A.

PD-L1 MHCI MHCII PD-L1 MHCI MHCII

CMT + Vehicle (N=3) CMT + IFNγ (N=3)

10
10

0 1 0 1.25 0 1.25 0 1.5* 0 3* 0 5*

pSTAT1 pERK 1/2 pp38 pSTAT1 pERK 1/2 pp38

tSNE2

tSNE2
0 0

-10 0 1.5 0 2.5 0 4 -10 0 2.5* 0 2.5 1 4

IkBa Ly6A/E Ly6C IkBa Ly6A/E Ly6C

-10 0 10 -10 -20 0 0 10 20

tSNE1 tSNE1

0 1.5 0 3.5 0 3 0 1.5 2 4.5* 1 5*

B. C. Clusters dominant in CMT + Vehicle

50 *** Cluster #12
CMT + Vehicle Cluster #14
**
Cluster #16
40 * CMT + IFN

MHCII
iNOS
Ly6C
BCL6
IkBa
Arginase-1
pERK 1/2
Ki67
TIGIT
pStat1
pp38
pStat3
CD122
b−Catenin
pH3
CD11c
PARPc
MHCI
CD24
CD11b
pRb
pSHP2
pH2AX
p4EBP1
pAKT
Ly6AE
CD44
pS6
CD117
pStat4
PD-L1
% of events

**
30
Clusters dominant in CMT + IFNγ
Cluster #2
20 * Cluster #3
* Cluster #4
** *
10 *** Cluster #5
Cluster #6 (<1%)
** ** * Cluster #7
0 Cluster #8 (<1%)
Cluster #9
2

6
#2

#3

#4

#5

#6

#7

#8

#9

#1

#1

#1

#1

Cluster #15
Cluster ID
MHCII
iNOS
Ly6C
BCL6
IkBa
Arginase-1
pERK 1/2
Ki67
TIGIT
pStat1
pp38
pStat3
CD122
b−Catenin
pH3
CD11c
PARPc
MHCI
CD24
CD11b
pRb
pH2AX
p4EBP1
pAKT
Ly6AE
CD44

CD117
pStat4
PD-L1
pS6
D. Protein Expression
Low High
ns
CMT + Vehicle
ns
3
CMT + IFN
E. Clusters conserved in both conditions
% of events

2 Cluster #1 (<1%)
Cluster #10
Cluster #11 (<1%)
Cluster #13
1
TIGIT
MHCII
iNOS
Ly6C
BCL6
IkBa

pStat1
pp38
pStat3

MHCI
CD24
CD11b
pRb
pH2AX
p4EBP1
pAKT
Arginase-1
pERK 1/2
Ki67

CD122
b−Catenin
pH3
CD11c
PARPc

Ly6AE
CD44
pS6
CD117
pStat4
PD-L1

ns ns
Protein Expression
0 High
Low
#1

1
0

3
#1
#1

#1

Cluster ID