Protocol for generating human tonsil immune organoids with epithelial and germinal center layers using low-Matrigel culture

Tonsil immune organoids traditionally include either epithelial layers or immune compartments, failing to recapitulate the integrated physiological microenvironment of human tonsils. Here, we present a protocol to generate tonsil immune organoids that recapitulate both epithelial and germinal center-like structures using a low-concentration Matrigel transwell system. We describe organoid assembly, immune stimulation, and evaluation of epithelial architecture and germinal center formation. This platform provides a versatile tool for dissecting human immune responses, assessing vaccines, discovering antibodies, and exploring autoimmune mechanisms. • Instructions for generating epithelial-immune organoids in low-concentration Matrigel • Preparation of L-WRN conditioned medium and optimized organoid culture medium • Guidance on organoid characterization by immunofluorescence and flow cytometry Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Tonsil immune organoids traditionally include either epithelial layers or immune compartments, failing to recapitulate the integrated physiological microenvironment of human tonsils. Here, we present a protocol to generate tonsil immune organoids that recapitulate both epithelial and germinal center-like structures using a low-concentration Matrigel transwell system. We describe organoid assembly, immune stimulation, and evaluation of epithelial architecture and germinal center formation. This platform provides a versatile tool for dissecting human immune responses, assessing vaccines, discovering antibodies, and exploring autoimmune mechanisms.