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Rauth S, Ganguly K, Atri P, Parte S, Nimmakayala RK, Varadharaj V, Nallasamy P, Vengoji R, Ogunleye AO, Lakshmanan I, Chirravuri R, Bessho M, Cox JL, Foster JM, Talmon GA, Bessho T, Ganti AK, Batra SK, Ponnusamy MP. Elevated PAF1-RAD52 axis confers chemoresistance to human cancers. Cell Rep 2023; 42:112043. [PMID: 36709426 PMCID: PMC10374878 DOI: 10.1016/j.celrep.2023.112043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/11/2022] [Accepted: 01/13/2023] [Indexed: 01/30/2023] Open
Abstract
Cisplatin- and gemcitabine-based chemotherapeutics represent a mainstay of cancer therapy for most solid tumors; however, resistance limits their curative potential. Here, we identify RNA polymerase II-associated factor 1 (PAF1) as a common driver of cisplatin and gemcitabine resistance in human cancers (ovarian, lung, and pancreas). Mechanistically, cisplatin- and gemcitabine-resistant cells show enhanced DNA repair, which is inhibited by PAF1 silencing. We demonstrate an increased interaction of PAF1 with RAD52 in resistant cells. Targeting the PAF1 and RAD52 axis combined with cisplatin or gemcitabine strongly diminishes the survival potential of resistant cells. Overall, this study shows clinical evidence that the expression of PAF1 contributes to chemotherapy resistance and worse clinical outcome for lethal cancers.
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Affiliation(s)
- Sanchita Rauth
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Seema Parte
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Venkatesh Varadharaj
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Palanisamy Nallasamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Ayoola O Ogunleye
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Ramakanth Chirravuri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Mika Bessho
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Jesse L Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Jason M Foster
- Department of Surgery, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Tadayoshi Bessho
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Apar Kishor Ganti
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA Nebraska Western Iowa Health Care System, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA.
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center at Omaha, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center at Omaha, Omaha, NE, USA.
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2
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Avsar O. Analysis of missense SNPs in the SLC47A1 and SLC47A2 genes affecting the pharmacokinetics of metformin: Computational approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Metformin as an anti-hyperglycaemic drug is commonly used for the treatment of type 2 diabetes mellitus (T2DM). The metformin response is variable due to the interindividual variation of pharmacokinetics which is based on strong genetic background. MATE1 and MATE2 proteins are significantly implicated in the pharmacokinetics of metformin. Missense SNPs with high risk of pathogenicity are expected to affect response to metformin via pharmacokinetics. Therefore, the aim of the current study is to determine the effects of missense SNPs in the SLC47A1 and SLC47A2 genes. The structural and functional consequences of all known SLC47A1 and SLC47A2 missense SNPs of the human MATE1 and MATE2 proteins were identified by various bioinformatics methods (SIFT, PhD-SNP, PolyPhen-2, PROVEAN, PMut, MUpro, I-Mutant 3.0, COACH, RaptorX Binding, ConSurf, STRING).
Results
The SLC47A1 variants P186T, L116P and the SLC47A2 variants I158N, L112P, V118G exhibited ΔΔG values less than − 1 kcal/mol, and these variants are considered to disrupt the structure and function of MATE1 and MATE2 proteins. SLC47A1 R118Q and SLC47A2 Y273C, V118G may significantly disturb protein function and transporting activities according to the analysis of ligand-binding regions.
Conclusion
It is suggested that high-risk deleterious missense SNPs may mediate the pharmacokinetics of metformin and may be associated with altered tissue distribution, renal clearance and metformin toxicity. We suppose that our results might serve as potential targets for the studies composed of the development of potential diagnostic and therapeutic strategies based on the relationship between mutations and metformin response.
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3
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MALAT1 enhances gemcitabine resistance in non-small cell lung cancer cells by directly affecting miR-27a-5p/PBOV1 axis. Cell Signal 2022; 94:110326. [DOI: 10.1016/j.cellsig.2022.110326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
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4
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Lee H, Kwon Y, Jin H, Liu H, Kang W, Chun Y, Bae J, Choi H. Anticancer activity and metabolic profile alterations by ortho‐topolin riboside in in vitro and in vivo models of non‐small cell lung cancer. FASEB J 2022; 36:e22127. [DOI: 10.1096/fj.202101333r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Hwanhui Lee
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Yeo‐Jung Kwon
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Hanyong Jin
- Key Laboratory of Natural Medicines of the Changbai Mountain Ministry of Education College of Pharmacy Yanbian University Yanji China
| | - Heifeng Liu
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Wonku Kang
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Young‐Jin Chun
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Jeehyeon Bae
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
| | - Hyung‐Kyoon Choi
- College of Pharmacy Chung‐Ang University Seoul Republic of Korea
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5
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Potential role of CMPK1, SLC29A1, and TLE4 polymorphisms in gemcitabine-based chemotherapy in HER2-negative metastatic breast cancer patients: pharmacogenetic study results from the prospective randomized phase II study of eribulin plus gemcitabine versus paclitaxel plus gemcitabine (KCSG-BR-13-11). ESMO Open 2021; 6:100236. [PMID: 34438242 PMCID: PMC8390551 DOI: 10.1016/j.esmoop.2021.100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/06/2021] [Accepted: 07/19/2021] [Indexed: 11/25/2022] Open
Abstract
Background In this study, we evaluated the association between genetic polymorphisms of 23 genes associated with gemcitabine metabolism and the clinical efficacy of gemcitabine in breast cancer patients. Patients and methods This prospective, pharmacogenetic study was conducted in cooperation with a phase II clinical trial. A total of 103 genetic polymorphisms of the 23 genes involved in gemcitabine transport and metabolism were selected for genotyping. The associations of genetic polymorphisms with overall survival, progression-free survival (PFS), and 6-month PFS were analyzed. Results A total of 91 breast cancer patients were enrolled in this study. In terms of 6-month PFS, rs1044457 in CMPK1 was the most significant genetic polymorphism [55.9% for CT and TT and 78.9% for CC, P < 0.001, hazard ratio (HR): 4.444, 95% confidence interval (CI): 1.905-10.363]. For the rs693955 in SLC29A1, the median duration of PFS was 5.4 months for AA and 10.5 months for CA and CC (P = 0.002, HR: 3.704, 95% CI: 1.615-8.497). For the rs2807312 in TLE4, the median duration of PFS was 5.7 months for TT and 10.4 months for CT and CC (P = 0.005, HR: 4.948, 95% CI: 1.612-15.190). In survival analysis with a multi-gene model, the TT genotype of rs2807312 had the worst PFS regardless of other genetic polymorphisms, whereas the CA genotype of rs693955 or the CT genotype of rs2807312 without the AA genotype of rs693955 had the best PFS compared with those of other genetic groups (P < 0.001). Conclusions Genetic polymorphisms of rs1044457 in CMPK1, rs693955 in SLC29A1, and rs2807312 in TLE4 were significantly associated with the 6-month PFS rate and/or the duration of PFS. Further studies with a larger sample size and expression study would be helpful to validate the association of genetic polymorphisms and clinical efficacy of gemcitabine. This is the largest pharmacogenetic study of gemcitabine-based breast cancer treatment in a prospective clinical trial. Several genetic polymorphisms in CMPK1, SLC29A1, and TLE4 were associated with 6-month PFS rate and the duration of PFS. The result of this study may contribute to the personalized treatment of breast cancer.
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Kim JE, Choi J, Park J, Park C, Lee SM, Park SE, Song N, Chung S, Sung H, Han W, Lee JW, Park SK, Kim MK, Noh DY, Yoo KY, Kang D, Choi JY. Associations between genetic polymorphisms of membrane transporter genes and prognosis after chemotherapy: meta-analysis and finding from Seoul Breast Cancer Study (SEBCS). THE PHARMACOGENOMICS JOURNAL 2018; 18:633-645. [PMID: 29618765 DOI: 10.1038/s41397-018-0016-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/13/2017] [Accepted: 12/04/2017] [Indexed: 12/30/2022]
Abstract
Membrane transporters can be major determinants of the pharmacokinetic profiles of anticancer drugs. The associations between genetic variations of ATP-binding cassette (ABC) and solute carrier (SLC) genes and cancer survival were investigated through a meta-analysis and an association study in the Seoul Breast Cancer Study (SEBCS). Including the SEBCS, the meta-analysis was conducted among 38 studies of genetic variations of transporters on various cancer survivors. The population of SEBCS consisted of 1338 breast cancer patients who had been treated with adjuvant chemotherapy. A total of 7750 SNPs were selected from 453 ABC and/or SLC genes typed by an Affymetrix 6.0 chip. ABCB1 rs1045642 was associated with poor progression-free survival in a meta-analysis (HR = 1.33, 95% CI: 1.07-1.64). ABCB1, SLC8A1, and SLC12A8 were associated with breast cancer survival in SEBCS (Pgene < 0.05). ABCB1 rs1202172 was differentially associated with survival depending on the chemotherapy (Pinteraction = 0.035). Our finding provides suggestive associations of membrane transporters on cancer survival.
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Affiliation(s)
- Ji-Eun Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Jaesung Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - JooYong Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Chulbum Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Se Mi Lee
- College of Pharmacy Chonnam National University, Gwangju, Korea
| | - Seong Eun Park
- College of Pharmacy, Duksung Women's university, Seoul, Korea
| | - Nan Song
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Seokang Chung
- Division for New Health Technology Assessment, National Evidence-based Healthcare Collaborating Agency, Seoul, Korea
| | - Hyuna Sung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Keun-Young Yoo
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.,The Armed Forces Capital Hospital, Seongnam, Korea
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.,Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea. .,Cancer Research Institute, Seoul National University, Seoul, Korea. .,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.
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7
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Toffalorio F, Santarpia M, Radice D, Jaramillo CA, Spitaleri G, Manzotti M, Catania C, Jordheim LP, Pelosi G, Peters GJ, Tibaldi C, Funel N, Spaggiari L, de Braud F, De Pas T, Giovannetti E. 5'-nucleotidase cN-II emerges as a new predictive biomarker of response to gemcitabine/platinum combination chemotherapy in non-small cell lung cancer. Oncotarget 2018; 9:16437-16450. [PMID: 29662657 PMCID: PMC5893252 DOI: 10.18632/oncotarget.24505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/02/2018] [Indexed: 02/04/2023] Open
Abstract
A number of pharmacogenetic studies have been carried out in non-small-cell lung cancer (NSCLC) to identify and characterize genes involved in chemotherapy activity. However, the results obtained so far are controversial and no reliable biomarker is currently used to predict clinical benefit from platinum-based chemotherapy, which represents the cornerstone of treatment of advanced NSCLC. This study investigated the expression levels of ERCC1 and of six genes (RRM1, RRM2, hENT1, dCK, cN-II and CDA) involved in gemcitabine metabolism in locally/advanced NSCLC patients treated with gemcitabine/platinum combination. Gene expression was assessed by quantitative-PCR in laser-microdissected specimens and correlated with tumor response. Frequency distribution of responses above and below the median expression level of biomarkers was compared using a two-sided Fisher’s test. 5′-nucleotidase (cN-II) was the only gene differently expressed (p = 0.016) in the responders (complete/partial-response) compared to non-responders (stable/progressive disease). In the multivariate analysis, overexpression of this catabolic enzyme of gemcitabine remained a significant negative predictive factor. Patients with low cN-II had a modest trend toward increased survival, while both survival and progression-free survival were significantly longer in a more homogenous validation cohort of 40 advanced NSCLC (8.0 vs. 5.1 months, p = 0.026). Moreover, in vitro studies showed that silencing or pharmacological inhibition of cN-II increased the cytotoxicity of gemcitabine. This is the first study demonstrating the role of cN-II as a predictor of response to gemcitabine/platinum combinations in NSCLC. Its validation in prospective studies may improve clinical outcome of selected patients.
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Affiliation(s)
- Francesca Toffalorio
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Affairs, Roche Spa, Monza, Italy
| | - Mariacarmela Santarpia
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Oncology Unit, Department of Human Pathology, University of Messina, Messina, Italy
| | - Davide Radice
- Epidemiology and Biostatistics Division, European Institute of Oncology, Milan, Italy
| | | | - Gianluca Spitaleri
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Michela Manzotti
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Chiara Catania
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Lars Petter Jordheim
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052/CNRS UMR 5286, Lyon, France
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Carmelo Tibaldi
- Division of Oncology, Department of Oncology, S. Luca Hospital, Lucca, Italy
| | - Niccola Funel
- CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Lorenzo Spaggiari
- Thoracic Surgery Division, European Institute of Oncology, Milan, Italy
| | - Filippo de Braud
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Tommaso De Pas
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
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8
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Snezhkina AV, Krasnov GS, Zaretsky AR, Zhavoronkov A, Nyushko KM, Moskalev AA, Karpova IY, Afremova AI, Lipatova AV, Kochetkov DV, Fedorova MS, Volchenko NN, Sadritdinova AF, Melnikova NV, Sidorov DV, Popov AY, Kalinin DV, Kaprin AD, Alekseev BY, Dmitriev AA, Kudryavtseva AV. Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer. BMC Genomics 2016; 17:1011. [PMID: 28105922 PMCID: PMC5249009 DOI: 10.1186/s12864-016-3351-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. CRC molecular pathogenesis is heterogeneous and may be followed by mutations in oncogenes and tumor suppressor genes, chromosomal and microsatellite instability, alternative splicing alterations, hypermethylation of CpG islands, oxidative stress, impairment of different signaling pathways and energy metabolism. In the present work, we have studied the alterations of alternative splicing patterns of genes related to energy metabolism in CRC. RESULTS Using CrossHub software, we analyzed The Cancer Genome Atlas (TCGA) RNA-Seq datasets derived from colon tumor and matched normal tissues. The expression of 1014 alternative mRNA isoforms involved in cell energy metabolism was examined. We found 7 genes with differentially expressed alternative transcripts whereas overall expression of these genes was not significantly altered in CRC. A set of 8 differentially expressed transcripts of interest has been validated by qPCR. These eight isoforms encoded by OGDH, COL6A3, ICAM1, PHPT1, PPP2R5D, SLC29A1, and TRIB3 genes were up-regulated in colorectal tumors, and this is in concordance with the bioinformatics data. The alternative transcript NM_057167 of COL6A3 was also strongly up-regulated in breast, lung, prostate, and kidney tumors. Alternative transcript of SLC29A1 (NM_001078177) was up-regulated only in CRC samples, but not in the other tested tumor types. CONCLUSIONS We identified tumor-specific expression of alternative spliced transcripts of seven genes involved in energy metabolism in CRC. Our results bring new knowledge on alternative splicing in colorectal cancer and suggest a set of mRNA isoforms that could be used for cancer diagnosis and development of treatment methods.
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Affiliation(s)
| | - George Sergeevich Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University Eastern Campus, Baltimore, Maryland, USA
| | | | - Alexey Alexandrovich Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | | | | | | | | | | | - Asiya Fayazovna Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | | | | | | | - Andrey Dmitrievich Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris Yakovlevich Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Anna Viktorovna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia.
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9
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Koh V, Kwan HY, Tan WL, Mah TL, Yong WP. Knockdown of POLA2 increases gemcitabine resistance in lung cancer cells. BMC Genomics 2016; 17:1029. [PMID: 28155658 PMCID: PMC5260101 DOI: 10.1186/s12864-016-3322-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Gemcitabine is used as a standard drug treatment for non-small cell lung cancer (NSCLC), but treatment responses vary among patients. Our previous studies demonstrated that POLA2 + 1747 GG/GA single nucleotide polymorphism (SNP) improves differential survivability and mortality in NSCLC patients. Here, we determined the association between POLA2 and gemcitabine treatment in human lung cancer cells. RESULTS Human PC9, H1299 and H1650 lung cancer cell lines were treated with 0.01-100 μM gemcitabine for 72 h. Although all 3 cell lines showed decreased cell viability upon gemcitabine treatment, H1299 was found to be the most sensitive to gemcitabine treatment. Next, sequencing was performed to determine if POLA2 + 1747 SNP might be involved in gemcitabine sensitivity. Data revealed that all 3 cell lines harbored the wild-type POLA2 + 1747 GG SNP, indicating that the POLA2 + 1747 SNP might not be responsible for gemcitabine sensitivity in the cell lines studied. Silencing of POLA2 gene in H1299 was then carried out by siRNA transfection, followed by gemcitabine treatment to determine the effect of POLA2 knockdown on chemosensitivity to gemcitabine. Results showed that H1299 exhibited increased resistance to gemcitabine after POLA2 knockdown, suggesting that POLA2 does not act alone and may cooperate with other interacting partners to cause gemcitabine resistance. CONCLUSIONS Collectively, our findings showed that knockdown of POLA2 increases gemcitabine resistance in human lung cancer cells. We propose that POLA2 may play a role in gemcitabine sensitivity and can be used as a prognostic biomarker of patient outcome in NSCLC pathogenesis.
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Affiliation(s)
- Vivien Koh
- National University Cancer Institute Singapore, National University Health System, Singapore, Singapore
| | - Hsueh Yin Kwan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Woei Loon Tan
- National University Cancer Institute Singapore, National University Health System, Singapore, Singapore
| | - Tzia Liang Mah
- Institute for Infocomm Research, Agency for Science, Technology and Research, Singapore, Singapore.
| | - Wei Peng Yong
- National University Cancer Institute Singapore, National University Health System, Singapore, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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10
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Shinozuka K, Tang H, Jones RB, Li D, Nieto Y. Impact of Polymorphic Variations of Gemcitabine Metabolism, DNA Damage Repair, and Drug-Resistance Genes on the Effect of High-Dose Chemotherapy for Relapsed or Refractory Lymphoid Malignancies. Biol Blood Marrow Transplant 2015; 22:843-9. [PMID: 26743341 DOI: 10.1016/j.bbmt.2015.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
Abstract
The goal of this study was to determine whether single nucleotide polymorphisms (SNPs) in genes involved in gemcitabine metabolism, DNA damage repair, multidrug resistance, and alkylator detoxification influence the clinical outcome of patients with refractory/relapsed lymphoid malignancies receiving high-dose gemcitabine/busulfan/melphalan (Gem/Bu/Mel) with autologous stem cell support. We evaluated 21 germline SNPs of the gemcitabine metabolism genes CDA, deoxycytidine kinase, and hCNT3; DNA damage repair genes RECQL, X-ray repair complementing 1, RAD54L, ATM, ATR, MLH1, MSH2, MSH3, TREX1, EXO1, and TP73; and multidrug-resistance genes MRP2 and MRP5; as well as glutathione-S-transferase GSTP1 in 153 patients with relapsed or refractory lymphoma or myeloma receiving Gem/Bu/Mel. We studied the association of genotypes with overall survival (OS), progression-free survival (PFS), and nonhematological grade 3 or 4 toxicity. CDA C111T and TREX1 Ex14-460C>T genotypes had a significant effect on OS (P = .007 and P = .005, respectively), and CDA C111T, ATR C340T, and EXO1 P757L genotypes were significant predictors for severe toxicity (P = .037, P = .024, and P = .025, respectively) in multivariable models that adjusted for clinical variables. The multi-SNP risk score analysis identified the combined genotypes of TREX1 Ex14-460 TT and hCNT3 Ex5 +25A>G AA as significant predictors for OS and the combination of MRP2 Ex10 + 40GG/GA and MLH1 IVS12-169 TT as significant predictor for PFS. Polymorphic variants of certain genes involved in gemcitabine metabolism and DNA damage repair pathways may be potential biomarkers for clinical outcome in patients with refractory/relapsed lymphoid tumors receiving Gem/Bu/Mel.
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Affiliation(s)
- Keiji Shinozuka
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hongwei Tang
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roy B Jones
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yago Nieto
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas.
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Niu N, Wang L. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics 2015; 16:273-85. [PMID: 25712190 DOI: 10.2217/pgs.14.170] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In vitro human cell line models have been widely used for cancer pharmacogenomic studies to predict clinical response, to help generate pharmacogenomic hypothesis for further testing, and to help identify novel mechanisms associated with variation in drug response. Among cell line model systems, immortalized cell lines such as Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) have been used most often to test the effect of germline genetic variation on drug efficacy and toxicity. Another model, especially in cancer research, uses cancer cell lines such as the NCI-60 panel. These models have been used mainly to determine the effect of somatic alterations on response to anticancer therapy. Even though these cell line model systems are very useful for initial screening, results from integrated analyses of multiple omics data and drug response phenotypes using cell line model systems still need to be confirmed by functional validation and mechanistic studies, as well as validation studies using clinical samples. Future models might include the use of patient-specific inducible pluripotent stem cells and the incorporation of 3D culture which could further optimize in vitro cell line models to improve their predictive validity.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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12
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Wang Y, An X, Liu J, Zhang N, Liu Z, Liang S, Yu J. [NT5C2 expression in children with acute leukemia and its clinical significance]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2015; 36:748-53. [PMID: 26462774 PMCID: PMC7342695 DOI: 10.3760/cma.j.issn.0253-2727.2015.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To investigate the expression level and analyze the clinical significance of NT5C2, which is an nucleoside analogues metabolism related gene, in children with acute leukemia (AL). METHODS Real-time PCR and immunohistochemistry were presented to detect the level of NT5C2 mRNA and its protein product cN- Ⅱ in bone marrow samples of 63 patients initially diagnosed with AL, 15 patients who achieved complete remission, 7 patients who relapsed and 16 non- hematologic malignancie controls. The expression of NT5C2 mRNA in different groups of AL and its relevance with clinical indicators were analyzed. RESULTS ①The expression of NT5C2 mRNA in newly diagnosed B-ALL, TALL, AML and controls were 1.16 (0.89-2.25, 0.96 (0.74-1.25, 1.66 (0.84-3.15) and 0.88 (0.61-1.21), respectively. NT5C2 mRNA expression in AML (P<0.01) and B-ALL (P<0.05) cases were higher than that in controls; NT5C2 mRNA expression in T- ALL and in controls showed no significant difference (P>0.05). Changes of NT5C2 mRNA level were observed between preliminary diagnosis and complete remission in 15 patients. NT5C2 mRNA levels were significantly decreased in complete remission stage than that in newly diagnosis AL (P<0.01). NT5C2 mRNA levels of relapsed-refractory group were higher than that of complete remission group and controls (P<0.01). ② Immunohistochemical staining results revealed that NT5C2 protein levels were consistent with the trend of mRNA levels. ③NT5C2 mRNA levels in AML (r=0.434) and T-ALL (r=0.389) were positively correlated with risk classification (P<0.05). ④ During chemotherapy of patients with AML, the NR rate of bone marrow in NT5C2 high expression group was higher than that of low expression group after 9 days induction chemotherapy (35.2% vs 0) and before consolidation therapy (25.0% vs 0); The positive rate of minimal-residual disease (36.4% vs 14.3%) and relapse rate of AL (38.5% vs 28.6%) were increased in NT5C2 high expressed patients than that in low expressed patients, but all the differences were insignificant (P>0.05). CONCLUSION High expression of NT5C2 was found to be a related risk factor of AL children with unfavourable prognosis. NT5C2 promises a new target for guiding individualized chemotherapy and evaluating the prognosis of childhood acute leukemia and monitoring recurrence.
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Affiliation(s)
- Yanzhen Wang
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Xizhou An
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Jianghua Liu
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Ni Zhang
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Zhijuan Liu
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Shaoyan Liang
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Jie Yu
- Department of Hematologic Neoplasm, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
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Abstract
The severity of the toxic side effects of chemotherapy shows a great deal of interindividual variability, and much of this variation is likely genetically based. Simple DNA tests predictive of toxic side effects could revolutionize the way chemotherapy is carried out. Due to the challenges in identifying polymorphisms that affect toxicity in humans, we use Drosophila fecundity following oral exposure to carboplatin, gemcitabine and mitomycin C as a model system to identify naturally occurring DNA variants predictive of toxicity. We use the Drosophila Synthetic Population Resource (DSPR), a panel of recombinant inbred lines derived from a multiparent advanced intercross, to map quantitative trait loci affecting chemotoxicity. We identify two QTL each for carboplatin and gemcitabine toxicity and none for mitomycin. One QTL is associated with fly orthologs of a priori human carboplatin candidate genes ABCC2 and MSH2, and a second QTL is associated with fly orthologs of human gemcitabine candidate genes RRM2 and RRM2B. The third, a carboplatin QTL, is associated with a posteriori human orthologs from solute carrier family 7A, INPP4A&B, and NALCN. The fourth, a gemcitabine QTL that also affects methotrexate toxicity, is associated with human ortholog GPx4. Mapped QTL each explain a significant fraction of variation in toxicity, yet individual SNPs and transposable elements in the candidate gene regions fail to singly explain QTL peaks. Furthermore, estimates of founder haplotype effects are consistent with genes harboring several segregating functional alleles. We find little evidence for nonsynonymous SNPs explaining mapped QTL; thus it seems likely that standing variation in toxicity is due to regulatory alleles.
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Abraham A, Varatharajan S, Karathedath S, Philip C, Lakshmi KM, Jayavelu AK, Mohanan E, Janet NB, Srivastava VM, Shaji RV, Zhang W, Abraham A, Viswabandya A, George B, Chandy M, Srivastava A, Mathews V, Balasubramanian P. RNA expression of genes involved in cytarabine metabolism and transport predicts cytarabine response in acute myeloid leukemia. Pharmacogenomics 2015; 16:877-90. [PMID: 26083014 DOI: 10.2217/pgs.15.44] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Variation in terms of outcome and toxic side effects of treatment exists among acute myeloid leukemia (AML) patients on chemotherapy with cytarabine (Ara-C) and daunorubicin (Dnr). Candidate Ara-C metabolizing gene expression in primary AML cells is proposed to account for this variation. METHODS Ex vivo Ara-C sensitivity was determined in primary AML samples using MTT assay. mRNA expression of candidate Ara-C metabolizing genes were evaluated by RQPCR analysis. Global gene expression profiling was carried out for identifying differentially expressed genes between exvivo Ara-C sensitive and resistant samples. RESULTS Wide interindividual variations in ex vivo Ara-C cytotoxicity were observed among samples from patients with AML and were stratified into sensitive, intermediately sensitive and resistant, based on IC50 values obtained by MTT assay. RNA expression of deoxycytidine kinase (DCK), human equilibrative nucleoside transporter-1 (ENT1) and ribonucleotide reductase M1 (RRM1) were significantly higher and cytidine deaminase (CDA) was significantly lower in ex vivo Ara-C sensitive samples. Higher DCK and RRM1 expression in AML patient's blast correlated with better DFS. Ara-C resistance index (RI), a mathematically derived quotient was proposed based on candidate gene expression pattern. Ara-C ex vivo sensitive samples were found to have significantly lower RI compared with resistant as well as samples from patients presenting with relapse. Patients with low RI supposedly highly sensitive to Ara-C were found to have higher incidence of induction death (p = 0.002; RR: 4.35 [95% CI: 1.69-11.22]). Global gene expression profiling undertaken to find out additional contributors of Ara-C resistance identified many apoptosis as well as metabolic pathway genes to be differentially expressed between Ara-C resistant and sensitive samples. CONCLUSION This study highlights the importance of evaluating expression of candidate Ara-C metabolizing genes in predicting ex vivo drug response as well as treatment outcome. RI could be a predictor of ex vivo Ara-C response irrespective of cytogenetic and molecular risk groups and a potential biomarker for AML treatment outcome and toxicity. Original submitted 22 December 2014; Revision submitted 9 April 2015.
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Affiliation(s)
- Ajay Abraham
- Department of Haematology, Christian Medical College, Vellore, India
| | | | | | - Chepsy Philip
- Department of Haematology, Christian Medical College, Vellore, India
| | - Kavitha M Lakshmi
- Department of Haematology, Christian Medical College, Vellore, India
| | | | | | - Nancy Beryl Janet
- Department of Haematology, Christian Medical College, Vellore, India
| | | | | | - Wei Zhang
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, India
| | - Auro Viswabandya
- Department of Haematology, Christian Medical College, Vellore, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, India
| | - Mammen Chandy
- Department of Haematology, Christian Medical College, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College, Vellore, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
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Determination of the enzymatic activity of cytosolic 5'-nucleotidase cN-II in cancer cells: development of a simple analytical method and related cell line models. Anal Bioanal Chem 2015; 407:5747-58. [PMID: 25998135 DOI: 10.1007/s00216-015-8757-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/04/2015] [Indexed: 01/03/2023]
Abstract
The cytosolic 5'-nucleotidase (cN-II) has been shown to be involved in the response of cancer cells to cytotoxic agents, and the quantification of its activity in biological samples is of great interest. In this context, we developed and validated an analytical method for determination of cN-II activity in cultured cancer cells. This non-radioactive method, using a Hypercarb column as stationary phase, was validated with a lower limit of quantification of 0.1 μM inosine. We used it to characterize cell line models with modified cN-II expression obtained with stable transfections. We show that the short hairpin RNA (shRNA)-mediated inhibition of cN-II expression in various malignant blood cells is associated with decreased protein expression and enzymatic activity (1.7-6.2-fold) as well as an increased sensitivity to cytotoxic agents (up to 14-fold). On the other hand, expression of green fluorescent protein (GFP)-fused wild type or hyperactive mutant (R367Q) cN-II increased the activity and also decreased the sensitivity to nucleoside analogues. Our results confirm the biological relevance of modulating cN-II in cancer cells, and we present a straightforward validated method for the determination of cN-II activity in cellular samples.
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Ding X, Chen W, Fan H, Zhu B. Cytidine deaminase polymorphism predicts toxicity of gemcitabine-based chemotherapy. Gene 2015; 559:31-7. [PMID: 25582275 DOI: 10.1016/j.gene.2015.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
BACKGROUND The aim of this study was to ascertain whether single nucleotide polymorphisms of cytidine deaminase (CDA), a key enzyme in the metabolism pathway of gemcitabine, could predict clinical outcomes of cancer patients with gemcitabine-based chemotherapy. METHODS We searched MEDLINE and EMBASE up to January 2013 to identify eligible studies. A rigorous quality assessment of eligible studies was conducted according to the Newcastle-Ottawa Quality Assessment Scale. For each included study, the overall survival (OS), overall response rate (ORR) and toxicities were extracted and pooled using random-effects model. RESULTS In total, data from 13 studies were included. CDA 208A>G and CDA 435C>T were not included in quantified synthesis due to limited data. CDA 79A>C polymorphism was not significantly associated with OS; however, patients carrying the variant CDA 79C allele were likely to have a poor survival, hazard ratio (HR)=1.03, 95% CI 0.957-1.27 (AC+CC vs. AA). CDA 79A>C polymorphism did not correlated with ORR, odds ratio (OR)=0.719, 95% CI 0.363-1.425 (AC+CC vs. AA). However, patients with the variant CDA 79C allele would experience more grade ≥ 3 leucopenia (OR=2.933, 95% CI 1.357-6.605) and tended to have more severe neutropenia (OR=1.313, 95% CI 0.157-10.981). CONCLUSIONS These results suggest that CDA 79A>C polymorphisms is a potential biomarker for toxicity of gemcitabine-based chemotherapy and a CDA testing before gemcitabine administration is preferred.
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Affiliation(s)
- Xiangxiang Ding
- First Clinical College, Nanjing Medical University, Nanjing 210029, China; Department of Radiology, Nanjing Drum Tower Hospital, Nanjing 210008, China
| | - Wenwei Chen
- First Clinical College, Nanjing Medical University, Nanjing 210029, China; Department of Oncology, Nanjing Drum Tower Hospital, Nanjing 210008, China
| | - Haijian Fan
- Department of Radiology, Nanjing Drum Tower Hospital, Nanjing 210008, China
| | - Bin Zhu
- Department of Radiology, Nanjing Drum Tower Hospital, Nanjing 210008, China.
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Meng X, Wang G, Guan R, Jia X, Gao W, Wu J, Yu J, Liu P, Yu Y, Sun W, Dong H, Fu S. Predicting chemosensitivity to gemcitabine and cisplatin based on gene polymorphisms and mRNA expression in non-small-cell lung cancer cells. Pharmacogenomics 2015; 16:23-34. [DOI: 10.2217/pgs.14.159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: We used a panel of 17 non-small-cell lung cancer cell lines to investigate whether the presence of polymorphisms in the RRM1, ERCC1, ABCB1 and MTHFR genes and alterations in their mRNA expression can affect the in vitro chemosensitivity to cisplatin and gemcitabine. Materials & methods: Polymorphisms in these genes were evaluated by direct sequencing. mRNA expression levels were assessed by realtime PCR. In vitro chemosensitivity to cisplatin and gemcitabine was expressed as IC50 values, using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay. Results: There was a significant, positive correlation between RRM1 mRNA expression and IC50 values for gemcitabine (r = 0.6533, p = 0.0045), and there was a significant, negative correlation between ABCB1 mRNA expression and IC50 values for cisplatin (r = -0.5459, p = 0.0287). When examining the association between the polymorphisms and IC50, we found that only the MTHFR 1298A>C polymorphism showed a tendency to be more chemosensitive to gemcitabine (p = 0.0440). Conclusion: These in vitro results suggest that mRNA expression levels of the RRM1 and ABCB1 genes may be useful indicators of chemosensitivity to gemcitabine and cisplatin, respectively. The MTHFR 1298A>C polymorphism was associated with gemcitabine chemosensitivity, which require further functional analysis with co-expressed genes and should be explored in prospective clinical studies to determine its potential clinical application as a predictive biomarker. Original submitted 11 February 2014; Revision submitted 3 November 2014
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Affiliation(s)
- Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Geng Wang
- Department of Anatomy, Harbin Medical University, Harbin 150081, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Wei Gao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jingcui Yu
- The Second Affiliated Hospital, Harbin Medical University, Harbin 150081, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Haiying Dong
- Department of Internal Medicine-Oncology, Zhejiang Province People's Hospital, Hangzhou 310014, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
- Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin 150081, China
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Wan H, Zhu J, Chen F, Xiao F, Huang H, Han X, Zhong L, Zhong H, Xu L, Ni B, Zhong J. SLC29A1 single nucleotide polymorphisms as independent prognostic predictors for survival of patients with acute myeloid leukemia: an in vitro study. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:90. [PMID: 25398670 PMCID: PMC4234887 DOI: 10.1186/s13046-014-0090-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/20/2014] [Indexed: 12/12/2022]
Abstract
Background The mechanism behind poor survival of acute myeloid leukemia (AML) patients with 1-barabinofuranosylcytosine (Ara-C) based treatment remains unclear. This study aimed to assess the pharmacogenomic effects of Ara-C metabolic pathway in patients with AML. Methods The genotypes of 19 single nucleotide polymorphisms (SNPs) of DCK, CDA and SLC29A1from 100 AML patients treated with Ara-C were examined. All the SNPs were screened with ligase detection reaction assay. The transcription analysis of genes was examined by quantitative real time polymerase chain reaction. The association between clinical outcome and gene variants was evaluated by Kaplan-Meier method. Results Genotypes of rs9394992 and rs324148 for SLC29A1 in remission patients were significantly different from those in relapsed ones. Post-induction overall survival (OS) significantly decreased in patients with the CC genotype of rs324148 compared with CT and TT genotypes (hazard ratio [HR] = 2.997 [95% confidence interval (CI): 1.71-5.27]). As compared with CT and TT genotype, patients with the CC genotype of rs9394992 had longer survival time (HR = 0.25 [95% CI: 0.075-0.81]; HR = 0.43 [95% CI: 0.24-0.78]) and longer disease-free survival (DFS) (HR = 0.52 [95% CI: 0.29-0.93]; HR = 0.15 [95% CI: 0.05-0.47]) as well As compared with CT and TT genotype, patients with the CC genotype of rs324148 had shorter DFS (HR = 3.18 [95% CI: 1.76-5.76]). Additionally, patients with adverse karyotypes had shorter DFS (HR = 0.17 [95% CI: 0.05-0.54]) and OS (HR = 0.18 [95% CI: 0.05-0.68]). Conclusions AML patients with low activity of SLC29A1 genotype have shorter DFS and OS in Ara-C based therapy. Genotypes of rs9394992 and rs324148 may be independent prognostic predictors for the survival of AML patients. Electronic supplementary material The online version of this article (doi:10.1186/s13046-014-0090-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haixia Wan
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Jianyi Zhu
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Fangyuan Chen
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Fei Xiao
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Honghui Huang
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Xiaofeng Han
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Lu Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Hua Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Lan Xu
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Beiwen Ni
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Jihua Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
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Effect of hENT1 polymorphism G-706C on clinical outcomes of gemcitabine-containing chemotherapy for Chinese non-small-cell lung cancer patients. Cancer Epidemiol 2014; 38:728-32. [PMID: 25246379 DOI: 10.1016/j.canep.2014.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 11/21/2022]
Abstract
AIM To identify the single-nucleotide polymorphism (SNP) of hENT1 G-706C that is associated with response to gemcitabine-containing chemotherapy, and to determine the prognosis in patients with non-small-cell lung cancer (NSCLC). METHODS Patients with stage III (A+B) or IV NSCLC were recruited for this study (n=225). Each subject received gemcitabine-containing chemotherapy. The association between human equilibrative nucleoside transporter 1 (hENT1) polymorphism G-706C (rs61758845) and therapeutic effect was evaluated. The SNP hENT1 G-706C was genotyped by polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) assays. RESULTS The polymorphic genotype and the allele frequency of hENT1 G-706C was significantly different between chemotherapy responders and non-responders; to be specific, the response rate of patients carrying an hENT1-706 GG allele was higher than that of patients with a GC or CC genotype. Logistic regression analysis showed that having the GC or CC genotypes was associated with a higher risk of being a non-responder compared with having the GG genotype (OR=2.34, 95% CI: 1.14-4.80; P=0.02). The overall survival in patients with the GG genotype was significantly longer than in those with GC or CC genotype (19.0 versus 15.1 months, P<0.001). The hazard ratio for the (GC+CC) genotype was 1.89 (95% CI: 1.23-2.90) compared with GG carriers (P=0.004). CONCLUSIONS The hENT1 genetic polymorphism of hENT1 G-706C was associated with response to the gemcitabine-containing chemotherapy and prognosis of NSCLC. Moreover, assaying this SNP in blood cells may represent a valuable biomarker for individualized treatment for NSCLC patients.
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Zhao H, Zhang H, Du Y, Gu X. Prognostic significance of BRCA1, ERCC1, RRM1, and RRM2 in patients with advanced non-small cell lung cancer receiving chemotherapy. Tumour Biol 2014; 35:12679-88. [PMID: 25227663 DOI: 10.1007/s13277-014-2592-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/03/2014] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to examine the prognostic value of breast cancer susceptibility gene 1 (BRCA1), excision repair cross-complementation 1 (ERCC1), ribonucleotide reductase subunit M1 (RRM1), and ribonucleotide reductase subunit M2 (RRM2) in patients with advanced non-small cell lung cancer (NSCLC) who received platinum-based chemotherapy. A total of 214 patients with histologically or cytologically confirmed advanced NSCLC were enrolled in this study. The relative complementary DNA (cDNA) quantification for BRCA1, ERCC1, RRM1, and RRM2 was conducted using a fluorescence-based, real-time detection method, and β-actin was used as a reference gene. A strong correlation was observed between ERCC1 and RRM1 messenger RNA (mRNA) levels (P = 0.0385). There were inverse significant correlations between BRCA1 and ERCC1 (P < 0.0001) or RRM1 (P < 0.0001) mRNA levels. As BRCA1 levels increased, the probability of response increased (odds ratio [OR] = 0.49; P < 0.001) and the risk of progression (hazard ratio [HR] = 1.52; P = 0.034) and death (HR = 1.45; P = 0.024) decreased. As ERCC1, RRM1, and RRM2 levels increased, the probability of response decreased (ERCC1, OR = 0.42, P < 0.001; RRM1, OR = 0.85, P = 0.083; RRM2, OR = 0.42, P = 0.005) and the risk of progression (ERCC1, HR = 1.59, P = 0.002; RRM1, HR = 1.48, P = 0.039; RRM2, HR = 1.49, P = 0.041) and death (ERCC1, HR = 1.62, P = 0.008; RRM1, HR = 1.52, P = 0.023; RRM2, HR = 1.48, P = 0.017) increased. At multivariate analysis, low expression of ERCC1 was shown to be an independent predictive factor for response to chemotherapy (P = 0.018), time to progression (P = 0.025), and overall survival (P = 0.038). Furthermore, concomitant low expression levels of ERCC1, RRM1, and RRM2 and the high expression level of BRCA1 were predictive of a better outcome (P = 0.014). This study suggests that the efficacy of platinum-based chemotherapy can be improved when customized according to the mRNA expression of BRCA1, ERCC1, RRM1, and RRM2.
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Affiliation(s)
- Hui Zhao
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong, China
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Lemstrová R, Souček P, Melichar B, Mohelnikova-Duchonova B. Role of solute carrier transporters in pancreatic cancer: a review. Pharmacogenomics 2014; 15:1133-45. [DOI: 10.2217/pgs.14.80] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nucleoside analogs such as gemcitabine and 5-fluorouracil are currently the cornerstone of chemotherapy in patients with pancreatic ductal adenocarcinoma (PDAC). Decreased drug transport into tumor cells that may be caused by low expression of membrane proteins, such as solute carrier transporters, represents one of the principal mechanisms of chemotherapy resistance. Individual diversity of multidrug resistance is the major challenge limiting the success of anticancer treatment. Novel biomarkers and pharmacogenomic approaches could further optimize treatment algorithms leading to better survival and lower treatment toxicity in PDAC patients. In this review, the most promising predictive biomarkers from the solute carrier transporter family of membrane transporters and the potential applications for PDAC therapy with nucleoside analogues are summarized.
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Affiliation(s)
- Radmila Lemstrová
- Department of Oncology, Palacky University Medical School & Teaching Hospital, Olomouc, Czech Republic
| | - Pavel Souček
- Biomedical Centre, Faculty of Medicine in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - Bohuslav Melichar
- Department of Oncology, Palacky University Medical School & Teaching Hospital, Olomouc, Czech Republic
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Lee SY, Im SA, Park YH, Woo SY, Kim S, Choi MK, Chang W, Ahn JS, Im YH. Genetic polymorphisms of SLC28A3, SLC29A1 and RRM1 predict clinical outcome in patients with metastatic breast cancer receiving gemcitabine plus paclitaxel chemotherapy. Eur J Cancer 2013; 50:698-705. [PMID: 24361227 DOI: 10.1016/j.ejca.2013.11.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 10/17/2013] [Accepted: 11/25/2013] [Indexed: 12/29/2022]
Abstract
BACKGROUND Paclitaxel and gemcitabine (PG) combination chemotherapy is effective as a maintenance chemotherapeutic regimen in metastatic breast cancer (MBC) patients because it increases progression-free survival (PFS), which increases overall survival (OS). The primary purpose of our study was to investigate the association between genetic polymorphisms in the genes involved in PG pathways and clinical outcomes in MBC patients treated with PG chemotherapy. METHODS A total of 324 MBC patients were enrolled in this prospective multicenter trial of PG as the first-line chemotherapy. Eighty-five of the 324 patients from two institutes were available for analysis of single nucleotide polymorphisms (SNPs). Germline DNA was extracted from peripheral blood mononuclear cells. Thirty-eight SNPs in 15 candidate genes selected from pathways that may influence the metabolism and transport of, or sensitivity, to PG were analysed. RESULTS The median PFS and OS of all 324 patients were 8.7 months (95% confidence interval [CI]: 7.5-9.6 months) and 26.9 months (95% CI: 23.6-30.1 months), respectively. An SNP in SLC28A3 (rs7867504, C/T) was associated with OS (CC or CT versus TT: 37 versus 21 months, p = 0.027, hazard ratio [HR] 2.6, 95% CI: 1.1-6.3). SLC29A1 GA haplotype had a significantly shorter OS (p = 0.030, HR 3.391, 95% CI: 1.13-10.19). RRM1 (ribonucleotide reductase large subunit M1) SNP (rs9937), and haplotypes ATAA and ATGA were significantly associated with neurotoxicity. CONCLUSION Genetic polymorphisms in SLC28A3, SLC29A1 and RRM1 can influence the clinical outcome of MBC patients treated with PG chemotherapy. Further studies on the functional mechanisms relating to these germline polymorphisms in these genes are warranted.
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Affiliation(s)
- Soo-Youn Lee
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University Hospital, Cancer Research Institute, Seoul National University, College of Medicine, Seoul, Republic of Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Sook Young Woo
- Biostatistics Team, Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seonwoo Kim
- Biostatistics Team, Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Moon Ki Choi
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Wonjin Chang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Expression of RRM1 and RRM2 as a novel prognostic marker in advanced non-small cell lung cancer receiving chemotherapy. Tumour Biol 2013; 35:1899-906. [DOI: 10.1007/s13277-013-1255-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022] Open
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24
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Impact of polymorphisms in drug pathway genes on disease-free survival in adults with acute myeloid leukemia. J Hum Genet 2013; 58:353-61. [PMID: 23677058 PMCID: PMC4068832 DOI: 10.1038/jhg.2013.38] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a clinically heterogeneous disease, with 5-year disease-free survival (DFS) ranging from under 10% to over 70% for distinct groups of patients. At our institution, cytarabine, etoposide and busulfan are used in first or second remission patients treated with a 2-step approach to autologous stem cell transplantation (ASCT). In this study, we tested the hypothesis that polymorphisms in the pharmacokinetic and pharmacodynamic pathway genes of these drugs are associated with DFS in AML patients. A total of 1659 variants in 42 genes were analyzed for their association with DFS using a Cox proportional hazards model. 154 genetically European patients were used for the primary analysis. An intronic SNP in ABCC3 (rs4148405) was associated with a significantly shorter DFS (HR=3.2, p=5.6 x 10(-6)) in our primary cohort. In addition a SNP in the GSTM1-GSTM5 locus, rs3754446, was significantly associated with a shorter DFS in all patients (HR=1.8, p=0.001 for 154 European ancestry; HR=1.7, p=0.028 for 125 non-European patients). Thus for the first time, genetic variants in drug pathway genes are shown to be associated with DFS in AML patients treated with chemotherapy-based autologous ASCT.
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Mitra AK, Kirstein MN, Khatri A, Skubitz KM, Dudek AZ, Greeno EW, Kratzke RA, Lamba JK. Pathway-based pharmacogenomics of gemcitabine pharmacokinetics in patients with solid tumors. Pharmacogenomics 2013; 13:1009-21. [PMID: 22838949 DOI: 10.2217/pgs.12.81] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The aim of this study was to evaluate the association of gemcitabine pathway SNPs with detailed pharmacokinetic measures obtained from solid tumor patients receiving gemcitabine-based therapy. MATERIALS & METHODS SNPs within nine gemcitabine pathway genes, namely CDA, CMPK, DCK, DCTD, NT5C2, NT5C3, SLC28A1, SLC28A3 and SLC29A1 were analyzed for association with gemcitabine pharmacokinetics. RESULTS Significant association of gemcitabine clearance with SNPs in NT5C2 was identified. Clearance of 2´,2´-difluorodeoxyuridine, a gemcitabine metabolite was significantly predicted by CDA, SLC29A1 and NT5C2 SNPs. This study reports an association of formation clearance of 2´,2´-difluoro-2´-deoxycytidine triphosphate, an active form of gemcitabine with SNPs within uptake transporters SLC28A1, SLC28A3 and SLC29A1. CONCLUSION Genetic variation in gemcitabine pathway genes is associated with its pharmacokinetics and hence could influence gemcitabine response. Our study identified pharmacogenetic markers that could be further tested in larger patient cohorts and could open up opportunities to individualize therapy in solid tumor patients.
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Affiliation(s)
- Amit K Mitra
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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Giovannetti E, Toffalorio F, De Pas T, Peters GJ. Pharmacogenetics of conventional chemotherapy in non-small-cell lung cancer: a changing landscape? Pharmacogenomics 2013; 13:1073-86. [PMID: 22838953 DOI: 10.2217/pgs.12.91] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Pharmacogenetics might be used to select patients who may benefit from specific chemotherapy that best matches the individual and tumor genetic profile, thus allowing maximum activity and minimal toxicity. Even if most studies in non-small-cell lung cancer yielded contradictory results, several potential biomarkers for sensitivity/resistance to platinum compounds, gemcitabine, taxanes and pemetrexed have been proposed. However, these markers need to be validated within larger prospective randomized trials of customized chemotherapy in homogeneous populations. Other critical points include the optimization/standardization of technical procedures, and further studies to unravel the extremely complex regulation of gene function. From this perspective, the evaluation of key factors influencing genotype-phenotype relationships, such as miRNAs, and functional studies to clarify pharmacokinetic/pharmacodynamic interactions, are fundamental for the pharmacogenetic optimization of cancer chemotherapy. Finally, limitation of the traditional pharmacogenetic approach relying only on candidate genes suspected of affecting drug response is now being overcome by the use of novel genome-wide studies.
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Affiliation(s)
- Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
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