New Bioinformatics Method Revolutionizes Colorectal Cancer Detection with Stool mRNA Markers

New Bioinformatics Method Revolutionizes CRC Detection

A recent peer-reviewed study published in Scientific Reports, part of the renowned Nature Portfolio, unveils an innovative bioinformatics approach for identifying messenger RNA (mRNA) biomarkers found in stool samples. This promising method shows significant potential for non-invasive detection of colorectal cancer (CRC) and advanced adenomas (AA), the most prevalent precancerous lesions.

The research was orchestrated by scientists associated with El Capitan Biosciences (ECB), in collaboration with various partners. In this investigation, a dual-step methodology was adopted. Initially, a computational screen scrutinizing public tissue databases facilitated the ranking of genes based on their differential expression in colorectal cancer compared to normal colon tissue. Following this analysis, the most promising candidate genes identified through this in silico method underwent validation via RT-qPCR on a cohort of 114 clinical stool samples, which included 33 CRC samples, 28 from individuals with advanced adenomas, and 53 control samples.

The results were impressive. The multi-gene mRNA panel demonstrated a robust predictive performance, achieving an Area Under the Curve (AUC) of 0.94 for distinguishing CRC patients from controls, with a sensitivity of 75.5% and specificity reaching 95%. Equally noteworthy was the panel's capacity to detect advanced adenomas, which are often missed by conventional non-invasive tests. This detection was marked by an AUC of 0.83, manifesting a sensitivity of 55.8% and specificity of 92.6%. This level of sensitivity for advanced adenomas is significantly better compared to the 10-40% sensitivity typically associated with fecal immunochemical tests (FIT).

The study's findings underscore the efficacy of leveraging expansive public genomic datasets for prioritizing biomarker candidates, which can streamline clinical validation processes for the development of next-generation diagnostics. Dr. Wenying Pan, Co-founder and CEO of El Capitan Biosciences, emphasized the importance of improving the detection rates of precancerous lesions, stating, "This is a critical unmet need in colorectal cancer screening, as timely intervention can prevent the progression to cancer."

Building on ECB's expertise in stool mRNA testing, the company has pioneered a proprietary platform engineered to extract human-host RNA from stool samples, coupled with a comprehensive whole-transcriptome biomarker discovery platform. This innovation not only fills a significant gap in the available understanding of the human stool transcriptome but also offers pharmaceutical companies investigating intestinal diseases a more holistic omics data perspective. When combined with ECB's unique bioinformatics algorithms, this platform empowers researchers to unearth novel biomarkers and targets effectively. This advancement is positioned to expedite drug target discovery and enhance the clinical trial efficiencies and success rates for ECB’s partners.

The study—entitled ``Bioinformatic screen with clinical validation for the identification of novel stool based mRNA biomarkers for the detection of colorectal lesions including advanced adenoma''—is accessible online with the DOI 10.1038/s41598-025-13074-4.

Disclaimer: The investigational approach discussed has not received clearance or approval from the U.S. FDA and is not available for clinical use.

About El Capitan Biosciences

El Capitan Biosciences (ECB), located in California, concentrates on the discovery of gut multi-omics biomarkers along with the production of diagnostic and screening products for various gastrointestinal diseases. Their cutting-edge method for stool RNA extraction, alongside a whole-transcriptome biomarker discovery framework, heightens the progression of clinical solutions directed at early disease detection, precision medication, and monitoring of intestinal disorders. For additional information, visit www.elcapitanbio.com.