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Varamo C, Peraldo-Neia C, Ostano P, Basiricò M, Raggi C, Bernabei P, Venesio T, Berrino E, Aglietta M, Leone F, Cavalloni G. Establishment and Characterization of a New Intrahepatic Cholangiocarcinoma Cell Line Resistant to Gemcitabine. Cancers (Basel) 2019; 11:cancers11040519. [PMID: 30979003 PMCID: PMC6520787 DOI: 10.3390/cancers11040519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 12/19/2022] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is one of the most lethal liver cancers. Late diagnosis and chemotherapy resistance contribute to the scarce outfit and poor survival. Resistance mechanisms are still poorly understood. Here, we established a Gemcitabine (GEM) resistant model, the MT-CHC01R1.5 cell line, obtained by a GEM gradual exposure (up to 1.5 µM) of the sensitive counterpart, MT-CHC01. GEM resistance was irreversible, even at high doses. The in vitro and in vivo growth was slower than MT-CHC01, and no differences were highlighted in terms of migration and invasion. Drug prediction analysis suggested that Paclitaxel and Doxycycline might overcome GEM resistance. Indeed, in vitro MT-CHC01R1.5 growth was reduced by Paclitaxel and Doxycycline. Importantly, Doxycycline pretreatment at very low doses restored GEM sensitivity. To assess molecular mechanisms underlying the acquisition of GEM resistance, a detailed analysis of the transcriptome in MT-CHC01R1.5 cells versus the corresponding parental counterpart was performed. Transcriptomic analysis showed that most up-regulated genes were involved in cell cycle regulation and in the DNA related process, while most down-regulated genes were involved in the response to stimuli, xenobiotic metabolism, and angiogenesis. Furthermore, additional panels of drug resistance and epithelial to mesenchymal transition genes (n = 168) were tested by qRT-PCR and the expression of 20 genes was affected. Next, based on a comparison between qRT-PCR and microarray data, a list of up-regulated genes in MT-CHC01R1.5 was selected and further confirmed in a primary cell culture obtained from an ICC patient resistant to GEM. In conclusion, we characterized a new GEM resistance ICC model that could be exploited either to study alternative mechanisms of resistance or to explore new therapies.
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Affiliation(s)
- Chiara Varamo
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, B3000 Leuven, Belgium.
| | | | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900 Biella, Italy.
| | - Marco Basiricò
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Chiara Raggi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, 20089 Rozzano, Italy.
- Dept. Medicina Sperimentale e Clinica, Università di Firenze, 50100 Florence, Italy.
| | - Paola Bernabei
- Flow Cytometry Center, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Tiziana Venesio
- Molecular Pathology Lab, Unit of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Enrico Berrino
- Molecular Pathology Lab, Unit of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126 Turin, Italy.
| | - Massimo Aglietta
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Francesco Leone
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Giuliana Cavalloni
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
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Dorman SN, Baranova K, Knoll JHM, Urquhart BL, Mariani G, Carcangiu ML, Rogan PK. Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Mol Oncol 2015; 10:85-100. [PMID: 26372358 DOI: 10.1016/j.molonc.2015.07.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/31/2015] [Indexed: 12/21/2022] Open
Abstract
Increasingly, the effectiveness of adjuvant chemotherapy agents for breast cancer has been related to changes in the genomic profile of tumors. We investigated correspondence between growth inhibitory concentrations of paclitaxel and gemcitabine (GI50) and gene copy number, mutation, and expression first in breast cancer cell lines and then in patients. Genes encoding direct targets of these drugs, metabolizing enzymes, transporters, and those previously associated with chemoresistance to paclitaxel (n = 31 genes) or gemcitabine (n = 18) were analyzed. A multi-factorial, principal component analysis (MFA) indicated expression was the strongest indicator of sensitivity for paclitaxel, and copy number and expression were informative for gemcitabine. The factors were combined using support vector machines (SVM). Expression of 15 genes (ABCC10, BCL2, BCL2L1, BIRC5, BMF, FGF2, FN1, MAP4, MAPT, NFKB2, SLCO1B3, TLR6, TMEM243, TWIST1, and CSAG2) predicted cell line sensitivity to paclitaxel with 82% accuracy. Copy number profiles of 3 genes (ABCC10, NT5C, TYMS) together with expression of 7 genes (ABCB1, ABCC10, CMPK1, DCTD, NME1, RRM1, RRM2B), predicted gemcitabine response with 85% accuracy. Expression and copy number studies of two independent sets of patients with known responses were then analyzed with these models. These included tumor blocks from 21 patients that were treated with both paclitaxel and gemcitabine, and 319 patients on paclitaxel and anthracycline therapy. A new paclitaxel SVM was derived from an 11-gene subset since data for 4 of the original genes was unavailable. The accuracy of this SVM was similar in cell lines and tumor blocks (70-71%). The gemcitabine SVM exhibited 62% prediction accuracy for the tumor blocks due to the presence of samples with poor nucleic acid integrity. Nevertheless, the paclitaxel SVM predicted sensitivity in 84% of patients with no or minimal residual disease.
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Affiliation(s)
- Stephanie N Dorman
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Katherina Baranova
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada; Molecular Diagnostics Division, Laboratory Medicine Program, London Health Sciences Centre, ON, Canada; Cytognomix Inc., London, ON, Canada
| | - Brad L Urquhart
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Gabriella Mariani
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Luisa Carcangiu
- Department of Diagnostic and Laboratory Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada; Cytognomix Inc., London, ON, Canada; Department of Computer Science, University of Western Ontario, London, ON, Canada; Department of Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.
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Anomalous altered expressions of downstream gene-targets in TP53-miRNA pathways in head and neck cancer. Sci Rep 2014; 4:6280. [PMID: 25186767 PMCID: PMC5385823 DOI: 10.1038/srep06280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/11/2014] [Indexed: 01/21/2023] Open
Abstract
The prevalence of head and neck squamous cell carcinoma, HNSCC, continues to grow. Change in the expression of TP53 in HNSCC affects its downstream miRNAs and their gene targets, anomalously altering the expressions of the five genes, MEIS1, AGTR1, DTL, TYMS and BAK1. These expression alterations follow the repression of TP53 that upregulates miRNA-107, miRNA- 215, miRNA-34 b/c and miRNA-125b, but downregulates miRNA-155. The above five so far unreported genes are the targets of these miRNAs. Meta-analyses of microarray and RNA-Seq data followed by qRT-PCR validation unravel these new ones in HNSCC. The regulatory roles of TP53 on miRNA-155 and miRNA-125b differentiate the expressions of AGTR1 and BAK1in HNSCC vis-à-vis other carcinogenesis. Expression changes alter cell cycle regulation, angiogenic and blood cell formation, and apoptotic modes in affliction. Pathway analyses establish the resulting systems-level functional and mechanistic insights into the etiology of HNSCC.
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