Sinem Saka (EMBL): 'A DNA toolbox for spatial biology from imaging to sequencing'

Speaker: Sinem Saka (EMBL)

Abstract: Our group at EMBL develops and applies spatial biology and spatial omics methods to understand how the cellular and molecular organization affect function. We have previously developed multiplexed imaging approaches such as SABER-FISH and Immuno-SABER that utilize DNA barcoding and a flexible in situ signal amplification system for efficient visualisation of many protein, DNA or RNA targets in cells and tissues. More recently, we started to leverage DNA barcoding for a new spatial transcriptomics approach, Light-Seq, which directly integrates fluorescence imaging and whole-transcriptome next-generation sequencing of the same cells in fixed biological samples. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables imaging-based in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three adjacent cellular layers and discovered new biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.