A blood-based test for detection of advanced adenomas and colorectal cancer (DENEB): a multicentre diagnostic...

Colorectal cancer is the third most common and second deadliest cancer in the USA, but cases and deaths are preventable through appropriate screening. Blood-based screening tests hold promise for increasing participation in colorectal cancer screening; however, their preventive effect remains limited if premalignant lesions are missed. Detection of advanced adenomas is essential to reduce both colorectal cancer incidence and mortality. The DENEB study aimed to develop and evaluate a novel blood-based assay for this purpose.

The DENEB study was an outcome-enriched case-controlled multicentre biomarker study, conducted according to the Early Detection Research Network phase I-III framework to discover circulating biomarkers associated with colorectal cancer and advanced adenomas (phase I) and then train (phase II) and test a blood-based assay (phase III) in non-overlapping cohorts. Discovery cohort 1 (n=274; March 16, 2010 to Dec 20, 2017; Barcelona, Spain) and discovery cohort 2 (n=307; Sept 9, 2013 to Dec 26, 2017; Tsu, Japan) and in silico cohorts (n=99, GSE39833, Japan; n=61, GSE25609, Spain; and n=107, GSE41655, China) were used for biomarker discovery; clinical cohort 1 (n=535; July 2, 2018, to Sept 27, 2023; Barcelona, Spain and Tsu, Japan) was used for training and clinical cohort 2 (n=230; July 2, 2018, to Sept 27, 2023; Barcelona, Spain and Tsu, Japan) for testing. In each cohort, data from average-risk individuals (aged 18-100 years) with colonoscopy findings from screening or diagnostic colonoscopy were included in the analyses, including data from treatment-naive patients with colorectal cancer recruited before surgery to enrich for this outcome. Individuals were classified according to their colonoscopy findings and histopathology as having colorectal cancers, advanced adenomas, low-risk adenomas, or as non-disease controls (negative colonoscopy findings). To develop the test, candidate miRNAs overexpressed in the blood of patients with colorectal cancer and adenomas were identified via small RNA sequencing in discovery cohorts 1 and 2. The in-silico cohorts were used as a biological validation and reproducibility filter. Only those biomarkers with significant overexpression in at least two of the discovery and in-silico cohorts were retained. The identified biomarkers were measured with reverse transcription quantitative PCR (RT-qPCR) in clinical cohorts 1 and 2. In clinical cohort 1, using an XGBoost machine-learning model, we built and locked two separate models (one for colorectal cancer and one for advanced adenomas) and established their diagnostic thresholds. These thresholds were then tested in clinical cohort 2. The primary outcome measures were sensitivity for colorectal cancer and advanced adenomas, and specificity for advanced neoplasia assessed in all eligible participants aged 45 years or older. This study is registered with ClinicalTrial.gov, NCT06342440.

The blood-based test developed through discovery and training interrogated the transcriptional expression of 19 cell-free and 20 exosomal miRNAs using RT-qPCR. In the testing cohort (clinical cohort 2), the test showed an area under the receiver operating characteristic curve of 95% (95% CI 92-98) for distinguishing colorectal cancers and advanced adenomas from non-disease controls. Sensitivity for colorectal cancer of any stage was 91% (95% CI 80-96; 89% [75-96] for males and 95% [75-99] for females), while sensitivity for stage I, II, or III colorectal cancers was 92% (80-97). Sensitivity for advanced adenomas was 81% (69-89; 82% [67-91] for males and 79% [57-92] for females). The specificity for advanced neoplasia was 85% (95% CI 77-90). Specificity for a negative colonoscopy was 83% (95% CI 72-91).

These findings provide the rationale for advancing this assay into large-scale prospective studies to determine its performance, clinical utility, and potential role within population-based screening strategies.

National Institutes of Health and AIRC Foundation.