Inflammatory Bowel Disease
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Systems and Chemical Biology Approaches to Study Cell Function and Response to Toxins
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by MSc. Yingying Jiang born in Shandong, China Oral-examination: Systems and chemical biology approaches to study cell function and response to toxins Referees: Prof. Dr. Rob Russell Prof. Dr. Stefan Wölfl CONTRIBUTIONS The chapter III of this thesis was submitted for publishing under the title “Drug mechanism predominates over toxicity mechanisms in drug induced gene expression” by Yingying Jiang, Tobias C. Fuchs, Kristina Erdeljan, Bojana Lazerevic, Philip Hewitt, Gordana Apic & Robert B. Russell. For chapter III, text phrases, selected tables, figures are based on this submitted manuscript that has been originally written by myself. i ABSTRACT Toxicity is one of the main causes of failure during drug discovery, and of withdrawal once drugs reached the market. Prediction of potential toxicities in the early stage of drug development has thus become of great interest to reduce such costly failures. Since toxicity results from chemical perturbation of biological systems, we combined biological and chemical strategies to help understand and ultimately predict drug toxicities. First, we proposed a systematic strategy to predict and understand the mechanistic interpretation of drug toxicities based on chemical fragments. Fragments frequently found in chemicals with certain toxicities were defined as structural alerts for use in prediction. Some of the predictions were supported with mechanistic interpretation by integrating fragment- chemical, chemical-protein, protein-protein interactions and gene expression data. Next, we systematically deciphered the mechanisms of drug actions and toxicities by analyzing the associations of drugs’ chemical features, biological features and their gene expression profiles from the TG-GATEs database. -
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. -
Enteric Alpha Defensins in Norm and Pathology Nikolai a Lisitsyn1*, Yulia a Bukurova1, Inna G Nikitina1, George S Krasnov1, Yuri Sykulev2 and Sergey F Beresten1
Lisitsyn et al. Annals of Clinical Microbiology and Antimicrobials 2012, 11:1 http://www.ann-clinmicrob.com/content/11/1/1 REVIEW Open Access Enteric alpha defensins in norm and pathology Nikolai A Lisitsyn1*, Yulia A Bukurova1, Inna G Nikitina1, George S Krasnov1, Yuri Sykulev2 and Sergey F Beresten1 Abstract Microbes living in the mammalian gut exist in constant contact with immunity system that prevents infection and maintains homeostasis. Enteric alpha defensins play an important role in regulation of bacterial colonization of the gut, as well as in activation of pro- and anti-inflammatory responses of the adaptive immune system cells in lamina propria. This review summarizes currently available data on functions of mammalian enteric alpha defensins in the immune defense and changes in their secretion in intestinal inflammatory diseases and cancer. Keywords: Enteric alpha defensins, Paneth cells, innate immunity, IBD, colon cancer Introduction hydrophobic structure with a positively charged hydro- Defensins are short, cysteine-rich, cationic peptides philic part) is essential for the insertion into the micro- found in vertebrates, invertebrates and plants, which bial membrane and the formation of a pore leading to play an important role in innate immunity against bac- membrane permeabilization and lysis of the microbe teria, fungi, protozoa, and viruses [1]. Mammalian [10]. Initial recognition of numerous microbial targets is defensins are predominantly expressed in epithelial cells a consequence of electrostatic interactions between the of skin, respiratory airways, gastrointestinal and geni- defensins arginine residues and the negatively charged tourinary tracts, which form physical barriers to external phospholipids of the microbial cytoplasmic membrane infectious agents [2,3], and also in leukocytes (mostly [2,5]. -
Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis
fgene-12-697514 July 5, 2021 Time: 19:1 # 1 ORIGINAL RESEARCH published: 09 July 2021 doi: 10.3389/fgene.2021.697514 Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis Zi-An Chen1, Yu-Feng Sun1, Quan-Xu Wang1, Hui-Hui Ma1, Zhi-Zhao Ma2* and Chuan-Jie Yang1* 1 Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China, 2 Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China Background: Ulcerative colitis (UC) is a chronic, complicated, inflammatory disease with an increasing incidence and prevalence worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of UC have not yet been fully elucidated. Methods: All UC datasets published in the GEO database were analyzed and Edited by: Shulan Tian, summarized. Subsequently, the robust rank aggregation (RRA) method was used to Mayo Clinic, United States identify differentially expressed genes (DEGs) between UC patients and controls. Gene Reviewed by: functional annotation and PPI network analysis were performed to illustrate the potential Espiridión Ramos-Martínez, Universidad Nacional Autónoma functions of the DEGs. Some important functional modules from the protein-protein de México, Mexico interaction (PPI) network were identified by molecular complex detection (MCODE), Panwen Wang, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), and Mayo Clinic Arizona, United States analyses were performed. The results of CytoHubba, a plug for integrated algorithm for *Correspondence: Zhi-Zhao Ma biomolecular interaction networks combined with RRA analysis, were used to identify [email protected] the hub genes. Finally, a mouse model of UC was established by dextran sulfate sodium Chuan-Jie Yang [email protected] salt (DSS) solution to verify the expression of hub genes. -
DEFA6 (NM 001926) Human Recombinant Protein Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP310229 DEFA6 (NM_001926) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human defensin, alpha 6, Paneth cell-specific (DEFA6) Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 8.9 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_001917 Locus ID: 1671 UniProt ID: Q01524 RefSeq Size: 479 Cytogenetics: 8p23.1 RefSeq ORF: 300 Synonyms: DEF6; HD-6 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 DEFA6 (NM_001926) Human Recombinant Protein – TP310229 Summary: Defensins are a family of antimicrobial and cytotoxic peptides thought to be involved in host defense. They are abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the intestine, respiratory tract, urinary tract, and vagina. Members of the defensin family are highly similar in protein sequence and distinguished by a conserved cysteine motif. -
Downloaded from the Protein Data Bank (PDB
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.451411; this version posted July 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells Dongjie Guo 1, 2, #, Ruifang Guo1, 2, #, Zhaoyang Li 1, 2, Yuyang Zhang 1, 2, Wei Zheng 3, Xiaoqiang Huang 3, Tursunjan Aziz 1, 2, Yang Zhang 3, 4, Lijun Liu 1, 2, * 1 College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China 2 Key Laboratory of Data Analytics and Optimization for Smart Industry (Ministry of Education), Northeastern University, Shenyang, Liaoning, China 3 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA 4 Department of Biological Chemistry, University of Michigan, Ann Arbor, USA * Corresponding author. College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China. E-mail address: [email protected] (L. Liu) # These authors contributed equally to this work. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.451411; this version posted July 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Since December 2019, the COVID-19 caused by SARS-CoV-2 has been widely spread all over the world. -
The Transition from Primary Colorectal Cancer to Isolated Peritoneal Malignancy
medRxiv preprint doi: https://doi.org/10.1101/2020.02.24.20027318; this version posted February 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . The transition from primary colorectal cancer to isolated peritoneal malignancy is associated with a hypermutant, hypermethylated state Sally Hallam1, Joanne Stockton1, Claire Bryer1, Celina Whalley1, Valerie Pestinger1, Haney Youssef1, Andrew D Beggs1 1 = Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, B15 2TT. Correspondence to: Andrew Beggs, [email protected] KEYWORDS: Colorectal cancer, peritoneal metastasis ABBREVIATIONS: Colorectal cancer (CRC), Colorectal peritoneal metastasis (CPM), Cytoreductive surgery and heated intraperitoneal chemotherapy (CRS & HIPEC), Disease free survival (DFS), Differentially methylated regions (DMR), Overall survival (OS), TableFormalin fixed paraffin embedded (FFPE), Hepatocellular carcinoma (HCC) ARTICLE CATEGORY: Research article NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.02.24.20027318; this version posted February 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . NOVELTY AND IMPACT: Colorectal peritoneal metastasis (CPM) are associated with limited and variable survival despite patient selection using known prognostic factors and optimal currently available treatments. -
A New Vision of Iga Nephropathy: the Missing Link
International Journal of Molecular Sciences Review A New Vision of IgA Nephropathy: The Missing Link Fabio Sallustio 1,2,* , Claudia Curci 2,3,* , Vincenzo Di Leo 3 , Anna Gallone 2, Francesco Pesce 3 and Loreto Gesualdo 3 1 Interdisciplinary Department of Medicine (DIM), University of Bari “Aldo Moro”, 70124 Bari, Italy 2 Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari “Aldo Moro”, 70124 Bari, Italy; [email protected] 3 Nephrology, Dialysis and Transplantation Unit, DETO, University “Aldo Moro”, 70124 Bari, Italy; [email protected] (V.D.L.); [email protected] (F.P.); [email protected] (L.G.) * Correspondence: [email protected] (F.S.); [email protected] (C.C.) Received: 7 December 2019; Accepted: 24 December 2019; Published: 26 December 2019 Abstract: IgA Nephropathy (IgAN) is a primary glomerulonephritis problem worldwide that develops mainly in the 2nd and 3rd decade of life and reaches end-stage kidney disease after 20 years from the biopsy-proven diagnosis, implying a great socio-economic burden. IgAN may occur in a sporadic or familial form. Studies on familial IgAN have shown that 66% of asymptomatic relatives carry immunological defects such as high IgA serum levels, abnormal spontaneous in vitro production of IgA from peripheral blood mononuclear cells (PBMCs), high serum levels of aberrantly glycosylated IgA1, and an altered PBMC cytokine production profile. Recent findings led us to focus our attention on a new perspective to study the pathogenesis of this disease, and new studies showed the involvement of factors driven by environment, lifestyle or diet that could affect the disease. -
Ontogeny of the Intestinal Circadian Clock and Its Role in the Response to Clostridium Difficile Toxin B
Ontogeny of the intestinal circadian clock and its role in the response to Clostridium difficile toxin B A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfilment of the requirements for the degree of Doctor of Philosophy In the Department of Pharmacology & Systems Physiology of the College of Medicine by Andrew Rosselot B.S. Biology, Wittenberg University October 2019 Committee Chair: Christian I. Hong Ph.D. Abstract: The endogenous clock of the intestine regulates physiological processes ranging from nutrient absorption to the pathogenic response. The developmental timepoint when the human intestinal clock becomes active is unknown. We investigated intestinal circadian clock ontogeny using in vitro samples that are representative of distinct developmental timepoints. Induced pluripotent stem cells (iPSCs) were differentiated into 3D human intestinal organoids (HIOs) to mimic intestinal embryonic development in vitro. HIOs were then matured beyond their early fetal state via kidney capsule transplantation. Differentiation of iPSCs into HIOs did not activate robust circadian clock activity. Enteroids isolated from kidney capsule matured HIOs possessed a functional circadian clock, similar to adult biopsy derived human intestinal enteroids (bHIEs). Samples were challenged with toxin B (TcdB) from Clostridium difficile to provide functional insights on intestinal clock activity. The necrotic cell death response to TcdB was clock phase- dependent in samples that possessed an active clock and anti-phasic between mouse enteroids and bHIEs. RNA-seq analysis of mouse enteroids and bHIEs showed both possess robust rhythmic gene expression with up to 20% and 8% of their transcriptome oscillating, respectively. The phase and identity of rhythmic genes was however species-dependent. -
Product Datasheet DEFA6 Antibody NBP1-84281
Product Datasheet DEFA6 Antibody NBP1-84281 Unit Size: 0.1 ml Store at 4C short term. Aliquot and store at -20C long term. Avoid freeze-thaw cycles. Publications: 3 Protocols, Publications, Related Products, Reviews, Research Tools and Images at: www.novusbio.com/NBP1-84281 Updated 1/6/2021 v.20.1 Earn rewards for product reviews and publications. Submit a publication at www.novusbio.com/publications Submit a review at www.novusbio.com/reviews/destination/NBP1-84281 Page 1 of 4 v.20.1 Updated 1/6/2021 NBP1-84281 DEFA6 Antibody Product Information Unit Size 0.1 ml Concentration Concentrations vary lot to lot. See vial label for concentration. If unlisted please contact technical services. Storage Store at 4C short term. Aliquot and store at -20C long term. Avoid freeze-thaw cycles. Clonality Polyclonal Preservative 0.02% Sodium Azide Isotype IgG Purity Immunogen affinity purified Buffer PBS (pH 7.2) and 40% Glycerol Product Description Host Rabbit Gene ID 1671 Gene Symbol DEFA6 Species Human Reactivity Notes Reactivity reported in scientific literature (PMID: 23519454) Specificity/Sensitivity Specificity of human DEFA6 antibody verified on a Protein Array containing target protein plus 383 other non-specific proteins. Immunogen This antibody was developed against Recombinant Protein corresponding to amino acids: PLQAEDDPLQAKAYEADAQEQRGANDQDFAVSFAEDASSSLRALGSTRAFTC HCRRSCYSTEYSYGTCTVMGINHRFC Product Application Details Applications Western Blot, Simple Western, Immunohistochemistry, Immunohistochemistry- Paraffin Recommended Dilutions Western Blot 0.04 - 0.4 ug/ml, Simple Western, Immunohistochemistry 1:5000 - 1:10000, Immunohistochemistry-Paraffin 1:5000 - 1:10000 Application Notes For IHC-Paraffin, HIER pH 6 retrieval is recommended. Images Western Blot: DEFA6 Antibody [NBP1-84281] - Analysis in control (vector only transfected HEK293T lysate) and DEFA6 over-expression lysate (Co-expressed with a C-terminal myc-DDK tag (3.1 kDa) in mammalian HEK293T cells). -
Crosstalk Between H9N2 Avian Influenza Virus and Crypt-Derived
Huang et al. Vet Res (2017) 48:71 DOI 10.1186/s13567-017-0478-6 RESEARCH ARTICLE Open Access Crosstalk between H9N2 avian infuenza virus and crypt‑derived intestinal organoids Lulu Huang, Qihang Hou, Lulu Ye, Qian Yang and Qinghua Yu* Abstract The spread of Avian infuenza virus via animal feces makes the virus difcult to prevent, which causes great threat to human health. Therefore, it is imperative to understand the survival and invasion mechanism of H9N2 virus in the intestinal mucosa. In this study, we used mouse threedimensional intestinal organoids that contained intestinal crypts and villi diferentiated from intestinal stem cells to explore interactions between H9N2 avian infuenza virus and the intestinal mucosa. The HA, NA, NP and PB1 genes of H9N2 viruses could be detected in intestinal organoids at 1 h, and reached peak levels at 48 h post-infection. Moreover, the HA and NP proteins of H9N2 virus could also be detected in organoids via immunofuorescence. Virus invasion caused damage to intestinal organoids with reduced mRNA tran- script expression of Wnt3, Dll1 and Dll4. The abnormal growth of intestinal organoids may be attributed to the loss of Paneth cells, as indicated by the low mRNA transcript levels of lyz1 and defcr1. This present study demonstrates that H9N2 virus could invade intestinal organoids and then cause damage, as well as afect intestinal stem cell proliferation and diferentiation, promoting the loss of Paneth cells. Introduction Caco-2 cells, and cause severe epithelial apoptosis [5, 6]. In China, low pathogenicity avian infuenza (LPAI) viruses However, the intestinal mucosa contains intestinal crypt of the H9N2 subtype have become endemic. -
Severity of Experimental Autoimmune Uveitis Is Reduced by Pretreatment with Live Probiotic Escherichia Coli Nissle 1917
cells Article Severity of Experimental Autoimmune Uveitis Is Reduced by Pretreatment with Live Probiotic Escherichia coli Nissle 1917 Otakar Dusek 1, Alena Fajstova 2, Aneta Klimova 1, Petra Svozilkova 1 , Tomas Hrncir 3 , Miloslav Kverka 2,* , Stepan Coufal 2 , Johan Slemin 2, Helena Tlaskalova-Hogenova 2, John V. Forrester 4,5,6 and Jarmila Heissigerova 1 1 Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic; [email protected] (O.D.); [email protected] (A.K.); [email protected] (P.S.); [email protected] (J.H.) 2 Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague, Czech Republic; [email protected] (A.F.); [email protected] (S.C.); [email protected] (J.S.); [email protected] (H.T.-H.) 3 Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 549 22 Novy Hradek, Czech Republic; [email protected] 4 Section of Immunology and Infection, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK; [email protected] 5 Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia 6009, Australia 6 Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia * Correspondence: [email protected]; Tel.: +420-24106-2452 Abstract: Non-infectious uveitis is considered an autoimmune disease responsible for a significant burden of blindness in developed countries and recent studies have linked its pathogenesis to dys- regulation of the gut microbiota.