The identification of autophagy‐related genes in the prognosis of oral squamous cell carcinoma

Zhu, Lucheng; Yan, Donglin; Chen, Yan; Chen, Sheng; Chen, Ning; Han, Jing

doi:10.1111/odi.13492

Cited by 19 publications

(16 citation statements)

References 23 publications

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“…In the very recent years, autophagy-related genes (ARGs) have been investigated in both inflammatory diseases (including pulmonary diseases) ( Wang, 2015 ; Racanelli et al, 2018 ; Kim et al, 2019 ; Larabi et al, 2020 ) and various cancers ( Wang et al, 2019a ; Wan et al, 2019 ; Zhu et al, 2020a ). For lung cancer, there are some newly released studies that have identified ARG prognostic signatures in LUAD and lung squamous cell carcinoma (LUSC) ( Zhu et al, 2020b ; Zhang et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Various ARGs are involved in the maintenance of intestinal homeostasis, such as ATG16L1, IRGM, LRRK2, ATG7, p62, optineurin, and TFEB (Kim et al, 2019). A six autophagy-related gene expression signature (including EIF4EBP1, TP63, BNIP3, ATIC, ERO1A, and FADD) showed better performance for predicting the survival of LUAD and LUSC patients than other clinicopathological variables (Zhu et al, 2020b). Another study constructed a risk model based on five autophagy-related gene expression levels, which could also predict the prognosis and serve as a prognostic biomarker in LUAD patients (Zhang et al, 2020).…”

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confidence: 99%

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Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma

Zhang

Chen

Liu

et al. 2021

Front. Cell Dev. Biol.

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Background: Autophagy plays an important role in lung adenocarcinoma (LUAD). In this study, we aimed to explore the autophagy-related gene (ARG) expression pattern and to identify promising autophagy-related biomarkers to improve the prognosis of LUAD.Methods: The gene expression profiles and clinical information of LUAD patients were downloaded from the Cancer Genome Atlas (TCGA), and validation cohort information was extracted from the Gene Expression Omnibus database. The Human Autophagy Database (HADb) was used to extract ARGs. Gene expression data were analyzed using the limma package and visualized using the ggplot2 package as well as the pheatmap package in R software. Functional enrichment analysis was also performed for the differentially expressed ARGs (DEARGs). Then, consensus clustering revealed autophagy-related tumor subtypes, and differentially expressed genes (DEGs) were screened according to the subtypes. Next, the univariate Cox and multivariate Cox regression analyses were used to identify independent prognostic ARGs. After overlapping DEGs and the independent prognostic ARGs, the predictive risk model was established and validated. Correlation analyses between ARGs and clinicopathological variables were also explored. Finally, the TIMER and TISIDB databases were used to further explore the correlation analysis between immune cell infiltration levels and the risk score as well as clinicopathological variables in the predictive risk model.Results: A total of 222 genes from the HADb were identified as ARGs, and 28 of the 222 genes were pooled as DEARGs. The most significant GO term was autophagy (p = 3.05E-07), and KEGG analysis results indicated that 28 DEARGs were significantly enriched in the ErbB signaling pathway (p < 0.001). Then, consensus clustering analysis divided the LUAD into two clusters, and a total of 168 DEGs were identified according to cluster subtypes. Then univariate and multivariate Cox regression analyses were used to identify 12 genes that could serve as independent prognostic indicators. After overlapping 168 DEGs and 12 genes, 10 genes (ATG4A, BAK1, CAPNS1, CCR2, CTSD, EIF2AK3, ITGB1, MBTPS2, SPHK1, ST13) were selected for the further exploration of the prognostic pattern. Survival analysis results indicated that this risk model identified the prognosis (p = 4.379E-10). Combined with the correlation analysis results between ARGs and clinicopathological variables, five ARGs were screened as prognostic genes. Among them, SPHK1 expression levels were positively correlated with CD4+ T cells and dendritic cell infiltration levels.Conclusions: In this study, we constructed a predictive risk model and identified a five autophagy subtype-related gene expression pattern to improve the prognosis of LUAD. Understanding the subtypes of LUAD is helpful to accurately characterize the LUAD and develop personalized treatment.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma

Zhang

Chen

Liu

et al. 2021

Front. Cell Dev. Biol.

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“…For IHC, the identification of the staining was semiquantitative. Based on the results, score zero represented <5% positively stained cells, score one 6%-25% cells, score two 26-50%, and score three >50% [ 16 ]. For the final score, zero was considered negative, and 1-3 as positive.…”

Section: Resultsmentioning

confidence: 99%

Development and Validation of an Autophagy-Related Signature for Head and Neck Squamous Cell Carcinoma

Liu

et al. 2021

BioMed Research International

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Introduction. HNSCC is the sixth most frequent type of malignant carcinoma with a low prognosis rate. In addition, autophagy is important in cancer development and progression. The purpose of this study is to investigate the potential significance of ARGs in the diagnosis and treatment of HNSCC. Materials and Methods. Expression data and clinical information of HNSCC samples were collected from the TCGA database, and a list of ARGs was obtained from the MSigDB. Then, we used R software to perform differential expression analysis and functional enrichment analysis. Further analysis was also performed to find out the survival-related ARGs in HNSCC, and two prognosis-related ARGs, FADD and NKX2-3, were selected to construct a prognosis prediction model. Moreover, some methods were applied to validate the prognosis prediction model. Finally, we used cell lines and clinical tissue samples of HNSCC to analyze the importance of FADD and NKX2-3. Results. We screened a total of 38 differentially expressed ARGs, and enrichment analysis showed that these genes were mainly involved in autophagy. Then, we selected FADD and NKX2-3 to construct a prognosis model and the risk score calculated by the model was proved to be effective in predicting the survival of HNSCC patients. Additionally, significant differences of the clinicopathological parameters could also be observed in the risk scores and the expression of NKX2-3 and FADD. The expression of FADD and NKX2-3 in cell lines and HNSCC tissue samples also showed the same trends. Conclusions. ARGs may be a potential biomarker for HNSCC prognosis, and targeted therapies for FADD and NKX2-3 are possible to be a new strategy of HNSCC treatment.

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“… 22 However, BAK1 is regarded as an unfavorable prognostic factor in some studies for Hepatocellular Carcinoma and Head and Neck Squamous Cell Carcinoma. 23 , 24 In the study, BAK1 seems to be a cancer-promoting gene, because its expression in tumor tissues is significantly higher than that in normal tissues; however, it helps to prolong patient survival for that it is enriched in the low-risk group. Given that the data provided by BC is limited and the results of different tumors are often contradictory, our results on BAK1 provide some insights for further research.…”

Section: Discussionmentioning

confidence: 99%

A Newly Defined Pyroptosis-Related Gene Signature for the Prognosis of Bladder Cancer

Chen

Zhang

Zhou

et al. 2021

IJGM

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The identification of autophagy‐related genes in the prognosis of oral squamous cell carcinoma

Cited by 19 publications

References 23 publications

Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma

Identification of a Five Autophagy Subtype-Related Gene Expression Pattern for Improving the Prognosis of Lung Adenocarcinoma

Development and Validation of an Autophagy-Related Signature for Head and Neck Squamous Cell Carcinoma

A Newly Defined Pyroptosis-Related Gene Signature for the Prognosis of Bladder Cancer

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