supplementary table 1 growth conditions for xenograft samples modelin vitro growth mediasource mouse...
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Supplementary Table 1 Growth conditions for xenograft samples
Model In vitro growth media SourceMouse Strain
n
A375 DMEM, 5% FCS, 1% LG ECACC Nude 5A375M DMEM, 10% FCS, 10% M1, 1% LG Prof Ian Hart ICRF Nude 5
A375v DMEM, 5% FCS, 1% LGProQinase,
GMBH, Breisacher Strasse , Germany
Nude 5
A431 DMEM, 5% FCS, 1% NEAA, 1% LG ECACC Nude 5A549 DMEM, 10% FCS, 10% M1, 1% LG ATCC Nude 5
BT-474 c1DMEM, 10% FCS, 10% M1, 1mM OAA, 1% LG
Dr. Albavell, Barcelona
Nude 5
Calu-6 RPMI 1640, 10% FCS, 1% LG ATCC Nude 5Colo205 RPMI 1640, 10% FCS, 1% LG ECACC Nude 5FaDu EMEM, 10% FCS, 1% NEAA, 1% LG ATCC Nude 5HCT 116 EMEM, 10% FCS, 1% NEAA, 1% LG ATCC Nude 5HT29 McCoy's 5A, 10% FCS, 1% LG ECACC Nude 5LoVo DMEM, 10% FCS, 1% LG ECACC Nude 5MCF7 RPMI 1640, 10% FCS, 1% LG ICRF LONDON SCID 5MDA-MB-468
DMEM, 10% FCS, 1% LG ATCC SCID Bg 5
MES-SA McCoy's 5A, 10% FCS, 1% LG ECACC SCID 5
MKN 45 DMEM, 10% FCS, 1% LGNOTTINGHAM UNIVERSITY
Nude 5
NCI N87 RPMI 1640, 10% FCS, 10% M1, 1% LG ATCC SCID 5
OVCAR 3 DMEM, 20% FCS, 10 ug/ml insulin, 1% LGApplied Cell
SciencesSCID 4
PC-3 Iscoves, 10% FCS, 1% LG ATCC Nude 5
PC-9 RPMI 1640, 10% FCS, 10% M1, 1% LGDr Nishio; National
Cancer Cetnre, Japan
SCID 5
Sw620 L-15, 10% FCS, 1% LG ECACC Nude 5
U87-MGEMEM, 10% FCS, 1% NEAA, 1% Na Pyr, 1% LG
ATCC Nude 5
Farren et al Supplementary Table1.
a
b
A37
5
A37
5M
A37
5v
A43
1
A54
9
BT-
474
c1
Calu
-6
Colo
205
FaD
u
HC
T 11
6
HT2
9
LoV
o
MC
F7
MD
A-M
B-4
68
ME
S-SA
MK
N 4
5
NCI
N87
OV
CAR3
PC
-3
PC
-9
Sw62
0
U87
-MG
100 %
90 %
80 %
70 %
60 %
50 %
40 %
30 %
20 %
10 %
0 %
Farren et al Supplementary Figure 1
Human Proportion
Mouse Proportion
% H
uman
: Mou
se m
RNA
Farren et al Supplementary Figure 2
HT29xFaDuvii BT474clIix
A431iv
PC9xi
HCT116vi
LoVoii
SW620viii
Calu-6v
A375Miii
A375xiii
U87MGi
M I M
M
M
I I
E I E I
I E
NCIN87xv MCF7xviA549xiv PC3xvii
I E E I
High α-SMA staining >15%
Medium α-SMA staining 5% to 15%
Low α-SMA staining <5%
Colo205xii
Farren et al Supplementary Figure 3
IHC Comparisons p-value R2
-SMA vs F4/80 0.176 0.111 -SMA vs MVD 0.231 0.088F4/80 vs MVD 0.005 0.400
Farren et al Supplementary Table 2; Linear regression analysis of the quantified histological staining for α-SMA, F4/80 and MVD.
Farren et al Supplementary Figure 4
Tumour PCA Scores Plot Normalised to total 18sPC
-2
PC-1
EpithelialMesenchymalMetastableN/A
SIMCA-P+ 12.0.1 - 2012-04-05 12:37:15 (UTC+0)
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
-7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7
t[2]
t[1]
BT-474-c1
BT-474-c1
BT-474-c1
BT-474-c1BT-474-c1
Colo-205
Colo-205
Colo-205
Colo-205Colo-205
FaDu
FaDu
FaDu
FaDuFaDu
HT29
HT29
HT29
HT29
HT29
MCF7
MCF7MCF7MCF7
MCF7
NCI-N87
NCI-N87
NCI-N87NCI-N87
NCI-N87
A375A375A375A375
A375
A375MA375MA375MA375M
A375M
Calu-6
Calu-6
Calu-6
Calu-6Calu-6
MES-SAMES-SA
MES-SA
MES-SAMES-SA
U87-MG
U87-MGU87-MG
U87-MG
U87-MG
A431
A431
A431
A431
A431
A549
A549
A549A549
A549
HCT 116
HCT 116
HCT 116
HCT 116
HCT 116
LoVo
LoVoLoVoLoVoLoVo
MKN 45MKN 45MKN 45MKN 45
MKN 45
OVCAR 3OVCAR 3OVCAR 3OVCAR 3PC-3
PC-3
PC-3PC-3
PC-3
PC-9PC-9PC-9PC-9
PC-9
Sw620Sw620Sw620
Sw620Sw620
A375vA375v
A375vA375vA375v
MDA-MB-468
MDA-MB-468
MDA-MB-468MDA-MB-468
MDA-MB-468
SIMCA-P+ 12.0.1 - 2012-04-12 08:28:25 (UTC+0)
Farren et al Supplementary Figure 5
-6
-4
-2
0
2
4
6
-12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12
t[2]
t[1]
EpithelialMesenchymalMetastableN/A
BT-474 c1
HT 29
MCF7
A375
A375M
Calu-6
MES-SA
U87-MG
A431
A549
LoVo
MKN 45
PC-3
PC-9Sw620
A375v
SIMCA-P+ 12.0.1 - 2012-03-27 09:18:06 (UTC+0)
-6
-4
-2
0
2
4
6
-7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7
t[2]
t[1]
EpithelialMesenchymalMetastableN/ABT-474-c1
BT-474-c1
BT-474-c1
BT-474-c1BT-474-c1
Colo-205
Colo-205
Colo-205
Colo-205Colo-205
FaDu
FaDu
FaDu
FaDuFaDu
HT29
HT29
HT29
HT29HT29
MCF7MCF7MCF7
MCF7MCF7
NCI-N87NCI-N87
NCI-N87
NCI-N87
NCI-N87
A375A375A375A375
A375
A375M
A375MA375M
A375MA375MCalu-6
Calu-6Calu-6
Calu-6Calu-6
MES-SA
MES-SA
MES-SA
MES-SAMES-SA
U87-MG
U87-MG
U87-MG
U87-MG
U87-MG
A431
A431
A431
A431
A431
A549
A549
A549A549
A549
HCT 116
HCT 116
HCT 116
HCT 116
HCT 116
LoVo
LoVoLoVo
LoVoLoVo
MKN 45MKN 45MKN 45MKN 45
MKN 45
OVCAR 3OVCAR 3
OVCAR 3OVCAR 3PC-3
PC-3
PC-3PC-3
PC-3
PC-9PC-9PC-9PC-9
PC-9Sw620Sw620Sw620
Sw620Sw620
A375vA375v
A375vA375v
A375v
MDA-MB-468
MDA-MB-468
MDA-MB-468
MDA-MB-468
MDA-MB-468
SIMCA-P+ 12.0.1 - 2012-03-27 09:42:26 (UTC+0)
A. PCA analysis of human cell line transcript profile
B. PCA analysis of human xenograft transcript profile
Farren et al Supplementary Figure 6.
Human Species Specific 18s Normalisation (Negatively Associated)MVD (CD31) F4/80+ αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2FLT3 0.027 0.271 ACVR1B 0.046 0.227 FGF1 0.058 0.207
ACVR1B 0.042 0.234 IL8RB 0.049 0.220 PDGFRB 0.133 0.135CXCR4 0.050 0.219 PDGFA 0.097 0.163 TEK 0.271 0.075
KIT 0.057 0.209 ITGAV 0.116 0.147 FGF2 0.341 0.057ITGAV 0.085 0.174 CXCR4 0.262 0.078 PDGFC 0.379 0.049FLT1 0.125 0.140 FLT3 0.270 0.075 ANGPT1 0.384 0.048
EFNB2 0.143 0.129 PGF 0.329 0.060 EFNB2 0.384 0.048IL8RB 0.206 0.098 ANGPT2 0.401 0.044 ITGA5 0.476 0.032
PDGFD 0.284 0.071 EFNB2 0.407 0.043 VEGF 0.497 0.029PDGFA 0.294 0.069 PDGFD 0.446 0.037 IL8RB 0.499 0.029TGFBR1 0.296 0.068 CXCL1 0.454 0.036 CXCR4 0.532 0.025CXCL1 0.311 0.064 IL8RA 0.524 0.026 PGF 0.574 0.020IL8RA 0.315 0.063 VEGF 0.585 0.019 FLT4 0.612 0.016EPHB4 0.324 0.061 TGFB1 0.659 0.012 ENG 0.620 0.016VEGF 0.351 0.054 CXCL10 0.670 0.012 TGFB1 0.658 0.013
PDGFRA 0.357 0.053 TGFBR1 0.762 0.006 ANGPT2 0.707 0.009CXCL10 0.392 0.046 THBS1 0.789 0.005 TGFBR1 0.955 <0.001
IL8 0.436 0.038 PDGFRA 0.813 0.004KDR 0.467 0.034 KIT 0.825 0.003
CXCL12 0.481 0.031 CXCL5 0.939 <0.001ANGPT2 0.533 0.025 FLT1 0.956 <0.001CXCL5 0.534 0.025 EPHB4 0.978 <0.001
ANGPT1 0.590 0.019 FGF2 0.991 <0.001F2R 0.685 0.011
VEGFB 0.803 0.004FGF1 0.833 0.003HIF1A 0.846 0.002TGFB1 0.916 0.001
PGF 0.939 <0.001Human Species Specific 18s Normalisation (Positively Associated)
MVD (CD31) F4/80+ αSMAGene P-Value R2 Gene P-Value R2 Gene P-Value R2EDG1 0.034 0.250 EDG1 0.025 0.275 EDG1 0.011 0.343ENG 0.069 0.192 VEGFC 0.033 0.253 PDGFD 0.092 0.167TEK 0.160 0.119 ENG 0.069 0.192 CXCL5 0.101 0.159TIE1 0.187 0.106 PDGFRB 0.070 0.191 EPHB4 0.107 0.154
PDGFRB 0.238 0.086 KDR 0.073 0.187 PDGFA 0.143 0.129VEGFC 0.254 0.080 TIE1 0.081 0.178 VEGFC 0.160 0.119PDGFC 0.354 0.054 EDG3 0.094 0.166 CSF1R 0.171 0.114CCL2 0.411 0.043 TEK 0.208 0.097 EDG3 0.223 0.091
CSF1R 0.498 0.029 PDGFC 0.276 0.074 CXCL12 0.275 0.074FLT4 0.723 0.008 CCL2 0.291 0.069 KDR 0.298 0.067FGF2 0.871 0.002 VEGFB 0.398 0.045 THBS1 0.299 0.067
THBS1 0.873 0.002 F2R 0.517 0.027 CCL2 0.320 0.062ITGA5 0.928 0.001 FGF1 0.555 0.022 FLT3 0.357 0.053EDG3 0.649 0.013 CXCL12 0.562 0.021 IL8 0.446 0.037
HIF1A 0.564 0.021 TIE1 0.458 0.035FLT4 0.579 0.020 HIF1A 0.530 0.025
CSF1R 0.699 0.010 VEGFB 0.530 0.025ANGPT1 0.897 0.001 KIT 0.532 0.025
IL8 0.939 <0.001 CXCL1 0.582 0.019ITGA5 0.962 <0.001 IL8RA 0.668 0.012
PDGFRA 0.672 0.011ACVR1B 0.673 0.011
FLT1 0.809 0.004ITGAV 0.818 0.003
F2R 0.836 0.003CXCL10 0.873 0.002
Farren et al Supplementary Table 3
Human Total 18s Normalisation (Negatively Associated) MVD (CD31) F4/80+ αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2FLT3 0.021 0.291 IL8RB 0.030 0.261 FGF1 0.052 0.217KIT 0.037 0.244 ACVR1B 0.032 0.256 PDGFRB 0.123 0.142
ACVR1B 0.043 0.231 PDGFA 0.084 0.175 TEK 0.229 0.089CXCR4 0.049 0.221 ITGAV 0.088 0.171 FGF2 0.333 0.059ITGAV 0.088 0.171 FLT3 0.114 0.148 ANGPT1 0.350 0.055FLT1 0.126 0.140 CXCR4 0.233 0.088 PDGFC 0.361 0.052
EFNB2 0.139 0.132 PGF 0.303 0.066 EFNB2 0.363 0.052IL8RB 0.207 0.098 ANGPT2 0.362 0.052 VEGF 0.433 0.039
PDGFD 0.280 0.072 IL8RA 0.367 0.051 IL8RB 0.435 0.039IL8RA 0.282 0.072 PDGFD 0.372 0.050 ITGA5 0.455 0.035
PDGFA 0.291 0.069 EFNB2 0.372 0.050 CXCR4 0.506 0.028TGFBR1 0.294 0.068 CXCL1 0.426 0.040 FLT4 0.514 0.027CXCL1 0.313 0.064 VEGF 0.478 0.032 PGF 0.554 0.022EPHB4 0.315 0.063 KIT 0.527 0.026 ENG 0.600 0.018VEGF 0.334 0.058 CXCL10 0.580 0.020 TGFB1 0.629 0.015
PDGFRA 0.350 0.055 TGFB1 0.606 0.017 ANGPT2 0.677 0.011CXCL10 0.387 0.047 TGFBR1 0.661 0.012 TGFBR1 0.892 0.001
IL8 0.435 0.038 PDGFRA 0.721 0.008KDR 0.458 0.035 THBS1 0.745 0.007
CXCL12 0.470 0.033 EPHB4 0.865 0.002ANGPT2 0.531 0.025 FLT1 0.892 0.001CXCL5 0.532 0.025 CXCL5 0.902 0.001
ANGPT1 0.584 0.019 FGF2 0.954 <0.001F2R 0.683 0.011 ITGA5 0.987 <0.001
VEGFB 0.788 0.005FGF1 0.829 0.003HIF1A 0.835 0.003TGFB1 0.912 0.001
PGF 0.936 <0.001
Human Total 18s NormalisationMVD (CD31) F4/80+ (Positively Associated) αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2EDG1 0.036 0.246 EDG1 0.037 0.245 EDG1 0.014 0.322ENG 0.069 0.191 VEGFC 0.038 0.243 CXCL5 0.108 0.153TEK 0.167 0.116 ENG 0.077 0.182 PDGFD 0.111 0.151TIE1 0.193 0.103 PDGFRB 0.083 0.176 EPHB4 0.126 0.140
PDGFRB 0.241 0.085 KDR 0.084 0.175 PDGFA 0.152 0.124VEGFC 0.254 0.080 TIE1 0.102 0.158 VEGFC 0.167 0.116PDGFC 0.359 0.053 EDG3 0.102 0.158 CSF1R 0.195 0.103CCL2 0.420 0.041 TEK 0.287 0.070 EDG3 0.231 0.088
CSF1R 0.501 0.029 PDGFC 0.309 0.065 CXCL12 0.298 0.067EDG3 0.650 0.013 CCL2 0.343 0.056 KDR 0.313 0.064FLT4 0.738 0.007 VEGFB 0.535 0.025 THBS1 0.321 0.062FGF2 0.876 0.002 F2R 0.579 0.020 CCL2 0.352 0.054
THBS1 0.878 0.002 FGF1 0.608 0.017 IL8 0.469 0.033ITGA5 0.933 <0.001 CXCL12 0.632 0.015 FLT3 0.492 0.030
HIF1A 0.687 0.010 TIE1 0.492 0.030FLT4 0.758 0.006 HIF1A 0.598 0.018
CSF1R 0.801 0.004 CXCL1 0.606 0.017ANGPT1 0.981 <0.001 VEGFB 0.618 0.016
IL8 0.985 <0.001 KIT 0.666 0.012PDGFRA 0.723 0.008ACVR1B 0.738 0.007
IL8RA 0.751 0.006FLT1 0.847 0.002F2R 0.876 0.002
ITGAV 0.886 0.001CXCL10 0.931 <0.001
Farren et al Supplementary Table 4
VEGF-A (log pg/ml)
VE
GF
-Hs0
0900
054_
m1
2 2.2 2.4 2.6 2.8 3 3.2 3.4
-8.5
-9
-9.5
-10
-10.5
-11
-11.5
-12
-12.5
-13
-13.5
Ang-1 (log pg/ml)
AN
GP
T1-
Hs0
0375
823_
m1
2.3 2.4 2.5 2.6 2.7 2.8 2.9 3 3.1 3.2 3.3 3.4 3.5 3.6 3.7
-15.5
-16
-16.5
-17
-17.5
-18
-18.5
-19
-19.5
-20
-20.5
Ang-2 (log pg/ml)
AN
GP
T2-
Hs0
1048
043_
m1
2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3 3.1 3.2 3.3
-13
-14
-15
-16
-17
-18
-19
-20
FGF-2 (log pg/ml)
FG
F2-
Hs0
0266
645_
m1
2.4 2.5 2.6 2.7 2.8 2.9 3 3.1 3.2 3.3 3.4 3.5 3.6
-12
-13
-14
-15
-16
-17
-18
-19
-20
IL-8 (log pg/ml)
IL8-
Hs0
0174
103_
m1
0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8
-9
-10
-11
-12
-13
-14
-15
-16
-17
PGF (log pg/ml)
PG
F-H
s011
1926
2_m
1
0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4
-11
-12
-13
-14
-15
-16
-17
-18
VEG
F (-∆
CT)
VEGF (log pg/ml)
ANG
PT-2
(-∆C
T)
ANGPT-2 (log pg/ml)
IL-8
(-∆C
T)
IL-8 (log pg/ml)
PGF
(-∆CT
)
PGF (log pg/ml)
FGF-
2 (-∆
CT)
FGF-2 (log pg/ml)
P Value = <0.001R2 = 0.50
P Value = <0.001R2 = 0.91
P Value = 0.004R2 = 0.36
P Value = <0.001R2 = 0.61
P Value = <0.001R2 = 0.71
P Value = <0.001R2 = 0.73
Farren et al Supplementary Figure 7
A375A375MA375vA431A549BT-474-c1
LoVoMCF7MDA-MB-468MES-SAMKN 45NCI-N87
Calu-6Colo-205FaDuHCT 116HT29
OVCAR 3PC-3PC-9Sw620U87-MG
Xenografts
ANG
PT-1
(-∆C
T)
ANGPT-1 (log pg/ml)
Ratio of CXCL10 expression over tumour derived transcripts
Vs. MVD
Ratio of THBS-1 expression over tumour derived transcripts Vs.
MVD
Ratio of ANGPT2 expression over tumour derived transcripts
Vs. MVD
Ratio of ANGPT1 expression over tumour derived transcripts
Vs. MVD
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2 Gene p-value RSq
EDG1 0.03 0.40 ENG 0.17 0.11 EDG1 0.07 0.29 EDG1 0.04 0.32
PDGFC 0.14 0.14 FLT1 0.19 0.10 VEGFC 0.15 0.18 TIE1 0.05 0.39
TEK 0.15 0.17 CXCR4 0.21 0.10 CXCR4 0.17 0.13 ENG 0.07 0.26
TIE1 0.16 0.17 CXCL1 0.31 0.07 ENG 0.21 0.13 PDGFRB 0.10 0.27
ENG 0.18 0.16 EFNB2 0.31 0.06 TIE1 0.26 0.20 VEGFC 0.12 0.22
ACVRL1 0.20 0.20 VEGFC 0.34 0.06 PDGFC 0.27 0.08 CXCR4 0.12 0.15
FLT4 0.22 0.13 EDG1 0.35 0.05 TEK 0.29 0.12 PDGFC 0.19 0.11
CXCR4 0.25 0.09 ITGAV 0.36 0.05 PDGFRB 0.33 0.13 TEK 0.26 0.12
CSF1R 0.28 0.10 ACVR1B 0.37 0.05 EFNB2 0.34 0.06 EFNB2 0.27 0.08
PDGFRB 0.32 0.09 PDGFA 0.37 0.05 FLT4 0.36 0.10 FLT1 0.32 0.11
EFNB2 0.35 0.06 IL8 0.43 0.04 CSF1R 0.42 0.07 CSF1R 0.40 0.06
CCL2 0.36 0.08 TIE1 0.47 0.03 ACVRL1 0.44 0.12 CCL2 0.44 0.08
IL8RB 0.36 0.10 PDGFD 0.50 0.03 CCL2 0.47 0.07 CXCL1 0.47 0.03
VEGFC 0.38 0.07 KDR 0.51 0.03 KIT 0.56 0.06 FLT4 0.49 0.05
FLT1 0.40 0.07 CXCL5 0.51 0.03 FLT3 0.57 0.06 ACVR1B 0.55 0.02
PDGFA 0.41 0.05 CXCL10 0.53 0.02 CXCL1 0.57 0.02 ITGAV 0.55 0.02
CXCL1 0.43 0.04 PDGFRB 0.54 0.02 VEGFB 0.57 0.02 IL8 0.63 0.01
IL8RA 0.46 0.06 PDGFC 0.56 0.02 HIF1A 0.59 0.02 THBS1 0.65 0.01
HIF1A 0.49 0.03 PDGFRA 0.57 0.02 THBS1 0.60 0.02 VEGFB 0.66 0.01
KIT 0.50 0.05 TGFBR1 0.57 0.02 TGFB1 0.63 0.01 ITGA5 0.68 0.01
ACVR1B 0.52 0.03 EPHB4 0.58 0.02 PDGFA 0.64 0.02 CXCL5 0.68 0.02
VEGFB 0.52 0.03 IL8RB 0.59 0.02 FLT1 0.64 0.03 HIF1A 0.72 0.01
FLT3 0.52 0.04 CXCL12 0.59 0.02 EDG3 0.68 0.01 TGFB1 0.73 0.01
THBS1 0.53 0.02 ANGPT2 0.60 0.02 PGF 0.70 0.01 KDR 0.76 0.01
ITGA5 0.60 0.02 VEGF 0.61 0.02 ACVR1B 0.71 0.01 FLT3 0.78 0.01
ITGAV 0.62 0.02 FLT3 0.64 0.01 IL8RA 0.71 0.02 PDGFA 0.80 0.00
PGF 0.67 0.01 ANGPT1 0.65 0.01 ITGA5 0.79 0.00 EDG3 0.80 0.01
TGFB1 0.67 0.01 KIT 0.65 0.01 IL8RB 0.80 0.01 PGF 0.80 0.00
CXCL5 0.67 0.02 ACVRL1 0.67 0.01 IL8 0.80 0.00 IL8RB 0.83 0.01
FGF2 0.68 0.01 F2R 0.70 0.01 F2R 0.81 0.00 PDGFD 0.83 0.01
EDG3 0.70 0.01 IL8RA 0.71 0.01 FGF2 0.83 0.00 ANGPT2 0.83 0.00
KDR 0.70 0.02 CCL2 0.75 0.01 ANGPT1 0.83 0.00 TGFBR1 0.84 0.00
IL8 0.70 0.01 EDG3 0.77 0.01 CXCL12 0.83 0.01 PDGFRA 0.85 0.01
CXCL12 0.87 0.00 FGF1 0.78 0.01 ITGAV 0.83 0.00 IL8RA 0.86 0.00
F2R 0.88 0.00 TEK 0.79 0.00 CXCL5 0.85 0.00 FGF2 0.88 0.00
ANGPT2 0.89 0.00 TGFB1 0.79 0.00 FGF1 0.86 0.00 EPHB4 0.90 0.00
PDGFRA 0.92 0.00 VEGFB 0.79 0.00 CXCL10 0.89 0.00 CXCL12 0.91 0.00
PDGFD 0.94 0.00 HIF1A 0.80 0.00 VEGF 0.90 0.00 VEGF 0.92 0.00
VEGF 0.95 0.00 PGF 0.82 0.00 KDR 0.92 0.00 FGF1 0.94 0.00
TGFBR1 0.95 0.00 CSF1R 0.88 0.00 EPHB4 0.93 0.00 KIT 0.95 0.00
ANGPT1 0.95 0.00 FLT4 0.94 0.00 PDGFRA 0.93 0.00 CXCL10 0.95 0.00
FGF1 0.96 0.00 ITGA5 0.95 0.00 TGFBR1 0.95 0.00 F2R 0.97 0.00
EPHB4 0.99 0.00 FGF2 0.98 0.00 PDGFD 0.98 0.00 ACVRL1 0.98 0.00
Farren et al Supplementary Table 5:
Mouse Total 18s Normalisation (Negatively Associated)MVD (CD31) F4/80+ αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2Fgf2 0.152 0.124 Fgf2 0.031 0.259 Efnb2 0.845 0.002
Pdgfra 0.251 0.081 Vegfa 0.318 0.062Edg3 0.310 0.064 Thbs1 0.357 0.053
Pdgfrb 0.328 0.060 Edg3 0.596 0.018F2r 0.352 0.054 Cxcl2 0.611 0.017Flt3 0.476 0.032 Pgf 0.747 0.007
Pdgfd 0.494 0.030 Acvr1b 0.762 0.006Thbs1 0.498 0.029 Fgf1 0.798 0.004Acvr1b 0.530 0.025 Flt3 0.829 0.003Acta2 0.593 0.018 Pdgfc 0.872 0.002Itgav 0.599 0.018 Pdgfrb 0.878 0.002
Cxcl12 0.601 0.017 Il8rb 0.988 <0.001Il8rb 0.684 0.011
Pdgfc 0.725 0.008Angpt1 0.761 0.006Cxcl2 0.829 0.003Tgfbr1 0.982 <0.001
Mouse Total 18s Normalisation (Positively Associated)MVD (CD31) F4/80+ αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2Angpt2 <0.001 0.543 Flt4 0.001 0.511 Tgfb1 0.001 0.496
Flt4 0.007 0.372 Tie1 0.002 0.452 Pdgfc 0.004 0.420Edg1 0.035 0.249 Kdr 0.008 0.363 Tgfbr1 0.006 0.382Tie1 0.036 0.247 Ephb4 0.015 0.318 Acta2 0.011 0.343
Pecam1 0.047 0.225 Edg1 0.015 0.317 Cxcl10 0.011 0.343Kdr 0.054 0.213 Csf1r 0.017 0.307 Thbs1 0.011 0.342Pgf 0.065 0.197 Pecam1 0.018 0.302 Vegfa 0.021 0.291Kit 0.100 0.160 Tek 0.020 0.296 Flt4 0.022 0.286
Cxcl10 0.107 0.154 Itgam 0.031 0.260 Angpt2 0.025 0.276Pdgfb 0.182 0.108 Angpt2 0.039 0.241 Pdgfrb 0.026 0.274Ccl2 0.192 0.104 Kit 0.051 0.218 Fgf1 0.032 0.256Flt1 0.211 0.096 Nrp1 0.052 0.216 Vegfb 0.033 0.254
Tgfb1 0.244 0.084 Acvrl1 0.057 0.208 Angpt1 0.034 0.250Tek 0.266 0.077 Eng 0.064 0.199 Vegfc 0.040 0.239
Itgam 0.288 0.070 Pdgfb 0.067 0.195 Pdgfd 0.043 0.232Acvrl1 0.358 0.053 Vegfb 0.096 0.164 Flt3 0.043 0.232Pdgfa 0.366 0.051 Flt1 0.098 0.161 Itgav 0.046 0.226Hif1a 0.425 0.040 Cxcl10 0.182 0.108 Acvr1b 0.048 0.222Eng 0.500 0.029 Efnb2 0.183 0.108 Hif1a 0.068 0.193Fgf1 0.514 0.027 Tgfbr1 0.205 0.099 Nrp1 0.077 0.183Nrp1 0.520 0.026 Pdgfd 0.221 0.092 Acvrl1 0.082 0.177Csf1r 0.535 0.025 Hif1a 0.238 0.086 Pdgfra 0.096 0.163Ephb4 0.537 0.024 Vegfc 0.247 0.083 Cxcl12 0.103 0.157Vegfb 0.637 0.014 Tgfb1 0.289 0.070 F2r 0.103 0.157Itga5 0.780 0.005 Ccl2 0.351 0.054 Pdgfa 0.104 0.156Efnb2 0.809 0.004 F2r 0.459 0.035 Csf1r 0.109 0.153Vegfc 0.887 0.001 Cxcl12 0.488 0.031 Eng 0.120 0.144Vegfa 0.995 <0.001 Pdgfra 0.640 0.014 Itga5 0.172 0.113
Pdgfa 0.674 0.011 Pgf 0.175 0.112Angpt1 0.838 0.003 Il8rb 0.228 0.090Acta2 0.978 <0.001 Kdr 0.237 0.086Itga5 0.984 <0.001 Itgam 0.249 0.082
Pecam1 0.269 0.076Ephb4 0.270 0.075Fgf2 0.301 0.067
Pdgfb 0.339 0.057Ccl2 0.372 0.050Tie1 0.400 0.045Flt1 0.670 0.012Kit 0.701 0.009
Edg3 0.702 0.009Tek 0.704 0.009
Cxcl2 0.914 0.001Farren et al Supplementary Table 6.
Mouse Species Specific 18s Normalisation (Negatively Associated)MVD (CD31) F4/80+ αSMA
Gene P-Value R2 Gene P-Value R2 Gene P-Value R2Pdgfra 0.154 0.123 Fgf2 0.006 0.388 Flt1 0.258 0.079
F2r 0.266 0.077 Acvr1b 0.023 0.282 Efnb2 0.299 0.067Edg3 0.277 0.073 Thbs1 0.027 0.271 Tek 0.360 0.053
Pdgfrb 0.298 0.067 Pdgfc 0.038 0.242 Kit 0.383 0.048Pdgfd 0.314 0.063 Vegfa 0.041 0.235 Fgf2 0.480 0.032Thbs1 0.499 0.029 Edg3 0.058 0.207 Pdgfb 0.516 0.027Fgf2 0.524 0.026 Flt3 0.061 0.202 Edg3 0.570 0.021
Acta2 0.561 0.022 Itga5 0.088 0.171 Cxcl2 0.649 0.013Itgav 0.569 0.021 Acta2 0.093 0.166 Tie1 0.808 0.004
Cxcl12 0.579 0.020 Itgav 0.097 0.163 Pecam1 0.887 0.001Acvr1b 0.586 0.019 Pdgfrb 0.105 0.156 Itgam 0.926 0.001
Flt3 0.659 0.013 Fgf1 0.180 0.110 Edg1 0.980 <0.001Il8rb 0.715 0.009 Angpt1 0.211 0.096
Pdgfc 0.725 0.008 Pdgfa 0.233 0.088Angpt1 0.742 0.007 Cxcl2 0.246 0.083Cxcl2 0.862 0.002 Pgf 0.280 0.072
Tgfb1 0.407 0.043Il8rb 0.522 0.026
Vegfc 0.542 0.024F2r 0.594 0.018
Tgfbr1 0.683 0.011Pdgfra 0.727 0.008Hif1a 0.745 0.007
Cxcl12 0.827 0.003Ccl2 0.895 0.001
Pdgfb 0.897 0.001Flt1 0.915 0.001
Acvrl1 0.961 <0.001Mouse Species Specific 18s Normalisation (Positively Associated)
MVD (CD31) F4/80+ αSMAGene P-Value R2 Gene P-Value R2 Gene P-Value R2Flt4 0.006 0.382 Flt4 0.041 0.235 Cxcl10 0.062 0.201
Angpt2 0.007 0.377 Tie1 0.087 0.172 Pdgfc 0.108 0.153Tie1 0.009 0.360 Ephb4 0.121 0.144 Thbs1 0.111 0.151Kdr 0.009 0.358 Kdr 0.144 0.129 Pdgfd 0.112 0.150
Edg1 0.012 0.334 Tek 0.291 0.069 Vegfa 0.125 0.141Pecam1 0.015 0.319 Pecam1 0.416 0.042 Acta2 0.148 0.126
Kit 0.081 0.178 Edg1 0.455 0.035 Flt4 0.159 0.120Pgf 0.098 0.161 Efnb2 0.476 0.032 Vegfb 0.190 0.105
Cxcl10 0.100 0.160 Cxcl10 0.524 0.026 Fgf1 0.197 0.102Pdgfb 0.114 0.149 Itgam 0.540 0.024 Angpt1 0.200 0.100Flt1 0.120 0.144 Nrp1 0.545 0.023 Pdgfra 0.205 0.098Tek 0.134 0.135 Angpt2 0.608 0.017 Pdgfrb 0.239 0.086Ccl2 0.185 0.107 Csf1r 0.611 0.017 Tgfb1 0.259 0.079Itgam 0.199 0.101 Kit 0.729 0.008 Tgfbr1 0.312 0.064Nrp1 0.254 0.081 Eng 0.753 0.006 Vegfc 0.319 0.062
Acvrl1 0.254 0.080 Vegfb 0.876 0.002 Cxcl12 0.337 0.058Tgfb1 0.255 0.080 Pdgfd 0.895 0.001 Angpt2 0.410 0.043Pdgfa 0.268 0.076 Nrp1 0.424 0.040Hif1a 0.306 0.065 F2r 0.446 0.037Eng 0.321 0.061 Hif1a 0.495 0.030
Vegfb 0.371 0.050 Il8rb 0.539 0.024Ephb4 0.391 0.046 Itgav 0.576 0.020Csf1r 0.459 0.035 Pgf 0.587 0.019Fgf1 0.469 0.033 Pdgfa 0.657 0.013Itga5 0.721 0.008 Eng 0.739 0.007Efnb2 0.734 0.007 Acvr1b 0.754 0.006Vegfc 0.772 0.005 Ephb4 0.796 0.004Vegfa 0.970 <0.001 Acvrl1 0.861 0.002Tgfbr1 0.974 <0.001 Kdr 0.875 0.002
Itga5 0.944 <0.0014 0.986 <0.001
Flt3 0.998 <0.001Farren et al Supplementary Table 7.
PC-1
PC-2
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
-13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13
t[2]
t[1]
A375A375
A375A375A375
A375M
A375M
A375M
A375MA375M
A375v
A375v A375vA375vA375v
A431A431
A431 A431A431
A549A549
A549A549
A549
BT-474-c1BT-474-c1
BT-474-c1
BT-474-c1BT-474-c1
Calu-6Calu-6
Calu-6Calu-6
Calu-6
Colo-205
Colo-205
Colo-205Colo-205
Colo-205FaDu
FaDu
FaDuFaDu
FaDuHCT 116
HCT 116HCT 116
HCT 116
HCT 116
HT29HT29HT29
HT29HT29
LoVo
LoVo
LoVoLoVo
LoVo
MCF7
MCF7MCF7
MCF7MCF7MDA-MB-468
MDA-MB-468
MDA-MB-468
MDA-MB-468MDA-MB-468
MES-SA
MES-SAMES-SA
MES-SA
MES-SA
MKN 45 MKN 45MKN 45
MKN 45MKN 45
NCI-N87
NCI-N87NCI-N87NCI-N87NCI-N87
OVCAR 3
OVCAR 3
OVCAR 3
OVCAR 3
PC-3
PC-3PC-3
PC-3
PC-3
PC-9PC-9
PC-9
PC-9PC-9
Sw620
Sw620Sw620
Sw620Sw620
U87-MG
U87-MG
U87-MG
U87-MGU87-MG
SIMCA-P+ 12.0.1 - 2012-04-05 12:31:07 (UTC+0)
Farren et al Supplementary Figure 8
-0.30
-0.25
-0.20
-0.15
-0.10
-0.05
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19
p[2
]
p[1]
Acta2
Acvr1b
Acvrl1
Angpt1
Angpt2
Ccl2 Csf1r
Cxcl10
Cxcl12Cxcl2
Edg1
Edg3
Efnb2
Eng
Ephb4
F2r
Fgf1Fgf2
Flt1
Flt3
Flt4
Hif1a
Il8rb
Itga5
Itgam
Itgav
KdrKit
Nrp1
Pdgfa
Pdgfb
Pdgfc
Pdgfd
Pdgfra
Pdgfrb
Pecam1
Pgf
Tek
Tgfb1
Tgfbr1
Thbs1
Tie1
Vegfa
Vegfb Vegfc
SIMCA-P+ 12.0.1 - 2012-04-05 12:20:24 (UTC+0)
PC-2
PC-1
B Stromal PCA Loading Plot Normalised to total 18s
A Stromal PCA Scores Plot Normalised to total 18s
XenograftAverage % of TGI of
cediranib at (1.5 mg/kg) n StdDevA431 61 1
Calu-6 54 9 11HCT-15 28 1
LoVo 44 2 1PC-3 49 2 9
SW620 60 4 10
Farren et al Supplementary Table 8:
Farren et al Supplementary Figure 9