Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation.
Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into...
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Public Library of Science (PLoS)
2013
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oai:doaj.org-article:6bda563f480e4d239955d6a664541f262021-11-18T05:52:16ZComputational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation.1553-734X1553-735810.1371/journal.pcbi.1002963https://doaj.org/article/6bda563f480e4d239955d6a664541f262013-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23592955/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac rejection may offer a relevant post-transplant monitoring tool to effectively guide clinical care. The proposed computational pipeline is highly applicable to a wide range of biomarker proteomic studies.Gabriela V Cohen FreueAnna MeredithDerek SmithAxel BergmanMayu SasakiKaren K Y LamZsuzsanna HollanderNina OpushnevaMandeep TakharDavid LinJanet Wilson-McManusRobert BalshawPaul A KeownChristoph H BorchersBruce McManusRaymond T NgW Robert McMasterBiomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence TeamsPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 4, p e1002963 (2013) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Biology (General) QH301-705.5 |
| spellingShingle |
Biology (General) QH301-705.5 Gabriela V Cohen Freue Anna Meredith Derek Smith Axel Bergman Mayu Sasaki Karen K Y Lam Zsuzsanna Hollander Nina Opushneva Mandeep Takhar David Lin Janet Wilson-McManus Robert Balshaw Paul A Keown Christoph H Borchers Bruce McManus Raymond T Ng W Robert McMaster Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| description |
Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac rejection may offer a relevant post-transplant monitoring tool to effectively guide clinical care. The proposed computational pipeline is highly applicable to a wide range of biomarker proteomic studies. |
| format |
article |
| author |
Gabriela V Cohen Freue Anna Meredith Derek Smith Axel Bergman Mayu Sasaki Karen K Y Lam Zsuzsanna Hollander Nina Opushneva Mandeep Takhar David Lin Janet Wilson-McManus Robert Balshaw Paul A Keown Christoph H Borchers Bruce McManus Raymond T Ng W Robert McMaster Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams |
| author_facet |
Gabriela V Cohen Freue Anna Meredith Derek Smith Axel Bergman Mayu Sasaki Karen K Y Lam Zsuzsanna Hollander Nina Opushneva Mandeep Takhar David Lin Janet Wilson-McManus Robert Balshaw Paul A Keown Christoph H Borchers Bruce McManus Raymond T Ng W Robert McMaster Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams |
| author_sort |
Gabriela V Cohen Freue |
| title |
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| title_short |
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| title_full |
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| title_fullStr |
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| title_full_unstemmed |
Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| title_sort |
computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/6bda563f480e4d239955d6a664541f26 |
| work_keys_str_mv |
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