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Page DB. The Human Tumor Atlas Network's beginning steps toward the future of collaborative multi-omic discovery. Cell Rep Med 2022; 3:100532. [PMID: 35243426 PMCID: PMC8861967 DOI: 10.1016/j.xcrm.2022.100532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Human Tumor Atlas Network is a multi-institutional effort to generate genomic and histologic datasets spanning thousands of patients. Johnson et al., in this issue of Cell Reports Medicine, illustrate how disparate data types from a single case can be combined to discover novel therapeutic directions.
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Affiliation(s)
- David B. Page
- Providence Cancer Institute, Earle A. Chiles Research Institute, Portland, OR, USA
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Lin S, Yue J, Guan X, Yuan P, Wang J, Luo Y, Fan Y, Cai R, Li Q, Chen S, Zhang P, Li Q, Ma F, Xu B. Polymorphisms of MTHFR and TYMS predict capecitabine-induced hand-foot syndrome in patients with metastatic breast cancer. Cancer Commun (Lond) 2019; 39:57. [PMID: 31601265 PMCID: PMC6787984 DOI: 10.1186/s40880-019-0399-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/20/2019] [Indexed: 02/08/2023] Open
Abstract
Background Breast cancer is a global problem, and a large number of new cases are diagnosed every year. Capecitabine is effective in patients with metastatic breast cancer (MBC). Hand-foot syndrome (HFS) is a common adverse effect of capecitabine. In this study, we investigated the association between single nucleotide polymorphisms (SNPs) in genes involved in capecitabine metabolism pathways and capecitabine-induced HFS in Chinese patients with MBC to identify some predictive genetic biomarkers. Methods We selected 3 genes involved in capecitabine metabolism and screened genetic variants in these target genes. We genotyped a total of 22 SNPs in the thymidylate synthase gene (TYMS), the methylene tetrahydrofolate reductase gene (MTHFR), and the ribonucleotide reductase M1 gene (RRM1) in 342 MBC patients treated with capecitabine-based chemotherapy. The genotype distributions of each SNP in patients with and without HFS were assessed using Pearson’s χ2 test, and the relationship between HFS and genotypes of SNPs was determined using logistic regression analysis. The association between SNPs and their corresponding gene expression was analyzed using the Blood expression quantitative trait loci (eQTL) browser online tools. Results We found 4 positive sites for HFS in the TYMS and MTHFR genes: TYMS rs2606241 (P = 0.022), TYMS rs2853741 (P = 0.019), MTHFR rs3737964 (P = 0.029), and MTHFR rs4846048 (P = 0.030). Logistic regression analyses showed that the genotype AG of MTHFR rs3737964 [odds ratio (OR) = 0.54, 95% confidence interval (CI) 0.31–0.97, P = 0.038] and MTHFR rs4846048 (OR = 0.54, 95% CI 0.30–0.98, P = 0.042) were protective factors of HFS, whereas the genotype CT of TYMS rs2853741 (OR = 2.25, 95% CI 1.31–3.87, P = 0.012) increased the risk of HFS. The association between the genotype GT of TYMS rs2606241 (OR = 1.27, 95% CI 0.73–2.23, P = 0.012) and HFS was uncertain. Further eQTL analyses confirmed that the alleles of rs3737964 and rs4846048 affected the gene expression levels of MTHFR in cis. Conclusions We have identified four potentially useful pharmacogenetic markers, TYMS rs2606241, TYMS rs2853741, MTHFR rs3737964, and MTHFR rs4846048 to predict capecitabine-induced HFS in MBC patients.
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Affiliation(s)
- Shaoyan Lin
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, P. R. China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100021, P. R. China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Ying Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Ruigang Cai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Pin Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Qing Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China.
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, P. R. China.
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Herrmann S, Zhan T, Betge J, Rauscher B, Belle S, Gutting T, Schulte N, Jesenofsky R, Härtel N, Gaiser T, Hofheinz RD, Ebert MP, Boutros M. Detection of mutational patterns in cell-free DNA of colorectal cancer by custom amplicon sequencing. Mol Oncol 2019; 13:1669-1683. [PMID: 31254442 PMCID: PMC6670011 DOI: 10.1002/1878-0261.12539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Monitoring the mutational patterns of solid tumors during cancer therapy is a major challenge in oncology. Analysis of mutations in cell-free (cf) DNA offers a noninvasive approach to detect mutations that may be prognostic for disease survival or predictive for primary or secondary drug resistance. A main challenge for the application of cfDNA as a diagnostic tool is the diverse mutational landscape of cancer. Here, we developed a flexible end-to-end experimental and bioinformatic workflow to analyze mutations in cfDNA using custom amplicon sequencing. Our approach relies on open-software tools to select primers suitable for multiplex PCR using minimal cfDNA as input. In addition, we developed a robust linear model to identify specific genetic alterations from sequencing data of cfDNA. We used our workflow to design a custom amplicon panel suitable for detection of hotspot mutations relevant for colorectal cancer and analyzed mutations in serial cfDNA samples from a pilot cohort of 34 patients with advanced colorectal cancer. Using our method, we could detect recurrent and patient-specific mutational patterns in the majority of patients. Furthermore, we show that dynamic changes of mutant allele frequencies in cfDNA correlate well with disease progression. Finally, we demonstrate that sequencing of cfDNA can reveal mechanisms of resistance to anti-Epidermal Growth Factor Receptor(EGFR) antibody treatment. Thus, our approach offers a simple and highly customizable method to explore genetic alterations in cfDNA.
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Affiliation(s)
- Simon Herrmann
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Germany.,Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tianzuo Zhan
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Germany.,Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Betge
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Germany.,Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Benedikt Rauscher
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Germany
| | - Sebastian Belle
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tobias Gutting
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nadine Schulte
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ralf Jesenofsky
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nicolai Härtel
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Medical Faculty Mannheim, Institute of Pathology, Heidelberg University, Mannheim, Germany
| | - Ralf-Dieter Hofheinz
- Medical Faculty Mannheim, Interdisciplinary Tumor Centre, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg University, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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Webber JT, Kaushik S, Bandyopadhyay S. Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics. Cell Syst 2018; 7:526-536.e6. [PMID: 30414925 DOI: 10.1016/j.cels.2018.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 08/01/2018] [Accepted: 10/04/2018] [Indexed: 02/08/2023]
Abstract
Leveraging insights from genomic studies of patient tumors is limited by the discordance between these tumors and the cell line models used for functional studies. We integrate omics datasets using functional networks to identify gene modules reflecting variation between tumors and show that the structure of these modules can be evaluated in cell lines to discover clinically relevant biomarkers of therapeutic responses. Applied to breast cancer, we identify 219 gene modules that capture recurrent alterations and subtype patients and quantitate various cell types within the tumor microenvironment. Comparison of modules between tumors and cell lines reveals that many modules composed primarily of gene expression and methylation are poorly preserved. In contrast, preserved modules are highly predictive of drug responses in a manner that is robust and clinically relevant. This work addresses a fundamental challenge in pharmacogenomics that can only be overcome by the joint analysis of patient and cell line data.
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Affiliation(s)
- James T Webber
- Department of Bioengineering and Therapeutic Sciences, Institute for Computational Health Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Swati Kaushik
- Department of Bioengineering and Therapeutic Sciences, Institute for Computational Health Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sourav Bandyopadhyay
- Department of Bioengineering and Therapeutic Sciences, Institute for Computational Health Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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McDonald M, Oktaria S, Konstantinov K, Rosenfeld A, Lerch M, Corde S, Tehei M. Radiosensitisation enhancement effect of BrUdR and Ta
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NSPs in combination with 5-Fluorouracil antimetabolite in kilovoltage and megavoltage radiation. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aabab2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Nagase H, Nakagawa F, Uchida J. Antitumor Efficacy of Combination Therapy Consisting of S-1, Leucovorin, and Oxaliplatin against Human Gastric Cancer Xenografts. Chemotherapy 2018; 63:46-52. [PMID: 29393100 DOI: 10.1159/000486029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/04/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM A phase 3 trial of S-1, leucovorin (LV), and oxaliplatin for treating gastric cancer is now underway. However, the antitumor efficacy of the combination has not yet been examined in an in vivo preclinical study. This study examined the antitumor efficacy of combination therapy consisting of S-1, LV, and oxaliplatin against 4 human gastric cancer xenografts: NUGC-4, St-40, SC-2, and SC-4. METHODS The antitumor efficacy was evaluated using human gastric cancer xenograft-bearing nude mice. S-1 and LV were administered orally once daily on days 1-7 at doses of 6.9 and 10 mg/kg, respectively. Oxaliplatin was administered intravenously at a dose of 8.3 mg/kg on day 1. The tumor volume was measured on day 15, and the relative tumor volume (RTV) was calculated. RESULTS In all 4 xenograft models, S-1 alone and oxaliplatin alone, but not LV alone, had significant antitumor activities (p < 0.001). Combination therapy consisting of S-1 and LV resulted in a significantly smaller RTV than S-1 alone (p < 0.001). Combination therapy consisting of S-1 and oxaliplatin also resulted in a significantly smaller RTV than either S-1 alone (p < 0.001) or oxaliplatin alone (p < 0.001). Furthermore, combination therapy consisting of S-1, LV, and oxaliplatin resulted in the highest antitumor activity in these models (p < 0.001 vs. S-1 + LV; p < 0.001 or p = 0.003 vs. S-1 + oxaliplatin). CONCLUSION Combination therapy consisting of S-1, LV, and oxaliplatin administered according to a 1-week-on/1-week-off schedule may be useful for the treatment of patients with gastric cancer.
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Affiliation(s)
- Hideki Nagase
- Pharmacology Laboratory, Taiho Pharmaceutical Co., Ltd., Tokushima, Japan
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Steding CE. Creating chemotherapeutic-resistant breast cancer cell lines: advances and future perspectives. Future Oncol 2016; 12:1517-27. [DOI: 10.2217/fon-2016-0059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The development of resistance remains the most significant impediment to generating effective treatments for cancer. In the modern age of personalized medicine, it is of critical importance to understand the principles of both innate and acquired resistance to achieve the most effective therapeutic outcomes. Significant differences exist between cancer cells that exhibit innate resistance verses those that acquire resistance over time. Studying the acquisition of resistance is essential to obtaining a complete understanding of how treatments contribute to disease recurrence and progression. This review will evaluate the current understanding of chemotherapeutic resistance and its role in personalized medicine. This review will also explore how generating resistant cells in culture is essential to the development of improved cancer therapeutics.
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Affiliation(s)
- Catherine E Steding
- The Center for Genomic Advocacy, Indiana State University, 600 Chestnut St., Terre Haute, IN 47809, USA
- The Department of Biology, Indiana State University, 600 Chestnut St., Terre Haute, IN 47809, USA
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Inside the biochemical pathways of thymidylate synthase perturbed by anticancer drugs: Novel strategies to overcome cancer chemoresistance. Drug Resist Updat 2015; 23:20-54. [PMID: 26690339 DOI: 10.1016/j.drup.2015.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 10/08/2015] [Accepted: 10/23/2015] [Indexed: 12/11/2022]
Abstract
Our current understanding of the mechanisms of action of antitumor agents and the precise mechanisms underlying drug resistance is that these two processes are directly linked. Moreover, it is often possible to delineate chemoresistance mechanisms based on the specific mechanism of action of a given anticancer drug. A more holistic approach to the chemoresistance problem suggests that entire metabolic pathways, rather than single enzyme targets may better explain and educate us about the complexity of the cellular responses upon cytotoxic drug administration. Drugs, which target thymidylate synthase and folate-dependent enzymes, represent an important therapeutic arm in the treatment of various human malignancies. However, prolonged patient treatment often provokes drug resistance phenomena that render the chemotherapeutic treatment highly ineffective. Hence, strategies to overcome drug resistance are primarily designed to achieve either enhanced intracellular drug accumulation, to avoid the upregulation of folate-dependent enzymes, and to circumvent the impairment of DNA repair enzymes which are also responsible for cross-resistance to various anticancer drugs. The current clinical practice based on drug combination therapeutic regimens represents the most effective approach to counteract drug resistance. In the current paper, we review the molecular aspects of the activity of TS-targeting drugs and describe how such mechanisms are related to the emergence of clinical drug resistance. We also discuss the current possibilities to overcome drug resistance by using a molecular mechanistic approach based on medicinal chemistry methods focusing on rational structural modifications of novel antitumor agents. This paper also focuses on the importance of the modulation of metabolic pathways upon drug administration, their analysis and the assessment of their putative roles in the networks involved using a meta-analysis approach. The present review describes the main pathways that are modulated by TS-targeting anticancer drugs starting from the description of the normal functioning of the folate metabolic pathway, through the protein modulation occurring upon drug delivery to cultured tumor cells as well as cancer patients, finally describing how the pathways are modulated by drug resistance development. The data collected are then analyzed using network/netwire connecting methods in order to provide a wider view of the pathways involved and of the importance of such information in identifying additional proteins that could serve as novel druggable targets for efficacious cancer therapy.
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Thymidylate synthase polymorphisms are associated to therapeutic outcome of advanced non-small cell lung cancer patients treated with platinum-based chemotherapy. Mol Biol Rep 2014; 41:3349-57. [PMID: 24554028 DOI: 10.1007/s11033-014-3197-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 01/24/2014] [Indexed: 12/11/2022]
Abstract
Thymidylate synthase (TYMS) has three polymorphisms that may modulate thymidylate synthase (TS) expression levels: (1) 28 base pairs (bp) variable number tandem repeat (VNTR) (rs34743033); (2) single nucleotide polymorphism (SNP) C>G at the twelfth nucleotide of the second repeat of 3R allele (rs2853542); and (3) 6 bp sequence deletion (1494del6, rs34489327). This study was conducted to evaluate the influence of TYMS polymorphisms on the survival of Portuguese patients with advanced non-small cell lung cancer (NSCLC) undergoing platinum-based chemotherapy. Our results showed no statistically significant differences between VNTR genotypes; although, considering the SNP C>G, homozygotes 3RG presented a better prognostic at 36 months (p=0.004) and overall survival (p=0.003) when compared to 2R3RG patients. Patients with "median/high expression genotypes" demonstrated a better survival at 12 months (p=0.041) when compared to "low expression genotypes". Furthermore, 6 bp- carriers (p=0.006) showed a better survival at 12 months when compared to 6 bp+ homozygotes patients. When analyzing TYMS haplotypes, better survival at 12 months was observed for patients carrying haplotypes with the 6 bp- allele (2R6 bp-; p=0.026 and 3RG6 bp-; p=0.045). This is the first report that evaluates the three major TYMS polymorphisms in the therapeutic outcome of NSCLC in Portugal. According to our results, the TYMS polymorphisms may be useful tools to predict which advanced NSCLC patients could benefit more from platinum-based chemotherapy regimens.
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Nakamura A, Nakajima G, Okuyama R, Kuramochi H, Kondoh Y, Kanemura T, Takechi T, Yamamoto M, Hayashi K. Enhancement of 5-fluorouracil-induced cytotoxicity by leucovorin in 5-fluorouracil-resistant gastric cancer cells with upregulated expression of thymidylate synthase. Gastric Cancer 2014; 17:188-95. [PMID: 23494117 PMCID: PMC3889291 DOI: 10.1007/s10120-013-0249-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 02/19/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND Elucidation of the mechanisms by which gastric cancer cells acquire resistance to 5-fluorouracil (5FU) may provide important clues to the development of effective chemotherapy for 5FU-resistant gastric cancer METHODS Four 5FU-resistant cell lines (MKN45/5FU, MKN74/5FU, NCI-N87/5FU, and KATOIII/5FU) were established by continuous exposure of the cells to progressively increasing concentrations of 5FU for about 1 year. Then, mRNA expression levels of four genes associated with 5FU metabolism, i.e., thymidylate synthase (TS), dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase, were quantitatively evaluated by real-time reverse transcriptase-polymerase chain reaction. In addition, TS protein expression was measured by Western blot analysis. RESULTS As compared with the parent cell lines, the 5FU-resistant cell lines showed 3.8- to 11.6-fold higher resistance to 5FU, as well as 1.9- to 3.5-fold higher TS mRNA expression and 1.6- to 7.1-fold higher TS protein expression. In contrast, the expressions of other genes did not differ significantly among the cell lines. The cytotoxicity of 5FU was enhanced 2.3- to 2.8 fold by leucovorin (LV) against three of the four 5FU-resistant cell lines. CONCLUSIONS Collectively, LV enhanced the cytotoxicity of 5FU not only against the parent gastric cancer cell lines, but also against the 5FU-resistant cell lines, even those with elevated TS expression levels. These results suggest that clinical studies of a combination of 5FU and LV are warranted in patients who have recurrent gastric cancer after 5FU-based therapy.
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Affiliation(s)
- Ayako Nakamura
- Field of Chemotherapy on Digestive Organs Division of Gastrointestinal Surgery, Tokyo Women’s Medical University Graduate School of Medicine, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan ,Oncology Medical Affairs Department, Taiho Pharmaceutical Co., Ltd, 1-2-4 Uchikanda, Chiyoda-ku, Tokyo, 101-0047 Japan
| | - Go Nakajima
- Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Ryuji Okuyama
- Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Hidekazu Kuramochi
- Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Yurin Kondoh
- Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Toshinori Kanemura
- Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Teiji Takechi
- Laboratory for Oncology Medication Management and Development, Taiho Pharmaceutical Co., Ltd, 1-2-4 Uchikanda, Chiyoda-ku, Tokyo, 101-0047 Japan
| | - Masakazu Yamamoto
- Department of Surgery, Institute of Gastroenterology, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Kazuhiko Hayashi
- Field of Chemotherapy on Digestive Organs Division of Gastrointestinal Surgery, Tokyo Women’s Medical University Graduate School of Medicine, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan ,Department of Chemotherapy and Palliative Care, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
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Thymidylate synthase protein expression by IHC and gene copy number by SISH correlate and show great variability in non-small cell lung cancer. J Thorac Oncol 2012; 7:982-92. [PMID: 22551903 DOI: 10.1097/jto.0b013e31824fe95a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Increased expression of thymidylate synthase (TS) is thought to be associated with resistance to TS-targeting drugs, e.g., pemetrexed. METHODS TS protein expression (PE) and gene copy number (GCN) were assayed using immunohistochemistry and silver in situ hybridization, respectively, on primary tumors of 189 resected non-small cell lung patients. Associations with pathological and clinical features and prognosis were explored. RESULTS Median immunohistochemistry H-score was 220 (range, 10-380) on a 0 to 400 scale; 17% of the patients had a TS expression of 300 or more. TS PE expression did not significantly differ by histology and did not significantly associate with disease-free survival (DFS) or overall survival (OS). However, there was a tendency for increased DFS (p = 0.12) and OS (p = 0.12) in PE positive (>median) squamous-cell carcinoma (SCC) patients. Median GCN was 2.5 genes/nucleus (range, 1.4-9.6); 29% of patients had GCN of 3 or more, 7% of 4 or more and 0.8% amplification. GCN differed by histology (p = 0.015); 50% of SCCs having GCN more than 2.5 versus 32% of adenocarcinomas. There was no significant relationship between TS GCN and DFS or OS; however, a trend toward better DFS (p = 0.18) and OS (p = 0.10) with increased GCN in SCCs was observed. TS GCN was significantly correlated with PE (r = 0.30, p = 0.0009). CONCLUSIONS TS PE and GCN vary widely in non-small cell lung and correlate significantly with each other. TS GCN is higher in SCCs, whereas TS PE does not associate with histological subtypes, clinical features, or survival. Variability of TS PE and GCN may indicate potential benefit from pemetrexed therapy in selected SCC patients.
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López-Mateo I, Villaronga MÁ, Llanos S, Belandia B. The transcription factor CREBZF is a novel positive regulator of p53. Cell Cycle 2012; 11:3887-95. [PMID: 22983008 DOI: 10.4161/cc.22133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
CREBZF is a member of the mammalian ATF/CREB family of transcription factors. Here, we describe a novel functional interaction between CREBZF and the tumor suppressor p53. CREBZF was identified in a yeast two-hybrid screen using HEY1, recently characterized as an indirect p53 activator, as bait. CREBZF interacts in vitro with both HEY1 and p53, and CREBZF expression stabilizes and activates p53. Moreover, CREBZF cooperates synergistically with HEY1 to enhance p53 transcriptional activity. On the other hand, partial depletion of endogenous CREBZF diminishes p53 protein levels and inhibits HEY1-mediated activation of p53. CREBZF-positive effects on p53 signaling may reflect, at least in part, an observed induction of posttranslational modifications in p53 known to prevent its degradation. CREBZF expression protects HCT116 cells from UV radiation-induced cell death. In addition, CREBZF expression confers sensitivity to 5-fluorouracil, a p53-activating chemotherapeutic drug. Our study suggests that CREBZF may participate in the modulation of p53 tumor suppressor function.
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Affiliation(s)
- Irene López-Mateo
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain
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Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer. PLoS One 2011; 6:e24662. [PMID: 21931799 PMCID: PMC3170379 DOI: 10.1371/journal.pone.0024662] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/16/2011] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Gastric cancer continues to be one of the deadliest cancers in the world and therefore identification of new drugs targeting this type of cancer is thus of significant importance. The purpose of this study was to identify and validate a therapeutic agent which might improve the outcomes for gastric cancer patients in the future. METHODOLOGY/PRINCIPAL FINDINGS Using microarray technology, we generated a gene expression profile of human gastric cancer-specific genes from human gastric cancer tissue samples. We used this profile in the Broad Institute's Connectivity Map analysis to identify candidate therapeutic compounds for gastric cancer. We found the histone deacetylase inhibitor vorinostat as the lead compound and thus a potential therapeutic drug for gastric cancer. Vorinostat induced both apoptosis and autophagy in gastric cancer cell lines. Pharmacological and genetic inhibition of autophagy however, increased the therapeutic efficacy of vorinostat, indicating that a combination of vorinostat with autophagy inhibitors may therapeutically be more beneficial. Moreover, gene expression analysis of gastric cancer identified a collection of genes (ITGB5, TYMS, MYB, APOC1, CBX5, PLA2G2A, and KIF20A) whose expression was elevated in gastric tumor tissue and downregulated more than 2-fold by vorinostat treatment in gastric cancer cell lines. In contrast, SCGB2A1, TCN1, CFD, APLP1, and NQO1 manifested a reversed pattern. CONCLUSIONS/SIGNIFICANCE We showed that analysis of gene expression signature may represent an emerging approach to discover therapeutic agents for gastric cancer, such as vorinostat. The observation of altered gene expression after vorinostat treatment may provide the clue to identify the molecular mechanism of vorinostat and those patients likely to benefit from vorinostat treatment.
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Amplification of thymidylate synthetase in metastatic colorectal cancer patients pretreated with 5-fluorouracil-based chemotherapy. Eur J Cancer 2010; 46:3358-64. [PMID: 20727737 DOI: 10.1016/j.ejca.2010.07.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/18/2010] [Accepted: 07/14/2010] [Indexed: 12/14/2022]
Abstract
Resistance to 5-fluorouracil (5-FU) represents a major contributor to cancer-related mortality in advanced colorectal cancer patients. Genetic variations and expression alterations in genes involved in 5-FU metabolism and effect have been shown to modulate 5-FU sensitivity in vitro, however these alterations do not fully explain clinical resistance to 5-FU-based chemotherapy. To determine if alterations of DNA copy number in genes involved in 5-FU metabolism-impacted clinical resistance to 5-FU-based chemotherapy, we assessed thymidylate synthetase (TYMS) and thymidine phosphorylase (TYMP) copy number in colorectal liver metastases. DNA copy number of TYMS and TYMP was evaluated using real time quantitative PCR in frozen colorectal liver metastases procured from 62 patients who were pretreated with 5-FU-based chemotherapy prior to surgical resection (5-FU exposed) and from 51 patients who received no pretreatment (unexposed). Gain of TYMS DNA copy number was observed in 18% of the 5-FU exposed metastases, while only 4% of the unexposed metastases exhibited TYMS copy gain (p = 0.036). No significant differences were noted in TYMP copy number alterations between 5-FU-exposed and -unexposed metastases. Median survival time was similar in 5-FU-exposed patients with metastases containing TYMS amplification and those with no amplification. However, TYMS amplification was associated with shorter median survival in patients receiving post-resection chemotherapy (hazard ratio = 2.7, 95% confidence interval = 1.1-6.6; p = 0.027). These results suggest amplification of TYMS amplification as a putative mechanism for clinical resistance to 5-FU-based chemotherapy and may have important ramifications for the post-resection chemotherapy choices for metastatic colorectal cancer.
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Balboa E, Duran G, Lamas MJ, Gomez-Caamaño A, Celeiro-Muñoz C, Lopez R, Carracedo A, Barros F. Pharmacogenetic analysis in neoadjuvant chemoradiation for rectal cancer: high incidence of somatic mutations and their relation with response. Pharmacogenomics 2010; 11:747-61. [DOI: 10.2217/pgs.10.51] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Aims: The identification of predictive markers of response to chemoradiotherapy treatment remains a promising approach for patient management in order to obtain the best response with minor side effects. Initially, we investigated whether the analysis of several markers previously studied and others not yet evaluated could predict response to 5-fluorouracil- and capecitabine-based neoadjuvant treatment in locally advanced rectal cancer. Methods & materials: We studied germline and tumoral samples of 65 stage II/III rectal patients. A panel of pharmacogenetic markers was genotyped in paired peripheral blood samples and rectal cancer tumors. Results: Our results seem to confirm the previously described association of thymidylate synthase and the prediction of chemoradiotherapy response in rectal cancer. However, it failed to confirm the clinical utility proposed for XRCC1, ERCC1, ERCC2, MTHFR and EGFR polymorphisms in blood/germline samples. Subsequently, with the aim of improving prediction of individual response and assessing the role of studied polymorphisms in response to treatment, we determined if changes in tumor response to these markers could predict clinical outcome. We found a high degree of changes between germline and tumor samples, mainly somatic mutations without microsatellite instability, and a minor frequency of loss-of-heterozygosity events. In tumoral samples, XRCC1 appeared to be significantly associated (p = 0.006) with downstaging of the tumor (odds ratio: 7.93; 95% CI: 1.03–60.83), but the increasing of TYMS low-expression alleles contradict the previous results observed in germline samples. Conclusion: The detection of somatic mutations in rectal cancer tumors led us to re-evaluate the utility of the tests performed in blood samples for these polymorphisms in rectal cancer. Furthermore, studies aimed at assessing the influence of pharmacogenetic markers in treatment response performed in blood samples should take into account the particular pattern of hypermutability present in each tumor type. We hypothesize that different patterns of hypermutability present in each tumor type would be related to the different results in association studies related to response to the treatment.
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Affiliation(s)
- Emilia Balboa
- Grupo Medicina Xenomica–CIBERER, Fundación Publica Galega de Medicina Xenómica, Santiago de Compostela, Spain and Fundación Publica Galega de Medicina Xenómica, Hospital Clinico Universitario, 15706, Santiago de Compostela, Spain
| | - Goretti Duran
- Complejo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Maria Jesus Lamas
- Complejo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Antonio Gomez-Caamaño
- Complejo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Catuxa Celeiro-Muñoz
- Complejo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Rafael Lopez
- Complejo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo Medicina Xenomica–CIBERER, Fundación Publica Galega de Medicina Xenómica, Santiago de Compostela, Spain and Fundación Publica Galega de Medicina Xenómica, Hospital Clinico Universitario, 15706, Santiago de Compostela, Spain
- Grupo Medicina Xenomica–CIBERER, Universidad de Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo Medicina Xenomica–CIBERER, Fundación Publica Galega de Medicina Xenómica, Santiago de Compostela, Spain and Fundación Publica Galega de Medicina Xenómica, Hospital Clinico Universitario, 15706, Santiago de Compostela, Spain
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Ozasa H, Oguri T, Uemura T, Miyazaki M, Maeno K, Sato S, Ueda R. Significance of thymidylate synthase for resistance to pemetrexed in lung cancer. Cancer Sci 2010; 101:161-6. [PMID: 19811498 PMCID: PMC11159671 DOI: 10.1111/j.1349-7006.2009.01358.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Pemetrexed (MTA) is a multitargeted antifolate with promising clinical activity in lung cancer. We exposed the small cell lung cancer cell line PC6 to stepwise-increasing pemetrexed concentrations of 0.4, 1.6, and 4.0 microm, and established three pemetrexed-resistant lung cancer cell lines: PC6/MTA-0.4, PC6/MTA-1.6, and PC6/MTA-4.0 cells. To investigate the mechanisms of acquired resistance to pemetrexed, we measured the expression levels of the thymidylate synthase (TS), reduced folate carrier (RFC), and folylpoly-gamma-glutamate synthetase (FPGS) genes. TS gene expression was significantly increased in PC6/MTA-1.6 and PC6/MTA-4.0 cells relative to parental cells in a pemetrexed dose-dependent manner. In contrast, the levels of RFC gene expression in PC6/MTA-0.4 cells and FPGS in PC6/MTA-1.6 cells were significantly decreased, whereas the levels of both genes were restored in PC6/MTA-4.0 cells. Knockdown of TS expression using siRNA enhanced pemetrexed cytotoxicity in PC6/MTA-4.0 cells. The expression level of the TS gene was significantly correlated with the concentration of pemetrexed for 50% cell survival (IC(50)) in 11 non-small cell lung cancer cell lines. These results suggest that the alteration of molecular pharmacological factors in relation with pemetrexed resistance is dose-dependent, and that up-regulation of the expression of the TS gene may have an important role in the acquired resistance to pemetrexed. In addition, TS may be a predictive marker for pemetrexed sensitivity in lung cancer.
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Affiliation(s)
- Hiroaki Ozasa
- Department of Medical Oncology and Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Ruderfer DM, Roberts DC, Schreiber SL, Perlstein EO, Kruglyak L. Using expression and genotype to predict drug response in yeast. PLoS One 2009; 4:e6907. [PMID: 19730698 PMCID: PMC2731853 DOI: 10.1371/journal.pone.0006907] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 07/30/2009] [Indexed: 02/03/2023] Open
Abstract
Personalized, or genomic, medicine entails tailoring pharmacological therapies according to individual genetic variation at genomic loci encoding proteins in drug-response pathways. It has been previously shown that steady-state mRNA expression can be used to predict the drug response (i.e., sensitivity or resistance) of non-genotyped mammalian cancer cell lines to chemotherapeutic agents. In a real-world setting, clinicians would have access to both steady-state expression levels of patient tissue(s) and a patient's genotypic profile, and yet the predictive power of transcripts versus markers is not well understood. We have previously shown that a collection of genotyped and expression-profiled yeast strains can provide a model for personalized medicine. Here we compare the predictive power of 6,229 steady-state mRNA transcript levels and 2,894 genotyped markers using a pattern recognition algorithm. We were able to predict with over 70% accuracy the drug sensitivity of 104 individual genotyped yeast strains derived from a cross between a laboratory strain and a wild isolate. We observe that, independently of drug mechanism of action, both transcripts and markers can accurately predict drug response. Marker-based prediction is usually more accurate than transcript-based prediction, likely reflecting the genetic determination of gene expression in this cross.
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Affiliation(s)
- Douglas M. Ruderfer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Eli & Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - David C. Roberts
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Stuart L. Schreiber
- Eli & Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Ethan O. Perlstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (LK); (EOP)
| | - Leonid Kruglyak
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (LK); (EOP)
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Thymidylate synthetase allelic imbalance in clear cell renal carcinoma. Cancer Chemother Pharmacol 2009; 64:1195-200. [PMID: 19306093 DOI: 10.1007/s00280-009-0986-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 03/06/2009] [Indexed: 10/21/2022]
Abstract
PURPOSE To investigate the allelic status of the thymidylate synthetase (TYMS) gene, located at chromosome band 18p11.32, in renal cell carcinoma (RCC). TYMS is a key target of the 5-fluorouracil (5-FU)-based class of drugs, frequently considered in combination therapies in advanced RCC. TYMS variants, such as the TYMS polymorphic 5'-untranslated region variable number tandem repeat sequence (VNTR), are under investigation to guide 5-FU treatment. Yet, no information is available with regard to changes in TYMS allele frequencies in RCC malignances. METHODS Blood and matched tumor samples were collected from 41 histological proven clear cell RCC affected patients (30 males, 11 females.). TYMS VNTR genotype was first determined in blood to identify heterozygotes employing PCR techniques. To evaluate for allelic imbalance, fragment analysis was performed both in blood and matched tumor DNA of the heterozygote patients. Microsatellite analysis, employing the markers D18S59 and D18S476 mapping, respectively, at the TYMS locus (18p11.32) and 1.5 Mb downstream of the TYMS gene sequence (18p11.31), was performed to confirm TYMS allelic imbalance in tumors. RESULTS Germ-line TYMS VNTR distribution was: 2R/2R (19.5%), TYMS 2R/3R (36.6%) and TYMS 3R/3R (43.9%). Allelic imbalance for the TYMS tandem repeat region was detected in 26.6% of the heterozygote patients. Microsatellite analysis confirmed the allelic imbalance detected by TYMS VNTR analysis and revealed that the overall frequence of allelic imbalance of chromosome band 18p11.32 was 35%, while the overall allelic imbalance of chromosome band 18p11.31 was 28%. CONCLUSIONS By focusing on the TYMS polymorphic variants in renal cancer, we here provide evidence, to our knowledge, for the first time showing loss of 18p11.32 and 18p11.31 in renal cell carcinomas. As allelic imbalances involving TYMS locus may be an important variable affecting 5-FU responsiveness, this study may contribute to explain different responses of advanced RCC in combined chemotherapeutic regimens incorporating fluoropyridines.
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Bleibel WK, Duan S, Huang RS, Kistner EO, Shukla SJ, Wu X, Badner JA, Dolan ME. Identification of genomic regions contributing to etoposide-induced cytotoxicity. Hum Genet 2008; 125:173-80. [PMID: 19089452 DOI: 10.1007/s00439-008-0607-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 12/06/2008] [Indexed: 01/25/2023]
Abstract
Etoposide is routinely used in combination-based chemotherapy for testicular cancer and small-cell lung cancer; however, myelosuppression, therapy-related leukemia and neurotoxicity limit its utility. To determine the genetic contribution to cellular sensitivity to etoposide, we evaluated cell growth inhibition in Centre d' Etude du Polymorphisme Humain lymphoblastoid cell lines from 24 multi-generational pedigrees (321 samples) following treatment with 0.02-2.5 microM etoposide for 72 h. Heritability analysis showed that genetic variation contributes significantly to the cytotoxic phenotypes (h (2) = 0.17-0.25, P = 4.9 x 10(-5)-7.3 x 10(-3)). Whole genome linkage scans uncovered 8 regions with peak LOD scores ranging from 1.57 to 2.55, with the most significant signals being found on chromosome 5 (LOD = 2.55) and chromosome 6 (LOD = 2.52). Linkage-directed association was performed on a subset of HapMap samples within the pedigrees to find 22 SNPs significantly associated with etoposide cytotoxicity at one or more treatment concentrations. UVRAG, a DNA repair gene, SEMA5A, SLC7A6 and PRMT7 are implicated from these unbiased studies. Our findings suggest that susceptibility to etoposide-induced cytotoxicity is heritable and using an integrated genomics approach we identified both genomic regions and SNPs associated with the cytotoxic phenotypes.
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Affiliation(s)
- Wasim K Bleibel
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, Box MC2115, Chicago, IL 60637, USA
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20
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Hagmann W, Jesnowski R, Faissner R, Guo C, Löhr JM. ATP-binding cassette C transporters in human pancreatic carcinoma cell lines. Upregulation in 5-fluorouracil-resistant cells. Pancreatology 2008; 9:136-44. [PMID: 19077464 DOI: 10.1159/000178884] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 07/01/2008] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pancreatic cancer is characterized by high resistance to chemotherapy. Such chemoresistance can be mediated by multidrug resistance proteins (MRPs), breast cancer resistance protein (BCRP), and MDR1 P-glycoprotein. However, the contribution of individual MRP isoforms to chemoresistance in pancreatic carcinoma is unclear. We studied ATP-binding cassette (ABC) transporter expression in human pancreatic carcinoma cell lines as compared to primary pancreatic duct cells, and analyzed the MRP expression profile in 5-fluorouracil-resistant cells. METHODS Transporter expression was analyzed by quantitative and qualitative RT-PCR, by immunoblot, and chemoresistance by cytotoxicity assay. RESULTS Primary pancreatic duct cells expressed MRP1, MRP3, MRP4, and MRP5, but not MRP2 mRNA. The established carcinoma cell lines expressed MRP1, MRP4, and MRP5, most of them also MRP2, MRP3, MRP7, and BCRP, but none contained detectable amounts of MRP6, MRP8, or MRP9 mRNA. Immunoblot analyses demonstrated presence of MRP1, MRP4, and MRP5 protein in all, but MRP3 and BCRP protein only in some of these cells. Compared to parental Capan-1 cells, Capan-1 cells with acquired chemoresistance towards 5-fluorouracil showed an upregulated mRNA and protein expression of MRP3, MRP4, and MRP5. In addition, silencing of MRP5 by RNA interference resulted in enhanced sensitivity of parental Capan-1 cells towards 5-fluorouracil cytotoxicity. CONCLUSION MRP3, MRP4, and MRP5 are upregulated in 5-fluorouracil-resistant cells, and MRP5 contributes to 5-FU resistance in pancreatic carcinoma cells.
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Affiliation(s)
- Wolfgang Hagmann
- Clinical Cooperation Unit of Molecular Gastroenterology, German Cancer Research Center, Heidelberg, Germany.
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Shirasaki T, Maruya SI, Mizukami H, Kakehata S, Kurotaki H, Yagihashi S, Shinkawa H. Effects of small interfering RNA targeting thymidylate synthase on survival of ACC3 cells from salivary adenoid cystic carcinoma. BMC Cancer 2008; 8:348. [PMID: 19036131 PMCID: PMC2628925 DOI: 10.1186/1471-2407-8-348] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 11/26/2008] [Indexed: 11/29/2022] Open
Abstract
Background Thymidylate synthase (TS) is an important target for chemotherapeutic treatment of cancer and high expression of TS has been associated with poor prognosis or refractory disease in several cancers including colorectal and head and neck cancer. Although TS is known to regulate cell cycles and transcription factors, its potency as a therapeutic target has not been fully explored in adenoid cystic carcinoma (ACC). Methods An ACC cell line (ACC3) was transfected with siRNA targeting the TS gene and inhibition of cell growth and induction of apoptosis-associated molecules were evaluated in vitro. In addition, the in vivo effect of TS siRNA on tumor progression was assessed using a xenograft model. Results Our results demonstrated that ACC3 cells showed significantly higher TS expression than non-cancer cell lines and the induction of TS siRNA led to inhibition of cell proliferation. The effect was associated with an increase in p53, p21, and active caspase-3 and S-phase accumulation. We also found up-regulation of spermidine/spermine N1-acetyltransferase (SSAT), a polyamine metabolic enzyme. Furthermore, treatment with TS siRNA delivered by atelocollagen showed a significant cytostatic effect through the induction of apoptosis in a xenograft model. Conclusion TS may be an important therapeutic target and siRNA targeting TS may be of potential therapeutic value in ACC.
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Affiliation(s)
- Takashi Shirasaki
- Department of Otolaryngology, Hirosaki University School of Medicine, Hirosaki, Japan.
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Zhang N, Yin Y, Xu SJ, Chen WS. 5-Fluorouracil: mechanisms of resistance and reversal strategies. Molecules 2008; 13:1551-69. [PMID: 18794772 PMCID: PMC6244944 DOI: 10.3390/molecules13081551] [Citation(s) in RCA: 467] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/01/2008] [Accepted: 07/15/2008] [Indexed: 11/24/2022] Open
Abstract
The purpose of this work is to review the published studies on the mechanisms of action and resistance of 5-fluorouracil. The review is divided into three main sections: mechanisms of anti-tumor action, studies of the resistance to the drug, and procedures for the identification of new genes involved in resistance with microarray techniques. The details of the induction and reversal of the drug resistance are also described.
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Affiliation(s)
- Ning Zhang
- Department of Orthopaedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, #88 Jiefang Road, Hangzhou, 310009, P.R. China; E-mail:
| | - Ying Yin
- Institute of Clinical Research, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, #3 East Qingchun Road, Hangzhou, 310016, P.R. China; E-mails: ;
| | - Sheng-Jie Xu
- Institute of Clinical Research, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, #3 East Qingchun Road, Hangzhou, 310016, P.R. China; E-mails: ;
| | - Wei-Shan Chen
- Department of Orthopaedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, #88 Jiefang Road, Hangzhou, 310009, P.R. China; E-mail:
- Author to whom correspondence should be addressed; E-Mail:
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Hamaguchi J, Nakagawa H, Takahashi M, Kudo T, Kamiyama N, Sun B, Oshima T, Sato Y, Deguchi K, Todo S, Nishimura SI. Swainsonine reduces 5-fluorouracil tolerance in the multistage resistance of colorectal cancer cell lines. Mol Cancer 2007; 6:58. [PMID: 17883871 PMCID: PMC2071919 DOI: 10.1186/1476-4598-6-58] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 09/21/2007] [Indexed: 01/11/2023] Open
Abstract
Background Drug resistance is a major problem in cancer chemotherapy. Acquisition of chemo-resistance not only reduces the effectiveness of drugs, but also promotes side effects and markedly reduces the patient's quality of life. However, a number of resistance mechanisms have been reported and are thought to be the reason for the difficulties in solving drug-resistance problems. Result To investigate the mechanisms of drug resistance, a set of cell lines with different levels of sensitivity and possessing different mechanisms of resistance to 5-fluorouracil (5-FU) was established from a colorectal cancer cell line. The expression of thymidylate synthase, orotic acid phosphoribosyltransferase and dihydropyrimidine dehydrogenase, which are well known to be related to drug resistance, differed among these cell lines, indicating that these cell lines acquired different resistance mechanisms. However, swainsonine, an inhibitor of N-glycan biosynthesis, reduced 5-FU-tolerance in all resistant cells, whereas the sensitivity of the parental cells was unchanged. Further analysis of the N-glycan profiles of all cell lines showed partial inhibition of biosynthesis and no cytotoxicity at the swainsonine dosage tested. Conclusion These observations suggest that N-linked oligosaccharides affect 5-FU resistance more widely than do drug-resistance related enzymes in colorectal cancer cells, and that the N-glycan could be a universal target for chemotherapy. Further, swainsonine may enhance the performance of chemotherapy by reducing tolerance.
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Affiliation(s)
- Jun Hamaguchi
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Hiroaki Nakagawa
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, 001-0021, Japan
| | - Masato Takahashi
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Takeaki Kudo
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Naoya Kamiyama
- Department of Sensory Physiology, Asahikawa Medical College, Asahikawa 078-8510, Japan
| | - Bailong Sun
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Takahiro Oshima
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Yuji Sato
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Kisaburo Deguchi
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, 001-0021, Japan
| | - Satoru Todo
- Department of General Surgery, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Shin-Ichiro Nishimura
- Graduate School of Advanced Life Science, Hokkaido University, Sapporo 001-0021, 001-0021, Japan
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