An immune-associated gene prognostic index risk model for stomach adenocarcinoma

Abstract Background Stomach adenocarcinoma (STAD) is one of the most common malignant tumors worldwide. In this study, we attempt to construct a valid immune-associated gene prognostic index risk model which could predict the survival of HCC patients and the efficacy of immune check point inhibitors (ICIs) treatment. Methods The transcriptome, clinical and gene mutational data were obtained from the TCGA database. And immune-related genes were downloaded from the ImmPort and InnateDB databases. Functional and enrichment analysis was performed to identify the potential molecular function and mechanism of these differentially expressed immune-associated genes. And then candidates genes related to overall survival (OS) of STAD was obtained by weighted gene co-expression network analysis (WGCNA). Next, the immune prognostic risk model was constructed via multivariate Cox regression analysis and verified with GEO STAD cohort. Afterwards, the association between the risk model and the immune characteristics and was estimated. Finally, the correlation between the risk model and efficacy of ICIs therapy. Results A total of 493 immune-related genes were identified to enriched in function associated to immune response as well as in immune and tumor-related pathways. Based on the cox regression analysis, we constructed an immune-associated gene prognostic index (IAGPI) risk model based on 8 genes (RNASE2, CGB5, INHBE, PTGER3, CTLA4, DUSP1, APOA1 and CD36). Patients were divided into two subsets according to risk score. Patients in low risk set had a better OS than those in high. In the low risk set, there were more CD8 T cells, activated memory CD4 T cells, follicular helper T cells and M1 macrophages, while monocytes, M2 macrophages, eosinophils and neutrophils were more plentiful in the high. And patients in the low risk set were more sensitive to ICIs therapy. Conclusion The IAGPI risk model can precisely predict prognosis, reflect tumor immune microenvironment and predict the efficacy of ICIs therapy in STAD patients.

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Identification of Immune-Related Prognostic mRNA and lncRNA in Patients with Hepatocellular Carcinoma

Journal of Oncology ◽

10.1155/2022/5313149 ◽

2022 ◽

Vol 2022 ◽

pp. 1-16

Author(s):

Dan Chen ◽

Xiaoting Li ◽

Hui Li ◽

Kai Wang ◽

Xianghua Tian

Keyword(s):

Hepatocellular Carcinoma ◽

Flow Cytometry ◽

T Cells ◽

Regression Analysis ◽

Survival Analysis ◽

Immune Cells ◽

Cox Regression ◽

Differentially Expressed ◽

Cox Regression Analysis ◽

Immune Related Genes

Background. As the most common hepatic malignancy, hepatocellular carcinoma (HCC) has a high incidence; therefore, in this paper, the immune-related genes were sought as biomarkers in liver cancer. Methods. In this study, a differential expression analysis of lncRNA and mRNA in The Cancer Genome Atlas (TCGA) dataset between the HCC group and the normal control group was performed. Enrichment analysis was used to screen immune-related differentially expressed genes. Cox regression analysis and survival analysis were used to determine prognostic genes of HCC, whose expression was detected by molecular experiments. Finally, important immune cells were identified by immune cell infiltration and detected by flow cytometry. Results. Compared with the normal group, 1613 differentially expressed mRNAs (DEmRs) and 1237 differentially expressed lncRNAs (DElncRs) were found in HCC. Among them, 143 immune-related DEmRs and 39 immune-related DElncRs were screened out. These genes were mainly related to MAPK cascade, PI3K-AKT signaling pathway, and TGF-beta. Through Cox regression analysis and survival analysis, MMP9, SPP1, HAGLR, LINC02202, and RP11-598F7.3 were finally determined as the potential diagnostic biomarkers for HCC. The gene expression was verified by RT-qPCR and western blot. In addition, CD4 + memory resting T cells and CD8 + T cells were identified as protective factors for overall survival of HCC, and they were found highly expressed in HCC through flow cytometry. Conclusion. The study explored the dysregulation mechanism and potential biomarkers of immune-related genes and further identified the influence of immune cells on the prognosis of HCC, providing a theoretical basis for the prognosis prediction and immunotherapy in HCC patients.

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

10.21203/rs.3.rs-123214/v1 ◽

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.

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Identification of a Pyroptosis-Related lncRNA Risk Model for Predicting Prognosis and Immune Response in Colon Adenocarcinoma

10.21203/rs.3.rs-1234682/v1 ◽

2022 ◽

Author(s):

Yuying Tan ◽

Liqing Lu ◽

Xujun Liang ◽

Yongheng Chen

Keyword(s):

Regression Analysis ◽

Risk Model ◽

Cox Regression ◽

Malignant Tumors ◽

Colon Adenocarcinoma ◽

Sequencing Data ◽

Cox Regression Analysis ◽

Immune Infiltration ◽

Cerna Network ◽

Kaplan Meier

Abstract Background: Colon adenocarcinoma (COAD) is one of the most common malignant tumors and diagnosed at an advanced stage with poor prognosis in the world. Pyroptosis is involved in the initiation and progression of tumors. This research focused on constructing a pyroptosis-related ceRNA network to generate a reliable risk model for risk prediction and immune infiltration analysis of COAD.Methods: Transcriptome data, miRNA-sequencing data and clinical information were downloaded from the TCGA database. Firstly, differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and lncRNAs (DElncRNAs) were identified to construct a pyroptosis-related ceRNA network. Secondly, a pyroptosis-related lncRNA risk model was developed applying univariate Cox regression analysis and least absolute shrinkage and selection operator method (LASSO) regression analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were utilized to functionally annotate RNAs contained in the ceRNA network. In addition, Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, univariate and multivariate Cox regression, and nomogram were applied to validate this risk model. Finally, the relationship of this risk model with immune cells and immune checkpoint blockade (ICB) related genes were analyzed.Results: Totally 5373 DEmRNAs, 1159 DElncRNAs and 355 DEmiRNAs were identified. A pyroptosis-related ceRNA regulatory network containing 132 lncRNAs, 7miRNAs and 5 mRNAs was constructed and a ceRNA-based pyroptosis-related risk model including 11 lncRNAs was built. Tumor tissues were classified into high- and low- risk groups according to the median risk score. Kaplan-Meier analysis showed that the high-risk group had a shorter survival time; ROC analysis, independent prognostic analysis and nomogram further indicated the risk model was a significant independent prognostic factor which had excellent ability to predict patients’ risk. Moreover, immune infiltration analysis indicated that the risk model was related to immune infiltration cells (i.e., B cells naïve, T cells follicular helper, Macrophages M1, etc.) and ICB-related genes (i.e., PD-1, CTLA4, HAVCR2, etc).Conclusions: This pyroptosis-related lncRNA risk model possessed good prognostic value and the ability to predict the outcome of ICB immunotherapy in COAD.

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Comprehensive Analysis of Ferroptosis-Related LncRNAs in Breast Cancer Patients Reveals Prognostic Value and Relationship With Tumor Immune Microenvironment

Frontiers in Surgery ◽

10.3389/fsurg.2021.742360 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhengjie Xu ◽

Suxiao Jiang ◽

Juan Ma ◽

Desheng Tang ◽

Changsheng Yan ◽

...

Keyword(s):

Breast Cancer ◽

T Cells ◽

Regression Analysis ◽

Cox Regression ◽

Comprehensive Analysis ◽

Low Risk ◽

Gene Set Enrichment Analysis ◽

Prognostic Signature ◽

Immune Microenvironment ◽

Cox Regression Analysis

Background: Breast cancer (BC) is a heterogeneous malignant tumor, leading to the second major cause of female mortality. This study aimed to establish an in-depth relationship between ferroptosis-related LncRNA (FRlncRNA) and the prognosis as well as immune microenvironment of the patients with BC.Methods: We downloaded and integrated the gene expression data and the clinical information of the patients with BC from The Cancer Genome Atlas (TCGA) database. The co-expression network analysis and univariate Cox regression analysis were performed to screen out the FRlncRNAs related to prognosis. A cluster analysis was adopted to explore the difference of immune microenvironment between the clusters. Furthermore, we determined the optimal survival-related FRLncRNAs for final signature by LASSO Cox regression analysis. Afterward, we constructed and validated the prediction models, which were further tested in different subgroups.Results: A total of 31 FRLncRNAs were filtrated as prognostic biomarkers. Two clusters were determined, and C1 showed better prognosis and higher infiltration level of immune cells, such as B cells naive, plasma cells, T cells CD8, and T cells CD4 memory activated. However, there were no significantly different clinical characters between the clusters. Gene Set Enrichment Analysis (GSEA) revealed that some metabolism-related pathways and immune-associated pathways were exposed. In addition, 12 FRLncRNAs were determined by LASSO analysis and used to construct a prognostic signature. In both the training and testing sets, patients in the high-risk group had a worse survival than the low-risk patients. The area under the curves (AUCs) of receiver operator characteristic (ROC) curves were about 0.700, showing positive prognostic capacity. More notably, through the comprehensive analysis of heatmap, we regarded LINC01871, LINC02384, LIPE-AS1, and HSD11B1-AS1 as protective LncRNAs, while LINC00393, AC121247.2, AC010655.2, LINC01419, PTPRD-AS1, AC099329.2, OTUD6B-AS1, and LINC02266 were classified as risk LncRNAs. At the same time, the patients in the low-risk groups were more likely to be assigned to C1 and had a higher immune score, which were consistent with a better prognosis.Conclusion: Our research indicated that the ferroptosis-related prognostic signature could be used as novel biomarkers for predicting the prognosis of BC. The differences in the immune microenvironment exhibited by BC patients with different risks and clusters suggested that there may be a complementary synergistic effect between ferroptosis and immunotherapy.

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Identification of Prognosis-Related RBPs to Reveal The Role of RNA Binding Proteins in the Progression and Prognosis of Wilms’ Tumor

10.21203/rs.3.rs-135539/v1 ◽

2021 ◽

Author(s):

Xuejiao Qi ◽

Shuyu Wang ◽

Yihui Dong ◽

Xiaojie Lin ◽

Jingqiu Chen

Keyword(s):

Regression Analysis ◽

Cox Regression ◽

Wilms Tumor ◽

Prognostic Index ◽

Low Risk ◽

Gene Set Enrichment Analysis ◽

Risk Scores ◽

Clinical Parameters ◽

Cox Regression Analysis ◽

The Relationship

Abstract Background: Despite the various key functions of RBPs in posttranscriptional events, the mechanism of their influence on Wilms’ tumor has not been well elucidated. Therefore, we constructed the research to identify several RBPs related to Wilmes’ tumor progression and prognosis, for the better understanding of RBPs’ role in the occurrence and development of Wilmes’ tumor, and to provide effective reference targets for new drug development.Methods: A total of 127 samples of different clinical characteristics including gender, race and stage were selected from TARGET to carry out our study. After the gene functional enrichment pathways, univariate Cox regression analysis and lasso regression analysis were performed to test the prognostic effect of the differentially-expressed genes and establish the prognostic index . Further Cox regression analyses were utilized to identify the independence of our model and to analyze the relationship between our model and clinical parameters. What’s more, gene set enrichment analysis (GSEA) was also performed to elucidate the biological characteristics of genes involved in Wilms’ tumor. P< 0.05 was considered to be statistically significant.Results: 20 RBPs were statistically correlated with Wilms’ tumor. After the construction of a prognostic index , patients were divided into high-and low-risk scores group. Kaplan-Meier (K-M) analyses showed that patients with high risk scores possessed poorer survival probability than patients with low risk scores in both training group and test group. Furthermore, multivariate Cox regression analysis explored the relationship between our prognostic model and clinical parameters and confirmed that our model was an independent predicted factor for Wilms’ tumor. Conclusion: Our study clarifies the application of RBPs in the prognosis of Wilms’ tumor. We are confident that our risk scoring model can provide ideas for the development of new targets for broad-spectrum anticancer drugs and has great potential in clinical practice.

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Identification of Prognosis-related RBPs to Reveal the Role of RNA Binding Proteins in the Progression and Prognosis of Wilms’ Tumor

10.21203/rs.3.rs-115860/v1 ◽

2020 ◽

Author(s):

Xuejiao Qi ◽

Yihui Dong ◽

Xiaojie Lin ◽

Jingqiu Chen

Keyword(s):

Regression Analysis ◽

Binding Proteins ◽

Cox Regression ◽

Wilms Tumor ◽

Prognostic Index ◽

Low Risk ◽

Risk Scores ◽

Clinical Parameters ◽

Cox Regression Analysis ◽

The Relationship

Abstract BackgroundRNA-binding proteins (RBPs), the ubiquitous regulators that can bind to RNA, mediate the function of RNA in the process of its maturation, translation, transport and localization [1, 2]. Despite the various key functions of RBPs in posttranscriptional events, the mechanism of their influence on Wilms’ tumor has not been well elucidated. So we construct the research to identify several RBPs related to Wilmes’ tumor progression and prognosis, for the better understanding of RBPs’ role in the occurrence and development of Wilmes’ tumor, and to provide effective reference targets for new drug development.MethodsA total of 127 samples of different clinical characteristics including gender, race and stage were selected from TCGA to carry out our study. After the gene functional enrichment pathways, univariate Cox regression analysis and lasso regression analysis were performed to test the prognostic effect of the differentially-expressed genes and establish the prognostic index . Further Cox regression analyses were utilized to identify the independence of our model and to analyze the relationship between our model and clinical parameters. What’s more, gene set enrichment analysis (GSEA) was also performed to elucidate the biological characteristics of genes involved in Wilms’ tumor. P< 0.05 was considered to be statistically significant.Results26 RBPs were statistically correlated with Wilms’ tumor. After the construction of a prognostic index , patients were divided into high-and low-risk scores group. Kaplan-Meier (K-M) analyses showed that patients with high risk scores possessed poorer survival probability than patients with low risk scores in both training group and test group. Furthermore, multivariate Cox regression analysis explored the relationship between our prognostic model and clinical parameters and confirmed that our model was an independent predicted factor for Wilms’ tumor. ConclusionOur study clarifies the application of RBPs in the prognosis of Wilms’ tumor. We are confident that our risk scoring model can provide ideas for the development of new targets for broad-spectrum anticancer drugs and has great potential in clinical practice.Trial registrationretrospectively registered

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Identification of immune-related genes as prognostic factors in bladder cancer

Scientific Reports ◽

10.1038/s41598-020-76688-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Jie Zhu ◽

Han Wang ◽

Ting Ma ◽

Yan He ◽

Meng Shen ◽

...

Keyword(s):

Bladder Cancer ◽

Regression Analysis ◽

Prognostic Model ◽

Immune Cell ◽

Cox Regression ◽

Kegg Pathway ◽

Prognostic Index ◽

Immune Cell Infiltration ◽

Cox Regression Analysis ◽

Immune Related Genes

AbstractBladder cancer is one of the most common cancers worldwide. The immune response and immune cell infiltration play crucial roles in tumour progression. Immunotherapy has delivered breakthrough achievements in the past decade in bladder cancer. Differentially expressed genes and immune-related genes (DEIRGs) were identified by using the edgeR package. Gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for functional enrichment analysis of DEIRGs. Survival-associated IRGs were identified by univariate Cox regression analysis. A prognostic model was established by univariate COX regression analysis, and verified by a validation prognostic model based on the GEO database. Patients were divided into high-risk and low-risk groups based on the median risk score value for immune cell infiltration and clinicopathological analyses. A regulatory network of survival-associated IRGs and potential transcription factors was constructed to investigate the potential regulatory mechanisms of survival-associated IRGs. Nomogram and ROC curve to verify the accuracy of the model. Quantitative real-time PCR was performed to validate the expression of relevant key genes in the prognostic model. A total of 259 differentially expressed IRGs were identified in the present study. KEGG pathway analysis of IRGs showed that the “cytokine-cytokine receptor interaction” pathway was the most significantly enriched pathway. Thirteen survival-associated IRGs were selected to establish a prognostic index for bladder cancer. In both TCGA prognostic model and GEO validation model, patients with high riskscore had worse prognosis compared to low riskscore group. A high infiltration level of macrophages was observed in high-risk patients. OGN, ELN, ANXA6, ILK and TGFB3 were identified as hub survival-associated IRGs in the network. EBF1, WWTR1, GATA6, MYH11, and MEF2C were involved in the transcriptional regulation of these survival-associated hub IRGs. The present study identified several survival-associated IRGs of clinical significance and established a prognostic index for bladder cancer outcome evaluation for the first time.

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Identification of IGF2BP2 as a Prognostic Biomarker and Immunotherapeutic Target Based on Alternative Splicing Events in Glioblastoma

10.21203/rs.3.rs-900457/v1 ◽

2021 ◽

Author(s):

Xin-Yu Li ◽

Lei Hou ◽

Lu-yu Zhang ◽

Xue-yuan Li ◽

xi-tao Yang

Keyword(s):

Regression Analysis ◽

High Risk ◽

Prognostic Model ◽

Prognostic Markers ◽

Risk Model ◽

Cox Regression ◽

Prognostic Biomarker ◽

Low Risk ◽

Lasso Regression ◽

Cox Regression Analysis

Abstract Aim: A glioblastoma (GBM) prognostic model was developed with GBM -related alternative splicing (AS) data and prognostic markers were identified. Methods: AS data and clinical data of GBM patients were retrieved from The Cancer Genome Atlas (TCGA) SpliceSeq database and TCGA database, respectively. The data from these two databases were intersected to screen the prognosis-associated AS events, which was subsequently examined in Univariate Cox regression models. To avoid model overfitting, LASSO regression analysis was conducted. On the basis of these AS events, we established a prognostic model of GBM with the use of multivariate Cox regression analysis. On the strength of this model, the patients were assigned into high-risk and low-risk groups with a median risk score as the threshold. Kaplan-Meier survival, receiver operating characteristic (ROC), and calibration curves were applied to evaluate the performance of this model. Finally, combined with the risk model and clinicopathological characteristics, Cox regression analysis was utilized to identify the independent prognostic markers of GBM, and a nomogram was constructed. Results: The AS and clinical data of 169 GBM patients from the TCGA SpliceSeq and TCGA databases were collected. Univariate Cox regression analysis identified 1000 prognosis-related AS events in GBM, and then Lasso regression analysis identified 16 AS events. A GBM prognostic risk model was constructed based on AS events of 7 genes (FAM86B1, ZNF302, C19orf57, RPL39L, CBLL1, RWDD1, IGF2BP2). Through this model, we found lower overall survival (OS) rates of the high-risk population versus the low-risk population (p < 0.05). ROC and calibration curve analyses demonstrated the good ability of this model to predict the OS of GBM patients. Cox regression analysis suggested risk score as an independent prognostic factor for GBM. We also found that IGF2BP2 is associated with patient prognosis and have a strong relationship with immunotherapy response. Conclusion: The prognostic model based on AS events can significantly distinguish the survival rate of high-risk and low-risk GBM patients and IGF2BP2 were identified as a novel prognostic biomarker and immunotherapeutic target.

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Identification and development of an independent immune-related genes prognostic model for breast cancer

BMC Cancer ◽

10.1186/s12885-021-08041-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lin Chen ◽

Yuxiang Dong ◽

Yitong Pan ◽

Yuhan Zhang ◽

Ping Liu ◽

...

Keyword(s):

Breast Cancer ◽

Regression Analysis ◽

Cox Regression ◽

Gene Set Enrichment Analysis ◽

Risk Scores ◽

Validation Dataset ◽

Immune Gene ◽

Cox Regression Analysis ◽

Immune Genes ◽

Immune Related Genes

Abstract Background Breast cancer is one of the main malignant tumors that threaten the lives of women, which has received more and more clinical attention worldwide. There are increasing evidences showing that the immune micro-environment of breast cancer (BC) seriously affects the clinical outcome. This study aims to explore the role of tumor immune genes in the prognosis of BC patients and construct an immune-related genes prognostic index. Methods The list of 2498 immune genes was obtained from ImmPort database. In addition, gene expression data and clinical characteristics data of BC patients were also obtained from the TCGA database. The prognostic correlation of the differential genes was analyzed through Survival package. Cox regression analysis was performed to analyze the prognostic effect of immune genes. According to the regression coefficients of prognostic immune genes in regression analysis, an immune risk scores model was established. Gene set enrichment analysis (GSEA) was performed to probe the biological correlation of immune gene scores. P < 0.05 was considered to be statistically significant. Results In total, 556 immune genes were differentially expressed between normal tissues and BC tissues (p < 0. 05). According to the univariate cox regression analysis, a total of 66 immune genes were statistically significant for survival risk, of which 30 were associated with overall survival (P < 0.05). Finally, a 15 immune genes risk scores model was established. All patients were divided into high- and low-groups. KM survival analysis revealed that high immune risk scores represented worse survival (p < 0.001). ROC curve indicated that the immune genes risk scores model had a good reliability in predicting prognosis (5-year OS, AUC = 0.752). The established risk model showed splendid AUC value in the validation dataset (3-year over survival (OS) AUC = 0.685, 5-year OS AUC = 0.717, P = 0.00048). Moreover, the immune risk signature was proved to be an independent prognostic factor for BC patients. Finally, it was found that 15 immune genes and risk scores had significant clinical correlations, and were involved in a variety of carcinogenic pathways. Conclusion In conclusion, our study provides a new perspective for the expression of immune genes in BC. The constructed model has potential value for the prognostic prediction of BC patients and may provide some references for the clinical precision immunotherapy of patients.

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Identification of Prognostic RBPs in Osteosarcoma

Technology in Cancer Research & Treatment ◽

10.1177/15330338211004918 ◽

2021 ◽

Vol 20 ◽

pp. 153303382110049

Author(s):

Bei Li ◽

Long Fang ◽

Baolong Wang ◽

Zengkun Yang ◽

Tingbao Zhao

Keyword(s):

Regression Analysis ◽

Prognostic Factors ◽

Differential Expression ◽

Ribosome Biogenesis ◽

Rna Binding ◽

Cox Regression ◽

Rna Binding Proteins ◽

Malignant Tumors ◽

Differential Expression Analysis ◽

Cox Regression Analysis

Osteosarcoma often occurs in children and adolescents and causes poor prognosis. The role of RNA-binding proteins (RBPs) in malignant tumors has been elucidated in recent years. Our study aims to identify key RBPs in osteosarcoma that could be prognostic factors and treatment targets. GSE33382 dataset was downloaded from Gene Expression Omnibus (GEO) database. RBPs extraction and differential expression analysis was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to explore the biological function of differential expression RBPs. Moreover, we constructed Protein-protein interaction (PPI) network and obtained key modules. Key RBPs were identified by univariate Cox regression analysis and multiple stepwise Cox regression analysis combined with the clinical information from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Risk score model was generated and validated by GSE16091 dataset. A total of 38 differential expression RBPs was identified. Go and KEGG results indicated these RBPs were significantly involved in ribosome biogenesis and mRNA surveillance pathway. COX regression analysis showed DDX24, DDX21, WARS and IGF2BP2 could be prognostic factors in osteosarcoma. Spearman’s correlation analysis suggested that WARS might be important in osteosarcoma immune infiltration. In conclusion, DDX24, DDX21, WARS and IGF2BP2 might play key role in osteosarcoma, which could be therapuetic targets for osteosarcoma treatment.

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