Dataset Information

Identification and Validation of a Proliferation-Associated Score Model Predicting Survival in Lung Adenocarcinomas

ABSTRACT:

Aim

This study is aimed at building a risk model based on the genes that significantly altered the proliferation of lung adenocarcinoma cells and exploring the underlying mechanisms.

Methods

The data of 60 lung adenocarcinoma cell lines in the Cancer Dependency Map (Depmap) were used to identify the genes whose knockout led to dramatical acceleration or deacceleration of cell proliferation. Then, univariate Cox regression was performed using the survival data of 497 patients with lung adenocarcinoma in The Cancer Genome Atlas (TCGA). The least absolute shrinkage and selection operator (LASSO) model was used to construct a risk prediction score model. Patients with lung adenocarcinoma from TCGA were classified into high- or low-risk groups based on the scores. The differences in clinicopathologic, genomic, and immune characteristics between the two groups were analyzed. The prognosis of the genes in the model was verified with immunohistochemical staining in 100 samples from the Department of Thoracic Surgery, Zhongshan Hospital, and the alteration in the proliferation rate was checked after these genes were knocked down in lung adenocarcinoma cells (A549 and H358).

Results

A total of 55 genes were found to be significantly related to survival by combined methods, which were crucial to tumor progression in functional enrichment analysis. A six-gene-based risk prediction score, including the proteasome subunit beta type-6 (PSMB6), the heat shock protein family A member 9 (HSPA9), the deoxyuridine triphosphatase (DUT), the cyclin-dependent kinase 7 (CDK7), the polo-like kinases 1 (PLK1), and the folate receptor beta 2 (FOLR2), was built using the LASSO method. The high-risk group classified with the score model was characterized by poor overall survival (OS), immune infiltration, and relatively higher mutation load. A total of 9864 differentially expressed genes and 138 differentially expressed miRNAs were found between the two groups. Also, a nomogram comparing score model, age, and the stage was built to predict OS for patients with lung adenocarcinoma. Using immunohistochemistry, the expression levels of PSMB6, HSPA9, DUT, CDK7, and PLK1 were found to be higher in lung adenocarcinoma tissues of patients, while the expression of FOLR2 was low, which was consistent with survival prediction. The knockdown of PSMB6 and HSPA9 by siRNA significantly downregulated the proliferation of A549 and H358 cells.

Conclusion

The proposed score model may function as a promising risk prediction tool for patients with lung adenocarcinoma and provide insights into the molecular regulation mechanism of lung adenocarcinoma.

SUBMITTER: Bian Y

PROVIDER: S-EPMC8554523 | biostudies-literature |

REPOSITORIES: biostudies-literature

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