SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis I

We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D solid-tumour models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq simultaneously reveals both inter- and intra-cellular signalling in tumour microenvironment organoids. HELA spheroids were grown in 96-well Eplasia plates for 48 hours in DMEM high-glucose with supplemented with 2 mM L-Glutamine and 10% FBS. Spheroids were serum starved for 4hrs and pre-treated with inhibitors 100nM Trametinib and 500nM GDC0941 Pictilisib or vehicle (DMSO) for 10 minutes prior to growth factor treatment. Spheroids were then treated for 30 minutes with 100nM Human IGF1 and 100nM Human EGF or vehicle (water) before fixation in-situ. Spheroids were fixed in-situ using an adapted SPLiT-seq protocol and dispersed by mechanical dissociation using a TissueGrinder. Single-cells were permeabilised using an adapted SPLiT-seq protocol and frozen before processing with SIGNAL-seq. The RNA and ADT libraries were sequenced separately. Further information on the SIGNAL-seq barcoding layout and processed data can be found at: https://github.com/TAPE-Lab/SIGNAL-seq