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8 fig. s210.1038/s41422-020-035… · c3_ca4 c2_ackr1 c1_esm1 singlet doublet 0 50 100 fraction of...

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  • 8 Fig. S210.1038/s41422-020-035… · C3_CA4 C2_ACKR1 C1_ESM1 Singlet Doublet 0 50 100 Fraction of cells (%) c d e Fig. S2 i j k 8. Fig. S2. Profiling of endothelial cells a t-SNE
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Normal Tumour Normal Tumour CRC LC OvC CRC LC OvC Unaligned CCA aligned _ _ __ _ __ _ _ _ ___ __ NEC1 NEC2 NEC3 NEC4 TEC Carbonic acid metabolism Glycolysis & gluconeogenesis Oxidative phosphorylation f g h l 0 1 2 3 4 5 PLVAP 0 1 2 3 SDPR 0 1 2 3 4 COL4A1 0 1 2 3 4 TIMP3 0 1 2 3 4 5 HSPG2 0 1 2 3 4 APOC1 0 1 2 3 4 GJA4 0 1 2 3 4 5 ADIRF 0 1 2 3 RBP1 0 1 2 3 APOC1 C5_PROX1 C4_FBLN5 C3_CA4 C2_ACKR1 C1_ESM1 Tumour Normal Tumour Normal Wnt_beta_catenin_signaling Uv_response_dn Unfolded_protein_response Tgf_beta_signaling Reactive_oxigen_species_pathway Protein_secretion Pi3k_akt_mtor_signaling Peroxisome Pancreas_beta_cells P53_pathway Oxidative_phosphorylation Notch_signaling Myogenesis Myc_targets_v2 Myc_targets_v1 Mtorc1_signaling Mitotic_spindle Heme_metabolism Hedgehog_signaling Glycolysis G2m_checkpoint Fatty_acid_metabolism Estrogen_response_late Epithelial_mesenchymal_transition E2f_targets Dna_repair Coagulation Cholesterol_homeostasis Apical_junction Androgen_response Adipogenesis Xenobiotic_metabolism Uv_response_up Tnfa_signaling_via_nfkb Kras_signaling_up Interferon_gamma_response Interferon_alpha_response Inflammatory_response Il6_jak_stat3_signaling Il2_stat5_signaling Hypoxia Estrogen_response_early Complement Apoptosis Apical_surface Angiogenesis Allograft_rejection Kras_signaling_dn Spermatogenesis C3_NEC1 C3_NEC2 C3_NEC3 C3_NEC4 C3_TEC -1 0 1 Row Z-score Heme_metabolism Estrogen_response_late Bile_acid_metabolism Cholesterol_homeostasis Apoptosis Spermatogenesis Kras_signaling_dn Interferon_alpha_response Il6_jak_stat3_signaling Xenobiotic_metabolism Uv_response_up Uv_response_dn Unfolded_protein_response Tnfa_signaling_via_nfkb Reactive_oxigen_species_pathway Peroxisome Pancreas_beta_cells P53_pathway Myc_targets_v2 Myc_targets_v1 Interferon_gamma_response Inflammatory_response Il2_stat5_signaling Hypoxia Estrogen_response_early E2f_targets Dna_repair Angiogenesis Androgen_response Allograft_rejection Wnt_beta_catenin_signaling Tgf_beta_signaling Protein_secretion Pi3k_akt_mtor_signaling Oxidative_phosphorylation Notch_signaling Myogenesis Mtorc1_signaling Mitotic_spindle Kras_signaling_up Hedgehog_signaling Glycolysis G2m_checkpoint Fatty_acid_metabolism Epithelial_mesenchymal_transition Complement Coagulation Apical_surface Apical_junction Adipogenesis C1_ESM1 C2_ACKR1 C3_CA4 C4_FBLN5 C5_PROX1 -1 0 1 Row Z-score CRC LC OvC C3_TEC RBP7 HLA−DRB5 CLU XIST CTSD C10orf10 IFNGR1 EPAS1 TNFSF10 TMEM100 SERPINB6 FCN3 APOC1 GPX3 SPRY1 LGALS1 JUN CD320 COL15A1 PLVAP MALL CXCL12 FABP5 -2 0 2 Normal Tumour CRC LC OvC C5_PROX1 C4_FBLN5 C3_CA4 C2_ACKR1 C1_ESM1 Fraction of cells (%) 0 50 100 0 50 100 0 50 100 EC EDNRB IL1RL1 EDN1 IL6 CCL2 ICAM1 FABP4 TIMP4 PLVAP IGFBP7 NEC1 NEC2 NEC3 NEC4 TEC CA4 ACKR1 ESM1 FBLN5 PROX1 CD3D RGS5 AIF1 Unaligned C5_PROX1 C4_FBLN5 C3_TEC C3_NEC4 C3_NEC3 C3_NEC2 C3_NEC1 C2_ACKR1 C1_ESM1 Unaligned LC OvC CRC 0 50 100 Fraction of cells (%) a C1_ESM1 C2_ACKR1 C3_CA4 C4_FBLN5 C5_PROX1 C6_CD3D C7_RGS5 C8_AIF C9_low_quality 6000 4000 2000 0 Number of detected genes b C9_low_quality C8_AIF C7_RGS5 C6_CD3D C5_PROX1 C4_FBLN5 C3_CA4 C2_ACKR1 C1_ESM1 Singlet Doublet 0 50 100 Fraction of cells (%) c d e Fig. S2 i j k 8

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Page 1: 8 Fig. S210.1038/s41422-020-035… · C3_CA4 C2_ACKR1 C1_ESM1 Singlet Doublet 0 50 100 Fraction of cells (%) c d e Fig. S2 i j k 8. Fig. S2. Profiling of endothelial cells a t-SNE

NormalTumour

NormalTumour

CRCLCOvC

CRCLCOvC

Unaligned CCA aligned

_ _ _ _ _

_ _ _ _ _

_ _ _ _ _

NEC

1

NEC

2

NEC

3

NEC

4TEC

Carbonic acidmetabolism

Glycolysis &gluconeogenesis

Oxidativephosphorylation

f g h

l

012345

PLVAP

0

1

2

3

SDPR

01234

COL4A1

01234

TIMP3

012345

HSPG2

01234

APOC1

01234

GJA4

012345

ADIRF

0

1

2

3

RBP1

0

1

2

3

APOC1

C5

_P

RO

X1

C

4_

FB

LN

5

C3

_C

A4

C

2_

AC

KR

1

C

1_

ES

M1

Tumou

r

Nor

mal

Tumou

r

Nor

mal

Wnt_beta_catenin_signalingUv_response_dnUnfolded_protein_responseTgf_beta_signalingReactive_oxigen_species_pathwayProtein_secretionPi3k_akt_mtor_signalingPeroxisomePancreas_beta_cellsP53_pathwayOxidative_phosphorylationNotch_signalingMyogenesisMyc_targets_v2Myc_targets_v1Mtorc1_signalingMitotic_spindleHeme_metabolismHedgehog_signalingGlycolysisG2m_checkpointFatty_acid_metabolismEstrogen_response_lateEpithelial_mesenchymal_transitionE2f_targetsDna_repairCoagulationCholesterol_homeostasisApical_junctionAndrogen_responseAdipogenesisXenobiotic_metabolismUv_response_upTnfa_signaling_via_nfkbKras_signaling_upInterferon_gamma_responseInterferon_alpha_responseInflammatory_responseIl6_jak_stat3_signalingIl2_stat5_signalingHypoxiaEstrogen_response_earlyComplementApoptosisApical_surfaceAngiogenesisAllograft_rejectionKras_signaling_dnSpermatogenesis

C3_

NEC

1

C3_

NEC

2

C3_

NEC

3

C3_

NEC

4

C3_

TEC

-1 0 1Row Z-score

Heme_metabolismEstrogen_response_lateBile_acid_metabolismCholesterol_homeostasisApoptosisSpermatogenesisKras_signaling_dnInterferon_alpha_responseIl6_jak_stat3_signalingXenobiotic_metabolismUv_response_upUv_response_dnUnfolded_protein_responseTnfa_signaling_via_nfkbReactive_oxigen_species_pathwayPeroxisomePancreas_beta_cellsP53_pathwayMyc_targets_v2Myc_targets_v1Interferon_gamma_responseInflammatory_responseIl2_stat5_signalingHypoxiaEstrogen_response_earlyE2f_targetsDna_repairAngiogenesisAndrogen_responseAllograft_rejectionWnt_beta_catenin_signalingTgf_beta_signalingProtein_secretionPi3k_akt_mtor_signalingOxidative_phosphorylationNotch_signalingMyogenesisMtorc1_signalingMitotic_spindleKras_signaling_upHedgehog_signalingGlycolysisG2m_checkpointFatty_acid_metabolismEpithelial_mesenchymal_transitionComplementCoagulationApical_surfaceApical_junctionAdipogenesis

C1_

ESM1

C2_

ACKR

1

C3_

CA4

C4_

FBLN5

C5_

PROX1

-1 0 1Row Z-score

CRC LC OvC

C3_TEC

RBP7HLA−DRB5CLUXISTCTSDC10orf10IFNGR1EPAS1TNFSF10TMEM100SERPINB6FCN3APOC1GPX3SPRY1LGALS1JUNCD320COL15A1PLVAPMALLCXCL12FABP5

-2 0 2

NormalTumour

CRC LC OvC

C5_PROX1C4_FBLN5

C3_CA4C2_ACKR1

C1_ESM1

Fraction of cells (%)

0 50 100 0 50 100 0 50 100

ECEDNRB

IL1RL1

EDN1

IL6

CCL2

ICAM1

FABP4

TIMP4

PLVAP

IGFBP7

NEC

1

NEC

2

NEC

3

NEC

4TEC

CA4 ACKR1

ESM1 FBLN5

PROX1 CD3D

RGS5 AIF1

Unaligned

C5_PROX1C4_FBLN5

C3_TECC3_NEC4C3_NEC3C3_NEC2C3_NEC1

C2_ACKR1C1_ESM1

Un

alig

ne

d

LC OvCCRC

0 50 100Fraction of cells (%)

a

C1

_E

SM

1

C2

_A

CK

R1

C3

_C

A4

C4

_F

BL

N5

C5

_P

RO

X1

C6

_C

D3

D

C7

_R

GS

5

C8

_A

IF

C9

_lo

w_

qu

alit

y

6000

4000

2000

0

Nu

mb

er

of

de

tect

ed

ge

ne

sb

C9_low_qualityC8_AIF

C7_RGS5C6_CD3D

C5_PROX1C4_FBLN5

C3_CA4C2_ACKR1

C1_ESM1

Singlet Doublet

0 50 100Fraction of cells (%)

c d e

Fig. S2

i

j

k

8

Page 2: 8 Fig. S210.1038/s41422-020-035… · C3_CA4 C2_ACKR1 C1_ESM1 Singlet Doublet 0 50 100 Fraction of cells (%) c d e Fig. S2 i j k 8. Fig. S2. Profiling of endothelial cells a t-SNE

Fig. S2. Profiling of endothelial cells

a t-SNE plots showing EC marker gene expressions for unaligned clusters. b t-SNE plots

showing unaligned or CCA aligned clusters colour-coded by sample origin (upper panels)

and cancer type (low panels). c Fraction of cells for unaligned EC clusters per cancer type.

d Fraction of singlet and doublet cells in each EC subcluster calculated by DoubletFinder.

e Box plot showing number of detected genes for each EC subcluster. f Fraction of cells

derived from normal (red) or tumour tissue (green) for each EC subcluster in each cancer

type. g Violin plots of genes specifically expressed in tumour or normal tissue for each of

the 5 EC subclusters. h Violin plot showing marker gene expressions for capillary EC

subclusters. i Heatmap of differentially expressed genes between CRC, LC and OvC in

the C3_TEC clusters. j Violin plot for metabolic activity for capillary EC subclusters scored

by AUCell. k-l Differences in cancer hallmark pathway activities scored per cell by AUCell

for all major EC subclusters (k) or subclusters of capillary ECs (l).

9


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