Gene pair based prognostic signature for colorectal colon cancer

Shu, Ping; Wu, Jianping; Tong, Yao; Xu, Chunxia; Zhang, Xingguo

doi:10.1097/md.0000000000012788

Cited by 12 publications

(4 citation statements)

References 36 publications

(41 reference statements)

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“…The RPS6KA5 gene encodes for a tyrosine kinase and has been indicated as a biomarker for colon cancer (38) through interaction with hsa-miR-130a (39). In our colon-specific network, the lncRNA MIR17HG sponges hsa-miR-130a and interacts with RPS6KA5.…”

Section: Discussionmentioning

confidence: 87%

Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction

Vieira

Jorge²,

Sousa

et al. 2021

Front. Oncol.

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BackgroundColorectal cancer (CRC) is a heterogeneous cancer. Its treatment depends on its anatomical site and distinguishes between colon, rectum, and rectosigmoid junction cancer. This study aimed to identify diagnostic and prognostic biomarkers using networks of CRC-associated transcripts that can be built based on competing endogenous RNAs (ceRNA).MethodsRNA expression and clinical information data of patients with colon, rectum, and rectosigmoid junction cancer were obtained from The Cancer Genome Atlas (TCGA). The RNA expression profiles were assessed through bioinformatics analysis, and a ceRNA was constructed for each CRC site. A functional enrichment analysis was performed to assess the functional roles of the ceRNA networks in the prognosis of colon, rectum, and rectosigmoid junction cancer. Finally, to verify the ceRNA impact on prognosis, an overall survival analysis was performed.ResultsThe study identified various CRC site-specific prognosis biomarkers: hsa-miR-1271-5p, NRG1, hsa-miR-130a-3p, SNHG16, and hsa-miR-495-3p in the colon; E2F8 in the rectum and DMD and hsa-miR-130b-3p in the rectosigmoid junction. We also identified different biological pathways that highlight differences in CRC behavior at different anatomical sites, thus reinforcing the importance of correctly identifying the tumor site.ConclusionsSeveral potential prognostic markers for colon, rectum, and rectosigmoid junction cancer were found. CeRNA networks could provide better understanding of the differences between, and common factors in, prognosis of colon, rectum, and rectosigmoid junction cancer.

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Section: Discussionmentioning

confidence: 87%

Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction

Vieira

Jorge²,

Sousa

et al. 2021

Front. Oncol.

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“…scaling and normalization) is required, and this method could produce reliable results in various studies. 49–51 Therefore, our prognostic characteristics can be used as precision therapy estimates of BC life and can be easily converted to clinical application.…”

Section: Discussionmentioning

confidence: 99%

Development and verification of a personalized immune prognostic feature in breast cancer

Wang

2020

Exp Biol Med (Maywood)

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Immune-related genes have great potential as prognostic markers in many types of cancer. Therefore, we have attempted to develop immune-related gene markers to enhance the prognosis of breast cancer; 1159 samples of breast cancer gene expression data and clinical follow-up messages were downloaded from TCGA and GEO, which were classified into training set, test set, and validation set. In the training set, the gene pairs are established according to the relative expression levels between 320 immune genes, in which the prognosis-related gene pairs are screened, and Lasso is used for feature selection to screen the robust biomarkers. A prognostic model of immune gene correlation was set up and verified. Sixty-six IRGPs were obtained, and 17-IRGPs signature was established. 17-IRGPs signature is an independent prognostic indicator for BC patients, which can stratify the risk in the training set and testing series, and AUC of five years survival was greater than 0.7; 17-IRGPs signature had better classification performance in patients with advanced BC. In addition, we compared the prognostic characteristics of 17-IRGPs with four reported breast cancers and clinical stages; 17-IRGPs achieved the highest average C index (0.7, P < 0.05), and functional analysis found that the dysregulated immune environment may be the cause of the observed difference in survival between patient groups defined by our characteristics. 17-IRGPs signature was constructed as a newly developed prognostic indicator to calculate the survival of BC patients. Impact statement Breast cancer is among the highest prevalent malignant tumors worldwide with a low survival ratio. Immune-related genes have great potential as prognostic indicator in many types of tumors. Therefore, we have attempted to develop immune-related gene markers to enhance the prognosis of breast cancer. 17-IRGPs signature was constructed as a newly developed prognostic indicator to predict the survival of BC patients.

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“…So, there were many studies by others and us developing several prognostic and predictive biomarkers based on this method for different cancers [38][39][40][41][42][43][44][45][46][47][48][49][50][51]. It indicated that the clinical applicability of the signatures based on the robust qualitative REO information extracted from the quantitative measurements of gene expression, rather than the "exact" quantitative measurements themselves [52].…”

Section: Discussionmentioning

confidence: 99%

A Qualitative Transcriptional Signature for Predicting Microsatellite Instability Status of Right-sided Colon Cancer

Guo

et al. 2019

Preprint

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Background: Microsatellite instability (MSI) accounts for about 15% of colorectal cancer and is associated with prognosis. Today, MSI is usually detected by polymerase chain reaction amplification of specific microsatellite markers. However, the instability is identified by comparing the length of microsatellite repeats in tumor and normal samples. In this work, we developed a qualitative transcriptional signature to individually predict MSI status for right-sided colon cancer (RCC) based on tumor samples. Results: Using RCC samples, based on the relative expression orderings (REOs) of gene pairs, we extracted a signature consisting of 10 gene pairs (10-GPS) to predict MSI status for RCC through a feature selection process. A sample is predicted as MSI when the gene expression orderings of at least 7 gene pairs vote for MSI; otherwise the microsatellite stability (MSS). The classification performance reached the largest F-score in the training dataset. This signature was verified in four independent datasets of RCCs with the F-scores of 1, 0.9630, 0.9412 and 0.8798, respectively. Additionally, the hierarchical clustering analyses and molecular features also supported the correctness of the reclassifications of the MSI status by 10-GPS. Conclusions: The qualitative transcriptional signature can be used to classify MSI status of RCC samples at the individualized level.

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Gene pair based prognostic signature for colorectal colon cancer

Abstract: Supplemental Digital Content is available in the text

Cited by 12 publications

References 36 publications

Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction

Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction

Development and verification of a personalized immune prognostic feature in breast cancer

A Qualitative Transcriptional Signature for Predicting Microsatellite Instability Status of Right-sided Colon Cancer

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