Table 1.

Intestinal epithelial culture methods and potential applications.

Culture	Source	Applications	Read-outs	Future applications	Cost
Cancer cell lines (CaCo-2, HT-29, SW480, T84, etc.)	Cancer tissues, adapted to cell culture	– Basic physiology (limited)  – Host-microbe interactions	– RNA levels (+)  – Western blot (+)  – Immunostainings (+)  – Transport of molecules (+)  – TEER measurement (+)  – Multiple cell types (−/+)  – Cell viability/proliferation (+)	– Limited	Low
Primary 2D monolayers	– Crypts from mucosal biopsies  – Resected tissue	– Basic physiology  – Host-microbe interactions	– RNA levels (+)  – Western blot (+)  – Immunostainings (+)  – Transport of molecules (+)  – TEER measurement (+)  – Multiple cell types (−/+)  – Cell viability/proliferation (+)	– Pathway-based patient stratification  – Gut-on-a-chip  – Co-culture with other patient-derived cell types, microbiota	Low–Moderate
Primary 3D organoids	– Crypts or LGR5+ stem cells from mucosal biopsies  – Resected tissue  – iPSC-derived	– Basic physiology  – Drug efficacy (e.g. CF)  – Host-microbe interactions	– RNA levels (+)  – Western blot (–/+)  – Immunostainings (+)  – Transport of molecules (+/−)  – TEER measurement (+)  – Multiple cell types (+)  – Cell viability/proliferation (+)	– Co-culture systems (enteric nervous system, immune cells, myofibroblasts, microbiota)  – Drug efficacy/toxicity screening	Expensive
Primary explants	– Mucosal biopsies  – Resected tissue	– Ussing chambers (barrier function)  – Effect on epithelium  – Immune system and CNS in one system	– RNA levels (+)  – Western blot (+)  – Immunostainings (+)  – Transport of molecules (+)  – TEER measurement (+)  – Multiple cell types (+)  – Cell viability/proliferation (+)	– Limited/to be explored	Moderate

TEER: transepithelial electrical resistance; 2D: two-dimensional; 3D: three-dimensional; LGR5: Leucin-rich repeat containing G-protein coupled receptor 5; CF: cystic fibrosis; CNS: central nervous system.