【생물정보학】 리간드-수용체 상호작용 분석

리간드-수용체 상호작용 분석(ligand-receptor interaction analysis; 세포-세포 상호작용, cell-cell interaction, CCI)

 

추천글 : 【생물학】 생물정보학 분석 목차

---

1. 알고리즘 및 데이터베이스 [본문]

2. 리간드-수용체 라이브러리 [본문]

---

a. 유전자 라이브러리

b. 유전자 스코어 라이브러리

c. 셀 타입 마커 유전자

---

 

1. 알고리즘 및 데이터베이스 [목차]

① LR 상호작용 스코어 (ref)

 

 

② scRNA-seq 기반

○ CellTalkDB (human DB file, mouse DB file)

○ CellPhoneDB  

○ CellChat

○ ICELLNET

○ NicheNet

○ SoptSC

○ CytoTalk

○ scTensor

○ CCCExplorer

○ Connectome

③ ST 기반

○ spata2

○ CellPhoneDB v3

○ stLearn

○ SCVA

○ MISTy

○ NCEM

○ COMMOT 

④ 기타

○ squidy

○ IPA (upstream regulator analysis of ingenuity pathway analysis)

 

 

2. 리간드-수용체 라이브러리 [목차]

○ 단백질-단백질 상호작용 

○ 일반적인 target receptor와 target ligand

 

Organ	Cell type	Receptor	Ligand	Common targeting applications	Ref.
Liver	Hepatocytes, cancer cells	Asialoglyco-protein	Galactose	Cancer, Wilson's disease, hemochromatosis	.
.	.	.	Galactosamine	.	.
.	.	.	Lactose	.	.
Liver	Endothelial cells and Kupffer cells	Mannose receptor (C-type lectin receptor)	Mannose	Bacterial infections, inflammation, cardiovascular disease, cancer, cerebral ischemia/stroke, genetic metabolic diseases, Leishmaniasis	.
Liver	Hepatocytes	Galactosyl receptor	Galactose	Blood filtration	.
Liver	Kupffer cells	Fucose receptor, Lectin B	Fucose	Tissue binding, bio film formation	.
Liver, spleen, brain, bone marrow, and lungs	Macrophages	Mannose receptor (C-type lectin receptor)	Mannose	Bacterial infections, inflammation, cardiovascular disease, cancer, cerebral ischemia/stroke, genetic metabolic diseases, Leishmaniasis	.
Spleen, lymph nodes, blood, skin	Dendritic cells	Mannose receptor (C-type lectin receptor)	Mannose	Adaptive immune respose/vaccination	.
Tumor sites	Malignant cells	Lectin-like receptors (e.g., galectins)	Galactose, lactose, mannose, fucose, Sialic Lewis' glycosides	Anti-proliferation	.
Oral cavity	Buccal cells	Lectin receptors	Lactose and mannose	Bioadhesion	.
Eye	Corneal/conjunctival cells	Lectin receptors	Glucose and galactose, chitosan	Conjunctivitis	.
Colon	Epithelial cells	Galectin	Galactose	Cancer, bioadhesion	.
Lung	Pulmonary cells	Lectin receptors	Galactose	Cystic fibrosis, lung cancer, and pulmonary tuberculosis	.
Brain	Neurons	Anionic membranes and lectins	Trimethylated chitosan	Crossing the blood brain barrier, memory impairment	.

 

Table. 1. 일반적인 target receptor와 target ligand

 

○ ALOX5 ↔︎ ALOX5AP : proinflammatory interaction

○ ANGPTL4 ↔︎ SDC1 : adhesive. Wnt signaling을 억제하는 것으로 여겨짐 

○ BST2 ↔️ LILRA4 : anti-inflammatory interaction

○ C3 ↔️ C3AR1 : proinflammatory interaction

○ CCL5 ↔️ CCR1 : proinflammatory interaction

○ CD28 ↔️ CD80 : co-stimulatory 

○ CD47 ↔️ SIRPA : innate immunity suppressor 

○ COL1A1 ↔︎ SDC1 : adhesive

○ CTLA4 ↔️ CD80 : co-inhibitory 

○ CTLA4 ↔️ CD86 : co-inhibitory 

○ CX3CL1 ↔️ CX3CR1 : anti-inflammatory interaction

○ CXCR3 ↔️ CXCL9 : T cell homing interaction

○ CXCR3 ↔️ CXCL10 : T cell homing interaction

○ CXCR3 ↔️ CXCL11 : T cell homing interaction

○ DNAM1 ↔️ CD155, CD112 : cell mediated cytotoxicity

○ DSC2 ↔︎ DSG1 : adhesive 

○ FGF9 ↔︎ FGFR3 : astrocyte에서 관찰

○ FN1 ↔︎ SDC1 : adhesive

○ GAS6 ↔︎ TYRO3 : innate immunity suppressor 

○ HAVCR2 (TIM3) ↔️ LGALS9 (Galectin9) : co-inhibitory 

○ HLA-F ↔️ LILRB1 : anti-inflammatory interaction

○ ICOS ↔️ ICOSLG : co-stimulatory 

○ LAIR1 ↔️ LILRB4 : suppressive interactions with myeloid cells

○ LAMB3 ↔︎ ITGA6_ITGB1 : adhesive

○ LAMB3 ↔︎ ITGA6_ITGB4 : adhesive

○ LFA1 ↔️ ICAM1 : T cell recruitment 

○ MIF ↔︎ CD74_CD44 : inflammatory

○ NECTIN1 ↔︎ FGFR3 : astrocyte에서 관찰

○ PDCD1 (PD1) ↔️ CD274 (PDL1) : co-inhibitory  

○ PDCD1 (PD1) ↔️ PDCD1LG2 (PDL2) : co-inhibitory  

○ POMC ↔️ MC1R : anti-inflammatory interaction

○ PROS1 ↔️ AXL : anti-inflammatory interaction

○ PSAP ↔️ GPR37L1: oligodendrocytes에서 관찰

○ TGFBR3 ↔️ TGFB1 : suppressive interactions with myeloid cells

○ TIM-3 (T-cell Ig and mucin domain 3) 수용체 ↔️ galectin-9 리간드

○ TNFRSF9 ↔️ TNFSF9 : co-stimulatory 

○ TNFSF10 ↔️ TNFRSF10A : pro-apoptotic interaction

○ VEGF ↔️ NRP1

○ VEGF ↔️ NRP2

 

입력: 2023.06.12 18:19

수정: 2024.09.07 11:50