scholarly journals Prognostic Model of Head and Neck Squamous Cell Carcinoma Based on 12 Ferroptosis-related Genes

2021 ◽  
Author(s):  
Sijia Li ◽  
Hongyang Zhang ◽  
Wei Li
Keyword(s):  
Regression Analysis ◽  
Risk Score ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Risk Scores ◽  
Cox Regression Analysis ◽  
Normal Tissues ◽  
Model Based ◽  
Cox Analysis

Abstract Background: The purpose of our study is establishing a model based on ferroptosis-related genes predicting the prognosis of patients with head and neck squamous cell carcinoma (HNSCC).Methods: In our study, transcriptome and clinical data of HNSCC patients were from The Cancer Genome Atlas, ferroptosis-related genes and pathways were from Ferroptosis Signatures Database. Differentially expressed genes (DEGs) were screened by comparing tumor and adjacent normal tissues. Functional enrichment analysis of DEGs, protein-protein interaction network and gene mutation examination were applied. Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to identified DEGs. The model was constructed by multivariate Cox regression analysis and verified by Kaplan-Meier analysis. The relationship between risk scores and other clinical features was also analyzed. Univariate and multivariate Cox analysis was used to verified the independence of our model. The model was evaluated by receiver operating characteristic analysis and calculation of the area under the curve (AUC). A nomogram model based on risk score, age, gender and TNM stages was constructed. Our model was also validated in the Gene Expression Omnibus (GEO) verification set. Results: We analyzed data including 500 tumor tissues and 44 adjacent normal tissues and 259 ferroptosis-related genes, then obtained 73 DEGs. Univariate Cox regression analysis screened out 16 genes related to overall survival, and LASSO analysis fingered out 12 of them with prognostic value. A risk score model based on these 12 genes was constructed by multivariate Cox regression analysis. According to the median risk score, patients were divided into high-risk group and low-risk group. The survival rate of high-risk group was significantly lower than that of low-risk group in Kaplan-Meier curve. Risk scores were related to T and grade. Univariate and multivariate Cox analysis showed our model was an independent prognostic factor. The AUC was 0.669. Those all could prove our model had great predictive ability of HNSCC prognosis and it could be validated in GEO dataset. The nomogram showed high accuracy predicting the prognosis of HNSCC patients.Conclusion: Our model based on 12 ferroptosis-related genes performed excellently in predicting the prognosis of HNSCC patients. Ferroptosis-related genes may be promising biomarkers for HNSCC treatment and prognosis.

scholarly journals Prognostic model of head and neck squamous cell carcinoma based on 12 ferroptosis-related genes

2021 ◽  
Author(s):  
Sijia Li ◽  
Hongyang Zhang ◽  
Wei Li
Keyword(s):  
Regression Analysis ◽  
Risk Score ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Risk Scores ◽  
Cox Regression Analysis ◽  
Normal Tissues ◽  
Model Based ◽  
Cox Analysis

Abstract Background: The purpose of our study is establishing a model based on ferroptosis-related genes predicting the prognosis of patients with head and neck squamous cell carcinoma (HNSCC).Methods: In our study, transcriptome and clinical data of HNSCC patients were from The Cancer Genome Atlas, ferroptosis-related genes and pathways were from Ferroptosis Signatures Database. Differentially expressed genes (DEGs) were screened by comparing tumor and adjacent normal tissues. Functional enrichment analysis of DEGs, protein-protein interaction network and gene mutation examination were applied. Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to identified DEGs. The model was constructed by multivariate Cox regression analysis and verified by Kaplan-Meier analysis. The relationship between risk scores and other clinical features was also analyzed. Univariate and multivariate Cox analysis was used to verified the independence of our model. The model was evaluated by receiver operating characteristic analysis and calculation of the area under the curve (AUC). A nomogram model based on risk score, age, gender and TNM stages was constructed.Results: We analyzed data including 500 tumor tissues and 44 adjacent normal tissues and 259 ferroptosis-related genes, then obtained 73 DEGs. Univariate Cox regression analysis screened out 16 genes related to overall survival, and LASSO analysis fingered out 12 of them with prognostic value. A risk score model based on these 12 genes was constructed by multivariate Cox regression analysis. According to the median risk score, patients were divided into high-risk group and low-risk group. The survival rate of high-risk group was significantly lower than that of low-risk group in Kaplan-Meier curve. Risk scores were related to T and grade. Univariate and multivariate Cox analysis showed our model was an independent prognostic factor. The AUC was 0.669. The nomogram showed high accuracy predicting the prognosis of HNSCC patients.Conclusion: Our model based on 12 ferroptosis-related genes performed excellently in predicting the prognosis of HNSCC patients. Ferroptosis-related genes may be promising biomarkers for HNSCC treatment and prognosis.

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 Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinzhi Lai ◽  
Hainan Yang ◽  
Tianwen Xu
Keyword(s):  
Overall Survival ◽  
Regression Analysis ◽  
Risk Score ◽  
Regulatory Network ◽  
Immune Cell ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Immune Cell Infiltration ◽  
Cox Regression Analysis

Abstract Background Malignant mesothelioma (MM) is a relatively rare and highly lethal tumor with few treatment options. Thus, it is important to identify prognostic markers that can help clinicians diagnose mesothelioma earlier and assess disease activity more accurately. Alternative splicing (AS) events have been recognized as critical signatures for tumor diagnosis and treatment in multiple cancers, including MM. Methods We systematically examined the AS events and clinical information of 83 MM samples from TCGA database. Univariate Cox regression analysis was used to identify AS events associated with overall survival. LASSO analyses followed by multivariate Cox regression analyses were conducted to construct the prognostic signatures and assess the accuracy of these prognostic signatures by receiver operating characteristic (ROC) curve and Kaplan–Meier survival analyses. The ImmuCellAI and ssGSEA algorithms were used to assess the degrees of immune cell infiltration in MM samples. The survival-related splicing regulatory network was established based on the correlation between survival-related AS events and splicing factors (SFs). Results A total of 3976 AS events associated with overall survival were identified by univariate Cox regression analysis, and ES events accounted for the greatest proportion. We constructed prognostic signatures based on survival-related AS events. The prognostic signatures proved to be an efficient predictor with an area under the curve (AUC) greater than 0.9. Additionally, the risk score based on 6 key AS events proved to be an independent prognostic factor, and a nomogram composed of 6 key AS events was established. We found that the risk score was significantly decreased in patients with the epithelioid subtype. In addition, unsupervised clustering clearly showed that the risk score was associated with immune cell infiltration. The abundances of cytotoxic T (Tc) cells, natural killer (NK) cells and T-helper 17 (Th17) cells were higher in the high-risk group, whereas the abundances of induced regulatory T (iTreg) cells were lower in the high-risk group. Finally, we identified 3 SFs (HSPB1, INTS1 and LUC7L2) that were significantly associated with MM patient survival and then constructed a regulatory network between the 3 SFs and survival-related AS to reveal potential regulatory mechanisms in MM. Conclusion Our study provided a prognostic signature based on 6 key events, representing a better effective tumor-specific diagnostic and prognostic marker than the TNM staging system. AS events that are correlated with the immune system may be potential therapeutic targets for MM.

scholarly journals Identification and Prognostic Value Exploration of Radiotherapy Sensitivity-Associated Genes in Non-Small-Cell Lung Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Qing Ma ◽  
Kai Geng ◽  
Ping Xiao ◽  
Lili Zeng
Keyword(s):  
Lung Cancer ◽  
Regression Analysis ◽  
Risk Score ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Small Cell ◽  
Small Cell Lung ◽  
Cox Regression Analysis ◽  
Nsclc Patients

Background. Non-small-cell lung cancer (NSCLC) is a prevalent malignancy with high mortality and poor prognosis. The radiotherapy is one of the most common treatments of NSCLC, and the radiotherapy sensitivity of patients could affect the individual prognosis of NSCLC. However, the prognostic signatures related to radiotherapy response still remain limited. Here, we explored the radiosensitivity-associated genes and constructed the prognostically predictive model of NSCLC cases. Methods. The NSCLC samples with radiotherapy records were obtained from The Cancer Genome Atlas database, and the mRNA expression profiles of NSCLC patients from the GSE30219 and GSE31210 datasets were obtained from the Gene Expression Omnibus database. The Weighted Gene Coexpression Network Analysis (WGCNA), univariate, least absolute shrinkage and selection operator (LASSO), multivariate Cox regression analysis, and nomogram were conducted to identify and validate the radiotherapy sensitivity-related signature. Results. WGCNA revealed that 365 genes were significantly correlated with radiotherapy response. LASSO Cox regression analysis identified 8 genes, including FOLR3, SLC6A11, ALPP, IGFN1, KCNJ12, RPS4XP22, HIST1H2BH, and BLACAT1. The overall survival (OS) of the low-risk group was better than that of the high-risk group separated by the Risk Score based on these 8 genes for the NSCLC patients. Furthermore, the immune infiltration analysis showed that monocytes and activated memory CD4 T cells had different relative proportions in the low-risk group compared with the high-risk group. The Risk Score was correlated with immune checkpoints, including CTLA4, PDL1, LAG3, and TIGIT. Conclusion. We identified 365 genes potentially correlated with the radiotherapy response of NSCLC patients. The Risk Score model based on the identified 8 genes can predict the prognosis of NSCLC patients.

scholarly journals Identification and Validation of Angiogenesis-Related Gene Expression for Predicting Prognosis in Patients With Ovarian Cancer

2022 ◽  
Vol 11 ◽  
Author(s):  
Yue Wang ◽  
Bao Xuan Li ◽  
Xiang Li
Keyword(s):  
Ovarian Cancer ◽  
Overall Survival ◽  
Regression Analysis ◽  
Risk Score ◽  
Clinical Decision Making ◽  
Cox Regression ◽  
Risk Group ◽  
Cancer Genome ◽  
Risk Scores ◽  
Cox Regression Analysis

Ovarian cancer (OC) is a highly heterogeneous disease with different cellular origins reported; thus, precise prognostic strategies and effective new therapies are urgently needed for patients with OC. A growing number of studies have shown that most malignancies have intensive angiogenesis and rapid growth. Therefore, angiogenesis plays an important role in the development of tumor metastasis. However, the prognostic value of angiogenesis-related genes (ARGs) in OC remains to be further elucidated. In this study, the expression data and corresponding clinical data from patients with OC and normal control samples were downloaded with UCSC XENA. A total of 1,960 differentially expressed ARGs were screened and functionally annotated through Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Univariate Cox regression analysis was performed to identify ARGs associated with prognosis. New ARGs signatures (including ESM1, CXCL13, TPCN2, PTPRD, FOXO1, and ELK3) were constructed for the prediction of overall survival (OS) in OC based on the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis. Patients were divided based on their median risk score. In the The Cancer Genome Atlas (TCGA) training dataset, the survival analysis showed that overall survival was lower in the high-risk group than that in the low-risk group (p < 0.0001). The International Cancer Genome Consortium (ICGC) database was used for validation, and the receiver operating characteristic (ROC) curves showed good performance. Univariate and multivariate Cox analyses were conducted to identify independent predictors of OS. The nomogram, including the risk score, age, stage, grade, and position, can not only show good predictive ability but also can explore the correlation analysis based on ARGs for immunogenicity, immune components, and immune phenotypes with risk score. Risk scores were correlated strongly with the type of immune infiltration. Furthermore, homologous recombination defect (HRD), NtAIscore, LOH score, LSTm score, stemness index (mRNAsi), and stromal cells were significantly correlated with risk score. The present study suggests that the novel signature constructed from six ARGs may serve as effective prognostic biomarkers for OC and contribute to clinical decision making and personalized prognostic monitoring of OC.

scholarly journals Development of a prognostic signature of patients with esophagus adenocarcinoma by using immune-related genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiangxin Zhang ◽  
Liu Yang ◽  
Ming Kong ◽  
Jian Ma ◽  
Yutao Wei
Keyword(s):  
Risk Score ◽  
Cox Regression ◽  
Risk Group ◽  
Survival Rates ◽  
High Risk Group ◽  
Survival Prediction ◽  
Cox Regression Analysis ◽  
Related Data ◽  
Cox Analysis ◽  
Immune Related Genes

Abstract Background Esophageal adenocarcinoma (EAC) is an aggressive malignancy with a poor prognosis. The immune-related genes (IRGs) are crucial to immunocytes tumor infiltration. This study aimed to construct a IRG-related prediction signature in EAC. Methods The related data of EAC patients and IRGs were obtained from the TCGA and ImmPort database, respectively. The cox regression analysis constructed the prediction signature and explored the transcription factors regulatory network through the Cistrome database. TIMER database and CIBERSORT analytical tool were utilized to explore the immunocytes infiltration analysis. Results The prediction signature with 12 IRGs (ADRM1, CXCL1, SEMG1, CCL26, CCL24, AREG, IL23A, UCN2, FGFR4, IL17RB, TNFRSF11A, and TNFRSF21) was constructed. Overall survival (OS) curves indicate that the survival rate of the high-risk group is significantly shorter than the low-risk group (P = 7.26e−07), and the AUC of 1-, 3- and 5- year survival prediction rates is 0.871, 0.924, and 0.961, respectively. Compared with traditional features, the ROC curve of the risk score in the EAC patients (0.967) is significant than T (0.57), N (0.738), M (0.568), and Stage (0.768). Moreover, multivariate Cox analysis and Nomogram of risk score are indicated that the 1-year and 3-year survival rates of patients are accurate by the combined analysis of the risk score, Sex, M stage, and Stage (The AUC of 1- and 3-years are 0.911, and 0.853). Conclusion The 12 prognosis-related IRGs might be promising therapeutic targets for EAC.

scholarly journals Endothelial Cells Immune-Related Genes Risk Signature Correlated With Tumor Immune Microenvironment Predicts Therapeutic Response and Prognosis in Glioblastoma

2021 ◽  
Author(s):  
Qijun Xie ◽  
Yuwei Zhang ◽  
Wu Huang ◽  
Haoran Wang ◽  
Fang Liu
Keyword(s):  
Endothelial Cells ◽  
Regression Analysis ◽  
Risk Score ◽  
Therapeutic Response ◽  
Immune Cell ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Cox Regression Analysis ◽  
Immune Related Genes

Abstract Glioblastoma (GBM) is the most common and aggressive primary tumor of the central nervous system with high recurrence and extremely poor prognosis. Multiple recent studies have indicated a pivotal correlation between GBM prognosis and immune-related risk signature. Nevertheless, the potential value of endothelial cells (ECs) immune-related genes (EIRGs) in prognosis, immune infiltration, and their correlation with therapeutic response to immunotherapy and TMZ chemotherapy remain obscure, especially in GBM. Here, we screened out 11 EIRGs after intersecting the identified 59 GBM ECs related prognostic genes and the identified 438 immune-related prognostic genes. A prognostic-related 6-EIRGs signature was established through univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis, and patients in the high-risk group were significantly worse overall survival (OS) compared to those in the low-risk group. Additionally, univariate and multivariate Cox regression analysis confirmed that risk score was an independent predictor of OS in patients with GBM. The nomogram which comprised age, gender, IDH mutation status, radiation therapy, and risk score yielded a strong predictive ability of 0.5-, 1-, and 2-year OS for GBM patients. Our results demonstrate that the EIRGs signature, which is associated with immune cell infiltration, may play a regulatory role in the immunobiological process of TIME. Prognostic-related 6-EIRGs signature is a promising classification index for predicting the drug sensitivity to immunotherapy and TMZ chemotherapy, suggesting that EIRGs signature may serve as a biomarker to stratify patients who will benefit from immunotherapy and chemotherapy.

A Six CT83-Related Genes Based Prognostic Signature for Lung Adenocarcinoma

2021 ◽  
Vol 24 ◽  
Author(s):  
Yongmei Wang ◽  
Guimin Zhang ◽  
Ruixian Wang
Keyword(s):  
Regression Analysis ◽  
Lung Adenocarcinoma ◽  
Differential Expression ◽  
Risk Score ◽  
Prognostic Model ◽  
Cox Regression ◽  
Differential Expression Analysis ◽  
Functional Enrichment ◽  
Risk Scores ◽  
Cox Regression Analysis

Background: This study aims to explore the prognostic values of CT83 and CT83-related genes in lung adenocarcinoma (LUAD). Methods: We downloaded the mRNA profiles of 513 LUAD patients (RNA sequencing data) and 246 NSCLC patients (Affymetrix Human Genome U133 Plus 2.0 Array) from TCGA and GEO databases. According to the median expression of CT83, the TCGA samples were divided into high and low expression groups, and differential expression analysis between them was performed. Functional enrichment analysis of differential expression genes (DEGs) was conducted. Univariate Cox regression analysis and LASSO Cox regression analysis were performed to screen the optimal prognostic DEGs. Then we established the prognostic model. A Nomogram model was constructed to predict the overall survival (OS) probability of LUAD patients. Results: CT83 expression was significantly correlated to the prognosis of LUAD patients. A total of 59 DEGs were identified, and a predictive model was constructed based on six optimal CT83-related DEGs, including CPS1, RHOV, TNNT1, FAM83A, IGF2BP1, and GRIN2A, could effectively predict the prognosis of LUAD patients. The nomogram could reliably predict the OS of LUAD patients. Moreover, the six important immune checkpoints (CTLA4, PD1, IDO1, TDO2, LAG3, and TIGIT) were closely correlated with the Risk Score, which was also differentially expressed between the LUAD samples with high and low-Risk Scores, suggesting that the poor prognosis of LUAD patients with high-Risk Score might be due to the immunosuppressive microenvironments. Conclusion: A prognostic model based on six optimal CT83 related genes could effectively predict the prognosis of LUAD patients.

scholarly journals A Transcription Factor Signature Predicts Prognosis of Patients with Adrenocortical Carcinoma

2021 ◽  
Author(s):  
Jianyu Zhao ◽  
Bo Liu ◽  
Xiaoping Li
Keyword(s):  
Overall Survival ◽  
High Risk ◽  
Risk Score ◽  
Adrenocortical Carcinoma ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Prognostic Signature ◽  
Abdominal Masses ◽  
Cox Analysis

Abstract Background: Adrenocortical carcinoma (ACC) is a rare endocrine cancer that manifests as abdominal masses and excessive steroid hormone levels. Transcription factors (TFs) deregulation is found to be involved in adrenocortical tumorigenesis and cancer progression. This study aimed to construct a TF-based prognostic signature for prediction of survival of ACC patients.Methods: The gene expression profile for ACC patients were downloaded from TCGA and GEO datasets. The univariate Cox analysis was applied to identify survival-related TFs and the LASSO Cox regression was conducted to construct the TF signature. The multivariate analysis was used to reveal the independent prognostic factors.Results: We identified a 13-TF prognostic signature comprised of CREB3L3, NR0B1, CENPA, FOXM1, E2F2, MYBL2, HOXC11, ZIC2, ZNF282, DNMT1, TCF3, ELK4, and KLF6 using the univariate Cox analysis and LASSO Cox regression. The risk score based on the TF-signature could classify patients into low- and high-risk group. Kaplan-Meier analyses showed that patients in the high-risk group had significantly shorter overall survival compared to the low-risk patients. ROC curves showed that the prognostic signature predicted the overall survival of ACC patients with good sensitivity and specificity. Furthermore, the TF-risk score was an independent prognostic factor.Conclusion: Taken together, we identified a 13-TF prognostic marker to predict overall survival in ACC patients.

scholarly journals Identification of a Novel Glycolysis-Related Signature to Predict the Prognosis of Patients with Breast Cancer

2021 ◽  
Author(s):  
Menglin He ◽  
Cheng Hu ◽  
Jian Deng ◽  
Hui Ji ◽  
Weiqian Tian
Keyword(s):  
Breast Cancer ◽  
Risk Score ◽  
Cox Regression ◽  
Risk Group ◽  
Gene Signature ◽  
High Risk Group ◽  
Low Risk ◽  
Cox Regression Analysis ◽  
Expression Levels ◽  
Incidence And Mortality

Abstract Background: Breast cancer (BC) is a kind of cancer with high incidence and mortality in female. Conventional clinical characteristics are far from accurate to predict individual outcomes. Therefore, we aimed to develop a novel signature to predict the survival of patients with BC. Methods: We analyzed the data of a training cohort from the TCGA database and a validation cohort from GEO database. After the applications of GSEA and Cox regression analyses, a glycolysis-related signature for predicting the survival of patients with BC was developed. The signature contains AK3, CACNA1H, IL13RA1, NUP43, PGK1, and SDC1. Then, we constructed a risk score formula to classify the patients into high and low-risk groups based on the expression levels of six-gene in patients. The receiver operating characteristic (ROC) curve and the Kaplan-Meier curve were used to assess the predicted capacity of the model. Next, a nomogram was developed to predict the outcomes of patients with risk score and clinical features in 1, 3, and 5 years. We further used Human Protein Atlas (HPA) database to validate the expressions of the six biomarkers in tumor and sample tissues.Results: We constructed a six-gene signature to predict the outcomes of patients with BC. The patients in high-risk group showed poor prognosis than that in low-risk group. The AUC values were 0.719 and 0.702, showing that the prediction performance of the signature is acceptable. Additionally, Cox regression analysis revealed that these biomarkers could independently predict the prognosis of BC patients without being affected by clinical factors. The expression levels of all six biomarkers in BC tissues were higher than that in normal tissues except AK3. Conclusion: We developed a six-gene signature to predict the prognosis of patients with BC. Our signature has been proved to have the ability to make an accurate and obvious prediction and might be used to expand the prediction methods in clinical.

Sign in / Sign up

Export Citation Format

Share Document