scholarly journals Signature based on metabolic‐related gene pairs can predict overall survival of osteosarcoma patients

2021 ◽  
Author(s):  
Long‐Qing Li ◽  
Liang‐Hao Zhang ◽  
Yao‐bo Yuan ◽  
Xin‐Chang Lu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Related Gene ◽  
Gene Pairs

scholarly journals Development of an immune-related gene pairs signature for predicting clinical outcome in lung adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunlei Wu ◽  
Quanteng Hu ◽  
Dehua Ma
Keyword(s):  
Overall Survival ◽  
Regression Analysis ◽  
Lung Adenocarcinoma ◽  
Risk Score ◽  
Cox Regression ◽  
Related Gene ◽  
Cox Regression Analysis ◽  
Gene Pairs ◽  
Immune Related Gene ◽  
Pathological Subtype

AbstractLung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. We downloaded the gene expression profile and immune-related gene set from the TCGA and ImmPort database, respectively, to establish immune-related gene pairs (IRGPs). Then, IRGPs were subjected to univariate Cox regression analysis, LASSO regression analysis, and multivariable Cox regression analysis to screen and develop an IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from the GEO set was used to validate this signature. The relationship of 22 tumor-infiltrating immune cells (TIICs) to the immune risk score was also investigated. An IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in the TCGA set was 0.867 and 0.870, respectively. Similar results were observed in the AUCs of GEO set 1, 2 and 3 (GEO set 1 [1-year: 0.819; 3-year: 0.803]; GEO set 2 [1-year: 0.834; 3-year: 0.870]; GEO set 3 [1-year: 0.955; 3-year: 0.827]). Survival analysis demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that the risk score was an independent prognostic factor. The immune risk score was highly associated with several TIICs (Plasma cells, memory B cells, resting memory CD4 T cells, and activated NK cells). We developed a novel IRGPs signature for predicting 1- and 3- year overall survival in LUAD, which would be helpful for prognosis assessment of LUAD.

scholarly journals An immune-related gene pairs signature predicts overall survival in serous ovarian carcinoma

2019 ◽  
Vol Volume 12 ◽  
pp. 7005-7014 ◽  
Author(s):  
Liuyan Zhang ◽  
Ping Zhu ◽  
Yao Tong ◽  
Yuzhuo Wang ◽  
Haifen Ma ◽  
...  
Keyword(s):  
Overall Survival ◽  
Ovarian Carcinoma ◽  
Related Gene ◽  
Gene Pairs ◽  
Serous Ovarian Carcinoma ◽  
Immune Related Gene

An Immune-Related Gene Pairs Signature Predicts Overall Survival in Melanoma

2021 ◽  
Author(s):  
Ding Pan ◽  
Qi-Feng Ou ◽  
Pan-Feng Wu ◽  
Fang Yu ◽  
Ju-Yu Tang
Keyword(s):  
Overall Survival ◽  
High Risk ◽  
Risk Group ◽  
High Risk Group ◽  
Low Risk ◽  
Related Gene ◽  
Immune Genes ◽  
Gene Pairs ◽  
Immune Related Gene ◽  
Public Data

Abstract Background:The incidence rate and mortality rate of melanoma have been increasing in recent decades. Increasing evidence has depicted the correlation between melanoma prognosis and immune signature. Therefore, the aim of this study is to develop a robust prognostic immune-related gene pairs (IRGPs) signature for estimating overall survival (OS) of melanoma.Methods:Gene expression profiling and clinical information of melanoma patients were derived from two public data sets, divided into training and validation cohorts. Immune genes significantly associated with prognosis were selected. Results:Among 1,646 immune genes, a 25 IRGPs signature was built which was significantly associated with OS in the training cohort (P=1.80×10−22; hazard ratio [HR] =9.50 [6.04, 14.93]). In the validation datasets, the IRGPs signature significantly divided patients into high- vs low- risk groups considering their prognosis (P=2.47×10−4; HR =2.99 [1.66, 5.38]) and was prognostic in multivariate analysis. Functional analysis showed that several biological processes, including keratinization and pigment phenotype-related pathways, enriched in the high-risk group. Macrophages M0, NK cells resting and T cells gamma delta were significantly higher in the high-risk group compared with the low-risk group. Conclusions:We successfully constructed a robust IRGPs signature with prognostic values for melanoma, providing new insights into post-operational treatment strategies.

scholarly journals Construction of immune-related gene pairs signature to predict the overall survival of osteosarcoma patients

Aging ◽  
2020 ◽  
Author(s):  
Long-Qing Li ◽  
Liang-Hao Zhang ◽  
Yan Zhang ◽  
Xin-Chang Lu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Related Gene ◽  
Gene Pairs ◽  
Immune Related Gene

scholarly journals A hypoxia-related gene pairs signature for predicting overall survival in lung adenocarcinoma

2021 ◽  
Author(s):  
Kang Li ◽  
Bo Zhang
Keyword(s):  
Overall Survival ◽  
Lung Adenocarcinoma ◽  
Clinical Decision Making ◽  
Immune Status ◽  
Risk Model ◽  
Expression Profiles ◽  
High Risk Group ◽  
Related Gene ◽  
Gene Pairs ◽  
Public Data

Abstract Background: Increasing evidence has depicted the clinical importance of the correlation between hypoxia and immune status in lung adenocarcinoma environment (LUAD). However, the reliable prognostic signatures based on the interaction of hypoxia and immune status are still limited. Therefore, we strived to construct a hypoxia-immune-related gene pairs signature for risk assessment and stratification for patients with LUAD.Methods: Gene expression profiles and clinical data of patients with lung adenocarcinoma were acquired from two public data sets, used as training and validation cohorts respectively. Different bioinformatics and statistical methods were applied to construct a robust hypoxia-related gene pairs (HRGPs) signatures for predicting overall survival in lung adenocarcinoma. Furthermore, we explored the correlation between HRGPs signature and infiltrating immune cells using the CIBERSORT algorithm in LUAD samples.Results: Among 146 hypoxia-related genes, a 13 HRGPs signature was built that was significantly associated with OS in the training cohort (P<0.01). In the validation cohort, the HRGPs signature stratified patients into high- and low-risk groups with a significant OS difference (P=0.04). After adjusting the other clinical factors, the developed HRGPs signature remained independent in multivariate analysis. Plasma cells and NK cells resting were significantly correlated with the OS of patients with LUAD. Functional analysis showed that the high-risk group was enriched in terms of DNA replication, lymphocyte apoptotic process, and cell cycle-related pathways.Conclusion: The HRGPs signature represents a promising risk model for patient’s stratification in LUAD. It might provide new insights into clinical decision-making regarding individualized treatment.

scholarly journals Development and Verification of an Immune-Related Gene Pairs Prognostic Signature in Hepatocellular Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaofei Feng ◽  
Shanshan Mu ◽  
Yao Ma ◽  
Wenji Wang
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Expression Profiles ◽  
Low Risk ◽  
Gene Set Enrichment Analysis ◽  
Related Gene ◽  
Prognostic Signature ◽  
Gene Pairs ◽  
Immune Related Gene ◽  
Risk Patients

With the increasing prevalence of Hepatocellular carcinoma (HCC) and the poor prognosis of immunotherapy, reliable immune-related gene pairs (IRGPs) prognostic signature is required for personalized management and treatment of patients. Gene expression profiles and clinical information of HCC patients were obtained from the TCGA and ICGC databases. The IRGPs are constructed using immune-related genes (IRGs) with large variations. The least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct IRGPs signature. The IRGPs signature was verified through the ICGC cohort. 1,309 IRGPs were constructed from 90 IRGs with high variability. We obtained 50 IRGPs that were significantly connected to the prognosis and constructed a signature that included 17 IRGPs. In the TCGA and ICGC cohorts, patients were divided into high and low-risk patients by the IRGPs signature. The overall survival time of low-risk patients is longer than that of high-risk patients. After adjustment for clinical and pathological factors, multivariate analysis showed that the IRGPs signature is an independent prognostic factor. The Receiver operating characteristic (ROC) curve confirmed the accuracy of the signature. Besides, gene set enrichment analysis (GSEA) revealed that the signature is related to immune biological processes, and the immune microenvironment status is distinct in different risk patients. The proposed IRGPs signature can effectively assess the overall survival of HCC, and provide the relationship between the signature and the reactivity of immune checkpoint therapy and the sensitivity of targeted drugs, thereby providing new ideas for the diagnosis and treatment of the disease.

scholarly journals Development and verification of an immune‐related gene pairs prognostic signature in ovarian cancer

2021 ◽  
Vol 25 (6) ◽  
pp. 2918-2930
Author(s):  
Bao Zhang ◽  
Xiaocui Nie ◽  
Xinxin Miao ◽  
Shuo Wang ◽  
Jing Li ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Related Gene ◽  
Prognostic Signature ◽  
Gene Pairs ◽  
Immune Related Gene

scholarly journals Development of an immune-related gene pairs index for the prognosis analysis of metastatic melanoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rong-zhi Huang ◽  
Min Mao ◽  
Jie Zheng ◽  
Hai-qi Liang ◽  
Feng-ling Liu ◽  
...  
Keyword(s):  
Decision Making ◽  
Skin Cancer ◽  
Metastatic Melanoma ◽  
Clinical Decision Making ◽  
Clinical Decision ◽  
Gene Set Enrichment Analysis ◽  
Comprehensive Treatment ◽  
Related Gene ◽  
Gene Pairs ◽  
Immune Related Gene

AbstractMelanoma is a skin cancer with great metastatic potential, which is responsible for the major deaths in skin cancer. Although the prognosis of melanoma patients has been improved with the comprehensive treatment, for patients with metastasis, the complexity and heterogeneity of diffuse diseases make prognosis prediction and systematic treatment difficult and ineffective. Therefore, we established a novel personalized immune-related gene pairs index (IRGPI) to predict the prognosis of patients with metastatic melanoma, which was conducive to provide new insights into clinical decision-making and prognostic monitoring for metastatic melanoma. Through complex analysis and filtering, we identified 24 immune-related gene pairs to build the model and obtained the optimal cut-off value from receiver operating characteristic curves, which divided the patients into high and low immune-risk groups. Meantime, the Kaplan–Meier analysis, Cox regression analysis and subgroup analysis showed that IRGPI had excellent prognostic value. Furthermore, IRGPI was shown that was closely associated with immune system in the subsequent tumor microenvironment analysis and gene set enrichment analysis. In addition, we broken through the data processing limitations of traditional researches in different platforms through the application of gene pairs, which would provide great credibility for our model. We believe that our research would provide a new perspective for clinical decision-making and prognostic monitoring in metastatic melanoma.

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