American Association of Immunologists

Table II.

CD3⁺CD4⁺ Th and Treg baseline cell population subsets identified using viSNE

Baseline Cell Population	Subset	Shared/Defining Markers	Differential Expression Profile	Annotation
Th1	2	CXCR3⁺CCR4−	T-bet⁺PD-1⁺CD226⁺	Bona fide Th1
	3		CD45RA⁺	CD45RA⁺ Th1
Th2	2	CCR4⁺CXCR3⁻GATA3⁺CD45RA⁻	CCR6⁺CD127⁺CD226⁺LAG3⁺	CCR6⁺ Th2
	3		CD127⁺ICOS⁺CD226⁺LAG3⁺	Bona fide Th2
Th17	1	CCR6⁺CD161⁺CD127⁺CD45RA⁻CD226⁺	CXCR3⁺CCR4⁺ICOS⁺LAG3⁺CD49b⁺	CCR4⁺CXCR3⁺ Th17
	Th17(2)-Th1(1)		CXCR3⁺CCR4⁻T-bet⁺GATA3^low	Th1-like Th17
	Th17(2)-Tfh(2)		CXCR5⁺RORC2⁺ICOS⁺CD49b⁺	Tfh-like Th17
Tfh	1	CXCR5⁺RORC2^+/lowCD45RA^−/low	CXCR3⁺CCR4⁺CCR6⁺CD161⁺CD127⁺ICOS⁺LAG3⁺CD62L⁺	CXCR3⁺CCR4⁺ Th17-like Tfh
	3		CXCR3⁺T-bet⁺PD-1⁺TIGIT⁺ICOS⁺CD226⁺	Tfh1
	4		CD161⁺PD-1⁺	Tfh
	5			CD45RA^low Tfh
Treg	Treg(1)-Th2(1)	CD25⁺CD127^low/−FOXP3⁺TIGIT^+/lowCTLA4⁺	CXCR3⁻CCR4⁺CCR6⁺CD45RA⁻GATA3⁺ICOS⁺CD62L⁺	Th2-like Treg
	2		CXCR3⁺CCR4⁺CCR6⁺CD45RA⁺CD49b⁺	CXCR3⁺CCR4⁺CCR6⁺ Treg
	3		CXCR3⁺CD45RA⁺RORC2⁺CD62L⁺	CXCR3⁺ Treg
	4		CD45RA⁺CD49b⁺	Bona fide Treg

Baseline Cell Population	Subset	Shared/Defining Markers	Differential Expression Profile	Annotation
Th1	2	CXCR3⁺CCR4−	T-bet⁺PD-1⁺CD226⁺	Bona fide Th1
	3		CD45RA⁺	CD45RA⁺ Th1
Th2	2	CCR4⁺CXCR3⁻GATA3⁺CD45RA⁻	CCR6⁺CD127⁺CD226⁺LAG3⁺	CCR6⁺ Th2
	3		CD127⁺ICOS⁺CD226⁺LAG3⁺	Bona fide Th2
Th17	1	CCR6⁺CD161⁺CD127⁺CD45RA⁻CD226⁺	CXCR3⁺CCR4⁺ICOS⁺LAG3⁺CD49b⁺	CCR4⁺CXCR3⁺ Th17
	Th17(2)-Th1(1)		CXCR3⁺CCR4⁻T-bet⁺GATA3^low	Th1-like Th17
	Th17(2)-Tfh(2)		CXCR5⁺RORC2⁺ICOS⁺CD49b⁺	Tfh-like Th17
Tfh	1	CXCR5⁺RORC2^+/lowCD45RA^−/low	CXCR3⁺CCR4⁺CCR6⁺CD161⁺CD127⁺ICOS⁺LAG3⁺CD62L⁺	CXCR3⁺CCR4⁺ Th17-like Tfh
	3		CXCR3⁺T-bet⁺PD-1⁺TIGIT⁺ICOS⁺CD226⁺	Tfh1
	4		CD161⁺PD-1⁺	Tfh
	5			CD45RA^low Tfh
Treg	Treg(1)-Th2(1)	CD25⁺CD127^low/−FOXP3⁺TIGIT^+/lowCTLA4⁺	CXCR3⁻CCR4⁺CCR6⁺CD45RA⁻GATA3⁺ICOS⁺CD62L⁺	Th2-like Treg
	2		CXCR3⁺CCR4⁺CCR6⁺CD45RA⁺CD49b⁺	CXCR3⁺CCR4⁺CCR6⁺ Treg
	3		CXCR3⁺CD45RA⁺RORC2⁺CD62L⁺	CXCR3⁺ Treg
	4		CD45RA⁺CD49b⁺	Bona fide Treg