DOCSLIB.ORG

Cancer Gene Discovery Using Digital Differential Display1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cancer Gene Discovery Using Digital Differential Display1 [CANCER RESEARCH 60, 4037–4043, August 1, 2000] Advances in Brief Cancer Gene Discovery Using Digital Differential Display1 Daniela Scheurle, Maurice Phil DeYoung, David M. Binninger, Holly Page, Mohammad Jahanzeb, and Ramaswamy Narayanan2 Center for Molecular Biology and Biotechnology and Department of Biology, Florida Atlantic University, Boca Raton, Florida 33431 [D. S., M. P. D., D. M. B., H. P., R. N.], and Eugene M. and Christine E. Lynn Clinical Research Center, Boca Raton Community Hospital Cancer Center, Boca Raton, Florida 33486 [M. J.] Abstract cancer-specific gene discovery (13). The Human Tumor Gene Index was initiated by the NCI in 1997 with a primary goal of identifying The Cancer Gene Anatomy Project database of the National Cancer genes expressed during development of human tumors in five major Institute has thousands of expressed sequences, both known and novel, in cancer sites: (a) breast; (b) colon; (c) lung; (d) ovary; and (e) prostate. the form of expressed sequence tags (ESTs). These ESTs, derived from This database consists of expression information (mRNA) of thou- diverse normal and tumor cDNA libraries, offer an attractive starting point for cancer gene discovery. Using a data-mining tool called Digital sands of known and novel genes in diverse normal and tumor tissues. Differential Display (DDD) from the Cancer Gene Anatomy Project da- By monitoring the electronic expression profile of many of these tabase, ESTs from six different solid tumor types (breast, colon, lung, sequences, it is possible to compile a list of genes that are selectively ovary, pancreas, and prostate) were analyzed for differential expression. expressed in the cancers. Data-mining tools are becoming available to An electronic expression profile and chromosomal map position of these extract expression information about the ESTs derived from various hits were generated from the Unigene database. The hits were categorized CGAP libraries (9, 10, 12, 14). Currently, there are 1.5 million ESTs into major classes of genes including ribosomal proteins, enzymes, cell in the CGAP database, of which 73,000 are novel sequences. These surface molecules, secretory proteins, adhesion molecules, and immuno- sequences are also subclassified into those derived from libraries of globulins and were found to be differentially expressed in these tumor- normal, precancerous, or cancer tissues. We chose the DDD at the derived libraries. Genes known to be up-regulated in prostate, breast, and CGAP database to identify genes (both novel and known ESTs) that pancreatic carcinomas were discovered by DDD, demonstrating the utility of this technique. Two hundred known genes and 500 novel sequences are selectively up- or down-regulated in six major solid tumor types were discovered to be differentially expressed in these select tumor- (breast, colon, lung, ovary, pancreas, and prostate). Survey sequenc- derived libraries. Test genes were validated for expression specificity by ing of mRNA gene products can provide an indirect means of gener- reverse transcription-PCR, providing a proof of concept for gene discov- ating gene expression fingerprints for cancer cells and their normal ery by DDD. A comprehensive database of hits can be accessed at http:// counterparts. DDD is a computer method of comparing these finger- www.fau.edu/cmbb/publications/cancergenes.htm. This solid tumor DDD prints. DDD is a quantitative method that enables the user to deter- database should facilitate target identification for cancer diagnostics and mine the fold differences between the libraries being compared, using therapeutics. a statistical method to quantitate the transcript levels. ESTs present in tumor-derived libraries were compared against all other libraries or Introduction against the corresponding normal libraries by DDD, and the hits showing Ͼ10-fold differences were compiled for each of the organ With the expected completion of the human genome sequencing types. These hits were functionally classified into major classes of efforts in the next few years, over 100,000 new genes are likely to be proteins. Genes belonging to ribosomal proteins, enzymes, receptors, discovered (1–3). From these vast numbers of new genes, new diag- binding proteins, secretory proteins, and cell adhesion molecules were nostic and therapeutic targets for diseases like cancer are predicted to identified to be differentially expressed in these tumor types. A emerge (4). Only a subset of genes is expressed in a given cell, and the comprehensive database of hits was created, providing additional level of expression governs function. High-throughput gene expres- electronic expression data as well as novel ESTs that were thus sion technology is becoming a possibility for analyzing expression of identified. This database can be accessed on the World Wide Web.4 a large number of sequences in diseased and normal tissues with the use of microarrays and gene chips (5–8). A parallel way to initiate a Materials and Methods search for genes relevant to cancer diagnostics and therapy is to data mine the sequence database (9–13). A large number of expressed Data-mining of CGAP Database. The CGAP database was accessed,5 and sequences from diverse organ-, species-, and disease-derived cDNA the DDD tool was used according to the database instructions. DDD takes libraries are being deposited in the form of ESTs3 in different data- advantage of the UniGene database by comparing the number of times ESTs bases. from different libraries were assigned to a particular UniGene cluster. Six The CGAP database of the NCI is an attractive starting point for different solid tumor-derived EST libraries (breast, colon, lung, ovary, pan- creas, and prostate) with corresponding normal tissue-derived libraries were chosen for DDD (N ϭ 110). To identify tumor- and organ-specific ESTs, all Received 2/2/00; accepted 6/8/00. ϭ The costs of publication of this article were defrayed in part by the payment of page the other organ- and tumor-derived EST libraries (N 327) were chosen for charges. This article must therefore be hereby marked advertisement in accordance with comparison with each of the six tumor types. The nature of the libraries 18 U.S.C. Section 1734 solely to indicate this fact. (normal, pretumor, or tumor) was authenticated by comparison of the CGAP 1 Supported by an institutional startup grant (to R. N.). D. S. was supported by a grant data with UniGene database.6 Those few libraries showing discrepancies of from the Boca Raton Community Hospital Foundation. Colon tumor and normal tissues were provided by the Cooperative Human Tissue Network, which is funded by the definition between the two databases were excluded. The DDD was performed National Cancer Institute. for each organ type individually. DDD was performed using ESTs from tumors 2 To whom requests for reprints should be addressed, at Center for Molecular Biology (pool A) and corresponding normal organ (pool B) for DDD2 method or and Biotechnology, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431. Phone: (561) 297-2018; Fax: (561) 297-2099; E-mail: [email protected]. 3 The abbreviations used are: EST, expressed sequence tag; CGAP, Cancer Gene 4 http://www.fau.edu/cmbb/publications/cancergenes.htm. Anatomy Project; DDD, Digital Differential Display; RT, reverse transcription; Hs., 5 http://www.cgap.gov. human sequence; NCI, National Cancer Institute. 6 http://www.ncbi.nlm.nih.gov/UniGene/. 4037 Downloaded from cancerres.aacrjournals.org on September 30, 2021. © 2000 American Association for Cancer Research. BIOINFORMATICS OF CANCER Table 1 DDD of up-regulated genes in tumors Hits (known ESTs) showing Ͼ10-fold differences in the indicated tumor-derived libraries in comparison with normal tissue-derived cDNA library and all other organ- and tumor-derived cDNA libraries were compiled. ESTs belonging to specific classes of genes were subclassified as indicated. UniGene number for each hit is shown. Electronic expression (E-Northern) for each of these hits was inferred from the UniGene database from the cDNA sources, and the chromosomal map position for each of these hits was inferred from the cytogenetic map.4 Name Hs.# Br Co Lu Ov Pa Pr Enzymes (n ϭ 35) CYB561 153028 29 P450, subfamily XVII 1363 26 ATP synthase, isoform 2 155751 20 Proteosome non-ATPase, 7 155543 10 18 Glu. peroxidase 2a 2702 17 Carbonic anhydrase I 23118 18 Dopa decarboxylase 150403 10 Tryptophan Hydroxylase 144563 27 ATPase, lysosomal 24322 13 Serine protease 9 79361 28 Serine-like protease, 1 69423 25 28 Myosin IXBB 159629 17 ATPase isoform 1 64173 15 ADH 8 87539 15 ATPase, 9 kD 24322 13 PKR 177574 10 Cathepsin E 1355 80 Panc. lipase 102876 47 Ser. protease 2 241561 39 Ser. protease 1 241395 34 Elastase 1 21 38 Carboxy peptidase A2 89717 34 Carboxy peptidase A1 2879 33 Elastase 3 181289 32 Chymotrypsino-gen B1 74502 32 Pancreatic lipase-related protein 1 73923 30 Carboxy peptidase B1 180884 28 DNase II 118243 14 Elastase 3B 183864 13 Urokinase 77274 13 Ribosomal proteins (N ϭ 6) S15a 2953 11 S17 5174 11 S19 126707 16 L31 184014 10 L35 182825 10 L41 108124 10 Receptor/surface/membrane (N ϭ 17) Claudin 25640 33 Tumor necrosis factor receptor, 6b 194676 17 Plakophilin 3 26557 11 Lymphocyte antigen complex 77667 17 Mesothelin 155981 40 Chloride channel 1A 84974 12 Folate receptor 1 73769 10 CD74 84298 10 Keratin 19 182265 24 CEA 220529 21 Keratin 17 2785 17 Trans membrane 4 superfamily 3 84072 13 Trans membrane 4 superfamily 4 11881 17 Non-specific cross-reacting antigen 73848
Load more

Recommended publications
  • Proteomic Profile of Human Spermatozoa in Healthy And
    Cao et al. Reproductive Biology and Endocrinology (2018) 16:16 https://doi.org/10.1186/s12958-018-0334-1 REVIEW Open Access Proteomic profile of human spermatozoa in healthy and asthenozoospermic individuals Xiaodan Cao, Yun Cui, Xiaoxia Zhang, Jiangtao Lou, Jun Zhou, Huafeng Bei and Renxiong Wei* Abstract Asthenozoospermia is considered as a common cause of male infertility and characterized by reduced sperm motility. However, the molecular mechanism that impairs sperm motility remains unknown in most cases. In the present review, we briefly reviewed the proteome of spermatozoa and seminal plasma in asthenozoospermia and considered post-translational modifications in spermatozoa of asthenozoospermia. The reduction of sperm motility in asthenozoospermic patients had been attributed to factors, for instance, energy metabolism dysfunction or structural defects in the sperm-tail protein components and the differential proteins potentially involved in sperm motility such as COX6B, ODF, TUBB2B were described. Comparative proteomic analysis open a window to discover the potential pathogenic mechanisms of asthenozoospermia and the biomarkers with clinical significance. Keywords: Proteome, Spermatozoa, Sperm motility, Asthenozoospermia, Infertility Background fertilization failure [4] and it has become clear that iden- Infertility is defined as the lack of ability to achieve a tifying the precise proteins and the pathways involved in clinical pregnancy after one year or more of unprotected sperm motility is needed [5]. and well-timed intercourse with the same partner [1]. It is estimated that around 15% of couples of reproductive age present with infertility, and about half of the infertil- Application of proteomic techniques in male ity is associated with male partner [2, 3].
    [Show full text]
  • Anti-Ps2 / Trefoil Factor 1 Antibody (ARG41084)
    Product datasheet [email protected] ARG41084 Package: 100 μl anti-pS2 / Trefoil factor 1 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes pS2 / Trefoil factor 1 Tested Reactivity Hu Tested Application FACS, ICC/IF, IHC-P, IP, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name pS2 / Trefoil factor 1 Antigen Species Human Immunogen Synthetic peptide derived from Human pS2 / Trefoil factor 1. Conjugation Un-conjugated Alternate Names D21S21; pNR-2; Trefoil factor 1; PNR-2; BCEI; hP1.A; HPS2; pS2; Polypeptide P1.A; HP1.A; Protein pS2; Breast cancer estrogen-inducible protein Application Instructions Application table Application Dilution FACS 1:50 ICC/IF 1:50 - 1:200 IHC-P 1:50 - 1:200 IP 1:50 WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 9 kDa Observed Size 11 kDa Properties Form Liquid Purification Affinity purified. Buffer PBS (pH 7.4), 150 mM NaCl, 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol www.arigobio.com 1/2 Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol TFF1 Gene Full Name trefoil factor 1 Background Members of the trefoil family are characterized by having at least one copy of the trefoil motif, a 40-amino acid domain that contains three conserved disulfides.
    [Show full text]
  • Location Analysis of Estrogen Receptor Target Promoters Reveals That
    Location analysis of estrogen receptor ␣ target promoters reveals that FOXA1 defines a domain of the estrogen response Jose´ e Laganie` re*†, Genevie` ve Deblois*, Ce´ line Lefebvre*, Alain R. Bataille‡, Franc¸ois Robert‡, and Vincent Gigue` re*†§ *Molecular Oncology Group, Departments of Medicine and Oncology, McGill University Health Centre, Montreal, QC, Canada H3A 1A1; †Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6; and ‡Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montre´al, Montreal, QC, Canada H2W 1R7 Communicated by Ronald M. Evans, The Salk Institute for Biological Studies, La Jolla, CA, July 1, 2005 (received for review June 3, 2005) Nuclear receptors can activate diverse biological pathways within general absence of large scale functional data linking these putative a target cell in response to their cognate ligands, but how this binding sites with gene expression in specific cell types. compartmentalization is achieved at the level of gene regulation is Recently, chromatin immunoprecipitation (ChIP) has been used poorly understood. We used a genome-wide analysis of promoter in combination with promoter or genomic DNA microarrays to occupancy by the estrogen receptor ␣ (ER␣) in MCF-7 cells to identify loci recognized by transcription factors in a genome-wide investigate the molecular mechanisms underlying the action of manner in mammalian cells (20–24). This technology, termed 17␤-estradiol (E2) in controlling the growth of breast cancer cells. ChIP-on-chip or location analysis, can therefore be used to deter- We identified 153 promoters bound by ER␣ in the presence of E2. mine the global gene expression program that characterize the Motif-finding algorithms demonstrated that the estrogen re- action of a nuclear receptor in response to its natural ligand.
    [Show full text]
  • Folate Receptor Alpha Defect Causes Cerebral Folate Transport Deficiency: a Treatable Neurodegenerative Disorder Associated with Disturbed Myelin Metabolism
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector ARTICLE Folate Receptor Alpha Defect Causes Cerebral Folate Transport Deficiency: A Treatable Neurodegenerative Disorder Associated with Disturbed Myelin Metabolism Robert Steinfeld,1,5,* Marcel Grapp,1,5 Ralph Kraetzner,1 Steffi Dreha-Kulaczewski,1 Gunther Helms,2 Peter Dechent,2 Ron Wevers,3 Salvatore Grosso,4 and Jutta Ga¨rtner1 Sufficient folate supplementation is essential for a multitude of biological processes and diverse organ systems. At least five distinct in- herited disorders of folate transport and metabolism are presently known, all of which cause systemic folate deficiency. We identified an inherited brain-specific folate transport defect that is caused by mutations in the folate receptor 1 (FOLR1) gene coding for folate receptor alpha (FRa). Three patients carrying FOLR1 mutations developed progressive movement disturbance, psychomotor decline, and epilepsy and showed severely reduced folate concentrations in the cerebrospinal fluid (CSF). Brain magnetic resonance imaging (MRI) demon- strated profound hypomyelination, and MR-based in vivo metabolite analysis indicated a combined depletion of white-matter choline and inositol. Retroviral transfection of patient cells with either FRa or FRb could rescue folate binding. Furthermore, CSF folate concen- trations, as well as glial choline and inositol depletion, were restored by folinic acid therapy and preceded clinical improvements. Our studies not only characterize
    [Show full text]
  • B Vitamin Polymorphisms and Behavior: Evidence of Associations
    G Model NBR 2010 1–14 ARTICLE IN PRESS Neuroscience and Biobehavioral Reviews xxx (2014) xxx–xxx Contents lists available at ScienceDirect Neuroscience and Biobehavioral Reviews jou rnal homepage: www.elsevier.com/locate/neubiorev 1 Review 2 B vitamin polymorphisms and behavior: Evidence of associations 3 with neurodevelopment, depression, schizophrenia, bipolar disorder 4 and cognitive decline ∗ 5 Q1 E. Siobhan Mitchell , Nelly Conus, Jim Kaput 6 Nestle Institute of Health Science, Innovation Park, EPFL Campus, Lausanne 1015, Switzerland 7 298 a r t i c l e i n f o a b s t r a c t 9 10 Article history: The B vitamins folic acid, vitamin B12 and B6 are essential for neuronal function, and severe deficiencies 11 Received 16 December 2013 have been linked to increased risk of neurodevelopmental disorders, psychiatric disease and dementia. 12 Received in revised form 11 July 2014 Polymorphisms of genes involved in B vitamin absorption, metabolism and function, such as methylene 13 Accepted 18 August 2014 tetrahydrofolate reductase (MTHFR), cystathionine ␤ synthase (C␤S), transcobalamin 2 receptor (TCN2) 14 Available online xxx and methionine synthase reductase (MTRR), have also been linked to increased incidence of psychiatric 15 and cognitive disorders. However, the effects of these polymorphisms are often quite small and many 16 Keywords: studies failed to show any meaningful or consistent associations. This review discusses previous findings 17 Folate from clinical studies and highlights gaps in knowledge. Future studies assessing B vitamin-associated 18 Vitamin B9 polymorphisms must take into account not just traditional demographics, but subjects’ overall diet, 19 Vitamin B12 20 Vitamin B6 relevant biomarkers of nutritional status and also analyze related genetic factors that may exacerbate 21 Dementia behavioral effects or nutritional status.
    [Show full text]
  • Molecular Alterations in the Stomach of Tffl-Deficient Mice
    International Journal of Molecular Sciences Article Molecular Alterations in the Stomach of Tff1-Deficient Mice: Early Steps in Antral Carcinogenesis Eva B. Znalesniak, Franz Salm and Werner Hoffmann * Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany; [email protected] (E.B.Z.) * Correspondence: werner.hoff[email protected] Received: 2 December 2019; Accepted: 14 January 2020; Published: 18 January 2020 Abstract: TFF1 is a peptide of the gastric mucosa co-secreted with the mucin MUC5AC. It plays a key role in gastric mucosal protection and repair. Tff1-deficient (Tff1KO) mice obligatorily develop antropyloric adenoma and about 30% progress to carcinomas. Thus, these mice represent a model for gastric tumorigenesis. Here, we compared the expression of selected genes in Tff1KO mice and the corresponding wild-type animals (RT-PCR analyses). Furthermore, we systematically investigated the different molecular forms of Tff1 and its heterodimer partner gastrokine-2 (Gkn2) in the stomach (Western blot analyses). As a hallmark, a large portion of murine Tff1 occurs in a monomeric form. This is unexpected because of its odd number of seven cysteine residues. Probably the three conserved acid amino acid residues (EEE) flanking the 7th cysteine residue allow monomeric secretion. As a consequence, the free thiol of monomeric Tff1 could have a protective scavenger function, e.g., for reactive oxygen/nitrogen species. Furthermore, a minor subset of Tff1 forms a disulfide-linked heterodimer with IgG Fc binding protein (Fcgbp). Of special note, in Tff1KO animals a homodimeric form of Gkn2 was observed. In addition, Tff1KO animals showed strongly reduced Tff2 transcript and protein levels, which might explain their increased sensitivity to Helicobacter pylori infection.
    [Show full text]
  • 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.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • (FOLR1) Mrna Expression, Its Specific Promoter
    Notaro et al. BMC Cancer (2016) 16:589 DOI 10.1186/s12885-016-2637-y RESEARCH ARTICLE Open Access Evaluation of folate receptor 1 (FOLR1) mRNA expression, its specific promoter methylation and global DNA hypomethylation in type I and type II ovarian cancers Sara Notaro1,2, Daniel Reimer1, Heidi Fiegl1, Gabriel Schmid1, Annamarie Wiedemair1, Julia Rössler1, Christian Marth1 and Alain Gustave Zeimet1* Abstract Background: In this retrospective study we evaluated the respective correlations and clinical relevance of FOLR1 mRNA expression, FOLR1 promoter specific methylation and global DNA hypomethylation in type I and type II ovarian cancer. Methods: Two hundred fifty four ovarian cancers, 13 borderline tumours and 60 samples of healthy fallopian epithelium and normal ovarian epithelium were retrospectively analysed for FOLR1 expression with RT-PCR. FOLR1 DNA promoter methylation and global DNA hypomethylation (measured by means of LINE1 DNA hypomethylation) were evaluated with MethyLight technique. Results: No correlation between FOLR1 mRNA expression and its specific promoter DNA methylation was found neither in type I nor in type II cancers, however, high FOLR1 mRNA expression was found to be correlated with global DNA hypomethylation in type II cancers (p = 0.033). Strong FOLR1 mRNA expression was revealed for Grades 2-3, FIGO stages III-IV, residual disease > 0, and serous histotype. High FOLR1 expression was found to predict increased platinum sensitivity in type I cancers (odds ratio = 3.288; 1.256-10.75; p = 0.020). One-year survival analysis showed in type I cancers an independent better outcome for strong expression of FOLR1 in FIGO stage III and IV.
    [Show full text]
  • Growth and Gene Expression Profile Analyses of Endometrial Cancer Cells Expressing Exogenous PTEN
    [CANCER RESEARCH 61, 3741–3749, May 1, 2001] Growth and Gene Expression Profile Analyses of Endometrial Cancer Cells Expressing Exogenous PTEN Mieko Matsushima-Nishiu, Motoko Unoki, Kenji Ono, Tatsuhiko Tsunoda, Takeo Minaguchi, Hiroyuki Kuramoto, Masato Nishida, Toyomi Satoh, Toshihiro Tanaka, and Yusuke Nakamura1 Laboratories of Molecular Medicine [M. M-N., M. U., K. O., T. M., T. Ta., Y. N.] and Genome Database [T. Ts.], Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Department of Obstetrics and Gynecology, School of Medicine, Kitasato University, Sagamihara 228-8555, Japan [H. K.]; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tsukuba, Tsukuba 305-8576, Japan [M. N.]; and Department of Obstetrics and Gynecology, Ibaraki Seinan Central Hospital, Tsukuba 306-0433, Japan [T. S.] ABSTRACT Akt/protein kinase B, cell survival, and cell proliferation (8). Over- expression of PTEN can decrease cell proliferation and tumorigenicity The PTEN tumor suppressor gene encodes a multifunctional phospha- (9, 10), an observation attributed to the ability of PTEN to induce cell tase that plays an important role in inhibiting the phosphatidylinositol-3- cycle arrest and apoptosis (11, 12). kinase pathway and downstream functions that include activation of Akt/protein kinase B, cell survival, and cell proliferation. Enforced ex- Thus, lack of PTEN expression may affect a complex set of pression of PTEN in various cancer cell lines decreases cell proliferation transcriptional targets. However, no systematic assessment of PTEN- through arrest of the cell cycle, accompanied in some cases by induction regulated targets in cancer cells has been reported to date.
    [Show full text]
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
    [Show full text]
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
    [Show full text]