scholarly journals BRCA1-Associated Protein Is a Potential Prognostic Biomarker and Is Correlated With Immune Infiltration in Liver Hepatocellular Carcinoma: A Pan-Cancer Analysis

2020 ◽  
Vol 7 ◽  
Author(s):  
Qiang Ju ◽  
Xin-mei Li ◽  
Heng Zhang ◽  
Yan-jie Zhao
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarker ◽  
Immune Infiltration ◽  
Liver Hepatocellular Carcinoma ◽  
Pan Cancer

scholarly journals A novel prognostic index model constructed with five autophagy-related genes may be a potential prognostic biomarker and therapeutic target in liver hepatocellular carcinoma

2020 ◽  
Author(s):  
Qingqing Zhu ◽  
Jia Wang ◽  
Menghan Liu ◽  
Qiujing Zhang ◽  
Miaomiao Shen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Survival Rate ◽  
Therapeutic Target ◽  
Prognostic Biomarker ◽  
Prognostic Index ◽  
Cancer Genome ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Liver Hepatocellular Carcinoma ◽  
Testing Group

Abstract Background Early diagnosis and effective treatment of liver hepatocellular carcinoma (LIHC) are keys to improving the prognosis of patients. Increasing evidences clarify that autophagy-related genes (ARGs) make great differences to the generation and progression of LIHC, and may serve as prognostic biomarkers for LIHC. Methods We randomly divided the LIHC patients in The Cancer Genome Atlas (TCGA) into the training and testing group. Next, use the training group to perform univariate Cox, LASSO and multivariate Cox analysis to construct our prognostic index (PI) model for LIHC; use the testing group and the whole TCGA set to make internal validations; use the International Cancer Genome Consortium to make external validations; and use the whole TCGA, GSE14520 and Oncomine to exam the expression patterns of the five ARGs. Then, we performed the ROC curve as well as univariate and multivariate analysis to evaluate the independent prognostic prediction power of the PI model, and made nomograms to estimate 1,3,5-year survival rate of LIHC patients. Besides, we conducted functional enrichment analyses of differentially expressed ARGs with GO, KEGG and GSEA, and made drug sensitivity analysis for the PI model via the GDSC database. Results A novel PI model which was composed of five key ARGs ( ATG9A , EIF2S1 , GRID1 , SAR1A and SQSTM1 ) succeeded to be constructed. All the internal and external validations testified that the PI model could well distinguish high-risk patients from low-risk ones, with AUC values > 0.60. Further comparison analysis showed that the PI model was no less than some common prognostic factors. People can estimate the 1,3,5-year survival rate of individual LIHC patient with the nomograms. Additionally, we obtained 62 differentially expressed ARGs and studied the potential mechanisms or pathways. Furthermore, we also found some potential targeted drugs associated to the five ARGs for LIHC patients. Conclusions The novel five-ARGs PI model has great potential to serve as a diagnostic or prognostic biomarker and therapeutic target in LIHC, which may guide future clinical applications to some extent and improve the outcome of LIHC patients.

scholarly journals SERPINH1 is a Potential Prognostic Biomarker and Correlated With Immune Infiltration: A Pan-Cancer Analysis

2022 ◽  
Vol 12 ◽  
Author(s):  
Yu Wang ◽  
Weigang Gu ◽  
Weiwei Wen ◽  
Xiaofeng Zhang
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Prognostic Biomarker ◽  
Proteinase Inhibitors ◽  
Pearson Correlation ◽  
Lower Grade ◽  
Immune Infiltration ◽  
Pan Cancer

Background: Serpin peptidase inhibitor clade H, member 1 (SERPINH1) is a gene encoding a member of the serpin superfamily of serine proteinase inhibitors. The upregulated of SERPINH1 was associated with poor prognosis in breast cancer, stomach adenocarcinoma, and esophageal carcinoma. However, the role of SERPINH1 in pan-cancer is largely unexplored.Methods: SERPINH1 expression and the correlation with prognosis in human pan-cancer were analyzed by the Cancer Genome Atlas and the Genotype-Tissue Expression dataset. Pearson correlation analysis was applied to evaluate the role of SERPINH1 expression in tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR), DNA methyltransferase, and common immunoregulators. Spearman’s correlation test was used to analysis SERPINH1 expression in tumor immune infiltration and infiltrating immune cells via the Tumor Immune Evaluation Resource database. Furtherly, immunohistochemistry staining of SERPINH1 was acquired from the Human Protein Atlas database for validation.Results: SERPINH1 was abnormally expressed in fourteen cancers. The high expression of SERPINH1 significantly reduced the overall survival (OS), disease-specific survival, and progression free interval in eleven cancers. Moreover, SERPINH1 expression was correlated with MMR, MSI, TMB, and DNA methylation in multiple types of cancer. Also, SERPINH1 expression showed strong association with immunoregulators and immune checkpoint markers in testicular germ cell tumors, brain lower grade glioma (LGG), pheochromocytoma and paraganglioma. In addition, SERPINH1 expression was related to immune cell infiltration in multiple cancers, particularly in breast invasive carcinoma, LGG, and liver hepatocellular carcinoma. The result of immunohistochemistry verification shown that SERPINH1 staining was higher in tumor samples than in normal tissue in colon adenocarcinoma, head and neck squamous cell carcinoma, kidney renal papillary cell carcinoma and cervical squamous cell carcinoma, which was consistent with the result of OS.Conclusion: Overall, these results indicate that SERPINH1 may serve as an important prognostic biomarker and correlate with tumor immunity in human pan-cancer.

scholarly journals Diagnostic significance and carcinogenic mechanism of pan-cancer gene POU5F1 in liver hepatocellular carcinoma

2020 ◽  
Author(s):  
Dingdong He ◽  
Xiaokang Zhang ◽  
Jiancheng Tu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Meta Analysis ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
Clinicopathological Parameters ◽  
Cancer Gene ◽  
Hub Genes ◽  
Liver Hepatocellular Carcinoma ◽  
The Impact ◽  
Pan Cancer

Abstract Background The prognostic and clinicopathological significance of POU Class 5 Homeobox 1 (POU5F1) among various cancers is disputable heretofore. The diagnostic value and function mechanism of POU5F1 in liver hepatocellular carcinoma (LIHC) have not been studied thoroughly. Methods An integrative strategy of meta-analysis, bioinformatics and wet-lab approach was used to explore the diagnostic and prognostic significance of POU5F1 in various types of tumors, especially in LIHC. Meta-analysis was utilized to investigate the impact of POU5F1 on prognosis and clinicopathological parameters in various cancers. The expression level and diagnostic value of POU5F1 were assessed by qPCR in plasma collected from LIHC patients and controls. The correlation between POU5F1 and tumor infiltrating immune cells (TIICs) in LIHC was evaluated by CIBERSORT. Gene set enrichment analysis (GSEA) was performed based on TCGA. Hub genes and related pathways were identified on the basis of co-expression genes of POU5F1. Results Elevated POU5F1 was associated with poor OS, DFS, RFS and DSS in various cancers. POU5F1 was confirmed as an independent risk factor for LIHC and correlated with tumor occurrence, stage and invasion depth. The combination of POU5F1 and AFP in plasma was with high diagnostic validity (AUC = 0.902, P < 0.001). Specifically, the level of POU5F1 was correlated with infiltrating levels of B cells, T cells, dendritic cells and monocytes in LIHC. GSEA indicated POU5F1 participated in multiple cancer related pathways and cell proliferation pathways. Moreover, CBX3, CCHCR1 and NFYC were filtered as the central hub genes of POU5F1. Conclusions Our study identified POU5F1 as a pan-cancer gene could not only be a prognostic and diagnostic biomarker in various cancers, especially in LIHC, but functionally carcinogenic in LIHC.

scholarly journals Comprehensive Analysis to Identify SPP1 as a Prognostic Biomarker in Cervical Cancer

2022 ◽  
Vol 12 ◽  
Author(s):  
Kaidi Zhao ◽  
Zhou Ma ◽  
Wei Zhang
Keyword(s):  
Cervical Cancer ◽  
Roc Curve ◽  
Immune Cell ◽  
Cox Regression ◽  
Prognostic Biomarker ◽  
R Package ◽  
Cancer Data ◽  
Immune Infiltration ◽  
Pan Cancer ◽  
Geo Database

Background:SPP1, secreted phosphoprotein 1, is a member of the small integrin-binding ligand N-linked glycoprotein (SIBLING) family. Previous studies have proven SPP1 overexpressed in a variety of cancers and can be identified as a prognostic factor, while no study has explored the function and carcinogenic mechanism of SPP1 in cervical cancer.Methods: We aimed to demonstrate the relationship between SPP1 expression and pan-cancer using The Cancer Genome Atlas (TCGA) database. Next, we validated SPP1 expression of cervical cancer in the Gene Expression Omnibus (GEO) database, including GSE7803, GSE63514, and GSE9750. The receiver operating characteristic (ROC) curve was used to evaluate the feasibility of SPP1 as a differentiating factor by the area under curve (AUC) score. Cox regression and logistic regression were performed to evaluate factors associated with prognosis. The SPP1-binding protein network was built by the STRING tool. Enrichment analysis by the R package clusterProfiler was used to explore potential function of SPP1. The single-sample GSEA (ssGSEA) method from the R package GSVA and TIMER database were used to investigate the association between the immune infiltration level and SPP1 expression in cervical cancer.Results: Pan-cancer data analysis showed that SPP1 expression was higher in most cancer types, including cervical cancer, and we got the same result in the GEO database. The ROC curve suggested that SPP1 could be a potential diagnostic biomarker (AUC = 0.877). High SPP1 expression was associated with poorer overall survival (OS) (P = 0.032). Further enrichment and immune infiltration analysis revealed that high SPP1 expression was correlated with regulating the infiltration level of neutrophil cells and some immune cell types, including macrophage and DC.Conclusion:SPP1 expression was higher in cervical cancer tissues than in normal cervical epithelial tissues. It was significantly associated with poor prognosis and immune cell infiltration. Thus, SPP1 may become a promising prognostic biomarker for cervical cancer patients.

scholarly journals CDKN2A is a Prognostic Biomarker and Correlated with Immune Infiltrates in Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Jun-peng Luo ◽  
Jing Wang ◽  
Jin-hua Huang
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cell ◽  
Immune Cell ◽  
Kinase Inhibitor ◽  
Prognostic Biomarker ◽  
Disease Free Survival ◽  
Cyclin Dependent Kinase ◽  
Strong Correlations ◽  
Immune Infiltration ◽  
Cyclin Dependent Kinase Inhibitor

Cyclin Dependent Kinase Inhibitor 2A (CDKN2A) is an essential regulator of immune cell functionality, but the mechanisms whereby it drives immune infiltration in hepatocellular carcinoma (HCC) remain unclear. In the current study, we studied the association with CDKN2A expression and immune invasion with the risk of developing HCC. A totally of 2207 different genes were found between HCC and adjacent liver tissues from TCGA and GEO databases. CDKN2A was highly expressed in HCC and associated with poorer overall survival and disease-free survival. Notably, CDKN2A expression was positively correlated with infiltrating levels into purity, B cell, CD+8 T cell, CD+4 T cell, macrophage, neutrophil, and dendritic cells in HCC. CDKN2A expression showed strong correlations between diverse immune marker sets in HCC. These findings suggest that CDKN2A expression potentially contributes to regulation of tumor-associated macrophages and can be used as a prognostic biomarker for determining prognosis and immune infiltration in HCC.

scholarly journals Prognostic and Immunological Role of mRNA ac4C Regulator NAT10 in Pan-Cancer: New Territory for Cancer Research?

2021 ◽  
Vol 11 ◽  
Author(s):  
Chuanxi Yang ◽  
Tingting Wu ◽  
Jing Zhang ◽  
Jinhui Liu ◽  
Kun Zhao ◽  
...  
Keyword(s):  
T Cells ◽  
Cell Carcinoma ◽  
Marker Gene ◽  
Gene Marker ◽  
Immune Infiltration ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Positive Correlations ◽  
Liver Hepatocellular Carcinoma ◽  
Pan Cancer

BackgroundNAT10 (also known as human N-acetyltransferase-like protein) is a critical gene that regulates N4-acetylcytidine formation in RNA, similar to the multiple regulators of N6-methyladenosine. However, the underlying functions and mechanisms of NAT10 in tumor progression and immunology are unclear.MethodsIn this study, we systematically analyzed the pan-cancer expression and correlations of NAT10, using databases including Oncomine, PrognoScan, GEPIA2, and Kaplan-Meier Plotter. The potential correlations of NAT10 with immune infiltration stages and gene marker sets were analyzed using the Tumor Immune Estimation Resource and GEPIA2.ResultsCompared with normal tissues, NAT10 showed higher expression in most cancers based on combined data from TCGA and GTEx. In different datasets, high NAT10 expression was significantly correlated with poor prognosis in adrenocortical carcinoma, head and neck squamous cell carcinoma, liver hepatocellular carcinoma, kidney renal papillary cell carcinoma, and pheochromocytoma and paraganglioma. Moreover, there were significant positive correlations between NAT10 expression and immune infiltrates, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, endothelial cells, and fibroblasts in LIHC. NAT10 expression showed strong correlations with diverse immune marker gene sets in LIHC.ConclusionNAT10 expression affects the prognosis of pan-cancer patients and is significantly correlated with tumor immune infiltration. Furthermore, it represents a potential target for cancer therapy.

scholarly journals Prognostic and Immunological Role of mRNA ac4C Regulator NAT10 in Pan-Cancer: New Territory for Cancer Research?

2020 ◽  
Author(s):  
Chuanxi Yang ◽  
Tingting Wu ◽  
Jing Zhang ◽  
Jinghui Liu ◽  
Kun Zhao ◽  
...  
Keyword(s):  
T Cells ◽  
Cell Carcinoma ◽  
Marker Gene ◽  
Gene Marker ◽  
Immune Infiltration ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Positive Correlations ◽  
Liver Hepatocellular Carcinoma ◽  
Pan Cancer

Abstract BackgroundNAT10 (also known as human N-acetyltransferase-like protein) is a critical gene that regulates N4-acetylcytidine formation in RNA, similar to the multiple regulators of N6-methyladenosine. However, the underlying functions and mechanisms of NAT10 in tumor progression and immunology are unclear.MethodsIn this study, we systematically analyzed the pan-cancer expression and correlations of NAT10, using databases including Oncomine, PrognoScan, GEPIA, and Kaplan-Meier Plotter. The potential correlations of NAT10 with immune infiltration stages and gene marker sets were analyzed using the Tumor Immune Estimation Resource and GEPIA.ResultsCompared with normal tissues, NAT10 showed higher expression in 26 of 27 cancers based on combined data from TCGA and GTEx. In different datasets, high NAT10 expression was significantly correlated with poor prognosis in adrenocortical carcinoma, head and neck squamous cell carcinoma, liver hepatocellular carcinoma, kidney renal papillary cell carcinoma, and pheochromocytoma and paraganglioma. Moreover, there were significant positive correlations between NAT10 expression and immune infiltrates, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, endothelial cells, and fibroblasts in LIHC. NAT10 expression showed strong correlations with diverse immune marker gene sets in LIHC.ConclusionNAT10 expression affects the prognosis of pan-cancer patients and is significantly correlated with tumor immune infiltration. Furthermore, it represents a potential target for cancer therapy.

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