DOCSLIB.ORG

Simultaneous Confidence Intervals to Compare Gene Expression Profiles Using ABC Transporter Taqman Microfluidic Cards

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Simultaneous Confidence Intervals to Compare Gene Expression Profiles Using ABC Transporter Taqman Microfluidic Cards 853-860.qxd 20/1/2010 12:25 ÌÌ Page 853 ONCOLOGY REPORTS 23: 853-860, 2010 853 Simultaneous confidence intervals to compare gene expression profiles using ABC transporter TaqMan microfluidic cards SARA PIZZAMIGLIO1*, GIACOMO COSSA2*, LAURA GATTI2, GIOVANNI L. BERETTA2, ELISABETTA CORNA2, STELLA TINELLI2, PAOLO VERDERIO1** and PAOLA PEREGO2** 1Medical Statistics and Biometry Unit, 2Preclinical Chemotherapy and Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Via Venezian 1, 20133 Milan, Italy Received September 14, 2009; Accepted November 20, 2009 DOI: 10.3892/or_00000707 Abstract. The rapid evolution of techniques for measuring Introduction gene expression makes available substantial data which require careful analysis. In particular, relative quantification Ovarian carcinoma is a major cause of death from gynaeco- based on microfluidic cards allows performing of rapid large logical cancers in the Western world. This disease is usually scale analyses. In the present study, we employed ovarian diagnosed at advanced stage when surgery cannot be curative carcinoma cell lines resistant to cisplatin (IGROV-1/Pt1) or and, after debulking surgery, patients are treated with platinum- to a camptothecin (IGROV-1CPT/L), both characterized by a taxane combination chemotherapy, which has become a complex pattern of resistance to multiple agents, to examine standard treatment for advanced-stage disease (1). A large the expression of genes of the superfamily of ATP binding- number of cytotoxic agents including camptothecins, the cassette (ABC) transporters by TaqMan microfluidic cards clinically available DNA topoisomerase I inhibitors, are used with the aim of developing an analytical tool to process data in the treatment of recurrence, but most therapies have failed in this particular framework. The transcript quantification to improve survival (2). Drug resistance represents a major was based on the comparative threshold cycle method, which cause of treatment failure, but the cellular bases of resistance compares the expression of a target gene normalized to the to cytotoxic agents remain to be defined. Although extensive expression of one or more reference genes (relative quantifi- cellular studies have underlined that resistance is multi- cation). To process expression of ABC transporters, we applied factorial in nature, a major impact of defence mechanisms a statistical procedure based on multivariate approaches and i.e., factors regulating antitumor drug influx and efflux has re-sampling techniques. The transporters that were signi- been recognized (3,4). Indeed, for all cytotoxic agents, ficantly modulated included members of the ABCA, ABCB, inadequate intra-tumor concentration could explain at least ABCC and ABCG subgroups. A consistent up-regulation in part the ‘pharmacological’ resistance to treatment. of ABCC2 as compared with the parental IGROV-1 cell line Selected components of the super-family of ATP binding- was observed in the IGROV-1/Pt1 cells, whereas down- cassette (ABC) transporters have been implicated in conferring regulation of ABCC6 and ABCG1 was found in IGROV-1/ resistance to structurally unrelated antitumor drugs including CPT-L cells. The use of rigorous analytic tools for gene cisplatin and camptothecins (5,6). The recent achievement expression data in preclinical models may lead to the identi- that ABC transporters are a large family of genes supports fication of signatures to test in ovarian carcinoma clinical the need for novel studies directed at clarifying the relation- samples. Moreover, the developed procedure may be useful ship between less characterized transporters and resistance. in the analysis of relative quantification data obtained with Thus, the availability of techniques allowing the simultaneous microfluidic cards in different experimental settings. analysis of a large number of transcripts with minimal quantity of total RNA may be useful in an attempt to establish pro- cedures to translate to the clinical setting. In this context, it is _________________________________________ important to define rigorous analytical procedures to analyze consistently the gene expression data in an attempt to define Correspondence to: Dr Laura Gatti, Preclinical Chemotherapy tools to translate insights from preclinical models into the and Pharmacology Unit, Department of Experimental Oncology and clinical practise (7). Based on this rationale, we used ovarian Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, carcinoma cell systems including a parental cell line and two Via Venezian 1, 20133 Milan, Italy E-mail: [email protected] drug-resistant sublines exhibiting a variable pattern of response to structurally unrelated antitumor agents to *Contributed equally examine the expression of the whole ABC transporters super- **Senior co-authorship family. The amount of ABC transporter transcripts were quantified by means of TaqMan microfluidic cards, a tool Key words: simultaneous confidence intervals, microfluidic cards, that allows simultaneous real-time PCR analysis of a large ABC transporters, ovarian carcinoma number of mRNAs because TaqMan gene expression assays are carried out on a microfluidic card with minimal quantity 853-860.qxd 20/1/2010 12:25 ÌÌ Page 854 854 PIZZAMIGLIO et al: STATISTICAL ANALYSIS AND GENE EXPRESSION PROFILES of total RNA. The transcript quantification is based on and DNase digestion were carried out with the RNAqueous®- the comparative threshold cycle (Ct) method (8), which 4PCR Kit (Ambion Europe LTD, Huntingdon, UK), according compares the expression of a target gene normalized to the to the manufacturer's instructions. RNA purity and integrity expression of one or more reference genes (relative quanti- were assessed with denaturing gel electrophoresis and the fication). Although relative quantification based on micro- RNA was quantified spectrophotometrically and then stored fluidic cards enables researchers to perform rapidly large at -80˚C. cDNA synthesis was performed with the High- scale analyses, its statistical background needs to be better Capacity cDNA Reverse Transcription Kit (Applied Bio- investigated. Currently, the software programs supplied systems, Foster City, CA, USA) with a Master Mix containing along with the various qPCR instruments usually do not 2.5 U/μl of MultiScribe Reverse Transcriptase and 1 μg provide an adequate solution for the processing of the raw of total RNA. The reaction mixture was incubated at 25˚C data into meaningful results due to their intrinsic restrictions for 10 min, followed by 120 min at 37˚C and then by heat mainly related to a closed software architecture. Consequently, inactivation of the enzyme at 85˚C for 5 sec. We then mixed we applied an ad hoc statistical procedure based on multi- 2 μl of single-stranded cDNA (equivalent to around 100 ng variate approaches and re-sampling techniques specifically of total RNA) with 48 μl of nuclease-free water and 50 μl developed to process gene expression data obtained using of TaqMan Universal PCR Master Mix. After loading TaqMan microfluidic cards. This procedure, exploiting the 100 μl of the sample-specific PCR mixture into one sample comparative Ct method (8), is based on the following steps: port of the microfluidic cards (Human ABC Transporter data cleaning, outlier detection, data normalization and Panel; Applied Biosystems), the cards were centrifuged twice selection of a small subset of genes confidently inferred to for 1 min at 280 g and sealed to prevent well-to-well conta- be involved in the multidrug-resistant phenotype. mination. The cards were placed in the microfluidic card Sample Block of an ABI Prism 7900 HT Sequence Detection Materials and methods System (Applied Biosystems). The thermal cycling conditions were 2 min at 50˚C and 10 min at 95˚C, followed by 40 cycles Cell culture and drugs. The human ovarian carcinoma of 30 sec at 97˚C and 1 min at 59.7˚C. The assay for each IGROV-1 cell line and the cisplatin- and camptothecin- gene on the microfluidic card was carried out in triplicate, resistant sublines, IGROV-1/Pt1 and IGROV-1/CPT-L, were due to the design of this specific panel. The calculation of the maintained in RPMI-1640 medium (BioWhittaker Lonza, threshold cycle (Ct) values was performed using the SDS 2.2 Lonza Milano S.r.l., Italy) supplemented with 10% fetal software (Applied Biosystems), after automatically setting bovine serum (Gibco, Invitrogen, San Giuliano M, Italy). the baseline and the threshold. The IGROV-1/Pt1 variant was generated as described (9). IGROV-1/CPT-L cells were developed by exposure of the Methodological background. Microfluidic card experiments parental cell line to increasing concentrations of the lipo- allow the detection and quantification of a large number philic camptothecin gimatecan. Resistance was stable for of genes by taking advantage of the real-time PCR method. at least 6 months when cells were grown in the absence Usually, each j-th (j=1,2,...J) Ct replicate is processed of selecting agent. Cell cultures were routinely checked for according to the comparative Ct method to compute the being mycoplasma-free and experiments were carried out relative quantity (RQ) of the i-th (i=1,2,...I) transcript in the using cell lines at similar passages following thawing from a k-th (k=1,2,...K) sample, normalized to an endogenous gene frozen stock. Cisplatin (Teva Italia S.r.l., Milan, Italy) was (R) and relative to a calibrator sample
Load more

Recommended publications
  • ABCC12 Monoclonal Antibody, Clone M9II-3
    ABCC12 monoclonal antibody, Gene Symbol: ABCC12 clone M9II-3 Gene Alias: MGC27071, MRP9 Catalog Number: MAB6675 Gene Summary: This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters Regulatory Status: For research use only (RUO) and the encoded protein contains two ATP-binding domains and 12 transmembrane regions. ABC proteins Product Description: Rat monoclonal antibody raised transport various molecules across extra- and against partial recombinant ABCC12. intracellular membranes. ABC genes are divided into Clone Name: M9II-3 seven distinct subfamilies: ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White. This gene is a member of Immunogen: Recombinant protein corresponding to the MRP subfamily which is involved in multi-drug amino acids 690-734 of human ABCC12. resistance. This gene and another subfamily member are arranged head-to-tail on chromosome 16q12.1. Host: Rat Increased expression of this gene is associated with breast cancer. [provided by RefSeq] Reactivity: Human References: Applications: ICC, IHC-Fr, WB 1. Multidrug resistance-associated protein 9 (ABCC12) is (See our web site product page for detailed applications present in mouse and boar sperm. Ono N, Van der information) Heijden I, Scheffer GL, Van de Wetering K, Van Deemter E, De Haas M, Boerke A, Gadella BM, De Rooij Protocols: See our web site at DG, Neefjes JJ, Groothuis TA, Oomen L, Brocks L, http://www.abnova.com/support/protocols.asp or product Ishikawa T, Borst P. Ono N, Van der Heijden I, Scheffer page for detailed protocols GL, Van de Wetering K, Van Deemter E, De Haas M, Boerke A, Gadella BM, De Rooij DG, Neefjes JJ, Specificity: M9II-3 reacts with an internal epitope of Groothuis TA, Oomen L, Brocks L, Ishikawa T, Borst P.
    [Show full text]
  • CFTR Inhibition by Glibenclamide Requires a Positive Charge in Cytoplasmic Loop Three ⁎ Patricia Melin A, , Eric Hosy B, Michel Vivaudou B, Frédéric Becq A
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com Biochimica et Biophysica Acta 1768 (2007) 2438–2446 www.elsevier.com/locate/bbamem CFTR inhibition by glibenclamide requires a positive charge in cytoplasmic loop three ⁎ Patricia Melin a, , Eric Hosy b, Michel Vivaudou b, Frédéric Becq a a Institut de Physiologie et Biologie Cellulaires, Université de Poitiers, CNRS UMR 6187, 86022 Poitiers cedex, France b CEA, DRDC, Biophysique Moléculaire et Cellulaire, UMR CNRS/UJF/CEA 5090, 17 Rue, des Martyrs, 38054, Grenoble, France Received 20 February 2007; received in revised form 2 May 2007; accepted 14 May 2007 Available online 21 May 2007 Abstract The sulfonylurea glibenclamide is widely used as an open-channel blocker of the CFTR chloride channel. Here, we used site-directed mutagenesis to identify glibenclamide site of interaction: a positively charged residue K978, located in the cytoplasmic loop 3. Charge- neutralizing mutations K978A, K978Q, K978S abolished the inhibition of forskolin-activated CFTR chloride current by glibenclamide but not by CFTRinh-172. The charge-conservative mutation K978R did not alter glibenclamide sensitivity of CFTR current. Mutations of the neighbouring R975 (R975A, R975S, R975Q) did not affect electrophysiological and pharmacological properties of CFTR. No alteration of halide selectivity was observed with any of these CFTR mutant channels. This study identifies a novel potential inhibitor site within the CFTR molecule, and suggests a novel role of cytoplasmic loop three, within the second transmembrane domain of CFTR protein. This work is the first to report on the role of a residue in a cytoplasmic loop in the mechanism of action of the channel blocker glibenclamide.
    [Show full text]
  • Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
    Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice.
    [Show full text]
  • Interindividual Differences in the Expression of ATP-Binding
    Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2018/02/02/dmd.117.079061.DC1 1521-009X/46/5/628–635$35.00 https://doi.org/10.1124/dmd.117.079061 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 46:628–635, May 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Special Section on Transporters in Drug Disposition and Pharmacokinetic Prediction Interindividual Differences in the Expression of ATP-Binding Cassette and Solute Carrier Family Transporters in Human Skin: DNA Methylation Regulates Transcriptional Activity of the Human ABCC3 Gene s Tomoki Takechi, Takeshi Hirota, Tatsuya Sakai, Natsumi Maeda, Daisuke Kobayashi, and Ichiro Ieiri Downloaded from Department of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan (T.T., T.H., T.S., N.M., I.I.); Drug Development Research Laboratories, Kyoto R&D Center, Maruho Co., Ltd., Kyoto, Japan (T.T.); and Department of Clinical Pharmacy and Pharmaceutical Care, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan (D.K.) Received October 19, 2017; accepted January 30, 2018 dmd.aspetjournals.org ABSTRACT The identification of drug transporters expressed in human skin and levels. ABCC3 expression levels negatively correlated with the methylation interindividual differences in gene expression is important for understanding status of the CpG island (CGI) located approximately 10 kilobase pairs the role of drug transporters in human skin. In the present study, we upstream of ABCC3 (Rs: 20.323, P < 0.05). The reporter gene assay revealed evaluated the expression of ATP-binding cassette (ABC) and solute carrier a significant increase in transcriptional activity in the presence of CGI.
    [Show full text]
  • ABCC11 Antibody (F48871)
    ABCC11 Antibody (F48871) Catalog No. Formulation Size F48871-0.4ML In 1X PBS, pH 7.4, with 0.09% sodium azide 0.4 ml F48871-0.08ML In 1X PBS, pH 7.4, with 0.09% sodium azide 0.08 ml Bulk quote request Availability 1-3 business days Species Reactivity Human Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit Ig Purity Antigen affinity UniProt Q96J66 Localization Cytoplasmic, membranous Applications Western blot : 1:1000 IHC (Paraffin) : 1:50-1:100 Limitations This ABCC11 antibody is available for research use only. ABCC11 antibody IHC analysis in formalin fixed and paraffin embedded breast carcinoma. Western blot analysis of ABCC11 antibody and WiDr lysate. Predicted molecular weight: ~154/150kDa (isoforms 1/2). Description ATP-binding cassette sub-family C member 11 is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Application Notes Titration of the ABCC11 antibody may be required due to differences in protocols and secondary/substrate sensitivity. Immunogen A portion of amino acids 343-372 from the human protein was used as the immunogen for this ABCC11 antibody.
    [Show full text]
  • View a Copy of This Licence, Visit
    Robertson et al. BMC Biology (2020) 18:103 https://doi.org/10.1186/s12915-020-00826-z RESEARCH ARTICLE Open Access Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets Matthew J. Robertson1,2, Katarzyna Kent3,4,5, Nathan Tharp3,4,5, Kaori Nozawa3,5, Laura Dean3,4,5, Michelle Mathew3,4,5, Sandra L. Grimm2,6, Zhifeng Yu3,5, Christine Légaré7,8, Yoshitaka Fujihara3,5,9,10, Masahito Ikawa9, Robert Sullivan7,8, Cristian Coarfa1,2,6*, Martin M. Matzuk1,3,5,6 and Thomas X. Garcia3,4,5* Abstract Background: The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive targets have so far reached clinical trials. To advance product development, further identification of novel reproductive tract-specific genes leading to potentially druggable protein targets is imperative. Results: In this study, we expand on previous single tissue, single species studies by integrating analysis of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. We detected a combined total of 1178 genes for which no previous evidence of male reproductive tract-specific expression was annotated, many of which are potentially druggable targets.
    [Show full text]
  • Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Citation Varas, Florencio, Matthias Stadtfeld, Luisa de Andres-Aguayo, Nimet Maherali, Alessandro di Tullio, Lorena Pantano, Cedric Notredame, et al. 2009. Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions. Stem Cells 27(2): 300-306. Published Version doi:10.1634/stemcells.2008-0696 Accessed February 18, 2015 8:46:59 PM EST Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:4459933 Terms of Use This article was downloaded from Harvard University's DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn- 3:HUL.InstRepos:dash.current.terms-of-use#OAP (Article begins on next page) EMBRYONIC STEM CELLS/INDUCED PLURIPOTENT STEM CELLS Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions FLORENCIO VARAS,a MATTHIAS STADTFELD,b LUISA DE ANDRES-AGUAYO,a NIMET MAHERALI,b ALESSANDRO DI TULLIO,a LORENA PANTANO,c CEDRIC NOTREDAME,c KONRAD HOCHEDLINGER,b THOMAS GRAFa,d aDifferentiation and Cancer and cBioinformatics Program, Center for Genomic Regulation and Pompeu Fabra University, Barcelona, Spain; bCancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Stem Cell Institute, Boston, Massachusetts, USA; dInstitucio´ Catalana de Recerca i Estudis Avanc¸ats Key Words.
    [Show full text]
  • Categorization and Classification of Different ABCA3 Variants Causing Interstitial Lung Disease
    Categorization and classification of different ABCA3 variants causing interstitial lung disease Dissertation der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen zur Erlangung des Doktorgrades Doktor der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Thomas Wittmann aus Neumarkt in der Oberpfalz, Deutschland Tübingen 2016 Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen. Tag der mündlichen Qualifikation: 15.07.2016 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Dominik Hartl 2. Berichterstatter: Prof. Dr. Andreas Peschel Table of contents Table of contents Table of contents ..........................................................................................................I List of tables.................................................................................................................II List of figures................................................................................................................II Abbreviations ..............................................................................................................III Summary..................................................................................................................... V Zusammenfassung .................................................................................................... VI Publications.............................................................................................................
    [Show full text]
  • Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response
    International Journal of Molecular Sciences Article Role of Genetic Variation in ABC Transporters in Breast Cancer Prognosis and Therapy Response Viktor Hlaváˇc 1,2 , Radka Václavíková 1,2, Veronika Brynychová 1,2, Renata Koževnikovová 3, Katerina Kopeˇcková 4, David Vrána 5 , Jiˇrí Gatˇek 6 and Pavel Souˇcek 1,2,* 1 Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic; [email protected] (V.H.); [email protected] (R.V.); [email protected] (V.B.) 2 Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic 3 Department of Oncosurgery, Medicon Services, 140 00 Prague, Czech Republic; [email protected] 4 Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, 150 06 Prague, Czech Republic; [email protected] 5 Department of Oncology, Medical School and Teaching Hospital, Palacky University, 779 00 Olomouc, Czech Republic; [email protected] 6 Department of Surgery, EUC Hospital and University of Tomas Bata in Zlin, 760 01 Zlin, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-267-082-711 Received: 19 November 2020; Accepted: 11 December 2020; Published: 15 December 2020 Abstract: Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105).
    [Show full text]
  • View See Ref
    Finelli et al. Molecular Cytogenetics 2012, 5:16 http://www.molecularcytogenetics.org/content/5/1/16 RESEARCH Open Access Juxtaposition of heterochromatic and euchromatic regions by chromosomal translocation mediates a heterochromatic long- range position effect associated with a severe neurological phenotype Palma Finelli1,2*, Silvia Maria Sirchia3,4, Maura Masciadri1, Milena Crippa1, Maria Paola Recalcati1, Daniela Rusconi1, Daniela Giardino1, Laura Monti3, Francesca Cogliati1, Francesca Faravelli5, Federica Natacci6, Leonardo Zoccante7, Bernardo Dalla Bernardina7, Silvia Russo1 and Lidia Larizza1,3 Abstract Background: The term “position effect” is used when the expression of a gene is deleteriously affected by an alteration in its chromosomal environment even though the integrity of the protein coding sequences is maintained. We describe a patient affected by epilepsy and severe neurodevelopment delay carrying a balanced translocation t(15;16)(p11.2;q12.1)dn that we assume caused a position effect as a result of the accidental juxtaposition of heterochromatin in the euchromatic region. Results: FISH mapped the translocation breakpoints (bkps) to 15p11.2 within satellite III and the 16q12.1 euchromatic band within the ITFG1 gene. The expression of the genes located on both sides of the translocation were tested by means of real-time PCR and three, all located on der(16), were found to be variously perturbed: the euchromatic gene NETO2/BTCL2 was silenced, whereas VPS35 and SHCBP1, located within the major heterochromatic block of chromosome 16q11.2, were over-expressed. Pyrosequencing and chromatin immunoprecipitation of NETO2/BTCL2 and VPS35 confirmed the expression findings. Interphase FISH analysis showed that der(16) localised to regions occupied by the beta satellite heterochromatic blocks more frequently than der(15).
    [Show full text]
  • Gene Section Review
    Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST -CNRS Gene Section Review ABCC11 (ATP-binding cassette, sub-family C (CFTR/MRP), member 11) Akimitsu Yamada, Kazuaki Takabe, Krista P Terracina, Takashi Ishikawa, Itaru Endo Department of Breast and Oncological Surgery, Yokohama City University School of Medicine, Kanagawa, Japan (AY, IE), Department of Surgery, Virginia Commonwealth University, Richmond, Virginia, USA (AY, KT, KPT), Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Kanagawa, Japan (TI) Published in Atlas Database: December 2013 Online updated version : http://AtlasGeneticsOncology.org/Genes/ABCC11ID538ch16q12.html DOI: 10.4267/2042/54005 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2014 Atlas of Genetics and Cytogenetics in Oncology and Haematology genes were classified into the multidrug resistant- Abstract associated protein (MRP) family. Review on ABCC11, with data on DNA/RNA, on Description the protein encoded and where the gene is implicated. The ABCC11 gene is encoded by a 68 kb gene consisting of 30 exons (Yabuuchi et al., 2001). According to the August 2013, NCBI database, Identity there are three ABCC11 variants. Variant 1 consists Other names: EWWD, MRP8, WW of 4576 bp (NM_032583.3) while variant 2 consists of 4862 bp (NM_033151.3). Both variant 1 and 2 HGNC (Hugo): ABCC11 genes encode an ABCC11 protein (isoform a) Location: 16q12.1 consisting of 1382 amino acids. Variant 3 (isoform b) consists of 4462 bp (NM_145186.2) and encodes DNA/RNA a protein consisting of 1344 amino acids. This variant 3 lacks an alternate in-frame exon compared Note to variant 1, resulting in a shorter protein (isoform In 2001, three research groups independently b), compared to isoform a.
    [Show full text]
  • Repositioning of Tyrosine Kinase Inhibitors As Antagonists of ATP-Binding Cassette Transporters in Anticancer Drug Resistance
    Cancers 2014, 6, 1925-1952; doi:10.3390/cancers6041925 OPEN ACCESS cancers ISSN 2072-6694 www.mdpi.com/journal/cancers Review Repositioning of Tyrosine Kinase Inhibitors as Antagonists of ATP-Binding Cassette Transporters in Anticancer Drug Resistance Yi-Jun Wang, Yun-Kai Zhang, Rishil J. Kathawala and Zhe-Sheng Chen * Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA; E-Mails: [email protected] (Y.-J.W.); [email protected] (Y.-K.Z.); [email protected] (R.J.K.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-718-990-1432; Fax: +1-718-990-1877. Received: 31 July 2014; in revised form: 4 September 2014 / Accepted: 11 September 2014 / Published: 29 September 2014 Abstract: The phenomenon of multidrug resistance (MDR) has attenuated the efficacy of anticancer drugs and the possibility of successful cancer chemotherapy. ATP-binding cassette (ABC) transporters play an essential role in mediating MDR in cancer cells by increasing efflux of drugs from cancer cells, hence reducing the intracellular accumulation of chemotherapeutic drugs. Interestingly, small-molecule tyrosine kinase inhibitors (TKIs), such as AST1306, lapatinib, linsitinib, masitinib, motesanib, nilotinib, telatinib and WHI-P154, have been found to have the capability to overcome anticancer drug resistance by inhibiting ABC transporters in recent years. This review will focus on some of the latest and clinical developments with ABC transporters, TKIs and anticancer drug resistance. Keywords: multidrug resistance; ABC transporters; tyrosine kinase inhibitor; clinical relevance; pharmacogenomics 1. Introduction Cancer, also known as malignant neoplasm or tumor, is the second most leading cause of death after cardiovascular diseases in United States and developing countries.
    [Show full text]