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Jado JC, Dow M, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep 2024; 14:13989. [PMID: 38886371 PMCID: PMC11183241 DOI: 10.1038/s41598-024-63943-7] [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: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
In vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cells could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
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Affiliation(s)
- Juan Carlos Jado
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michelle Dow
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
- Health Science, Department of Biomedical Informatics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Krypton Carolino
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Adam Klie
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gregory J Fonseca
- Department of Medicine, Meakins-Christie Laboratories, McGill University Health Centre, 1001 Decaire Blvd, Montreal, QC, H4A 3J1, Canada
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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Imyanitov EN, Iyevleva AG. Molecular tests for prediction of tumor sensitivity to cytotoxic drugs. Cancer Lett 2022; 526:41-52. [PMID: 34808283 DOI: 10.1016/j.canlet.2021.11.021] [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: 09/25/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/15/2022]
Abstract
Chemotherapy constitutes the backbone of cancer treatment. Several predictive assays assist personalized administration of cytotoxic drugs and are recommended for use in a clinical setting. The deficiency of DNA repair by homologous recombination (HRD), which is caused by inactivation of BRCA1/2 genes or other genetic events, is associated with high tumor responsiveness to platinum compounds, bifunctional alkylating agents and topoisomerase II poisons. Low activity of MGMT predicts the efficacy of nitrosoureas and tetrazines. Some clinically established pharmacogenetic tests allow for the adjustment of drug dosage, for example, the analysis of DPYD allelic variants for administration of fluoropyrimidines and UGT1A1 genotyping for the use of irinotecan. While there are promising molecular predictors of tumor sensitivity to pemetrexed, gemcitabine and taxanes, they remain in the investigational stage and require additional validation. Comprehensive molecular analysis of tumors obtained from drug responders and non-responders is likely to reveal new clinically useful predictive markers for cytotoxic therapy.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, 191015, Russia.
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, 194100, Russia
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Zhu CM, Lian XY, Bi YH, Hu CC, Liang YW, Li QS. Prognostic value of ribonucleotide reductase subunit M1 (RRM1) in non-small cell lung cancer: A meta-analysis. Clin Chim Acta 2018; 485:67-73. [PMID: 29803896 DOI: 10.1016/j.cca.2018.05.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Ribonucleotide reductase subunit 1 (RRM1) is a potential prognostic factor for non-small cell lung cancer (NSCLC). This study evaluates prognostic value of RRM1 in NSCLC patients by meta-analyzing outcomes reported in literature. METHOD Data were acquired from research articles retrieved after literature search in online databases. Random effects meta-analyses were conducted by pooling hazard ratios (HR). Meta-analyses of standardized mean differences (SMD) were used to evaluate overall survival (OS) and progression-free survival (PFS) between low and high RRM1 expression groups. Metaregression analyses were conducted to evaluate the factors that could affect prognostic relationship of RRM1 with treatment and survival outcomes. RESULTS 23 studies (3148 patients) were included. RRM1 expression was not meaningfully associated with prognosis of NSCLC even when the reference (HR = 1) was either low RRM1 expression (0.918 [95% CI 0.833, 1.003]) or high RRM1 expression (0.834 [0.625, 1.043]). OS was significantly longer in low RRM1 expression group compared to high RRM1 expression group (SMD 0.73 [0.36, 1.09]; P < 0.0001). PFS was not significantly different between low and high RRM1 expression groups (SMD 0.08 [-0.29, 0.45]; p = 0.68). Age was inversely associated with HR (p = 0.001) even when reference was low RRMI (p = 0.027) or high RRM1 (p = 0.006). Age was positively associated with OS in both low and high RRM1 groups. CONCLUSION In meta-analysis of studies which used gemcitabine-based therapies, higher RRM1 expression is found to associated with shorter OS but not PFS. HR depicting relationship between RRM1 expression and OS/PFS/treatment response could not demonstrate a prognostic role of RRM1 in NSCLC patients.
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Affiliation(s)
- Cui-Min Zhu
- Department of Oncology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Xiang-Yao Lian
- Department of Oncology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Ying-Hui Bi
- Department of Oncology, Qingdao Municipal Hospital, Qingdao, Shandong 266000, China
| | - Chan-Chan Hu
- Department of Oncology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Yun-Wei Liang
- Department of Oncology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China
| | - Qing-Shan Li
- Department of Oncology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, China.
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Chen Z, Zheng Y, Shi Y, Cui Z. Overcoming tumor cell chemoresistance using nanoparticles: lysosomes are beneficial for (stearoyl) gemcitabine-incorporated solid lipid nanoparticles. Int J Nanomedicine 2018; 13:319-336. [PMID: 29391792 PMCID: PMC5768424 DOI: 10.2147/ijn.s149196] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Despite recent advances in targeted therapies and immunotherapies, chemotherapy using cytotoxic agents remains an indispensable modality in cancer treatment. Recently, there has been a growing emphasis in using nanomedicine in cancer chemotherapy, and several nanomedicines have already been used clinically to treat cancers. There is evidence that formulating small molecular cancer chemotherapeutic agents into nanomedicines significantly modifies their pharmacokinetics and often improves their efficacy. Importantly, cancer cells often develop resistance to chemotherapy, and formulating anticancer drugs into nanomedicines also helps overcome chemoresistance. In this review, we briefly describe the different classes of cancer chemotherapeutic agents, their mechanisms of action and resistance, and evidence of overcoming the resistance using nanomedicines. We then emphasize on gemcitabine and our experience in discovering the unique (stearoyl) gemcitabine solid lipid nanoparticles that are effective against tumor cells resistant to gemcitabine and elucidate the underlying mechanisms. It seems that lysosomes, which are an obstacle in the delivery of many drugs, are actually beneficial for our (stearoyl) gemcitabine solid lipid nanoparticles to overcome tumor cell resistance to gemcitabine.
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Affiliation(s)
- Zhe Chen
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yuanqiang Zheng
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yanchun Shi
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Zhengrong Cui
- Inner Mongolia Key Lab of Molecular Biology, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China.,Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
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Dragoj M, Milosevic Z, Bankovic J, Tanic N, Pesic M, Stankovic T. Targeting CXCR4 and FAK reverses doxorubicin resistance and suppresses invasion in non-small cell lung carcinoma. Cell Oncol (Dordr) 2016; 40:47-62. [DOI: 10.1007/s13402-016-0304-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2016] [Indexed: 12/12/2022] Open
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Tekpli X, Skaug V, Bæra R, Phillips DH, Haugen A, Mollerup S. Estrogen receptor expression and gene promoter methylation in non-small cell lung cancer - a short report. Cell Oncol (Dordr) 2016; 39:583-589. [PMID: 27572263 DOI: 10.1007/s13402-016-0295-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2016] [Indexed: 11/29/2022] Open
Abstract
PURPOSE In the past, anomalous estrogen receptor (ER) regulation has been associated with various lung pathologies, but so far its involvement in lung cancer initiation and/or progression has remained unclear. Here, we aimed at assessing in vivo and in vitro ER expression and its possible epigenetic regulation in non-small cell lung cancer (NSCLC) samples and their corresponding normal tissues and cells. METHODS ERα and ERβ gene expression levels were assessed using real time quantitative PCR (RT-qPCR), whereas ERα and ERβ gene promoter methylation levels were assessed using DNA bisulfite conversion followed by pyrosequencing. We included NSCLC (n = 87) and adjacent histologically normal lung tissue samples from lung cancer patients (n = 184), primary normal bronchial epithelial-derived cell cultures (n = 11), immortalized bronchial epithelial-derived cell lines (n = 3) and NSCLC derived cell lines (n = 9). RESULTS Using RT-qPCR we found significantly lower ERα and ERβ expression levels in the NSCLC tissue samples compared to their normal adjacent tissue samples. These lower ER expression levels were confirmed in vitro using primary normal bronchial epithelial-derived cell cultures, immortalized bronchial epithelial-derived cell lines and NSCLC-derived cell lines. By using this latter panel of cells, we found that ER gene promoter hypermethylation was associated with decreased ER expression. In addition we found that in tumor and normal lung tissues, smoking was associated with decreased ER expression and that normal lung tissues with a low ERβ expression level exhibited increased smoking-related DNA adducts. CONCLUSIONS Taken together, our results indicate that decreased ER expression mediated by DNA methylation may play a role in NSCLC development.
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Affiliation(s)
- Xavier Tekpli
- Section for Toxicology and Biological Working Environment, Department of Biological and Chemical Working Environment, National Institute of Occupational Health, PO box 8149, Dep., Gydas vei 8, N-0033, Oslo, Norway. .,Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Vidar Skaug
- Section for Toxicology and Biological Working Environment, Department of Biological and Chemical Working Environment, National Institute of Occupational Health, PO box 8149, Dep., Gydas vei 8, N-0033, Oslo, Norway
| | - Rita Bæra
- Section for Toxicology and Biological Working Environment, Department of Biological and Chemical Working Environment, National Institute of Occupational Health, PO box 8149, Dep., Gydas vei 8, N-0033, Oslo, Norway
| | - David H Phillips
- Analytical and Environmental Sciences, MRC-PHE Centre for Environment and Health, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Aage Haugen
- Section for Toxicology and Biological Working Environment, Department of Biological and Chemical Working Environment, National Institute of Occupational Health, PO box 8149, Dep., Gydas vei 8, N-0033, Oslo, Norway
| | - Steen Mollerup
- Section for Toxicology and Biological Working Environment, Department of Biological and Chemical Working Environment, National Institute of Occupational Health, PO box 8149, Dep., Gydas vei 8, N-0033, Oslo, Norway
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The functional status of DNA repair pathways determines the sensitization effect to cisplatin in non-small cell lung cancer cells. Cell Oncol (Dordr) 2016; 39:511-522. [PMID: 27473273 DOI: 10.1007/s13402-016-0291-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Cisplatin can cause a variety of DNA crosslink lesions including intra-strand and inter-strand crosslinks (ICLs), which are associated with the sensitivity of cancer cells to cisplatin. Here, we aimed to assess the contribution of the Fanconi anemia (FA), homologous recombination (HR) and nucleotide excision repair (NER) pathways to cisplatin resistance in non-small cell lung cancer (NSCLC)-derived cells. METHODS The expression of FA, HR and NER pathway-associated genes was assessed by RT-qPCR and Western blotting. siRNAs were used to knock down the expression of these genes. CCK-8 and flow cytometry assays were used to assess the viability and apoptotic rate of NSCLC-derived cells, respectively. Immunofluorescence and alkaline comet assays were used to assess the repair of ICLs. RESULTS We found that acquired cisplatin-resistant NSCLC-derived A549/DR cells exhibited markedly enhanced FA and HR repair pathway capacities compared to its parental A549 cells and another independent NSCLC-derived cell line, Calu-1, which possesses a moderate innate resistance to cisplatin. siRNA-mediated silencing of the FA-associated genes FANCL and RAD18 and the HR-associated genes BRCA1 and BRCA2 significantly potentiated the sensitivity of A549/DR cells to cisplatin compared to A549 and Calu-1 cells, suggesting that the acquired cisplatin resistance in A549/DR cells may be attributed to enhanced FA and HR pathway capacities responsible for ICL repair. Although we found that expression knockdown of the NER-associated genes XPA and ERCC1 sensitized the three NSCLC-derived cell lines to cisplatin, the sensitization effect was more significant in Calu-1 cells than in A549 and A549/DR cells, implying that the innate cisplatin resistance in Calu-1 cells may result from an increased NER activity. CONCLUSIONS Our results indicate that the functional status of DNA repair pathways determine the sensitivity of NSCLC cells to cisplatin. Direct targeting of the pathway that is involved in cisplatin resistance may be an effective strategy to surmount cisplatin resistance in NSCLC.
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Saisongkorh V, Maiuthed A, Chanvorachote P. Nitric oxide increases the migratory activity of non-small cell lung cancer cells via AKT-mediated integrin αv and β1 upregulation. Cell Oncol (Dordr) 2016; 39:449-462. [PMID: 27376838 DOI: 10.1007/s13402-016-0287-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previously, nitric oxide (NO) has been found to affect the metastatic behavior of various types of cancer. In addition, it has been found that alterations in integrin expression may have profound effects on cancer cell survival and migration. Here, we aimed at assessing the effects of non-toxic concentrations of NO on human non-small cell lung cancer (NSCLC) cells, including the expression of integrins and the migration of these cells. METHODS The cytotoxic and proliferative effects of NO on human NSCLC-derived H460, H292 and H23 cells were tested by MTT assay. The migration capacities of these cells was evaluated by wound healing and transwell migration assays. The expression of integrins and migration-associated proteins was determined by Western blot analyses. RESULTS We found that NO treatment caused a significant increase in the expression of integrin αv and β1 in all three NSCLC-derived cell lines tested. Known migration-associated proteins acting downstream of these integrins, including focal adhesion kinase (FAK), active RhoA (Rho-GTP) and active cell division control 42 (Cdc42-GTP), were found to be significantly activated in response to NO. In addition, we found that NO-treated cells showed an increased motility and that this motility was associated with a significant increase in the number of filopodia per cell. We also found that NO-treated cells exhibited increased active protein kinase G (PKG), protein kinase B (AKT) and FAK expression levels. Using a pharmacological approach, we found that the integrin-modulating effect of NO is most likely brought about by a PKG/AKT-dependent mechanism, since the observed changes in integrin expression were abolished by AKT inhibitors, but not by FAK inhibitors. CONCLUSION Our data suggest a novel role of NO in the regulation of integrin expression and, concomitantly, the migratory capacity of NSCLC cells.
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Affiliation(s)
- Vhudhipong Saisongkorh
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.,Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Arnatchai Maiuthed
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.,Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pithi Chanvorachote
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand. .,Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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Hypoxia can impair doxorubicin resistance of non-small cell lung cancer cells by inhibiting MRP1 and P-gp expression and boosting the chemosensitizing effects of MRP1 and P-gp blockers. Cell Oncol (Dordr) 2016; 39:411-433. [PMID: 27306525 DOI: 10.1007/s13402-016-0285-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Non-small cell lung cancers (NSCLCs) frequently exhibit resistance to therapeutic drugs, which seriously hampers their treatment. Here, we set out to assess the roles of the multidrug resistance protein 1 (MRP1) and P-glycoprotein (P-gp) in the doxorubicin (DOX) resistance of NSCLC cells, as well as the putative therapeutic efficacy of MRP1 and P-gp blockers on DOX-treated NSCLC cells. METHODS The impact of DOX on cell survival, DOX efflux and MRP1 and P-gp expression was assessed in 5 different NSCLC-derived cell lines (parental CH27, A549, H1299, H460, and DOX resistant CH27) in the absence or presence of MK571 (MRP1 inhibitor) or Verapamil (P-gp inhibitor), under both normoxic and hypoxic conditions. RESULTS We found that in response to DOX treatment, NSCLC cells that express high levels of MRP1 and P-gp (such as CH27) showed a better DOX efflux and a higher DOX resistance. MK571 and Verapamil were found to abolish DOX resistance and to act as chemosensitizers for DOX therapy in all cell lines tested. We also found that hypoxia could inhibit MRP1 and P-gp expression in a HIF-1α-dependent manner, abolish DOX resistance and boost the chemosensitizer effect of MK571 and Verapamil on DOX treatment of all the NSCLC cells tested, except the DOX-resistant CH27 cells. CONCLUSIONS From our data we conclude that MRP1 and P-gp play critical roles in the DOX resistance of the NSCLC cells tested. MRP1 and P-gp targeted therapy using MK571, Verapamil, CoCl2 or ambient hypoxia appeared to be promising in abolishing the DOX efflux and DOX resistance of the NSCLC cells. The putative therapeutic efficacies of MRP1 and/or P-gp blockers on NSCLC cells are worthy of note.
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MiR-613 induces cell cycle arrest by targeting CDK4 in non-small cell lung cancer. Cell Oncol (Dordr) 2016; 39:139-47. [DOI: 10.1007/s13402-015-0262-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2015] [Indexed: 10/22/2022] Open
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