Single-Cell and Spatial Analysis of Emergent Organoid Platforms

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 pat...

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Bibliographic Details
Published in:	Methods in molecular biology (Clifton, N.J.) Vol. 2660; p. 311
Main Authors:	Kumar, Aditi, Cai, Shuangyi, Allam, Mayar, Henderson, Samuel, Ozbeyler, Melissa, Saiontz, Lilly, Coskun, Ahmet F
Format:	Journal Article
Language:	English
Published:	United States 2023
Subjects:	Humans Organogenesis Organoids Regenerative Medicine Spatial Analysis Stem Cells Regenerative medicine Imaging mass cytometry (IMC) High-dimensional immunophenotyping Embryonic stem cells (ESCs) Sequential fluorescence in situ hybridization (seqFISH) Matrix-assisted laser desorption/ionization (MALDI) Multivariate-barcoded mass cytometry (MC) Precision medicine Cyclic immunofluorescence (CycIF) Light-sheet fluorescence microscopy (LSFM) Multiplexed error-robust fluorescence in situ hybridization (MERFISH) Patient-derived xenograft (PDX) Organoid heterogeneity Pluripotent stem cells (PSCs) Organogenesis Three-dimensional (3D) tissues Adult stem cells (ASCs) Epi-illumination selective-plane illumination microscope (eSPIM) Time-of-flight secondary ion mass spectrometry (TOF-SIMS) Extracellular matrix (ECM) Single-cell RNA-sequencing (scRNA-seq) Open-top light-sheet (OTLS) microscopes Single-cell and spatial analysis Induced pluripotent stem cells (iPSC) Organoid atlas
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Summary:	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.
ISSN:	1940-6029
DOI:	10.1007/978-1-0716-3163-8_22