scholarly journals Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of colorectal cancer

Aging ◽  
2021 ◽  
Author(s):  
Wei Li ◽  
Xiaojing Jin ◽  
Shang Guo ◽  
Fei Xu ◽  
Xingkai Su ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Comprehensive Analysis ◽  
Immune Related Genes

Comprehensive analysis of prognostic immune‐related genes in the tumor microenvironment of cutaneous melanoma

2019 ◽  
Vol 235 (2) ◽  
pp. 1025-1035 ◽  
Author(s):  
Sheng Yang ◽  
Tong Liu ◽  
Hongmei Nan ◽  
Yan Wang ◽  
Hao Chen ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Cutaneous Melanoma ◽  
Comprehensive Analysis ◽  
Immune Related Genes

scholarly journals Identification of prognostic immune-related gene signature associated with tumor microenvironment of colorectal cancer

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuanyuan Wang ◽  
Wei Li ◽  
Xiaojing Jin ◽  
Xia Jiang ◽  
Shang Guo ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Expression Profiles ◽  
Functional Enrichment ◽  
Clinical Parameters ◽  
Cox Regression Analysis ◽  
Ppi Networks ◽  
Tumor Purity ◽  
Immune Related Genes ◽  
Immune Score

Abstract Background The tumor microenvironment (TME) has significantly correlation with tumor occurrence and prognosis. Our study aimed to identify the prognostic immune-related genes (IRGs)in the tumor microenvironment of colorectal cancer (CRC). Methods Transcriptome and clinical data of CRC cases were downloaded from TCGA and GEO databases. Stromal score, immune score, and tumor purity were calculated by the ESTIMATE algorithm. Based on the scores, we divided CRC patients from the TCGA database into low and high groups, and the differentially expressed genes (DEGs) were identified. Immune-related genes (IRGs) were selected by venn plots. To explore underlying pathways, protein-protein interaction (PPI) networks and functional enrichment analysis were used. After utilizing LASSO Cox regression analysis, we finally established a multi-IRGs signature for predicting the prognosis of CRC patients. A nomogram consists of the thirteen-IRGs signature and clinical parameters was developed to predict the overall survival (OS). We investigated the association between prognostic validated IRGs and immune infiltrates by TIMER database. Results Gene expression profiles and clinical information of 1635 CRC patients were collected from the TCGA and GEO databases. Higher stromal score, immune score and lower tumor purity were observed positive correlation with tumor stage and poor OS. Based on stromal score, immune score and tumor purity, 1517 DEGs, 1296 DEGs, and 1892 DEGs were identified respectively. The 948 IRGs were screened by venn plots. A thirteen-IRGs signature was constructed for predicting survival of CRC patients. Nomogram with a C-index of 0.769 (95%CI, 0.717–0.821) was developed to predict survival of CRC patients by integrating clinical parameters and thirteen-IRGs signature. The AUC for 1-, 3-, and 5-year OS were 0.789, 0.783 and 0.790, respectively. Results from TIMER database revealed that CD1B, GPX3 and IDO1 were significantly related with immune infiltrates. Conclusions In this study, we established a novel thirteen immune-related genes signature that may serve as a validated prognostic predictor for CRC patients, thus will be conducive to individualized treatment decisions.

Crosstalk between the MSI status and tumor microenvironment in colorectal cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15236-e15236
Author(s):  
Peng Luo ◽  
Anqi Lin ◽  
Jian Zhang
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Microsatellite Instability ◽  
Immune Cell ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Immune Microenvironment ◽  
Mutation Data ◽  
Immune Related Genes

e15236 Background: In recent years, cancer immunotherapy has been extensively studied, and colorectal cancer (CRC) patients have also derived clinical benefits from immunotherapy, especially CRC patients with mismatch repair deficiency (dMMR)/microsatellite instability-high (MSI-H), whose sensitivity to immune checkpoint inhibitors (ICIs) is significantly higher than that of patients with microsatellite-stable (MSS)/microsatellite instability-low (MSI-L) disease. This study suggests that patients with MSI-H CRC have a higher mutational burden and more immune cell infiltration than those with MSS/MSI-L disease. However, most studies have not systematically evaluated the immune characteristics and immune microenvironments of MSI-H and MSS/MSI-L CRC. Methods: A published CRC cohort with mutation and immunotherapy-related prognostic data was collected. We analyzed the relationship between the MSI status and prognosis of ICI treatment in an immunotherapy cohort. We then further used mutation data for the immunotherapy and The Cancer Genome Atlas (TCGA)-CRC (colon adenocarcinoma (COAD) + rectum adenocarcinoma (READ) cohorts. For mRNA expression, mutation data analysis of the immune microenvironment and immunogenicity under different MSI status was performed. Results: Compared with MSS/MSI-L CRC patients, patients with MSI-H CRC significantly benefited from ICI treatment. We found that MSI-H CRC had more immune cell infiltration, higher expression of immune-related genes and higher immunogenicity than MSS/MSI-L disease. The MANTIS score used to predict the MSI status was positively correlated with immune cells, immune-related genes, and immunogenicity. In addition, subtype analysis showed that COAD and READ might have different tumor immune microenvironments. Conclusions: MSI-H CRC may have an inflammatory tumor microenvironment and increased sensitivity to ICIs. Unlike those of MSI-H READ, the immune characteristics of MSI-H COAD may be consistent with those of MSI-H CRC. Furthermore, the possible mechanism underlying the prognostic differences among CRC patients receiving ICIs in relation to the immune microenvironment were elucidated to provide theoretical guidance for further improving the curative effect of ICIs treatment on MSI-H CRC patients in the future and solve the problems underlying why MSS/MSI-L CRC patients do not benefit from ICIs treatment.

scholarly journals Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of hepatocellular carcinoma (HCC)

Medicine ◽  
2021 ◽  
Vol 100 (39) ◽  
pp. e27332
Author(s):  
Mengting Li ◽  
Hongliang Li ◽  
Canxin Zhou ◽  
Xianpeng Li ◽  
Jiande Gong ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Tumor Microenvironment ◽  
Comprehensive Analysis ◽  
Immune Related Genes

scholarly journals Identification of prognostic immune‐related gene signature associated with tumor microenvironment of colorectal cancer

2020 ◽  
Author(s):  
Yuanyuan Wang ◽  
Wei Li ◽  
Xiaojing Jin ◽  
Xia Jiang ◽  
Shang Guo ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Expression Profiles ◽  
Functional Enrichment ◽  
Clinical Parameters ◽  
Cox Regression Analysis ◽  
Ppi Networks ◽  
Tumor Purity ◽  
Immune Related Genes ◽  
Immune Score

Abstract Background The tumor microenvironment (TME) has significantly correlation with tumor occurrence and prognosis. Our study aimed to identify the prognostic immune-related genes (IRGs)in the tumor microenvironment of colorectal cancer (CRC). Methods Transcriptome and clinical data of CRC cases were downloaded from TCGA and GEO databases. Stromal score, immune score, and tumor purity were calculated by the ESTIMATE algorithm. Based on the scores, we divided CRC patients from the TCGA database into low and high groups, and the differentially expressed genes (DEGs) were identified. Immune-related genes (IRGs) were selected by venn plots. To explore underlying pathways, protein-protein interaction (PPI) networks and functional enrichment analysis were used. After utilizing LASSO Cox regression analysis, we finally established a multi-IRGs signature for predicting the prognosis of CRC patients. A nomogram consists of the thirteen-IRGs signature and clinical parameters was developed to predict the overall survival (OS). We investigated the association between prognostic validated IRGs and immune infiltrates by TIMER database. Results Gene expression profiles and clinical information of 1635 CRC patients were collected from the TCGA and GEO databases. Higher stromal score, immune score and lower tumor purity were observed positive correlation with tumor stage and poor OS. Based on stromal score, immune score and tumor purity, 1517 DEGs, 1296 DEGs, and 1892 DEGs were identified respectively. The 948 IRGs were screened by venn plots. A thirteen-IRGs signature was constructed for predicting survival of CRC patients. Nomogram with a C‐index of 0.769 (95%CI, 0.717–0.821) was developed to predict survival of CRC patients by integrating clinical parameters and thirteen‐IRGs signature. The AUC for 1‐, 3‐, and 5‐year OS were 0.789, 0.783 and 0.790, respectively. Results from TIMER database revealed that CD1B, GPX3 and IDO1 were significantly related with immune infiltrates. Conclusions In this study, we established a novel thirteen immune-related genes signature that may serve as a validated prognostic predictor for CRC patients, thus will be conducive to individualized treatment decisions.

scholarly journals Prognostic Signatures Based on Thirteen Immune-Related Genes in Colorectal Cancer

2021 ◽  
Vol 10 ◽  
Author(s):  
Xiao-Bo Ma ◽  
Yuan-Yuan Xu ◽  
Meng-Xuan Zhu ◽  
Lu Wang
Keyword(s):  
Colorectal Cancer ◽  
High Risk ◽  
Tumor Microenvironment ◽  
Risk Group ◽  
Risk Groups ◽  
Low Risk ◽  
Gene Set Enrichment Analysis ◽  
Cox Regression Analysis ◽  
Immune Infiltration ◽  
Immune Related Genes

BackgroundThe immunosuppressive microenvironment is closely related to tumorigenesis and cancer development, including colorectal cancer (CRC). The aim of the current study was to identify new immune biomarkers for the diagnosis and treatment of CRC.Materials and MethodsCRC data were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas databases. Sequences of immune-related genes (IRGs) were obtained from the ImmPort and InnateDB databases. Gene set enrichment analysis (GSEA) and transcription factor regulation analysis were used to explore potential mechanisms. An immune-related classifier for CRC prognosis was conducted using weighted gene co-expression network analysis (WGCNA), Cox regression analysis, and least absolute shrinkage and selection operator (LASSO) analysis. ESTIMATE and CIBERSORT algorithms were used to explore the tumor microenvironment and immune infiltration in the high-risk CRC group and the low-risk CRC group.ResultsBy analyzing the IRGs that were significantly associated with CRC in the module, a set of 13 genes (CXCL1, F2RL1, LTB4R, GPR44, ANGPTL5, BMP5, RETNLB, MC1R, PPARGC1A, PRKDC, CEBPB, SYP, and GAB1) related to the prognosis of CRC were identified. An IRG-based prognostic signature that can be used as an independent potentially prognostic indicator was generated. The ROC curve analysis showed acceptable discrimination with AUCs of 0.68, 0.68, and 0.74 at 1-, 3-, and 5- year follow-up respectively. The predictive performance was validated in the train set. The potential mechanisms and functions of prognostic IRGs were analyzed, i.e., NOD-like receptor signaling, and transforming growth factor beta (TGFβ) signaling. Besides, the stromal score and immune score were significantly different in high-risk group and low-risk group (p=4.6982e-07, p=0.0107). Besides, the proportions of resting memory CD4+ T cells was significantly higher in the high-risk groups.ConclusionsThe IRG-based classifier exhibited strong predictive capacity with regard to CRC. The survival difference between the high-risk and low-risk groups was associated with tumor microenvironment and immune infiltration of CRC. Innovative biomarkers for the prediction of CRC prognosis and response to immunological therapy were identified in the present study.

scholarly journals Recent Advancements on Immunomodulatory Mechanisms of Resveratrol in Tumor Microenvironment

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1343
Author(s):  
Gagan Chhabra ◽  
Chandra K. Singh ◽  
Deeba Amiri ◽  
Neha Akula ◽  
Nihal Ahmad
Keyword(s):  
Tumor Microenvironment ◽  
Immune Cell ◽  
Cancer Therapies ◽  
Regulatory Cells ◽  
Immunomodulatory Effects ◽  
Cancer Management ◽  
Natural Agents ◽  
Anticancer Effects ◽  
Cancer Types ◽  
Immune Related Genes

Immunomodulation of the tumor microenvironment is emerging as an important area of research for the treatment of cancer patients. Several synthetic and natural agents are being investigated for their ability to enhance the immunogenic responses of immune cells present in the tumor microenvironment to impede tumor cell growth and dissemination. Among them, resveratrol, a stilbenoid found in red grapes and many other natural sources, has been studied extensively. Importantly, resveratrol has been shown to possess activity against various human diseases, including cancer. Mechanistically, resveratrol has been shown to regulate an array of signaling pathways and processes involving oxidative stress, inflammation, apoptosis, and several anticancer effects. Furthermore, recent research suggests that resveratrol can regulate various cellular signaling events including immune cell regulation, cytokines/chemokines secretion, and the expression of several other immune-related genes. In this review, we have summarized recent findings on resveratrol’s effects on immune regulatory cells and associated signaling in various cancer types. Numerous immunomodulatory effects of resveratrol suggest it may be useful in combination with other cancer therapies including immunotherapy for effective cancer management.

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