Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer
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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. -
Genomic and Expression Profiling of Chromosome 17 in Breast Cancer Reveals Complex Patterns of Alterations and Novel Candidate Genes
[CANCER RESEARCH 64, 6453–6460, September 15, 2004] Genomic and Expression Profiling of Chromosome 17 in Breast Cancer Reveals Complex Patterns of Alterations and Novel Candidate Genes Be´atrice Orsetti,1 Me´lanie Nugoli,1 Nathalie Cervera,1 Laurence Lasorsa,1 Paul Chuchana,1 Lisa Ursule,1 Catherine Nguyen,2 Richard Redon,3 Stanislas du Manoir,3 Carmen Rodriguez,1 and Charles Theillet1 1Ge´notypes et Phe´notypes Tumoraux, EMI229 INSERM/Universite´ Montpellier I, Montpellier, France; 2ERM 206 INSERM/Universite´ Aix-Marseille 2, Parc Scientifique de Luminy, Marseille cedex, France; and 3IGBMC, U596 INSERM/Universite´Louis Pasteur, Parc d’Innovation, Illkirch cedex, France ABSTRACT 17q12-q21 corresponding to the amplification of ERBB2 and collinear genes, and a large region at 17q23 (5, 6). A number of new candidate Chromosome 17 is severely rearranged in breast cancer. Whereas the oncogenes have been identified, among which GRB7 and TOP2A at short arm undergoes frequent losses, the long arm harbors complex 17q21 or RP6SKB1, TBX2, PPM1D, and MUL at 17q23 have drawn combinations of gains and losses. In this work we present a comprehensive study of quantitative anomalies at chromosome 17 by genomic array- most attention (6–10). Furthermore, DNA microarray studies have comparative genomic hybridization and of associated RNA expression revealed additional candidates, with some located outside current changes by cDNA arrays. We built a genomic array covering the entire regions of gains, thus suggesting the existence of additional amplicons chromosome at an average density of 1 clone per 0.5 Mb, and patterns of on 17q (8, 9). gains and losses were characterized in 30 breast cancer cell lines and 22 Our previous loss of heterozygosity mapping data pointed to the primary tumors. -
REG Gene Expression in Inflamed and Healthy Colon Mucosa Explored by in Situ Hybridisation
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Crossref Cell Tissue Res (2013) 352:639–646 DOI 10.1007/s00441-013-1592-z REGULAR ARTICLE REG gene expression in inflamed and healthy colon mucosa explored by in situ hybridisation Atle van Beelen Granlund & Ann Elisabet Østvik & Øystein Brenna & Sverre H. Torp & Bjørn I. Gustafsson & Arne Kristian Sandvik Received: 10 December 2012 /Accepted: 14 February 2013 /Published online: 22 March 2013 # The Author(s) 2013. This article is published with open access at Springerlink.com Abstract The regenerating islet-derived (REG) gene family used in situ hybridisation to demonstrate the cellular encodes a group of proteins highly expressed in several localisation of REG expression in healthy and diseased human pathologies, many of which are associated with colonic mucosa. Samples drawn from an IBD cohort includ- epithelial inflammation. All human family members, name- ing both inflamed and un-inflamed colonic mucosa are ly REG1A, REG1B, REG3A and REG4, are closely related described, as are samples from non-IBD inflammation and in genomic sequence and all are part of the c-type lectin healthy controls. Immunohistochemistry against known superfamily. REGs are highly expressed during inflamma- cell-type markers on serial sections has localised the expres- tory bowel disease (IBD)-related colonic inflammation and sion of REGs to metaplastic Paneth cells (REG1A, REG1B the in vivo expression pattern of REG1A and REG4 has and REG3A) and enteroendocrine cells (REG4), with a been localised by using immunohistochemistry. However, marked expansion of expression during inflammation. The the function of the encoded proteins is largely unknown and group of REGs can, based on gene expression patterns, be the cellular localisation of REG expression during colonic divided into at least two groups; REG1A, REG1B and inflammation has not been described. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Itraq Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment
International Journal of Molecular Sciences Article iTRAQ Quantitative Proteomic Analysis of Vitreous from Patients with Retinal Detachment Fátima Milhano Santos 1,2,3 ID , Leonor Mesquita Gaspar 1,2, Sergio Ciordia 4, Ana Sílvia Rocha 1,2, João Paulo Castro e Sousa 1,5, Alberto Paradela 4, Luís António Passarinha 1,3 ID and Cândida Teixeira Tomaz 1,2,* ID 1 CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; [email protected] (F.M.S.); [email protected] (L.M.G.); [email protected] (A.S.R.); [email protected] (J.P.C.e.S.); [email protected] (L.A.P.) 2 Chemistry Department, Faculty of Sciences, University of Beira Interior, 6201-001 Covilhã, Portugal 3 Laboratory of Pharmacology and Toxicology—UBIMedical, University of Beira Interior, 6200-284 Covilhã, Portugal 4 Unidad de Proteomica, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain; [email protected] (S.C.); [email protected] (A.P.) 5 Hospital Center Leiria-Pombal, 3100-462 Pombal, Portugal * Correspondence: [email protected]; Tel.: +351-275-242-021 Received: 8 February 2018; Accepted: 8 April 2018; Published: 11 April 2018 Abstract: Rhegmatogenous retinal detachment (RRD) is a potentially blinding condition characterized by a physical separation between neurosensory retina and retinal pigment epithelium. Quantitative proteomics can help to understand the changes that occur at the cellular level during RRD, providing additional information about the molecular mechanisms underlying its pathogenesis. In the present study, iTRAQ labeling was combined with two-dimensional LC-ESI-MS/MS to find expression changes in the proteome of vitreous from patients with RRD when compared to control samples. -
Datasheet Blank Template
SAN TA C RUZ BI OTEC HNOL OG Y, INC . Reg lll α/γ (S-13): sc-103862 BACKGROUND APPLICATIONS The regeneration (Reg) family consists of secretory proteins involved in liver, Reg III α/γ (S-13) is recommended for detection of Reg III α and Reg III γ of pancreatic, gastric and intestinal cell proliferation or differentiation. Members human origin by Western Blotting (starting dilution 1:200, dilution range of the Reg family are divided into four subclasses, designated types I, II, III 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein and IV, all of which share a common gene structure containing five introns and (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution six exons. Members of the Reg family have been implicated in the regulation range 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution of cell growth, tumorigenesis and the progression of cancer. Reg lll γ (regen - range 1:30-1:3000). erating islet-derived 3 γ), also known as pancreatitis-associated protein 1B, PA P1B or UNQ429, is a 175 amino acid secreted protein that is expressed Molecular Weight of Reg III α: 19 kDa. almost exclusively in pancreas, with low levels of expression in testis. Reg lll γ Molecular Weight of Reg lll γ: 16 kDa. functions as an antimicrobial protein involved in controlling bacterial prolifera - Positive Controls: human pancreas extract: sc-363770. tion and may be induced during acute pancreatitis. The gene encoding Reg lll γ maps to human chromosome 2, which houses over 1,400 genes and comprises nearly 8% of the human genome. -
Reg Proteins Promote Acinar-To-Ductal Metaplasia and Act As Novel Diagnostic and Prognostic Markers in Pancreatic Ductal Adenocarcinoma
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 47 Research Paper Reg proteins promote acinar-to-ductal metaplasia and act as novel diagnostic and prognostic markers in pancreatic ductal adenocarcinoma Qing Li1,*, Hao Wang2,*, George Zogopoulos3,4, Qin Shao5, Kun Dong6, Fudong Lv6, Karam Nwilati1, Xian-yong Gui7, Adeline Cuggia4, Jun-Li Liu1, Zu-hua Gao5 1Fraser Laboratories for Diabetes Research, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada 2Department of Oncology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, China 3Department of Surgery, McGill University Health Centre, Montreal, QC, Canada 4Quebec Pancreas Cancer Study, McGill University Health Centre, Montreal, QC, Canada 5Department of Pathology, McGill University Health Centre, Montreal, QC, Canada 6Department of Pathology, You An Hospital, Capital Medical University, Beijing, China 7Department of Pathology, University of Calgary, Calgary, AB, Canada *These authors have contributed equally Correspondence to: Zu-hua Gao, email: [email protected] Jun-Li Liu, email: [email protected] Keywords: Reg family proteins, pancreatic ductal adenocarcinoma, acinar-to-ductal metaplasia, pancreatic intraepithelial neoplasia, cholangiocarcinoma Received: March 01, 2016 Accepted: October 13, 2016 Published: October 24, 2016 ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignant tumor. Acinar-to-ductal metaplasia (ADM) and pancreatic intraepithelial neoplasia (PanIN) are both precursor lesions that lead to the development of PDAC. Reg family proteins (Reg1A, 1B, 3A/G, 4) are a group of calcium-dependent lectins that promote islet growth in response to inflammation and/or injuries. The aim of this study was to establish a role for Reg proteins in the development of PDAC and their clinical value as biomarkers. -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
Human Lectins, Their Carbohydrate Affinities and Where to Find Them
biomolecules Review Human Lectins, Their Carbohydrate Affinities and Where to Review HumanFind Them Lectins, Their Carbohydrate Affinities and Where to FindCláudia ThemD. Raposo 1,*, André B. Canelas 2 and M. Teresa Barros 1 1, 2 1 Cláudia D. Raposo * , Andr1 é LAQVB. Canelas‐Requimte,and Department M. Teresa of Chemistry, Barros NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829‐516 Caparica, Portugal; [email protected] 12 GlanbiaLAQV-Requimte,‐AgriChemWhey, Department Lisheen of Chemistry, Mine, Killoran, NOVA Moyne, School E41 of ScienceR622 Co. and Tipperary, Technology, Ireland; canelas‐ [email protected] NOVA de Lisboa, 2829-516 Caparica, Portugal; [email protected] 2* Correspondence:Glanbia-AgriChemWhey, [email protected]; Lisheen Mine, Tel.: Killoran, +351‐212948550 Moyne, E41 R622 Tipperary, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +351-212948550 Abstract: Lectins are a class of proteins responsible for several biological roles such as cell‐cell in‐ Abstract:teractions,Lectins signaling are pathways, a class of and proteins several responsible innate immune for several responses biological against roles pathogens. such as Since cell-cell lec‐ interactions,tins are able signalingto bind to pathways, carbohydrates, and several they can innate be a immuneviable target responses for targeted against drug pathogens. delivery Since sys‐ lectinstems. In are fact, able several to bind lectins to carbohydrates, were approved they by canFood be and a viable Drug targetAdministration for targeted for drugthat purpose. delivery systems.Information In fact, about several specific lectins carbohydrate were approved recognition by Food by andlectin Drug receptors Administration was gathered for that herein, purpose. plus Informationthe specific organs about specific where those carbohydrate lectins can recognition be found by within lectin the receptors human was body. -
Development and Validation of an Individualized Immune Prognostic Signature in Early-Stage Nonsquamous Non–Small Cell Lung Cancer
Supplementary Online Content Li B, Cui Y, Diehn M, Li R. Development and validation of an individualized immune prognostic signature in early-stage nonsquamous non–small cell lung cancer. JAMA Oncol. Published online July 6, 2017. doi:10.1001/jamaoncol.2017.1609 eMethods. Data Preprocessing, Assessment of Robustness, and Comparison With Commercialized Lung Biomarker eResults. Analysis and Robustness of IRGPs eTable 1. Details About the Data Sets Used in This Study eTable 2. Clinical and Pathologic Features of Patients in Meta-training, Meta-testing, and Independent Validation Cohorts eTable 3. Model Information About IRGPI eTable 4. Univariate and Multivariate Analyses of Prognostic Factors in Meta-training, Meta-testing, and Independent Validation Data Sets eTable 5. Biological Processes Overrepresented by Genes Consisting of IRGPI eTable 6. RMS Time Ratio Between Low- and High-Risk Groups Based on IRGPI or ICPI in Different Data Sets eFigure 1. Overview of the Construction and Validation of Immune and Composite Immune/Clinical Signatures eFigure 2. Time-Dependent ROC Curve for IRGPI in the Meta-training Data Set at 5 Years eFigure 3. Kaplan-Meier Curve of Overall Survival for Patients With Different IRGPI Risks eFigure 4. Kaplan-Meier Curve of Overall Survival for Early- and Late-Stage Patients With Different IRGPI Risks eFigure 5. Kaplan-Meier Curve of Overall Survival for Stage IA and IB Patients With Different IRGPI Risks eFigure 6. C-index Comparison Between IRGPI and 2 Existing Biomarkers eFigure 7. Time-Dependent ROC for ICPI and RMS Curve for ICPI and IRGPI in Meta-training Data Set eFigure 8. Kaplan-Meier Curves for Overall Survival of All Patients Stratified by the IRGPI and the ICPI eFigure 9. -
Immunoproteomic Analysis of the Excretory-Secretory Products Of
Wang et al. Parasites & Vectors (2017) 10:579 DOI 10.1186/s13071-017-2522-9 RESEARCH Open Access Immunoproteomic analysis of the excretory-secretory products of Trichinella pseudospiralis adult worms and newborn larvae Yang Wang1†, Xue Bai1†, Haichao Zhu1†, Xuelin Wang1, Haining Shi2, Bin Tang1, Pascal Boireau1,3, Xuepeng Cai4,5, Xuenong Luo5, Mingyuan Liu1,6* and Xiaolei Liu1* Abstract Background: The nematode Trichinella pseudospiralis is an intracellular parasite of mammalian skeletal muscle cells and exists in a non-encapsulated form. Previous studies demonstrated that T. pseudospiralis could induce a lower host inflammatory response. Excretory-secretory (ES) proteins as the most important products of host-parasite interaction may play the main functional role in alleviating host inflammation. However, the ES products of T. pseudospiralis early stage are still unknown. The identification of the ES products of the early stage facilitates the understanding of the molecular mechanisms of the immunomodulation and may help finding early diagnostic markers. Results: In this study, we used two-dimensional gel electrophoresis (2-DE)-based western blotting coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS/MS) to separate and identify the T. pseudospiralis adult worms ES products immunoreaction-positive proteins. In total, 400 protein spots were separated by 2-DE. Twenty-eight protein spots were successfully identified using the sera from infected pigs and were characterized to correlate with 12 different proteins of T. pseudospiralis, including adult-specific DNase II-10, poly-cysteine and histidine-tailed protein isoform 2, serine protease, serine/threonine-protein kinase ULK3, enolase, putative venom allergen 5, chymotrypsin-like elastase family member 1, uncharacterized protein, peptidase inhibitor 16, death-associated protein 1, deoxyribonuclease II superfamily and golgin-45. -
Cysteine‑Rich 61‑Associated Gene Expression Profile Alterations in Human Glioma Cells
MOLECULAR MEDICINE REPORTS 16: 5561-5567, 2017 Cysteine‑rich 61‑associated gene expression profile alterations in human glioma cells RUI WANG1, BO WEI2, JUN WEI3, YU TIAN2 and CHAO DU2 Departments of 1Radiology, 2Neurosurgery and 3Science and Education Section, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China Received January 28, 2016; Accepted February 20, 2017 DOI: 10.3892/mmr.2017.7216 Abstract. The present study aimed to investigate gene be critical for maintaining the role of CYR61 during cancer expression profile alterations associated with cysteine‑rich 61 progression. (CYR61) expression in human glioma cells. The GSE29384 dataset, downloaded from the Gene Expression Omnibus, Introduction includes three LN229 human glioma cell samples expressing CYR61 induced by doxycycline (Dox group), and three Cysteine‑rich 61 (CYR61) is a secreted, cysteine‑rich, control samples not exposed to doxycycline (Nodox group). heparin‑binding protein (1) involved in a variety of cellular Differentially expressed genes (DEGs) between the Dox and functions including adhesion, migration and proliferation (2). Nodox groups were identified with cutoffs of |log2 fold change Previously, Xie et al (3) reported that CYR61 was overexpressed (FC)|>0.5 and P<0.05. Gene ontology and Kyoto Encyclopedia in 66 primary gliomas compared with healthy brain samples, of Genes and Genomes pathway enrichment analyses for and that CYR61 expression was significantly correlated with DEGs were performed. Protein‑protein interaction (PPI) tumor grade and patient survival (3). CYR61‑overexpressing network and module analyses were performed to identify glioma cells were observed to have an increased proliferation the most important genes.