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Background <p>RUNX3 acts as a tumor suppressor gene in non-small-cell lung cancer (NSCLC), yet its specific biological mechanism is still unclear. This study aimed to uncover tumor microenvironment (TME) changes in NSCLC with varying RUNX3 expression statuses through single-cell RNA sequencing.</p> Patients and Methods <p>In total, seven patients with NSCLC with detailed pathological data were involved, with three both paracancerous and cancerous tissue samples. After sequencing, the “Seurat” package was used to analyze differentially expressed genes, annotate cell clusters with marker genes, and compare cell proportion differences at different RUNX3 expression levels. Observed-over-expected cell number ratios (<i>R</i><sub>o/e</sub>) assessed cell type enrichment among three pathological types.</p> Results <p>Immunohistochemical staining of RUNX3 categorized three patients into the RUNX3-negative group (RUNX3_Neg) and four into the RUNX3 positive group (RUNX3_Pos). All cells were classified into 13 types based on marker genes. <i>R</i><sub>o/e</sub> results showed fibroblasts were the only enriched cell type in RUNX3_Pos cancer tissue, while club cells, ciliated cells, and so on were enriched in RUNX3_Neg cancer tissue. RUNX3_Neg tissues were more likely to accumulate certain immune cells compared with RUNX3_Pos tissues. <i>R</i><sub>o/e</sub> also indicated RUNX3_Neg cancer tissues were more prone to macrophage depletion, while RUNX3_Pos tissues were more prone to macrophage enrichment.</p> Conclusions <p>Through single-cell sequencing, our study found that RUNX3 expression status is closely related to NSCLC TME. Mononuclear phagocytes may be an important target cell population for RUNX3 to change TME.</p>

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Single-Cell RNA Sequencing Reveals Potential Mechanism of RUNX3 Reshaping Tumor Microenvironment in Non-small-cell Lung Cancer

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年9月7日

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  • Weijin Xiao,
  • Jianqing Zheng,
  • Yujie Deng,
  • Bifen Huang,
  • Weibin Liu,
  • Xuejin Zheng,
  • Kaijia Zhou,
  • Weimin Fang,
  • Xiaohui Chen

摘要

Background

RUNX3 acts as a tumor suppressor gene in non-small-cell lung cancer (NSCLC), yet its specific biological mechanism is still unclear. This study aimed to uncover tumor microenvironment (TME) changes in NSCLC with varying RUNX3 expression statuses through single-cell RNA sequencing.

Patients and Methods

In total, seven patients with NSCLC with detailed pathological data were involved, with three both paracancerous and cancerous tissue samples. After sequencing, the “Seurat” package was used to analyze differentially expressed genes, annotate cell clusters with marker genes, and compare cell proportion differences at different RUNX3 expression levels. Observed-over-expected cell number ratios (Ro/e) assessed cell type enrichment among three pathological types.

Results

Immunohistochemical staining of RUNX3 categorized three patients into the RUNX3-negative group (RUNX3_Neg) and four into the RUNX3 positive group (RUNX3_Pos). All cells were classified into 13 types based on marker genes. Ro/e results showed fibroblasts were the only enriched cell type in RUNX3_Pos cancer tissue, while club cells, ciliated cells, and so on were enriched in RUNX3_Neg cancer tissue. RUNX3_Neg tissues were more likely to accumulate certain immune cells compared with RUNX3_Pos tissues. Ro/e also indicated RUNX3_Neg cancer tissues were more prone to macrophage depletion, while RUNX3_Pos tissues were more prone to macrophage enrichment.

Conclusions

Through single-cell sequencing, our study found that RUNX3 expression status is closely related to NSCLC TME. Mononuclear phagocytes may be an important target cell population for RUNX3 to change TME.