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Single-cell Transcriptomic Analysis Reveals an Immunosuppressive Network Between POSTN CAFs and ACKR1 ECs in
Zhiyi Wang1, Ning Yan1, Hailong Sheng1
1Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China.
Background/Aim:
Tyrosine kinase inhibitor (TKI) therapy, a principal treatment for advanced non-small cell lung cancer (NSCLC), frequently encounters the development of drug resistance. The tumor microenvironment (TME) plays a critical role in the progression of NSCLC, yet the relationship between endothelial cells (ECs) and cancer-associated fibroblasts (CAFs) subpopulations in TKI treatment resistance remains largely unexplored.
Materials And Methods:
The BioProject database PRJNA591860 project was used to analyze scRNA-seq data including 49 advanced-stage NSCLC samples across three different time points: pre-targeted therapy (naïve), post-partial response (PR) to targeted therapy, and post-progressive disease (PD) stage. The data involved clustering stromal cells into multiple CAFs and ECs subpopulations. The abundance changes and functions of each cluster during TKI treatment were investigated by KEGG and GO analysis. Additionally, we identified specific transcription factors and metabolic pathways via DoRothEA and scMetabolism. Moreover, cell-cell communications between PD and PR stages were compared by CellChat.
Results:
ECs and CAFs were clustered and annotated using 49 scRNA-seq samples. We identified seven ECs subpopulations, with OIT3 ECs showing enrichment in the PR phase with a drug-resistance phenotype, and ACKR1 ECs being prevalent in the PD phase with enhanced cell adhesion. Similarly, CAFs were clustered into 7 subpopulations. PLA2G2A CAFs were predominant in PR, whereas POSTN CAFs were prevalent in PD, characterized by an immunomodulatory phenotype and increased collagen secretion. CellChat analysis showed that ACKR1 ECs strongly interacted with macrophage through the CD39 pathway and POSTN CAFs secreted Tenascin-C (TNC) to promote the progression of epithelial cells, primarily malignant ones, in PD.
Conclusion:
This study reveals that POSTN CAFs and ACKR1 ECs are associated with resistance to TKI treatment, based on single-cell sequencing.
Insights
This study identifies specific endothelial cells (ECs) and cancer-associated fibroblasts (CAFs) linked to drug resistance in non-small cell lung cancer (NSCLC) treated with tyrosine kinase inhibitors (TKIs). These findings offer new insights into TKI resistance mechanisms within the tumor microenvironment.
Area of Science:
- Oncology
- Molecular Biology
- Immunology
Background:
- Tyrosine kinase inhibitor (TKI) therapy is a primary treatment for advanced non-small cell lung cancer (NSCLC).
- Drug resistance is a significant challenge in NSCLC treatment.
- The tumor microenvironment (TME), including endothelial cells (ECs) and cancer-associated fibroblasts (CAFs), influences treatment outcomes, but its role in TKI resistance is not fully understood.
Purpose of the Study:
- To investigate the subpopulations of ECs and CAFs within the TME and their association with TKI treatment resistance in NSCLC.
- To identify specific EC and CAF subtypes that emerge during TKI treatment and contribute to disease progression.
Main Methods:
- Analysis of single-cell RNA sequencing (scRNA-seq) data from 49 advanced NSCLC samples at different treatment stages (naïve, partial response, progressive disease).
- Clustering and functional annotation of ECs and CAFs subpopulations using KEGG and GO analysis.
- Identification of key transcription factors and metabolic pathways using DoRothEA and scMetabolism.
- Comparison of cell-cell communications between treatment stages using CellChat.
Main Results:
- Seven EC subpopulations were identified, with OIT3 ECs associated with partial response and ACKR1 ECs prevalent in progressive disease, exhibiting enhanced cell adhesion.
- Seven CAF subpopulations were identified, with PLA2G2A CAFs predominant in partial response and POSTN CAFs prevalent in progressive disease, showing immunomodulatory properties and increased collagen secretion.
- ACKR1 ECs interact with macrophages via the CD39 pathway, and POSTN CAFs secrete Tenascin-C (TNC), promoting malignant epithelial cell progression in the progressive disease stage.
Conclusions:
- POSTN CAFs and ACKR1 ECs are identified as key cellular components associated with resistance to TKI treatment in NSCLC.
- These findings highlight the critical role of specific EC and CAF subpopulations in mediating TKI resistance and suggest potential therapeutic targets within the TME.
