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Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. Genome position and gene amplification. Genome Biol 2008; 8:R120. [PMID: 17584934 PMCID: PMC2394771 DOI: 10.1186/gb-2007-8-6-r120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 05/15/2007] [Accepted: 06/21/2007] [Indexed: 01/05/2023] Open
Abstract
Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
Background Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. Results We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. Conclusion These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
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Affiliation(s)
- Pavla Gajduskova
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská, Brno, 612 65, Czech Republic
| | - Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Serena Kwek
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Ritu Roydasgupta
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane Fridlyand
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Taku Tokuyasu
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Kündig C, Leblanc E, Papadopoulou B, Ouellette M. Role of the locus and of the resistance gene on gene amplification frequency in methotrexate resistant Leishmania tarentolae. Nucleic Acids Res 1999; 27:3653-9. [PMID: 10471733 PMCID: PMC148619 DOI: 10.1093/nar/27.18.3653] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The protozoan parasite Leishmania resists the antifolate methotrexate (MTX) by amplifying the R locus dihydrofolate reductase-thymidylate synthase ( dhfr-ts ) gene, the H locus ptr1 pterin reductase gene, and finally by mutation in a common folate/MTX transporter. Amplification of dhfr-ts has never been observed in Leishmania tarentolae MTX resistant mutants while ptr1 amplification is common. We have selected a L.tarentolae ptr1 null mutant for MTX resistance and observed dhfr-ts amplification in this mutant demonstrating that once a preferred resistance mechanism is unavailable, a second one will take over. By introducing the ptr1 gene at the R locus and the dhfr-ts gene at the H locus by gene targeting, we investigated the role of the resistance gene and the locus on the rate of gene amplification. Transfection studies indicated that ptr1 gave higher levels of MTX resistance than dhfr-ts. Consistent with this, when ptr1 was present as part of either the H locus or the R locus it was invariably amplified, while dhfr-ts was only amplified when ptr1 was inactivated. When dhfr-ts was present in a ptr1 null background on both the H locus and the R locus, amplification from the H locus was more frequent suggesting that both the gene and the locus are determining the frequency of gene amplification in Leishmania.
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Affiliation(s)
- C Kündig
- Centre de Recherche en Infectiologie du CHUL and Département de Biologie Médicale, Division de Microbiologie, Faculté de Médecine, Université Laval, Québec, Canada
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