Study of LY9 as a potential biomarker for prognosis and prediction of immunotherapy efficacy in lung adenocarcinoma

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Differential expression and prognostic value analysis of LY9 in pan-cancer

Gene Set Enrichment Analysis and correlation of LY9 expression in LUAD with clinical features from TCGA

Construction of the lncRNA-miRNA-LY9 ceRNA network

Correlation analyses of LY9 expression in LUAD with immune cells infiltration and immune checkpoints

Validation of GEO dataset, qRT-PCR and IHC experiments

Statistical analyses

Results

The mRNA expression levels of LY9 in pan-cancer

Prognostic value of LY9 in pan-cancer

GSEA and correlation analysis of clinical characteristics in LUAD

Construction of the lncRNA-miRNA-LY9 ceRNA network

Correlation of LY9 expression levels in LUAD with immune cell infiltration and immune checkpoints

Validation using GEO dataset, qRT-PCR and IHC experiments

Discussion

Conclusion

Supplemental Information

Bioinformatics Analysis

DOI: 10.7717/peerj.17816/supp-4

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Kun Deng conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Liqiang Yuan conceived and designed the experiments, prepared figures and/or tables, and approved the final draft.

Zhanyu Xu conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Fanglu Qin analyzed the data, prepared figures and/or tables, and approved the final draft.

Zhiwen Zheng performed the experiments, prepared figures and/or tables, and approved the final draft.

Liuliu Huang performed the experiments, prepared figures and/or tables, and approved the final draft.

Wei Jiang performed the experiments, prepared figures and/or tables, and approved the final draft.

Junqi Qin analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Yu Sun analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Tiaozhan Zheng analyzed the data, prepared figures and/or tables, and approved the final draft.

Xinhuai Ou analyzed the data, prepared figures and/or tables, and approved the final draft.

Liping Zheng analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Shikang Li conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

the Ethics Committee of the First Affiliated Hospital of Guangxi Medical University

Data Availability

The following information was supplied regarding data availability:

The raw data and worksheets are available in the Supplemental Files.

The data from third parties are available at:

(1). UCSC Xena database: GDC TCGA (gene expression RNAseq, HTSeq - FPKM);

(2). Kaplan-Meier plotter: LY9 and select cancer type;

(3). Gene Expression Profiling Interactive Analysis (GEPIA): LY9 and select cancer type; LY9,CD274, PDCD1, and CTLA4, LUAD

(4). TargetScan 7.2 database: LY9;

(5). DIANA-tools database LncBase Experimental v.2: hsa-miR-141-3p

(6). TIMER 2.0 database: LY9,CD274, PDCD1, and CTLA4, LUAD

Funding

This study is supported by Natural Science Foundation of Guangxi Province (2021JJA141242). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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