Micrornas As New Regulators of Neutrophil Extracellular Trap Formation
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The Expression of Non-Coding Rnas and Their Target Molecules in Rheumatoid Arthritis
International Journal of Molecular Sciences Review The Expression of Non-Coding RNAs and Their Target Molecules in Rheumatoid Arthritis: A Molecular Basis for Rheumatoid Pathogenesis and Its Potential Clinical Applications Chang-Youh Tsai 1,*,† , Song-Chou Hsieh 2,†, Chih-Wei Liu 1, Cheng-Hsun Lu 2,3 , Hsien-Tzung Liao 1, Ming-Han Chen 1, Ko-Jen Li 2, Cheng-Han Wu 2,3, Cheih-Yu Shen 2,3 , Yu-Min Kuo 2,3 and Chia-Li Yu 2,* 1 Division of Allergy, Immunology & Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei 11217, Taiwan; [email protected] (C.-W.L.); [email protected] (H.-T.L.); [email protected] (M.-H.C.) 2 Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 10002, Taiwan; [email protected] (S.-C.H.); [email protected] (C.-H.L.); [email protected] (K.-J.L.); [email protected] (C.-H.W.); [email protected] (C.-Y.S.); [email protected] (Y.-M.K.) 3 Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan * Correspondence: [email protected] (C.-Y.T.); [email protected] (C.-L.Y.) † The two co-first authors contributed equally in the preparation of the manuscript. Abstract: Rheumatoid arthritis (RA) is a typical autoimmune-mediated rheumatic disease presenting Citation: Tsai, C.-Y.; Hsieh, S.-C.; Liu, C.-W.; Lu, C.-H.; Liao, H.-T.; Chen, as a chronic synovitis in the joint. The chronic synovial inflammation is characterized by hyper- M.-H.; Li, K.-J.; Wu, C.-H.; Shen, C.-Y.; vascularity and extravasation of various immune-related cells to form lymphoid aggregates where an Kuo, Y.-M.; et al. -
A Machine Learning Tool for Predicting Protein Function Anna
The Woolf Classifier Building Pipeline: A Machine Learning Tool for Predicting Protein Function Anna Farrell-Sherman Submitted in Partial Fulfillment of the Prerequisite for Honors in Computer Science under the advisement of Eni Mustafaraj and Vanja Klepac-Ceraj May 2019 © 2019 Anna Farrell-Sherman Abstract Proteins are the machinery that allow cells to grow, reproduce, communicate, and create multicellular organisms. For all of their importance, scientists still have a hard time understanding the function of a protein based on its sequence alone. For my honors thesis in computer science, I created a machine learning tool that can predict the function of a protein based solely on its amino acid sequence. My tool gives scientists a structure in which to build a � Nearest Neighbor or random forest classifier to distinguish between proteins that can and cannot perform a given function. Using default Min-Max scaling, and the Matthews Correlation Coefficient for accuracy assessment, the Woolf Pipeline is built with simplified choices to guide users to success. i Acknowledgments There are so many people who made this thesis possible. First, thank you to my wonderful advisors, Eni and Vanja, who never gave up on me, and always pushed me to try my hardest. Thank you also to the other members of my committee, Sohie Lee, Shikha Singh, and Rosanna Hertz for supporting me through this process. To Kevin, Sophie R, Sophie E, and my sister Phoebe, thank you for reading my drafts, and advising me when the going got tough. To all my wonderful friends, who were always there with encouraging words, warm hugs, and many congratulations, I cannot thank you enough. -
The C718T Polymorphism in the 3″-Untranslated
Hypertension Research (2012) 35, 507–512 & 2012 The Japanese Society of Hypertension All rights reserved 0916-9636/12 www.nature.com/hr ORIGINAL ARTICLE The C718T polymorphism in the 3¢-untranslated region of glutathione peroxidase-4 gene is a predictor of cerebral stroke in patients with essential hypertension Alexey V Polonikov1, Ekaterina K Vialykh2, Mikhail I Churnosov3, Thomas Illig4, Maxim B Freidin5, Oksana V Vasil¢eva1, Olga Yu Bushueva1, Valentina N Ryzhaeva1, Irina V Bulgakova1 and Maria A Solodilova1 In the present study we have investigated the association of three single nucleotide polymorphisms in glutathione peroxidase (GPx) genes GPX1 rs1050450 (P198L), GPX3 rs2070593 (G930A) and GPX4 rs713041 (T718C) with the risk of cerebral stroke (CS) in patients with essential hypertension (EH). A total of 667 unrelated EH patients of Russian origin, including 306 hypertensives (the EH–CS group) who suffered from CS and 361 people (the EH–CS group) who did not have cerebrovascular accidents, were enrolled in the study. The variant allele 718C of the GPX4 gene was found to be significantly associated with an increased risk of CS in hypertensive patients (odds ratio (OR) 1.53, 95% confidence interval (CI) 1.23–1.90, Padj¼0.0003). The prevalence of the 718TC and 718CC genotypes of the GPX4 gene was higher in the EH–CS group than the EH-alone group (OR¼2.12, 95%CI 1.42–3.16, Padj¼0.0018). The association of the variant GPX4 genotypes with the increased risk of CS in hypertensives remained statistically significant after adjusting for confounding variables such as sex, body mass index (BMI), blood pressure and antihypertensive medication use (OR¼2.18, 95%CI 1.46–3.27, P¼0.0015). -
Editorial: Functions of Non-Coding RNA in Innate Immunity
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector EDITORIAL published: 14 December 2015 doi: 10.3389/fimmu.2015.00622 Editorial: Functions of Non-Coding RNA in Innate Immunity Susan Carpenter* Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA Keywords: innate immunity, long non-coding RNAs, miRNAs, inflammation, extracellular RNA Our understanding of the functions that non-coding RNAs play in shaping the immune response is still in its infancy. The breakthroughs in deep sequencing technology have provided us with an unprecedented view of the human genome. The deeper we sequence the more non-coding genes we identify, while the number of protein coding genes remains constant. GENCODE represents the gene set of the ENCODE project and there are currently 15,931 long non-coding RNA (lncRNA) genes, 9,882 small non-coding RNA genes, and 14,477 Pseudogenes cataloged in GENCODE version 231. The contribution of each of these genes to biological processes still remains to be determined. In this research topic, we explore recent data surrounding the functions for microRNA (miRNA) as well as lncRNA within Innate Immunity. Innate immune responses to infection involve the production of pro-inflammatory cytokines such as IL-6 and TNFα in addition to the Type I Interferons (IFNs) that play critical roles in anti-viral immunity. In recent years, there have been huge strides made in understanding the contributions of small RNAs such as miRNA to the Innate Immune processes. More recently, our attention has also been drawn to the growing catalog of lncRNAs. -
Interactome of Mirnas and Transcriptome of Human Umbilical Cord Endothelial Cells Exposed to Short-Term Simulated Microgravity
www.nature.com/npjmgrav ARTICLE OPEN Interactome of miRNAs and transcriptome of human umbilical cord endothelial cells exposed to short-term simulated microgravity Dharanibalan Kasiviswanathan1,2,4, Rajadurai Chinnasamy Perumal 3,4, Srinivasan Bhuvaneswari1,2, Pavitra Kumar1, ✉ Lakshmikirupa Sundaresan 1,2, Manuel Philip 3, Sajesh Puthenpurackal Krishnankutty3 and Suvro Chatterjee1,2 Adaptation of humans in low gravity conditions is a matter of utmost importance when efforts are on to a gigantic leap in human space expeditions for tourism and formation of space colonies. In this connection, cardiovascular adaptation in low gravity is a critical component of human space exploration. Deep high-throughput sequencing approach allowed us to analyze the miRNA and mRNA expression profiles in human umbilical cord vein endothelial cells (HUVEC), cultured under gravity (G), and stimulated microgravity (MG) achieved with a clinostat. The present study identified totally 1870 miRNAs differentially expressed in HUVEC under MG condition when compared to the cells subjected to unitary G conditions. The functional association of identified miRNAs targeting specific mRNAs revealed that miRNAs, hsa-mir-496, hsa-mir-151a, hsa-miR-296-3p, hsa-mir-148a, hsa-miR-365b-5p, hsa- miR-3687, hsa-mir-454, hsa-miR-155-5p, and hsa-miR-145-5p differentially regulated the genes involved in cell adhesion, angiogenesis, cell cycle, JAK-STAT signaling, MAPK signaling, nitric oxide signaling, VEGF signaling, and wound healing pathways. Further, the q-PCR based experimental studies of upregulated and downregulated miRNA and mRNAs demonstrate that the above 1234567890():,; reported miRNAs influence the cell proliferation and vascular functions of the HUVEC in MG conditions effectively. -
Characterization of Cytosolic Glutathione Peroxidase And
Aquatic Toxicology 130–131 (2013) 97–111 Contents lists available at SciVerse ScienceDirect Aquatic Toxicology jou rnal homepage: www.elsevier.com/locate/aquatox Characterization of cytosolic glutathione peroxidase and phospholipid-hydroperoxide glutathione peroxidase genes in rainbow trout (Oncorhynchus mykiss) and their modulation by in vitro selenium exposure a a b a d c a,∗ D. Pacitti , T. Wang , M.M. Page , S.A.M. Martin , J. Sweetman , J. Feldmann , C.J. Secombes a Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom b Integrative and Environmental Physiology, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom c Trace Element Speciation Laboratory, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom d Alltech Biosciences Centre, Sarney, Summerhill Rd, Dunboyne, Country Meath, Ireland a r t i c l e i n f o a b s t r a c t Article history: Selenium (Se) is an oligonutrient with both essential biological functions and recognized harmful effects. Received 4 July 2012 As the selenocysteine (SeCys) amino acid, selenium is integrated in several Se-containing proteins Received in revised form (selenoproteins), many of which are fundamental for cell homeostasis. Nevertheless, selenium may exert 19 December 2012 toxic effects at levels marginally above those required, mainly through the generation of reactive oxygen Accepted 20 December 2012 species (ROS). The selenium chemical speciation can strongly affect the bioavailability of this metal and its impact on metabolism, dictating the levels that can be beneficial or detrimental towards an organism. -
Molecular Characterization, Protein–Protein Interaction Network, and Evolution of Four Glutathione Peroxidases from Tetrahymena Thermophila
antioxidants Article Molecular Characterization, Protein–Protein Interaction Network, and Evolution of Four Glutathione Peroxidases from Tetrahymena thermophila Diana Ferro 1,2, Rigers Bakiu 3 , Sandra Pucciarelli 4, Cristina Miceli 4 , Adriana Vallesi 4 , Paola Irato 5 and Gianfranco Santovito 5,* 1 BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA; [email protected] 2 Department of Pediatrics, Children’s Mercy Hospital and Clinics, Kansas City, MO 64108, USA 3 Department of Aquaculture and Fisheries, Agricultural University of Tirana, 1000 Tiranë, Albania; [email protected] 4 School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; [email protected] (S.P.); [email protected] (C.M.); [email protected] (A.V.) 5 Department of Biology, University of Padova, 35131 Padova, Italy; [email protected] * Correspondence: [email protected] Received: 6 September 2020; Accepted: 1 October 2020; Published: 2 October 2020 Abstract: Glutathione peroxidases (GPxs) form a broad family of antioxidant proteins essential for maintaining redox homeostasis in eukaryotic cells. In this study, we used an integrative approach that combines bioinformatics, molecular biology, and biochemistry to investigate the role of GPxs in reactive oxygen species detoxification in the unicellular eukaryotic model organism Tetrahymena thermophila. Both phylogenetic and mechanistic empirical model analyses provided indications about the evolutionary relationships among the GPXs of Tetrahymena and the orthologous enzymes of phylogenetically related species. In-silico gene characterization and text mining were used to predict the functional relationships between GPxs and other physiologically-relevant processes. The GPx genes contain conserved transcriptional regulatory elements in the promoter region, which suggest that transcription is under tight control of specialized signaling pathways. -
Extracellular Glutathione Peroxidase Gpx3 and Its Role in Cancer
cancers Review Extracellular Glutathione Peroxidase GPx3 and Its Role in Cancer Caroline Chang 1, Beth L. Worley 2,Rébécca Phaëton 3 and Nadine Hempel 2,* 1 Department of Comparative Medicine, Penn State University College of Medicine, Hershey, PA 17033, USA; [email protected] 2 Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; [email protected] 3 Department of Obstetrics & Gynecology & Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA 17033, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-717-531-4037 Received: 29 June 2020; Accepted: 4 August 2020; Published: 6 August 2020 Abstract: Mammalian cells possess a multifaceted antioxidant enzyme system, which includes superoxide dismutases, catalase, the peroxiredoxin/thioredoxin and the glutathione peroxidase systems. The dichotomous role of reactive oxygen species and antioxidant enzymes in tumorigenesis and cancer progression complicates the use of small molecule antioxidants, pro-oxidants, and targeting of antioxidant enzymes as therapeutic approaches for cancer treatment. It also highlights the need for additional studies to investigate the role and regulation of these antioxidant enzymes in cancer. The focus of this review is on glutathione peroxidase 3 (GPx3), a selenoprotein, and the only extracellular GPx of a family of oxidoreductases that catalyze the detoxification of hydro- and soluble lipid hydroperoxides by reduced glutathione. In addition to summarizing the biochemical function, regulation, and disease associations of GPx3, we specifically discuss the role and regulation of systemic and tumor cell expressed GPx3 in cancer. From this it is evident that GPx3 has a dichotomous role in different tumor types, acting as both a tumor suppressor and pro-survival protein. -
Combined Effects of PVT1 and Mir-146A Single Nucleotide
Int. J. Biol. Sci. 2018, Vol. 14 1153 Ivyspring International Publisher International Journal of Biological Sciences 2018; 14(10): 1153-1162. doi: 10.7150/ijbs.25420 Research Paper Combined Effects of PVT1 and MiR-146a Single Nucleotide Polymorphism on the Lung Function of Smokers with Chronic Obstructive Pulmonary Disease Sijing Zhou1*, Yi Liu2*, Min Li3, Peipei Wu2, Gengyun Sun2, Guanghe Fei2, Xuan Xu4, Xuexin Zhou5, Luqian Zhou5, Ran Wang2 1. Hefei Prevention and Treatment Center for Occupational Diseases, Hefei 230022, China 2. Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei 230022, China 3. Department of oncology, the first affiliated hospital of Anhui medical university, Hefei 230022, China 4. Division of Pulmonary/Critical Care Medicine, Cedars sinai Medical Center, Los Angeles 90015, USA 5. The first clinical college of Anhui medical university, Hefei 230032, China *These authors contributed equally to the work. Corresponding author: Ran Wang Ph.D., Department of respiratory and critical care medicine, The first affiliated hospital of Anhui medical university, Hefei, 230022, China. Phone: 86-551-62922913; Fax: 86-551-62922913; E-mail: [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2018.02.07; Accepted: 2018.06.16; Published: 2018.06.23 Abstract Non-coding RNAs play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). This study was performed to investigate the role of PVT1 and miR-146a single nucleotide polymorphisms (SNPs) in the lung function of COPD smokers. -
Downloaded from 10X Genomics Datasets Available on Link
International Journal of Molecular Sciences Article Unravelling the Role of Trophoblastic-Derived Extracellular Vesicles in Regulatory T Cell Differentiation Árpád Ferenc Kovács 1,* ,Nóra Fekete 1, Lilla Turiák 2 , András Ács 2 ,László K˝ohidai 1 , Edit I. Buzás 1,3,4 and Éva Pállinger 1 1 Department of Genetics, Cell- and Immunobiology, Semmelweis University, H-1085 Budapest, Hungary 2 MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1051 Budapest, Hungary 3 MTA-SE Immune-Proteogenomics Extracellular Vesicle Research Group, H-1085 Budapest, Hungary 4 HCEMM-SE Extracellular Vesicle Research Group, H-1085 Budapest, Hungary * Correspondence: [email protected] Received: 21 June 2019; Accepted: 11 July 2019; Published: 14 July 2019 Abstract: Regulatory T cells (Treg) are mandatory elements in the maintenance of human pregnancy, but their de novo differentiation has not been completely exposed. HSPE1 chaperone expressing trophoblast cells may have a role in it. Trophoblast-derived extracellular vesicles (EVs), either at the feto–maternal interface or in circulation, target CD4+ T cells. We hypothesized that HSPE1-associated trophoblastic cell line (BeWo)-derived EVs are active mediators of Treg cell differentiation. We proved at first that recombinant HSPE1 promote human Treg cell differentiation in vitro. Developing a CRISPR-Cas9 based HSPE1 knockout BeWo cell line we could also demonstrate, that EV-associated HSPE1 induces Treg development. Next-generation sequencing of miRNA cargo of BeWo-EVs characterized the regulatory processes of Treg polarization. By the use of single-cell transcriptomics analysis, seven Treg cell subtypes were distinguished and we demonstrated for the first time that the expression level of HSPE1 was Treg subtype dependent, and CAPG expression is characteristic to memory phenotype of T cells. -
Functional Polymorphisms in Pre-Mir146a and Pre-Mir499 Are
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 54), pp: 91876-91886 Research Paper Functional polymorphisms in pre-miR146a and pre-miR499 are associated with systemic lupus erythematosus but not with rheumatoid arthritis or Graves’ disease in Mexican patients Isidro Alemán-Ávila1,2, Mayra Jiménez-Morales1, Olga Beltrán-Ramírez1, Rosa Elda Barbosa-Cobos3, Silvia Jiménez-Morales4, Fausto Sánchez-Muñoz5, Guillermo Valencia-Pacheco6, Luis M. Amezcua-Guerra5, Yaneli Juárez-Vicuña5, Dulce Milagro Razo-Blanco Hernández7, María Concepción Aguilera-Cartas8, Ricardo F. López-Villanueva9, Oscar Peralta-Zaragoza10, Carlos Tovilla-Zárate11 and Julian Ramírez-Bello1 1Endocrine and Metabolic Disease Unit Research, Hospital Juarez of Mexico, Mexico City, Mexico 2Superior School of Medicine Postgraduate Program, National Polytechnic Institute, Mexico City, Mexico 3Rheumatology Department, Hospital Juarez of Mexico, Mexico City, Mexico 4Laboratory of Cancer Genomics, National Institute of Genomic Medicine, Mexico City, Mexico 5Immunology Department, National Institute of Cardiology, Mexico City, Mexico 6Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico 7Research Direction, Hospital Juarez of Mexico, Mexico City, Mexico 8Endocrinology Department, Hospital Juarez of Mexico, Mexico City, Mexico 9Rheumatology Department, Regional Hospital General (ISSSTE), Health Service Yucatan, Yucatan, Mexico 10 Direction of Chronic Infections and Cancer, Research Center in Infection Diseases, National -
Associations of Mirna Polymorphisms and Expression Levels with Breast Cancer Risk in the Chinese Population
Associations of miRNA polymorphisms and expression levels with breast cancer risk in the Chinese population P. Qi1, L. Wang2, B. Zhou2, W.J. Yao3, S. Xu1, Y. Zhou1 and Z.B. Xie1 1Department of Head-Neck and Breast Surgery, Xinxiang Central Hospital, Xinxiang, China 2Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China 3Department of Thoracic Surgery, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China Corresponding author: P. Qi E-mail: [email protected] Genet. Mol. Res. 14 (2): 6289-6296 (2015) Received March 3, 2015 Accepted May 14, 2015 Published June 11, 2015 DOI http://dx.doi.org/10.4238/2015.June.11.2 ABSTRACT. Single-nucleotide polymorphisms in microRNAs (miRNAs) may dramatically affect gene expression and subsequently alter individual susceptibility to cancer, and thus has become a research hotspot for many cancer types, including breast cancer. We recruited 321 breast cancer patients and 290 controls in our study. Four established miRNA single-nucleotide polymorphisms (mir-499 rs3746444 A>G; miR-27a rs895819 A>G; miR-196a2 rs11614913 T>C; miR-146a rs2910164 G/C) were detected using Taqman assays. Mature miRNA expression, allele distribution, and the association with clinical features were further analyzed. Our results showed that the miR146a rs2910164 G/C polymorphism was associated with an elevated risk of breast cancer (odds ratio = 1.85, 95% confidence interval = 1.03-3.32; P < 0.05). Compared with the ancestral T allele Genetics and Molecular Research 14 (2): 6289-6296 (2015) ©FUNPEC-RP www.funpecrp.com.br P. Qi et al.