Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer

2020 ◽  
Author(s):  
Marc Clos-Garcia ◽  
Koldo Garcia ◽  
Cristina Alonso ◽  
Marta Iruarrizaga-Lejarreta ◽  
Mauro D’Amato ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Integrative Analysis

scholarly journals Prognostic Effect of Inflammatory Genes on Stage I–III Colorectal Cancer—Integrative Analysis of TCGA Data

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 751
Author(s):  
Eun Kyung Choe ◽  
Sangwoo Lee ◽  
So Yeon Kim ◽  
Manu Shivakumar ◽  
Kyu Joo Park ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Clinical Features ◽  
Cox Proportional Hazards ◽  
Integrative Analysis ◽  
Stage I ◽  
The Cancer Genome Atlas ◽  
Integrative Model ◽  
Inflammatory Status ◽  
Study Results

Background inflammatory status indicators have been reported as prognostic biomarkers of colorectal cancer (CRC). However, since inflammatory interactions with the colon involve various modes of action, the biological mechanism linking inflammation and CRC prognosis has not been fully elucidated. We comprehensively evaluated the predictive roles of the expression and methylation levels of inflammation-related genes for CRC prognosis and their pathophysiological associations. Method. An integrative analysis of 247 patients with stage I-III CRC from The Cancer Genome Atlas was conducted. Lasso-penalized Cox proportional hazards regression (Lasso-Cox) and statistical Cox proportional hazard regression (CPH) were used for the analysis. Results. Models to predict overall survival were designed with respective combinations of clinical variables, including age, sex, stage, gene expression, and methylation. An integrative model combining expression, methylation, and clinical features performed better (median C-index = 0.756) than the model with clinical features alone (median C-index = 0.726). Based on multivariate CPH with features from the best model, the methylation levels of CEP250, RAB21, and TNPO3 were significantly associated with overall survival. They did not share any biological process in functional networks. The 5-year survival rate was 29.8% in the low methylation group of CEP250 and 79.1% in the high methylation group (p < 0.001). Conclusion. Our study results implicate the importance of integrating expression and methylation information along with clinical information in the prediction of survival. CEP250, RAB21, and TNPO3 in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reactions and CRC progression.

scholarly journals Integrative analysis from multi‐centre studies identifies a function‐derived personalized multi‐gene signature of outcome in colorectal cancer

2019 ◽  
Vol 23 (8) ◽  
pp. 5270-5281 ◽  
Author(s):  
Jie Sun ◽  
Hengqiang Zhao ◽  
Shuting Lin ◽  
Siqi Bao ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gene Signature ◽  
Integrative Analysis

scholarly journals Integrative analysis identifies DNMTs against immune-infiltrating neutrophils and dendritic cells in colorectal cancer

Epigenetics ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. 392-404 ◽  
Author(s):  
Qili Shi ◽  
Libing Shen ◽  
Jun Gan ◽  
Lirong He ◽  
Jing Lin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dendritic Cells ◽  
Integrative Analysis

Prognostic effect of inflammatory genes on stage I-III colorectal cancer – integrative analysis of TCGA data

2020 ◽  
Author(s):  
Eun Kyung Choe ◽  
Sangwoo Lee ◽  
So Yeon Kim ◽  
Manu Shivakumar ◽  
Kyu Joo Park ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Clinical Features ◽  
Proportional Hazards ◽  
Cox Proportional Hazards ◽  
Integrative Analysis ◽  
Stage I ◽  
The Cancer Genome Atlas ◽  
Integrative Model ◽  
Inflammatory Status

Abstract Background Inflammatory status indicators have been reported as a prognostic biomarker of colorectal cancer (CRC). However, since the inflammatory interactions with colon involve various modes of action, the biological mechanism to link inflammation and CRC prognosis is not fully elucidated. We comprehensively evaluated the predictive role of the expression and methylation level of inflammation-related genes for CRC prognosis and their pathophysiological associations. Method An integrative analysis was conducted on 247 patients of stage I-III CRC from The Cancer Genome Atlas. Lasso-penalized Cox proportional hazards regression (Lasso-Cox) and statistical Cox proportional hazard regression (CPH) were used for analysis. Result Models to predict overall survival were designed with respective combinations of clinical variables, including age, sex, stage, gene expression, and methylation. An integrative model combining expression, methylation, and clinical features had the highest performance (median C-index=0.756), compared to the model with clinical features alone (median C-index=0.726). By multivariate CPH with features from the best model, methylation levels of CEP250, RAB21 and TNPO3 were significantly associated with overall survival. They did not share any biological process in functional networks. The 5-year survival rate was 29.8% in a low methylation group of CEP250 and 79.1% in a high (P <0.001). Conclusion Our study result implicates the importance of integrating the expression and methylation information along with clinical information in prediction of survival. CEP250, RAB21 and TNPO3, in the prediction model might have a crucial role in CRC prognosis and further improve our understanding of potential mechanisms linking inflammatory reaction and CRC progression.

Abstract 4930: Integrative analysis of genome-wide methylation and expression profiles for metastatic colorectal cancer

2012 ◽  
Author(s):  
Yutaka Midorikawa ◽  
Shingo Tsuji ◽  
Genta Nagae ◽  
Tadatoshi Takayama ◽  
Yasuyuki Sugiyama ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Expression Profiles ◽  
Integrative Analysis ◽  
Genome Wide
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