Although metastatic disease is the leading cause of cancer-related deaths, its tumor microenvironment remains poorly characterized due to technical and biospecimen limitations. In this study, we assembled a multi-modal spatial and cellular map of 67 tumor biopsies from 60 patients with metastatic breast cancer across diverse clinicopathological features and nine anatomic sites with detailed clinical annotations. We combined single-cell or single-nucleus RNA sequencing for all biopsies with a panel of four spatial expression assays (Slide-seq, MERFISH, ExSeq and CODEX) and H&E staining of consecutive serial sections from up to 15 of these biopsies. We leveraged the coupled measurements to provide reference points for the utility and integration of different experimental techniques and used them to assess variability in cell type composition and expression as well as emerging spatial expression characteristics across clinicopathological and methodological diversity. Finally, we assessed spatial expression and co-localization features of macrophage populations, characterized three distinct spatial phenotypes of epithelial-to-mesenchymal transition and identified expression programs associated with local T cell infiltration versus exclusion, showcasing the potential of clinically relevant discovery in such maps.

尽管转移性疾病是癌症相关死亡的主要原因，但由于技术和生物样本的限制，其肿瘤微环境的表征仍然很差。在这项研究中，我们收集了 60 名转移性乳腺癌患者的 67 例肿瘤活检的多模态空间和细胞图谱，这些肿瘤活检具有不同的临床病理特征和 9 个解剖部位，并附有详细的临床注释。我们将所有活检的单细胞或单核 RNA 测序与一组四种空间表达测定 （Slide-seq、MERFISH、ExSeq 和 CODEX） 和来自多达 15 个这些活检的连续连续切片的 H&E 染色相结合。我们利用耦合测量为不同实验技术的实用和整合提供参考点，并使用它们来评估细胞类型组成和表达的变异性，以及临床病理学和方法学多样性中新出现的空间表达特征。最后，我们评估了巨噬细胞群的空间表达和共定位特征，表征了上皮到间充质转化的三种不同的空间表型，并确定了与局部 T 细胞浸润与排除相关的表达程序，展示了此类图谱中临床相关发现的潜力。