Single-Cell Signalling Analysis of Heterocellular Organoids

Abstract

Organoids are powerful biomimetic tissue models. Despite their widespread adoption, methods to analyse cell-type specific post-translational modification (PTM) signalling networks in organoids are absent. Here we report multivariate single-cell analysis of cell-type specific signalling networks in organoids and organoid co-cultures. Simultaneous measurement of 28 PTMs in >1 million single small intestinal organoid cells by mass cytometry reveals cell-type and cell-state specific signalling networks in stem, Paneth, enteroendocrine, tuft, goblet cells, and enterocytes. Integrating single-cell PTM analysis with Thiol-reactive Organoid Barcoding in situ (TOBis) enables high-throughput comparison of signalling networks between organoid cultures. Multivariate cell-type specific PTM analysis of colorectal cancer tumour microenvironment organoids reveals that shApc, Kras G12D , and Trp53 R172H cell-autonomously mimic signalling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform highthroughput multivariate cell-type specific signalling analysis of healthy and cancerous organoids.

A developmental atlas of somatosensory diversification and maturation in the dorsal root ganglia by single-cell mass cytometry

“…This approach has been applied to immune cells in suspension 62 , but cell dissociation presents a challenge because it can induce artifactual stress-related signaling. These effects can be mitigated by rapid dissociation and fixation from 2D culture 26 , or by fixing cells before dissociation from epithelial sheets 63, 64 and organoids 65, 66 . DRG tissue is not compatible with these techniques due to the prolonged dissociation steps (Methods), but DRG explant cultures in vitro can be dissociated rapidly, and are therefore amenable to cell signaling analysis.…”

Mass Cytometry for Multivariate Organoid Signalling Analysis

“…TOBis barcoded conditions can be resolved into individual FCS files using: https://github.com/zunderlab/single-cell-debarcoder. All FCS files can be uploaded to the Cytobank platform (http://www.cytobank.org/) and proceed to single-cell signalling analysis 10 . All selection of tools to analyse organoid CyTOF data can be found at: https://github.com/TAPE-Lab.…”

Computational methods for single-cell omics across modalities

“…This opens up opportunities for reconstructing inter-and intracellular signaling networks. Methods for inference of signaling pathway architecture are already being applied on single-cell mass cytometry (CyTOF) data 15,16 .…”