An investigation of plasma cell-free RNA for the detection of colorectal cancer - From transcriptome marker selection to targeted validation

Sep 21, 2026

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Regular screening for colorectal cancer (CRC) is critical for early detection and long-term survival. Interest is growing in non-invasive plasma cell-free RNA (cfRNA) for diagnostic, prognostic, and predictive use. This study aims to identify and validate cfRNA candidates to improve early CRC diagnosis across discovery, targeted validation, and RT-qPCR phases. Differential expression and validation results are reported, along with an optimized methodological framework and the need for further clinical utility testing.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages15

Reading Time38 min

AccessFree to download

Abstract

Study phases and workflow (discovery, targeted validation, RT-qPCR)

Differential expression and marker validation results

Summary, methodological framework, and future work

PLOS ONE OPEN ACCESS Citation: Northrop-Albrecht EJ, Wu CW, Berger CK, Taylor WR, Foote PH, Doering KA, et al. (2024) An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. PLoS ONE 19(8): e0308711 . [https://doi.org/10.1371/journal](https://doi.org/10.1371/journal). pone.0308711 Editor: Alvaro Galli, CNR, ITALY Received: March 26, 2024 Accepted: July 29, 2024 Published: August 15, 2024 Copyright: © 2024 Northrop-Albrecht et al. This isan open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Most data arepresented within the paper and its Supporting Information files. However, Mayo Clinic and Exact Sciences have a Sponsored Research Contract and Intellectual Property Development Agreement, the terms of which preclude us from disseminating raw sequencing data publicly. Data and materials restrictions have been put in place by the Mayo Clinic institutional review board and Legal Contracts Administration, the contact for which is Randall Jones ([jones.randall@mayo.edu](jones.randall@mayo.edu)) . Additional data restrictions may be in place from RESEARCH ARTICLE An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation Emmalee J. Northrop-Albrecht1 *, Chung Wah Wu1¤, Calise K. Berger1, William R. Taylor1, Patrick H. Foote1, Karen A. Doering1, Anna M. Gonser1, Aditya Bhagwate2, Zhifu Sun2, Douglas W. Mahoney3, Kelli N. Burger3, Lisa A. Boardman1, John B. Kisiel1 * 1 Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America, 2 Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, United States of America, 3 Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America ¤ Current address: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America * [Kisiel.john@mayo.edu](Kisiel.john@mayo.edu) (JBK); [Northrop.emmalee@mayo.edu](Northrop.emmalee@mayo.edu) (EJNA) Abstract 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 impro

FAQs

What is the goal of the study on plasma cfRNA in colorectal cancer?

Identify and validate potential plasma cell-free RNA candidates that could improve early colorectal cancer diagnosis across multiple study phases.

How were cfRNA candidates validated in the study?

Discovery used total RNA sequencing, phase 2 used targeted capture sequencing to validate selected exons, and phase 3 used RT-qPCR on previously identified candidates.

What did the study find regarding differential expression and marker validation?

Across cancers versus controls, many exons were differentially expressed, but fewer markers than expected were validated in independent patient sets, often drawing from prior published literature.

Sep 21, 2026

Uploaded by Ezra