Novel DNA methylation biomarkers show high sensitivity and specificity for blood-based detection of colorectal cancer—a clinical biomarker discovery and validation study

Abstract

BackgroundEarly detection plays an essential role to reduce colorectal cancer (CRC) mortality. While current screening methods suffer from poor compliance, liquid biopsy-based strategies for cancer detection is rapidly gaining promise. Here, we describe the development of TriMeth, a minimal-invasive blood-based test for detection of early-stage colorectal cancer. The test is based on assessment of three tumour-specific DNA methylation markers in circulating cell-free DNA.ResultsA thorough multi-step biomarker discovery study based on DNA methylation profiles of more than 5000 tumours and blood cell populations identified CRC-specific DNA methylation markers. The DNA methylation patterns of biomarker candidates were validated by bisulfite sequencing and methylation-specific droplet digital PCR in CRC tumour tissue and peripheral blood leucocytes. The three best performing markers were first applied to plasma from 113 primarily early-stage CRC patients and 87 age- and gender-matched colonoscopy-verified controls. Based on this, the test scoring algorithm was locked, and then TriMeth was validated in an independent cohort comprising 143 CRC patients and 91 controls. Three DNA methylation markers, C9orf50, KCNQ5, and CLIP4, were identified, each capable of discriminating plasma from colorectal cancer patients and healthy individuals (areas under the curve 0.86, 0.91, and 0.88). When combined in the TriMeth test, an average sensitivity of 85% (218/256) was observed (stage I: 80% (33/41), stage II: 85% (121/143), stage III: 89% (49/55), and stage IV: 88% (15/17)) at 99% (176/178) specificity in two independent plasma cohorts.ConclusionTriMeth enables detection of early-stage colorectal cancer with high sensitivity and specificity. The reported results underline the potential utility of DNA methylation-based detection of circulating tumour DNA in the clinical management of colorectal cancer.

Epigenetic Analysis of Circulating Tumor DNA in Localized and Metastatic Prostate Cancer: Evaluation of Clinical Biomarker Potential

“…Extracted cell-free DNA was quantified by ddPCR using assays targeting two reference regions located on chromosome 1 (CF assay) and chromosome 3 (Chr3 assay), respectively, as previously described [35]. Both assays are located in regions that only rarely show copy number alterations in cancer, including PCa.…”

Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma

“…Studies show that tumor suppressor genes can be inhibited by hypermethylation, whereas oncogenes can be activated by hypomethylation [ 5 , 6 ]. Many studies have explored the abnormal DNA methylation in cervical [ 6 ] and breast [ 7 ] cancers, which may be possible markers for diagnoses, therapeutic targets, and prognosis [ 5 , 8 ]. The DNA methylation in KIRC has been studied for several years [ 9 ].…”

Triage May Improve Selection to Colonoscopy and Reduce the Number of Unnecessary Colonoscopies

“…Future screening concepts may focus on acceptability by the screening-relevant population. One such option may be screening based on various cancer-associated biomarkers in blood samples; emerging results have indicated that blood-based screening may improve the screening test sensitivity [ 23 , 24 , 25 , 26 , 27 , 28 ], in particular by combining various biomarker entities [ 29 ]. Blood-based screening appears to be preferred in comparison with feces-based testing [ 30 , 31 ], although the feces test performance is still the single most important attribute of a screening test [ 31 ].…”

“…Hitherto, the majority of emerging results on blood-based, cancer-associated biomarkers for early detection of malignant diseases, including CRC, have been based on studies of symptomatic patients at risk of having the disease or on patients with a diagnosis of the disease or even a mix of symptomatic and diagnosed patients [ 23 , 24 , 25 , 26 , 29 , 32 ]. It has been widely discussed whether such results might be interpreted to be used directly in screening settings.…”

“…One such opportunity is further validation of the Triage test suggested previously [ 49 , 50 ]. That specific test includes (1) the age of the subject; (2) the level of hemoglobin in the FIT test; and (3) combined biomarkers, which may be a mix of proteins and ctDNA methylations, mutations and/or fragmentations ( Figure 1 ) [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Particularly, the various possibilities for biomarker combinations require a high level of research attention to develop, test and validate the combinations with the highest and most reproducible impact.…”