A Genetic Snapshot of Small Cell Lung Cancer
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Atlas Antibodies in Breast Cancer Research Table of Contents
ATLAS ANTIBODIES IN BREAST CANCER RESEARCH TABLE OF CONTENTS The Human Protein Atlas, Triple A Polyclonals and PrecisA Monoclonals (4-5) Clinical markers (6) Antibodies used in breast cancer research (7-13) Antibodies against MammaPrint and other gene expression test proteins (14-16) Antibodies identified in the Human Protein Atlas (17-14) Finding cancer biomarkers, as exemplified by RBM3, granulin and anillin (19-22) Co-Development program (23) Contact (24) Page 2 (24) Page 3 (24) The Human Protein Atlas: a map of the Human Proteome The Human Protein Atlas (HPA) is a The Human Protein Atlas consortium cell types. All the IHC images for Swedish-based program initiated in is mainly funded by the Knut and Alice the normal tissue have undergone 2003 with the aim to map all the human Wallenberg Foundation. pathology-based annotation of proteins in cells, tissues and organs expression levels. using integration of various omics The Human Protein Atlas consists of technologies, including antibody- six separate parts, each focusing on References based imaging, mass spectrometry- a particular aspect of the genome- 1. Sjöstedt E, et al. (2020) An atlas of the based proteomics, transcriptomics wide analysis of the human proteins: protein-coding genes in the human, pig, and and systems biology. mouse brain. Science 367(6482) 2. Thul PJ, et al. (2017) A subcellular map of • The Tissue Atlas shows the the human proteome. Science. 356(6340): All the data in the knowledge resource distribution of proteins across all eaal3321 is open access to allow scientists both major tissues and organs in the 3. -
Amplification of Chromosome 8 Genes in Lung Cancer Onur Baykara1, Burak Bakir1, Nur Buyru1, Kamil Kaynak2, Nejat Dalay3
Journal of Cancer 2015, Vol. 6 270 Ivyspring International Publisher Journal of Cancer 2015; 6(3): 270-275. doi: 10.7150/jca.10638 Research Paper Amplification of Chromosome 8 Genes in Lung Cancer Onur Baykara1, Burak Bakir1, Nur Buyru1, Kamil Kaynak2, Nejat Dalay3 1. Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Turkey 2. Department of Chest Surgery, Cerrahpasa Medical Faculty, Istanbul University, Turkey 3. Department of Basic Oncology, I.U. Oncology Institute, Istanbul University, Turkey Corresponding author: Prof. Dr. Nejat Dalay, I.U.Oncology Institute, 34093 Capa, Istanbul, Turkey. e-mail : [email protected]; Phone : 90 542 2168861; Fax : 90 212 5348078 © 2015 Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions. Received: 2014.09.25; Accepted: 2014.12.18; Published: 2015.01.20 Abstract Chromosomal alterations are frequent events in lung carcinogenesis and usually display regions of focal amplification containing several overexpressed oncogenes. Although gains and losses of chromosomal loci have been reported copy number changes of the individual genes have not been analyzed in lung cancer. In this study 22 genes were analyzed by MLPA in tumors and matched normal tissue samples from 82 patients with non-small cell lung cancer. Gene amplifications were observed in 84% of the samples. Chromosome 8 was found to harbor the most frequent copy number alterations. The most frequently amplified genes were ZNF703, PRDM14 and MYC on chromosome 8 and the BIRC5 gene on chromosome 17. The frequency of deletions were much lower and the most frequently deleted gene was ADAM9. -
Sequence Variation in the Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) and Trypanothione Reductase (TR) Genes of Trypanosoma Cruzi
Molecular & Biochemical Parasitology 121 (2002) 33Á/47 www.parasitology-online.com Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi Carlos A. Machado *, Francisco J. Ayala Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA Received 15 November 2001; received in revised form 25 January 2002 Abstract Dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) are important enzymes for the metabolism of protozoan parasites from the family Trypanosomatidae (e.g. Trypanosoma spp., Leishmania spp.) that are targets of current drug-design studies. Very limited information exists on the levels of genetic polymorphism of these enzymes in natural populations of any trypanosomatid parasite. We present results of a survey of nucleotide variation in the genes coding for those enzymes in a large sample of strains from Trypanosoma cruzi, the agent of Chagas’ disease. We discuss the results from an evolutionary perspective. A sample of 31 strains show 39 silent and five amino acid polymorphisms in DHFR-TS, and 35 silent and 11 amino acid polymorphisms in TR. No amino acid replacements occur in regions that are important for the enzymatic activity of these proteins, but some polymorphisms occur in sites previously assumed to be invariant. The sequences from both genes cluster in four major groups, a result that is not fully consistent with the current classification of T. cruzi in two major groups of strains. Most polymorphisms correspond to fixed differences among the four sequence groups. Two tests of neutrality show that there is no evidence of adaptivedivergence or of selectiveevents having shaped the distribution of polymorphisms and fixed differences in these genes in T. -
Identification and Analysis of Single-Nucleotide Polymorphisms in the Gemcitabine Pharmacologic Pathway
The Pharmacogenomics Journal (2004) 4, 307–314 & 2004 Nature Publishing Group All rights reserved 1470-269X/04 $30.00 www.nature.com/tpj ORIGINAL ARTICLE Identification and analysis of single-nucleotide polymorphisms in the gemcitabine pharmacologic pathway AK Fukunaga1 ABSTRACT 2 Significant variability in the antitumor efficacy and systemic toxicity of S Marsh gemcitabine has been observed in cancer patients. However, there are 1 DJ Murry currently no tools for prospective identification of patients at risk for TD Hurley3 untoward events. This study has identified and validated single-nucleotide HL McLeod2 polymorphisms (SNP) in genes involved in gemcitabine metabolism and transport. Database mining was conducted to identify SNPs in 14 genes 1Department of Clinical Pharmacy and Pharmacy involved in gemcitabine metabolism. Pyrosequencing was utilized to Practice, Purdue University, W. Lafayette, IN, determine the SNP allele frequencies in genomic DNA from European and 2 USA; Departments of Medicine, Genetics, and African populations (n ¼ 190). A total of 14 genetic variants (including 12 Molecular Biology and Pharmacology, Washington University School of Medicine and SNPs) were identified in eight of the gemcitabine metabolic pathway genes. the Siteman Cancer Center, St Louis, MO, USA; The majority of the database variants were observed in population samples. 3Department of Biochemistry and Molecular Nine of the 14 (64%) polymorphisms analyzed have allele frequencies that Biology, Indiana University School of Medicine, were found to be significantly different between the European and African Indianapolis, IN, USA populations (Po0.05). This study provides the first step to identify markers Correspondence: for predicting variability in gemcitabine response and toxicity. Dr HL McLeod, Washington University The Pharmacogenomics Journal (2004) 4, 307–314. -
TITLE PAGE Oxidative Stress and Response to Thymidylate Synthase
Downloaded from molpharm.aspetjournals.org at ASPET Journals on October 2, 2021 -Targeted -Targeted 1 , University of of , University SC K.W.B., South Columbia, (U.O., Carolina, This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. The final version may differ from this version. This article has not been copyedited and formatted. -
Logistic Regression Analysis for the Identification of the Metastasis-Associated Signaling Pathways of Osteosarcoma
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 41: 1233-1244, 2018 Logistic regression analysis for the identification of the metastasis-associated signaling pathways of osteosarcoma YANG LIU1, WEI SUN2, XIAOJUN MA2, YUEDONG HAO3, GANG LIU3, XIAOHUI HU3, HOULAI SHANG3, PENGFEI WU3, ZEXUE ZHAO3 and WEIDONG LIU3 1Department of Orthopedics, Affiliated Hospital of Inner Mongolia University for The Nationalities, Tongliao, Inner Mongolia 028007; 2Department of Orthopaedics, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080; 3Department of Orthopedics, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu 223300, P.R. China Received February 20, 2017; Accepted September 26, 2017 DOI: 10.3892/ijmm.2018.3360 Abstract. Osteosarcoma (OS) is the most common histological migration were identified as the terms that were significantly type of primary bone cancer. The present study was designed different. ICAM1, PDGFB, PDGFRB and TGFB1 were iden- to identify the key genes and signaling pathways involved in the tified to be enriched in cell migration and regulation of cell metastasis of OS. Microarray data of GSE39055 were down- migration. Nucleotide excision repair and the Wnt signaling loaded from the Gene Expression Omnibus database, which pathway were the metastasis-associated pathways of OS. In included 19 OS biopsy specimens before metastasis (control addition, ICAM1, PDGFB, PDGFRB and TGFB1, which were group) and 18 OS biopsy specimens after metastasis (case involved in cell migration and regulation of cell migration may group). After the differentially expressed genes (DEGs) were affect the metastasis of OS. identified using the Linear Models for Microarray Analysis package, hierarchical clustering analysis and unsupervised Introduction clustering analysis were performed separately, using orange software and the self-organization map method. -
Role of MTDH, FOXM1 and Micrornas in Drug Resistance in Hepatocellular Carcinoma
Diseases 2014, 2, 209-225; doi:10.3390/diseases2030209 OPEN ACCESS diseases ISSN 2079-9721 www.mdpi.com/journal/diseases/ Review Role of MTDH, FOXM1 and microRNAs in Drug Resistance in Hepatocellular Carcinoma Xiangbing Meng 1,2,*, Eric J. Devor 1, Shujie Yang 1, Brandon M. Schickling 3 and Kimberly K. Leslie 1,2 1 Department of Obstetrics and Gynecology, The University of Iowa, Iowa City, IA 52242, USA 2 Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA 3 Department of Internal Medicine, The University of Iowa, Iowa City, IA 52242, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]. Received: 16 April 2014; in revised form: 24 June 2014 / Accepted: 25 June 2014 / Published: 1 July 2014 Abstract: Hepatocellular carcinoma (HCC) is one of the most lethal malignancies due to underlying co-morbid cirrhosis and chemo-resistance. Vaccination and improved treatment for hepatitis are the most effective means to reduce the burden of liver cancer worldwide. Expression of biomarkers such as AFP (alpha-fetoprotein), DDK1 (Dickkopf WNT Signaling Pathway Inhibitor 1) and microRNAs in blood are being tested for early screening of liver cancer. Since 2008, sorafenib has been used as the standard molecular targeting agent for HCC. However, overall outcomes for sorafenib alone or in combination with other tyrosine kinase inhibitors are unsatisfactory. Whether simultaneously or sequentially, addiction switches and compensatory pathway activation in HCC, induced by sorafenib treatment, may induce acquired resistance. Forkhead box M1 (FOXM1) and metadherin (MTDH) have been shown to be master regulators of different aspects of tumorigenesis, including angiogenesis, invasion, metastasis and drug resistance. -
Nicotinamide Phosphoribosyltransferase Deficiency Potentiates the Anti
JPET Fast Forward. Published on February 2, 2018 as DOI: 10.1124/jpet.117.246199 This article has not been copyedited and formatted. The final version may differ from this version. JPET #246199 Nicotinamide Phosphoribosyltransferase Deficiency Potentiates the Anti- proliferative Activity of Methotrexate through Enhanced Depletion of Intracellular ATP Rakesh K. Singh, Leon van Haandel, Daniel P. Heruth, Shui Q. Ye, J. Steven Leeder, Mara L. Becker, Ryan S. Funk Department of Pharmacy Practice, The University of Kansas Medical Center, Kansas City, KS Downloaded from 66160 (RKS and RSF) Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy jpet.aspetjournals.org Kansas City, Kansas City, MO 64108 (LVH, JSL, and MLB) Division of Rheumatology, Children’s Mercy Kansas City, Kansas City, MO 64108 (MLB) Division of Experimental and Translational Genetics, Children’s Mercy Kansas City, Kansas at ASPET Journals on September 27, 2021 City, MO 64108 (DPH and SQY) Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, KS 66160 (JSL and RSF) Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, Kansas City, MO 64108 (SQY) 1 JPET Fast Forward. Published on February 2, 2018 as DOI: 10.1124/jpet.117.246199 This article has not been copyedited and formatted. The final version may differ from this version. JPET #246199 Running title: NAMPT Deficiency Potentiates ATP Depletion by Methotrexate Corresponding -
Contribution of Alternative Splicing to Breast Cancer Metastasis
Meng et al. J Cancer Metastasis Treat 2019;5:21 Journal of Cancer DOI: 10.20517/2394-4722.2018.96 Metastasis and Treatment Review Open Access Contribution of alternative splicing to breast cancer metastasis Xiangbing Meng1,2, Shujie Yang1,2, Jun Zhang2,3, Huimin Yu1,4 1Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA. 2Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA. 3Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA. 4Department of Pathogenic Biology, Shenzhen University School of medicine, Shenzhen 518060,China. Correspondence to: Dr. Xiangbing Meng, Department of Obstetrics and Gynecology, The University of Iowa, 375 Newton Road, Iowa City, IA 52242, USA. E-mail: [email protected] How to cite this article: Meng X, Yang S, Zhang J, Yu H. Contribution of alternative splicing to breast cancer metastasis. J Cancer Metastasis Treat 2019;5:21. http://dx.doi.org/10.20517/2394-4722.2018.96 Received: 10 Dec 2018 Accepted: 25 Jan 2019 Published: 22 Mar 2019 Science Editor: William P. Schiemann Copy Editor: Cai-Hong Wang Production Editor: Huan-Liang Wu Abstract Alternative splicing is a major contributor to transcriptome and proteome diversity in eukaryotes. Comparing to normal samples, about 30% more alternative splicing events were recently identified in 32 cancer types included in The Cancer Genome Atlas database. Some alternative splicing isoforms and their encoded proteins contribute to specific cancer hallmarks. In this review, we will discuss recent progress regarding the contributions of alternative splicing to breast cancer metastasis. -
Genomics and Functional Genomics of Malignant Pleural Mesothelioma
International Journal of Molecular Sciences Review Genomics and Functional Genomics of Malignant Pleural Mesothelioma Ece Cakiroglu 1,2 and Serif Senturk 1,2,* 1 Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; [email protected] 2 Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey * Correspondence: [email protected] Received: 22 July 2020; Accepted: 20 August 2020; Published: 1 September 2020 Abstract: Malignant pleural mesothelioma (MPM) is a rare, aggressive cancer of the mesothelial cells lining the pleural surface of the chest wall and lung. The etiology of MPM is strongly associated with prior exposure to asbestos fibers, and the median survival rate of the diagnosed patients is approximately one year. Despite the latest advancements in surgical techniques and systemic therapies, currently available treatment modalities of MPM fail to provide long-term survival. The increasing incidence of MPM highlights the need for finding effective treatments. Targeted therapies offer personalized treatments in many cancers. However, targeted therapy in MPM is not recommended by clinical guidelines mainly because of poor target definition. A better understanding of the molecular and cellular mechanisms and the predictors of poor clinical outcomes of MPM is required to identify novel targets and develop precise and effective treatments. Recent advances in the genomics and functional genomics fields have provided groundbreaking insights into the genomic and molecular profiles of MPM and enabled the functional characterization of the genetic alterations. This review provides a comprehensive overview of the relevant literature and highlights the potential of state-of-the-art genomics and functional genomics research to facilitate the development of novel diagnostics and therapeutic modalities in MPM. -
Tumor Suppressive Microrna-375 Regulates Oncogene AEG-1&Sol;MTDH in Head and Neck Squamous Cell Carcinoma (HNSCC)
Journal of Human Genetics (2011) 56, 595–601 & 2011 The Japan Society of Human Genetics All rights reserved 1434-5161/11 $32.00 www.nature.com/jhg ORIGINAL ARTICLE Tumor suppressive microRNA-375 regulates oncogene AEG-1/MTDH in head and neck squamous cell carcinoma (HNSCC) Nijiro Nohata1,2, Toyoyuki Hanazawa2, Naoko Kikkawa1,2, Muradil Mutallip1,2, Daiju Sakurai2, Lisa Fujimura3, Kazumori Kawakami4, Takeshi Chiyomaru4, Hirofumi Yoshino4, Hideki Enokida4, Masayuki Nakagawa4, Yoshitaka Okamoto2 and Naohiko Seki1 Our microRNA (miRNA) expression signatures of hypopharyngeal squamous cell carcinoma, maxillary sinus squamous cell carcinoma and esophageal squamous cell carcinoma revealed that miR-375 was significantly reduced in cancer tissues compared with normal epithelium. In this study, we focused on the functional significance of miR-375 in cancer cells and identification of miR-375-regulated novel cancer networks in head and neck squamous cell carcinoma (HNSCC). Restoration of miR-375 showed significant inhibition of cell proliferation and induction of cell apoptosis in SAS and FaDu cell lines, suggesting that miR-375 functions as a tumor suppressor. We adopted genome-wide gene expression analysis to search for miR-375-regulated molecular targets. Gene expression data and luciferase reporter assays revealed that AEG-1/MTDH was directly regulated by miR-375. Cancer cell proliferation was significantly inhibited in HNSCC cells transfected with si-AEG-1/MTDH. In addition, expression levels of AEG-1/MTDH were significantly upregulated in cancer tissues. Therefore, AEG-1/MTDH may function as an oncogene in HNSCC. The identification of novel tumor suppressive miRNA and its regulated cancer pathways could provide new insights into potential molecular mechanisms of HNSCC oncogenesis. -
Folate Binding Site of Flavin-Dependent Thymidylate
Folate binding site of flavin-dependent thymidylate synthase Eric M. Koehna, Laura L. Perissinottia, Salah Moghrama, Arjun Prabhakarb, Scott A. Lesleyc, Irimpan I. Mathewsb,1, and Amnon Kohena,1 aDepartment of Chemistry, University of Iowa, Iowa City, IA 52242; bStanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025; and cThe Joint Center for Structural Genomics at The Genomics Institute of Novartis Research Foundation, San Diego, CA 92121 Edited* by Robert M. Stroud, University of California, San Francisco, CA, and approved August 14, 2012 (received for review April 12, 2012) The DNA nucleotide thymidylate is synthesized by the enzyme cofactor to reduce the bound flavin, but a reactive binding site for thymidylate synthase, which catalyzes the reductive methylation nicotinamides has not been identified or proposed. of deoxyuridylate using the cofactor methylene-tetrahydrofolate FDTS enzymes use a flavin adenine dinucleotide (FAD) pros- (CH2H4folate). Most organisms, including humans, rely on the thetic group to catalyze the redox chemistry, which can be divided thyA- or TYMS-encoded classic thymidylate synthase, whereas, into reductive and oxidative-half reactions. The FAD can be re- Rickettsia certain microorganisms, including all and other patho- duced to FADH2 by nicotinamides, ferrodoxin, and other small gens, use an alternative thyX-encoded flavin-dependent thymidy- molecule reductants (e.g., dithionite). Although the reductive half- late synthase (FDTS). Although several crystal structures of FDTSs reaction is activated by dUMP the conversion of dUMP to dTMP have been reported, the absence of a structure with folates limits occurs during the oxidative half-reaction (FADH2 →FAD) (8, 10, understanding of the molecular mechanism and the scope of drug 14, 18, 27).