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Untitled Document
CANCER GENOMICS & PROTEOMICS
Volume 3, Number
5, September-October 2006
| CONTENTS |
PAGE |
| Molecular Assessment of the Tumor Protein Microenvironment Using Imaging Mass Spectrometry. R.L. CALDWELL, A. GONZALEZ, S.R. OPPENHEIMER, H.S. SCHWARTZ, R.M. CAPRIOLI (Nashville, TN, USA) |
279 |
cDNA Microarray Analysis of Gene Expression in Ovarian Cancer Cells After Treatment with Carboplatin and Paclitaxel. L. RANDALL-WHITIS,
D.D. TAYLOR, Ç. GERÇEL-TAYLOR (Louisville, KY, USA) |
289 |
| Deregulated Pathways in a Human Lymphoblastoid Cell Line after Low Doses of Gamma Irradiation. S. CHEVILLARD, N. UGOLIN, O. RIGAUD, K. ORY, C. LEVALOIS, R. MAXIMILIEN, B. MALFOY (Fontenay-aux-Roses cedex; Paris, France) |
295 |
| *Basics of Diagnostic DNA Microarray Technology. Case Study: Hepatocellular Carcinoma. A. EL-ANEED, J. BANOUB (St. John’s, NL, Canada) |
311 |
| Non-coding MicroRNAs hsa-let-7g and hsa-miR-181b are Associated with Chemoresponse to S-1 in Colon Cancer. G. NAKAJIMA, K. HAYASHI, Y. XI, K. KUDO, K. UCHIDA, K. TAKASAKI, M. YAMAMOTO, J. JU (Mobile, AL, USA; Tokyo, Japan) |
317 |
The Proteome Profile of the Human Osteosarcome Saos2 Cell Line.
K.N. NIFOROU, A.K. ANAGNOSTOPOULOS, K. VOUGAS, C. KITTAS,
V.G. GORGOULIS, G.T. TSANGARIS (Athens, Greece) |
325 |
*Review
CANCER GENOMICS & PROTEOMICS 3: 325-346 (2006)
The Proteome Profile of the Human Osteosarcome Saos2 Cell Line
KATERINA N. NIFOROU1, ATHANASIOS K. ANAGNOSTOPOULOS2, KONSTANTINOS VOUGAS2, CHRISTOS KITTAS1, VASSILIS G. GORGOULIS1 and GEORGE T. TSANGARIS2
1 Department of Histology-Embryology, School of Medicine, University of Athens;
2 Division of Biotechnology, Centre of Basic Research II, Foundation
for Biomedical Research of the Academy of Athens, Athens, Greece
Abstract: The human Saos2 cell line was one of the first generated cell lines and is known to be used in all sorts of biomedical research. Knowledge of its protein expression is limited and no comprehensive study on the proteome of this cell type has been reported to date. Proteomics technologies were applied in order to analyse the proteins of the Saos2 cell line. Total protein extracts were separated by two dimensional gel electrophoresis (2-DE) and analysed by MALDI-MS and MALDI-MS-MS following in-gel digestion with trypsin and, finally, protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Approximately 4,000 spots were excised from four 2-DE gels and were analysed, resulting in the identification of 349 different gene products. The majority of the identified proteins were enzymes, regulatory proteins and transporters, while leukocyte markers and oncogenes were also included. Our findings include 10 protooncogenes (STRAP, FUBP1, SRC8, NPM, PARK7, DJ-1, PSD10, OXRP, GAGD2 and TPD54) related to the chromosomally instable character observed in the Saos2 cell line. Considering these, the Saos2 2-DE database shapes the basis for future expressional studies at the protein level and it forms a useful tool in anticancer research.
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CANCER GENOMICS & PROTEOMICS 3: 317-324 (2006)
Non-coding MicroRNAs hsa-let-7g and hsa-miR-181b areAssociated with Chemoresponse to S-1 in Colon Cancer
GO NAKAJIMA1, KAZUHIKO HAYASHI2, YAGUANG XI1, KENJI KUDO2, KAZUMI UCHIDA2, KEN TAKASAKI2, MASAKAZU YAMAMOTO2 and JINGFANG JU1
1 USA-Mitchell Cancer Institute, Mobile, AL 36688, U.S.A.; 2 Department of Surgery,
Institute of Gastroenterology, Tokyo Women's Medical University,
Tokyo 162-8666, Japan
Abstract: Background: MicroRNAs (miRNAs) are small non-coding RNAs (~22 nucleotides) that regulate gene expression at a post-transcriptional level via imperfect base pairing to the 3'-UTR of their target mRNAs. Previous studies from our group identified a number of deregulated miRNAs due to the loss of p53 tumor suppressor in colon cancer cell lines. To further investigate the in vivo biological significance of these miRNAs, the expressions of hsa-let-7g, hsa-miR-143, hsa-miR-145, hsa-miR-181b and hsa-miR-200c were investigated using formalin-fixed paraffin-embedded (FFPE) colon cancer specimens to evaluate the potential relationship with chemosensitivity and tumorigenesis. Patients and Methods: Forty-six patients with recurrent or residual colon cancer lesions were treated with the 5-fluorouracil-based antimetabolite S-1. This includes twenty-one pairs of tumor and normal samples. Total RNAs were isolated and the expression level of each particular miRNA was quantified using real time qRT-PCR analysis. Results: The expression levels of hsa-let-7g, hsa-miR-181b and hsa-miR-200c were over-expressed in tumor tissues compared to normal tissues. The expression levels of hsa-let-7g (p=0.03; Mann-Whitney test) and hsa-miR-181b (p=0.02; Mann-Whitney test) were strongly associated with clinical response to S-1. Although hsa-let-7g and hsa-miR-181b are strongly associated with patient's response to S-1 treatment, they are not significant prognostic factors for predicting survival. Conclusion: hsa-let-7g, hsa-miR-181b and hsa-miR-200c may be associated with tumorigenesis in colon cancer. In addition, hsa-let-7g and hsa-miR-181b may be potential indicators for chemoresponse to S-1 based chemotherapy.
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CANCER GENOMICS & PROTEOMICS 3: 279-288 (2006)
Molecular Assessment of the Tumor Protein Microenvironment Using Imaging Mass Spectrometry
ROBERT L. CALDWELL1,2, ADRIANA GONZALEZ3, STACEY R. OPPENHEIMER1, HERBERT S. SCHWARTZ4 and RICHARD M. CAPRIOLI1,2
1Mass Spectrometry Research Center, Departments of 2Biochemistry and 3Pathology and 4Vanderbilt Orthopaedic Institute, Vanderbilt University School of Medicine, Nashville, TN, U.S.A.
Abstract: Tumor cells or other bioreactive compounds derived from the tumor can migrate beyond the tumor margin and may be significant contributing factors in tumor recurrence. Local recurrence of cancer occurs quite often, despite microscopically-confirmed negative surgical resection margins, and is likely related to the presence of abnormal, fully neoplastic or pre-neoplastic cells adjacent to the tumor that cannot be recognized by conventional light microscopy. Identification of proteins that define the molecular tumor microenvironment of the neoplastic process may become an important part of the evaluation of cancer tissue, potentially helping guide surgical resection procedures. Tissue-based matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry is a molecular analysis technology that can significantly improve the assessment of tumor microenvironment at the molecular level. In the current study, this is illustrated with the analysis of an invasive soft tissue sarcoma. Marked differences in protein distribution between tumor and immediate adjacent tissue are shown, and these differences persist far into histologically normal appearing adjacent tissue. Several of these proteins are confirmed using immunohistochemistry. This study demonstrates that tissue-based MALDI imaging mass spectrometry is ideally suited for the molecular analysis of tumor microenvironment and could potentially augment histologic interpretation of tumor margins.
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CANCER GENOMICS & PROTEOMICS 3: 295-310 (2006)
Deregulated Pathways in a Human Lymphoblastoid Cell Line after Low Doses of Gamma Irradiation
SYLVIE CHEVILLARD1, NICOLAS UGOLIN1, ODILE RIGAUD1, KATHY ORY1, CÉLINE LEVALOIS1, RÉMI MAXIMILIEN1 and BERNARD MALFOY2,3,4
1CEA, DSV, DRR, Laboratoire de Cancérologie Expérimentale, Fontenay-aux-Roses cedex;
2Institut Curie, Centre de Recherche, Paris; 3CNRS, UMR7147, Paris; 4Université Paris VI, Paris, France
Abstract: Transcriptome analysis now permits the exploration of the effects of low doses of radiation and potentially can provide a global view of radiation responsive pathways. The present work focuses on the comparison of the variation of gene expression with regard to the cellular response induced after either 0.02 or 2 Gy gamma radiation exposure of a human lymphoblastoid cell line. It was observed that: a) a lower number of genes was deregulated after 0.02 compared to 2 Gy, b) some genes were specifically deregulated according to the dose while others were similarly deregulated whatever the dose, c) functional grouping of all ionizing radiations responsive genes after high or low doses showed that the pathways most frequently involved are the same and correspond to signal transduction, cytoskeleton, protein metabolism catabolism and modification, intracellular trafficking and transcription factors, d) genes specifically deregulated at the high dose did not present specificity regarding their functional grouping compared to pathways described above while genes specifically deregulated after 0.02 Gy were mainly involved in signal transduction, cytoskeleton, stress response, ionic transport and channel and e) after both doses, responsive genes related to cell survival and death were in good agreement with data obtained on cell survival and death. Overall, the results support the hypothesis that low doses of ionizing radiation lead to a typical stress-induced translation inhibition and RNA processing alteration. The utility of DNA microarray to obtain an integrated view of the radiation response is emphasized and the need for further efforts to explore the effects of low doses of radiation is underlined. The results suggest that part of the response at low doses cannot be predicted by extrapolation from data obtained at high doses.
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CANCER GENOMICS & PROTEOMICS 3: 289-294 (2006)
cDNA Microarray Analysis of Gene Expression in Ovarian Cancer Cells After Treatment with Carboplatin and Paclitaxel
L. RANDALL-WHITIS, DOUGLAS D. TAYLOR and C. GERCEL-TAYLOR
Department of Obstetrics, Gynecology and Women's Health, Division of Gynecologic Oncology, University of Louisville School of Medicine, Louisville, KY 40202, U.S.A.
Abstract: Background: Tumor resistance to chemotherapy results in ovarian cancer treatment failures. To understand the role of DNA damage, expression profiling was performed in ovarian cancer cells following suboptimal carboplatin (Carbo) and paclitaxel (Tax) treatments. Materials and Methods: Cell lines isolated from one patient were used. UL-3A was isolated at initial diagnosis, UL-3B after failure to cisplatin and Tax, and UL-3C at the final stages of the disease. Five clones isolated from UL-3A were also included. Sulforhodamine B assay was used to determine drug sensitivities. Gene expression was studied by DNA repair pathway specific microarray. Results: The cytotoxic phase was induced in all cells with Carbo and/or Tax treatments. Some cells recovered after individual drug treatments with the UL-3B cells surviving all modalities. Significant changes in the sensitivity of some surviving cells to chemotherapeutic agents were demonstrated. Carbo or Tax treatments resulted in significantly increased MDM2 and MSH6 and decreased 53BP1, EXT1, H2AFL and UNG expression. Combined Carbo and Tax treatment resulted in decreased ATR, CHEK1, PPM1D and PRKDC and increased RAD1, CDS1 and ATRX expression. Conclusion: Differential gene expression patterns were identified in cells that survived Carbo and Tax treatment that may be involved in ovarian cancer drug resistance.
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CANCER GENOMICS & PROTEOMICS 3: 311-316 (2006)
Basics of Diagnostic DNA Microarray Technology. Case Study: Hepatocellular Carcinoma
ANAS EL-ANEED and JOSEPH BANOUB
Memorial University of Newfoundland, Biochemistry Department, St. John's, NL,
A1C 5S7, Canada
Abstract: The DNA microarray technique is capable of identifying the expression of thousands of genes simultaneously. This technology has become instrumental in cancer research for diagnosis and biomarker discovery purposes. This mini-review will introduce DNA microarrays at the basic technical level and will focus on high risk Hepatocellular Carcinoma (HCC) patients, namely hepatitis B and C infected individuals.
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