Detection of colorectal cancer in urine using DNA methylation analysis

AbstractColorectal cancer (CRC) is the second leading cause for cancer-related death globally. Clinically, there is an urgent need for non-invasive CRC detection. This study assessed the feasibility of CRC detection by analysis of tumor-derived methylated DNA fragments in urine. Urine samples, including both unfractioned and supernatant urine fractions, of 92 CRC patients and 63 healthy volunteers were analyzed for DNA methylation levels of 6 CRC-associated markers (SEPT9, TMEFF2, SDC2, NDRG4, VIM and ALX4). Optimal marker panels were determined by two statistical approaches. Methylation levels of SEPT9 were significantly increased in urine supernatant of CRC patients compared to controls (p < 0.0001). Methylation analysis in unfractioned urine appeared inaccurate. Following multivariate logistic regression and classification and regression tree analysis, a marker panel consisting of SEPT9 and SDC2 was able to detect up to 70% of CRC cases in urine supernatant at 86% specificity. First evidence is provided for CRC detection in urine by SEPT9 methylation analysis, which combined with SDC2 allows for an optimal differentiation between CRC patients and controls. Urine therefore provides a promising liquid biopsy for non-invasive CRC detection.

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Multiplexed DNA Methylation Analysis in Colorectal Cancer Using Liquid Biopsy and Its Diagnostic and Predictive Value

Current Issues in Molecular Biology ◽

10.3390/cimb43030100 ◽

2021 ◽

Vol 43 (3) ◽

pp. 1419-1435

Author(s):

Walter Pulverer ◽

Kristi Kruusmaa ◽

Silvia Schönthaler ◽

Jasmin Huber ◽

Marko Bitenc ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Therapy Monitoring ◽

Methylation Status ◽

Methylation Analysis ◽

Microarray Experiments ◽

Specific Pcr ◽

Colonic Adenomas ◽

Methylation Sensitive Restriction Enzyme ◽

Dna Methylation Analysis

Early diagnosis of colorectal cancer (CRC) is of high importance as prognosis depends on tumour stage at the time of diagnosis. Detection of tumour-specific DNA methylation marks in cfDNA has several advantages over other approaches and has great potential for solving diagnostic needs. We report here the identification of DNA methylation biomarkers for CRC and give insights in our methylation-sensitive restriction enzyme coupled qPCR (MSRE-qPCR) system. Targeted microarrays were used to investigate the DNA methylation status of 360 cancer-associated genes. Validation was done by qPCR-based approaches. A focus was on investigating marker performance in cfDNA from 88 patients (44 CRC, 44 controls). Finally, the workflow was scaled-up to perform 180plex analysis on 110 cfDNA samples, to identify a DNA methylation signature for advanced colonic adenomas (AA). A DNA methylation signature (n = 44) was deduced from microarray experiments and confirmed by quantitative methylation-specific PCR (qMSP) and by MSRE-qPCR, providing for six genes’ single areas under the curve (AUC) values of >0.85 (WT1, PENK, SPARC, GDNF, TMEFF2, DCC). A subset of the signatures can be used for patient stratification and therapy monitoring for progressed CRC with liver metastasis using cfDNA. Furthermore, we identified a 35-plex classifier for the identification of AAs with an AUC of 0.80.

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13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients

Journal of Clinical Medicine ◽

10.3390/jcm8122107 ◽

2019 ◽

Vol 8 (12) ◽

pp. 2107 ◽

Cited By ~ 4

Author(s):

Davide B. Gissi ◽

Achille Tarsitano ◽

Andrea Gabusi ◽

Roberto Rossi ◽

Giuseppe Attardo ◽

...

Keyword(s):

Dna Methylation ◽

Oral Cancer ◽

Cancer Treatment ◽

Sample Collection ◽

Methylation Analysis ◽

Non Invasive ◽

Locoregional Relapse ◽

Positive Score ◽

Dna Methylation Analysis

Background: This study aimed to evaluate the prognostic value of a non-invasive sampling procedure based on 13-gene DNA methylation analysis in the follow-up of patients previously treated for oral squamous cell carcinoma (OSCC). Methods: The study population included 49 consecutive patients treated for OSCC. Oral brushing sample collection was performed at two different times: before any cancer treatment in the tumor mass and during patient follow-up almost 6 months after OSCC treatment, within the regenerative area after OSCC resection. Each sample was considered positive or negative in relation to a predefined cut-off value. Results: Before any cancer treatment, 47/49 specimens exceeded the score and were considered as positive. Six months after OSCC resection, 16/49 specimens also had positive scores in the samples collected from the regenerative area. During the follow-up period, 7/49 patients developed locoregional relapse: 6/7 patients had a positive score in the regenerative area after OSCC resection. The presence of a positive score after oral cancer treatment was the most powerful variable related to the appearance of locoregional relapse. Conclusion: 13-gene DNA methylation analysis by oral brushing may have a clinical application as a prognostic non-invasive tool in the follow-up of patients surgically treated for OSCC.

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On-Chip DNA Methylation Analysis Using Osmium Complexation

Journal of Nucleic Acids ◽

10.4061/2011/480570 ◽

2011 ◽

Vol 2011 ◽

pp. 1-5 ◽

Cited By ~ 4

Author(s):

Kaori Sugizaki ◽

Tadashi Umemoto ◽

Akimitsu Okamoto

Keyword(s):

Dna Methylation ◽

Research Subject ◽

Methylation Analysis ◽

Methylated Dna ◽

Chemical Assay ◽

Challenging Research ◽

Detection Probe ◽

On Chip ◽

Dna Strand ◽

Dna Methylation Analysis

The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.

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