Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells.
Using transcriptomic and metabolomic measurements from the NCI60 cell line panel, together with a novel approach to integration of molecular profile data, we show that the biochemical pathways associated with tumour cell chemosensitivity to platinum-based drugs are highly coincident, i.e. they descr...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001113&type=printable |
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| _version_ | 1849331168489504768 |
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| author | Rachel Cavill Atanas Kamburov James K Ellis Toby J Athersuch Marcus S C Blagrove Ralf Herwig Timothy M D Ebbels Hector C Keun |
| author_facet | Rachel Cavill Atanas Kamburov James K Ellis Toby J Athersuch Marcus S C Blagrove Ralf Herwig Timothy M D Ebbels Hector C Keun |
| author_sort | Rachel Cavill |
| collection | DOAJ |
| description | Using transcriptomic and metabolomic measurements from the NCI60 cell line panel, together with a novel approach to integration of molecular profile data, we show that the biochemical pathways associated with tumour cell chemosensitivity to platinum-based drugs are highly coincident, i.e. they describe a consensus phenotype. Direct integration of metabolome and transcriptome data at the point of pathway analysis improved the detection of consensus pathways by 76%, and revealed associations between platinum sensitivity and several metabolic pathways that were not visible from transcriptome analysis alone. These pathways included the TCA cycle and pyruvate metabolism, lipoprotein uptake and nucleotide synthesis by both salvage and de novo pathways. Extending the approach across a wide panel of chemotherapeutics, we confirmed the specificity of the metabolic pathway associations to platinum sensitivity. We conclude that metabolic phenotyping could play a role in predicting response to platinum chemotherapy and that consensus-phenotype integration of molecular profiling data is a powerful and versatile tool for both biomarker discovery and for exploring the complex relationships between biological pathways and drug response. |
| format | Article |
| id | doaj-art-9ece8c5eb9264645a076bcc09d13201d |
| institution | Kabale University |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2011-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-9ece8c5eb9264645a076bcc09d13201d2025-08-20T03:46:42ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582011-03-0173e100111310.1371/journal.pcbi.1001113Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells.Rachel CavillAtanas KamburovJames K EllisToby J AthersuchMarcus S C BlagroveRalf HerwigTimothy M D EbbelsHector C KeunUsing transcriptomic and metabolomic measurements from the NCI60 cell line panel, together with a novel approach to integration of molecular profile data, we show that the biochemical pathways associated with tumour cell chemosensitivity to platinum-based drugs are highly coincident, i.e. they describe a consensus phenotype. Direct integration of metabolome and transcriptome data at the point of pathway analysis improved the detection of consensus pathways by 76%, and revealed associations between platinum sensitivity and several metabolic pathways that were not visible from transcriptome analysis alone. These pathways included the TCA cycle and pyruvate metabolism, lipoprotein uptake and nucleotide synthesis by both salvage and de novo pathways. Extending the approach across a wide panel of chemotherapeutics, we confirmed the specificity of the metabolic pathway associations to platinum sensitivity. We conclude that metabolic phenotyping could play a role in predicting response to platinum chemotherapy and that consensus-phenotype integration of molecular profiling data is a powerful and versatile tool for both biomarker discovery and for exploring the complex relationships between biological pathways and drug response.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001113&type=printable |
| spellingShingle | Rachel Cavill Atanas Kamburov James K Ellis Toby J Athersuch Marcus S C Blagrove Ralf Herwig Timothy M D Ebbels Hector C Keun Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PLoS Computational Biology |
| title | Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. |
| title_full | Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. |
| title_fullStr | Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. |
| title_full_unstemmed | Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. |
| title_short | Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. |
| title_sort | consensus phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1001113&type=printable |
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