Supplementary Table 1 Growth conditions for xenograft samples ModelIn vitro growth mediaSource Mouse Strain n A375DMEM, 5% FCS, 1% LGECACCNude5 A375MDMEM,

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


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


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.


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)


-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


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)


-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:


Documents

Supplementary Table 1 Growth conditions for xenograft samples ModelIn vitro growth mediaSource Mouse Strain n A375DMEM, 5% FCS, 1% LGECACCNude5 A375MDMEM,