Development and validation of a novel epigenetic signature for predicting prognosis in colon cancer

Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. Public microarray datasets were acquired from th...

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Published inJournal of cellular physiology Vol. 235; no. 11; pp. 8714 - 8723
Main Authors Luo, Dakui, Liu, Qi, Shan, Zezhi, Cai, Sanjun, Li, Qingguo, Li, Xinxiang
Format Journal Article
LanguageEnglish
Published United States Wiley Subscription Services, Inc 01.11.2020
Subjects
Biomarkers
Biomarkers, Tumor - genetics
Carcinogenesis
Carcinogens
Chemotherapy
Chromatin
Colon
Colon cancer
Colonic Neoplasms - diagnosis
Colonic Neoplasms - genetics
Colonic Neoplasms - pathology
Colorectal cancer
DNA microarrays
epigenetic regulation
Epigenetics
Epigenomics - methods
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation, Neoplastic
gene signature
GEO database
Humans
Medical prognosis
Neoplasm Recurrence, Local - diagnosis
Neoplasm Recurrence, Local - genetics
Nomograms
Prognosis
relapse‐free survival
Reproducibility of Results
Risk
Risk groups
ROC Curve
Time dependence
Training
relapse-free survival
GEO database
gene signature
epigenetic regulation
colon cancer
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Abstract Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high‐risk and low‐risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time‐dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow‐up and aggressive therapeutic intervention. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. This biomarker would aid in identifying patients who require an intensive follow‐up and aggressive therapeutic intervention.
AbstractList Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high‐risk and low‐risk groups in training series based on a set of 11 epigenetic factors ( p  < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series ( p  < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p  = .018), and entire series ( p  < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time‐dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow‐up and aggressive therapeutic intervention.
Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse-free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high-risk and low-risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time-dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow-up and aggressive therapeutic intervention.
Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse-free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high-risk and low-risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time-dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow-up and aggressive therapeutic intervention.Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse-free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high-risk and low-risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time-dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow-up and aggressive therapeutic intervention.
Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. Public microarray datasets were acquired from the Gene Expression Omnibus databases: GSE39582, GSE17538, GSE33113, and GSE37892 set. Patients from GSE39582 set were randomized 1:1 into training and internal validation series. Patients were divided into high‐risk and low‐risk groups in training series based on a set of 11 epigenetic factors (p < .001). The good reproducibility for the prognostic value of the epigenetic signature was confirmed in the internal validation series (p < .001), external validation series (a combination of GSE17538 set, GSE33113 set, and GSE37892 set; p = .018), and entire series (p < .001). Furthermore, a nomogram, which integrated the epigenetic signature, pathological stage, and postoperative chemotherapy, was developed based on the GSE39582 set. The time‐dependent receiver operating characteristic curve at 1 year demonstrated that the comprehensive signature presented superior prognostic value than the pathological stage. In conclusion, an epigenetic signature, which could be utilized to divide colon cancer patients into two groups with significantly different risk of relapse, was established. This biomarker would aid in identifying patients who require an intensive follow‐up and aggressive therapeutic intervention. The present study aimed to develop a novel epigenetic signature for evaluating the relapse‐free survival of colon cancer patients. This biomarker would aid in identifying patients who require an intensive follow‐up and aggressive therapeutic intervention.
Author Cai, Sanjun
Li, Xinxiang
Shan, Zezhi
Li, Qingguo
Luo, Dakui
Liu, Qi
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CitedBy_id crossref_primary_10_1038_s41598_023_39412_y
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Keywords relapse-free survival
GEO database
gene signature
epigenetic regulation
colon cancer
Language English
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Notes Dakui Luo, Qi Liu, and Zezhi Shan contributed equally.
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Snippet Epigenetic factors play a critical role in carcinogenesis by imparting a distinct feature to the chromatin architecture. The present study aimed to develop a...
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SubjectTerms Biomarkers
Biomarkers, Tumor - genetics
Carcinogenesis
Carcinogens
Chemotherapy
Chromatin
Colon
Colon cancer
Colonic Neoplasms - diagnosis
Colonic Neoplasms - genetics
Colonic Neoplasms - pathology
Colorectal cancer
DNA microarrays
epigenetic regulation
Epigenetics
Epigenomics - methods
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation, Neoplastic
gene signature
GEO database
Humans
Medical prognosis
Neoplasm Recurrence, Local - diagnosis
Neoplasm Recurrence, Local - genetics
Nomograms
Prognosis
relapse‐free survival
Reproducibility of Results
Risk
Risk groups
ROC Curve
Time dependence
Training
Title Development and validation of a novel epigenetic signature for predicting prognosis in colon cancer
URI https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fjcp.29715
https://www.ncbi.nlm.nih.gov/pubmed/32329069
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https://www.proquest.com/docview/2394888062
Volume 235
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