Human Defensin-5 Blocks Ethanol and Colitis-Induced Dysbiosis, Tight
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Network Medicine Approach for Analysis of Alzheimer's Disease Gene Expression Data
International Journal of Molecular Sciences Article Network Medicine Approach for Analysis of Alzheimer’s Disease Gene Expression Data David Cohen y, Alexander Pilozzi y and Xudong Huang * Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; [email protected] (D.C.); [email protected] (A.P.) * Correspondence: [email protected]; Tel./Fax: +1-617-724-9778 These authors contributed equally to this work. y Received: 15 November 2019; Accepted: 30 December 2019; Published: 3 January 2020 Abstract: Alzheimer’s disease (AD) is the most widespread diagnosed cause of dementia in the elderly. It is a progressive neurodegenerative disease that causes memory loss as well as other detrimental symptoms that are ultimately fatal. Due to the urgent nature of this disease, and the current lack of success in treatment and prevention, it is vital that different methods and approaches are applied to its study in order to better understand its underlying mechanisms. To this end, we have conducted network-based gene co-expression analysis on data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. By processing and filtering gene expression data taken from the blood samples of subjects with varying disease states and constructing networks based on that data to evaluate gene relationships, we have been able to learn about gene expression correlated with the disease, and we have identified several areas of potential research interest. Keywords: Alzheimer’s disease; network medicine; gene expression; neurodegeneration; neuroinflammation 1. Introduction Alzheimer’s disease (AD) is the most widespread diagnosed cause of dementia in the elderly [1]. -
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. -
Duplications and Copy Number Variants of 8P23.1 Are Cytogenetically Indistinguishable but Distinct at the Molecular Level
European Journal of Human Genetics (2005) 13, 1131–1136 & 2005 Nature Publishing Group All rights reserved 1018-4813/05 $30.00 www.nature.com/ejhg ARTICLE Duplications and copy number variants of 8p23.1 are cytogenetically indistinguishable but distinct at the molecular level John CK Barber*,1,2,3, Viv Maloney2, Edward J Hollox4, Annegret Stuke-Sontheimer5, Gabi du Bois6, Eva Daumiller6, Ute Klein-Vogler7, Andreas Dufke7, John AL Armour4 and Thomas Liehr8 1Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Trust, Salisbury, Wiltshire, UK; 2National Genetics Reference Laboratory (Wessex), Salisbury Hospital NHS Trust, Salisbury, Wiltshire, UK; 3Human Genetics Division, Southampton University School of Medicine, Southampton General Hospital, Southampton, UK; 4Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham, UK; 5Genetics Clinic, Wernigerode, Germany; 6Institute for Chromosome Diagnostics and Genetic Counselling, Boeblingen, Germany; 7Department of Medical Genetics, Eberhard-Karls University, Tuebingen, Germany; 8Institute for Human Genetics and Anthropology, Friedrich-Schiller University, Jena, Germany It has been proposed that duplications of 8p23.1 are either euchromatic variants of the 8p23.1 defensin domain with no phenotypic consequences or true duplications associated with developmental delay and heart defects. Here, we provide evidence for both alternatives in two new families. A duplication of most of band 8p23.1 (circa 5 Mb) was found in a girl of 8 years with pulmonary stenosis and mild language delay. BAC fluorescence in situ hybridisation (FISH) and multiplex amplifiable probe hybridisation (MAPH) showed that the two copies of the duplicated segment were sited, in an alternating fashion, between three copies of a circa 300–450 kb segment from 8p23.1 distal to REPD. -
Paneth Cell Α-Defensins HD-5 and HD-6 Display Differential Degradation Into Active Antimicrobial Fragments
Paneth cell α-defensins HD-5 and HD-6 display differential degradation into active antimicrobial fragments D. Ehmanna, J. Wendlera, L. Koeningera, I. S. Larsenb,c, T. Klaga, J. Bergerd, A. Maretteb,c, M. Schallere, E. F. Stangea, N. P. Maleka, B. A. H. Jensenb,c,f, and J. Wehkampa,1 aInternal Medicine I, University Hospital Tübingen, 72076 Tübingen, Germany; bQuebec Heart and Lung Institute, Department of Medicine, Faculty of Medicine, Cardiology Axis, Laval University, G1V 4G5 Quebec, QC, Canada; cInstitute of Nutrition and Functional Foods, Laval University, G1V 4G5 Quebec, QC, Canada; dElectron Microscopy Unit, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany; eDepartment of Dermatology, University Hospital Tübingen, 72076 Tübingen, Germany; and fNovo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Genomics, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark Edited by Lora V. Hooper, The University of Texas Southwestern, Dallas, TX, and approved January 4, 2019 (received for review October 9, 2018) Antimicrobial peptides, in particular α-defensins expressed by Paneth variety of AMPs but most abundantly α-defensin 5 (HD-5) and -6 cells, control microbiota composition and play a key role in intestinal (HD-6) (2, 17, 18). These secretory Paneth cells are located at the barrier function and homeostasis. Dynamic conditions in the local bottom of the crypts of Lieberkühn and are highly controlled by microenvironment, such as pH and redox potential, significantly af- Wnt signaling due to their differentiation and their defensin regu- fect the antimicrobial spectrum. In contrast to oxidized peptides, lation and expression (19–21). -
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. -
Functional Interaction of Human Neutrophil Peptide-1 with the Cell Wall Precursor Lipid II
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 584 (2010) 1543–1548 journal homepage: www.FEBSLetters.org Functional interaction of human neutrophil peptide-1 with the cell wall precursor lipid II Erik de Leeuw a,*, Changqing Li a, Pengyun Zeng b, Chong Li b, Marlies Diepeveen-de Buin c, Wei-Yue Lu b, Eefjan Breukink c, Wuyuan Lu a,** a University of Maryland Baltimore School of Medicine, Institute of Human Virology and Department of Biochemistry and Molecular Biology, 725 West Lombard Street, Baltimore, MD 21201, USA b Fudan University School of Pharmacy, Shanghai, China c Utrecht University, Department of Biochemistry of Membranes, Bijvoet Center for Biomolecular Research, Padualaan 8, 3585 CH, Utrecht, The Netherlands article info abstract Article history: Defensins constitute a major class of cationic antimicrobial peptides in mammals and vertebrates, Received 11 January 2010 acting as effectors of innate immunity against infectious microorganisms. It is generally accepted Revised 1 March 2010 that defensins are bactericidal by disrupting the anionic microbial membrane. Here, we provide evi- Accepted 2 March 2010 dence that membrane activity of human a-defensins does not correlate with antibacterial killing. Available online 7 March 2010 We further show that the a-defensin human neutrophil peptide-1 (HNP1) binds to the cell wall pre- Edited by Renee Tsolis cursor lipid II and that reduction of lipid II levels in the bacterial membrane significantly reduces bacterial killing. The interaction between defensins and lipid II suggests the inhibition of cell wall synthesis as a novel antibacterial mechanism of this important class of host defense peptides. -
Avian Antimicrobial Host Defense Peptides: from Biology to Therapeutic Applications
Pharmaceuticals 2014, 7, 220-247; doi:10.3390/ph7030220 OPEN ACCESS pharmaceuticals ISSN 1424-8247 www.mdpi.com/journal/pharmaceuticals Review Avian Antimicrobial Host Defense Peptides: From Biology to Therapeutic Applications Guolong Zhang 1,2,3,* and Lakshmi T. Sunkara 1 1 Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA 2 Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA 3 Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-405-744-6619; Fax: +1-405-744-7390. Received: 6 February 2014; in revised form: 18 February 2014 / Accepted: 19 February 2014 / Published: 27 February 2014 Abstract: Host defense peptides (HDPs) are an important first line of defense with antimicrobial and immunomoduatory properties. Because they act on the microbial membranes or host immune cells, HDPs pose a low risk of triggering microbial resistance and therefore, are being actively investigated as a novel class of antimicrobials and vaccine adjuvants. Cathelicidins and β-defensins are two major families of HDPs in avian species. More than a dozen HDPs exist in birds, with the genes in each HDP family clustered in a single chromosomal segment, apparently as a result of gene duplication and diversification. In contrast to their mammalian counterparts that adopt various spatial conformations, mature avian cathelicidins are mostly α-helical. Avian β-defensins, on the other hand, adopt triple-stranded β-sheet structures similar to their mammalian relatives. Besides classical β-defensins, a group of avian-specific β-defensin-related peptides, namely ovodefensins, exist with a different six-cysteine motif.