An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation.
Regular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Despite the current screening options available and advancements in therapies there will be around 53,000 CRC related deaths this year. There is great interest in non-invasive alternatives such as p...
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| Format: | Article |
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0308711 |
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| author | Emmalee J Northrop-Albrecht Chung Wah Wu Calise K Berger William R Taylor Patrick H Foote Karen A Doering Anna M Gonser Aditya Bhagwate Zhifu Sun Douglas W Mahoney Kelli N Burger Lisa A Boardman John B Kisiel |
| author_facet | Emmalee J Northrop-Albrecht Chung Wah Wu Calise K Berger William R Taylor Patrick H Foote Karen A Doering Anna M Gonser Aditya Bhagwate Zhifu Sun Douglas W Mahoney Kelli N Burger Lisa A Boardman John B Kisiel |
| author_sort | Emmalee J Northrop-Albrecht |
| collection | DOAJ |
| description | Regular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Despite the current screening options available and advancements in therapies there will be around 53,000 CRC related deaths this year. There is great interest in non-invasive alternatives such as plasma cell-free RNA (cfRNA) for diagnostic, prognostic, and predictive applications. In the current study, our aim was to identify and validate potential cfRNA candidates to improve early CRC diagnosis. In phase 1 (n = 49; 25 controls, 24 cancers), discovery total RNA sequencing was performed. Select exons underwent validation in phase 2 (n = 73; 35 controls, 29 cancers, 9 adenomas) using targeted capture sequencing (n = 10,371 probes). In phase 3 (n = 57; 30 controls, 27 cancers), RT-qPCR was performed on previously identified candidates (n = 99). There were 895 exons that were differentially expressed (325 upregulated, 570 downregulated) among cancers versus controls. In phases 2 and 3, fewer markers were validated than expected in independent sets of patients, most of which were from previously published literature (FGA, FGB, GPR107, CDH3, and RP23AP7). In summary, we optimized laboratory processes and data analysis strategies which can serve as methodological framework for future plasma RNA studies beyond just the scope of CRC detection. Additionally, further exploration is needed in order to determine if the few cfRNA candidates identified in this study have clinical utility for early CRC detection. Over time, advancements in technologies, data analysis, and RNA preservation methods at time of collection may improve the biological and technical reproducibility of cfRNA biomarkers and enhance the feasibility of RNA-based liquid biopsies. |
| format | Article |
| id | doaj-art-6d7a94ddfe824517a2e217f4cc9f03f0 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-6d7a94ddfe824517a2e217f4cc9f03f02025-08-20T02:46:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-01198e030871110.1371/journal.pone.0308711An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation.Emmalee J Northrop-AlbrechtChung Wah WuCalise K BergerWilliam R TaylorPatrick H FooteKaren A DoeringAnna M GonserAditya BhagwateZhifu SunDouglas W MahoneyKelli N BurgerLisa A BoardmanJohn B KisielRegular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Despite the current screening options available and advancements in therapies there will be around 53,000 CRC related deaths this year. There is great interest in non-invasive alternatives such as plasma cell-free RNA (cfRNA) for diagnostic, prognostic, and predictive applications. In the current study, our aim was to identify and validate potential cfRNA candidates to improve early CRC diagnosis. In phase 1 (n = 49; 25 controls, 24 cancers), discovery total RNA sequencing was performed. Select exons underwent validation in phase 2 (n = 73; 35 controls, 29 cancers, 9 adenomas) using targeted capture sequencing (n = 10,371 probes). In phase 3 (n = 57; 30 controls, 27 cancers), RT-qPCR was performed on previously identified candidates (n = 99). There were 895 exons that were differentially expressed (325 upregulated, 570 downregulated) among cancers versus controls. In phases 2 and 3, fewer markers were validated than expected in independent sets of patients, most of which were from previously published literature (FGA, FGB, GPR107, CDH3, and RP23AP7). In summary, we optimized laboratory processes and data analysis strategies which can serve as methodological framework for future plasma RNA studies beyond just the scope of CRC detection. Additionally, further exploration is needed in order to determine if the few cfRNA candidates identified in this study have clinical utility for early CRC detection. Over time, advancements in technologies, data analysis, and RNA preservation methods at time of collection may improve the biological and technical reproducibility of cfRNA biomarkers and enhance the feasibility of RNA-based liquid biopsies.https://doi.org/10.1371/journal.pone.0308711 |
| spellingShingle | Emmalee J Northrop-Albrecht Chung Wah Wu Calise K Berger William R Taylor Patrick H Foote Karen A Doering Anna M Gonser Aditya Bhagwate Zhifu Sun Douglas W Mahoney Kelli N Burger Lisa A Boardman John B Kisiel An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. PLoS ONE |
| title | An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. |
| title_full | An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. |
| title_fullStr | An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. |
| title_full_unstemmed | An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. |
| title_short | An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. |
| title_sort | investigation of plasma cell free rna for the detection of colorectal cancer from transcriptome marker selection to targeted validation |
| url | https://doi.org/10.1371/journal.pone.0308711 |
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