Analysis and identification of mRNAsi‑related expression signatures via RNA sequencing in lung cancer

Yan,Bo; Chen,Yong; Wang,Zhouyu; Li,Jing; Wang,Ruiru; Pan,Xufeng; Li,Boyi; Li,Rong

doi:10.3892/ol.2024.14682

Analysis and identification of mRNAsi‑related expression signatures via RNA sequencing in lung cancer

Authors:
- Bo Yan
- Yong Chen
- Zhouyu Wang
- Jing Li
- Ruiru Wang
- Xufeng Pan
- Boyi Li
- Rong Li
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Affiliations: Clinical Research Unit, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China, Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200050, P.R. China, Berry Oncology Corporation, Beijing 100102, P.R. China, Kanghui Biotechnology Corporation, Shenyang, Liaoning 110042, P.R. China
Published online on: September 13, 2024 https://doi.org/10.3892/ol.2024.14682
Article Number: 549
Copyright: © Yan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

High stemness index scores are associated with poor survival in patients with lung cancer. Studies on the mRNA expression‑based stemness index (mRNAsi) are typically conducted using tumor tissues; however, mRNAsi‑related expression signatures based on cell‑free RNA (cfRNA) are yet to be comprehensively investigated. The present study aimed to elucidate the gene expression profiles of tumor stemness in lung cancer tissues and corresponding cfRNAs in blood, and to assess their links with immune infiltration. Tumor tissue, paracancerous tissue, peripheral blood and lymph node samples were collected from patients with stage I‑III non‑small cell lung cancer and RNA sequencing was performed. The TCGAbiolinks package was used to calculate the mRNAsi for each of these four types of sample. Weighted gene co‑expression network analysis and differentially expressed gene analyses were performed to investigate mRNAsi‑related genes, and pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology‑based annotation system. In addition, the STAR‑Fusion tool was used to detect fusion variants, and CIBERSORT was used to analyze the correlations of stemness signatures in tissues and blood with immune cell infiltration. The mRNAsi values in peripheral blood and lymph nodes were found to be higher than those in cancer tissues. ‘Hematopoietic cell lineage’ was the only KEGG pathway enriched in mRNAsi‑related genes in both lung cancer tissues and peripheral blood. In addition, the protein tyrosine phosphatase receptor type C associated protein gene was the only gene commonly associated with the mRNAsi in these two types of sample. The expression of mRNAsi‑related genes was increased in the dendritic and Treg cells in tumor tissues, but was elevated in Treg and CD8 cells in the blood. In conclusion, cfRNAs in the blood exhibit unique stemness signatures that have potential for use in the diagnosis of lung cancer.

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