Multiplex digital spatial profiling of proteins and RNA in fixed tissue
Multiplex digital spatial profiling of proteins and RNA in fixed tissue
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DOI：
10.1038/s41587-020-0472-9
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发表时间：
2020-05-01
影响因子：
46.9
通讯作者：
Beechem, Joseph M.
中科院分区：
文献类型：
--
作者：
Merritt, Christopher R.;Ong, Giang T.;Beechem, Joseph M.
数字空间分析（DSP）是一种对蛋白质或rna进行高度多重空间分析的方法，适用于福尔马林固定石蜡包埋（FFPE）样品。该方法依赖于(1)使用寡核苷酸标签对蛋白质或rna进行多路读取；(2)寡核苷酸标签通过光切割（PC）连接物附着在亲和试剂（抗体或RNA探针）上；(3)光切割光投射到组织样品上，释放PC寡核苷酸在覆盖1到5000个细胞的感兴趣区域（ROI）的任何空间模式中。DSP能够在ROI内使用抗体读出单细胞灵敏度，RNA检测可低至类似600个mRNA转录物。我们利用nCounter系统对淋巴组织、结直肠肿瘤组织和自身免疫组织中多达44个蛋白和96个基因（928个RNA探针）进行了空间分析，利用下一代测序（NGS）对1,412个基因（4,998个RNA探针）进行了空间分析。DSP不仅可用于分析生物库样品中的蛋白质和rna，还可用于分析患者样品中的免疫标记物，具有临床决策的潜在预后和预测潜力。
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 similar to 5,000 cells. DSP is capable of single-cell sensitivity within an ROI using the antibody readout, with RNA detection feasible down to similar 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 bio-banked samples but also immune markers in patient samples, with potential prognostic and predictive potential for clinical decision-making.