Association Between Inflammation and Function of Cell Adhesion Molecules Influence on Gastrointestinal Cancer Development
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
A61K9/00 (2006.01) G01N 2 7/447 (2006.01) Chusetts 02139 (US)
( (51) International Patent Classification: (74) Agent: SCARR, Rebecca B. et al.; McNeill Baur PLLC, C07K 16/28 (2006.01) A61K 35/00 (2006.01) 125 Cambridge Park Drive, Suite 301, Cambridge, Massa¬ A61K9/00 (2006.01) G01N 2 7/447 (2006.01) chusetts 02139 (US). A61K9/19 (2006.01) C07K 19/00 (2006.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection av ailable) . AE, AG, AL, AM, PCT/US2020/036035 AO, AT, AU, AZ , BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, (22) International Filing Date: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, 04 June 2020 (04.06.2020) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (25) Filing Language: English KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (26) Publication Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (30) Priority Data: SC, SD, SE, SG, SK, SL, ST, SV, SY, TH, TJ, TM, TN, TR, 62/857,364 05 June 2019 (05.06.2019) US TT, TZ, UA, UG, US, UZ, VC, VN, WS, ZA, ZM, ZW. 62/906,862 27 September 2019 (27.09.2019) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: SEATTLE GENETICS, INC. [US/US]; kind of regional protection available) . ARIPO (BW, GH, 21823 30th Drive SE, Bothell, Washington 98021 (US). -
Peripheral Mononuclear Blood Cells Contribute to The
Genes Nutr (2015) 10:11 DOI 10.1007/s12263-015-0460-8 RESEARCH PAPER Peripheral mononuclear blood cells contribute to the obesity- associated inflammatory state independently of glycemic status: involvement of the novel proinflammatory adipokines chemerin, chitinase-3-like protein 1, lipocalin-2 and osteopontin 1,2,3 1,2,3 1,2,3 Victoria Catala´n • Javier Go´mez-Ambrosi • Amaia Rodrı´guez • 1,2,3 2,4 3,5 2,3,6 Beatriz Ramı´rez • Vı´ctor Valentı´ • Rafael Moncada • Camilo Silva • 2,6 1,2,3,6 Javier Salvador • Gema Fru¨hbeck Received: 24 December 2014 / Accepted: 28 March 2015 / Published online: 14 April 2015 Ó Springer-Verlag Berlin Heidelberg 2015 Abstract Inflammation is a critical contributor to the including chemerin, chitinase-3-like protein 1 (YKL-40), pathogenesis of metabolic disorders with adipose tissue lipocalin-2 (LCN-2) and osteopontin (OPN), and their being crucial in the inflammatory response by releasing circulating concentrations were also determined by ELISA. multiple adipokines with either pro- or anti-inflammatory We show, for the first time, that PBMC gene expression activities with potential functions as metabolic regulators. levels of chemerin (P \ 0.0001), chitinase-3-like protein 1 Peripheral blood mononuclear cells (PBMC) have been (P = 0.010), lipocalin-2 (P \ 0.0001) and osteopontin proposed as representative of the inflammatory status in (P \ 0.0001) were strongly upregulated in obesity inde- obesity. The aim of the present study was to evaluate the pendently of the glycemic state. Circulating concentrations contribution of PBMC to the obesity-associated chronic of these adipokines followed the same trend being sig- inflammation analyzing the expression of novel adipokines. -
Semaphorin7a Promotes Tumor Growth and Exerts a Pro-Angiogenic Effect in Macrophages of Mammary Tumor-Bearing Mice
ORIGINAL RESEARCH ARTICLE published: 05 February 2014 doi: 10.3389/fphys.2014.00017 Semaphorin7A promotes tumor growth and exerts a pro-angiogenic effect in macrophages of mammary tumor-bearing mice Ramon Garcia-Areas 1, Stephania Libreros 1, Samantha Amat 1, Patricia Keating 2, Roberto Carrio 3, Phillip Robinson 4, Clifford Blieden 5 and Vijaya Iragavarapu-Charyulu 1* 1 Tumor Immunology, Department of Biomedical Sciences, Florida Atlantic University, Boca Raton, FL, USA 2 Immunology, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA 3 Tumor Immunology, Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA 4 Department of Clinical Sciences, Florida Atlantic University, Boca Raton, FL, USA 5 Department of Pathology and Laboratory Medicine, Jackson Memorial Hospital, University of Miami Miller School of Medicine, Miami, FL, USA Edited by: Semaphorins are a large family of molecules involved in axonal guidance during the Michal A. Rahat, Technion - Israel development of the nervous system and have been recently shown to have both Institute for Technology, Israel angiogenic and anti-angiogenic properties. Specifically, semaphorin 7A (SEMA7A) has Reviewed by: been reported to have a chemotactic activity in neurogenesis and to be an immune Andrea Foskett, Texas A&M Health α β Science Center, USA modulator through 1 1integrins. SEMA7A has been shown to promote monocyte Jincai Luo, The University of Tokyo, chemotaxis and induce them to produce proinflammatory mediators. In this study we Japan explored the role of SEMA7A in a murine model of breast cancer. We show that SEMA7A Zahava Vadasz, Bnai-Zion Medical is highly expressed by DA-3 murine mammary tumor cells in comparison to normal Center, Israel mammary cells (EpH4), and that peritoneal elicited macrophages from mammary tumor- *Correspondence: Vijaya Iragavarapu-Charyulu, Tumor bearing mice also express SEMA7A at higher levels compared to those derived from Immunology, Department of normal mice. -
Genome-Wide Analysis Identifies Critical DNA Methylations Within
Chen et al. J Transl Med (2021) 19:73 https://doi.org/10.1186/s12967-021-02740-6 Journal of Translational Medicine RESEARCH Open Access Genome-wide analysis identifes critical DNA methylations within NTRKs genes in colorectal cancer Zijian Chen1,3† , Zenghong Huang2,3†, Yanxin Luo2,3, Qi Zou3,4, Liangliang Bai3, Guannan Tang3, Xiaolin Wang3, Guangwen Cao5, Meijin Huang2,3, Jun Xiang1* and Huichuan Yu3* Abstract Background: Neurotrophic tropomyosin receptor kinases (NTRKs) are a gene family function as oncogene or tumor suppressor gene in distinct cancers. We aimed to investigate the methylation and expression profles and prognostic value of NTRKs gene in colorectal cancer (CRC). Methods: An analysis of DNA methylation and expression profles in CRC patients was performed to explore the critical methylations within NTRKs genes. The methylation marker was validated in a retrospectively collected cohort of 229 CRC patients and tested in other tumor types from TCGA. DNA methylation status was determined by quantita- tive methylation-specifc PCR (QMSP). Results: The profles in six CRC cohorts showed that NTRKs gene promoter was more frequently methylated in CRC compared to normal mucosa, which was associated with suppressed gene expression. We identifed a specifc methylated region within NTRK3 promoter targeted by cg27034819 and cg11525479 that best predicted survival outcome in CRC. NTRK3 promoter methylation showed independently predictive value for survival outcome in the validation cohort (P 0.004, HR 2.688, 95% CI [1.355, 5.333]). Based on this, a nomogram predicting survival outcome was developed with= a C-index of 0.705. Furthermore, the addition of NTRK3 promoter methylation improved the performance of currently-used prognostic model (AIC: 516.49 vs 513.91; LR: 39.06 vs 43.64, P 0.032). -
Chitinase 3-Like-1, a Novel Regulator of Th1/CTL Responses, As a Therapeutic Target for Increasing Anti-Tumor Immunity
BMB Rep. 2018; 51(5): 207-208 BMB www.bmbreports.org Reports Perspective Chitinase 3-like-1, a novel regulator of Th1/CTL responses, as a therapeutic target for increasing anti-tumor immunity Do-Hyun Kim1,2 & Je-Min Choi1,2,* 1Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, 2Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea Chitinase-Like Proteins (CLPs) are an evolutionarily conserved Chitinase is an enzyme that degrades chitin macromolecules, protein which lose their enzymatic activity for degrading chitin which are long-chain polymers of N-acetylglucosamine, a macromolecules. Chitinase-3-like-1 (Chi3l1) is a type of CLP component of cell walls in fungi and the exoskeletons of that is highly expressed in epithelial cells, macrophages, etc., arthropods. Surprisingly, several chitinase and chitinase-like and is known to have correlations with type 2 inflammation proteins (CLPs) have been identified in mammals, and their and cancer. Although the increased level of Chi3l1 in the expression is upregulated in various inflammatory diseases and blood was reported in various disease patients, the function of tumors. Ym1/2 (Chi3l3, Chi3l4) are well-known CLPs as Chi3l1 in adaptive immunity has been totally unknown. markers of alternative activated macrophages and contributors Recently, we found that Chi3l1 is expressed in T cells and has to allergic diseases. A recent study suggests that these CLPs a negative regulatory role in T-cell activation and proliferation. promote T-cell mediated-IL-17 production and neutrophilia A genetic ablation study of Chi3l1 in T cells showed in parasite infection. -
Curriculum Vitae
Revised 08/14/2019 Yang Zhou, Ph.D. CURRICULUM VITAE NAME Yang Zhou, Ph.D. DATE OF BIRTH March 11, 1983 CITIZENSHIP Chinese (U.S. Permanent Resident) CURRENT POSITION Assistant Professor of Molecular Microbiology & Immunology Division of Biology and Medicine, Brown University Sidney Frank Hall, Room 258 Box G-B5, 185 Meeting Street Providence, RI 02912 401-863-5933 Email: [email protected] ACADEMIC APPOINTMENTS 07/01/2014 Assistant Professor Department of Molecular Microbiology and Immunology Division of Biology and Medicine, Brown University Providence, RI 09/01/2011 Associate Research Scientist Section of Pulmonary, Critical Care and Sleep Medicine Department of Internal Medicine Yale University School of Medicine, New Haven, CT EDUCATION 2010-2011 Postdoctoral Associate Section of Pulmonary and Critical Care Medicine Department of Internal Medicine Yale University School of Medicine, New Haven, CT Mentor, Jack A. Elias, M.D. 2005-2010 Ph.D. in Biochemistry and Molecular Biology The University of Texas Health Sciences Center Houston, TX Advisor, Michael R. Blackburn, Ph.D. 2001-2005 B.S. in Biochemistry Nanjing University, Nanjing, China 1 Revised 08/14/2019 Yang Zhou, Ph.D. AWARDS AND HONORS 2013-2014 American Thoracic Society Abstract Scholarship Award 2011 American Thoracic Society Hermansky-Pudlak Syndrome Network Research Award 2010 President’s Research Scholarship The University of Texas Health Science Center 2010 Graduate Student Education Committee Poster Competition The University of Texas Health Sciences Center 2009 Dean’s -
In Vivo Imaging of Tgfβ Signalling Components Using Positron
REVIEWS Drug Discovery Today Volume 24, Number 12 December 2019 Reviews KEYNOTE REVIEW In vivo imaging of TGFb signalling components using positron emission tomography 1 1 2 Lonneke Rotteveel Lonneke Rotteveel , Alex J. Poot , Harm Jan Bogaard , received her MSc in drug 3 1 discovery and safety at the Peter ten Dijke , Adriaan A. Lammertsma and VU University in 1 Amsterdam. She is Albert D. Windhorst currently finishing her PhD at the VU University 1 Department of Radiology and Nuclear Medicine, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands Medical Center (VUmc) 2 under the supervision of A. Pulmonary Medicine, Institute for Cardiovascular Research, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands D. Windhorst and Adriaan A. Lammertsma. Her 3 research interest is on the development of positron Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The emission tomography (PET) tracers that target Netherlands selectively the activin receptor-like kinase 5 in vitro and in vivo. Alex J. Poot obtained his The transforming growth factor b (TGFb) family of cytokines achieves PhD in medicinal chemistry homeostasis through a careful balance and crosstalk with complex from Utrecht University. As postdoctoral researcher at signalling pathways. Inappropriate activation or inhibition of this pathway the VUmc, Amsterdam, he and mutations in its components are related to diseases such as cancer, developed radiolabelled anticancer drugs for PET vascular diseases, and developmental disorders. Quantitative imaging of imaging. In 2014, he accepted a research expression levels of key regulators within this pathway using positron fellowship from Memorial Sloan Kettering Cancer 13 emission tomography (PET) can provide insights into the role of this Center, New York to develop C-labelled probes for tumour metabolism imaging with magnetic resonance in vivo pathway , providing information on underlying pathophysiological imaging (MRI). -
Dipeptidase As Biomarkers Associated With
Cantó et al. Journal of Neuroinflammation 2014, 11:181 JOURNAL OF http://www.jneuroinflammation.com/content/11/1/181 NEUROINFLAMMATION RESEARCH Open Access Validation of semaphorin 7A and ala-β-his- dipeptidase as biomarkers associated with the conversion from clinically isolated syndrome to multiple sclerosis Ester Cantó1, Mar Tintoré1, Luisa Maria Villar2, Eva Borrás3, Jose Carlos Álvarez-Cermeño2, Cristina Chiva3, Eduard Sabidó3, Alex Rovira4, Xavier Montalban1 and Manuel Comabella1,5* Abstract Background: In a previous proteomics study using pooled cerebrospinal fluid (CSF) samples, we proposed apolipoprotein AI, apolipoprotein AIV, vitronectin, plasminogen, semaphorin 7A, and ala-β-his-dipeptidase as candidate biomarkers associated with the conversion to clinically definite multiple sclerosis (CDMS) in patients with clinically isolated syndromes (CIS). Here, we aimed to validate these results in individual CSF samples using alternative techniques. Methods: In a first replication study, levels of apolipoproteins AI and AIV, vitronectin, and plasminogen were measured by ELISA in CSF and serum of 56 CIS patients (29 patients who converted to CDMS (MS converters) and 27 patients who remained with CIS during follow-up (MS non-converters)) and 26 controls with other neurological disorders. Semaphorin 7A and ala-β-his-dipeptidase levels were determined by selected reaction monitoring (SRM) in CSF of 36 patients (18 MS converters, 18 non-converters) and 20 controls. In a second replication study, apolipoprotein AI levels were measured by ELISA in CSF of 74 CIS patients (47 MS converters, 27 non-converters) and 50 individual controls, and levels of semaphorin 7A and ala-beta-his-dipeptidase were determined by SRM in 49 patients (24 MS converters, 25 non-converters) and 22 controls. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Learning from Cadherin Structures and Sequences: Affinity Determinants and Protein Architecture
Learning from cadherin structures and sequences: affinity determinants and protein architecture Klára Fels ıvályi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Klara Felsovalyi All rights reserved ABSTRACT Learning from cadherin structures and sequences: affinity determinants and protein architecture Klara Felsovalyi Cadherins are a family of cell-surface proteins mediating adhesion that are important in development and maintenance of tissues. The family is defined by the repeating cadherin domain (EC) in their extracellular region, but they are diverse in terms of protein size, architecture and cellular function. The best-understood subfamily is the type I classical cadherins, which are found in vertebrates and have five EC domains. Among the five different type I classical cadherins, the binding interactions are highly specific in their homo- and heterophilic binding affinities, though their sequences are very similar. As previously shown, E- and N-cadherins, two prototypic members of the subfamily, differ in their homophilic K D by about an order of magnitude, while their heterophilic affinity is intermediate. To examine the source of the binding affinity differences among type I cadherins, we used crystal structures, analytical ultracentrifugation (AUC), surface plasmon resonance (SPR), and electron paramagnetic resonance (EPR) studies. Phylogenetic analysis and binding affinity behavior show that the type I cadherins can be further divided into two subgroups, with E- and N-cadherin representing each. In addition to the affinity differences in their wild-type binding through the strand-swapped interface, a second interface also shows an affinity difference between E- and N-cadherin. -
Chitinase-3-Like 1 Protein (CHI3L1) Locus Influences Cerebrospinal Fluid Levels of YKL-40 Yuetiva Deming1 , Kathleen Black1, David Carrell1, Yefei Cai1, Jorge L
Deming et al. BMC Neurology (2016) 16:217 DOI 10.1186/s12883-016-0742-9 RESEARCH ARTICLE Open Access Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40 Yuetiva Deming1 , Kathleen Black1, David Carrell1, Yefei Cai1, Jorge L. Del-Aguila1, Maria Victoria Fernandez1, John Budde1, ShengMei Ma1, Benjamin Saef1, Bill Howells1, Sarah Bertelsen2, Kuan-lin Huang3, Courtney L. Sutphen4, Rawan Tarawneh4,5,6, Anne M. Fagan4,5,6, David M. Holtzman4,5,6,7, John C. Morris4,5,6,7, Alison M. Goate2, Joseph D. Dougherty1,3 and Carlos Cruchaga1,6* Abstract Background: Alzheimer’s disease (AD) pathology appears several years before clinical symptoms, so identifying ways to detect individuals in the preclinical stage is imperative. The cerebrospinal fluid (CSF) Tau/Aβ42 ratio is currently the best known predictor of AD status and cognitive decline, and the ratio of CSF levels of chitinase-3-like 1 protein (CHI3L1, YKL-40) and amyloid beta (Aβ42) were reported as predictive, but individual variability and group overlap inhibits their utility for individual diagnosis making it necessary to find ways to improve sensitivity of these biomarkers. Methods: We used linear regression to identify genetic loci associated with CSF YKL-40 levels in 379 individuals (80 cognitively impaired and 299 cognitively normal) from the Charles F and Joanne Knight Alzheimer’s Disease Research Center. We tested correlations between YKL-40 and CSF Tau/Aβ42 ratio, Aβ42, tau, and phosphorylated tau (ptau181). We used studentized residuals from a linear regression model of the log-transformed, standardized protein levels and the additive reference allele counts from the most significant locus to adjust YKL-40 values and tested the differences in correlations with CSF Tau/Aβ42 ratio, Aβ42, tau, and ptau181.