DOCSLIB.ORG

The Roles of KCNQ1 (Potassium Voltage-Gated Channel, KQT-Like Subfamily, Member 1) and CFTR (Cystic Fibrosis Transmembrane Condu

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Roles of KCNQ1 (Potassium Voltage-Gated Channel, KQT-Like Subfamily, Member 1) and CFTR (Cystic Fibrosis Transmembrane Condu The Roles of KCNQ1 (Potassium Voltage-Gated Channel, KQT-like Subfamily, Member 1) and CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) in Mouse and Human GI Cancers A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA By Bich Le Ngoc Than IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Thesis Advisors: Robert Cormier, Ph.D. and Patricia Scott, Ph.D. September, 2013 Copyright © 2013 Bich Le Ngoc Than Acknowledgements I would like to thank and acknowledge my thesis advisors, Drs. Robert Cormier and Patricia Scott, for their mentorship on this thesis research project. They have been instrumental in my scientific development, from experimental design to writing. They have also provided support and guidance during the course of my graduate journey, for which I greatly appreciate. I am thankful for the service of my committee members: Drs. Kendall Wallace, Lester Drewes, David Largaespada and Fekadu Kassie. I greatly appreciate the helpful comments and advice they provided during my graduate training experience. i Dedication I would like to dedicate this dissertation to my family. Without their trust and constant encouragement, I would not be the way I am today. I would like to thank my mother, Kim-Chung Le, for her unyielding support. She has been with me every step of the way and given me the inspiration to keep moving forward. I thank my brother, Thanh Than, for his encouragement and confidence in me to follow all of my aspirations. I thank my sister, Phuong-Cac Than, for her support to pursue and complete this degree. I would also like to dedicate this work to my late father who passed away during the first year of my graduate training. He instilled in me a sense of hard work and dedication toward my goals. For my family, I have propelled my career towards the field of medicine, knowing, step by step, my research may help thousands of cancer patients out of the place where those more fortunate have never ventured. ii Abstract The ion-channel genes Kcnq1 and Cftr were identified as gastrointestinal (GI) tract cancer susceptibility genes in multiple Sleeping Beauty DNA transposon-based forward genetic screens in mice. Kcnq1 encodes for the pore-forming alpha subunit of a voltage- gated potassium channel and Cftr encodes for the chloride conductance channel. These ion channels act together to maintain ion homeostasis in the cellular and extracellular environment. To confirm that Kcnq1 and Cftr have a functional role in GI tract cancer, mouse models in which targeted mutant alleles of Kcnq1 and Cftr were intogressed into the intestinal tumor susceptible ApcMin strain of mice. Results demonstrated that Kcnq1 mutant mice developed significantly more intestinal tumors, especially in the proximal small intestine and colon, with some of these tumors in the proximal small intestine progressing to adenocarcinomas. Gross tissue abnormalities and neoplasia were also observed in the rectum, pancreas and stomach. Similarly, Cftr mutant mice developed significantly more intestinal tumors, both in the colon and the entire small intestine. Colon organoid formation was significantly increased in organoids created from Kcnq1 mutant and Cftr mutant mice compared with wildtype littermate controls, suggesting a role for Kcnq1 and Cftr in regulation of the intestinal crypt stem cell compartment. To identify gene expression changes due to loss of Kcnq1 and Cftr, we carried out microarray studies in the colon and proximal small intestine. We identified an overlapping set of altered genes involved in innate immune responses, goblet and Paneth cell function, ion channels, intestinal stem cells, EGFR and other growth regulatory signaling pathways. We also found genes implicated in inflammation and in cellular detoxification. Pathway analysis using Ingenuity Pathway Analysis (IPA) and gene set enrichment analysis (GSEA) confirmed the importance of these gene clusters and further identified significant overlap with genes regulated by MUC2, another important regulator of intestinal homeostasis. To investigate the role of KCNQ1 in human colorectal cancer (CRC) we measured protein levels of KCNQ1 by immunohistochemistry in tissue microarrays containing samples from CRC patients with liver metastases who had undergone hepatic resection. Results showed that low expression of KCNQ1 expression was significantly associated with poor overall survival (OS). Our results indicate that both KCNQ1 and CFTR are potent tumor suppressor genes in GI cancer. Defining the mechanisms of action of KCNQ1 and CFTR, and elucidating the nature of their interactions in GI cancer can lead to their use as prognostic biomarkers and potential therapeutic targets for human cancers. iii Table of Contents ACKNOWLEDGEMENTS………………………………………………………..………i DEDICATION……………………………………………………………………...……..ii ABSTRACT………………………………………………………………………..…….iii TABLE OF CONTENTS…………………………………………………………...……iv LIST OF TABLES……………………………………………………………………….vi LIST OF FIGURES………………………………………………………………..……viii ABBREVIATIONS……………………………………………………………………...xii CHAPTER 1. Introduction – Battle against gastrointestinal cancer and the importance of targeted therapies The impact of CRC on society ………………………………………………….1 Risk factors contributing to CRC 1) Genetic factors…………………………………………………....……2 2) Environmental factors…………………………………………....…….3 The biology of the GI tract……………………………………………….………4 The biology of intestinal cancer…………………………………………….……8 Analysis of CRC mutational spectra……………………………………………17 Sleeping Beauty mutagenesis…………………………………………………...20 Ion channels……………………………………………………………...……...26 KCNQ1 (Kv7.1)………………………………………………………….29 CFTR…………………………………………………….……………….36 2. The role of KCNQ1 in mouse and human GI cancer……………………………..45 iv 3. The cystic fibrosis transmembrane conductance regulator (CFTR) is a tumor suppressor in the gastrointestinal tract…………………………………….…...141 4. Discussion Challenges in GI cancer…………………………………………..…………..164 Environmental Influences on GI cancer………………………………………165 KCNQ1 and CFTR………………………………………………..…………..166 Limitations in Our Studies…………………………………………..………..167 Implications for Human Diseases………………………………...…………..168 Potential Mechanisms of Action of KCNQ1 and CFTR…………..…………170 BIBLIOGRAPHY…………………………………………………………..…………..175 APPENDICES 1. A Sleeping Beauty transposon-mediated screen identifies murine susceptibility genes for adenomatous polyposis coli (Apc)-dependent intestinal tumorigenesis…………...…………………197 2. Loss of Kcnq1 delayed organoid differentiation in the small intestine of Apcwt mice……………………………………………….233 3. TCGA Report of: KCNQ1……………………………………………………………….…236 CFTR…………………………………………………………………....237 v List of Tables Chapter 2 Min Table 1. Loss of Kcnq1 enhances tumor multiplicity in Apc mice……………..…49 Min -/- Table 2. Apc Kcnq1 tumor phenotype is strongest in the proximal quarter of the small intestine……………………………………………..…49 Table 3. List of top known genes 1.5 fold (A) up-regulated and (B) down-regulated in -/- Kcnq1 mouse colons……………………..…..………..76-86 Table 4. List of top known genes 1.5 fold (A) up-regulated and (B) down-regulated in -/- Kcnq1 mouse small intestines……………….………86-118 Table 5. IPA Analysis of Colon Microarray……………………….……….…118-125 Table 6. IPA Analysis of Proximal Small Intestine Microarray……………………….…..126-136 Table 7. Core genes enriched in Kcnq1 KO…………………………………..136-137 Table 8. Expression of Areg……………………………………………….…..…..138 Table 9. Patient characteristics……………………………………………..…138-139 vi Chapter 3 Table 10. Top upregulated and downregulated genes identified by microarray in the small intestine………………….…..........151 Table 11. Top upregulated and downregulated genes identified by microarray in the colon…………………………..…………152 Appendices Table 12. Polyp number and age of death for transgenic mice………………….…202 Table 13. List of 33 CIS……………………………………………………………206 Table 14. LOH and MOH in ApcMin tumors based on the ratio of T:A trace peaks……………...………230 Table 15. Sequence read overlap between duplicate regions of a single GS FLX sequencing run………………230 Table 16. Human orthologous regions to the mouse CIS with recurrent chromosomal copy number changes based on published data………………..…230-231 Table 17. Knockdown of ApcMin CIS candidate genes affects viability of human colon cancer cells…………………………………………...…232 Table 18. Mapped transposon insertions in 96 tumors…………………………….232 vii List of Figures Chapter 1 Figure 1. The Anatomy of the Gastrointestinal Tract……………………………….5-6 Figure 2. The multi-layered organization of the mature GI tract…………………...6-7 Figure 3. Progression from Polyps to Cancer…………………………………………9 Figure 4. The organization of the small intestinal crypt-villus and the colon crypt…………………………………………………..…......10-11 Figure 5. Organization of the intestinal epithelium and the crypts of Lieberkühn and cell lineage determination in the intestinal epithelium……...…….12-13 Figure 6. Contribution of EMT to cancer progression………………………….…....17 Figure 7. Vogelgram……………………………………………………………...….18 Figure 8. Human Colorectal Cancer genome landscape……………………………..19 Figure 9. SB Transposon (T2/Onc2) can deregulate the expression of an oncogene or inactivate expression of a tumor suppressor gene…….…..21-22 Figure 10. Tissue-specific expression of the SB transposase…………………….….23 Figure 11. Scheme for validation of intestinal candidate cancer genes…...…………25 Figure 12. Structures of KCNE and KCNQ1 proteins………………………………30 Figure 13. CIS map of Kcnq1 in Apcwt screen………………………………………36 Figure 14. Proposed model of CFTR structure in the cell
Load more

Recommended publications
  • (ALDH1A3) for the Maintenance of Non-Small Cell Lung Cancer Stem Cells Is Associated with the STAT3 Pathway
    Author Manuscript Published OnlineFirst on June 6, 2014; DOI: 10.1158/1078-0432.CCR-13-3292 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Essential role of aldehyde dehydrogenase 1A3 (ALDH1A3) for the maintenance of non-small cell lung cancer stem cells is associated with the STAT3 pathway Chunli Shao1,2, James P. Sullivan3, Luc Girard1,2, Alexander Augustyn1,2, Paul Yenerall1,2, Jaime Rodriguez4, Hui Liu4, Carmen Behrens4, Jerry W. Shay5, Ignacio I. Wistuba4, John D. Minna 1,2,6,7 1Hamon Center for Therapeutic Oncology Research, 2Simmons Comprehensive Cancer Center, 3Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, 02114, 4Department of Translational Molecular Pathology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77054, 5Department of Cell Biology, 6Department of Pharmacology, 7Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA. Running Title: ALDH1A3 in non-small cell lung cancer stem cells Keywords: Lung cancer, cancer stem cells, ALDH1A3, STAT3, Stattic Financial Support This project was supported by CPRIT, NCI SPORE P50CA70907, UTSW Cancer Center Support Grant 5P30-CA142543, and the Gillson-Longenbaugh Foundation. Address Correspondence: John D. Minna, M.D. 6000 Harry Hines Blvd Dallas, TX 75390-8593 Hamon Center for Therapeutic Oncology Research UT Southwestern Medical Center Phone: 214-648-4900; Fax: 214-648-4940 [email protected] Disclosure of Potential Conflict of Interest The authors indicate no potential conflicts of interest. Word count: 4583 Total number of figures and tables: 6 figures Downloaded from clincancerres.aacrjournals.org on September 28, 2021. © 2014 American Association for Cancer Research.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2015/0337275 A1 Pearlman Et Al
    US 20150337275A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0337275 A1 Pearlman et al. (43) Pub. Date: Nov. 26, 2015 (54) BOCONVERSION PROCESS FOR Publication Classification PRODUCING NYLON-7, NYLON-7.7 AND POLYESTERS (51) Int. C. CI2N 9/10 (2006.01) (71) Applicant: INVISTATECHNOLOGIES S.a.r.l., CI2P 7/40 (2006.01) St. Gallen (CH) CI2PI3/00 (2006.01) CI2PI3/04 (2006.01) (72) Inventors: Paul S. Pearlman, Thornton, PA (US); CI2P 13/02 (2006.01) Changlin Chen, Cleveland (GB); CI2N 9/16 (2006.01) Adriana L. Botes, Cleveland (GB); Alex CI2N 9/02 (2006.01) Van Eck Conradie, Cleveland (GB); CI2N 9/00 (2006.01) Benjamin D. Herzog, Wichita, KS (US) CI2P 7/44 (2006.01) CI2P I 7/10 (2006.01) (73) Assignee: INVISTATECHNOLOGIES S.a.r.l., (52) U.S. C. St. Gallen (CH) CPC. CI2N 9/13 (2013.01); C12P 7/44 (2013.01); CI2P 7/40 (2013.01); CI2P 13/005 (2013.01); (21) Appl. No.: 14/367,484 CI2P 17/10 (2013.01); CI2P 13/02 (2013.01); CI2N 9/16 (2013.01); CI2N 9/0008 (2013.01); (22) PCT Fled: Dec. 21, 2012 CI2N 9/93 (2013.01); CI2P I3/04 (2013.01); PCT NO.: PCT/US2012/071.472 CI2P 13/001 (2013.01); C12Y 102/0105 (86) (2013.01) S371 (c)(1), (2) Date: Jun. 20, 2014 (57) ABSTRACT Embodiments of the present invention relate to methods for Related U.S. Application Data the biosynthesis of di- or trifunctional C7 alkanes in the (60) Provisional application No.
    [Show full text]
  • Autoantibodies in Neurological Diseases
    Autoantibodies in neurological diseases Hu, Ri, Yo, Tr CV2 Amphiphysin Amphiphysin GM1 Ma/Ta CV2 Amphiphysin Cerebellum Intestine Hippocampus Control transfection CV2 GM2 SOX1 PNMAP 2 (MMa2/Ta) Zic4 PNMP A2 GM3G ITPR1 (MMa2/Ta) RiR CARP YoY RiR GD1G a GAD Hippocampus HEp-2 cells Cerebellum NMDAR (transf. cells) Recoverin HuH Titin Anti-Hu positive Anti-NMDA-receptor positive YoY GD1G b Recoverin Gangliosides MAG HuH GT1b SOS X1 Myelin Aquaporin-4 Titin GQ1G b MOG Zic4 VGKC (LGI1 + CASPR2) Cerebellum Intestine Cerebellum Control transfection NMDA receptors GAD65G AMPA receptors Tr (DNER) GABAB receptors DPPX Control CoC ntrol CoC ntrol IgLON5 Hippocampus HEp-2 cells Optic nerve AQP-4 (transf. cells) Glycine receptors Anti-Yo positive Anti-aquaporin-4 positive AChR Indirect immunofl uorescence EUROLINE Examples of relevant target antigens EUROIMMUN AG · Seekamp 31 · 23560 Lübeck (Germany) · Tel +49 451/5855-0 · Fax 5855-591 · [email protected] · www.euroimmun.com 2 Autoantibodies IIFT pattern Test systems Anti-Hu (ANNA-1*) IIFT: Granular fl uorescence of almost all neuronal nuclei on the substrates cerebellum and hippocampus. The Autoantibodies against basic, RNA- cell nuclei of the plexus myentericus (intestinal tissue) binding proteins of the neuronal cell are also positive. nuclei of the central and peripheral nervous system EUROLINE: Positive reaction of the recombinant Hu antigen (HuD). Associated diseases: encephalomyelitis, subacute sensory neuronopathy (Denny-Brown syndrome), autonomous neuropathy Associated tumours: small-cell lung carcinoma, Cerebellum Intestine neuroblastoma Anti-Ri (ANNA-2*) IIFT: Granular fl uorescence of almost all neuronal nuclei on the substrates cerebellum and hippocampus. The Autoantibodies against neuronal cell substrate intestine (plexus myentericus) shows no reac- nuclei of the central nervous system tion.
    [Show full text]
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • A Cell Line P53 Mutation Type UM
    A Cell line p53 mutation Type UM-SCC 1 wt UM-SCC5 Exon 5, 157 GTC --> TTC Missense mutation by transversion (Valine --> Phenylalanine UM-SCC6 wt UM-SCC9 wt UM-SCC11A wt UM-SCC11B Exon 7, 242 TGC --> TCC Missense mutation by transversion (Cysteine --> Serine) UM-SCC22A Exon 6, 220 TAT --> TGT Missense mutation by transition (Tyrosine --> Cysteine) UM-SCC22B Exon 6, 220 TAT --> TGT Missense mutation by transition (Tyrosine --> Cysteine) UM-SCC38 Exon 5, 132 AAG --> AAT Missense mutation by transversion (Lysine --> Asparagine) UM-SCC46 Exon 8, 278 CCT --> CGT Missense mutation by transversion (Proline --> Alanine) B 1 Supplementary Methods Cell Lines and Cell Culture A panel of ten established HNSCC cell lines from the University of Michigan series (UM-SCC) was obtained from Dr. T. E. Carey at the University of Michigan, Ann Arbor, MI. The UM-SCC cell lines were derived from eight patients with SCC of the upper aerodigestive tract (supplemental Table 1). Patient age at tumor diagnosis ranged from 37 to 72 years. The cell lines selected were obtained from patients with stage I-IV tumors, distributed among oral, pharyngeal and laryngeal sites. All the patients had aggressive disease, with early recurrence and death within two years of therapy. Cell lines established from single isolates of a patient specimen are designated by a numeric designation, and where isolates from two time points or anatomical sites were obtained, the designation includes an alphabetical suffix (i.e., "A" or "B"). The cell lines were maintained in Eagle's minimal essential media supplemented with 10% fetal bovine serum and penicillin/streptomycin.
    [Show full text]
  • Towards Mutation-Specific Precision Medicine in Atypical Clinical
    International Journal of Molecular Sciences Review Towards Mutation-Specific Precision Medicine in Atypical Clinical Phenotypes of Inherited Arrhythmia Syndromes Tadashi Nakajima * , Shuntaro Tamura, Masahiko Kurabayashi and Yoshiaki Kaneko Department of Cardiovascular Medicine, Gunma University Graduate School of Medicine, Maebashi 371-8511, Gunma, Japan; [email protected] (S.T.); [email protected] (M.K.); [email protected] (Y.K.) * Correspondence: [email protected]; Tel.: +81-27-220-8145; Fax: +81-27-220-8158 Abstract: Most causal genes for inherited arrhythmia syndromes (IASs) encode cardiac ion channel- related proteins. Genotype-phenotype studies and functional analyses of mutant genes, using heterol- ogous expression systems and animal models, have revealed the pathophysiology of IASs and enabled, in part, the establishment of causal gene-specific precision medicine. Additionally, the utilization of induced pluripotent stem cell (iPSC) technology have provided further insights into the patho- physiology of IASs and novel promising therapeutic strategies, especially in long QT syndrome. It is now known that there are atypical clinical phenotypes of IASs associated with specific mutations that have unique electrophysiological properties, which raises a possibility of mutation-specific precision medicine. In particular, patients with Brugada syndrome harboring an SCN5A R1632C mutation exhibit exercise-induced cardiac events, which may be caused by a marked activity-dependent loss of R1632C-Nav1.5 availability due to a marked delay of recovery from inactivation. This suggests that the use of isoproterenol should be avoided. Conversely, the efficacy of β-blocker needs to be examined. Patients harboring a KCND3 V392I mutation exhibit both cardiac (early repolarization syndrome and Citation: Nakajima, T.; Tamura, S.; paroxysmal atrial fibrillation) and cerebral (epilepsy) phenotypes, which may be associated with a Kurabayashi, M.; Kaneko, Y.
    [Show full text]
  • Examining the Regulation of Kv7 K+ Channels in Airway Smooth Muscle Cells and Their Potential As Novel Therapeutic Targets for the Treatment of Asthma
    Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2017 Examining the Regulation of Kv7 K+ Channels in Airway Smooth Muscle Cells and Their Potential as Novel Therapeutic Targets for the Treatment of Asthma Jennifer Haick Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Pharmacology Commons Recommended Citation Haick, Jennifer, "Examining the Regulation of Kv7 K+ Channels in Airway Smooth Muscle Cells and Their Potential as Novel Therapeutic Targets for the Treatment of Asthma" (2017). Dissertations. 2588. https://ecommons.luc.edu/luc_diss/2588 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2017 Jennifer Haick LOYOLA UNIVERSITY CHICAGO EXAMINING THE REGULATION OF Kv7 K+ CHANNELS IN AIRWAY SMOOTH MUSCLE CELLS AND THEIR POTENTIAL AS NOVEL THERAPEUTIC TARGETS FOR THE TREATMENT OF ASTHMA A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN MOLECULAR PHARMACOLOGY AND THERAPEUTICS BY JENNIFER HAICK CHICAGO, IL MAY 2017 ACKNOWLEDGEMENTS I would like to take a moment to thank all of the people who have helped and supported me these past years while I have been working towards my Ph.D. First and foremost, I would like to thank Dr. Kenneth Byron for accepting me into his lab and for his mentorship these past years.
    [Show full text]
  • 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.
    [Show full text]
  • Transcriptomic Analysis of Native Versus Cultured Human and Mouse Dorsal Root Ganglia Focused on Pharmacological Targets Short
    bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. 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. Transcriptomic analysis of native versus cultured human and mouse dorsal root ganglia focused on pharmacological targets Short title: Comparative transcriptomics of acutely dissected versus cultured DRGs Andi Wangzhou1, Lisa A. McIlvried2, Candler Paige1, Paulino Barragan-Iglesias1, Carolyn A. Guzman1, Gregory Dussor1, Pradipta R. Ray1,#, Robert W. Gereau IV2, # and Theodore J. Price1, # 1The University of Texas at Dallas, School of Behavioral and Brain Sciences and Center for Advanced Pain Studies, 800 W Campbell Rd. Richardson, TX, 75080, USA 2Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine # corresponding authors [email protected], [email protected] and [email protected] Funding: NIH grants T32DA007261 (LM); NS065926 and NS102161 (TJP); NS106953 and NS042595 (RWG). The authors declare no conflicts of interest Author Contributions Conceived of the Project: PRR, RWG IV and TJP Performed Experiments: AW, LAM, CP, PB-I Supervised Experiments: GD, RWG IV, TJP Analyzed Data: AW, LAM, CP, CAG, PRR Supervised Bioinformatics Analysis: PRR Drew Figures: AW, PRR Wrote and Edited Manuscript: AW, LAM, CP, GD, PRR, RWG IV, TJP All authors approved the final version of the manuscript. 1 bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. 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]
  • Supplementary Table S1. Prioritization of Candidate FPC Susceptibility Genes by Private Heterozygous Ptvs
    Supplementary Table S1. Prioritization of candidate FPC susceptibility genes by private heterozygous PTVs Number of private Number of private Number FPC patient heterozygous PTVs in heterozygous PTVs in tumors with somatic FPC susceptibility Hereditary cancer Hereditary Gene FPC kindred BCCS samples mutation DNA repair gene Cancer driver gene gene gene pancreatitis gene ATM 19 1 - Yes Yes Yes Yes - SSPO 12 8 1 - - - - - DNAH14 10 3 - - - - - - CD36 9 3 - - - - - - TET2 9 1 - - Yes - - - MUC16 8 14 - - - - - - DNHD1 7 4 1 - - - - - DNMT3A 7 1 - - Yes - - - PKHD1L1 7 9 - - - - - - DNAH3 6 5 - - - - - - MYH7B 6 1 - - - - - - PKD1L2 6 6 - - - - - - POLN 6 2 - Yes - - - - POLQ 6 7 - Yes - - - - RP1L1 6 6 - - - - - - TTN 6 5 4 - - - - - WDR87 6 7 - - - - - - ABCA13 5 3 1 - - - - - ASXL1 5 1 - - Yes - - - BBS10 5 0 - - - - - - BRCA2 5 6 1 Yes Yes Yes Yes - CENPJ 5 1 - - - - - - CEP290 5 5 - - - - - - CYP3A5 5 2 - - - - - - DNAH12 5 6 - - - - - - DNAH6 5 1 1 - - - - - EPPK1 5 4 - - - - - - ESYT3 5 1 - - - - - - FRAS1 5 4 - - - - - - HGC6.3 5 0 - - - - - - IGFN1 5 5 - - - - - - KCP 5 4 - - - - - - LRRC43 5 0 - - - - - - MCTP2 5 1 - - - - - - MPO 5 1 - - - - - - MUC4 5 5 - - - - - - OBSCN 5 8 2 - - - - - PALB2 5 0 - Yes - Yes Yes - SLCO1B3 5 2 - - - - - - SYT15 5 3 - - - - - - XIRP2 5 3 1 - - - - - ZNF266 5 2 - - - - - - ZNF530 5 1 - - - - - - ACACB 4 1 1 - - - - - ALS2CL 4 2 - - - - - - AMER3 4 0 2 - - - - - ANKRD35 4 4 - - - - - - ATP10B 4 1 - - - - - - ATP8B3 4 6 - - - - - - C10orf95 4 0 - - - - - - C2orf88 4 0 - - - - - - C5orf42 4 2 - - - -
    [Show full text]
  • Analysis of Mouse Keratin 6A Regulatory Sequences in Transgenic Mice Reveals Constitutive, Tissue-Speci®C Expression by a Keratin 6A Minigene
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Analysis of Mouse Keratin 6a Regulatory Sequences in Transgenic Mice Reveals Constitutive, Tissue-Speci®c Expression by a Keratin 6a Minigene Donna Mahony, Seetha Karunaratne, Graham Cam,* and Joseph A. Rothnagel Department of Biochemistry and the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, and *Division of Animal Production, CSIRO, Blacktown, New South Wales, Australia The analysis of keratin 6 expression is complicated atin 6 expressing tissues, including the hair follicle, by the presence of multiple isoforms that are tongue, footpad, and nail bed, showing that both expressed constitutively in a number of internal stra- transgenes retained keratinocyte-speci®c expression. ti®ed epithelia, in palmoplantar epidermis, and in Quantitative analysis of b-galactosidase activity veri- the companion cell layer of the hair follicle. In addi- ®ed that both the 1.3 and 0.12 kb keratin 6a promo- tion, keratin 6 expression is inducible in interfollicu- ter constructs produced similar levels of the reporter. lar epidermis and the outer root sheath of the Notably, bothconstructs were constitutively follicle, in response to wounding stimuli, phorbol expressed in the outer root sheath and interfollicular esters, or retinoic acid. In order to establishthecriti- epidermis in the absence of any activating stimulus, cal regions involved in the regulation of keratin 6a suggesting that they lack the regulatory elements (the dominant isoform in mice), we generated trans- that normally silence transcription in these cells. This genic mice withtwo different-sized mouse keratin 6a study has revealed that a keratin 6a minigene con- constructs containing either 1.3 kb or 0.12 kb of 5¢ tains critical cis elements that mediate tissue-speci®c ¯anking sequence linked to the lacZ reporter gene.
    [Show full text]
  • Transcriptome Sequencing and Genome-Wide Association Analyses Reveal Lysosomal Function and Actin Cytoskeleton Remodeling in Schizophrenia and Bipolar Disorder
    Molecular Psychiatry (2015) 20, 563–572 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder Z Zhao1,6,JXu2,6, J Chen3,6, S Kim4, M Reimers3, S-A Bacanu3,HYu1, C Liu5, J Sun1, Q Wang1, P Jia1,FXu2, Y Zhang2, KS Kendler3, Z Peng2 and X Chen3 Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental disorders with high heritability. Clinicians have long noticed the similarities of clinic symptoms between these disorders. In recent years, accumulating evidence indicates some shared genetic liabilities. However, what is shared remains elusive. In this study, we conducted whole transcriptome analysis of post-mortem brain tissues (cingulate cortex) from SCZ, BPD and control subjects, and identified differentially expressed genes in these disorders. We found 105 and 153 genes differentially expressed in SCZ and BPD, respectively. By comparing the t-test scores, we found that many of the genes differentially expressed in SCZ and BPD are concordant in their expression level (q ⩽ 0.01, 53 genes; q ⩽ 0.05, 213 genes; q ⩽ 0.1, 885 genes). Using genome-wide association data from the Psychiatric Genomics Consortium, we found that these differentially and concordantly expressed genes were enriched in association signals for both SCZ (Po10 − 7) and BPD (P = 0.029). To our knowledge, this is the first time that a substantially large number of genes show concordant expression and association for both SCZ and BPD. Pathway analyses of these genes indicated that they are involved in the lysosome, Fc gamma receptor-mediated phagocytosis, regulation of actin cytoskeleton pathways, along with several cancer pathways.
    [Show full text]