ExSeq: Expansion Sequencing for Single-Cell Spatial Transcriptomics

Abstract

The innovation of spatial transcriptomics allows for the study of gene expression while preserving spatial information on the detected transcripts. Expansion Sequencing (ExSeq) is an advanced spatial transcriptomic method combining in situ sequencing with expansion microscopy, thus enablingthe sequencing of RNAs in a physically enlarged tissue. The experiment involves the steps of tissue expansion, RNA library preparation and multiplexed sequencing by rounds of fluorescent dye addition, imaging and fluorescent dye removal. ExSeq significantly enhances resolution capacity of RNA transcripts up to the nanoscale level, thus identifying subcellular location of RNAs. The method is applicable to exploring cellular RNA in an untargeted approach, as well as to specifically detecting certain RNA types in a targeted approach, thus making the method suitable for a variety of research questions. However, limitations to the method include referring to the readout length of transcripts obtainable during sequencing and the availability of the method. ExSeq has the potential to be used in multiple tissues to allow for new insights into cellular identity, heterogeneity, interactions and implications in diseases and could possibly be adapted to inquire other cellular molecules, such as DNA or proteins on a nanoscale level.