Revolutionary liquid biopsy detects early colorectal cancer via RNA

Researchers at the University of Chicago have pioneered a groundbreaking liquid biopsy technique that analyses RNA modifications from gut microbes in blood samples to detect early-stage colorectal cancer with 95% accuracy. The innovative LIME-seq method represents a significant advance over current non-invasive testing approaches, offering unprecedented sensitivity for identifying the disease at its most treatable stages.

University of Chicago scientists have developed a revolutionary liquid biopsy test that could transform early colorectal cancer detection by analysing RNA modifications from gut microorganisms circulating in blood. The innovative approach, detailed in Nature Biotechnology on 8 July 2025, achieves remarkable 95% accuracy in identifying the earliest stages of the disease – a substantial improvement over existing non-invasive screening methods.

liquid biopsy test to detect early-stage colorectal cancer

Addressing limitations of current liquid biopsies

Traditional liquid biopsies detect cancer by identifying DNA fragments from tumour cells in blood samples. However, these approaches face significant challenges in early-stage disease detection when tumour cell death is minimal, resulting in insufficient circulating DNA for reliable analysis.

“That has been a major challenge for early diagnosis. You just don’t have enough tumour DNA released into the blood,” explained Dr Chuan He, the John T. Wilson Distinguished Service Professor of Chemistry and Professor of Biochemistry and Molecular Biology at the University of Chicago and senior author of the study. “That was a challenge for us and everyone else to do early diagnosis of colon cancer, so we decided to look at RNA instead.”

The research team’s solution involved developing low-input multiple methylation sequencing (LIME-seq), a novel technique that analyses RNA modifications rather than abundance levels. This approach offers superior stability and reliability compared to measuring simple RNA quantities, which can vary dramatically based on sample timing and preparation.

Microbiome revelations drive diagnostic breakthrough

The most striking discovery emerged when researchers examined blood samples from colorectal cancer patients provided by gastroenterologist Dr Marc Bissonnette. The team found they could detect not only RNA from human cells but also RNA from gut microorganisms – opening an entirely new avenue for cancer detection.

“We found that RNA released from microbes has substantial differences between cancer patients versus healthy individuals,” Dr He noted. “In the gut when you have a tumour growing, the nearby microbiome must be reshaped in response to that inflammation. That affects the nearby microbes.”

The microbiome’s rapid cellular turnover proved advantageous for early detection. Microbial populations refresh much more frequently than human cells, releasing RNA fragments into the bloodstream at higher rates. This phenomenon enables detection of cancerous activity much earlier than tests relying solely on human tumour cell DNA.

Superior performance across cancer stages

The research involved comprehensive analysis of blood samples from 27 colorectal cancer patients across various stages (five stage 0, six stage I, eight stage II, and eight stage III) alongside 36 age-matched and sex-matched non-cancer controls. LIME-seq demonstrated exceptional performance, achieving 95% overall accuracy whilst maintaining high sensitivity even for the earliest disease stages.

Commercial stool-based tests measuring DNA or RNA abundance typically achieve approximately 90% accuracy for later-stage cancers but drop below 50% accuracy for early stages. The new RNA modification-based approach maintained consistent accuracy across all cancer stages, representing a significant diagnostic advancement.

Statistical validation through leave-one-out cross-validation yielded an area under the curve (AUC) of 0.98, substantially exceeding the 0.77 AUC achieved by models based solely on microbial abundance. Under rigorous validation frameworks including bootstrapping and k-fold cross-validation, the model maintained high accuracy with an AUC of 0.92.

Clinical implications and mechanistic insights

The authors noted that “RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.” Their analysis revealed that higher modification levels in microbiome RNA correlate with increased metabolic activity and external stress, suggesting dysregulation of microbiomes in cancer patients.

Using Shapley additive explanations (SHAP) analysis, researchers identified key microbial contributors to their diagnostic model. Among the most significant organisms, Burkholderia emerged as distinctly enriched in cancer patients, whilst Clostridium showed reduced methylation levels – organisms that align with previous research findings on cancer-associated microbiome changes.

Validation and future directions

The team validated their approach across two independent cohorts, achieving AUCs of 0.89 and 0.93 respectively. Notably, the model effectively distinguished both adenoma and stage I colorectal cancer from non-cancer controls, demonstrating robust early-detection capabilities.

Preliminary testing on pancreatic cancer samples suggested broader applicability beyond colorectal malignancies, though the researchers emphasise that further validation in larger cohorts is necessary.

The authors concluded that “methylation levels in microbiome-derived cfRNA are effective and promising biomarkers for CRC diagnosis, offering a notable advantage over microbial abundance profiles of cfRNA or cfDNA.” This approach achieved high accuracy particularly at the earliest disease stages, when therapeutic interventions are most effective.

Reference

Ju, C. W., Lyu, R., Li, H., et. al. (2025). Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples. Nature Biotechnology. https://doi.org/10.1038/s41587-025-02731-8