scholarly journals Construction of a Prognostic Immune-Related LncRNA Risk Model for Lung Adenocarcinoma

2021 ◽  
Vol 9 ◽  
Author(s):  
Yue Li ◽  
Ruoyi Shen ◽  
Anqi Wang ◽  
Jian Zhao ◽  
Jieqi Zhou ◽  
...  
Keyword(s):  
High Risk ◽  
Differentially Expressed Genes ◽  
Risk Model ◽  
Cox Regression ◽  
Risk Group ◽  
Enrichment Analysis ◽  
Risk Groups ◽  
Low Risk ◽  
Differentially Expressed ◽  
Cox Regression Analysis

BackgroundLung adenocarcinoma (LUAD) originates mainly from the mucous epithelium and glandular epithelium of the bronchi. It is the most common pathologic subtype of non-small cell lung cancer (NSCLC). At present, there is still a lack of clear criteria to predict the efficacy of immunotherapy. The 5-year survival rate for LUAD patients remains low.MethodsAll data were downloaded from The Cancer Genome Atlas (TCGA) database. We used Gene Set Enrichment Analysis (GSEA) database to obtain immune-related mRNAs. Immune-related lncRNAs were acquired by using the correlation test of the immune-related genes with R version 3.6.3 (Pearson correlation coefficient cor = 0.5, P < 0.05). The TCGA-LUAD dataset was divided into the testing set and the training set randomly. Based on the training set to perform univariate and multivariate Cox regression analyses, we screened prognostic immune-related lncRNAs and given a risk score to each sample. Samples were divided into the high-risk group and the low-risk group according to the median risk score. By the combination of Kaplan–Meier (KM) survival curve, the receiver operating characteristic (ROC) (AUC) curve, the independent risk factor analysis, and the clinical data of the samples, we assessed the accuracy of the risk model. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the differentially expressed mRNAs between the high-risk group and the low-risk group. The differentially expressed genes related to immune response between two risk groups were analyzed to evaluate the role of the model in predicting the efficacy and effects of immunotherapy. In order to explain the internal mechanism of the risk model in predicting the efficacy of immunotherapy, we analyzed the differentially expressed genes related to epithelial-mesenchymal transition (EMT) between two risk groups. We extracted RNA from normal bronchial epithelial cell and LUAD cells and verified the expression level of lncRNAs in the risk model by a quantitative real-time polymerase chain reaction (qRT-PCR) test. We compared our risk model with other published prognostic signatures with data from an independent cohort. We transfected LUAD cell with siRNA-LINC0253. Western blot analysis was performed to observed change of EMT-related marker in protein level.ResultsThrough univariate Cox regression analysis, 24 immune-related lncRNAs were found to be strongly associated with the survival of the TCGA-LUAD dataset. Utilizing multivariate Cox regression analysis, 10 lncRNAs were selected to establish the risk model. The K-M survival curves and the ROC (AUC) curves proved that the risk model has a fine predictive effect. The GO enrichment analysis indicated that the effect of the differentially expressed genes between high-risk and low-risk groups is mainly involved in immune response and intercellular interaction. The KEGG enrichment analysis indicated that the differentially expressed genes between high-risk and low-risk groups are mainly involved in endocytosis and the MAPK signaling pathway. The expression of genes related to the efficacy of immunotherapy was significantly different between the two groups. A qRT-PCR test verified the expression level of lncRNAs in LUAD cells in the risk model. The AUC of ROC of 5 years in the independent validation dataset showed that this model had superior accuracy. Western blot analysis verified the change of EMT-related marker in protein level.ConclusionThe immune lncRNA risk model established by us could better predict the prognosis of patients with LUAD.

Construction of a Prognostic Model Related to Ferroptosis and Iron-Metabolism and the Relationship with the Immune Microenvironment of Gastric Cancer

2021 ◽  
Author(s):  
Fang Wen ◽  
Xiaoxue Chen ◽  
Wenjie Huang ◽  
Shuai Ruan ◽  
Suping Gu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
High Risk ◽  
Iron Metabolism ◽  
Risk Model ◽  
Cox Regression ◽  
Risk Group ◽  
Risk Groups ◽  
High Risk Group ◽  
Low Risk ◽  
Immune Microenvironment

Abstract Background: The diagnosis rate and mortality of gastric cancer (GC) are among the highest in the global, so it is of great significance to predict the survival time of GC patients. Ferroptosis and iron-metabolism make a critical impact on tumor development and are closely linked to the treatment of cancer and the prognosis of patients. However, the predictive value of the genes involved in ferroptosis and iron-metabolism in GC and their effects on immune microenvironment remain to be further clarified.Methods: In this study, the RNA sequence information and general clinical indicators of GC patients were acquired from the public databases. We first systematically screen out 134 DEGs and 13 PRGs related to ferroptosis and iron-metabolism. Then, we identified six PRDEGs (GLS2, MTF1, SLC1A5, SP1, NOX4, and ZFP36) based on the LASSO-penalized Cox regression analysis. The 6-gene prognostic risk model was established in the TCGA cohort and the GC patients were separated into the high- and the low-risk groups through the risk score median value. GEO cohort was used for verification. The expression of PRDEGs was verified by quantitative QPCR.Results: Our study demonstrated that patients in the low-risk group had a higher survival probability compared with those in high-risk group. In addition, univariate and multivariate Cox regression analyses confirmed that the risk score was an independent prediction parameter. The ROC curve analysis and nomogram manifested that the risk model had the high predictive ability and was more sensitive than general clinical features. Furthermore, compared with the high-risk group, the low-risk group had higher TMB and a longer 5-year survival period. In the immune microenvironment of GC, there were also differences in immune function and highly infiltrated immune cells between the two risk groups.Conclusions: The prognostic risk model based on the six genes associated with ferroptosis and iron-metabolism has a good performance for predicting the prognosis of patients with GC. The treatment of cancer by inducing tumor ferroptosis or mediating tumor iron-metabolism, especially combined with immunotherapy, provides a new possibility for individualized treatment of GC patients.

scholarly journals Prognostic Immune-Related Analysis Based on Differentially Expressed Genes in Left- and Right-Sided Colon Adenocarcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Jun-Nan Guo ◽  
Ming-Qi Li ◽  
Shen-Hui Deng ◽  
Chen Chen ◽  
Yin Ni ◽  
...  
Keyword(s):  
High Risk ◽  
Differentially Expressed Genes ◽  
Cox Regression ◽  
Risk Group ◽  
Colon Adenocarcinoma ◽  
High Risk Group ◽  
Low Risk ◽  
Differentially Expressed ◽  
Model Group ◽  
Gene Pairs

BackgroundColon adenocarcinoma (COAD) can be divided into left-sided and right-sided COAD (LCCs and RCCs, respectively). They have unique characteristics in various biological aspects, particularly immune invasion and prognosis. The purpose of our study was to develop a prognostic risk scoring model (PRSM) based on differentially expressed immune-related genes (IRGs) between LCCs and RCCs, therefore the prognostic key IRGs could be identified.MethodsThe gene sets and clinical information of COAD patients were derived from TCGA and GEO databases. The comparison of differentially expressed genes (DEGs) of LCCs and RCCs were conducted with appliance of “Limma” analysis. The establishment about co-expression modules of DEGs related with immune score was conducted by weighted gene co-expression network analysis (WGCNA). Furthermore, we screened the module genes and completed construction of gene pairs. The analysis of the prognosis and the establishment of PRSM were performed with univariate- and lasso-Cox regression. We employed the PRSM in the model group and verification group for the purpose of risk group assignment and PRSM accuracy verification. Finally, the identification of the prognostic key IRGs was guaranteed by the adoption of functional enrichment, “DisNor” and protein-protein interaction (PPI).ResultsA total of 215 genes were screened out by differential expression analysis and WGCNA. A PRSM with 16 immune-related gene pairs (IRGPs) was established upon the genes pairing. Furthermore, we confirmed that the risk score was an independent factor for survival by univariate- and multivariate-Cox regression. The prognosis of high-risk group in model group (P < 0.001) and validation group (P = 0.014) was significantly worse than that in low-risk group. Treg cells (P < 0.001) and macrophage M0 (P = 0.015) were highly expressed in the high-risk group. The functional analysis indicated that there was significant up-regulation with regard of lymphocyte and cytokine related terms in low-risk group. Finally, we identified five prognostic key IRGs associated with better prognosis through PPI and prognostic analysis, including IL2RB, TRIM22, CIITA, CXCL13, and CXCR6.ConclusionThrough the analysis and screening of the DEGs between LCCs and RCCs, we constructed a PRSM which could predicate prognosis of LCCs and RCCs, and five prognostic key IRGs were identified as well. Therefore, the basis for identifying the benefits of immunotherapy and immunomodulatory was built.

scholarly journals Development of a prognostic scoring model for predicting the survival of elderly patients with hepatocellular carcinoma

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8497 ◽  
Author(s):  
Sizhe Wan ◽  
Yuan Nie ◽  
Xuan Zhu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Factors ◽  
High Risk ◽  
Cox Regression ◽  
Risk Group ◽  
Large Population ◽  
Risk Groups ◽  
Low Risk ◽  
Cox Regression Analysis ◽  
Scoring Model

Background The number of elderly hepatocellular carcinoma (HCC) patients is increasing, and precisely assessing of the prognosis of these patients is necessary. We developed a prognostic scoring model to predict survival in elderly HCC patients. Methods We extracted data from 4,076 patients ≥65 years old from the Surveillance, Epidemiology, and End Results (SEER) database and randomly divided them into training and validation groups. Cox regression analysis was used to screen for meaningful independent prognostic factors. The receiver operating characteristic curve reflected the model’s discrimination power. Results Age, race, American Joint Committee on Cancer stage, degree of tumour differentiation, tumour size, alpha-fetoprotein and tumour therapy were independent prognostic factors for survival in elderly HCC patients. We developed a prognostic scoring model based on the seven meaningful variables to predict survival in elderly HCC patients. The AUCs of the model were 0.805 (95% CI [0.788–0.821]) and 0.788 (95% CI [0.759–0.816]) in the training and validation groups, respectively. We divided the patients into low-risk groups and high-risk groups according to the optimal cut-off value. The Kaplan–Meier survival curve showed that in the training and validation groups, the survival rate of the low-risk group was significantly higher than that of the high-risk group (P < 0.001). Conclusion Based on a large population, we constructed a prognostic scoring model for predicting survival in elderly HCC patients. The model may provide a reference for clinicians for preoperative and postoperative evaluations of elderly HCC patients.

scholarly journals Identification of Five Immune-Related lncRNAs Predicting Survival and Tumor Microenvironment Characteristics in Breast Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Ran Xiao ◽  
Meng Yang ◽  
Yuanyuan Tan ◽  
Rumeng Ding ◽  
Duolu Li
Keyword(s):  
Breast Cancer ◽  
High Risk ◽  
Tumor Microenvironment ◽  
Risk Model ◽  
Risk Group ◽  
Risk Groups ◽  
Low Risk ◽  
Gene Set Enrichment Analysis ◽  
Clinical Samples ◽  
Cox Regression Analysis

A common cancer in females, breast cancer (BRCA) mortality has been recently reduced; however, the prognosis of BRCA patients remains poor. This study attempted to develop prognostic immune-related long noncoding RNAs (lncRNAs) for BRCA and identify the effects of these lncRNAs on the tumor microenvironment (TME). Gene expression data from The Cancer Genome Atlas (TCGA) database were collected in order to select differentially expressed lncRNAs. Immune-related lncRNAs were downloaded from the ImmLnc database, where 316 immune-related lncRNAs were identified, 12 of which were found to be significantly related to the prognosis of BRCA patients. Multivariate cox regression analysis was then applied to construct prognostic immune-related lncRNAs as the risk model, including C6orf99, LINC00987, SIAH2-AS1, LINC01010, and ELOVL2-AS1. High-risk and low-risk groups were distinguished according to the median of immune-related risk scores. Accordingly, the overall survival (OS) in the high-risk group was observed to be shorter than that in the low-risk group. qRT-PCR analysis demonstrated that lncRNA expression levels in BRCA cell lines were in basic agreement with predictions except for LINC00987. By validating numerous clinical samples, lncRNA C6orf99 was shown to be highly expressed in the advanced stage, while LINC01010 and SIAH2-AS1 decreased in the advanced T-stage and M-stage. Moreover, the expression of LINC0098 was found to be significantly decreased among the groups (>50 years old). Gene set enrichment analysis (GSEA) was applied to analyze the cancer hallmarks and immunological characteristics of the high-risk and low-risk groups. Importantly, the TIMER database demonstrated that this immune-related lncRNA risk model for breast cancer is related to the infiltration of immune cells. In conclusion, the results indicated that five immune-related lncRNAs could be used as a prognostic model and may even accelerate immunotherapy for BRCA patients.

scholarly journals A novel pyroptosis-related gene signature predicts the prognosis of glioma through immune infiltration

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moxuan Zhang ◽  
Yanhao Cheng ◽  
Zhengchun Xue ◽  
Qiang Sun ◽  
Jian Zhang
Keyword(s):  
High Risk ◽  
Risk Model ◽  
Cox Regression ◽  
Validation Cohort ◽  
Risk Group ◽  
High Risk Group ◽  
Low Risk ◽  
Related Gene ◽  
Cox Regression Analysis ◽  
Genome Atlas

Abstract Background Glioma is the most common primary intracranial tumour and has a very poor prognosis. Pyroptosis, also known as inflammatory necrosis, is a type of programmed cell death that was discovered in recent years. The expression and role of pyroptosis-related genes in gliomas are still unclear. Methods In this study, we analysed the RNA-seq and clinical information of glioma patients from The Cancer Genome Atlas (TCGA) database and Chinese Glioma Genome Atlas (CGGA) database. To investigate the prognosis and immune microenvironment of pyroptosis-related genes in gliomas, we constructed a risk model based on the TCGA cohort. The patients in the CGGA cohort were used as the validation cohort. Results In this study, we identified 34 pyroptosis-related differentially expressed genes (DEGs) in glioma. By clustering these DEGs, all glioma cases can be divided into two clusters. Survival analysis showed that the overall survival time of Cluster 1 was significantly higher than that of Cluster 2. Using the TCGA cohort as the training set, a 10-gene risk model was constructed through univariate Cox regression analysis and LASSO Cox regression analysis. According to the risk score, gliomas were divided into high-risk and low-risk groups. Survival analysis showed that the low-risk group had a longer survival time than the high-risk group. The above results were verified in the CGGA validation cohort. To verify that the risk model was independent of other clinical features, the distribution and the Kaplan-Meier survival curves associated with risk scores were performed. Combined with the characteristics of the clinical cases, the risk score was found to be an independent factor predicting the overall survival of patients with glioma. The analysis of single sample Gene Set Enrichment Analysis (ssGSEA) showed that compared with the low-risk group, the high-risk group had immune cell and immune pathway activities that were significantly upregulated. Conclusion We established 10 pyroptosis-related gene markers that can be used as independent clinical predictors and provide a potential mechanism for the treatment of glioma.

scholarly journals A prognostic model based on immune-related long noncoding RNAs for patients with epithelial ovarian cancer

2022 ◽  
Vol 15 (1) ◽  
Author(s):  
Yao Peng ◽  
Hui Wang ◽  
Qi Huang ◽  
Jingjing Wu ◽  
Mingjun Zhang
Keyword(s):  
High Risk ◽  
Immune Cell ◽  
Cox Regression ◽  
Risk Group ◽  
Principal Component ◽  
Risk Groups ◽  
Low Risk ◽  
Training Set ◽  
Cox Regression Analysis ◽  
Validation Set

Abstract Background Long noncoding RNAs (lncRNAs) are important regulators of gene expression and can affect a variety of physiological processes. Recent studies have shown that immune-related lncRNAs play an important role in the tumour immune microenvironment and may have potential application value in the treatment and prognosis prediction of tumour patients. Epithelial ovarian cancer (EOC) is characterized by a high incidence and poor prognosis. However, there are few studies on immune-related lncRNAs in EOC. In this study, we focused on immune-related lncRNAs associated with survival in EOC. Methods We downloaded mRNA data for EOC patients from The Cancer Genome Atlas (TCGA) database and mRNA data for normal ovarian tissue from the Genotype-Tissue Expression (GTEx) database and identified differentially expressed genes through differential expression analysis. Immune-related lncRNAs were obtained through intersection and coexpression analysis of differential genes and immune-related genes from the Immunology Database and Analysis Portal (ImmPort). Samples in the TCGA EOC cohort were randomly divided into a training set, validation set and combination set. In the training set, Cox regression analysis and LASSO regression were performed to construct an immune-related lncRNA signature. Kaplan–Meier survival analysis, time-dependent ROC curve analysis, Cox regression analysis and principal component analysis were performed for verification in the training set, validation set and combination set. Further studies of pathways and immune cell infiltration were conducted through Gene Set Enrichment Analysis (GSEA) and the Timer data portal. Results An immune-related lncRNA signature was identified in EOC, which was composed of six immune-related lncRNAs (KRT7-AS, USP30-AS1, AC011445.1, AP005205.2, DNM3OS and AC027348.1). The signature was used to divide patients into high-risk and low-risk groups. The overall survival of the high-risk group was lower than that of the low-risk group and was verified to be robust in both the validation set and the combination set. The signature was confirmed to be an independent prognostic biomarker. Principal component analysis showed the different distribution patterns of high-risk and low-risk groups. This signature may be related to immune cell infiltration (mainly macrophages) and differential expression of immune checkpoint-related molecules (PD-1, PDL1, etc.). Conclusions We identified and established a prognostic signature of immune-related lncRNAs in EOC, which will be of great value in predicting the prognosis of clinical patients and may provide a new perspective for immunological research and individualized treatment in EOC.

scholarly journals A Risk Signature of Nine Autophagy-Related Genes Associated With Immune Microenvironment and Clinical Prognosis in Wilms Tumor

2021 ◽  
Author(s):  
Shaopei Ye ◽  
Wenbin Tang ◽  
Ke Huang
Keyword(s):  
Regression Analysis ◽  
High Risk ◽  
Risk Score ◽  
Cox Regression ◽  
Wilms Tumor ◽  
Risk Group ◽  
High Risk Group ◽  
Differentially Expressed ◽  
Clinical Prognosis ◽  
Cox Regression Analysis

Abstract Background: Autophagy is a biological process to eliminate dysfunctional organelles, aggregates or even long-lived proteins. . Nevertheless, the potential function and prognostic values of autophagy in Wilms Tumor (WT) are complex and remain to be clarifed. Therefore, we proposed to systematically examine the roles of autophagy-associated genes (ARGs) in WT.Methods: Here, we obtained differentially expressed autophagy-related genes (ARGs) between healthy and Wilms tumor from Therapeutically Applicable Research To Generate Effective Treatments(TARGET) and The Cancer Genome Atlas (TCGA) database. The functionalities of the differentially expressed ARGs were analyzed using Gene Ontology. Then univariate COX regression analysis and multivariate COX regression analysis were performed to acquire nine autophagy genes related to WT patients’ survival. According to the risk score, the patients were divided into high-risk and low-risk groups. The Kaplan-Meier curve demonstrated that patients with a high-risk score tend to have a poor prognosis.Results: Eighteen DEARGs were identifed, and nine ARGs were fnally utilized to establish the FAGs based signature in the TCGA cohort. we found that patients in the high-risk group were associated with mutations in TP53. We further conducted CIBERSORT analysis, and found that the infiltration of Macrophage M1 was increased in the high-risk group. Finally, the expression levels of crucial ARGs were verifed by the experiment, which were consistent with our bioinformatics analysis.Conclusions: we emphasized the clinical significance of autophagy in WT, established a prediction system based on autophagy, and identified a promising therapeutic target of autophagy for WT.

scholarly journals Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8128 ◽  
Author(s):  
Cheng Yue ◽  
Hongtao Ma ◽  
Yubai Zhou
Keyword(s):  
High Risk ◽  
Lung Adenocarcinoma ◽  
Prognostic Model ◽  
Cox Regression ◽  
Risk Group ◽  
Expression Profiles ◽  
Gene Signature ◽  
Low Risk ◽  
Differentially Expressed ◽  
Lasso Regression

Background Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients. Methods The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model. Results A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven genes were screened out from the 23 DEGs by LASSO regression method and were further analyzed by step multivariate Cox regression. Finally, a three-gene (ADAM12, Bruton Tyrosine Kinase (BTK), ERG) signature was constructed, and ADAM12, BTK can be used as independent prognostic factors. The three-gene signature well stratified the LADC patients in both training (TCGA) and testing (GEO) datasets as high-risk and low-risk groups, the 3-year area under curve (AUC) of ROC curves of three GEO sets were 0.718 (GSE3141), 0.646 (GSE30219) and 0.643 (GSE50081). The GSEA analysis indicated that highly expressed ADAM12, BTK, ERG mainly correlated with the activation of pathways involving in focal adhesion, immune regulation. The immune analysis indicated that the low-risk group has more immune activities and higher expression of HLA genes than that of the high-risk group. In sum, we identified and constructed a three TME-related DEGs signature, which could be used to predict the prognosis of LADC patients.

scholarly journals Prognostic Value and Regulatory Network of Immune-Related Genes in Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Xiang Zhou ◽  
Keying Zhang ◽  
Fa Yang ◽  
Chao Xu ◽  
Jianhua Jiao ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Regression Analysis ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Risk Model ◽  
Cox Regression ◽  
Wilcoxon Test ◽  
Differentially Expressed ◽  
Cox Regression Analysis ◽  
Immune Related Genes

Abstract Background: Hepatocellular carcinoma (HCC) is a disease with higher morbidity, mortality, and poor prognosis in the whole world. Understanding the crosslink between HCC and the immune system is essential for people to uncover a few potential and valuable therapeutic strategies. This study aimed to reveal the correlation between HCC and immune-related genes and establish a clinical evaluation model. Methods: We had analyzed the clinical information consisted of 373 HCC and 49 normal samples from the cancer genome atlas (TCGA). The differentially expressed genes (DEGs) were selected by the Wilcoxon test and the immune-related differentially expressed genes (IRDEGs) in DEGs were identified by matching DEGs with immune-related genes downloaded from the ImmPort database. Furthermore, the univariate Cox regression analysis and multivariate Cox regression analysis were performed to construct a prognostic risk model. Then, twenty-two types of tumor immune-infiltrating cells (TIICs) were downloaded from Tumor Immune Estimation Resource (TIMER) and were used to construct the correlational graphs between the TIICs and risk score by the CIBERSORT. Subsequently, the transcription factors (TFs) were gained in the Cistrome website and the differentially expressed TFs (DETFs) were achieved. Finally, the KEGG pathway analysis and GO analysis were performed to further understand the molecular mechanisms between DETFs and PDIRGs.Results: In our study, 5839 DEGs, 326 IRDEGs, and 31 prognosis-related IRDEGs (PIRDEGs) were identified. And 8 optimal PIRDEGs were employed to construct a prognostic risk model by multivariate Cox regression analysis. The correlation between risk genes and clinical characterizations and TIICs has verified that the prognostic model was effective in predicting the prognosis of HCC patients. Finally, several important immune-related pathways and molecular functions of the eight PIRDEGs were significantly enriched and there was a distinct association between the risk IRDEGs and TFs. Conclusion: The prognostic risk model showed a more valuable predicting role for HCC patients, and produced many novel therapeutic targets and strategies for HCC.

A Novel Risk Classification Model Predicts Overall Survival and Locoregional Surgery Benefit in Colorectal Patients with Distant Metastasis at the Initial Diagnosis

2020 ◽  
Author(s):  
Mo Chen ◽  
Tian-en Li ◽  
Pei-zhun Du ◽  
Junjie Pan ◽  
Zheng Wang ◽  
...  
Keyword(s):  
Overall Survival ◽  
High Risk ◽  
Distant Metastasis ◽  
Cox Regression ◽  
Risk Group ◽  
Risk Groups ◽  
Risk Classification ◽  
Low Risk ◽  
Classification Model ◽  
Intermediate Risk

Abstract Background and aims: In this research, we aimed to construct a risk classification model to predict overall survival (OS) and locoregional surgery benefit in colorectal cancer (CRC) patients with distant metastasis.Methods: We selected a cohort consisting of 12741 CRC patients diagnosed with distant metastasis between 2010 and 2014, from the Surveillance, Epidemiology and End Results (SEER) database. Patients were randomly assigned into training group and validation group at the ratio of 2:1. Univariable and multivariable Cox regression models were applied to screen independent prognostic factors. A nomogram was constructed and assessed by the Harrell’s concordance index (C-index) and calibration plots. A novel risk classification model was further established based on the nomogram.Results: Ultimately 12 independent risk factors including race, age, marriage, tumor site, tumor size, grade, T stage, N stage, bone metastasis, brain metastasis, lung metastasis and liver metastasis were identified and adopted in the nomogram. The C-indexes of training and validation groups were 0.77 (95% confidence interval [CI] 0.73-0.81) and 0.75 (95% CI 0.72-0.78), respectively. The risk classification model stratified patients into three risk groups (low-, intermediate- and high-risk) with divergent median OS (low-risk: 36.0 months, 95% CI 34.1-37.9; intermediate-risk: 18.0 months, 95% CI 17.4-18.6; high-risk: 6.0 months, 95% CI 5.3-6.7). Locoregional therapies including surgery and radiotherapy could prognostically benefit patients in the low-risk group (surgery: hazard ratio [HR] 0.59, 95% CI 0.50-0.71; radiotherapy: HR 0.84, 95% CI 0.72-0.98) and intermediate risk group (surgery: HR 0.61, 95% CI 0.54-0.68; radiotherapy: HR 0.86, 95% CI 0.77-0.95), but not in the high-risk group (surgery: HR 1.03, 95% CI 0.82-1.29; radiotherapy: HR 1.03, 95% CI 0.81-1.31). And all risk groups could benefit from systemic therapy (low-risk: HR 0.68, 95% CI 0.58-0.80; intermediate-risk: HR 0.50, 95% CI 0.47-0.54; high-risk: HR 0.46, 95% CI 0.40-0.53).Conclusion: A novel risk classification model predicting prognosis and locoregional surgery benefit of CRC patients with distant metastasis was established and validated. This predictive model could be further utilized by physicians and be of great significance for medical practice.

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