DOCSLIB.ORG

Free PDF Download

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Free PDF Download European Review for Medical and Pharmacological Sciences 2020; 24: 1877-1886 Identification of lung adenocarcinoma-specific exosome RNAs in peripheral blood by RNA-Seq analysis X.-Q. LIU1, A. TUFMAN1, R. KIEFL1, G.-F. LI2, Q.-L. MA2, R.M. HUBER1 1Department of Internal Medicine V, Division of Respiratory Medicine and Thoracic Oncology, Ludwig-Maximilians University (LMU), Thoracic Oncology Centre Munich; Comprehensive Pneumology Center Munich, Member of the German Center for Lung Research (DZL), Munich, Bavaria, Germany 2Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center. Kunming, Yunnan, China Abstract. – OBJECTIVE: Several plasma-de- carcinoma patients, who were more abundant/ rived exosome RNAs have been identified as key detectable than healthy volunteers. regulators in cancer development. They have CONCLUSIONS: Our data indicate that been considered as potential biomarkers for a plasma-derived exosome RNAs, UGT1A1, non-invasive “liquid biopsy” to diagnose and and BAIAP2L1, as well as the eight isolated assess the progression of cancer. This study pseudogenes could serve as diagnostic and aimed to identify human lung adenocarcino- prognostic biomarkers for an effective non-inva- ma-specific exosome RNAs in peripheral blood, sive “liquid biopsy” of lung adenocarcinomas. while assessing the feasibility and efficiency of this recently developed deep-sequencing tech- Key Words: nology for transcriptome profiling. Lung adenocarcinoma, Pseudogenes, Exosome, PATIENTS AND METHODS: Plasma-derived Biomarkers. exosome RNAs were isolated from 13 lung ad- enocarcinoma patients, 3 patients with benign lung diseases, and 15 healthy volunteers. RNA- seq analysis of ribosomal RNA-depleted total RNA was performed. RNAs differentially ex- Introduction pressed between lung adenocarcinoma and be- nign lung diseases or healthy volunteers were Lung cancer is the predominant cause of identified, followed by GO and KEGG pathway cancer-related death worldwide1. Non-small cell enrichment analyses for the identification of key lung cancer (NSCLC) accounts for approxi- exosome RNAs associated with lung adenocar- mately 80% of all lung cancer cases, main- cinomas. RESULTS: Significant differentially ex ly including adenocarcinomas, squamous cell - 2-4 pressed RNAs, such as UDP glucuronosyl- carcinomas, and large cell carcinomas . In transferase family 1 member A1 (UGT1A1) and spite of great advances in NSCLC therapy, the BAI1-associated protein 2 like 1 (BAIAP2L1), prognosis for NSCLC patients remains poor5. A were identified as differentially expressed be- previous research6 has indicated that the use of tween lung adenocarcinoma patients and pa- biomarkers to guide lung cancer therapies will tients with benign lung diseases. Eight pseudogenes, including Tropomyosin 1 (Al- be beneficial for the treatment of this malignan- pha) Pseudogene (LOC100129096), Prothymo- cy. However, there are no reliable diagnostic and sin, Alpha Pseudogene 2 (PTMAP2), Cell Di- prognostic tools for the detection and identifica- vision Cycle 14C, Pseudogene (CDC14C), Tro- tion of changes in the disease status. Therefore, pomyosin 1 (Alpha) Pseudogene (LOC643634), seeking biomarkers is an important component Ferritin Heavy Chain 1 Pseudogene 2 (FTH1P2), of the lung cancer research. Actin Related Protein 2/3 Complex Subunit 3 Exosomes are 30-100 nm diameter mem- Pseudogene 3 (ARPC3P3), Ferritin Heavy Chain 1 Pseudogene 11 (FTH1P11), and Prothymosin brane-enclosed extracellular vesicles originating 7 Alpha Pseudogene 5 (PTMAP5) were identified from endosomes . Under normal and stressful from plasma-derived exosomes in lung adeno- conditions, almost all cell types can secrete exo- Corresponding Author: Rudolf M. Huber, MD; e-mail: [email protected] 1877 X.-Q. Liu, A. Tufman, R. Kiefl, G.-F. Li, Q.-L. Ma, R.M. Huber somes, and cancer cells are confirmed to pro- amine Tetraacetic Acid (EDTA)-anticoagulated duce more exosomes than normal cells from the blood collection tubes (BD Vacutainer, Plymouth, same organ8. Moreover, exosomes are found to UK). After centrifugation, plasma samples were carry various biological molecules, such as lip- then collected and saved at –80° C. Plasma-de- ids, proteins, and nucleic acid species, including rived exosome RNAs were isolated using the mRNAs, miRNA, lncRNAs, rRNAs, genomic exoRNeasy Serum Plasma Kit (cat. no. 77064; DNA, and pseudogenes8,9. Increasing evidence Qiagen GmbH, Hilden, Germany), which was has shown that those exosomal-derived mole- designed for the rapid purification of total vesic- cules play a crucial role in intercellular signal ular RNAs, including non-coding RNA, mRNA, transduction, immunoregulation, and tumorigen- miRNA, and other small RNAs from serum or esis. Also, these molecules, present in exosomes plasma. Sterility was maintained and all proce- in bodily fluids, are considered promising bio- dures were performed according to the protocols markers for the diagnosis and prognosis of many recommended by the manufacturers. diseases9,10, including a variety of cancers11-13. Authors14,15 have shown that several plasma-de- Construction of the cDNA Library and rived exosome cargoes, such as exosome RNAs High-Throughput Sequencing and proteins, are overexpressed in NSCLC and The rRNA removal reagents in the Ribo-Zero have been suggested as potential biomarkers Gold Kit (Epicentre Biotechnologies, Madison, for a non-invasive “liquid biopsy”. Noteworthy, WI, USA) were used for the rRNA removal. Us- exosomal LRG1 has been identified as a poten- ing the ScriptSeq™ mRNA-Seq Library Prepa- tial urinary biomarker for detecting NSCLC16. ration Kit (Epicentre, Biotechnologies, Madison, Meanwhile, a number of techniques have been WI, USA), the rRNA-depleted RNA was used for used and are under development for exosome the construction of cDNA libraries. The cDNA li- genetic cargo analysis, such as quantitative Real braries were then sequenced on Illumina® GAIIx Time Polymerase Chain Reaction (qRT-PCR), and HiSeq 2000 platforms. microarray analyses, and next-generation se- quencing. Due to the power of RNA sequencing, Preprocessing and Quality Control of which involves a combination of identification Sequencing Data and quantification in a single high-throughput For the retrieval of the clean reads, prepro- sequencing assay, the adoption of this technolo- cessing was performed to remove the adapt- gy has spread quickly. er sequences and the reads with a low quality In the present study, our findings provide a of < 16 were removed. The quality control of theoretical basis for the development of novel clean reads was then conducted using FastQC diagnostic and predictive biomarkers for lung (http://www.bioinformatics.bbsrc.ac.uk/projects/ adenocarcinomas. fastqc/). Moreover, RNA-seq intrinsic biases, such as nucleotide composition bias and GC bias, were assessed. Patients and Methods Sequence Alignment and Patient Samples and Exosome Transcriptome Assembly RNAs Isolation Genomic sequences of various organisms and A total of 13 lung adenocarcinoma cancer pa- their annotation information were deposited in tients with newly diagnosed, untreated, histolog- the UCSC Genome Browser database (http:// ically confirmed lung adenocarcinoma according genome.ucsc.edu)17. Thus, the clean reads were to the World Health Organization classification mapped to the human reference genome (hg19) were enrolled. Three patients with benign lung in the UCSC database using Tophat2.1.0 (http:// diseases and 15 healthy volunteers were recruited tophat.cbcb.umd.edu)18 with default parameters. as controls. All the patients and healthy volunteer According to the results of the sequence align- blood samples came from The Third Affiliated ment, transcript assembly was then performed Hospital of Kunming Medical University, Yun- using StringTie19. The transcript assemblies were nan Cancer Center, China. This investigation further merged using the Cuffmerge tool20. Cuff- was approved by the local Ethics Committee and merge results were compared with the Ensem- all participants gave informed consent. About 10 bl database (http://ensemblgenomes.org/) using ml blood samples were collected in Ethylene Di- Cuffcompare20 to find known and novel RNAs. 1878 Identification of lung adenocarcinoma-specific exosome RNAs Bioinformatics Analysis Notably, LOC100129096, PTMAP2, CDC14C, Differentially expressed RNAs (including LOC643634, FTH1P2, ARPC3P3, FTH1P11, and mRNAs and non-coding RNAs) were identified PTMAP5 were pseudogenes. in lung adenocarcinoma patient plasma-derived Differentially expressed RNAs between lung exosomes using the DESeq2 package21. The cut- adenocarcinoma and patients with benign lung off values were an absolute fold change ≥ 2, with diseases were significantly enriched in the GO p ≤ 0.05. BP functions, associated with steroid metabolic To understand the biological functions of processes, protein activation cascades, and the differentially expressed RNAs, functional en- acute inflammatory response. While, GO CC richment analyses were performed. Gene On- functions related to blood microparticles, the tology (GO, http://www.geneontology.org/)22 cytoplasmic membrane-bounded vesicle lumen, contains a set of terms for the unification and vesicle lumen, and GO MF functions were of the biology of large-scale gene lists. GO associated with monooxygenase activity, steroid terms mainly include cellular component (CC), hydroxylase activity, and iron ion binding (Table molecular function (MF), and biological pro- I, Figure 1). cess (BP).
Load more

Recommended publications
  • Analyses of Allele-Specific Gene Expression in Highly Divergent
    ARTICLES Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance James J Crowley1,10, Vasyl Zhabotynsky1,10, Wei Sun1,2,10, Shunping Huang3, Isa Kemal Pakatci3, Yunjung Kim1, Jeremy R Wang3, Andrew P Morgan1,4,5, John D Calaway1,4,5, David L Aylor1,9, Zaining Yun1, Timothy A Bell1,4,5, Ryan J Buus1,4,5, Mark E Calaway1,4,5, John P Didion1,4,5, Terry J Gooch1,4,5, Stephanie D Hansen1,4,5, Nashiya N Robinson1,4,5, Ginger D Shaw1,4,5, Jason S Spence1, Corey R Quackenbush1, Cordelia J Barrick1, Randal J Nonneman1, Kyungsu Kim2, James Xenakis2, Yuying Xie1, William Valdar1,4, Alan B Lenarcic1, Wei Wang3,9, Catherine E Welsh3, Chen-Ping Fu3, Zhaojun Zhang3, James Holt3, Zhishan Guo3, David W Threadgill6, Lisa M Tarantino7, Darla R Miller1,4,5, Fei Zou2,11, Leonard McMillan3,11, Patrick F Sullivan1,5,7,8,11 & Fernando Pardo-Manuel de Villena1,4,5,11 Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect.
    [Show full text]
  • Supplemental Information
    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.
    [Show full text]
  • Revostmm Vol 10-4-2018 Ingles Maquetaciûn 1
    108 ORIGINALS / Rev Osteoporos Metab Miner. 2018;10(4):108-18 Roca-Ayats N1, Falcó-Mascaró M1, García-Giralt N2, Cozar M1, Abril JF3, Quesada-Gómez JM4, Prieto-Alhambra D5,6, Nogués X2, Mellibovsky L2, Díez-Pérez A2, Grinberg D1, Balcells S1 1 Departamento de Genética, Microbiología y Estadística - Facultad de Biología - Universidad de Barcelona - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III (ISCIII) - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Instituto de Investigación Sant Joan de Déu (IRSJD) - Barcelona (España) 2 Unidad de Investigación en Fisiopatología Ósea y Articular (URFOA); Instituto Hospital del Mar de Investigaciones Médicas (IMIM) - Parque de Salud Mar - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Barcelona (España) 3 Departamento de Genética, Microbiología y Estadística; Facultad de Biología; Universidad de Barcelona - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Barcelona (España) 4 Unidad de Metabolismo Mineral; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC); Hospital Universitario Reina Sofía - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Córdoba (España) 5 Grupo de Investigación en Enfermedades Prevalentes del Aparato Locomotor (GREMPAL) - Instituto de Investigación en Atención Primaria (IDIAP) Jordi Gol - Centro de Investigación
    [Show full text]
  • Decoding DMD Transcriptional Networks Using Single‐Nucleus RNA Sequencing COMMENTARY Daniel J
    COMMENTARY Decoding DMD transcriptional networks using single‐nucleus RNA sequencing COMMENTARY Daniel J. Garrya,b,1, Satyabrata Dasa, and Wuming Gonga Duchenne muscular dystrophy (DMD) is an X chromosome-linked disease, and it is the most com- mon form of muscular dystrophy caused by genetic mutations in the Dmd gene (1). The Dmd gene contains 79 exons, spans 2.4 Mb, and is the single largest gene in the human genome (2). This gene encodes for dystro- phin, which is a component of the dystrophin– glycoprotein complex that provides structural stability to the cell membrane (by connecting the cytoskeleton and the extracellular matrix), and a dys- functional or absent dystrophin protein leads to pro- Fig. 1. Decoding the molecular mechanisms of DMD gressive muscle wasting with cycles of muscle pathogenesis utilizing snRNA-seq. This figure schematizes the discoveries outlined in Chemello et al. degeneration and regeneration that ultimately fail (3, (7) with the newly generated DMD mouse model 4). Young boys with DMD lose their ability to ambu- (ΔEx51) and the transcriptomic analysis of isolated late, become wheelchair bound, and die prematurely nuclei from skeletal muscle cells. The snRNA-seq (1, 5). This disease affects skeletal muscle, which is the analysis was used to discover factors and pathways underlying DMD pathogenesis from previously single largest organ in the body, and it normally has a unrecognized cell clusters. These results in remarkable capacity for regeneration (6). In response combination with other databases provide a platform to a severe injury caused by genetic disorders, trauma, for developing new therapeutic interventions or exposure to toxins that destroys over 90% of the mus- as well as an enhanced understanding of the gene-regulatory networks involved in muscle biology cle, the cytoarchitecture of the injured tissue is com- and DMD.
    [Show full text]
  • The Landscape of Human Mutually Exclusive Splicing
    bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. 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-ND 4.0 International license. The landscape of human mutually exclusive splicing Klas Hatje1,2,#,*, Ramon O. Vidal2,*, Raza-Ur Rahman2, Dominic Simm1,3, Björn Hammesfahr1,$, Orr Shomroni2, Stefan Bonn2§ & Martin Kollmar1§ 1 Group of Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany 2 Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany 3 Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Germany § Corresponding authors # Current address: Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland $ Current address: Research and Development - Data Management (RD-DM), KWS SAAT SE, Einbeck, Germany * These authors contributed equally E-mail addresses: KH: [email protected], RV: [email protected], RR: [email protected], DS: [email protected], BH: [email protected], OS: [email protected], SB: [email protected], MK: [email protected] - 1 - bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. 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.
    [Show full text]
  • WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Definition of the Landscape of Promoter DNA Hypomethylation in Liver Cancer
    Published OnlineFirst July 11, 2011; DOI: 10.1158/0008-5472.CAN-10-3823 Cancer Therapeutics, Targets, and Chemical Biology Research Definition of the Landscape of Promoter DNA Hypomethylation in Liver Cancer Barbara Stefanska1, Jian Huang4, Bishnu Bhattacharyya1, Matthew Suderman1,2, Michael Hallett3, Ze-Guang Han4, and Moshe Szyf1,2 Abstract We use hepatic cellular carcinoma (HCC), one of the most common human cancers, as a model to delineate the landscape of promoter hypomethylation in cancer. Using a combination of methylated DNA immunopre- cipitation and hybridization with comprehensive promoter arrays, we have identified approximately 3,700 promoters that are hypomethylated in tumor samples. The hypomethylated promoters appeared in clusters across the genome suggesting that a high-level organization underlies the epigenomic changes in cancer. In normal liver, most hypomethylated promoters showed an intermediate level of methylation and expression, however, high-CpG dense promoters showed the most profound increase in gene expression. The demethylated genes are mainly involved in cell growth, cell adhesion and communication, signal transduction, mobility, and invasion; functions that are essential for cancer progression and metastasis. The DNA methylation inhibitor, 5- aza-20-deoxycytidine, activated several of the genes that are demethylated and induced in tumors, supporting a causal role for demethylation in activation of these genes. Previous studies suggested that MBD2 was involved in demethylation of specific human breast and prostate cancer genes. Whereas MBD2 depletion in normal liver cells had little or no effect, we found that its depletion in human HCC and adenocarcinoma cells resulted in suppression of cell growth, anchorage-independent growth and invasiveness as well as an increase in promoter methylation and silencing of several of the genes that are hypomethylated in tumors.
    [Show full text]
  • Concordance of Copy Number Loss and Down-Regulation of Tumor Suppressor Genes: a Pan-Cancer Study Min Zhao1 and Zhongming Zhao2,3,4,5*
    The Author(s) BMC Genomics 2016, 17(Suppl 7):532 DOI 10.1186/s12864-016-2904-y RESEARCH Open Access Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study Min Zhao1 and Zhongming Zhao2,3,4,5* From The International Conference on Intelligent Biology and Medicine (ICIBM) 2015 Indianapolis, IN, USA. 13-15 November 2015 Abstract Background: Tumor suppressor genes (TSGs) encode the guardian molecules to control cell growth. The genomic alteration of TSGs may cause tumorigenesis and promote cancer progression. So far, investigators have mainly studied the functional effects of somatic single nucleotide variants in TSGs. Copy number variation (CNV) is another important form of genetic variation, and is often involved in cancer biology and drug treatment, but studies of CNV in TSGs are less represented in literature. In addition, there is a lack of a combinatory analysis of gene expression and CNV in this important gene set. Such a study may provide more insights into the relationship between gene dosage and tumorigenesis. To meet this demand, we performed a systematic analysis of CNVs and gene expression in TSGs to provide a systematic view of CNV and gene expression change in TSGs in pan-cancer. Results: We identified 1170 TSGs with copy number gain or loss in 5846 tumor samples. Among them, 207 TSGs tended to have copy number loss (CNL), from which fifteen CNL hotspot regions were identified. The functional enrichment analysis revealed that the 207 TSGs were enriched in cancer-related pathways such as P53 signaling pathway and the P53 interactome.
    [Show full text]
  • Redalyc.Loss of Heterozygosity in the Short Arm of Human Chromosome 3
    Colombia Médica ISSN: 0120-8322 [email protected] Universidad del Valle Colombia BARRERA, LINA MARCELA; ÁLVAREZ, LIZETH MARELLY; ROLDÁN, MIGUEL IGNACIO; ORTEGA, HÉCTOR; TRIANA, OMAR; MARTÍNEZ, ALONSO Loss of heterozygosity in the short arm of human chromosome 3 in sporadic lung cancer Colombia Médica, vol. 41, núm. 4, octubre-diciembre, 2010, pp. 358-366 Universidad del Valle Cali, Colombia Disponible en: http://www.redalyc.org/articulo.oa?id=28315594010 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Colombia Médica Vol. 41 Nº 4, 2010 (Octubre-Diciembre) Loss of heterozygosity in the short arm of human chromosome 3 in sporadic lung cancer* LINA MARCELA BARRERA, BIOL1**, LIZETH MARELLY ÁLVAREZ, BIOL.1**, MIGUEL IGNACIO ROLDÁN, MD2, HÉCTOR ORTEGA, MD3, OMAR TRIANA, PHD4, ALONSO MARTÍNEZ, PHD5 SUMMARY Introduction: Loss of Heterozygocity (LOH) in the short arm of human chromosome 3 (3p) is a frequent event in different types of sporadic tumors, including lung cancer (LC). Aim: To determine 3p LOH in LC samples using 17 microsatellite markers. Methodology: In a pilot study on volunteers, thirteen LC biopsies (tumor tissue) and 4 ml of blood (normal tissue) from the same patient were collected. DNA extraction and Polymerase Chain Reaction (PCR) were performed with 17 microsatellite markers to analyze LOH. Amplified fragments were run on 6% denaturalizing polyacrilamide gels and were visualized by using silver stain.
    [Show full text]
  • Mechanisms of FUS1/TUSC2 Deficiency in Mesothelioma and Its
    Molecular Cancer BioMed Central Research Open Access Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects Alla V Ivanova*1, Sergey V Ivanov2, Ljudmila Prudkin3, Daisuke Nonaka2, Zhandong Liu4, Anne Tsao3, Ignacio Wistuba3, Jack Roth5 and Harvey I Pass2 Address: 1Hematology/Oncology Division, Vanderbilt Medical Center, Nashville, TN, USA, 2Department of Cardiothoracic Surgery, NYU Langone Medical Center, New York, NY, USA, 3Department of Thoracic/Head and Neck Medical Oncology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Unit 432, Houston, TX, USA, 4Genomics and Computational Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA and 5Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA Email: Alla V Ivanova* - [email protected]; Sergey V Ivanov - [email protected]; Ljudmila Prudkin - [email protected]; Daisuke Nonaka - [email protected]; Zhandong Liu - [email protected]; Anne Tsao - [email protected]; Ignacio Wistuba - [email protected]; Jack Roth - [email protected]; Harvey I Pass - [email protected] * Corresponding author Published: 24 October 2009 Received: 6 August 2009 Accepted: 24 October 2009 Molecular Cancer 2009, 8:91 doi:10.1186/1476-4598-8-91 This article is available from: http://www.molecular-cancer.com/content/8/1/91 © 2009 Ivanova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • Stathmin 1 Is a Potential Novel Oncogene in Melanoma
    Oncogene (2013) 32, 1330–1337 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc SHORT COMMUNICATION Stathmin 1 is a potential novel oncogene in melanoma J Chen, M Abi-Daoud, A Wang , X Yang, X Zhang, HE Feilotter and VA Tron In previous studies, we demonstrated that miR-193b expression is reduced in melanoma relative to benign nevi, and also that miR- 193b represses cyclin D1 and Mcl-1 expression. We suggested that stathmin 1 (STMN1) might be a target of miR-193b. STMN1 normally regulates microtubule dynamics either by sequestering free tubulin heterodimers or by promoting microtubule catastrophe. Increased expression of STMN1 has been observed in a variety of human malignancies, but its association with melanoma is unknown. We now report that STMN1 is upregulated during the progression of melanoma relative to benign nevi, and that STMN1 is directly regulated by miR-193b. Using an experimental cell culture approach, overexpression of miR-193b using synthetic microRNAs repressed STMN1 expression, whereas inhibition of miR-193b with anti-miR oligos increased STMN1 expression in melanoma cells. The use of a luciferase reporter assay confirmed that miR-193b directly regulates STMN1 by targeting the 30-untranslated region of STMN1 mRNA. We further demonstrated that STMN1 is overexpressed in malignant melanoma compared with nevi in two independent melanoma cohorts, and that its level is inversely correlated with miR-193b expression. However, STMN1 expression was not significantly associated with patient survival, Breslow depth, mitotic count or patient age. STMN1 knockdown by small-interfering RNA in melanoma cells drastically repressed cell proliferation and migration potential, whereas ectopic expression of STMN1 using lentivirus increased cell proliferation and migration rates.
    [Show full text]
  • Epigenetic Remodelling of Gene Expression Profiles of Neoplastic and Normal Tissues: Immunotherapeutic Implications
    British Journal of Cancer (2012) 107, 1116–1124 & 2012 Cancer Research UK All rights reserved 0007 – 0920/12 www.bjcancer.com Epigenetic remodelling of gene expression profiles of neoplastic and normal tissues: immunotherapeutic implications S Coral1,4, A Covre1,2,4, HJMG Nicolay1,2, G Parisi1,2, A Rizzo1, F Colizzi1, S Dalla Santa3, E Fonsatti2, E Fratta1, L Sigalotti1 and M Maio*,1,2 1 2 Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy; Division of Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, Istituto Toscano Tumori, Strada delle Scotte 14, 53100 Siena, Italy; 3 Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Division, University of Padua, Padua, Italy Translational Therapeutics BACKGROUND Epigenetic remodelling of cancer cells is an attractive therapeutic strategy and distinct DNA hypomethylating agents : (DHA) are being actively evaluated in patients with hemopoietic or solid tumours. However, no studies have investigated the modulation of gene expression profiles (GEP) induced by DHA in transformed and benign tissues. Such information is mandatory to clarify the fine molecular mechanism(s) underlying the clinical efficacy of DHA, to identify appropriate therapeutic combinations, and to address safety issues related to their demethylating potential in normal tissues. Thus, utilising a syngeneic mouse model, we investigated the remodelling of GEP of neoplastic and normal tissues induced by systemic administration of DHA. METHODS: The murine mammary carcinoma cells TS/A were injected s.c. into female BALB/c mice that were treated i.p. with four 0 À 1 cycles of the DHA 5-aza-2 -deoxycytidine (5-AZA-CdR) at a fractioned daily dose of 0.75 mg kg (q8 h  3 days, every week).
    [Show full text]