. 2021 Oct 9;13(20):5042. doi: 10.3390/cancers13205042

Table 2.

ILC/NK classification using scRNA-seq analyses: gene markers of both humans and mice are reported. Dashed lines and upper/lower-case characters separate the genes markers of the two species.

Cell Populations	Specific Cluster Name ¹	Organism	Tissue	Cell Source	Gene Marker ²	Reference
ILCP	ALP	Mouse	BM of Tcf7^E^GFP mice	Lin⁻cKit⁺2B4⁺α4β7⁻Flt3hiIL-7Rα⁺	Tcf7 Flt3 H2dma Sp1 Mef2c	[198]
	sEILP		BM of Tcf7^EGFP mice	Lin⁻cKit⁺2B4⁺α4β7⁺Tcf7-GFP⁺	Tcf7 Irf8 Runx3	[198]
	cEILP		BM of Tcf7^EGFPmice	Lin⁻cKit⁺2B4⁺α4β7⁺Tcf7-GFP⁺	Tcf7 Runx3 Tox	[198]
	General		BM of Tcf7^EGFP mice	Lin⁻cKit⁺2B4⁺α4β7⁺Tcf7-GFP⁺	Zbtb16 Lmo4 Rora	[198]
	General		BM	Lin⁻Flt3lo/⁻IL⁻7Rαlo/⁺α4β7⁺	Zbtb16 Il7r Kit Itga4 Itgb7 but low Myc	[199]
	General		BM	Lin⁻Flt3lo/⁻IL⁻7Rαlo/⁺α4β7⁺	Tcf7 Il18r1	[199]
ILC1	General	Mouse	Colon-tumor-infiltrating ILCs	CD45⁺Lin⁻CD127⁺	Xcl1 Tbx21 Klrb1c Ncr1 Ifng Klrd Klrk1 Klrc1 Ctsw	[138]
	ILC1s and/or cNKs		BM	Lin⁻Flt3lo/⁻IL−7Rαlo/⁺α4β7⁺	Cish	[199]
	Bile duct-ILC1		Liver or EHDB after Il-33	CD45⁺Lin⁻	Cd28 Il12rb2 Thy1 Cd93 Tbx21 Ifngr1 Il2 Il10	[200]
	General		Salmonella-infected ceca of WT or Rora^sg/sg BM-transplanted (BMT) chimeric mice	CD45.2⁺Lin⁻CD90⁺	Xcl1	[201]
	General	Human	Tonsil	Lin⁻CD127⁺NKG2A⁻CD16⁻CD117⁻CRTH2⁻	CXCR3 IFNG	[202]
	General		CRC tissue	Lin⁻CD45⁺CD127⁺	CD3D CD3G CCL4 IFNG IKZF3 PRDM1	[203]
	General		Lung, blood, colon and tonsil	Lin⁻CD45⁺CD127⁺CD117⁻CRTH2⁻	IL7R	[204]
	General		PB	Lin⁻CD45⁺CD127⁺CD117⁻CRTH2⁻	ETS1 TBX21 EOMES IFNG BCL11BTCF7	[205]
ILC2	General	Mouse	BM	Lin⁻Flt3lo/⁻IL-7Rαlo/⁺α4β7⁺	Pdcd1 Bcl11b Icos Rora Gata3	[199]
	General (from clusters c8 to c10)		BM	Lin⁻Flt3lo/⁻IL-7Rαlo/⁺α4β7⁺	Il2ra Il1rl1 Bmp7 Pparg	[199]
	General (cluster c8)		BM	Lin⁻Flt3lo/⁻IL-7Rαlo/⁺α4β7⁺	Itgb3 Pbxip1 1700113H08Rik	[199]
	General (cluster c9)		BM	Lin⁻Flt3lo/⁻IL-7Rαlo/⁺α4β7⁺	Ccr8 Gclc	[199]
	General		Colon tumor infiltrating ILCs	Lin⁻CD45⁺CD127⁺	Gata3 Il4 Il5 Klrg1 Il1rl1 Il13 Il17rb Fosb Hes1 Itga4	[138]
	Liver-specific ILC2		Liver or EHDB after Il-33	CD45⁺Lin⁻	Ccr4 Tnfsf9 Il12rb1 IL10 NFil3 Idi1 IL9r	[200]
	Canonical ILC2		Liver or EHDB after Il-33	CD45⁺Lin⁻	Rora Gata3 Arg1 Ccr8 Klrg1 Icos Il17Rb Ccr2 Il5 Il13	[200]
	General		Adult and neonatal lung	CD45lo/⁺Lin^lo RORγt⁻YFP⁻YFP⁺	Areg Il7r Rora and Gata3 and the lack of expression of stromal NK/ILC1 B and T cell genes	[206]
	Conventional ILC2		Adult and neonatal lung	CD45lo/⁺Lin^lo RORγt⁻YFP⁻YFP⁺	Il1rl1 Tnfrsf18 Areg and Arg1	[206]
	General		Adult and neonatal lung	CD45lo/⁺Lin^loRORγt⁻YFP⁻and YFP⁺	Cd7 Runx3 Cd2 Tcf7 Il18r1	[206]
	ILC2 mature		Infected lung	(Lin⁻) CD45⁺Il7ra⁺Thy1⁺/lowNK1.1⁻	Gata3 Il1rl1 Klrg1 Bcl11b	[207]
	ILC2 effector		Infected lung	(Lin⁻) CD45⁺Il7ra⁺Thy1⁺/lowNK1.1⁻	Il5 Il13 Il17a	[207]
	Natural ILC2		Lung	Lin⁻CD3⁻TCRβ⁻Thy1⁺	Cd69 Nfkbid Fos Il13 Il1r2 Cxcl3 Calca Cxcl2 Il5 Csf2 Ccl1	[208]
	Inflammatory ILC2		Lung	Lin⁻CD3⁻TCRβ⁻Thy1⁺	Gzma Lgals1 Stmn1 Ccr9 Lgals3 Klrg1	[208]
	General		Salmonella-infected ceca of WT or Rora^sg/sg BM-transplanted (BMT) chimeric mice	CD45.2⁺Lin2CD90⁺	Gata3 Il4 Il17rb Il1rl1 Rora Il7r	[201]
	General	Human	Lung, blood, colon and tonsil	CD3⁻CD4⁻Lin⁻CD45⁺CD127⁺CD117⁺/⁻CRTH2⁺	IL7R GATA3 MAF PTGRD2 HPGDS	[204]
	c-kit- ILC2		Skin	CD45⁺Lin⁻CD127⁺CRTH2⁺CD117⁻/⁺	GATA3 CRLF2 IL17RB CCR6 RORA BCL11B	[205]
	c-kit+ ILC2		Skin	CD45⁺Lin⁻CD127⁺CRTH2⁺CD117⁻/⁺	CRLF2 IL17RB CCR6 RORA BCL11B ZBTB16 RORC	[205]
	General		Tonsil	Lin⁻CD127⁺NKG2A⁻CD16⁻CRTH2⁺	GATA3 IL1RL1 IL17RB PTGDR2	[202]
ILC3	General	Mouse	BM	Lin⁻Flt3lo/⁻IL-7Rαlo/⁺α4β7⁺	Tbx21 Il2rb Ncr1 Cxcr3 Ctsw	[199]
	General		Colon-tumor-infiltrating ILCs	Lin⁻CD45⁺CD127⁺	Rorc Il22 Ncr1 Sepp1 Ccr7 Fcer1g Cd74	[138]
	ILCreg		Colon-tumor-infiltrating ILCs	Lin⁻CD45⁺CD127⁺	Id3-Il10-Ctla4-Klf2-Tnfrsf18-Tnfrs8-Tnfrs9	[138]
	General		Salmonella-infected ceca of WT or Rora^sg/sg BM-transplanted (BMT) chimeric mice	CD45.2⁺Lin2CD90⁺	Rora Il7r Thy1 Gzmb Xcl1 Ncr1 Ifng Cxcr6 Cd4	[201]
	General	Human	Lung, blood, colon and tonsil	CD45⁺Lin⁻CD127⁺CD117⁺CRTH2⁻	KIT IL1R1 IL23R RORC	[204]
	General	Human	Tonsil	expression of NKp44 CD62L HLA-DR	IL1R1 IL23R RORC AHR NCR2	[202]
NK	mNK	Mouse	Blood	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Hbb-bs Smad7 Tgfb1 Qrfp Ifngr1	[209]
	mNK_Bl1		Blood	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Gzmb Klrg1 Ly6c2 Cma1 Klra9 Ncr1 Emp3 Fgl2	[209]
	mNK_Bl2		Blood	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Ctla2a Emb Ccr2 Socs3 Xlc1 Cd27 Cd7 Ltb	[209]
	General		Blood	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Ly6c2 Klrg1 Klra4	[210]
	NK (non-tissue- specific)		Blood, spleen, inguinal lymph node, liver, VAT, small intestine IEL/LPL, salivary gland and uterus	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Itgam S1pr5 Cma1 Zeb2	[210]
	General		Inguinal lymph node	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Il7r Ly6c2 Klra8 Klra4 Il18r1	[210]
	General		Liver	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Itga1	[210]
	NK (tissue-specific)		Liver, VAT, salivary gland, uterus, small intestine IEL/LPL and tumor	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Kit Itga1 Cd160 Asb2 S100a4m Fgl2 Gzmb Cd7m Ctla2 CCr2 Itgb1 Capg Tnfrsf9 Anxa2 Ldha Irf8	[210]
	NK (early Pec)		Peritoneal exudates	CD3ε⁻NKp46⁺CD49b⁺	Furin Ctla2a, Ifitm1 Ifng	[211]
	NK (late Pec)		Peritoneal exudates	CD3ε⁻NKp46⁺CD49b⁺	Spp1 Gzmb Lag3 Ly6a	[211]
	General		Salivary gland and uterus	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Klra4 Klra8 Itga1 Il7r	[210]
	General		Salmonella-infected ceca of WT or Rorasg/sg BM-transplanted (BMT) chimeric mice	CD45.2⁺Lin2CD90⁺	Ncr1 Sell Eomes Gzma	[201]
	General		Small-intestine IEL/LPL	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Kit Itga1 Il7r	[210]
	mNK		Spleen	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Jun Ccl3 Fos Ccl4 Fosb Klf2	[209]
	mNK_Sp1		Spleen	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Lgals1 Cma1 Gzmb Fgl2 Klra9 Lys6c2 Irf8 Klrg1	[209]
	mNK_Sp2		Spleen	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Ctla2a Ltb Emb Cd28 Xcl1 Cd7 Spry2 Fosb Cd27 Cebpb	[209]
	mNK_Sp3		Spleen	CD3⁻CD19⁻CD45.2NK1.1⁺NKp46⁺	Nfkbia Nr4a1 Pim1 Prr7 Ccl4	[209]
	General		Spleen	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Ly6c2 Klrg1 Klra4 Klra8 Il18r1	[210]
	General		Spleen	CD3⁻CD19⁻NK1.1⁺NKp46⁺Eomes-GFP⁺CD49a⁻	Eomes Itgam Zeb2 (no expression of Cd27 Itga1)	[212]
	NK (early Spl)		Spleen	CD3ε⁻NKp46⁺CD49b⁺	Xcl1 Ncr1 Jun Fos	[211]
	NK (resting Spl)		Spleen	CD3ε⁻NKp46⁺CD49b⁺	Cma1 Klf2 Zeb2 Itga4 Klrc2	[211]
	NK (proliferating Pec/Spl)		Spleen/peritoneal exudates	CD3ε⁻NKp46⁺CD49b⁺	Mki67 Top2a Stmn1	[211]
	Cd11bˡᵒʷCd27ʰᶦᵍʰ		TME	CD3ε⁻NK1.1⁺	Kit Pdcd1 Tigit Ctla4	[213]
	Cd11bʰᶦᵍʰCd27ˡᵒʷ		TME	CD3ε⁻NK1.1⁺	Klrg1 Ncr1 Klrb1c Itga2 Klra3 Klra9 Prf1 Gzma Gzmb	[213]
	NK(Hif1a−/−)		TME	CD3ε⁻NK1.1⁺	Ifng Cd69 Ccl4 Ccl3 Nr4a1	[213]
	General		VAT	CD45⁺Lin⁻NK1.1⁺NKp46⁺	Itga1 Il7r Ly6c2	[210]
	hNK	Human	Blood	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	PTMA S100A6 TGFB1 GNLY LDHA SCL75A	[209]
	hNK_Bl1		Blood	anti-CD3, -CD14, -CD19, -CD45, -CD56	FGFBP2 GZMB GZMA SPON2 CST7 FGCR3A GTF3C1	[209]
	hNK_Bl2		Blood	anti-CD3, -CD14, -CD19, -CD45, -CD56	GZMK CD44 CXCR3 SCML1 NCF1 XCL1 SCML1 ZFP36L2	[209]
	General		Blood	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	GZMK JUNB LTB LNFS	[214]
	bNK0		Blood	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	FCGR3A FCGR3B PRF1 GZMB	[214]
	bNK1		Blood	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	GZMK SELL	[214]
	bNK2		Blood	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14^–CD15⁻CD163⁻	SELL IL7R XCL1/2	[214]
	bNK3		Blood	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	PCNA MKI67	[214]
	h_NK_Bm1		BM	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	FGFBP2 GZMB GZMH PRF1 FCGR3A	[215]
	h_NK_Bm2		BM	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	CCL3 CCL4 XCL1 XCL2 GZMK CCL3L1 AREG CD160 CD69	[215]
	h_NK_Bm3		BM	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	GZMK XCL1 XCL2 AREG LTB SELL CD44	[215]
	h_NK_Bm4		BM	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	CCL5 GZMM GZMH ZEB2	[215]
	General		BM	Not provided	GZMH GZMK GNLY	[216]
	General		Bronchoalveolar lavage fluid	Not provided	TYROBP KLRD1 NKG7 FCER1G GNLY PRF1 GZMB KLRF1 XCL1/2 CCL3/4	[217]
	General		Liver/cirrhotic liver	CD45⁺	KLRF1 CCL3 XCL1 IL2RB XCL2 CD160 KDLR1 CLEBPD CLIC3 LAT2 CCL3L3	[218]
	cNK		Liver/cirrhotic liver	CD45⁺	KLRF1 GNLY PRF1 FGFBP3 SPON2	[218]
	General		Liver	Viable cells	NKG7 CCL4 CCL5 KLRD1 KLRK1 GZMA GZMB GZMH	[219]
	General		Liver	Viable cells	CD7 KLRB1 NKG7	[220]
	trNK		Liver	CD45⁺	KLRB1 TRDC CXCR6 EOMES GZMK KLRF1	[221]
	cNK		Liver	CD45⁺	TBX21 CX3CR1 GZMB TRDC FGCR3A KLRF1	[221]
	NK-GZMH		Intrahepatic cholangiocarcinoma	Viable cells	KLRF1 KLRB1 IL7R LTB CCR6 NCR3	[222]
	NK-GZMK		Intrahepatic cholangiocarcinoma	Viable cells	KLRF1 TYROBP FCER1G GZMK CD160	[222]
	General		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15CD163⁻	FGFBP2 FCGR3A PRF1 S1PR5 GZMB	[214]
	tNK0		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	AREG SELL XCL1/2 FOS	[214]
	tNK1		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	CCL3/4L2/5 CD160 TIGIT	[214]
	tNK2		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	FGFBP2 FGCR3A PRF1 GZMB	[214]
	tNK3		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	SELL SPTSSB KIR2DL4	[214]
	tNK4		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD16⁻	LST1 LTB	[214]
	tNK5		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	CCL5 HLA-DRBA GZMH	[214]
	tNK6		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	PCNA MKI67	[214]
	tNK7		Melanoma metastasis	CD45⁺CD56⁺CD3ε⁻CD4⁻CD8a⁻CD14⁻CD15⁻CD163⁻	ISG15 IFI6	[214]
	General		Ovarian cancer ascites	CD45⁺	KLRB1 KLRF1	[223]
	General		Ovarian cancer ascites	CD45⁺	FCGR3A FCGR3B NCAM1 KLRB1 KLRB1 KLRC1 KLRD1 KLRF1 KLRK1	[224]
	General		PBMC	Not provided	KLRF1 FCGR3A	[225]
	General		PBMC	Not provided	FCGR3A NCAM1 GZMB	[226]
	General		PBMC	Not provided	KLRF1	[227]
	hNK		Spleen	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	KLF6 NFKBIA TSC22D3 ADGRE5 NCL1 CD69 ANXA1	[209]
	hNK_Sp1		Spleen	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	FGFBP2 GZMB CST7 FGCR3A MYOM2 GNLY S100A4 CYBA PRF1	[209]
	hNK_Sp2		Spleen	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	GZMK XCL1 COTL1 CD160 TOX2 RGS1 LIF KLRB1 KLRB1 BCL2A1 SPRY2	[209]
	hNK_Sp3		Spleen	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	IL7R DUSP4 CD52 GRP183 SELL CD44 CAPG LTB YBX3	[209]
	hNK_Sp4		Spleen	CD3⁻CD14⁻CD19⁻CD45⁺CD56^low/+	TTC30B TXNIP ARRDC3 SDF2 INPP5F	[209]
	General		Tonsil	CD45⁺Lin⁻CD127⁻CD56⁺NKG2A⁺	KLRC1 GNLY GZMA EOMES	[202]
	General		TME/PBMC	CD3CD4CD8CD25	CD160 XCL1 XCL2 MYADAM CAPG RORA NR4A1/2/3 KLRC1/2/3 IKZF2 EDNTPD1 CD69 ITGAE	[228]
	NK-1		Tumor/blood	CD3CD19CD20⁻	IFIT1/3 IFI6 CD8a	[229]
	NK-1		Tumor/blood	CD14⁻CD34⁻CD68⁻CD56⁺/⁻CD127⁺/⁻	IFIT1/3 IFI6 CD8a	[229]
	NK-2		Tumor/blood	CD3⁻CD19⁻CD20⁻CD14⁻CD34⁻CD68⁻CD56⁺/⁻CD127⁺/⁻	NR4A2 REL CXCR4	[229]
	NK-ILC1		Tumor/blood	CD3⁻CD19⁻CD20⁻CD14⁻CD34⁻CD68⁻CD56⁺/⁻CD127⁺/⁻	CD83 IL7R SELL	[229]

¹ When provided and different from cell population (general). ² Selected on the basis of the relevance in the study.