Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.
Nat Commun. 2022 Jan 10;13(1):169. doi: 10.1038/s41467-021-27798-0.
Multiplexed mRNA profiling in the spatial context provides new information enabling basic research and clinical applications. Unfortunately, existing spatial transcriptomics methods are limited due to either low multiplexing or complexity. Here, we introduce a spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based decoding. We demonstrate MOSAICA's multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of five fluorophores with facile error-detection and removal of autofluorescence. MOSAICA's analysis is strongly correlated with sequencing data (Pearson's r = 0.96) and was further benchmarked using RNAscope and LGC Stellaris. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We finally demonstrate simultaneous co-detection of protein and mRNA in cancer cells.
在空间背景下进行多重 mRNA 分析提供了新的信息，使基础研究和临床应用成为可能。不幸的是，现有的空间转录组学方法由于低多重性或复杂性而受到限制。在这里，我们介绍了一种空间组学技术，称为多组学单扫描分析与组合分析集成（MOSAICA），它将细胞或组织中 mRNA 和蛋白质标记物的原位标记与组合荧光光谱和寿命编码探针、光谱和时间分辨荧光成像以及基于机器学习的解码相结合。我们通过使用易于检测错误的五种荧光团的组合标记以及去除自发荧光来证明 MOSAICA 在检测固定结直肠癌细胞中的 10 重靶标方面的可扩展性。MOSAICA 的分析与测序数据具有很强的相关性（Pearson r=0.96），并进一步使用 RNAscope 和 LGC Stellaris 进行了基准测试。我们进一步将 MOSAICA 应用于临床黑色素瘤福尔马林固定石蜡包埋（FFPE）组织的多重分析。我们最后证明了在癌细胞中同时检测蛋白质和 mRNA。
