NanoString Technologies, Inc., Seattle, WA, USA.
Precision Oncology, Oregon Health & Science University Knight Cancer Institute, Portland, OR, USA.
Nat Biotechnol. 2020 May;38(5):586-599. doi: 10.1038/s41587-020-0472-9. Epub 2020 May 11.
Digital Spatial Profiling (DSP) is a method for highly multiplex spatial profiling of proteins or RNAs suitable for use on formalin-fixed, paraffin-embedded (FFPE) samples. The approach relies on (1) multiplexed readout of proteins or RNAs using oligonucleotide tags; (2) oligonucleotide tags attached to affinity reagents (antibodies or RNA probes) through a photocleavable (PC) linker; and (3) photocleaving light projected onto the tissue sample to release PC oligonucleotides in any spatial pattern across a region of interest (ROI) covering 1 to ~5,000 cells. DSP is capable of single-cell sensitivity within an ROI using the antibody readout, with RNA detection feasible down to ~600 individual mRNA transcripts. We show spatial profiling of up to 44 proteins and 96 genes (928 RNA probes) in lymphoid, colorectal tumor and autoimmune tissues by using the nCounter system and 1,412 genes (4,998 RNA probes) by using next-generation sequencing (NGS). DSP may be used to profile not only proteins and RNAs in biobanked samples but also immune markers in patient samples, with potential prognostic and predictive potential for clinical decision-making.
数字空间分析（DSP）是一种适用于福尔马林固定、石蜡包埋（FFPE）样本的高度多重化蛋白质或 RNA 空间分析方法。该方法依赖于：(1) 通过寡核苷酸标签对蛋白质或 RNA 进行多重读出；(2) 通过光可裂解（PC）接头将寡核苷酸标签连接到亲和试剂（抗体或 RNA 探针）上；以及 (3) 将光投射到组织样本上，以在覆盖 1 至 ~5000 个细胞的感兴趣区域（ROI）中释放任何空间模式的 PC 寡核苷酸。在 ROI 中，DSP 可以使用抗体读出实现单细胞灵敏度，RNA 检测的可行性低至 ~600 个单个 mRNA 转录本。我们通过 nCounter 系统在淋巴样、结直肠肿瘤和自身免疫组织中实现了多达 44 种蛋白质和 96 种基因（928 个 RNA 探针）的空间分析，通过下一代测序（NGS）实现了多达 1412 种基因（4998 个 RNA 探针）的空间分析。DSP 不仅可用于分析生物样本库中的蛋白质和 RNA，还可用于分析患者样本中的免疫标志物，具有用于临床决策的潜在预后和预测潜力。
