APC	Antigen presenting cell
Card9	Caspase recruitment domain 9
CCL	Chemokine (C-C motif) ligand
CCR	C-C motif chemokine receptor
CD	Crohn’s disease
CitH3	Citrullination histone H3
CLA	Cutaneous lymphocyte antigen
CPD	Common dendritic progenitor
CXCL	Chemokine (C-X-C motif) ligand
CX3CR	Chemokine (C-X3-C motif) receptor
DAMPs	Damage-associated molecular patterns
DCs	Dendritic cells
DSS	Dextran sodium sulfate
ECM	Extracellular matrix
Flt3L	Fms-like tyrosine kinase 3 ligand
Foxp3	Forkhead Box P3
G-CSF	Granulocyte colony-stimulating factor
GM-CSF	Granulocyte-macrophage colony-stimulating factor
GWAS	Genome-wide association studies
IBD	Inflammatory bowel disease
IFN	Interferon
Ig	Immunoglobulin
IIC	Innate immune cells
iNOS	Inducible nitric oxide synthetase
ILCs	Innate lymphoid cells
IL	Interleukin
IRF	Interferon regulatory factor
MCP	Monocyte chemoattractant protein
MHCII	Major histocompatibility complex molecules class II
MIP	Macrophage inflammatory proteins
MMPs	Matrix metalloproteinases
MMT	Myofibroblast transition
MPO	Myeloperoxidase
mTOR	Mammalian target of rapamycin
NK	Natural killer
NETs	Neutrophil extracellular traps
NOD2	Nucleotide binding oligomerization domain containing 2
NLR	Nod-like receptors
PAD4	Protein arginine deiminase 4
PAMPs	Pathogen-associated molecular patterns
pDC	Plasmacytoid DCs
RA	Retinoic acid
PRRs	Pattern recognition receptors
RORγt	RAR-related orphan receptor gamma t
SCFAs	Short-chain fatty acids
scRNA-seq	Single cell RNA sequencing
SIPRα	Signal-regulatory protein alpha
STAT	Signal transducer and activator of transcription
Th	T-helper
TGF	Transforming growth factor
TL1A	TNF-like ligand 1 A
TLRs	Toll-like receptors
TNBS	2,4,6-trinitrobenzene sulfonic acid
TNF	Tumor necrosis factor
Treg	T regulatory
Tr1	T regulatory type 1
TWAS	Transcriptome-wide association studies
UC	Ulcerative colitis
WNT	Wingless-related integration site
XCR1	Chemokine (C motif) receptor 1