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Gene expression profiling using targeted RNA-sequencing to elucidate the progression from histologically normal lung tissues to non-invasive lesions in invasive lung adenocarcinoma

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Abstract

Lung adenocarcinoma (LUAD) shows heterogeneous morphological features and the stepwise progression from adenocarcinoma in situ to minimally invasive adenocarcinoma to invasive LUAD. Although multiple genetic alterations have been linked to the progression, the differences between the gene expression profiles of non-invasive lesions (non-ILs) and adjacent histologically normal lung (aNL) tissues within invasive LUAD have not been investigated. Herein, we analyzed differentially expressed genes (DEGs) specific to early-stage carcinogenesis in LUAD. Invasive LUAD tissue samples containing both non-ILs and aNL tissues were obtained from seven patients with pathological stage I LUAD, and each component was subjected to microdissection. Gene expression profiles of each component were determined using targeted RNA-sequencing. In total, 2536 DEGs, including 863 upregulated and 1673 downregulated genes, were identified in non-ILs. In non-ILs, the expression of SLC44A5, a choline transporter-like protein-coding gene, was significantly upregulated, and that of TMEM100, a gene encoding a transmembrane protein, was significantly downregulated. Reportedly, SLC44A5 plays an important role in the development and progression of hepatocellular carcinoma, whereas TMEM100 functions as a tumor suppressor in non-small cell lung cancer. Gene set enrichment analysis showed that DEGs in non-ILs were negatively enriched in cell death and immune response. Immunohistochemical analysis revealed that increased SLC44A5 expression and decreased TMEM100 expression were maintained in ILs. A protein–protein interaction (PPI) network analysis identified several upregulated and downregulated hub genes with high degrees in non-ILs. In conclusion, several new DEGs and key PPI network hub genes were identified in non-ILs, contributing to understanding of early-stage carcinogenesis in LUAD.

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Acknowledgements

The authors are grateful to Professor Eiji Nanba, Kaori Adachi, and Masachika Kai for technical assistance with the NGS experiment and Shoji Yashima and Yuko Urakami for pathological specimen preparation.

Funding

This work was supported by JSPS KAKENHI [Grant Number JP19K18214].

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Author notes

  1. Taichi Kadonaga and Tomohiko Sakabe contributed equally to this work.

Authors and Affiliations

  1. Department of Pathology, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan

    Taichi Kadonaga, Tomohiko Sakabe, Yoshiteru Kidokoro, Kanae Nosaka & Yoshihisa Umekita

  2. Division of General Thoracic Surgery and Breast and Endocrine Surgery, Department of Surgery, Faculty of Medicine, Tottori University, Tottori, Japan

    Taichi Kadonaga, Yoshiteru Kidokoro, Tomohiro Haruki & Hiroshige Nakamura

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  1. Taichi Kadonaga
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Contributions

T. Kadonaga: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing—original draft. T. Sakabe: Conceptualization, Data curation, Investigation, Methodology, Project administration, Supervision, Visualization, Writing—original draft. Y. Kidokoro: Funding acquisition, Methodology, Visualization, Writing—review and editing. T. Haruki: Data curation, Resources, Writing—review and editing. K. Nosaka: Data curation, Resources, Writing—review and editing. H. Nakamura: Funding acquisition, Resources, Writing—review and editing. Y. Umekita: Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, Writing—original draft.

Corresponding author

Correspondence to Yoshihisa Umekita.

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Ethics approval and consent to participate

Written informed consent for the use of clinical data in research was obtained from all patients, and the study was approved by the Ethical Review Board of Tottori University, Japan (approval number: 19A165, December 4, 2019).

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The authors declare no competing interests.

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Kadonaga, T., Sakabe, T., Kidokoro, Y. et al. Gene expression profiling using targeted RNA-sequencing to elucidate the progression from histologically normal lung tissues to non-invasive lesions in invasive lung adenocarcinoma. Virchows Arch 480, 831–841 (2022). https://doi.org/10.1007/s00428-021-03250-y

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