High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging
复制标题
固定组织中RNA和蛋白质亚细胞分辨率的空间分子成像
DOI：
10.1038/s41587-022-01483-z
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发表时间：
2022-10-06
影响因子：
46.9
通讯作者：
Beechem, Joseph M.
中科院分区：
文献类型：
--
作者：
He, Shanshan;Bhatt, Ruchir;Beechem, Joseph M.
以亚细胞分辨率解析组织中RNA和蛋白质的空间分布是空间生物学领域的一个挑战。我们描述了空间分子成像，这是一种通过执行荧光分子条形码核酸杂交的多个循环以亚细胞分辨率测量完整生物样品中的 RNA 和蛋白质的系统。我们证明空间分子成像具有高灵敏度（每个细胞一个或两个副本）和非常低的错误率（每个细胞 0.0092 个错误调用）和背景（类似于每个细胞 0.04 个计数）。成像系统生成分析物的三维超分辨率定位，每个样本大约有 200 万个细胞。细胞分割是基于形态学的抗体，与福尔马林固定、石蜡包埋的样品兼容。我们在福尔马林固定、石蜡包埋的组织（非小细胞肺癌和乳腺癌）中以亚细胞分辨率测量了多组学数据（980 个 RNA 和 108 个蛋白质），并鉴定了超过 18 种不同的细胞类型、10 种独特的肿瘤微环境和 100 种配对配体-受体相互作用。有关超过 800,000 个单细胞和大约 2.6 亿个转录本的数据可以在 访问。
Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes. We demonstrate that spatial molecular imaging has high sensitivity (one or two copies per cell) and very low error rate (0.0092 false calls per cell) and background (similar to 0.04 counts per cell). The imaging system generates three-dimensional, super-resolution localization of analytes at similar to 2 million cells per sample. Cell segmentation is morphology based using antibodies, compatible with formalin-fixed, paraffin-embedded samples. We measured multiomic data (980 RNAs and 108 proteins) at subcellular resolution in formalin-fixed, paraffin-embedded tissues (nonsmall cell lung and breast cancer) and identified >18 distinct cell types, ten unique tumor microenvironments and 100 pairwise ligand-receptor interactions. Data on >800,000 single cells and similar to 260 million transcripts can be accessed at .