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Identification of Novel Biomarkers and Candidate Small Molecule Drugs in Non-Small-Cell Lung Cancer by Integrated Microarray Analysis
OncoTargets and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis This article was published in the following Dove Press journal: OncoTargets and Therapy Qiong Wu1,2,* Background: Non-small-cell lung cancer (NSCLC) remains the leading cause of cancer Bo Zhang1,2,* morbidity and mortality worldwide. In the present study, we identified novel biomarkers Yidan Sun3 associated with the pathogenesis of NSCLC aiming to provide new diagnostic and therapeu- Ran Xu1 tic approaches for NSCLC. Xinyi Hu4 Methods: The microarray datasets of GSE18842, GSE30219, GSE31210, GSE32863 and Shiqi Ren4 GSE40791 from Gene Expression Omnibus database were downloaded. The differential Qianqian Ma5 expressed genes (DEGs) between NSCLC and normal samples were identified by limma Chen Chen6 package. The construction of protein–protein interaction (PPI) network, module analysis and Jian Shu7 enrichment analysis were performed using bioinformatics tools. The expression and prog- Fuwei Qi7 nostic values of hub genes were validated by GEPIA database and real-time quantitative fi Ting He7 PCR. Based on these DEGs, the candidate small molecules for NSCLC were identi ed by the CMap database. Wei Wang2 Results: A total of 408 overlapping DEGs including 109 up-regulated and 296 down- Ziheng Wang2 regulated genes were identified; 300 nodes and 1283 interactions were obtained from the 1 Medical School of Nantong University, PPI network. The most significant biological process and pathway enrichment of DEGs were Nantong 226001, People’s Republic of China; 2The Hand Surgery Research Center, response to wounding and cell adhesion molecules, respectively. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Early Growth Response 1 Regulates Hematopoietic Support and Proliferation in Human Primary Bone Marrow Stromal Cells
Hematopoiesis SUPPLEMENTARY APPENDIX Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells Hongzhe Li, 1,2 Hooi-Ching Lim, 1,2 Dimitra Zacharaki, 1,2 Xiaojie Xian, 2,3 Keane J.G. Kenswil, 4 Sandro Bräunig, 1,2 Marc H.G.P. Raaijmakers, 4 Niels-Bjarne Woods, 2,3 Jenny Hansson, 1,2 and Stefan Scheding 1,2,5 1Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, Lund, Sweden; 2Lund Stem Cell Center, Depart - ment of Laboratory Medicine, Lund University, Lund, Sweden; 3Division of Molecular Medicine and Gene Therapy, Department of Labora - tory Medicine, Lund University, Lund, Sweden; 4Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands and 5Department of Hematology, Skåne University Hospital Lund, Skåne, Sweden ©2020 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2019.216648 Received: January 14, 2019. Accepted: July 19, 2019. Pre-published: August 1, 2019. Correspondence: STEFAN SCHEDING - [email protected] Li et al.: Supplemental data 1. Supplemental Materials and Methods BM-MNC isolation Bone marrow mononuclear cells (BM-MNC) from BM aspiration samples were isolated by density gradient centrifugation (LSM 1077 Lymphocyte, PAA, Pasching, Austria) either with or without prior incubation with RosetteSep Human Mesenchymal Stem Cell Enrichment Cocktail (STEMCELL Technologies, Vancouver, Canada) for lineage depletion (CD3, CD14, CD19, CD38, CD66b, glycophorin A). BM-MNCs from fetal long bones and adult hip bones were isolated as reported previously 1 by gently crushing bones (femora, tibiae, fibulae, humeri, radii and ulna) in PBS+0.5% FCS subsequent passing of the cell suspension through a 40-µm filter. -
Pituitary Tumor Transforming Gene 1 Regulates Aurora Kinase a Activity
Oncogene (2008) 27, 6385–6395 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc ORIGINAL ARTICLE Pituitary tumor transforming gene 1 regulates Aurora kinase A activity Y Tong, A Ben-Shlomo, C Zhou, K Wawrowsky and S Melmed Department of Medicine, Cedars-Sinai Research Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA Pituitary tumor transforming gene 1 (PTTG1),a pathogenesis of estrogen-induced rat prolactinomas transforming gene highly expressed in several cancers,is (Heaney et al., 1999), and has been suggested as a a mammalian securin protein regulating both G1/S and prognostic marker for thyroid, breast (Solbach et al., G2/M phases. Using protein array screening,we showed 2004)and colon cancer invasiveness (Heaney et al., PTTG1 interacting with Aurora kinase A (Aurora-A), 2000). PTTG and HTLV-1 Tax exhibit a cooperative and confirmed the interaction using co-immunoprecipita- transforming activity (Sheleg et al., 2007), whereas small tion,His-tagged pull-down assays and intracellular interfering RNA (siRNA)directed against PTTG immunofluorescence colocalization. PTTG1 transfection suppressed lung cancer growth in nude mice (Kakar into HCT116 cells prevented Aurora-A T288 autopho- and Malik, 2006)and was also proposed as a subcellular sphorylation,inhibited phosphorylation of the histone H3 therapy for ovarian cancer (El-Naggar et al., 2007). Aurora-A substrate and resulted in abnormally condensed Overexpressed PTTG1 results in chromosome chromatin. PTTG1-null cell proliferation was more instability and aneuploidy, which has been suggested sensitive to Aurora-A knock down and to Aurora kinase as a mechanism underlying PTTG1 transforming Inhibitor III treatment. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
(PTTG1IP/PBF) Predicts Breast Cancer Survival
Repo et al. BMC Cancer (2017) 17:705 DOI 10.1186/s12885-017-3694-6 RESEARCHARTICLE Open Access PTTG1-interacting protein (PTTG1IP/PBF) predicts breast cancer survival Heli Repo1* , Natalia Gurvits1, Eliisa Löyttyniemi2, Marjukka Nykänen3, Minnamaija Lintunen1, Henna Karra4, Samu Kurki5, Teijo Kuopio3, Kati Talvinen1, Mirva Söderström1 and Pauliina Kronqvist1 Abstract Background: PTTG1-interacting protein (PTTG1IP) is an oncogenic protein, which participates in metaphase-anaphase transition of the cell cycle through activation of securin (PTTG1). PTTG1IP promotes the shift of securin from the cell cytoplasm to the nucleus, allowing the interaction between separase and securin. PTTG1IP overexpression has been previously observed in malignant disease, e.g. in breast carcinoma. However, the prognostic value of PTTG1IP in breast carcinoma patients has not previously been revealed. Methods: A total of 497 breast carcinoma patients with up to 22-year follow-up were analysed for PTTG1IP and securin immunoexpression. The results were evaluated for correlations with the clinical prognosticators and patient survival. Results: In our material, negative PTTG1IP immunoexpression predicted a 1.5-fold risk of breast cancer death (p =0.02). However, adding securin immunoexpression to the analysis indicated an even stronger and independent prognostic power in the patient material (HR = 2.5, p < 0.0001). The subcellular location of securin was found with potential prognostic value also among the triple-negative breast carcinomas (n = 96, p = 0.052). Conclusions: PTTG1IP-negativity alone and in combination with high securin immunoexpression indicates a high risk of breast cancer death, resulting in up to 14-year survival difference in our material. Keywords: PTTG1IP, PBF, Immunohistochemistry, Breast cancer, Prognosis Background nucleus, allowing the interaction between separase and Pituitary tumour transforming gene 1 interacting pro- securin [1]. -
Nuclear Localization of PTTG1 Promotes Migration and Invasion of Seminoma Tumor Through Activation of MMP-2
Nuclear Localization of PTTG1 Promotes Migration and Invasion of Seminoma Tumor Through Activation of MMP-2. Emanuela Teveroni International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Fiorella Di Nicuolo International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Giada Bianchetti Department of Neuroscience, section of Biophysics, Università Cattolica del Sacro Cuore Alan L. Epstein Department of Pathology, Keck school of medicine, University of Southern California, Los Angeles Giuseppe Grande International Scientic Institute "Paul VI", ISI, Fondazione Policlinico "A.Gemelli" IRCCS Giuseppe Maulucci Department of Neuroscience, section of Biophysics, Università Cattolica del Sacro Cuore Marco De Spirito Università Cattolica del Sacro Cuore: Universita Cattolica del Sacro Cuore Alfredo Pontecorvi Division of Endocrinology, Fondazione policlinico "A.Gemelli" IRCCS Domenico Milardi Division of Endocrinology, Fondazione policlinico "A.Gemelli" IRCCS Francesca Mancini ( [email protected] ) International Scientic Institute "Paul VI", ISI, Fondazione Policlinico 'A. Gemelli' IRCCS, Rome, Italy https://orcid.org/0000-0002-2459-8815 Research Keywords: PTTG1, seminoma cell lines, testicular cancer, PBF, MMP-2, invasiveness Posted Date: December 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-125309/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/53 Abstract Background: Seminoma is the most common subtype of testicular germ cell tumors (TGCTs) and its molecular patterns have not been fully claried. The pituitary tumor-transforming gene 1 (PTTG1) is a securin, inhibitor of premature sister chromatid segregation during mitosis and is overexpressed in many cancers. PTTG1 shows the ability to sustain the invasiveness of several cancer types through its transcriptional activity. -
Dissecting the DNA Binding Landscape and Gene Regulatory Network of P63 and P53
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.145540; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Dissecting the DNA binding landscape and gene regulatory network of p63 and p53 Konstantin Riege1, Helene Kretzmer2, Simon S. McDade3, Steve Hoffmann1, Martin Fischer1,# 1 Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany 2 Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany 3 Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK Running title: p63 GRN vs p53 GRN #To whom correspondence should be addressed. Email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.145540; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The transcription factor (TF) p53 is the best-known tumor suppressor, but its ancient sibling p63 (ΔNp63) is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available in recent years, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network (GRN). -
Atlas Journal
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 5, Sep-Oct 2008 Previous Issue / Next Issue Genes XAF1 (XIAP associated factor-1) (17p13.2). Stéphanie Plenchette, Wai Gin Fong, Robert G Korneluk. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 668-673. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/XAF1ID44095ch17p13.html WWP1 (WW domain containing E3 ubiquitin protein ligase 1) (8q21.3). Ceshi Chen. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 674-680. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/WWP1ID42993ch8q21.html TSPAN1 (tetraspanin 1) (1p34.1). David Murray, Peter Doran. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 681-683. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TSPAN1ID44178ch1p34.html TCL1B (T-cell leukemia/lymphoma 1B) (14q32.13). Herbert Eradat, Michael A Teitell. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 684-686. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/TCL1BID354ch14q32.html PVRL4 (poliovirus receptor-related 4) (1q23.3). Marc Lopez. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 687-690. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/PVRL4ID44141ch1q23.html PTTG1IP (pituitary tumor-transforming 1 interacting protein) (21q22.3). Vicki Smith, Chris McCabe. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (5): 691-694. -
An Integrated Data Analysis Approach to Characterize Genes Highly Expressed in Hepatocellular Carcinoma
Oncogene (2005) 24, 3737–3747 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma Mohini A Patil1,6, Mei-Sze Chua2,6, Kuang-Hung Pan3,6, Richard Lin3, Chih-Jian Lih3, Siu-Tim Cheung4, Coral Ho1,RuiLi2, Sheung-Tat Fan4, Stanley N Cohen3, Xin Chen1,5 and Samuel So2 1Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA; 2Department of Surgery and Asian Liver Center, Stanford University, Stanford, CA 94305, USA; 3Department of Genetics, Stanford University, Stanford, CA 94305, USA; 4Department of Surgery and Center for the Study of Liver Disease, University of Hong Kong, Hong Kong, China; 5Liver Center, University of California, San Francisco, CA 94143, USA Hepatocellular carcinoma (HCC) is one of the major cancer deaths worldwide (Parkin, 2001; Parkin et al., causes of cancer deaths worldwide. New diagnostic and 2001). Epidemiological and molecular genetic studies therapeutic options are needed for more effective and early have demonstrated that the development of HCC spans detection and treatment of this malignancy. We identified several decades, often starting with hepatitis B virus 703 genes that are highly expressed in HCC using DNA (HBV) or hepatitis C virus (HCV) infections. Chronic microarrays, and further characterized them in order to carriers of HBV or HCV are at much higher risk of uncover novel tumor markers, oncogenes, and therapeutic developing HCC, especially when infection has been targets for HCC. Using Gene Ontology annotations, genes accompanied by liver cirrhosis (El-Serag, H., 2001; El- with functions related to cell proliferation and cell cycle, Serag, H.B., 2002). -
PBF, a Proto-Oncogene in Esophageal Carcinoma Received November 18, 2018; Accepted July 26, 2019 1 Introduction
Open Med. 2019; 14: 748-756 Research Article Shi-hai Lian, Jun-ding Song, Yi Huang* PBF, a proto-oncogene in esophageal carcinoma https://doi.org/10.1515/med-2019-0086 received November 18, 2018; accepted July 26, 2019 1 Introduction Esophageal carcinoma (ESCA), with high invasiveness Abstract: Emerging evidence shows that the pituitary and lethality, is a type of malignant tumor occurring in tumour-transforming gene (PTTG)-binding factor (PBF) the digestive system. At present, ESCA is the eighth most functions as a proto-oncogene in some tumors. However, common cancer in the world and the sixth leading cause the precise functions of PBF in tumorigenesis and its of cancer-related deaths [1]. ESCA is classified into eso- action mechanisms remain largely unknown. Here for the phageal adenocarcinoma (EAC or EAD) and esophageal first time we demonstrated that PBF was associated with squamous cell carcinoma (ESCC) according to its histolog- a tumor-related cell phenotype in esophageal carcinoma ical type, while ESCC accounts for 90% of cases of ESCA (ESCA) and identified the involved signaling pathways. worldwide [1, 2]. Despite remarkable improvements in the PBF was up-regulated in ESCA tissues (Data from GEPIA) treatment of ESCA in recent years, the current prognosis and cells. Then we down-regulated PBF in ESCA cell lines, of ESCA is still poor because of the advanced diagnosis Eca-109 and TE-1, by using RNAi technology. Cell function and recurrence after cancer treatment. The 5-year survival analysis suggested that down-regulation of PBF could rate of patients is only 15%-25% [3, 4]. -
A Pathway of Targeted Autophagy Is Induced by DNA Damage In
A pathway of targeted autophagy is induced by DNA PNAS PLUS damage in budding yeast Vinay V. Eapena,1, David P. Watermana, Amélie Bernardb, Nathan Schiffmannc, Enrich Sayasd,e, Roarke Kamberf, Brenda Lemosa, Gonen Memisoglua, Jessie Anga, Allison Mazellaa, Silvia G. Chuartzmanc, Robbie J. Loewithd,e, Maya Schuldinerc, Vladimir Denicf, Daniel J. Klionskyb, and James E. Habera,2 aDepartment of Biology, Brandeis University, Waltham, MA 02454; bLife Sciences Institute, University of Michigan, Ann Arbor, MI 48109; cDepartment of Molecular Genetics, Weizmann Institute of Sciences, Rehovot, Israel 7610001; dDepartment of Molecular Biology, University of Geneva, CH-1211 Geneva 4, Switzerland; eInstitute of Genetics and Genomics in Geneva, University of Geneva, CH-1211 Geneva 4, Switzerland; and fMolecular and Cell Biology, Harvard University, Cambridge, MA 02138 Contributed by James E. Haber, December 5, 2016 (sent for review August 31, 2016; reviewed by Eric H. Baehrecke and Stephen J. Elledge) Autophagy plays a central role in the DNA damage response (DDR) by conditions. For example, in response to nutrient starvation, cells controlling the levels of various DNA repair and checkpoint proteins; recycle internal reserves of basic metabolites by the degradation however, how the DDR communicates with the autophagy pathway of proteins, or even whole organelles, by their digestion in the remains unknown. Using budding yeast, we demonstrate that global vacuole/lysosome. This process is initiated by the formation of genotoxic damage or even a single unrepaired double-strand break double-membraned cytosolic sequestering vesicles, termed phag- (DSB) initiates a previously undescribed and selective pathway of ophores, which can engulf either random portions of the cyto- autophagy that we term genotoxin-induced targeted autophagy plasm, organelles, or specific proteins (10).