Purpose

Single-cell transcriptional profiling reveals cell heterogeneity and clinically relevant traits in intra-operatively collected patient-derived tissue. So far, single-cell studies have been constrained by the requirement for prospectively collected fresh or cryopreserved tissue. This limitation might be overcome by recent technical developments enabling single-cell analysis of FFPE tissue.

Methods

We benchmark single-cell profiles from patient-matched fresh, cryopreserved and archival FFPE cancer tissue.

Results

We find that fresh tissue and FFPE routine blocks can be employed for the robust detection of clinically relevant traits on the single-cell level. Specifically, single-cell maps of fresh patient tissues and corresponding FFPE tissue blocks could be integrated into common low-dimensional representations, and cell subtype clusters showed highly correlated transcriptional strengths of signaling pathway, hallmark, and clinically useful signatures, although expression of single genes varied due to technological differences. FFPE tissue blocks revealed higher cell diversity compared to fresh tissue. In contrast, single-cell profiling of cryopreserved tissue was prone to artifacts in the clinical setting.

Conclusion

Our analysis highlights the potential of single-cell profiling in the analysis of retrospectively and prospectively collected archival pathology cohorts and increases the applicability in translational research.

中文翻译：

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对患者匹配的新鲜和福尔马林固定石蜡包埋 (FFPE) 肺癌组织的单细胞 RNA 谱中的临床相关特征进行稳健检测

目的

单细胞转录谱揭示了术中收集的患者来源组织中的细胞异质性和临床相关特征。到目前为止，单细胞研究受到前瞻性收集新鲜或冷冻保存组织的要求的限制。最近的技术发展可以对 FFPE 组织进行单细胞分析，从而克服这一限制。

方法

我们对来自患者匹配的新鲜、冷冻保存和存档 FFPE 癌症组织的单细胞概况进行基准测试。

结果

我们发现新鲜组织和 FFPE 常规块可用于在单细胞水平上稳健地检测临床相关性状。具体来说，新鲜患者组织和相应 FFPE 组织块的单细胞图谱可以整合到常见的低维表示中，并且细胞亚型簇显示出信号通路、标志和临床有用特征的高度相关的转录强度，尽管单基因的表达由于技术差异而有所不同。与新鲜组织相比，FFPE 组织块显示出更高的细胞多样性。相比之下，冷冻保存组织的单细胞分析在临床环境中很容易出现伪影。

结论

我们的分析强调了单细胞分析在分析回顾性和前瞻性收集的档案病理学队列中的潜力，并增加了在转化研究中的适用性。