Single-cell and spatial transcriptomics profile the interaction of SPP1+ macrophages and FAP+ fibroblasts in non-small cell lung cancer
Minqin Xiao, Yiqi Deng, Hang Guo, Zhixiang Ren, Yong He, Xia Ren, Li‐Bin Huang, Weihan Zhang, Hai‐Ning Chen, Shu Yang, Fanxin Zeng, Yan Zhang, Heng Xu, Lanlan Wang
Abstract
Background: Non-small cell lung cancer (NSCLC) remains one of the most prevalent malignancies. A series of differentially expressed genes (DEGs) have been identified in tumor samples and play critical roles in modulating the characteristics of tumor cells. However, some DEGs are specifically expressed in the tumor microenvironment (TME) cells. The underlying mechanisms of the functional DEGs warrant comprehensive investigation to elucidate their contributions to tumor biology of NSCLC. Therefore, the primary goal of our study is to systematically investigate TME-related DEGs using NSCLC as a model. Methods: DEG analysis was performed by comparing bulk transcriptomes of adjacent and tumor samples across 7 independent NSCLC cohorts. Expression pattern of these DEGs were annotated to specific cell types using a single-cell RNA sequencing (scRNA-seq) dataset from 13 NSCLC studies. Myeloid and stromal cells were re-clustered to achieve a detailed characterization of cell-cell interactions within the TME. Spatial co-localization of distinct subpopulations was validated by immunofluorescence staining and spatial transcriptomics (ST). Finally, functional relevance of these interactions was evaluated using a conditional knockout mouse model. Results: expression in tumor exhibited significantly poor prognosis for immunotherapy treatment. Conclusions: fibroblasts. Their interactions contribute to the formation of a tumor barrier that inhibits immune infiltration, reducing the immunotherapy efficacy in NSCLC.