Single-Cell and Spatial Analysis of Emergent Organoid Platforms

Abstract

Organoids have emerged as a promising advancement of the two-dimensional (2D) culture systems to improve studies in organogenesis, drug discovery, precision medicine, and regenerative medicine applications. Organoids can self-organize as three-dimensional (3D) tissues derived from stem cells and patient tissues to resemble organs. This chapter presents growth strategies, molecular screening methods, and emerging issues of the organoid platforms. Single-cell and spatial analysis resolve organoid heterogeneity to obtain information about the structural and molecular cellular states. Culture media diversity and varying lab-to-lab practices have resulted in organoid-to-organoid variability in morphology and cell compositions. An essential resource is an organoid atlas that can catalog protocols and standardize data analysis for different organoid types. Molecular profiling of individual cells in organoids and data organization of the organoid landscape will impact biomedical applications from basic science to translational use.

Keywords: Adult stem cells (ASCs); Cyclic immunofluorescence (CycIF); Embryonic stem cells (ESCs); Epi-illumination selective-plane illumination microscope (eSPIM); Extracellular matrix (ECM); High-dimensional immunophenotyping; Imaging mass cytometry (IMC); Induced pluripotent stem cells (iPSC); Light-sheet fluorescence microscopy (LSFM); Matrix-assisted laser desorption/ionization (MALDI); Multiplexed error-robust fluorescence in situ hybridization (MERFISH); Multivariate-barcoded mass cytometry (MC); Open-top light-sheet (OTLS) microscopes; Organogenesis; Organoid atlas; Organoid heterogeneity; Patient-derived xenograft (PDX); Pluripotent stem cells (PSCs); Precision medicine; Regenerative medicine; Sequential fluorescence in situ hybridization (seqFISH); Single-cell RNA-sequencing (scRNA-seq); Single-cell and spatial analysis; Three-dimensional (3D) tissues; Time-of-flight secondary ion mass spectrometry (TOF-SIMS).