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Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer.

Roperch JP, Incitti R, Forbin S, Bard F, Mansour H, Mesli F, Baumgaertner I, Brunetti F, Sobhani I - BMC Cancer (2013)

Bottom Line: We assessed the results by receiver operating characteristic curve (ROC), using cumulative methylation index (CMI) as variable threshold.We optimized a QM-MSP for simultaneously quantifying their methylation levels.Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination.

View Article: PubMed Central - HTML - PubMed

Affiliation: Profilome SAS, Paris Biotech 24 rue du Faubourg St Jacques, Paris 75014, France. jp.roperch@profilome-sas.com.

ABSTRACT

Background: DNA methylation is a well-known epigenetic mechanism involved in epigenetic gene regulation. Several genes were reported hypermethylated in CRC, althought no gene marker was proven to be individually of sufficient sensitivity or specificity in routine clinical practice. Here, we identified novel epigenetic markers and assessed their combined use for diagnostic accuracy.

Methods: We used methylation arrays on samples from several effluents to characterize methylation profiles in CRC samples and controls, as established by colonoscopy and pathology findings, and selected two differentially methylated candidate epigenetic genes (NPY, PENK). To this gene panel we added WIF, on the basis of being reported in literature as silenced by promoter hypermethylation in several cancers, including CRC. We measured their methylation degrees by quantitative multiplex-methylation specific PCR (QM-MSP) on 15 paired carcinomas and adjacent non-cancerous colorectal tissues and we subsequently performed a clinical validation on two different series of 266 serums, subdivided in 32 CRC, 26 polyps, 47 other cancers and 161 with normal colonoscopy. We assessed the results by receiver operating characteristic curve (ROC), using cumulative methylation index (CMI) as variable threshold.

Results: We obtained CRC detection on tissues with both sensitivity and specificity of 100%. On serum CRC samples, we obtained sensitivity/specificity values of, e.g., 87%/80%, 78%/90% and 59%/95%, and negative predictive value/positive predictive value figures of 97%/47%, 95%/61% and 92%/70%. On serum samples from other cancers we obtained sensitivity/specificity of, e.g, 89%/25%, 43%/80% and 28%/91%.

Conclusions: We showed the potential of NPY, PENK, and WIF1 as combined epigenetic markers for CRC diagnosis, both in tissue and serum and tested their use as serum biomarkers in other cancers. We optimized a QM-MSP for simultaneously quantifying their methylation levels. Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination. This panel of markers, if validated, can also be a cost effective screening tool for the detection of asymptomatic cancer patients for colonoscopy.

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ROC curve relative to the cumulative methylation index. Sum of three (WIF1, NPY, PENK) methylation indexes are used to establish ROC curves corresponding to Series 1 (A), Series 2 (B), total of both series (C) for CRC and Series 3 (D) for other cancers.
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Figure 4: ROC curve relative to the cumulative methylation index. Sum of three (WIF1, NPY, PENK) methylation indexes are used to establish ROC curves corresponding to Series 1 (A), Series 2 (B), total of both series (C) for CRC and Series 3 (D) for other cancers.

Mentions: CMI values were used for calculating the Specificity (Sp) versus the Sensitivity (Se) depending on various thresholds and the ROC (Receiver Operating Characteristic) diagrams were constructed. For each of the two series, we obtained similar ROC profiles for CRC detection (Figure 4A, 4B). To highlight key trade-offs between Se and Sp, we consider CMI thresholds for having high Se (e.g. Se about 90%) and high Sp (e.g. Sp about 90% or Sp about 95%). So, pooling the two series (Figure 4C), we obtain sensitivity/specificity figures of, respectively, 87%/80%, 78%/90% and 59%/95% (Table 3), and NPV/PPV figures of 97%/47%, 95%/61% and 92%/70% (as computed without factoring the prevalence, since the population is already symptomatic). No significant relationship could be identified between serum CMI rates and TNM staging (Additional file 6: Figure S3).


Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer.

Roperch JP, Incitti R, Forbin S, Bard F, Mansour H, Mesli F, Baumgaertner I, Brunetti F, Sobhani I - BMC Cancer (2013)

ROC curve relative to the cumulative methylation index. Sum of three (WIF1, NPY, PENK) methylation indexes are used to establish ROC curves corresponding to Series 1 (A), Series 2 (B), total of both series (C) for CRC and Series 3 (D) for other cancers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219483&req=5

Figure 4: ROC curve relative to the cumulative methylation index. Sum of three (WIF1, NPY, PENK) methylation indexes are used to establish ROC curves corresponding to Series 1 (A), Series 2 (B), total of both series (C) for CRC and Series 3 (D) for other cancers.
Mentions: CMI values were used for calculating the Specificity (Sp) versus the Sensitivity (Se) depending on various thresholds and the ROC (Receiver Operating Characteristic) diagrams were constructed. For each of the two series, we obtained similar ROC profiles for CRC detection (Figure 4A, 4B). To highlight key trade-offs between Se and Sp, we consider CMI thresholds for having high Se (e.g. Se about 90%) and high Sp (e.g. Sp about 90% or Sp about 95%). So, pooling the two series (Figure 4C), we obtain sensitivity/specificity figures of, respectively, 87%/80%, 78%/90% and 59%/95% (Table 3), and NPV/PPV figures of 97%/47%, 95%/61% and 92%/70% (as computed without factoring the prevalence, since the population is already symptomatic). No significant relationship could be identified between serum CMI rates and TNM staging (Additional file 6: Figure S3).

Bottom Line: We assessed the results by receiver operating characteristic curve (ROC), using cumulative methylation index (CMI) as variable threshold.We optimized a QM-MSP for simultaneously quantifying their methylation levels.Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination.

View Article: PubMed Central - HTML - PubMed

Affiliation: Profilome SAS, Paris Biotech 24 rue du Faubourg St Jacques, Paris 75014, France. jp.roperch@profilome-sas.com.

ABSTRACT

Background: DNA methylation is a well-known epigenetic mechanism involved in epigenetic gene regulation. Several genes were reported hypermethylated in CRC, althought no gene marker was proven to be individually of sufficient sensitivity or specificity in routine clinical practice. Here, we identified novel epigenetic markers and assessed their combined use for diagnostic accuracy.

Methods: We used methylation arrays on samples from several effluents to characterize methylation profiles in CRC samples and controls, as established by colonoscopy and pathology findings, and selected two differentially methylated candidate epigenetic genes (NPY, PENK). To this gene panel we added WIF, on the basis of being reported in literature as silenced by promoter hypermethylation in several cancers, including CRC. We measured their methylation degrees by quantitative multiplex-methylation specific PCR (QM-MSP) on 15 paired carcinomas and adjacent non-cancerous colorectal tissues and we subsequently performed a clinical validation on two different series of 266 serums, subdivided in 32 CRC, 26 polyps, 47 other cancers and 161 with normal colonoscopy. We assessed the results by receiver operating characteristic curve (ROC), using cumulative methylation index (CMI) as variable threshold.

Results: We obtained CRC detection on tissues with both sensitivity and specificity of 100%. On serum CRC samples, we obtained sensitivity/specificity values of, e.g., 87%/80%, 78%/90% and 59%/95%, and negative predictive value/positive predictive value figures of 97%/47%, 95%/61% and 92%/70%. On serum samples from other cancers we obtained sensitivity/specificity of, e.g, 89%/25%, 43%/80% and 28%/91%.

Conclusions: We showed the potential of NPY, PENK, and WIF1 as combined epigenetic markers for CRC diagnosis, both in tissue and serum and tested their use as serum biomarkers in other cancers. We optimized a QM-MSP for simultaneously quantifying their methylation levels. Our assay can be an effective blood test for patients where CRC risk is present but difficult to assess (e.g. mild symptoms with no CRC family history) and who would therefore not necessarily choose to go for further examination. This panel of markers, if validated, can also be a cost effective screening tool for the detection of asymptomatic cancer patients for colonoscopy.

Show MeSH
Related in: MedlinePlus