PO.TB10.08 · 肿瘤生物学
在FFPE肺鳞状细胞癌样本中对空间转录组学技术进行跨平台比较
Cross-platform comparison of spatial transcriptomics technologies in an FFPE lung squamous cell carcinoma sample
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摘要 Abstract
中文摘要
空间转录组学技术在方法学、空间分辨率、灵敏度以及与FFPE组织的兼容性方面差异巨大,然而来自同一临床标本生成的比较数据仍然有限。我们使用单个FFPE肺鳞状细胞癌组织块开展了一项基准研究,以评估Takara Trekker™以及Visium、Visium HD和Xenium。来自同一组织块的切片按照标准工作流程分别用各平台处理。Trekker采用独特的空间标记策略,保留完整细胞核的位置身份,并与10x Flex检测无缝整合,实现真正单细胞分辨率的空间谱分析。Visium HD和Visium提供基于阵列的mRNA捕获,Xenium实现靶向原位检测。数据使用平台特异性流程处理。在同一肿瘤区域内,Trekker实现了更高的基因回收率,并以与组织病理学大体一致的空间模式捕获了恶性、免疫和基质细胞群。与Visium HD的比较显示在主要肿瘤和基质特征上总体空间一致。相较于Visium HD和Visium,Trekker灵敏度的提升带来了更深的转录组覆盖度以及对转录上不同肿瘤状态更清晰的区分。基于细胞核的工作流程还支持对低表达基因的可靠检测。Xenium提供与Trekker主要空间特征一致的高分辨率靶向测量,尽管其面板限制了无偏的全转录组发现。跨平台整合分析显示,Trekker在保留来自FFPE的全转录组谱分析优势的同时,与高分辨率的成像信号和阵列水平结构均高度一致。这些发现表明,Trekker能够对存档肺癌组织实现高分辨率、可扩展且无偏的空间表征,并通过将灵活的FFPE兼容性与全面的分子检测相结合,补充现有的空间技术。
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Spatial transcriptomics technologies vary widely in methodology, spatial resolution, sensitivity, and compatibility with FFPE tissues, yet comparative data generated from the same clinical specimen remain limited. We conducted a benchmarking study using a single FFPE lung squamous cell carcinoma block to evaluate Takara Trekker™ alongside Visium, Visium HD, and Xenium. Sections from the same block were processed with each platform following standard workflows. Trekker employs a unique spatial-tagging strategy that preserves the positional identity of intact nuclei and integrates seamlessly with the 10x Flex assay, enabling true single-cell-resolution spatial profiling. Visium HD and Visium provide array-based mRNA capture and Xenium enabled targeted in situ detection. Data were processed with platform-specific pipelines.Within the same tumor region, Trekker delivered higher gene recovery and captured malignant, immune, and stromal populations with spatial patterns broadly aligned with histopathology. Comparisons with Visium HD showed overall spatial concordance in major tumor and stromal features. Trekker's increased sensitivity relative to Visium HD and Visium resulted in deeper transcriptome coverage and clearer separation of transcriptionally distinct tumor states. The nuclei-based workflow also supported reliable detection of lower expressing genes. Xenium offered high-resolution, targeted measurements that aligned with Trekker's major spatial features, though its panel limited unbiased transcriptome-wide discovery.Across platforms, integrated analysis showed that Trekker provided strong concordance with both high-resolution imaging-based signals and array-level structure while preserving the advantages of whole-transcriptome profiling from FFPE. These findings demonstrate that Trekker enables high-resolution, scalable, and unbiased spatial characterization of archival lung cancer tissue and complements existing spatial technologies by combining flexible FFPE compatibility with comprehensive molecular detection.
利益披露 Disclosure
B. Bell, None..
C. Uytingco, None..
A. Barrett, None..
B. Ngo, None..
J. Sakkos, None..
D. Kool, None..
W. Wang, None..
M. del Rosario, None..
C. Chang, None..
C. Fan, None..
A. Farmer, None.