Screening for Colorectal Cancer Based on the Promoter Methylation Status of the Septin 9 Gene in Plasma Cell Free DNA

BACKGROUND: Investigating aberrant tumor-specific methylation in plasma cell-free DNA provides a promising and noninvasive biomarker for cancer detection. OBJECTIVE: We aimed to investigate methylation status of some promoter regions in the plasma and tumor tissues to find biomarkers for early detection of colorectal cancer. METHODS: This case-control study on seventy colorectal cancer patients and fifty matched healthy controls used Methylation-Specific High-Resolution Melting Curve analysis to evaluate the methylation of the selected promoter regions in converted genomic tissue DNA and plasma cfDNA. RESULTS: The methylation levels in selected regions of SPG20 (+24375 to +24680, +24209 to +24399, and +23625 to +23883), SNCA (+807 to +1013, +7 to +162, and -180 to +7), FBN1 (+223 to +429, +1 to +245, and -18 to -175), ITF2 (+296 to +436 and -180 to +55), SEPT9 (-914412 to -91590 and -99083 to -92264), and MLH1 (-13 to +22) were significantly higher in tumor tissues compared with normal adjacent tissues. The methylation levels of FBN1, ITF2, SNCA, and SPG20 promoters were significantly higher in the patient’s plasma compared to patient’s normal tissue and plasma of healthy control subjects. FBN1, SPG20, and SEPT9 promoter methylation had a good diagnostic performance for discriminating CRC tissues from normal adjacent tissues (AUC > 0.8). A panel of SPG20, FBN1, and SEPT9 methylation had a higher diagnostic value than that of any single biomarker and other panels in tissue-based assay (AUC > 0.9). The methylation of FBN1(a) and SPG20(a) regions, as the closest region to the first coding sequence (CDS), had a good diagnostic performance in plasma cfDNA (AUC > 0.8) while a panel consisted of FBN1(a) and SPG20(a) regions showed excellent diagnostic performance for CRC detection in plasma cfDNA (AUC > 0.9). CONCLUSION: Methylation of FBN1(a) and SPG20(a) promoter regions in the plasma cfDNA can be an excellent simple, non-invasive blood-based test for early detection of CRC.

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Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA

BMC Cancer ◽

10.1186/s12885-019-6003-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Nathan Wan ◽

David Weinberg ◽

Tzu-Yu Liu ◽

Katherine Niehaus ◽

Eric A. Ariazi ◽

...

Keyword(s):

Colorectal Cancer ◽

Machine Learning ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Plasma Cell ◽

Early Stage ◽

Whole Genome ◽

Cell Free Dna ◽

Free Dna

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Plasma cell-free DNA and fraction of circulating KRAS mutations as prognostic in patients with metastatic colorectal cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2014.32.3_suppl.490 ◽

2014 ◽

Vol 32 (3_suppl) ◽

pp. 490-490 ◽

Cited By ~ 2

Author(s):

David Sefrioui ◽

Nasrin Vasseur ◽

Richard Sesboüé ◽

France Blanchard ◽

Alice Oden-Gangloff ◽

...

Keyword(s):

Colorectal Cancer ◽

Metastatic Colorectal Cancer ◽

Plasma Cell ◽

Circulating Tumor Dna ◽

Dna Fragments ◽

Wild Type ◽

Kras Mutations ◽

Cell Free Dna ◽

Free Dna ◽

Tumor Dna

490 Background: It has been suggested that detection of circulating tumor DNA may be relevant in patients with metastatic colorectal cancer (mCRC). The main objective of the present study was to evaluate a method based on the TaqMan Mutation Detection Assay (TMDA) for the detection of circulating KRAS mutations in mCRC patients. Moreover, we also investigated the prognostic impact of the plasma cell-free DNA and the fraction of circulating KRAS mutations. Methods: The study was conducted from April to July 2013 and plasma samples were prospectively collected in a series of 35 mCRC patients treated with chemotherapy (CT). QIAamp Circulating Nucleic Acid kit was used for DNA extraction and Quant-iT High Sensitivity dsDNA Assay for cf-DNA quantification. Detection of circulating tumor DNA was based on the KRAS mutations detected in tumour and was performed in plasma by the castPCR Technology TMDA. Response to CT was assessed according to RECIST criteria. The results of plasma cf-DNA and level of mutant DNA fragments were correlated with response and 3-months survival. Results: We isolated and quantified plasma cf-DNA in all patients with a mean concentration of 106 ng/mL. Among them, 18 were wild-type and 17 mutated for KRAS in the tumour. Detection of circulating KRAS mutations was performed with TMDA in 23 patients (10 KRAS wild-type and 13 KRAS mutated). The sensitivity was 62% (8/13) and specificity 100% (0/10) with a level of circulating mutant DNA fragments ranging from 0 to 29%. Plasma cf-DNA and level of circulating mutant DNA were both significantly correlated with the 3-months survival (mean 36 versus 524 ng/mL, p=0.0015 and 2% versus 29%, p<0.0001). There was a non significant trend for response to CT (respectively p=0.14 and p=0.12). Conclusions: TMDA method is a simple, accurate and non-invasive tool for the detection of circulating tumor DNA. Our preliminary results also suggest that plasma cf-DNA and fraction of mutant DNA fragments could be prognostic markers in mCRC patients.

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Differential survival trends of stage II colorectal cancer patients relate to promoter methylation status of PCDH10, SPARC, and UCHL1

Modern Pathology ◽

10.1038/modpathol.2013.204 ◽

2013 ◽

Vol 27 (6) ◽

pp. 906-915 ◽

Cited By ~ 16

Author(s):

Ellen Heitzer ◽

Monika Artl ◽

Martin Filipits ◽

Margit Resel ◽

Ricarda Graf ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Patients ◽

Promoter Methylation ◽

Methylation Status ◽

Stage Ii ◽

Differential Survival ◽

Promoter Methylation Status ◽

Stage Ii Colorectal Cancer ◽

Colorectal Cancer Patients

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Gene-Specific Methylation: Potential Markers for Colorectal Cancer

The International Journal of Biological Markers ◽

10.1177/172460080902400109 ◽

2009 ◽

Vol 24 (1) ◽

pp. 57-62 ◽

Cited By ~ 1

Author(s):

Jyothi S. Prabhu ◽

Aruna Korlimarla ◽

Arindam Banerjee ◽

Shivangi Wani ◽

K Payal ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Polymerase Chain Reaction ◽

Promoter Methylation ◽

Methylation Status ◽

Epigenetic Mechanism ◽

Aberrant Methylation ◽

Chain Reaction ◽

Promoter Methylation Status ◽

Polymerase Chain

Purpose Aberrant methylation of the promoter region is associated with silencing of many genes in neoplasia. CpG island methylation is an epigenetic mechanism for transcriptional silencing that occurs at various stages of colon tumorigenesis. In this study, we tested the promoter methylation and expression of seven genes from various pathways of DNA repair, apoptosis and inflammation, i.e., sFRP1, MLH1, RASSF1A, CDA, v-fgr, LYN-B, and TNFR10d. Method The genes were analyzed by quantitative polymerase chain reaction for the level of gene expression. The promoter methylation status of the genes was studied by methylation-specific polymerase chain reaction. Result The correlation of promoter methylation status with suppressed gene expression patterns suggested a potential role for the silencing these genes in colon cancer progression. Conclusion Promoter methylations of the studied genes could be explored as promising biomarkers for new diagnostic, prognostic and therapeutic targets of colorectal cancer.

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