Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma

Zhao, Yijie; Chen, Dongyi; Yin, Jian; Xie, Jian; Sun, Chengfei; Lu, Mengmeng

doi:10.3389/fgene.2022.788580

Cited by 11 publications

(11 citation statements)

References 49 publications

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“…The expression levels of FN1, ZEB1, ZEB2 , and TGFB1 were the highest in Immunity_H, suggesting that the activity of EMT was the highest in Immunity_H. This finding is consistent with those of previous studies [ 12 , 24 ] in that the higher the immune activity, the better the clinical prognosis. Some studies have indicated that immune infiltration and EMT are more accurate predictors of antitumor immunotherapy in lung cancer, and T cell infiltration negatively correlated with EMT signaling in NSCLC.…”

Section: Discussionsupporting

confidence: 91%

Analysis of immune subtypes in non-small-cell lung cancer based on TCGA database

Chen

Song

2023

Medicine

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Immunotherapy is one of the main therapeutic approaches for non-small-cell lung cancer (NSCLC). Based on the poor response of immunotherapy, it is crucial to determine the most accurate and widespread predictive characteristics of NSCLC. We retrieved lung squamous cell carcinoma and lung adenocarcinoma gene expression profiles and clinical data from the cancer genome atlas database and classified them into 3 subtypes based on 29 immune gene sets. Combined with previous studies, the expression differences of related pathways and genes in different subtypes were analyzed. We classified them into 3 subtypes: Immunity High, Immunity Medium, and Immunity Low. Immunity High had the strongest immune cell infiltration and antitumor immune activity. Gene ontology enrichment analyses revealed enriched immune-related signaling pathways in lung squamous cell carcinoma. The hyperactivation of cancer-related pathways did not occur in any NSCLC. In addition, the Hippo signaling pathway was negatively correlated with immune signature, whereas epithelial-to-mesenchymal transition was positively correlated. In addition, we found significant differences in immune signatures between males and females; however, no correlation was observed with other clinical data. The identification of NSCLC subtypes based on immune signatures has potential clinical implications for NSCLC treatment.

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Section: Discussionsupporting

confidence: 91%

Analysis of immune subtypes in non-small-cell lung cancer based on TCGA database

Chen

Song

2023

Medicine

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“…However, the role and biological function of FDX1 in gliomas are currently unclear. Currently, it is generally accepted that the tumor microenvironment (TME) is one of the key factors in tumor initiation and progression (7,(21)(22)(23)(24)(25)(26)(27)(28)(29). It is mainly composed of tumor cells, fibroblast cells, immune cells, various signal molecules, extracellular matrix, special physical and chemical factors (30)(31)(32)(33).…”

Section: Introductionmentioning

confidence: 99%

“…It is mainly composed of tumor cells, fibroblast cells, immune cells, various signal molecules, extracellular matrix, special physical and chemical factors (30)(31)(32)(33). Evidence shows that the tumor microenvironment significantly affects tumor diagnosis, survival outcomes, and clinical treatment sensitivity (21,23,(33)(34)(35). In recent years, related immunological studies have found that immune cell infiltration plays a key role in the tumor microenvironment in the formation, occurrence and development (31,(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47).…”

Section: Introductionmentioning

confidence: 99%

Cuproptosis key gene FDX1 is a prognostic biomarker and associated with immune infiltration in glioma

Zhou

Zhang

et al. 2022

Front. Med.

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Recent studies have found that the protein encoded by the FDX1 gene is involved in mediating Cuproptosis as a regulator of protein lipoylation and related to immune response process of tumors. However, the specific biological function of FDX1 in glioma is currently unclear. To explore the potential function of FDX1, this study explored the correlation between the expression of FDX1 in cancers and survival prognosis by analyzing the public databases of GEPIA and Cbioportal. Immune infiltration was analyzed by the TIMER2.0 database in tumors. The possible biological processes and functions of FDX1-related in glioma were annotated through gene enrichment. Relationship between Cuproptosis and autophagy was explored through gene co-expression studies. Summary and conclusions of this study: (1) FDX1 is highly expressed in gliomas and associated with poor prognosis in low-grade gliomas (LGG). (2) Gene annotation indicates that FDX1 is mainly involved in the tumor protein lipoylation and cell death. (3) FDX1 expression is positively correlated with the infiltration of immune cells. (4) LIPT2 and NNAT, two other genes involved in lipoylation, may be unidentified marker gene for Cuproptosis. And the Cuproptosis genes related to FDX1 were positively correlated with the expression of autophagy marker genes Atg5, Atg12, and BECN-1. This evidence suggests that there may be some interaction between FDX1 mediated Cuproptosis and autophagy. In summary, FDX1 may serve as a potential immunotherapy target and prognostic marker for Glioma.

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“…Two external HNSCC datasets GSE41613 ( n = 97) ( Zhao et al, 2022 ) and GSE42743 ( n = 103) ( Lohavanichbutr et al, 2013 ) were employed to validate the independently predictive accuracy of GILncRNAs signature. In the GSE41613 set, 21 patients were excluded from this study because they did not succumb to HNSCC.…”

Section: Methodsmentioning

confidence: 99%

Characterization of tumor immune microenvironment and cancer therapy for head and neck squamous cell carcinoma through identification of a genomic instability-related lncRNA prognostic signature

Jing

2022

Front. Genet.

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Head and neck squamous cell carcinoma (HNSCC) represents one of the most prevalent and malignant tumors of epithelial origins with unfavorable outcomes. Increasing evidence has shown that dysregulated long non-coding RNAs (lncRNAs) correlate with tumorigenesis and genomic instability (GI), while the roles of GI-related lncRNAs in the tumor immune microenvironment (TIME) and predicting cancer therapy are still yet to be clarified. In this study, transcriptome and somatic mutation profiles with clinical parameters were obtained from the TCGA database. Patients were classified into GI-like and genomic stable (GS)-like groups according to the top 25% and bottom 25% cumulative counts of somatic mutations. Differentially expressed lncRNAs (DElncRNAs) between GI- and GS-like groups were identified as GI-related lncRNAs. These lncRNA-related coding genes were enriched in cancer-related KEGG pathways. Patients totaling 499 with clinical information were randomly divided into the training and validation sets. A total of 18 DElncRNAs screened by univariate Cox regression analysis were associated with overall survival (OS) in the training set. A GI-related lncRNA signature that comprised 10 DElncRNAs was generated through least absolute shrinkage and selection operator (Lasso)-Cox regression analysis. Patients in the high-risk group have significantly decreased OS vs. patients in the low-risk group, which was verified in internal validation and entire HNSCC sets. Integrated HNSCC sets from GEO confirmed the notable survival stratification of the signature. The time-dependent receiver operating characteristic curve demonstrated that the signature was reliable. In addition, the signature retained a strong performance of OS prediction for patients with various clinicopathological features. Cell composition analysis showed high anti-tumor immunity in the low-risk group which was evidenced by increased infiltrating CD8+ T cells and natural killer cells and reduced cancer-associated fibroblasts, which was convinced by immune signatures analysis via ssGSEA algorithm. T helper/IFNγ signaling, co-stimulatory, and co-inhibitory signatures showed increased expression in the low-risk group. Low-risk patients were predicted to be beneficial to immunotherapy, which was confirmed by patients with progressive disease who had high risk scores vs. complete remission patients. Furthermore, the drugs that might be sensitive to HNSCC were identified. In summary, the novel prognostic GILncRNA signature provided a promising approach for characterizing the TIME and predicting therapeutic strategies for HNSCC patients.

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Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma

Cited by 11 publications

References 49 publications

Analysis of immune subtypes in non-small-cell lung cancer based on TCGA database

Analysis of immune subtypes in non-small-cell lung cancer based on TCGA database

Cuproptosis key gene FDX1 is a prognostic biomarker and associated with immune infiltration in glioma

Characterization of tumor immune microenvironment and cancer therapy for head and neck squamous cell carcinoma through identification of a genomic instability-related lncRNA prognostic signature

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