Ozirmak Lermi Nejla, Molina Ayala Max, Hernandez Sharia, Lu Wei, Khan Khaja, Serrano Alejandra, Lubo Idania, Hamana Leticia, Tomczak Katarzyna, Barnes Sean, Dou Jinzhuang, Liang Qingnan, Raso Maria Gabriela, Tang Ximing, Jiang Mei, Sanchez-Espiridion Beatriz, Weissferdt Annikka, Heymach John, Zhang Jianjun, Sepesi Boris, Cascone Tina, Tsao Anne, Altan Mehmet, Mehran Reza, Gibbons Don, Wistuba Ignacio, Haymaker Cara, Chen Ken, Solis Soto Luisa M
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Nat Commun. 2025 Sep 26;16(1):8499. doi: 10.1038/s41467-025-63414-1.
Imaging-based spatial transcriptomics (ST) is evolving as a pivotal technology in studying tumor biology and associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. We use serial 5 μm sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma samples in tissue microarrays to compare the performance of the ST platforms (CosMx, MERFISH, and Xenium (uni/multi-modal)) in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx, and hematoxylin and eosin staining data. In addition to an objective assessment of automatic cell segmentation and phenotyping, we perform a manual phenotyping evaluation to assess pathologically meaningful comparisons between ST platforms. Here, we show the intricate differences between the ST platforms, reveal the importance of parameters such as probe design in determining the data quality, and suggest reliable workflows for accurate spatial profiling and molecular discovery.
基于成像的空间转录组学（ST）正在发展成为研究肿瘤生物学及相关微环境的关键技术。然而，市售ST平台在研究空间生物学方面的优势尚未通过严格控制的实验进行系统评估。我们在组织微阵列中使用福尔马林固定、石蜡包埋的手术切除肺腺癌和胸膜间皮瘤样本的连续5μm切片，参照批量RNA测序、多重免疫荧光、GeoMx以及苏木精和伊红染色数据，比较ST平台（CosMx、MERFISH和Xenium（单/多模态））的性能。除了对自动细胞分割和表型分析进行客观评估外，我们还进行手动表型分析评估，以评估ST平台之间具有病理意义的比较。在此，我们展示了ST平台之间的复杂差异，揭示了诸如探针设计等参数在决定数据质量方面的重要性，并提出了用于准确空间分析和分子发现的可靠工作流程。
