Supplementary tables and figures Table S1: Clinical information for resected HCC from Y90-RE versus treatment naive patients, n=12

Post DFS Resection Treatment DFS Viral TNM No. No. Grade Sex Y90 RE (days) (days)* Naive (Days) Status Stage CyTOF NGS qPCR 1 HEP157 910 190 8 HEP174 664 Hep B I II M + + + 2 HEP165 332 148 9 HEP261 326 Hep C II II M + + 3 HEP210 229 232 10 HEP300 208 Hep B I III M + + + 4 HEP242 518 182 11 HEP304 289 Hep B I II F + + + 5 HEP279 89 89 12 HEP303 132 Hep B IIIa III M + + +* 6 HEP285 109 300 13 HEP200 694 NIL I III M + +* 7 HEP286 260 261 14 HEP125 97 Hep B I II M + Average 350 202 Average 344

FootNote: n=7 Post Y90 RE versus n=7 treatment-naive HCC tumors as controls (Ctl) with matched viral status, TNM Stage, Grade, Sex and average DFS= Disease-free survival. * number of days post Y90 RE when resection was performed + indicated the pair of samples taken for either CyTOF, NGS or qPCR experiments. * Two tumor specimens were collected and analysed from HEP279 and HEP285 Y90 RE-treated tumors. Table S2: Clinical and samples collection information for HCC patients treated with Y90-RE-1

No. Pat ID Pre 1mo 3mo 6mo TIL 3m RECIST 6m RECIST Location of Response Tumor Tumor size Stage PVTT AFP level Hepatitis Pre tx Post tx 1.1 1.1 progression status multiplicity (cm) (TNM) (µg/ml) status

1 HEP011 PD PD Non target NR Multifocal 3.2 IVB No 16841.0 B Yes No (Distant)

2 HEP023 PD PD Non target NR 1 9.1 IIIB Yes 2047.0 B Yes No (Distant)

3 HEP053 SD PD Target TR Multifocal 1.7 IIIB Yes 210.0 B Yes Yes

4 HEP099 PD PD Non target NR Multifocal 2.2 IIIB Yes 402.0 C Yes Yes (Distant)

5 HEP167 PD PD Non target NR Multifocal 7.2 IIIB Yes 171.0 Non Yes Yes (Distant)

6 HEP205 PD PD Non target NR 1 10.0 IIIA No 6.3 B No No (Distant)

7 HEP278 SD PD Non target TR Multifocal 3.0 II No 15.9 Non No Yes (liver)

8 HEP272 PD PD Target NR 1 16.0 I No 2.3 Non No No

9 HEP022 SD PD Non target TR Multifocal 2.5 II Yes 252.0 B Yes Yes (Distant)

10 HEP279 SD PD Non target TR Multifocal 8.4 IIIA No 202.0 B No Yes (liver)

11 HEP161 PD PD Target NR Multifocal 3.7 IIIb Yes 499.0 Non No Yes

12 HEP188 PD PD Non target NR Multifocal 10.6 IIIB Yes 62.4 Non No Yes (Distant)

13 HEP258 PD PD Non target NR Multifocal 2.7 IIIB Yes 60500.0 C Yes No (Distant)

14 HEP266 PD PD Non target NR Multifocal 8.3 IIIA No 122.0 B No No (Distant)

15 HEP291 PD PD Non target NR Multifocal 6.2 IIIB Yes 3.7 B No Yes (Distant)

16 HEP292 PD PD Non target NR Multifocal 5.7 IIIA No 17818.0 Non Yes No (Distant)

17 HEP294 SD PD Non target TR 1 9.9 I No 521.0 B Yes Yes (liver)

18 HEP313 PD PD Non target NR Multifocal 10.0 IIIA No 4281.0 Non Yes Yes (Distant)

19 HEP128 PR PR - SR 1 10.3 II Yes 97.5 B Yes Yes

20 HEP131 PR PR - SR 1 5.5 I Yes 9.9 B No Yes

21 HEP147 SD SD - SR Multifocal 9.8 IIIA Yes 67.7 Non No No

22 HEP056 SD SD - SR 1 10.0 I No 4718.0 C Yes Yes

23 HEP179 PR PR - SR 1 5.1 IIIB Yes 149.0 Non Yes Yes

24 HEP201 PR PR - SR Multifocal 3.9 II Yes 165.0 C Yes No

25 HEP132 SD SD - SR 1 12.6 I No 3.9 Non Yes No

26 HEP210 PR PR - SR Multifocal 6.4 I No 38.0 B No Yes

27 HEP242 PR PR - SR 1 11.1 I No 14.4 B No Yes

28 HEP281 SD SD - SR 1 6.0 I No 6.4 C No No

29 HEP286 PR PR - SR 1 6.7 I No 90.2 B No Yes

30 HEP298 PR PR - SR 1 6.4 I No 3.2 Non No No

31 HEP316 SD SD - SR Multifocal 7.0 IIIA No 4.0 C Yes No

Footnote: Samples used in CyTOF analysis 1mo, 37 to 53 days; 3mo, 75-146 days and 6mo, 157 to 233 days RECIST 1.1 criteria: CR, complete response is characterised by “disappearance of all target lesions”, PR, partial response is defined as “30% decrease in the sum of diameters of target lesions,” PD, progressive disease is defined as “20% increase in the sum of diameters of target lesions” and SD, stable disease is described as “neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD” (24). Location of progression: target means progression at lesion treated with Y90; non-target means progression at lesions not treated with Y90 either within the liver (Liver); for lesions outside of liver such as lungs (Distant). Response status: NR= non-responders, patients who are already PD at 3m; TR= transient-responders, patients who are SD, PR or CR (non-PD) at 3m but PD at 6m; and SR= sustained responders, patients who are non-PD at 6m. PVTT: Portal vein tumor thrombus; AFP: alpha-fetoprotein; Non: non hepatitis B nor hepatitis C; tx: therapy Table S3: Antibodies used for CyTOF staining

Isotopes Antibodies Clone Vendor

89 CD45 (Barcode 1) HI30 Fluidigm 112/114 CD14 TüK4 Lifetechnologies 115 CD45 (Barcode 2) HI30 Biolegend 139 CD3 UCHT1 Biolegend 141 CD19 HIB19 Biolegend 142 CD45RO UCHL1 Biolegend 143 HLA-DR L243 Biolegend 144 CD8 SK1 Biolegend 145 T-bet 4B10 Biolegend 146 CD28 CD28.2 Biolegend 147 PD-1 EH12.2H7 Biolegend 148 CD4 SK3 Biolegend 149 CD154 24-31 Biolegend 150 CD103 B-Ly7 Ebioscience 151 CXCR6 K041E5 Biolegend 152 TNF-a MAb11 Biolegend 153 CD25 2A3 BD bioscience 154 CD27 O323 Biolegend 155 CD152 BN13 BD bioscience 156 PD- 29E.2A3 Biolegend 157 CD244 CL7 Biolegend 158 IL-10 JES3-9D7 Biolegend 159 LAG-3 17B4 Abcam 160 TIM-3 F38-2E2 Biolegend 161 CCR7 G043H7 Biolegend 162 CD56 NCAM16.2 BD bioscience 163 CXCR3 G025H7 Biolegend 164 GITR 621 Biolegend 165 FoxP3 PCH101 Ebioscience 166 Ki67 20Raj1 Ebioscience 167 CD80 2D10 Biolegend 168 IFN-y B27 Biolegend 169 IL-17A BL168 Biolegend 170 EOMES 21Mags8 Ebioscience 171 CD45RA JS-83 Ebioscience 172 CD45 (Barcode 3) HI30 Biolegend 173 GranzymeB CLB-GB11 Abcam 174 CD137 4B4-1 Biolegend 175 CCR5 T21/8 Biolegend 176 CD69 FN50 Biolegend 191/193 Ir Intercalator Fluidigm Table S4: Primer sequence for target Targets Primer Sequence in 5’-3’ orientation CCL5-Forward ACACACTTGGCGGTTCTTTC CCL5-Reverse CCTGCTGCTTTGCCTACATT CXCL16-Forward CTACACGAGGTTCCAGCTCC CXCL16-Reverse CAATCCCCGAGTAAGCATGT GAPDH-Forward ACCACAGTCCATGCCATCAC GAPDH-Reverse TCCACCACCCTGTTGCTGTA A

Table S5: Selective list of significantly enriched in post-Y90-RE tumors genes from NGS data

LEUKOCYTE ACTIVATION

Ensembl ID Symbol Annotation logFC ENSG00000196839 ADA adenosine deaminase 2.9590 ENSG00000030110 BAK1 BCL2-antagonist/killer 1; BCL2-like 7 pseudogene 1 2.1519 ENSG00000198851 CD3E T-cell surface glycoprotein CD3 epsilon chain (CD3-TCR complex) 3.4588 ENSG00000117091 CD48 signaling lymphocytic activation molecule 2 (SLAMF2) 4.2027 ENSG00000114013 CD86 T-lymphocyte activation (B7-2) 3.5566 ENSG00000153563 CD8A T-cell surface glycoprotein CD8 alpha chain 3.9605 ENSG00000172243 CLEC7A C-type lectin domain family 7, member A 3.7015 ENSG00000172215 CXCR4 chemokine (C-X-C motif) receptor 4 3.8053 ENSG00000100867 DHRS2 dehydrogenase/reductase (SDR family) member 2 -5.9752 ENSG00000134516 DOCK2 dedicator of cytokinesis 2 3.1380 ENSG00000169508 GPR183 G -coupled receptor 183 5.1502 ENSG00000185811 IKZF1 IKAROS family zinc finger 1 (Ikaros) 2.3466 ENSG00000103522 IL21R interleukin 21 receptor 3.7686 ENSG00000106348 IMPDH1 IMP (inosine monophosphate) dehydrogenase 1 3.4897 ENSG00000115232 ITGA4 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) 2.4608 ENSG00000005844 ITGAL ; Lymphocyte function-associated antigen 1 (LFA-1) 2.3630 ENSG00000143772 ITPKB inositol 1,4,5-trisphosphate 3-kinase B 3.3828 ENSG00000182866 lymphocyte-specific protein tyrosine kinase 4.4954 ENSG00000136167 LCP1 lymphocyte cytosolic protein 1 (L-plastin) 3.4880 lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of ENSG00000043462 LCP2 76kDa) 2.6663

ENSG00000142347 MYO1F myosin IF 3.6385

ENSG00000235568 NFAM1 NFAT activating protein with ITAM motif 1 3.7751 ENSG00000124126 PREX1 phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1 2.7667 ENSG00000134242 PTPN22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid) 4.1690 ENSG00000081237 PTPRC protein tyrosine phosphatase, receptor type, C 2.8910 ENSG00000026751 SLAMF7 SLAM family member 7 4.6398 solute carrier family 11 (proton-coupled divalent metal ion transporters), ENSG00000018280 SLC11A1 member 1 4.4467 ENSG00000145335 SNCA synuclein, alpha (non A4 component of amyloid precursor) 6.3671 ENSG00000126561 STAT5A signal transducer and activator of transcription 5A 2.5439

ENSG00000165025 SYK spleen tyrosine kinase 3.5553

ENSG00000137462 TLR2 toll-like receptor 2 2.8924

ENSG00000196664 TLR7 toll-like receptor 7 4.5440

ENSG00000141968 VAV1 vav 1 guanine nucleotide exchange factor 3.0099 Table S5 (continued)

ANTIGEN PROCESSING AND PRESENTATION VIA MHC CLASS II

Ensembl ID Gene Symbol Annotation logFC

ENSG00000242574 HLA-DMB major histocompatibility complex, class II, DM beta 3.9071

ENSG00000204252 HLA-DOA major histocompatibility complex, class II, DO alpha 3.4570

ENSG00000223865 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 3.0601

ENSG00000196735 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 3.4422

ENSG00000237541 HLA-DQA2 major histocompatibility complex, class II, DQ alpha 2 4.3574

ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 3.7580

ENSG00000232629 HLA-DRB5 major histocompatibility complex, class II, DR beta 5 4.7493

POSITIVE REGULATION OF ACTIVATION

Ensembl ID Gene Symbol Annotation logFC ENSG00000196839 ADA adenosine deaminase 2.9590 ENSG00000198851 CD3E T-cell surface glycoprotein CD3 epsilon chain (CD3-TCR complex) 3.4588 ENSG00000117091 CD48 signaling lymphocytic activation molecule 2 (SLAMF2) 4.2027 ENSG00000114013 CD86 T-lymphocyte activation antigen (B7-2) 3.5566 ENSG00000153563 CD8A T-cell surface glycoprotein CD8 alpha chain 3.9605 ENSG00000172243 CLEC7A C-type lectin domain family 7, member A 3.7015 ENSG00000172215 CXCR4 chemokine (C-X-C motif) receptor 4 3.8053 ENSG00000134516 DOCK2 dedicator of cytokinesis 2 3.1380 ENSG00000185811 IKZF1 IKAROS family zinc finger 1 (Ikaros) 2.3466 ENSG00000005844 ITGAL Integrin alpha L; Lymphocyte function-associated antigen 1 (LFA-1) 2.3630 ENSG00000143772 ITPKB inositol 1,4,5-trisphosphate 3-kinase B 3.3828 ENSG00000182866 LCK lymphocyte-specific protein tyrosine kinase 4.4954 ENSG00000136167 LCP1 lymphocyte cytosolic protein 1 (L-plastin) 3.4880 ENSG00000134242 PTPN22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid) 4.1690 ENSG00000081237 PTPRC protein tyrosine phosphatase, receptor type, C 2.8910 solute carrier family 11 (proton-coupled divalent metal ion transporters), ENSG00000018280 SLC11A1 member 1 4.4467 ENSG00000126561 STAT5A signal transducer and activator of transcription 5A 2.5439 ENSG00000165025 SYK spleen tyrosine kinase 3.5553 ENSG00000141968 VAV1 vav 1 guanine nucleotide exchange factor 3.0099

POSITIVE REGULATION OF T CELL PROLIFERATION

Ensembl ID Gene Symbol Annotation logFC ENSG00000198851 CD3E T-cell surface glycoprotein CD3 epsilon chain (CD3-TCR complex) 3.4588 ENSG00000102879 CORO1A protein tyrosine phosphatase, receptor type, C 3.2727 ENSG00000103522 IL2RA IKAROS family zinc finger 1 (Ikaros) 3.5704 ENSG00000197646 PDCD1LG2 spleen tyrosine kinase 2.9272 ENSG00000081237 PTPRC protein tyrosine phosphatase, receptor type, C 2.8910 ENSG00000126561 STAT5A signal transducer and activator of transcription 5A 2.5439 ENSG00000165025 SYK spleen tyrosine kinase 3.5553 ENSG00000102524 TNFSF13B inositol 1,4,5-trisphosphate 3-kinase B 3.2932 Table S5 (continued)

CHEMOTAXIS

Ensembl ID Gene Symbol Annotation logFC ENSG00000126522 ASL argininosuccinate lyase -2.5285 ENSG00000171860 C3AR1 complement component 3a receptor 1 3.8846 ENSG00000197405 C5AR1 complement component 5a receptor 1 4.2604 ENSG00000275385 CCL18 chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated) 7.6359 ENSG00000277632 CCL3 chemokine (C-C motif) ligand 3 3.8563 ENSG00000271503 CCL5 chemokine (C-C motif) ligand 5 4.1328 ENSG00000163823 CCR1 chemokine (C-C motif) receptor 1 3.7753 ENSG00000183625 CCR3 chemokine (C-C motif) receptor 3 3.3132 ENSG00000121797 CCRL2 chemokine (C-C motif) receptor-like 2 4.4294 ENSG00000174600 CMKLR1 chemokine-like receptor 1 3.7571 ENSG00000140931 CMTM3 CKLF-like MARVEL transmembrane domain containing 3 3.0302 ENSG00000102879 CORO1A coronin, actin binding protein, 1A 3.2727 ENSG00000161921 CXCL16 chemokine (C-X-C motif) ligand 16 2.6270 ENSG00000121966 CXCR4 chemokine (C-X-C motif) receptor 4 3.8053 ENSG00000134516 DOCK2 dedicator of cytokinesis 2 3.1380 ENSG00000171051 FPR1 formyl peptide receptor 1 4.4761 ENSG00000187474 FPR3 formyl peptide receptor 3 3.1849 ENSG00000160255 ITGB2 integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) 4.3212 potassium large conductance calcium-activated channel, subfamily M, alpha ENSG00000156113 KCNMA1 member 1 2.3486 ENSG00000118257 NRP2 2 2.8811

ENSG00000122861 PLAU plasminogen activator, urokinase 5.7288

ENSG00000011422 PLAUR plasminogen activator, 5.1215 ENSG00000169403 PTAFR platelet-activating factor receptor 3.8327 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding ENSG00000128340 RAC2 protein Rac2) 3.4148

ENSG00000163220 S100A9 S100 calcium binding protein A9 4.8190 ENSG00000145335 SNCA synuclein, alpha (non A4 component of amyloid precursor) 6.3671 ENSG00000165025 SYK spleen tyrosine kinase 3.5553 ENSG00000025708 TYMP thymidine phosphorylase 2.9858 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 4 4 4 4 4 4 4 CD45RO CXCR3 CD154 CD103 CCR5 CD14 GITR node244(224)=86.5 6 6 6 6 6 6 6 node244(224)=3.5 node244(224)=2.1 node244(224)=3.6 node244(224)=4.1 node244(224)=5.4 node244(224)=93 All(119930)=19.6 All(119930)=43.7 All(119930)=6.2 All(119930)=2.7 All(119930)=4.9 All(119930)=4.8 All(119930)=4.7 8 8 8 8 8 8 8 10 10 10 10 10 10 10 12 12 12 12 12 12 12 Density Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 4 4 4 4 4 4 4 CD45RA CD152 FoxP3 IL17A CD69 CD56 PD.1 node244(224)=127.6 node244(224)=30.6 6 6 6 6 6 6 6 node244(224)=5.8 node244(224)=5.4 node244(224)=5.8 All(119930)=14.8 All(119930)=21.5 All(119930)=59.5 node244(224)=9 node244(224)=5 All(119930)=7.5 All(119930)=7.1 All(119930)=5.1 All(119930)=13 8 8 8 8 8 8 8 10 10 10 10 10 10 10 12 12 12 12 12 12 12 Density Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 4 4 4 4 4 4 4 PD.L1 TNFA CD27 Tim3 IL10 CD3 node244(224)=131.1 GB node244(224)=21.7 node244(224)=42.1 6 6 6 6 6 6 6 node244(224)=5.6 node244(224)=3.7 node244(224)=2.7 node244(224)=3.7 All(119930)=23.9 All(119930)=24.7 All(119930)=40.5 All(119930)=7.4 All(119930)=8.3 All(119930)=5.4 All(119930)=4 8 8 8 8 8 8 8 A B 10 10 10 10 10 10 10 B. A. Figure S1: Immune profiles of TILsnaive tumors. or from post-Y90-RE treatment 12 12 12 12 12 12 12 from post Y90-RE (Y90) and treatment naive (Ctl) TILs. Right, graphs shows percentage of Treg of by analyzed ±were means SDs and show Data cells. percentage shows graphs Right, TILs. (Ctl) naive treatment and (Y90) Y90-RE post from cells T CD4+ pre-gated on cells Treg Foxp3+CD152+ of gating and the showing plots Representative (Y90) Y90-RE post from Student’s t-test. *p<0.05. TILs by analyzed in were and SDs ± means cells the represent Graphs tumors. (Ctl) T naive treatment CXCR3+CD4+CD45RO+ of percentages show graphs marker. Right, each of level expression average the represent lines black and Red nodes. the all of profiles expression show plots black and node selected the from profiles expression show plots Red tumors. RE Y90 post from NODE TILs in enriched nodes, was that population representative CD4+ representing from 244 expression CD45RO and CXCR3 showing plots density Left, Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 Foxp3 2 2 2 2 2 2 4 4 4 4 4 4 HLA.DR LAG3 CD80 IFNG CD4 CD8 node244(224)=12.5 node244(224)=30.8 6 6 6 6 6 6 node244(224)=4.1 node244(224)=4.2 node244(224)=5.5 node244(224)=44 All(119930)=17.9 All(119930)=35.9 All(119930)=19.5 All(119930)=6.3 All(119930)=5.5 All(119930)=6.3 8 8 8 8 8 8 Y-90 2.29% 10 10 10 10 10 10 12 12 12 12 12 12 Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 CD152 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 4 4 4 4 4 4 4 4 4 CD45RO CXCR3 CD154 CD103 CD137 CD244 CCR5 CCR7 CD14 CD28 GITR Ki67 Tbet node244(224)=86.5 node244(224)=20.9 node244(224)=13.8 node244(224)=37.8 6 6 6 6 6 6 6 node244(224)=5.4 node244(224)=3.5 node244(224)=2.1 node244(224)=3.6 node244(224)=4.1 6 6 6 6 6 6 node244(224)=4.2 node244(224)=3.7 node244(224)=93 node244(224)=11 All(119930)=43.7 All(119930)=19.6 All(119930)=12.1 All(119930)=18.6 All(119930)=18.9 All(119930)=24.7 All(119930)=6.2 All(119930)=2.7 All(119930)=4.9 All(119930)=4.8 All(119930)=4.7 All(119930)=7.9 All(119930)=5.7 8 8 8 8 8 8 8 8 8 8 8 8 8 Ctl 10 10 10 10 10 10 10 10 10 10 10 10 10 29.6% 12 12 12 12 12 12 12 12 12 12 12 12 12 Density Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 unpaired Student’sunpaired t-test. *p<0.05. 4 4 4 4 4 4 4 4 4 4 4 4 4 4 CD45RA CD45RO CXCR3 CD152 CD154 CD103 FoxP3 IL17A %Foxp3+CD152+ CCR5 CD69 CD56 CD14 GITR PD.1 node244(224)=127.6 node244(224)=30.6 node244(224)=86.5 6 6 6 6 6 6 6 node244(224)=5.4 node244(224)=5.8 node244(224)=5.8 6 6 6 6 6 6 6 node244(224)=5.4 node244(224)=3.5 node244(224)=2.1 node244(224)=3.6 node244(224)=4.1 node244(224)=93 All(119930)=59.5 All(119930)=14.8 All(119930)=21.5 All(119930)=43.7 All(119930)=19.6 node244(224)=9 node244(224)=5 All(119930)=7.5 All(119930)=7.1 All(119930)=5.1 All(119930)=6.2 All(119930)=2.7 All(119930)=4.9 All(119930)=4.8 All(119930)=4.7 All(119930)=13 /CD4+ T cells Node 244 10 20 30 40 8 8 8 8 8 8 8 8 8 8 8 8 8 8 0 10 10 10 10 10 10 10 10 10 10 10 10 10 10 12 12 12 12 12 12 12 12 12 12 12 12 12 12

Density DensityDensity DensityDensity DensityDensity DensityDensity Y90 DensityDensity DensityDensity Density Treg cells 0.0 0.2 0.4 0.6 0.8 1.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 %CXCR3+ CXCR3+CD4+CD45RO+ 2 2 2 2 2 2 2 2 2 2 2 2 2 2 /CD4+CD45RO+ T cells 20 40 60 0 * 4 4 4 4 4 4 4 4 4 4 4 4 4 4 CD45RA CD152 FoxP3 PD.L1 IL17A TNFA CD27 CD69 CD56 Tim3 PD.1 IL10 CD3 node244(224)=131.1 node244(224)=127.6 GB node244(224)=21.7 node244(224)=42.1 node244(224)=30.6 6 6 6 6 6 6 6 node244(224)=5.6 node244(224)=3.7 node244(224)=2.7 node244(224)=3.7 6 6 6 6 6 6 6 node244(224)=5.8 node244(224)=5.4 node244(224)=5.8 Y90 All(119930)=23.9 All(119930)=24.7 All(119930)=40.5 All(119930)=59.5 All(119930)=21.5 All(119930)=14.8 node244(224)=9 node244(224)=5 All(119930)=7.4 All(119930)=8.3 All(119930)=5.4 All(119930)=5.1 All(119930)=7.5 All(119930)=7.1 All(119930)=13 Ctl All(119930)=4 8 8 8 8 8 8 8 8 8 8 8 8 8 8 10 10 10 10 10 10 10 10 10 10 10 10 10 10 * 12 12 12 12 12 12 12 12 12 12 12 12 12 12

DensityDensity DensityDensity DensityDensity DensityDensity DensityDensity Ctl DensityDensity Density unpaired unpaired 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 4 4 4 4 4 4 4 4 4 HLA.DR

PD.L1 LAG3

CD80 TNFA CD27

IFNG Tim3

CD4 CD8

IL10 CD3

node244(224)=131.1

GB

node244(224)=12.5 node244(224)=30.8

node244(224)=21.7 node244(224)=42.1

6

6 6 6 6 6 node244(224)=4.1 node244(224)=4.2 node244(224)=5.5

6 6 6 6 6 6 6

node244(224)=5.6 node244(224)=3.7 node244(224)=2.7 node244(224)=3.7

node244(224)=44

All(119930)=17.9

All(119930)=35.9 All(119930)=19.5

All(119930)=23.9 All(119930)=24.7 All(119930)=40.5

All(119930)=6.3 All(119930)=5.5 All(119930)=6.3 All(119930)=7.4

All(119930)=8.3 All(119930)=5.4

All(119930)=4 8 8 8 8 8 8 8 8 8 8 8 8 8 10 10 10 10 10 10 10 10 10 10 10 10 10 12 12 12 12 12 12 12 12 12 12 12 12 12 Density DensityDensity DensityDensity DensityDensity DensityDensity DensityDensity Density

0.0 0.2 0.4 0.6 0.8 1.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.00.0 0.20.2 0.40.4 0.60.6 0.80.8 1.01.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 4 4 4 4 4 4 4 4 HLA.DR CD137 CD244 CCR7 LAG3 CD28 CD80 IFNG Ki67 Tbet CD4 CD8 node244(224)=20.9 node244(224)=13.8 node244(224)=37.8 node244(224)=12.5 node244(224)=30.8 6 6 6 6 6 6 node244(224)=4.2 node244(224)=3.7 6 6 6 6 6 6 node244(224)=4.1 node244(224)=4.2 node244(224)=5.5 node244(224)=11 node244(224)=44 All(119930)=12.1 All(119930)=18.6 All(119930)=18.9 All(119930)=24.7 All(119930)=17.9 All(119930)=35.9 All(119930)=19.5 All(119930)=7.9 All(119930)=5.7 All(119930)=6.3 All(119930)=5.5 All(119930)=6.3 8 8 8 8 8 8 8 8 8 8 8 8 10 10 10 10 10 10 10 10 10 10 10 10 12 12 12 12 12 12 12 12 12 12 12 12 Density Density Density Density Density Density

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0 0 0 0 0 0 2 2 2 2 2 2 4 4 4 4 4 4 CD137 CD244 CCR7 CD28 Ki67 Tbet node244(224)=20.9 node244(224)=13.8 node244(224)=37.8 6 6 6 6 6 6 node244(224)=4.2 node244(224)=3.7 node244(224)=11 All(119930)=12.1 All(119930)=18.6 All(119930)=18.9 All(119930)=24.7 All(119930)=7.9 All(119930)=5.7 8 8 8 8 8 8 10 10 10 10 10 10 12 12 12 12 12 12 A Total gene enrichment 3% 9% Y-90 Ctl Pseudogenes 88%

B Clathrin coated Clathrin:AP-2 MHC class II alpha/ complex MHC class II beta/li nonamer alpha/beta/li Peptide loaded nonamer MHC class II Cytosol SH3GL2 Clathrin-coated endocytic vesicle SH3GL2 Transport vesicle Endocytic vesicle Clathrin coated MHC class II MHC class II Clathrin:AP-2 alpha/beta/li alpha/beta/li nonamer complex Nonameric nonamer complex AP-1 complex

Nonameric MHC complex AP-1 Clathrin II:lip22 coated nonamer TGN- nonameric MHC II:lip10 Lysosomal lysosome complex nonamer lumen vesicle with Cathepsin LGMN nonameric complex Nonameric MHC class IF130 complex Peptide II epitopes Antigen loaded MHC trans-Golgi Unfolded class II network antigen complex MHC II: CLIP

peptide-free MHC II: HLA-DM HLA-DM/ Legend HLA-DO Nonameric complex in COPII vesicle Protein complex ER to Golgi transport vesicle Small molecule/protein Invariant chain trimer MHC II alpha-beta Reaction heterodimer HLA II alpha Binding chain MHC II alpha- Nonameric beta alpha-beta: complex HLA II beta heterodimer Ii trimer: chain calnexin COP II Lumen of endoplasmic reticulum CANX

Figure S2: Major immune pathways enriched in RNA from post Y90-RE versus treatment naive HCC tumor tissues by Reactome pathway analysis. A. Pie chart showing higher percentages of genes enriched in Y90-RE treated versus treatment naive (Ctl) tumor tissues. B. Genes involved in antigen presenting pathways such as surface translocation of MHC II complex (green lines), antigen processing and loading on MHC II (blue lines) and MHC class II formation (red lines) were enriched in Y90-RE-treated patients. C Cytosol

CD80 (B7-1) CD86 Legend homodimer (B7-2) Protein complex Small molecule/protein Reaction CD28:B7-1 Binding

CD28 CD28:B7-2 homodimer

Cytosol D CD28:Grb2 phospho CD28:PI3K PI(4,5)P PI(3,4,5)P3 CD28:B7-1/ 2 CD28:B7-1, B7-2 CD28:Gads B7-2 ATP AKT:PIP3 ADP ATP PI3K alpha ADP PDPK1:PIP3 GRAP2 GRAB2-1

LCK, FYN PDPK1 AKT Src family tyrosine kinase (SFKs) VAV1 p-MAP3K14 MAP3K14 ATP p-S-AKT:PIP3

TORC2 RAC1:GDP GTP ADP ATP complex ADP p-S-AKT: PDPK1:PIP3 ATP

p-S400-MAP3K8 MAP3K8 ADP RAC1:GTP GDP

Active AKT CDC42:GTP GDP ADP ATP

VAV1:PIP3:CD ATP 28:GRB2 FYN Cytosol GTP CDC42:GDP ADP

p-Y142,160,174- VAV1:PIP3:CD28: GRB2

(continued) Figure S2

C.CD28-CD86 co-stimulatory pathways indicated by enriched genes in Y90-RE treated tumors. D. Post-Y90-RE enriched genes involved in the CD28-related activation pathway via Akt and Vav, denoted by red and blue line, respectively.

B-D. Protein molecules or complexes containing one or more genes identified by our NGS data are highlighted in yellow. Individual or molecules are represented in circles while protein complexes represented by boxes. A B

Cytosol

CD48

ICAM1-5

Cytosol CD244

Integrin LFA-1:ICAM1-5 alphaLbeta2 (LFA-1) CD48:CD244

Cytosol

Figure S3: NK cell and NKT cell pathways enriched in RNA from post Y90-RE versus treatment naive HCC tumor tissues

A. Enriched genes related to NK cell activation. B. Enriched genes related to NKT cell development and recruitment to liver

A and B. P Protein molecules or complexes containing one or more genes identified by our NGS data are colored in yellow. Individual proteins or molecules are represented in circles while protein complexes represented by boxes. Color Key Color Key

Color Key A Color Key −4 −2 0 2 4 3mo Row Z−Score −4 −2 0 −4 −2 2 0 2 4 4 Pre Row Z−Score Row Z−Score -4 -2 0 2 4 .CCR5 .LAG3 ..GITR ..GITRGITR .CR3 Row Z-Score .CD244 .PD.L1 .PD.L1PD-L1 ..HLA.DR CCR7 ..EOMES .CCR7 .CCR7 .IL17A IL10 .CD80 .IL10 .IL10 .CD45RA Foxp3 .CD56 .FoxP3 .FoxP3 .CD69 CD80 .Ki67 .CD80 .CD80Ki67 .IL10 .CD137 .Ki67 .Ki67CD45R ..GB ..Tbet .CD45RA .CD45RAA .Tim3 .CD244 .CD244CD244 .CD8 .CD103 .CD69 .CD69CD69 .CD154 .CD19 .CD56 .CD56CD56 .PD.1 .PD.L1 ..Tbet ..TbetTbet .CD14 Eomes GB+CD56+ ..TNFA ..EOMES ..EOMES ..IFNG IL17a .FoxP3 .IL17A .IL17A .CR6 .CD137 .CD137CD137 .CCR7 GB .CD27 ..GB ..GB .CD152 CXCR3 .CD3 .CR3 .CR3 .CD28 IFNg ..GITR ..IFNG ..IFNGHLA- .CD4 CD14+ .CD25 ..HLA.DR ..HLA.DR .CD45RO .Tim3 .Tim3DR

Tim3 161 471 459 449 513 506 490 100 206 431 462 507 501 324 232 370 331 365 371 338 296 312 259 266 .CD8 .CD8CD8 .CCR5 .CCR5CCR5 .CR6 .CR6CXCR6 ..TNFA ..TNFATNFa .PD.1 .PD.1PD-1 .CD45RO .CD45ROCD45R .CD3 .CD3O .CD27 .CD27CD3 CD27 .CD28 .CD28CD28 .CD25 .CD25CD25 .CD4 .CD4CD4 .CD152 .CD152CD152 .CD103 .CD103CD103 .CD154 .CD154CD154 .LAG3 .LAG3Lag3 .CD14 .CD14CD14 37 58 41 69 26 46 29 65 37 93 58 47 41 69 26 46 29 65 93 47 179 179 305 445 305 325 445 470 428 325 454 427 470 346 240 428 454 427 346 240 108 138 293 361 108 138 293 361

B CD14 HLA.DR Ki67 CD103 CD152 1.0 1.0 1.0 1.0 1.0 All(158751)=4.7 All(158751)=8.7 All(158751)=32.1 All(158751)=3.3 All(158751)=5.6 0.8 0.8 0.8 0.8 0.8 node43(351)=184.6 node43(351)=20.6 node43(351)=36.3 node43(351)=3 node43(351)=4.3

0.6 0.6 0.6 Node 293 0.6 0.6 Density Density Density Density 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12

GITR IFNG CD28 IL17A LAG3 1.0 1.0 1.0 1.0 1.0 All(158751)=7.6 All(158751)=4.5 All(158751)=13 All(158751)=9.1 All(158751)=5.5 0.8 0.8 0.8 0.8 0.8 node43(351)=5.5 node43(351)=3.4 node43(351)=7.9 node43(351)=5.9 node43(351)=3.9

Figure0.6 S4: Immune profiles0.6 of PBMCs from responders0.6 versus non0.6 responders to 0.6 Density Density Density Density Y90 RE.0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2

A. 2D0.0 heatmap showing enriched0.0 nodes in Pre-versus0.0 3 months (3mo)0.0 post-Y90 0.0 PBMCs.0 2 colour4 6 8 lines10 12 represent0 2 4GB+CD56+6 8 10 12 NK and0 2 CD14+4 6 8 populations10 12 0 enriched2 4 6 8 10 12 0 2 4 6 8 10 12

3mo after Y90IL10 RE. n=5 paired pre-CD45RO versus 3mo PBMCsEOMES from Y90 RE-responders.FoxP3 CD69

B. Density1.0 plots showing CD141.0 and HLA-DR expression1.0 from representative1.0 nodes, 1.0 All(158751)=9 All(158751)=25.4 All(158751)=10.8 All(158751)=8.9 All(158751)=8.5

NODE0.8 293 represents APCs0.8 enriched in TILs 0.8 from post Y90 RE tumors.0.8 Red plot 0.8 node43(351)=5.7 node43(351)=12.6 node43(351)=6.4 node43(351)=5.5 node43(351)=5.2

shows0.6 expression profile0.6 from the selected node0.6 and black shows that0.6 of all the 0.6 Density Density Density Density

nodes.0.4 Red and black lines0.4 represent the average0.4 expression levels0.4 of each 0.4

marker.0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12

GB PD.1 CD56 CD137 CD3 1.0 1.0 1.0 1.0 1.0 All(158751)=218.2 All(158751)=5 All(158751)=18.8 All(158751)=19.9 All(158751)=32.3 0.8 0.8 0.8 0.8 0.8 node43(351)=61.6 node43(351)=3.3 node43(351)=9.1 node43(351)=9.4 node43(351)=13.5 0.6 0.6 0.6 0.6 0.6 Density Density Density Density 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12

CD154 CD19 CD80 PD.L1 Tim3 1.0 1.0 1.0 1.0 1.0 All(158751)=2.6 All(158751)=4.5 All(158751)=6 All(158751)=4.3 All(158751)=9.3 0.8 0.8 0.8 0.8 0.8 node43(351)=2.1 node43(351)=3 node43(351)=3.8 node43(351)=2.9 node43(351)=5 0.6 0.6 0.6 0.6 0.6 Density Density Density Density 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12

CD244 CCR7 TNFA CD25 CD45RA 1.0 1.0 1.0 1.0 1.0 All(158751)=14 All(158751)=10.7 All(158751)=3.7 All(158751)=7.8 All(158751)=263.7 0.8 0.8 0.8 0.8 0.8 node43(351)=6 node43(351)=4.9 node43(351)=2.3 node43(351)=3.3 node43(351)=21.4 0.6 0.6 0.6 0.6 0.6 Density Density Density Density 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12

CXCR3 CCR5 CD27 CXCR6 CD4 1.0 1.0 1.0 1.0 1.0 All(158751)=11.1 All(158751)=4.3 All(158751)=96.8 All(158751)=3.3 All(158751)=156.6 0.8 0.8 0.8 0.8 0.8 node43(351)=3.7 node43(351)=2.1 node43(351)=9.2 node43(351)=1.8 node43(351)=9.6 0.6 0.6 0.6 0.6 0.6 Density Density Density Density 0.4 0.4 0.4 0.4 0.4 0.2 0.2 0.2 0.2 0.2 0.0 0.0 0.0 0.0 0.0

0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 0 2 4 6 8 10 12 Color Key Color Key Color Key Color Key Color Key A Pre −4 −2 0 2 4 Row Z−Score -4 -2 0 2 4 .CCR5 .LAG3 .CR3 Row Z-Score .CD244 −4 −2 0 2 4 −4 −2 0 2 4 −4 −2 0 2 4 Row Z−Score ..HLA.DR Row Z−Score Row Z−Score ..EOMES .IL17A .CCR5 .CCR5 CCR5 .CCR5.CD80 .CD45RA .LAG3 .LAG3 Lag3 .LAG3.CD56 .CD69 .CR3 .CR3 CXCR3 .CR3.Ki67 .IL10 .CD244 .CD244 CD244 .CD244.CD137 ..GB ..HLA.DR ..HLA.DR HLA-DR ..HLA.DR..Tbet .Tim3 ..EOMES ..EOMES Eomes ..EOMES.CD8 .CD103 .IL17A .IL17A IL17a .IL17A.CD154 .CD80.CD19 .CD80 .CD80 CD80 .PD.1 .CD45RA.PD.L1 .CD45RA .CD45RA CD45RA .CD14 CD56 .CD56..TNFA .CD56 .CD56 ..IFNG .CD69 .CD69 CD69 .CD69.FoxP3 .CR6 .Ki67 .Ki67 Ki67 .Ki67.CCR7 .CD27 .IL10 .IL10 IL10 .IL10.CD152 .CD3 .CD137 .CD137 CD137 .CD137.CD28 ..GITR ..GB ..GB GB ..GB.CD4 .CD25 ..Tbet ..Tbet Tbet ..Tbet.CD45RO .Tim3 .Tim3 Tim3 .Tim3 .CD8 .CD8 CD8 161 471 459 449 513 506 490 100 206 431 462 507 501 324 232 370 331 365 371 338 296 312 259 266 .CD8 .CD103 .CD103 CD103 .CD103 .CD154 .CD154 CD154 .CD154 .CD19 .CD19 CD19 .CD19 .PD.1 .PD.1 PD-1 .PD.1 .PD.L1 .PD.L1 PD-L1 .PD.L1 .CD14 .CD14 CD14 .CD14 ..TNFA ..TNFA TNFa ..TNFA ..IFNG ..IFNG IFNg ..IFNG .FoxP3 .FoxP3 Foxp3 .FoxP3 .CR6 .CR6 CXCR6 .CR6 .CCR7 .CCR7 CCR7 .CCR7 .CD27 .CD27 CD27 .CD27 .CD152 .CD152 CD152 .CD152 .CD3 .CD3 CD3 .CD3 .CD28 .CD28 CD28 .CD28 ..GITR ..GITR GITR ..GITR .CD4 .CD4 CD4 .CD4 .CD25 .CD25 CD25 .CD25 .CD45RO .CD45RO CD45RO .CD45RO 161 471 459 449 513 506 490 100 206 431 462 507 501 324 232 370 331 365 371 338 296 312 259 266 161 471 459 449 513 506 490 100 206 161 431 471 459 462 449 507 513 506 501 490 100 324 206 431 232 462 507 370 501 324 331 232 365 370 331 371 365 371 338 338 296 296 312 259 312 266 259 266 SRs NRs/TRs

Color Key Color Key Color Key Color Key Color Key Color Key

ColorColor Key Key

−4 −2 0 2 4 B 3mo Row Z−Score -4 -2 0 2 4 .CCR5 .LAG3 −4 −2 0 2 4 −4 −2 0 2 4 Row Z−Score −4 −2 0 2 4 Row Z−Score .CR3 Row Z−Score −4 −2 0 2 4 .CD244 −4 −2 0 2 4 Row Z−Score −4 −2 0 2 4 Row Z-Score Row Z−Score Row Z−Score ..HLA.DR .CD152 .CD152 .CD152..EOMES .CD152 .IL17A .CD3 .CD152.CD3 CD152 .CD152.CD3 .CD80 .CD3 .CD45RA .CD103 .CD3.CD103 CD3 .CD3.CD103.CD56 .CD103 .CD69 ..GITR .CD103..GITR CD103 .CD103..GITR.Ki67 ..GITR .IL10 .CD4 ..GITR.CD4 GITR ..GITR.CD4 .CD137 .CD4 .CD25 .CD25..GB .CD25 .CD4 CD4 .CD4 ..Tbet .CD25 .CD27 .CD25.CD27.Tim3 .CD27 .CD25 CD25 .CD8 .CD27.CD28 .CD27.CD28 .CD27.CD28.CD103 .CD28 CD27 .CD154 .CD45RA .CD28.CD45RA .CD28.CD45RA.CD19 .CD45RA CD28 .PD.1 .CCR7 .CD45RA.CCR7 .CD45RA.CCR7.PD.L1 .CCR7 CD45RA .CD14 ..IFNG .CCR7..IFNG .CCR7..IFNG..TNFA ..IFNG CCR7 ..IFNG ..TNFA ..IFNG..TNFA ..IFNG..TNFA.FoxP3 ..TNFA IFNg .CR6 .FoxP3 ..TNFA.FoxP3 TNFa ..TNFA.FoxP3.CCR7 .FoxP3 .PD.L1 .PD.L1.CD27 .PD.L1 .FoxP3 Foxp3 .FoxP3.CD152 .PD.L1 .CD14 .PD.L1.CD14.CD3 .CD14 .PD.L1 PD-L1 .CD28 .CD14 .CD14.CD19 .CD14.CD19..GITR .CD19 CD14 .CD4 .CD19..HLA.DR .CD19..HLA.DR .CD19..HLA.DR.CD25 ..HLA.DR HLA-DR .CD45RO .CCR5 ..HLA.DR.CCR5 CCR5 ..HLA.DR.CCR5 .CCR5 .CCR5.CD80 161 471 459 449 513 506 490 100 206 431 462 507 501 324 232 370 331 365 371 338 296 312 .CCR5.CD80259 266 .CD80.CD80 CD80 .PD.1 .CD80.PD.1 PD-1 .CD80.PD.1 .PD.1.CD45RO .PD.1.CD45RO .PD.1.CD45RO .CD45RO .CD45RO.CD137 CD45RO .CD45RO.CD137 .CD137.CD137 CD137 ..GB .CD137..GB GB .CD137..GB ..GB.Ki67 ..GB.Ki67 ..GB.Ki67 .Ki67 .Ki67.IL10 Ki67 .Ki67.IL10 .IL10.IL10 IL10 ..EOMES .IL10..EOMES Eomes .IL10..EOMES ..EOMES.IL17A ..EOMES.IL17A ..EOMES.IL17A .IL17A .CD244 IL17a .IL17A.CD244 .CD244 .IL17A CD244 .CD244..Tbet .CD244..Tbet .CD244..Tbet ..Tbet.CD69 ..Tbet.CD69 Tbet ..Tbet.CD69 .CD69.CD56 .CD69.CD56 CD69 .CD69.CD56 .CD56.Tim3 .CD56.Tim3 CD56 .CD56.Tim3 .Tim3 .CD8 Tim3 .Tim3.CD8 .CD8 .Tim3 CD8 .CD8.CR3 .CD8.CR3 .CD8.CR3 .CR3.LAG3 .CR3.LAG3 CXCR3 .CR3.LAG3 .LAG3.CR6 .LAG3.CR6 Lag3 .LAG3.CR6 .CR6.CD154 .CR6.CD154 CXCR6 .CR6.CD154 .CD154 .CD154 CD154 .CD154 82 76 82 76 82 76 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 82 76 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 82 76 82 76 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 142 158 202 195 198 191 187 281 271 249 330 350 130 121 336 351 305 274 342 278 382 404 381 367 423 399 391 288 333 306 400 439 455 443 407 SRs NRs/TRs

Figure S5: Immune profiles of PBMCs from responders versus non responders to Y90-RE.

A. 2D heatmap showing enriched nodes in PBMCs from sustained-responders (SRs) and non- or transient-responders (NRs/TRs) at Pre-Y90-RE. n=8 each group. B. 2D heatmap showing enriched nodes in PBMCs from SRs and NRs/TRs at 3 months after Y90-RE. n=6 each group. A D or transient responders (NRs/TRs). responders or transient non (SRs) versus responders sustained RE PBMCs in from A-D. subsets pre-Y90 Immune D. C. B. A. of percentages showing plots Representative non-/transient sustained versus toresponders Y90-RE. Figure from S6: Specific immune enrichedPBMCs subsets in pre-treatment CCR5+ or CXCR6+ CD8+ CD8+ or CXCR6+ CCR5+ T cells Foxp3+CD152+ Treg CD4+ on gated (pre cells T cells) PD1+CD4+ T CD4+CD45RO+ on gated (pre cells T cells) PD-1+CD8+ T and cells Tim3+CD8+ T cells Pre Tim-3 PD-1 Pre CCR5 52.7% SRs 16.3% SRs 22.6% CD8 CD8 CD8 NRs/TRs NRs/TRs 3.21% 2.08% 3.9% C B

CXCR6 Foxp3 PD-1 38.2% SRs SRs 12.2% 1.55% CD152 CD4 CD8 gated on CD4+CD45RO+ NRs/TRs NRs/TRs gated on CD4+ 0.27% 17.9% 12.2% ntree ntree A 500500 ● 10001000 ● 15001500 ● 20002000 ●

0.770.77 ● ● ● 0.768 ● ●

● ● 0.760.76

0.750.75

0.74 Validation) 0.74 Accuracy (Repeated Cross − Validation) Accuracy

0.73 0.73 ●

Accuracy(Repeated Cross- ●

0 55 1010 1515 2020 2525 3030 mtrymtry

B Prediction outcome for training cohort n=22

Pat ID Prob_SR (%) Prob_NR (%) Predicted Actual HEP011 15.02 84.98 NR NR HEP053 22.14 77.86 NR NR HEP056 88.92 11.08 R R HEP099 9.20 90.80 NR NR HEP128 61.03 38.97 R R HEP131 94.88 5.12 R R HEP147 86.71 13.29 R R Prediction outcome for testing cohort n=8 HEP161 3.73 96.27 NR NR Pat ID Prob_SR (%) Prob_NR (%) Predicted Actual HEP167 20.51 79.49 NR NR HEP022 11.03 88.97 NR NR HEP188 5.89 94.11 NR NR HEP023 28.73 71.27 NR NR HEP201 63.35 36.65 R R HEP266 8.08 91.92 NR NR HEP205 24.37 75.63 NR NR HEP272 35.00 65.00 NR NR HEP210 59.44 40.56 R R HEP278 12.41 87.59 NR NR HEP242 56.06 43.94 R R HEP294 19.30 80.70 NR NR HEP258 26.59 73.41 NR NR HEP179 46.04 53.96 NR R HEP279 11.97 88.03 NR NR HEP316 35.06 64.94 NR R HEP281 32.11 67.89 NR R HEP286 56.11 43.89 R R HEP291 8.55 91.45 NR NR HEP292 7.55 92.45 NR NR HEP298 57.98 42.02 R R HEP313 12.56 87.44 NR NR Figure S7: Random Forest prediction model A. Accuracy curve based on mtry (number of random variables) and ntree (number of trees) for the training model. The most accurate parameters selected was mtry=10 and ntree=2000 with an accuracy of 76.8% B. Probability table for training cohort n=22 and testing cohort=8. R=SRs; NR= TRs/NRs. Prob= probability. Highlighted in red were discrepancy in prediction and actual response status.