Sumoylation Ubiquitination Neddylation
n n n n n n o o o o tio tio ti ti ti ti a a a n a n a a c n n c n n ic n ic n c n n c n n fi io o fi io o if io io if io io fi io io fi io io li t ti li t ti l t t l t t li t t li t t p ta e p ta e p ta e p ta e p a e p a e l l l l G t l t l m u e m u e m u e m u e m u e m u e A M D A M D
G A M D A M D e
A M D A M D G
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% RAD18 5
METABRIC TCGA (
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n=2173 n=816 0 ) PCNA 0 ) SENP8 HLA0A NEDD8 RRAGA UCHL3 PAF1 UBE2H PUM2 SHPRH UBD PEX13 IL31RA VCP CCDC8 UBE2R2 CUL5 HIST1H2BA WDR61 RBX1 HIST1H2BB NAE1 CTR9 OBSL1 RNF152 MYEOV2 HLA0B UBA3 HIST1H2BC UBE2D1 UBE2F Sumoylation Ubiquitination UBE2Q2 Neddylation IL17RB HIST1H2BD SAG UCHL3 n n n n on on io io io io ti ti METABRIC TCGA t t t t HIST1H2BH a n n a n n ca n n ca n n ca n n ca n n fic io o fic io o ifi tio io ifi tio io fi io io fi io io UBE2A li t ti li t ti (n=2173) (n=816) l t l t li t t li t t p ta e p ta e p ta e p ta e G p a e p a e l l u l u l ut l ut l UBE2L3 m u e m u e m e m e e m e m e A M D A M D A M D A M D G
n
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) METABRIC TCGA RAD18 5 ) HIST1H2BN UBA52 HIST1HV2HBL n=2173 n=816 0 PCNA 0 HIST1SHE2NBPO8 HIST1H2BM HLA0A RNNEFD1D881 RRAGA HISTU1HC2HBLK3 PAF1 HIST1H2BJ UBE2H PPEUXM120 SHPRH UBEU2BED1 BCL10 PEX13 UILB3E12RJA2 VCP UCBCED2CD83 UBE2R2 CDCUCL354 HIST1H2BA UBE2E3 WDR61 URBBEX2B1 HIST1H2BB NUABEC1 TMEM129 CTR9 UOSBPS9LX1 RNF152 MUYBEO2GV21 HLA0B RNF20 UBA3 HIST1H2BC RTF1 UBE2D1 UBE2FK PEX14 UBE2Q2 ILU17SR1B1 HIST1H2BD OTUSLAIGN UCHL3 HIST1H2BH METABRIC TCGA UBE2A (n=2173) (n=816) UBE2L3 UBA1 UBE2N LEO1 UBB RPS27A UBE2D2 UBA6 HIST1H2BN HIST1H2BL HIST1H2BO HIST1H2BM RNF181 HIST1H2BK HIST1H2BJ PEX10 UBE2E1 BCL10 Suppl Figure 1 UBE2J2 UBE2D3 CDC34 UBE2E3 UBE2B UBC TMEM129 USP9X UBE2G1 RNF20 RTF1 UBE2K PEX14 US11 OTULIN (a) (b) (c)
p=1.07 E-01 p=7.97 E-04 p=8.28 E-03
p=2.79 E-01 p=1.12 E-04 p=8.31 E-01
p=8.82 E-02 p=3.04 E-06 p=1 E-12
p=3.092 E-01 p=2.01 E-02 p=9.44 E-01
Suppl Figure 2 (a) USP9X mutation signature USP7 mutation signature 5 5
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l - - 1 Downregulated 1 Downregulated Upregulated Upregulated 0 0 -4 -2 0 2 4 -6 -4 -2 0 2 4 Fold Change Fold Change
(b) USP9X mutation USP7 mutation
NGFR LOC401431 IGFBP6 PLEKHH2 BNIPL CDCA7 IQCA1 GABRP CCDC8 LASS2 APBB1 SSH3 PHYHD1 SNHG1 FES KIAA1257 COL16A1 LGR6 HIC1 SATB1 PNMAL2 SNHG12 IGFBP4 C20ORF54 OPRL1 GABBR1 SCD ZNF767 FAM176B CCT6P1 Total Total 0 1 2 0 1 2 HR RFS HR RFS
Suppl Figure 3 UBE2C log2(TPM+1) UBE2C log2(TPM+1) BIRC5 log2(TPM+1) UBE2C log2(TPM+1) BIRC5 log2(TPM+1) UBE2C log2(TPM+1)
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Chemotherapy - Luminal Endocrine therapy - Luminal
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BIRC5 log2(TPM+1) BIRC5 log2(TPM+1) BIRC5 log2(TPM+1) UBE2C log2(TPM+1) BIRC5 log2(TPM+1) UBE2C log2(TPM+1)
1
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0 0 UBE2C log2(TPM+1)
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2 UB0 E2C UBE2C BIRC5 log2(TPM+1) UBE2C BIRC5 log2(TPM+1) log2(TPM+1) 0 log2(TPM+1) log2(TPM+1)
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. BIRC5 logB2IR(TCP5Mllo+g12) (TPM+1) BIRC5 lo. gB2IIR(TCP5Mllo+g12) (TPM+1) BIRC5 logB2IIR(TCP5Mllo+g12) ((TPM+1)) UBE2C loUgB2E(T2PCMllo+g12) ((TPM+1)) BIRC5 logB2IIR(TCP55Mllo+og1g2)2((TTPM++11)) UBE2C loUgB2BE(ET22PCMllo+og1g2)2((TTPPM++11))
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0 BIRC5 log2(TPM+1) BIRC5 log2(TPM+1) BIRC5 log2(TPM+1) 0 UBE2C log2(TPM+1) BIRC5 log2(TPM+1) UBE2C log2(TPM+1)
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5 (a)
SUMO2 TCEB2 BIRC5 UBE2T DERL1 PRKDC UBE2C HR RFS 0.77 (0.61-0.98 0.82 (0.63-1.07) 1.7 (1.34-2.16) 1.7 (1.35-2.16) 1.42 (1.11-1.82) 1.4 (1.11-1.78) 1.95 (1.53-2.48) METABRIC p p=0.034 p=0.14 p=7.8e-06 p=7.5e-06 p=0.0057 p=0.0045 p=4.4e-08 FDR >50% 100% 2% 1% >50% >50% 1% ALL HR RFS 0.67 (0.44-1.03) 1.46 (0.95-2.26) 1.82 (1.18-2.8) 2.36 (1.4-3.99) 2.26 (1.33-3.86) 1.58 (1.03-2.44) 2.15 (1.38-3.36) TCGA p p=0.069 p=0.085 p=0.0058 p=0.00087 p=0.002 p=0.036 p=0.00054 FDR 100% 100% >50% 20% >50% >50% 5%
(b)
Clinical-Pathological TCGA METABRIC features Patient (n) 928 1976 Mean age (Q2-Q3) 58.1 (49.0-67.0) 61.1 (51.5-70.6) Nodal status positive 422 (47%) 935 (47%) negative 481 (53%) 1035 (53%) Tumor size (mm) - 26.1 (17-30) HER2 status positive 288 (31%) 245 (12.4%) negative 639 (69%) 1731 (87.6%) Molecular subtype (PAM50) Basal 162 (17.5%) 328 (16.6%) Luminal A 401 (43.2%) 718 (36.3%) Luminal B 277 (30%) 487 (24.6%) HER2 enriched 78 (8.5%) 238 (12%) Normal-like 10 (1%) 199 (10.1%) Survival follow-up (mo) 39.1 (14.7-53.5) 117.1 (51.4-175.5) Stage I 167 (18%) 501 (25.3%) II 541 (59%) 824 (41.7%) III 209 (23%) 117 (6%) IV 0 10 (0.5%)
(c)
ALL N+ N- G3 G1 HR RFS 1.26 (1.13-1.41) 1.32 (1.07-1.62) 0.88 (0.72-1.08) 0.97 (0.78-1.2) 0.61 (0.36-1.04) SUMO2 p p=3.06e-5 p=0.0089 p=0.23 p=0.76 p=0.065 FDR 1% >50% 100% 100% 100% HR RFS 1.32 (1.18-1.48) 0.5 (0.17-1.45) 0.6 (0.31-1.16) 1.35 (1.05-1.74) 0.63 (0.37-1.06) TCEB2 p p=7.4e-7 p=0.19 p=0.13 p=0.02 p=0.08 FDR 1% 100% 100% >50% 100% HR RFS 1.55 (1.36-1.76) 1.64 (1.34-2) 1.57 (1.3-1.89) 0.78 (0.62-0.98) 2.22 (1.31-3.76) BIRC5 p p=9.4e-12 p=8.9e-07 p=2.9e-06 p=0.036 p=0.0022 FDR 1% 1% 1% >50% 50% HR RFS 2.21 (1.89-2.59) 1.82 (1.38-2.39) 1.94 (1.28-2.92) 0.68 (0.47-0.98) 2.72 (0.61-12.15) UBE2T p p<1e-16 p=1.6e-05 p=0.0013 p=0.04 p=0.17 FDR 1% 1% 20% >50% 100% HR RFS 1.31 (1.12-1.54) 1.55 (1.2-1.99) 1.47 (1-2.15) 1.43 (1.03-1.99) 3.97 (0.52-30.32) DERL1 p p=0.00072 P=0.00069 p=0.05 p=0.032 p=0.15 FDR 10% 20% >50% >50% 100% HR RFS 1.38 (1.23-1.56) 0.79 (0.65-0.96) 1.34 (1.12-1.61) 1.19 (0.94-1.51) 0.53 (0.31-0.89) PRKDC p p=4.9e-8 p=0.017 p=0.0017 p=0.15 p=0.015 FDR 1% >50% 50% 100% >50% HR RFS 1.82 (1.63-2.04) 2.25 (1.75-2.9) 1.91 (1.6-2.27) 0.91 (0.73-1.13) 2.51 (1.49-4.21) UBE2C p p<1e-16 p=7.4e-11 p=2.8e-13 p=0.39 p=0.00032 FDR 1% 1% 1% 100% 5%
Suppl Table 1 LUM A LUM B BASAL UBE2T UBE2C BIRC5 UBE2T UBE2C UBE2T HR RFS 1.5 (1-2.27) 1.66 (1.1-2.49) 1.75 (1.12-2.74) 1.73 (1.18-2.56) 2.08 (1.42-3.04) 1.56 (0.89-2.73) METABRIC p p=0.05 p=0.014 p=0.013 p=0.0049 p=0.00013 p=0.12 FDR 100% >50% >50% >50% 10% 100% HR RFS 3.01 (1.46-6.23) 3.45 (1.64-7.28) 2.6 (1.25-5.4) 5.86 (0.78-43.75) 2.99 (0.88-10.16) 0.42 (0.14-1.24) TCGA p p=0.0018 p=0.00053 p=0.0081 p=0.051 p=0.065 p=0.11 FDR 50% >10% >50% >100% 100% 100%
Suppl Table 2 Gene Variation Consequence SIFT PolyPhen MutationTaster FATHMM-MKL CLINVAR ENST00000344836.4:c.3011G>A missense deleterious probably damaging disease causing damaging NR ENST00000344836.4:c.2941G>C missense tolerated benign disease causing damaging NR ENST00000344836.4:c.1861C>T stop NR NR disease causing damaging NR USP7 ENST00000344836.4:c.1223G>A missense deleterious probably damaging disease causing damaging NR ENST00000344836.4:c.556G>A missense tolerated benign disease causing damaging NR ENST00000344836.4:c.230G>A missense tolerated benign disease causing damaging NR ENST00000324545.8:c.273_274del frameshift NR. Expected deleterious NR ENST00000324545.8:c.283G>C missense deleterious probably damaging disease causing damaging NR ENST00000324545.8:c.1969C>T missense deleterious probably damaging disease causing damaging NR ENST00000324545.8:c.2084_2090del frameshift NR. Expected deleterious NR ENST00000324545.8:c.2225G>A missense deleterious probably damaging disease causing damaging NR ENST00000324545.8:c.2248C>T stop NR NR disease causing damaging NR ENST00000324545.8:c.3479C>G missense tolerated benign disease causing damaging NR USP9X ENST00000324545.8:c.3805G>C missense tolerated benign disease causing damaging NR ENST00000324545.8:c.3876G>A missense deleterious benign disease causing damaging NR ENST00000324545.8:c.3894G>C missense deleterious probably damaging disease causing damaging NR ENST00000324545.8:c.4104_4105del frameshift NR. Expected deleterious NR ENST00000324545.8:c.5331+1G>A splice donor NR. Unknown NR ENST00000324545.8:c.5800A>C missense tolerated benign disease causing damaging NR ENST00000324545.8:c.6586C>G missense deleterious probably damaging disease causing damaging NR
Suppl Table 3 Amplification Mutation Cell line Int Sub UBE2T UBE2C BIRC5 USP9X USP7 HCC1428 LA CAL-120 TN HCC1500 Incons MDA-MB-436 TN HCC1187 TN MDA-MB-157 TN HCC38 TN MDA-MB-231 TN CAMA-1 LA BT-549 TN MRK-nu-1 none HCC1419 Incons MDA-MB-468 TN HCC1937 TN MDA-MB-415 LA BT-483 LA DU-4475 TN HCC1395 TN EVSA-T Incons HCC2218 HER2 CAL-51 TN HCC70 TN CAL-85-1 TN JIMT-1 HER2 MFM-223 TN ZR-75-30 LB HCC2157 TN HCC1143 TN HDQ-P1 TN COLO-824 none UACC-812 LB Hs-578-T TN MCF7 LA EFM-192A LB AU565 HER2 HCC1569 HER2 MDA-MB-175-VII LA BT-474 LB T47D LA HCC1599 TN HCC1954 HER2 EFM-19 LA BT-20 TN CAL-148 TN UACC-893 HER2 MDA-MB-453 TN OCUB-M none MDA-MB-330 LB MDA-MB-361 LB
Suppl Table 4