Gao Yang, Li Bin, Jin Yuzhi, Cheng Jinlin, Tian Weihong, Ying Lixiong, Hong Libing, Xin Shan, Lin Bo, Liu Chuan, Sun Xuqi, Zhang Jun, Zhang Haibo, Xie Jindong, Deng Xinpei, Dai Xiaomeng, Liu Lulu, Zheng Yi, Zhao Peng, Yu Guangchuan, Fang Weijia, Bao Xuanwen
Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China.
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China.
Oncogene. 2025 Apr 15. doi: 10.1038/s41388-025-03388-y.
Primary breast cancer (BC) and metastatic tumors exhibit distinct tumor microenvironment (TME) ecosystems, and the heterogeneity of the TME of BC poses challenges to effective therapies. Evaluating the TME at the single-cell and spatial profiles offers potential for more precise treatments. However, due to the challenge of obtaining surgical specimens of both primary BC and oligo-recurrent lung metastasis simultaneously for high-resolution spatial analysis, the TME of lung-specific metastases using paired samples remains largely unexplored. In this study, we developed a comprehensive strategy using imaging mass cytometry (IMC), spatial proteomics, single-nucleus RNA-seq (snRNA-seq) and multiplex immunofluorescence to explore the spatial topology of lung-specific metastasis and the underlying biological mechanisms based on formalin-fixed paraffin-embedded (FFPE) samples from BC and paired lung metastasis. A total of 250,600 high-quality cells with spatial information revealed by IMC depicted the spatial differences in the TME between BC and lung metastasis. A significant increase in HLA-DR epithelial cells, endothelial cells and exhausted T cells was detected in lung metastases compared to primary sites, with this difference accentuated in the triple-negative subtype. Moreover, a distinct cellular hub comprising endothelial cells and HLA-DR epithelial cells implies the potential promising effect of anti-angiogenic therapy and immunotherapy in BC with lung metastasis, which was further validated by multiplex immunofluorescence analysis. Spatial proteomics further explored the underlying mechanism of TME components identified by IMC analysis. snRNA-seq validated the enrichment of endothelial cells in lung metastasis than that in BC at a whole FFPE slide level. In conclusion, this study determines the spatial multi-omics profiling of TME components at a single-cell resolution using paired samples of primary BC and lung oligo-metastasis. The comprehensive analysis may contribute to the development of therapeutic options.
原发性乳腺癌（BC）和转移性肿瘤表现出不同的肿瘤微环境（TME）生态系统，而BC的TME异质性对有效治疗构成挑战。在单细胞和空间层面评估TME为更精确的治疗提供了可能。然而，由于同时获取原发性BC和寡转移性肺转移的手术标本用于高分辨率空间分析存在挑战，使用配对样本对肺特异性转移的TME研究仍很有限。在本研究中，我们开发了一种综合策略，利用成像质谱流式细胞术（IMC）、空间蛋白质组学、单核RNA测序（snRNA-seq）和多重免疫荧光，基于来自BC和配对肺转移的福尔马林固定石蜡包埋（FFPE）样本，探索肺特异性转移的空间拓扑结构和潜在生物学机制。IMC揭示的总共250,600个具有空间信息的高质量细胞描绘了BC和肺转移之间TME的空间差异。与原发部位相比，肺转移中HLA-DR上皮细胞、内皮细胞和耗竭性T细胞显著增加，这种差异在三阴性亚型中更为明显。此外，由内皮细胞和HLA-DR上皮细胞组成的独特细胞枢纽表明抗血管生成疗法和免疫疗法对伴有肺转移的BC可能具有良好疗效，这通过多重免疫荧光分析得到进一步验证。空间蛋白质组学进一步探索了IMC分析确定的TME成分潜在机制。snRNA-seq在整个FFPE玻片水平上验证了肺转移中内皮细胞比BC中更富集。总之，本研究使用原发性BC和肺寡转移的配对样本，在单细胞分辨率下确定了TME成分的空间多组学图谱。综合分析可能有助于治疗方案的制定。
