Formalin-fixed paraffin-embedded (FFPE) tissues are the most abundant archivable specimens in clinical tissue banks, but unfortunately incompatible with single-cell level whole transcriptome sequencing due to RNA degradation in storage and RNA damage in extraction. We developed an in-tissue barcoding approach namely DBiT-seq for spatially revolved whole transcriptome sequencing at cellular level, which required no tissue dissociation or RNA exaction, thus potentially more suited for FFPE samples. Herein, we demonstrated spatial transcriptome sequencing of embryonic and adult mouse FFPE tissue sections at cellular level (25um pixel size) with high coverage (>1000 genes per pixel). Spatial transcriptome of an E10.5 mouse embryo identified all major anatomical features in the brain and abdominal region. Integration with single-cell RNAseq data for cell type identification indicated that most tissue pixels were dominated by single-cell transcriptional phenotype. Spatial mapping of adult mouse aorta, atrium, and ventricle tissues identified the spatial distribution of a variety of cell types. Spatial transcriptome sequencing of FFPE samples at cellular level may provide enormous opportunities in a wide range of biomedical research. It may allow us to exploit the huge resource of clinical tissue specimens to study human disease mechanisms and discover tissue biomarkers or therapeutic targets.

中文翻译：

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FFPE组织在细胞水平上的空间转录组测序

福尔马林固定石蜡包埋（FFPE）组织是临床组织库中可归档的最丰富的标本，但不幸的是，由于存储中的RNA降解和提取中的RNA损伤，与单细胞水平的完整转录组测序不兼容。我们开发了一种组织内条形码方法，即DBiT-seq，可在细胞水平上进行空间旋转的整个转录组测序，而无需组织解离或RNA提取，因此可能更适合FFPE样品。在这里，我们展示了在细胞水平（25um像素大小）下具有高覆盖率（每个像素> 1000个基因）的胚胎和成年小鼠FFPE组织切片的空间转录组测序。E10.5小鼠胚胎的空间转录组确定了大脑和腹部区域的所有主要解剖特征。与用于细胞类型识别的单细胞RNAseq数据整合表明，大多数组织像素主要由单细胞转录表型主导。成年小鼠的主动脉，心房和心室组织的空间作图确定了各种细胞类型的空间分布。在细胞水平上对FFPE样品进行空间转录组测序可能为广泛的生物医学研究提供巨大的机会。它可能使我们能够利用临床组织标本的巨大资源来研究人类疾病的机制并发现组织生物标志物或治疗靶标。在细胞水平上对FFPE样品进行空间转录组测序可能为广泛的生物医学研究提供巨大的机会。它可能使我们能够利用临床组织标本的巨大资源来研究人类疾病的机制并发现组织生物标志物或治疗靶标。在细胞水平上对FFPE样品进行空间转录组测序可能为广泛的生物医学研究提供巨大的机会。它可能使我们能够利用临床组织标本的巨大资源来研究人类疾病的机制并发现组织生物标志物或治疗靶标。