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Methylation of the Homeobox Gene, HOPX, Is Frequently Detected in Poorly Differentiated Colorectal Cancer
ANTICANCER RESEARCH 31: 2889-2892 (2011) Methylation of the Homeobox Gene, HOPX, Is Frequently Detected in Poorly Differentiated Colorectal Cancer YOSHIKUNI HARADA, KAZUHIRO KIJIMA, KAZUKI SHINMURA, MAKIKO SAKATA, KAZUMA SAKURABA, KAZUAKI YOKOMIZO, YOUHEI KITAMURA, ATSUSHI SHIRAHATA, TETSUHIRO GOTO, HIROKI MIZUKAMI, MITSUO SAITO, GAKU KIGAWA, HIROSHI NEMOTO and KENJI HIBI Gastroenterological Surgery, Showa University Fujigaoka Hospital, 1-30 Fujigaoka, Aoba-ku, Yokohama 227-8501, Japan Abstract. Background: Homeodomein only protein x pathogenesis of colorectal cancer (4-8). It is also known that (HOPX) gene methylation has frequently been detected in gene promoter hypermethylation is involved in the cancer tissues. The methylation status of the HOPX gene in development and progression of cancer (9). An investigation colorectal cancer was examined and compared to the of genetic changes is important in order to clarify the clinocopathological findings. Materials and Methods: tumorigenic pathway of colorectal cancer (10). Eighty-nine tumor samples and corresponding normal tissues The homeodomain only protein x (HOPX) gene, also were obtained from colorectal cancer patients who known as NECC1 (not expressed in choriocarcinoma clone underwent surgery at our hospital. The methylation status of 1), LAGY (lung cancer-associated gene Y), and OB1 (odd the HOPX gene in these samples was examined by homeobox 1 protein), was initially identified as an essential quantitative methylation-specific PCR (qMSP). Subsequently, gene for the modulation of cardiac growth and development the clinicopathological findings were correlated with the (11). Three spliced transcript variants, HOPX-α, HOPX-β methylation status of the HOPX gene. Results: HOPX gene and HOPX-γ, encode the same protein, which contains a methylation was found in 46 (52%) out of the 89 colorectal putative homeodomain motif that acts as an adapter protein carcinomas, suggesting that it was frequently observed in to mediate transcriptional repression (12). -
Investigation of Functional Genes at Homologous Loci Identified Based
Journal of Atherosclerosis and Thrombosis Vol.22, No.5 455 Original Article Investigation of Functional Genes at Homologous Loci Identified Based on Genome-wide Association Studies of Blood Lipids via High-fat Diet Intervention in Rats using an in vivo Approach Koichi Akiyama, Yi-Qiang Liang, Masato Isono and Norihiro Kato Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan Aim: It is challenging to identify causal (or target) genes at individual loci detected using genome- wide association studies (GWAS). In order to follow up GWAS loci, we investigated functional genes at homologous loci identified using human lipid GWAS that responded to a high-fat, high-choles- terol diet (HFD) intervention in an animal model. Methods: The HFD intervention was carried out for four weeks in male rats of the spontaneously hypertensive rat strain. The liver and adipose tissues were subsequently excised for analyses of changes in the gene expression as compared to that observed in rats fed normal rat chow (n=8 per group). From 98 lipid-associated loci reported in previous GWAS, 280 genes with rat orthologs were initially selected as targets for the two-staged analysis involving screening with DNA microarray and validation with quantitative PCR (qPCR). Consequently, genes showing a differential expression due to HFD were examined for changes in the expression induced by atorvastatin, which was indepen- dently administered to the rats. Results: Using the HFD intervention in the rats, seven known (Abca1, Abcg5, Abcg8, Lpl, Nr1h3, Pcsk9 and Pltp) and three novel (Madd, Stac3 and Timd4) genes were identified as potential signifi- cant targets, with an additional list of 23 suggestive genes. -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Prospective Isolation of NKX2-1–Expressing Human Lung Progenitors Derived from Pluripotent Stem Cells
The Journal of Clinical Investigation RESEARCH ARTICLE Prospective isolation of NKX2-1–expressing human lung progenitors derived from pluripotent stem cells Finn Hawkins,1,2 Philipp Kramer,3 Anjali Jacob,1,2 Ian Driver,4 Dylan C. Thomas,1 Katherine B. McCauley,1,2 Nicholas Skvir,1 Ana M. Crane,3 Anita A. Kurmann,1,5 Anthony N. Hollenberg,5 Sinead Nguyen,1 Brandon G. Wong,6 Ahmad S. Khalil,6,7 Sarah X.L. Huang,3,8 Susan Guttentag,9 Jason R. Rock,4 John M. Shannon,10 Brian R. Davis,3 and Darrell N. Kotton1,2 2 1Center for Regenerative Medicine, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA. 3Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA. 4Department of Anatomy, UCSF, San Francisco, California, USA. 5Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA. 6Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA. 7Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. 8Columbia Center for Translational Immunology & Columbia Center for Human Development, Columbia University Medical Center, New York, New York, USA. 9Department of Pediatrics, Monroe Carell Jr. Children’s Hospital, Vanderbilt University, Nashville, Tennessee, USA. 10Division of Pulmonary Biology, Cincinnati Children’s Hospital, Cincinnati, Ohio, USA. It has been postulated that during human fetal development, all cells of the lung epithelium derive from embryonic, endodermal, NK2 homeobox 1–expressing (NKX2-1+) precursor cells. -
Detailed Review Paper on Retinoid Pathway Signalling
1 1 Detailed Review Paper on Retinoid Pathway Signalling 2 December 2020 3 2 4 Foreword 5 1. Project 4.97 to develop a Detailed Review Paper (DRP) on the Retinoid System 6 was added to the Test Guidelines Programme work plan in 2015. The project was 7 originally proposed by Sweden and the European Commission later joined the project as 8 a co-lead. In 2019, the OECD Secretariat was added to coordinate input from expert 9 consultants. The initial objectives of the project were to: 10 draft a review of the biology of retinoid signalling pathway, 11 describe retinoid-mediated effects on various organ systems, 12 identify relevant retinoid in vitro and ex vivo assays that measure mechanistic 13 effects of chemicals for development, and 14 Identify in vivo endpoints that could be added to existing test guidelines to 15 identify chemical effects on retinoid pathway signalling. 16 2. This DRP is intended to expand the recommendations for the retinoid pathway 17 included in the OECD Detailed Review Paper on the State of the Science on Novel In 18 vitro and In vivo Screening and Testing Methods and Endpoints for Evaluating 19 Endocrine Disruptors (DRP No 178). The retinoid signalling pathway was one of seven 20 endocrine pathways considered to be susceptible to environmental endocrine disruption 21 and for which relevant endpoints could be measured in new or existing OECD Test 22 Guidelines for evaluating endocrine disruption. Due to the complexity of retinoid 23 signalling across multiple organ systems, this effort was foreseen as a multi-step process. -
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. -
A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Dent Res Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 October 01. Published in final edited form as: J Dent Res. 2017 October ; 96(11): 1322–1329. doi:10.1177/0022034517716914. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts L.M. Moreno Uribe1, T. Fomina2, R.G. Munger3, P.A. Romitti4, M.M. Jenkins5, H.K. Gjessing2,6, M. Gjerdevik2,6, K. Christensen7, A.J. Wilcox8, J.C. Murray9, R.T. Lie2,6,*, and G.L. Wehby10,* 1Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA 2Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway 3Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA 4Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA 5National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA 6Norwegian Institute of Public Health, Bergen and Oslo, Norway 7Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark 8Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA 9Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA 10Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA Abstract Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. -
Identification of Potential Markers for Type 2 Diabetes Mellitus Via Bioinformatics Analysis
1868 MOLECULAR MEDICINE REPORTS 22: 1868-1882, 2020 Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis YANA LU1, YIHANG LI1, GUANG LI1* and HAITAO LU2* 1Key Laboratory of Dai and Southern Medicine of Xishuangbanna Dai Autonomous Prefecture, Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, Yunnan 666100; 2Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China Received March 20, 2019; Accepted January 20, 2020 DOI: 10.3892/mmr.2020.11281 Abstract. Type 2 diabetes mellitus (T2DM) is a multifactorial and cell proliferation’. These candidate genes were also involved in multigenetic disease, and its pathogenesis is complex and largely different signaling pathways associated with ‘PI3K/Akt signaling unknown. In the present study, microarray data (GSE201966) of pathway’, ‘Rap1 signaling pathway’, ‘Ras signaling pathway’ β-cell enriched tissue obtained by laser capture microdissection and ‘MAPK signaling pathway’, which are highly associated were downloaded, including 10 control and 10 type 2 diabetic with the development of T2DM. Furthermore, a microRNA subjects. A comprehensive bioinformatics analysis of microarray (miR)-target gene regulatory network and a transcription data in the context of protein-protein interaction (PPI) networks factor-target gene regulatory network were constructed based was employed, combined with subcellular location information on miRNet and NetworkAnalyst databases, respectively. to mine the potential candidate genes for T2DM and provide Notably, hsa-miR‑192-5p, hsa-miR‑124-5p and hsa-miR‑335-5p further insight on the possible mechanisms involved. First, appeared to be involved in T2DM by potentially regulating the differential analysis screened 108 differentially expressed expression of various candidate genes, including procollagen genes. -
Compound Heterozygosity for Novel Truncating Variants in the LMOD3 Gene As the Cause of Polyhydramnios in Two Successive Fetuses
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Online Research @ Cardiff CASE REPORT published: 13 September 2019 doi: 10.3389/fgene.2019.00835 Compound Heterozygosity for Novel Truncating Variants in the LMOD3 Gene as the Cause of Polyhydramnios in Two Successive Fetuses Ye Wang 1, Caixia Zhu 1, Liu Du 2, Qiaoer Li 3, Mei-Fang Lin 2, Claude Férec 4,5, David N. Cooper 6, Jian-Min Chen 4† and Yi Zhou 1*† 1 Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China, 2 Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China, 3 Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, China, 4 EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France, 5 CHU Brest, Service de Génétique, Brest, France, 6Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom Polyhydramnios is sometimes associated with genetic defects. However, establishing an Edited by: Fan Jin, accurate diagnosis and pinpointing the precise genetic cause of polyhydramnios in any Zhejiang University, China given case represents a major challenge because it is known to occur in association with Reviewed by: over 200 different conditions. Whole exome sequencing (WES) is now a routine part of Liang-Liang Fan, Central South University, China the clinical workup, particularly with diseases characterized by atypical manifestations and Wenbin Zou, significant genetic heterogeneity. Here we describe the identification, by means of WES, Changhai Hospital, China of novel compound heterozygous truncating variants in the LMOD3 gene [i.e., c.1412delA *Correspondence: (p.Lys471Serfs*18) and c.1283dupC (p.Gly429Trpfs*35)] in a Chinese family with two Yi Zhou [email protected] successive fetuses affected with polyhydramnios, thereby potentiating the prenatal diagnosis of nemaline myopathy (NM) in the proband. -
Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis
Figure S1. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. A Figure S1. Continued. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. B Figure S2. Comparative analysis of the variant frequency found by the KCC71 panel and calculated from publicly available cBioPortal datasets. For each of the 71 genes in the KCC71 panel, the frequency of variants was calculated as the variant number found in the examined cases. Datasets marked with different colors and sample numbers of prostate cancer are presented in the upper right. *Significantly high in the present study. Figure S3. Seven subnetworks extracted from each of seven public prostate cancer gene networks in TCNG (Table SVI). Blue dots represent genes that include initial seed genes (parent nodes), and parent‑child and child‑grandchild genes in the network. Graphical representation of node‑to‑node associations and subnetwork structures that differed among and were unique to each of the seven subnetworks. TCNG, The Cancer Network Galaxy. Figure S4. REVIGO tree map showing the predicted biological processes of prostate cancer in the Japanese. Each rectangle represents a biological function in terms of a Gene Ontology (GO) term, with the size adjusted to represent the P‑value of the GO term in the underlying GO term database. -
Differentiation of the Human PAX7
© 2020. Published by The Company of Biologists Ltd | Development (2020) 147, dev187344. doi:10.1242/dev.187344 HUMAN DEVELOPMENT TECHNIQUES AND RESOURCES ARTICLE Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro Ziad Al Tanoury1,2,3, Jyoti Rao2,3, Olivier Tassy1,Bénédicte Gobert1,4, Svetlana Gapon2, Jean-Marie Garnier1, Erica Wagner2, Aurore Hick4, Arielle Hall5, Emanuela Gussoni5 and Olivier Pourquié1,2,3,6,* ABSTRACT SC derive from the paraxial mesoderm, the embryonic tissue that Satellite cells (SC) are muscle stem cells that can regenerate adult forms the vertebral column and skeletal muscles (Chal and Pourquié, muscles upon injury. Most SC originate from PAX7+ myogenic 2017; Gros et al., 2005; Hutcheson et al., 2009; Kassar-Duchossoy precursors set aside during development. Although myogenesis has et al., 2005; Lepper and Fan, 2010; Relaix et al., 2005; Schienda et al., + been studied in mouse and chicken embryos, little is known about 2006). Pax3 myogenic precursors arise from the dorsal epithelial + human muscle development. Here, we report the generation of human compartment of the somite called the dermomyotome. Pax3 cells of induced pluripotent stem cell (iPSC) reporter lines in which fluorescent the dermomyotome lips activate Myf5, then downregulate Pax3 and proteins have been introduced into the PAX7 and MYOG loci. We use delaminate and differentiate into elongated post-mitotic myocytes single cell RNA sequencing to analyze the developmental trajectory of expressing myogenin (Myog) to form the first embryonic muscles + the iPSC-derived PAX7+ myogenic precursors. We show that the called myotomes (Chal and Pourquié, 2017). At the same time, Pax3 PAX7+ cells generated in culture can produce myofibers and self- myogenic precursors delaminate from the lateral edge of the renew in vitro and in vivo. -
Genome-Wide Linkage and Admixture Mapping of Type 2 Diabetes In
ORIGINAL ARTICLE Genome-Wide Linkage and Admixture Mapping of Type 2 Diabetes in African American Families From the American Diabetes Association GENNID (Genetics of NIDDM) Study Cohort Steven C. Elbein,1,2 Swapan K. Das,1,2 D. Michael Hallman,3 Craig L. Hanis,3 and Sandra J. Hasstedt4 OBJECTIVE—We used a single nucleotide polymorphism (SNP) map in a large cohort of 580 African American families to identify regions linked to type 2 diabetes, age of type 2 diabetes ype 2 diabetes is marked by a clear genetic diagnosis, and BMI. propensity, a high concordance in identical twins, tendencies for both diabetes and age of RESEARCH DESIGN AND METHODS—After removing outli- onset to be familial (1), and marked differences ers and problematic samples, we conducted linkage analysis T in prevalence among ethnic groups (2). Despite consider- using 5,914 SNPs in 1,344 individuals from 530 families. Linkage analysis was conducted using variance components for type 2 able evidence for a genetic predisposition, unraveling the diabetes, age of type 2 diabetes diagnosis, and BMI and nonpara- genetic etiology has been daunting, with few confirmed metric linkage analyses. Ordered subset analyses were con- genes identified from genome-wide linkage scans. Recent ducted ranking on age of type 2 diabetes diagnosis, BMI, waist successes with genome-wide association scans (3) have circumference, waist-to-hip ratio, and amount of European ad- greatly increased the number of confirmed genetic loci, mixture. Admixture mapping was conducted using 4,486 markers but these successes have been limited primarily to Cauca- not in linkage disequilibrium.