Intestinal enteroids/organoids: A novel platform for drug discovery in inflammatory bowel diseases

Table 1 Enteroids/organoids retain the tissue specific transcriptional and epigenetic profiles

	Enteroidsderived from	Distinct genes	Transcriptional / epigenetic	Culture period / passage number of enteroids	Human / mouse	Ref.
Region-specific	Duodenum	Gata4, Cybrd1, Slc40a1	Increased mRNA	12 weeks	Mouse	[25]
	Jejunum	Gata4, Lct
	Ileum	Slc10a2, Ostb
Region- specific	Small bowel	CHGA, ATOH1	Increased mRNA	Not mentioned	Human fetus	[172]
	Large bowel	LGR5, MYC
Region-specific	Terminal ileum	SLC5A1, CLDN15	Increased mRNA	3 months / 11 passages	Human children and adults	[26]
		SATB2AS1	Increased methylation
	Sigmoid colon	CFTR, SATB2	Increased mRNA
		IL6R, CLDN15	Increased methylation
Disease-specific	Normal rectum	GATA2	Increased methylation	3-5 passages	Human children	[26]
	Gastric heterotopia in rectum	SATB2AS1
Disease-specific	Colon of non-IBD patients	PLA2G2A, ZG16, CLCA1, AQP8, MUC12	Increased mRNA	1 passage	Human	[14]
	Colon of UC patients	LYZ, ANXA10CLDN18
Disease-specific	Sigmoid colon of non-IBD patients	LYZ (low)	mRNA expression	Not mentioned	Human	[14]
	Sigmoid colon of CD patients	LYZ (High)
Disease-specific	Healthy control	GREB1, TMEM173	Increased methylation	Not mentioned	Human children: Terminal ileum, sigmoid colon	[28]
	CD patients	PDE1B

Gata4: GATA binding protein 4, transcription factor specific to duodenum and jejunum; Cybrd1: Cytochrome b reductase 1 specific for iron uptake; Slc40a1: Solute carrier family 40 member 1, Fe2⁺ transporter ferroportin for iron uptake; Lct: Lactase-phlorizin hydrolase for dissacharide digestion; Slc10a2: Solute carrier family 10 member 2, apical sodium-dependent bile acid transporter; Ostb: Organic solute transporter beta for bile acid uptake; CHGA: Chromogranin A, a marker of enteroendocrine cells; ATOH1: Atonal BHLH Transcription Factor 1, key regulator of the Notch pathway; LGR5: Leucine rich repeat containing G protein-coupled receptor 5; MYC: MYC Proto-Oncogene, BHLH Transcription Factor; SLC5A1: Solute carrier family 5 member 1; CLDN15: Claudin 15; SATB2AS1: Special AT-rich sequence-binding protein 2 antisense 1; CFTR: Cystic fibrosis transmembrane conductance regulator; SATB2: Special AT-rich sequence-binding protein 2; IL6R: Interleukin-6 receptor; GATA2: GATA binding protein 2; PLA2G2A: Phospholipase A2 Group IIA, antibacterial enzyme; ZG16: Zymogen Granule Protein 16, mucus secreting cell marker; CLCA1: Chloride Channel Accessory 1, mucus secreting cell marker; AQP8: Aquaporin-8, water transporter; MUC12: Transmembrane mucin 12; LYZ: Lysozyme C; ANXA10: Annexin-10; CLDN18: Claudin 18; GREB1: Growth regulation by estrogen in breast cancer 1; TMEM173: Transmembrane protein 173; PDE1B: Phosphodiesterase 1B.