Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis.
IF: 17.694
Cited by: 23


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 RNAscopeTM and LGC StellarisTM. 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.


Spatial Transcriptomics

MeSH terms

BRCA1 Protein
Cell Line, Tumor
DNA-Directed RNA Polymerases
Diagnostic Imaging
Fluorescent Dyes
Gene Expression Profiling
Gene Expression Regulation
HEK293 Cells
Ki-67 Antigen
Microscopy, Fluorescence
Nuclear Receptor Coactivator 3
RNA, Messenger
Skin Neoplasms
Spatial Analysis
TOR Serine-Threonine Kinases


Vu, Tam
Vallmitjana, Alexander
Gu, Joshua
La, Kieu
Xu, Qi
Flores, Jesus
Zimak, Jan
Shiu, Jessica
Hosohama, Linzi
Wu, Jie
Douglas, Christopher
Waterman, Marian L
Ganesan, Anand
Hedde, Per Niklas
Gratton, Enrico
Zhao, Weian

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