7.0) 2.5 (0.50–5.8) 10%, 70%, 20% CDM3 10 8.6 (2.3–16) 4/6 M3B–3C 600 (36–2858) 151 (9.0–781) 10%, 80%, 10% on December 21, 2020 at Linkopings Subjects in the M0 and CDM3 groups consumed a gluten- containing diet. Study subjects in group M0 did not receive a coeliac disease (CD) diagnosis, whereas a CD diagnosis was confirmed in study subjects in group CDM3. Group CDM0 contained subjects with a CD diagnosis who were followed- up after a period on a gluten- free diet. *Mean (min–max) †Levels of IgA autoantibodies against tissue transglutaminase (anti-TG2) in sera.
Load more

Recommended publications
  • A Genome-Wide Study of Blood Pressure in African Americans Accounting for Gene-Smoking Interaction Jacquelyn Y
    A Genome-wide study of blood pressure in African Americans accounting for gene-smoking interaction Jacquelyn Y. Taylor, Yale University Karen Schwander, Washington University in St. Louis Sharon L. R. Kardia, University of Michigan Donna Arnett, University of Alabama, Birmingham Jingjing Liang, Case Western Reserve University Steven C. Hunt, University of Utah D.C. Rao, Washington University in St. Louis Yan Sun, Emory University Journal Title: Scientific Reports Volume: Volume 6 Publisher: Nature Publishing Group | 2016-01-11, Pages 18812-18812 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.1038/srep18812 Permanent URL: https://pid.emory.edu/ark:/25593/rhb37 Final published version: http://dx.doi.org/10.1038/srep18812 Copyright information: © 2016, Macmillan Publishers Limited This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/). Accessed September 29, 2021 11:39 AM EDT www.nature.com/scientificreports OPEN A Genome-wide study of blood pressure in African Americans accounting for gene-smoking Received: 15 January 2015 Accepted: 09 November 2015 interaction Published: 11 January 2016 Jacquelyn Y. Taylor1, Karen Schwander2, Sharon L. R. Kardia3 & Donna Arnett4, Jingjing Liang5 Steven C. Hunt6, D.C. Rao2 & Yan V. Sun7,8 Cigarette smoking has been shown to be a health hazard. In addition to being considered a negative lifestyle behavior, studies have shown that cigarette smoking has been linked to genetic underpinnings of hypertension. Because African Americans have the highest incidence and prevalence of hypertension, we examined the joint effect of genetics and cigarette smoking on health among this understudied population.
    [Show full text]
  • Evolutionary Genomics of a Plastic Life History Trait: Galaxias Maculatus Amphidromous and Resident Populations
    EVOLUTIONARY GENOMICS OF A PLASTIC LIFE HISTORY TRAIT: GALAXIAS MACULATUS AMPHIDROMOUS AND RESIDENT POPULATIONS by María Lisette Delgado Aquije Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia August 2021 Dalhousie University is located in Mi'kma'ki, the ancestral and unceded territory of the Mi'kmaq. We are all Treaty people. © Copyright by María Lisette Delgado Aquije, 2021 I dedicate this work to my parents, María and José, my brothers JR and Eduardo for their unconditional love and support and for always encouraging me to pursue my dreams, and to my grandparents Victoria, Estela, Jesús, and Pepe whose example of perseverance and hard work allowed me to reach this point. ii TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ........................................................................................................... ix ABSTRACT ...................................................................................................................... xii LIST OF ABBREVIATION USED ................................................................................ xiii ACKNOWLEDGMENTS ................................................................................................ xv CHAPTER 1. INTRODUCTION ....................................................................................... 1 1.1 Galaxias maculatus ..................................................................................................
    [Show full text]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • Identification and Characterization of Tissue-Resident Memory T Cells in Humans Brahma Vencel Kumar
    Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar 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 2018 ©2017 Brahma Vencel Kumar All rights reserved ABSTRACT Identification and characterization of tissue-resident memory T cells in humans Brahma Vencel Kumar Memory T cells are critical for maintaining lifelong immunity by protecting against reinfection with previously encountered pathogens. In recent years, a subset of memory T cells termed tissue-resident memory T cells (TRM) has emerged as the primary mediator of protection at many tissue sites. Numerous studies in mice have demonstrated that TRM accelerate pathogen clearance compared with other subsets of memory T cells. The defining characteristic of TRM is that they are retained within tissues and do not circulate in the blood. The lack of TRM in blood has proved to be a barrier for investigating the role of TRM in healthy humans. As a result, there are many outstanding questions about TRM biology in humans, including which phenotypic markers identify TRM, if TRM represent a unique memory subset, as well as defining transcriptional and functional characteristics of this subset. Through a unique collaboration with the local organ procurement agency, we obtained samples from >15 tissue sites from healthy organ donors of all ages. We found that the surface marker CD69 was expressed by memory CD4 + and CD8 + T cells in multiple tissues including spleen and other lymphoid tissues, lung, and intestines, but not in blood, suggesting that this marker may identify TRM in human tissues.
    [Show full text]
  • 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
    [Show full text]
  • Table SI. Genes Upregulated ≥ 2-Fold by MIH 2.4Bl Treatment Affymetrix ID
    Table SI. Genes upregulated 2-fold by MIH 2.4Bl treatment Fold UniGene ID Description Affymetrix ID Entrez Gene Change 1558048_x_at 28.84 Hs.551290 231597_x_at 17.02 Hs.720692 238825_at 10.19 93953 Hs.135167 acidic repeat containing (ACRC) 203821_at 9.82 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 1559509_at 9.41 Hs.656636 202957_at 9.06 3059 Hs.14601 hematopoietic cell-specific Lyn substrate 1 (HCLS1) 202388_at 8.11 5997 Hs.78944 regulator of G-protein signaling 2 (RGS2) 213649_at 7.9 6432 Hs.309090 serine and arginine rich splicing factor 7 (SRSF7) 228262_at 7.83 256714 Hs.127951 MAP7 domain containing 2 (MAP7D2) 38037_at 7.75 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 224549_x_at 7.6 202672_s_at 7.53 467 Hs.460 activating transcription factor 3 (ATF3) 243581_at 6.94 Hs.659284 239203_at 6.9 286006 Hs.396189 leucine rich single-pass membrane protein 1 (LSMEM1) 210800_at 6.7 1678 translocase of inner mitochondrial membrane 8 homolog A (yeast) (TIMM8A) 238956_at 6.48 1943 Hs.741510 ephrin A2 (EFNA2) 242918_at 6.22 4678 Hs.319334 nuclear autoantigenic sperm protein (NASP) 224254_x_at 6.06 243509_at 6 236832_at 5.89 221442 Hs.374076 adenylate cyclase 10, soluble pseudogene 1 (ADCY10P1) 234562_x_at 5.89 Hs.675414 214093_s_at 5.88 8880 Hs.567380; far upstream element binding protein 1 (FUBP1) Hs.707742 223774_at 5.59 677825 Hs.632377 small nucleolar RNA, H/ACA box 44 (SNORA44) 234723_x_at 5.48 Hs.677287 226419_s_at 5.41 6426 Hs.710026; serine and arginine rich splicing factor 1 (SRSF1) Hs.744140 228967_at 5.37
    [Show full text]
  • Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
    Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus.
    [Show full text]
  • By Submitted in Partial Satisfaction of the Requirements for Degree of in In
    BCL6 maintains thermogenic capacity of brown adipose tissue during dormancy by Vassily Kutyavin DISSERTATION Submitted in partial satisfaction of the requirements for degree of DOCTOR OF PHILOSOPHY in Biomedical Sciences in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Approved: ______________________________________________________________________________Eric Verdin Chair ______________________________________________________________________________Ajay Chawla ______________________________________________________________________________Ethan Weiss ______________________________________________________________________________ ______________________________________________________________________________ Committee Members Copyright 2019 by Vassily Kutyavin ii Dedicated to everyone who has supported me during my scientific education iii Acknowledgements I'm very grateful to my thesis adviser, Ajay Chawla, for his mentorship and support during my dissertation work over the past five years. Throughout my time in his lab, I was always able to rely on his guidance, and his enthusiasm for science was a great source of motivation. Even when he was traveling, he could easily be reached for advice by phone or e- mail. I am particularly grateful for his help with writing the manuscript, which was probably the most challenging aspect of graduate school for me. I am also very grateful to him for helping me find a postdoctoral fellowship position. Ajay's inquisitive and fearless approach to science have been a great inspiration to me. In contrast to the majority of scientists who focus narrowly on a specific topic, Ajay pursued fundamental questions across a broad range of topics and was able to make tremendous contributions. My experience in his lab instilled in me a deep appreciation for thinking about the entire organism from an evolutionary perspective and focusing on the key questions that escape the attention of the larger scientific community. As I move forward in my scientific career, there is no doubt that I will rely on him as a role model.
    [Show full text]
  • Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Genomic Stress Response
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.08.330209; this version posted October 9, 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-ND 4.0 International license. 1 Isolating the role of corticosterone in the hypothalamic-pituitary-gonadal 2 genomic stress response 3 4 By: Suzanne H. Austin1, *, Rayna Harris1, April M. Booth1, Andrew S. Lang2, Victoria S. Farrar1, 5 Jesse S. Krause1, 3, Tyler A. Hallman4, Matthew MacManes2, and Rebecca M. Calisi1 6 7 1Department of Neurobiology, Physiology, and Behavior, University of California Davis, 1 8 Shields Avenue, Davis, CA, USA, 95616 9 2 Department of Molecular, Cellular and Biomedical Sciences, The University of New 10 Hampshire, 434 Gregg Hall, Durham, NH, USA, 03824 11 3 Department of Biology, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, USA, 12 89557-0314 13 4 Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, OR 14 97331 15 16 *Current address: 17 Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR, 18 USA, 97331; Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, 19 Corvallis, OR 97331 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.08.330209; this version posted October 9, 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.
    [Show full text]
  • Adaptive History of the Chimpanzee Subspecies in the Genomic Era
    Adaptive History of the Chimpanzee Subspecies in the Genomic Era Jessica Nye TESI DOCTORAL UPF 2018 Directors de la Tesi Jaume Bertranpetit i Hafid Laayouni CIÈNCIES EXPERIMENTALS I DE LA SALUT ii Acknowledgements I would like to thank my advisors Dr. Jaume Bertranpetit and Dr. Hafid Laayouni for guiding me during my doctoral research. I would like to thank my family and friends for supporting me during my many years of education. To my fellow lab mates, I am grateful for the theoretical discussions we had over the last four years. This work was supported by FI Agaur grant FI-DGR 2015. iii iv Abstract Chimpanzees are our closest living genetic cousins. The species consists of four subspecies, each with a unique demographic history. In order to better understand their species, a detailed map of signatures of selection will highlight important genetic differences between the four subspecies. Here, we interrogate the genome using 15 tests of selection. We simulate neutral and selective scenarios taking their unique demographic history into account in the model. We combine all these elements using a machine learning approach to highlight regions of interest in each subspecies. We specifically investigate the regions of the genome that have been selected after introgression with bonobo. We investigate the haplotype changes that have occurred since the divergence with humans in a few specially selected genes. From this, we find that the evolutionary history of each of the four subspecies is unique. That subtle differences in their demographic history and environment have greatly shaped their genetic diversity. In general, we observe signatures in selection in phenotypes involving immunity, muscle function, reproduction, and DNA repair.
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • Cellular and Molecular Aspects of the Response of the Testis to Nutrition In
    Cellular and molecular aspects of the response of the testis to nutrition in sexually mature sheep Yongjuan Guan 21004548 This thesis is presented for the degree of Doctor of Philosophy of The University of Western Australia School of Animal Biology Institute of Agriculture March 2015 Declaration Declaration The work presented in this thesis is original work of the author, and none of the material in this thesis has been submitted either in full, or part, for a degree at this university or any other universities or institutions before. The experimental designs and manuscript preparation were carried out by myself after discussion with my supervisors Prof Graeme Martin, A/Prof Irek Malecki and Dr Penny Hawken. Yongjuan Guan March 2015 1 Contents Contents Summary ....................................................................................................................................... 4 Acknowledgements ....................................................................................................................... 8 Publications ................................................................................................................................. 10 Chapter 1: General Introduction ................................................................................................. 12 Chapter 2: Literature Review ...................................................................................................... 16 2.1 Male reproduction ............................................................................................................
    [Show full text]