Development and validation of a novel survival model for head and neck squamous cell carcinoma based on autophagy-related genes

Ren, Ziying; Zhang, Long; Ding, Wei; Luo, Yilang; Shi, Zhiqiang; Shrestha, Bikal; Kan, Xuan; Zhang, Zhuhua; Jing, Ding; He, Haojie; Hu, Xuegang

doi:10.1016/j.ygeno.2020.11.017

Cited by 33 publications

(28 citation statements)

References 43 publications

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“…After 24-hour starvation, mRNA sequencing of SAS cells detected 12 up-regulated ARGs (ATP6V0A2, ATP6V1B1, ATP6V1C2, DDIT3, ERN1, NHLRC1, NUPR1, PIM2, TMEM150A, TRIB3, WIPI1, and XBP1) and 13 down-regulated ARGs (BNIP3, BNIP3L, C10orf10, DAPK2, GAPDH, HMOX1, MEFV, PLK2, RRAGD, SESN3, SRPX, S100A8, and S100A9). These genes differed from the ARGs previously reported to predict the prognosis of HNSCC patients 29,33,34 . This starvation-induced approach may be bene cial in extrapolating ARGs that have not been previously identi ed as differentially expressed genes.…”

Section: Discussioncontrasting

confidence: 74%

“…Similarly, Jin et al 33 determined 35 genes for HNSCC and identi ed ITGA3, CDKN2A, FADD, NKX2-3, BAK1, CXCR4, and HSPB8 as prognostic ARGs. Ren et al 34 also reported 13 ARGs as genes that predict prognosis. In the present study, HNSCC cells were cultured under serum starvation, which can e ciently induce autophagy, and RNA sequencing was used to examine the expression of ARGs.…”

Section: Discussionmentioning

confidence: 99%

“…The complex multi-step process of autophagy is tightly controlled by a set of autophagy-related genes (ARGs). Some ARGs have been shown to be associated with the prognosis of HNSCC patients using bioinformatics 29,[32][33][34] . However, it has not been clari ed how these ARGs exhibit their expression kinetics in an environment where autophagy occurs.…”

Section: Introductionmentioning

confidence: 99%

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Prognostic association of starvation-induced genes in head and neck cancer

Hamada

Inaba

Nishiyama

et al. 2021

Preprint

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Autophagy-related genes (ARGs) have been implicated in the initiation and progression of malignant tumor promotion. To investigate the dynamics of expression of genes, including ARGs, head and neck squamous cell carcinoma (HNSCC) cells were placed under serum-free conditions to induce growth retardation and autophagy, and these starved cells were subjected to transcriptome analysis. Among the 21 starvation-induced genes (SIGs) located in the autophagy, cell proliferation, and survival signaling pathways, we identified SIGs that showed prominent up-regulation or down-regulation. These included AGR2, BST2, CALR, CD22, DDIT3, FOXA2, HSPA5, PIWIL4, PYCR1, SGK3, and TRIB3. The Cancer Genome Atlas (TCGA) database of HNSCC patients was used to examine the expression of up-regulated genes, and CALR, HSPA5, and TRIB3 were highly expressed relative to solid normal tissue in cancer and the survival rate was found to be reduced in patients with high expression. Protein-protein interaction analysis demonstrated the formation of a dense network of these genes. Cox regression analysis revealed that high expression of CALR, HSPA5, and TRIB3 was associated with poor prognosis in patients with TCGA-HNSCC. Therefore, these SIGs up-regulated under serum starvation may be molecular prognostic markers in HNSCC patients.

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Section: Discussioncontrasting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Prognostic association of starvation-induced genes in head and neck cancer

Hamada

Inaba

Nishiyama

et al. 2021

Preprint

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“…So far, the focus of accurate genomic medicine was to find accurate and specific predictors of survival and prognosis from large medical data with clinical results. Therefore, in recent years, there were some studies aimed at using bioinformatics analysis to explore the prognostic factors related to autophagy 23‐25 . In the past year, three prognostic risk models of autophagy‐related genes in LUAD were established based on TCGA database and using different screening criteria and statistical methods 26‐28 .…”

Section: Discussionmentioning

confidence: 99%

A novel autophagy‐related lncRNA survival model for lung adenocarcinoma

Zhu

Song

et al. 2021

J Cellular Molecular Medi

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Long non‐coding RNA (lncRNA) is an important regulatory factor in the development of lung adenocarcinoma, which is related to the control of autophagy. LncRNA can also be used as a biomarker of prognosis in patients with lung adenocarcinoma. Therefore, it is important to determine the prognostic value of autophagy‐related lncRNA in lung adenocarcinoma. In this study, autophagy‐related mRNAs‐lncRNAs were screened from lung adenocarcinoma and a co‐expression network of autophagy‐related mRNAs‐lncRNAs was constructed by using The Cancer Genome Atlas (TCGA). The univariate and multivariate Cox proportional hazard analyses were used to evaluate the prognostic value of the autophagy‐related lncRNAs and finally obtained a survival model composed of 11 autophagy‐related lncRNAs. Through Kaplan‐Meier analysis, univariate and multivariate Cox regression analysis and time‐dependent receiver operating characteristic (ROC) curve analysis, it was further verified that the survival model was a new independent prognostic factor for patients with lung adenocarcinoma. In addition, based on the survival model, gene set enrichment analysis (GSEA) was used to illustrate the function of genes in low‐risk and high‐risk groups. These 11 lncRNAs were GAS6‐AS1, AC106047.1, AC010980.2, AL034397.3, NKILA, AL606489.1, HLA‐DQB1‐AS1, LINC01116, LINC01806, FAM83A‐AS1 and AC090559.1. The hazard ratio (HR) of the risk score was 1.256 (1.196‐1.320) (P < .001) in univariate Cox regression analysis and 1.215 (1.149‐1.286) (P < .001) in multivariate Cox regression analysis. And the AUC value of the risk score was 0.809. The 11 autophagy‐related lncRNA survival models had important predictive value for the prognosis of lung adenocarcinoma and may become clinical autophagy‐related therapeutic targets.

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“…ALGALS8 was demonstrated to be a biomarker predicting the prognosis of glioblastoma and ovarian cancer patients [ 48 , 49 ]. As for PTPRS , it has been proved that reduced expression of PTPRS is significantly associated with the poor prognosis of esophageal squamous cell carcinoma and malignant peripheral nerve sheath tumor [ 50 , 51 ]. Summarily, all of the ARGs incorporated in our risk model was closely correlated with tumors via autophagy-mediated molecular cascades.…”

Section: Discussionmentioning

confidence: 99%

Construction and Validation of an Autophagy-Related Prognostic Model for Osteosarcoma Patients

Lei

et al. 2021

Journal of Oncology

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While the prognostic value of autophagy-related genes (ARGs) in OS patients remains scarcely known, increasing evidence is indicating that autophagy is closely associated with the development and progression of osteosarcoma (OS). Therefore, we explored the prognostic value of ARGs in OS patients and illuminate associated mechanisms in this study. When the OS patients in the training/validation cohort were stratified into high- and low-risk groups according to the risk model established using least absolute shrinkage and selection operator (LASSO) regression analysis, we observed that patients in the low-risk group possessed better prognosis ( P < 0.0001 ). Univariate/Multivariate COX regression and subgroup analysis demonstrated that the ARGs-based risk model was an independent survival indicator for OS patients. The nomogram incorporating the risk model and clinical features exhibited excellent prognostic accuracy. GO, KEGG, and GSVA analyses collectively indicated that bone development-associated pathway mediated the contribution of ARGs to the malignance of OS. Immune infiltration analysis suggested the potential pivotal role of macrophage in OS. In summary, the risk model based on 12 ARGs possessed potent capacity in predicting the prognosis of OS patients. Our work may assist clinicians to map out more reasonable treatment strategies and facilitate individual-targeted therapy in osteosarcoma.

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Development and validation of a novel survival model for head and neck squamous cell carcinoma based on autophagy-related genes

Cited by 33 publications

References 43 publications

Prognostic association of starvation-induced genes in head and neck cancer

Prognostic association of starvation-induced genes in head and neck cancer

A novel autophagy‐related lncRNA survival model for lung adenocarcinoma

Construction and Validation of an Autophagy-Related Prognostic Model for Osteosarcoma Patients

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