scholarly journals HILPDA Is a Prognostic Biomarker and Correlates With Macrophage Infiltration in Pan-Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Chengdong Liu ◽  
Xiaohan Zhou ◽  
Hanyi Zeng ◽  
Dehua Wu ◽  
Li Liu
Keyword(s):  
Survival Data ◽  
Immune Cell ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Clinical Prognosis ◽  
Cancer Data ◽  
Tumor Types ◽  
Pan Cancer

Background: The protein hypoxia-inducible lipid droplet-associated (HILPDA) is differentially expressed in various tumors. However, its role and correlation with immune cell infiltration in most tumors remain unclear.Methods: HILPDA expression was analyzed in pan-cancer data from The Cancer Genome Atlas (TCGA) database. The influence of HILPDA in clinical prognosis was evaluated using clinical survival data from TCGA. Enrichment analysis of HILPDA was conducted using the R package “clusterProfiler.” We downloaded the immune cell infiltration score of TCGA samples from published articles and analyzed the correlation between the magnitude of immune cell infiltration and HILPDA expression.Results: HILPDA was highly expressed and associated with worse overall survival, disease-specific survival, and progression-free interval in most tumor types. In addition, HILPDA expression was significantly associated with the glycolysis pathway and infiltration of immune cells. Tumor-associated macrophage (TAM) infiltration increased in tissues with high HILPDA expression in most tumor types. Immunosuppressive genes, such as PD-L1, PD-1, TGFB1, and TGFBR1 were positively correlated with HILPDA.Conclusions: Our study suggests that HILPDA is a marker of poor prognosis. High HILPDA may contribute to TAM infiltration and be associated with tumor immunosuppression status.

A Pan-Cancer Analysis of the Tumorigenic Role of Yin-Yang1 (YY1) in Human Tumors

2021 ◽  
Author(s):  
Ke-Hao Pan ◽  
Nai-Peng Shi ◽  
Yi-Fan Liu ◽  
Ya-Li Wang ◽  
Ming Chen
Keyword(s):  
Survival Data ◽  
Immune Cell ◽  
High Expression ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Clinical Prognosis ◽  
Free Survival ◽  
Cancer Data ◽  
Pan Cancer

Abstract Background: Yin-yang1 (YY1) is a nuclear transcription factor possessing dual transcriptional activity, which has different expression in a variety of tumor tissues. However, it remains unclear that the role of YY1 in most tumors and its association with immune cell infiltration.Methods: The expression of YY1 was analyzed in pan-cancer data which were downloaded from The Cancer Genome Atlas (TCGA) database. The clinical survival data downloading from TCGA was used to analyze the effect of YY1 on clinical prognosis. We had access to the R package “clusterProfiler” to make the enrichment analysis of YY1. The score of the immune cell infiltration of TCGA samples was downloaded from published articles and the correlation between YY1 expression and the immune cell infiltration was analyzed.Results: YY1 had a high expression in 25 tumors and strongly associated with clinical stage. In most tumor types, the over-expression of YY1 was connected to the worse prognostic indicator, such as overall survival(OS), progression-free survival (PFS), disease-specific survival(DSS) and disease-free survival (DFS). Moreover, the expression of YY1 had a correlation with tumor mutation burden(TMB). Nearly all of immune-related genes had co-expression with YY1 and almost all genes had positive correlation with YY1 in all types of tumors. It's worth noting that the expression levels of B cells and T cells were lower in the group with high YY1 expression. In addition, 22 m6A methylation-related cells were co-expressed with YY1, such as METTL3, YTHDC1, FTO and so on. Conclusions: Our study leads to a suggestion that YY1 may be a marker of bad prognosis and high expression of YY1 may lead to immune infiltration and be connected to m6A methylation.

scholarly journals AHSA1 is a Prognostic Biomarker that Correlates with Macrophage Infiltration in Pan-Cancer

2021 ◽  
Author(s):  
Fulei Li ◽  
Chengdong Liu ◽  
Yanling Chen ◽  
Shasha Li ◽  
Lu Bai
Keyword(s):  
T Cells ◽  
Cd8 T Cells ◽  
Immune Cell ◽  
Enrichment Analysis ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Cancer Data ◽  
Pan Cancer

Abstract Background: Activator of heat shock 90 kDa protein ATPase homolog 1 (AHSA1) is differentially expressed in several tumor types. However, its association with immune cell infiltration remains elusive. Methods: AHSA1 expression was analyzed using The Cancer Genome Atlas (TCGA) pan-cancer data and normal tissue expression data from Genotype-Tissue Expression (GTEx). The clinical prognostic role of AHSA1 in pan-cancer was investigated, and an enrichment analysis of AHSA1 was performed using the R package “clusterProfiler.” We downloaded data regarding the immune cell infiltration level of TCGA pan-cancer tissues and analyzed the association between immune cell infiltration and AHSA1 expression. Results: The results of TCGA pan-cancer data analysis revealed that AHSA1 was overexpressed and associated with poor survival in patients with cancer. Furthermore, the infiltration levels of tumor-associated macrophages (TAMs) were higher, while those of CD8+ T cells were lower, in the high AHSA1 expression group. Conclusions: Our study suggests that AHSA1 is an oncogene and a risk factor for patient survival in cancer. AHSA1 may contribute to high infiltration levels of TAMs and low infiltration levels of CD8+ T cells, thus indicating that high AHSA1 expression may be associated with the tumor immunosuppressive microenvironment.

RNF24 is a Novel Biomarker of Prognosis and Immunological Cell Infiltration in Cancers

2021 ◽  
Author(s):  
Bin Yu ◽  
ma mei
Keyword(s):  
Survival Data ◽  
Immune Cell ◽  
Ring Finger ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Pathway Enrichment Analysis ◽  
Systematic Analysis ◽  
Ppi Networks ◽  
Pan Cancer

Abstract Background The RNF family engaged in diverse biological and pathological processes, including tumorigenesis and cancer advance. However, studies about Ring Finger Protein 24 (RNF24) were limited and have not been reported in cancer. A systematic analysis in pan-cancer is a benefit to understand the function of RNF24. Methods RNF24 expression was evaluated in pan-cancer based on the data from The Cancer Genome Atlas (TCGA) analyzed by TIMER, UALCAN, GEPIA, and HPA. Then, the effect of RNF24 on the prognostic value was assessed by clinical survival data in Kaplan–Meier Plotter and GEPIA. And mutation burden and related survival of RNF24 was observed in cBioPortal. Furthermore, protein-protein interaction (PPI) networks of RNF24 and pathway enrichment analysis were explored on multiple websites. Lastly, relationships between RNF24 expression and immune cells infiltration were analyzed in the TIMER2 online database with various algorithms. Results The mRNA and protein levels of RNF24 were significantly upregulated in most types of cancer compared to normal tissues. And RNF24 was a reliable biomarker to predict prognosis in at least 10 types of cancer, including liver hepatocellular carcinoma (LIHC). In addition, we showed the genetic alteration, PPI networks, and functional pathway of RNF24. Moreover, immune cell infiltration exhibited RNF24 expression negatively linked to CD8+ T cells, but positively to Tregs, MDSCs, HSC, and macrophages in pan-cancer.Conclusions Our pan-cancer analysis revealed RNF24 as an oncogene and its expression predicted OS in multiple human cancers, especially in LIHC. RNF24 might predict the immunotherapy response for cancer patients based on its expression with infiltration of immune and immunosuppressive cells.

scholarly journals P4HA1, a Prognostic Biomarker that Correlates With Immune Infiltrates in Lung Adenocarcinoma and Pan-Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Qi Zhao ◽  
Junfeng Liu
Keyword(s):  
Prognostic Value ◽  
Immune Cell ◽  
Prognostic Biomarker ◽  
Enrichment Analysis ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Pathway Enrichment Analysis ◽  
Immune Cell Infiltration ◽  
Pan Cancer

Objective: Prolyl 4-hydroxylase, alpha polypeptide I (P4HA1), a key enzyme in collagen synthesis, comprises two identical alpha subunits and two beta subunits. However, the immunomodulatory role of P4HA1 in tumor immune microenvironment (TIME) remains unclear. This study aimed to evaluate the prognostic value of P4HA1 in pan-cancer and explore the relationship between P4HA1 expression and TIME.Methods: P4HA1 expression, clinical features, mutations, DNA methylation, copy number alteration, and prognostic value in pan-cancer were investigated using the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression data. Pathway enrichment analysis of P4HA1 was performed using R package “clusterProfiler.” The correlation between immune cell infiltration level and P4HA1 expression was analyzed using three sources of immune cell infiltration data, including ImmuCellAI database, TIMER2 database, and a published work.Results: P4HA1 was substantially overexpressed in most cancer types. P4HA1 overexpression was associated with poor survival in patients. Additionally, we discovered that P4HA1 expression was positively associated with infiltration levels of immunosuppressive cells, such as tumor-associated macrophages, cancer-associated fibroblasts, nTregs, and iTregs, and negatively correlated with CD8+ T and NK cells in pan-cancer.Conclusions: Our results highlighted that P4HA1 might serve as a potential prognostic biomarker in pan-cancer. P4HA1 overexpression is indicative of an immunosuppressive microenvironment. P4HA1 may be a potential target of immunotherapy.

scholarly journals INHBA is a Prognostic Biomarker and Correlated With Immune Cell Infiltration in Cervical Cancer

2022 ◽  
Vol 12 ◽  
Author(s):  
Kaidi Zhao ◽  
Yuexiong Yi ◽  
Zhou Ma ◽  
Wei Zhang
Keyword(s):  
Cervical Cancer ◽  
Immune Cell ◽  
Enrichment Analysis ◽  
R Package ◽  
Gene Set Enrichment Analysis ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Cancer Data ◽  
Pan Cancer ◽  
Geo Database

Background: Inhibin A (INHBA), a member of the TGF-β superfamily, has been shown to be differentially expressed in various cancer types and is associated with prognosis. However, its role in cervical cancer remains unclear.Methods: We aimed to demonstrate the relationship between INHBA expression and pan-cancer using The Cancer Genome Atlas (TCGA) database. Next, we validated INHBA expression in cervical cancer using the Gene Expression Omnibus (GEO) database, including GSE7803, GSE63514, and GSE9750 datasets. Enrichment analysis of INHBA was performed using the R package “clusterProfiler.” We analyzed the association between immune infiltration level and INHBA expression in cervical cancer using the single-sample gene set enrichment analysis (ssGSEA) method by the R package GSVA. We explored the association between INHBA expression and prognosis using the R package “survival”.Results: Pan-cancer data analysis showed that INHBA expression was elevated in 19 tumor types, including cervical cancer. We further confirmed that INHBA expression was higher in cervical cancer samples from GEO database and cervical cancer cell lines than in normal cervical cells. Survival prognosis analysis indicated that higher INHBA expression was significantly associated with reduced Overall Survival (p = 0.001), disease Specific Survival (p = 0.006), and Progression Free Interval (p = 0.001) in cervical cancer and poorer prognosis in other tumors. GSEA and infiltration analysis showed that INHBA expression was significantly associated with tumor progression and some types of immune infiltrating cells.Conclusion:INHBA was highly expressed in cervical cancer and was significantly associated with poor prognosis. Meanwhile, it was correlated with immune cell infiltration and could be used as a promising prognostic target for cervical cancer.

scholarly journals RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Yimin Pan ◽  
Kai Xiao ◽  
Yue Li ◽  
Yuzhe Li ◽  
Qing Liu
Keyword(s):  
Immune Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Lasso Regression ◽  
Gene Set Enrichment ◽  
Clinical Prognosis ◽  
Prognostic Assessment ◽  
The Relationship

Glioblastoma (GBM) is a group of intracranial neoplasms with intra-tumoral heterogeneity. RNA N6-methyladenosine (m6A) methylation modification reportedly plays roles in immune response. The relationship between the m6A modification pattern and immune cell infiltration in GBM remains unknown. Utilizing expression data of GBM patients, we thoroughly explored the potential m6A modification pattern and m6A-related signatures based on 21 regulators. Thereafter, the m6A methylation modification-based prognostic assessment pipeline (MPAP) was constructed to quantitatively assess GBM patients’ clinical prognosis combining the Robustness and LASSO regression. Single-sample gene-set enrichment analysis (ssGSEA) was used to estimate the specific immune cell infiltration level. We identified two diverse clusters with diverse m6A modification characteristics. Based on differentially expressed genes (DEGs) within two clusters, m6A-related signatures were identified to establish the MPAP, which can be used to quantitatively forecast the prognosis of GBM patients. In addition, the relationship between 21 m6A regulators and specific immune cell infiltration was demonstrated in our study and the m6A regulator ELAVL1 was determined to play an important role in the anticancer response to PD-L1 therapy. Our findings indicated the relationship between m6A methylation modification patterns and tumor microenvironment immune cell infiltration, through which we could comprehensively understand resistance to multiple therapies in GBM, as well as accomplish precise risk stratification according to m6A-related signatures.

scholarly journals Cancer Stemness Associated With Prognosis and the Efficacy of Immunotherapy in Adrenocortical Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaoxi Shi ◽  
Yuanlin Liu ◽  
Shuai Cheng ◽  
Haidi Hu ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Adrenocortical Carcinoma ◽  
Immune Cell ◽  
Checkpoint Inhibitors ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Potential Biomarker ◽  
Lower Expression

BackgroundCancer stem cells (CSCs) have been proven to influence drug resistance, recurrence, and metastasis in tumors. Our study aimed to identify stemness-related prognostic biomarkers for new therapeutic strategies in adrenocortical carcinoma.MethodsRNA-seq data and clinical characteristics were downloaded from The Cancer Genome Atlas (TCGA). The stemness indexes, mDNAsi and mRNAsi, were calculated to classify all samples into low-score and high-score groups. Two algorithms, based on the R language, ESTIMATE and single-sample Gene Set Enrichment Analysis (ssGSEA) were used to assess the immune cell infiltration states of adrenocortical carcinoma patients. Weighted Gene Co-expression Network Analysis (WGCNA) was used to find genes that were related to the stemness of cancer. By bioinformatics methods, the correlations between biomarkers capable of predicting immune checkpoint inhibitors (ICIs) responses and stemness of cancer were explored.ResultsHigh-mRNAsi predicted shorter overall survival (OS) and a higher metastatic trend in adrenocortical carcinoma (ACC) patients. Compared with the low-mRNAsi group, the high-mRNAsi group had a lower ImmuneScore and StromalScroe. Twenty-two stemness-related prognostic genes were obtained by WGCNA, which focused on the function of the cell cycle and cell mitosis. Immune cell infiltration, especially CD8+T cell, increased in the low-mRNAsi group compared with the high-mRNAsi group. Lower expression of PD-L1, CTLA-4, and TIGHT was evaluated in the high-mRNAsi group.ConclusionsACC patients with high-mRNAsi have poor prognosis and less immune cell infiltration. Combined with the finding of lower expression of CTLA-4, TIGHT, and PD-L1 in the high-mRNAsi group, we came to the conclusion that stemness index is a potential biomarker to predict the effectiveness of ICIs.

scholarly journals CRYAB predicts clinical prognosis and is associated with immunocyte infiltration in colorectal cancer

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12578
Author(s):  
Junsheng Deng ◽  
Xiaoli Chen ◽  
Ting Zhan ◽  
Mengge Chen ◽  
Xisheng Yan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Immune Cell ◽  
Malignant Tumors ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
Gene Marker ◽  
Immune Cell Infiltration ◽  
Clinical Prognosis ◽  
Advanced Tumor

Background αB-Crystallin (CRYAB) is differentially expressed in various tumors. However, the correlation between CRYAB and immune cell infiltration in colorectal cancer (CRC) remains unclear. Materials & Methods Kaplan–Meier survival curves in The Cancer Genome Atlas (TCGA) were used to evaluate the relationship between CRYAB expression and both overall survival and progression-free survival. The relationships between CRYAB expression and infiltrating immune cells and their corresponding gene marker sets were examined using the TIMER database. Results The expression of CRYAB was lower in CRC tumor tissues than in normal tissues (P < 0.05). High CRYAB gene expression and high levels of CRYAB gene methylation were correlated with high-grade malignant tumors and more advanced tumor, nodes and metastasis (TNM) cancer stages. In addition, in colorectal cancer, there was a positive correlation between CRYAB expression and immune infiltrating cells including neutrophils, macrophages, CD8 + T cells, and CD4 + T cells, as well as immune-related genes including CD2, CD3D, and CD3E. Methylation sites such as cg13084335, cg15545878, cg13210534, and cg15318568 were positively correlated with low expression of CRYAB. Conclusion Because CRYAB likely plays an important role in immune cell infiltration, it may be a potential tumor-suppressor gene in CRC and a potential novel therapeutic target and predictive biomarker for colorectal cancer (CRC).

scholarly journals CCDC137 Is a Prognostic Biomarker and Correlates With Immunosuppressive Tumor Microenvironment Based on Pan-Cancer Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Lihao Guo ◽  
Boxin Li ◽  
Zhaohong Lu ◽  
Hairong Liang ◽  
Hui Yang ◽  
...  
Keyword(s):  
Survival Data ◽  
Immune Cell ◽  
Coiled Coil ◽  
The Cancer Genome Atlas ◽  
Pathway Enrichment Analysis ◽  
Lower Grade ◽  
Coiled Coil Domain ◽  
Tumor Types ◽  
Pan Cancer

BackgroundThe coiled-coil domain containing (CCDC) family proteins have important biological functions in various diseases. However, the coiled-coil domain containing 137 (CCDC137) was rarely studied. We aim to investigate the role of CCDC137 in pan-cancer.MethodsCCDC137 expression was evaluated in RNA sequence expression profilers of pan-cancer and normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. The influence of CCDC137 on the prognosis of tumor patients was analyzed using clinical survival data from TCGA. Function and pathway enrichment analysis was performed to explore the role of CCDC137 using the R package “clusterProfiler.” We further analyzed the correlation of immune cell infiltration score of TCGA samples and CCDC137 expression using TIMER2 online database.ResultsCCDC137 was over-expressed and associated with worse survival status in various tumor types. CCDC137 expression was positively correlated with tumor associated macrophages (TAMs) and cancer associated fibroblasts (CAFs) in Lower Grade Glioma (LGG) and Uveal Melanoma (UVM). In addition, high CCDC137 expression was positively correlated with most immunosuppressive genes, including TGFB1, PD-L1, and IL10RB in LGG and UVM.ConclusionsOur study identified CCDC137 as an oncogene and predictor of worse survival in most tumor types. High CCDC137 may contribute to elevated infiltration of TAMs and CAFs and be associated with tumor immunosuppressive status.

scholarly journals Pan-Cancer Analyses Reveal Oncogenic and Immunological Role of Dickkopf-1 (DKK1)

2021 ◽  
Vol 12 ◽  
Author(s):  
Shuang Gao ◽  
Ye Jin ◽  
Hongmei Zhang
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Immune Cell ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Dickkopf 1 ◽  
Pan Cancer

WNT signaling pathway inhibitor Dickkopf-1 (DKK1) is related to cancer progression; however, its diagnostic and prognostic potential have not been investigated in a pan-cancer perspective. In this study, multiple bioinformatic analyses were conducted to evaluate therapeutic value of DKK1 in human cancers. The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project served as data resources. The Wilcoxon rank test was performed to evaluate the expression difference of DKK1 between cancer tissues and normal tissues. A Kaplan-Meier curve and Cox regression were used for prognosis evaluation. Single-sample gene set enrichment analysis (ssGSEA) was used to evaluate the association of DKK1 expression with the immune cell infiltration. The potential function of DKK1 was explored by STRING and clusterProfiler. We found that the expression level of DKK1 is significantly different in different cancer types. Importantly, we demonstrated that DKK1 is an independent risk factor in ESCA, LUAD, MESO, and STAD. Further analysis revealed that DKK1 had a large effect on the immune cell infiltration and markers of certain immune cells, such as Th1 and Th2 cells. PPI network analysis and further pathway enrichment analysis indicated that DKK1 was mainly involved in the WNT signaling pathway. Our findings suggested that DKK1 might serve as a marker of prognosis for certain cancers by affecting the WNT signaling pathway and tumor immune microenvironment.

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