supplementary figure 1a. r 2 = 0.9694 p < 0.0001 qrt-pcr illumina beadchip supplementary figure...
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Control Trastuzumab Pertuzumab Combination0
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Control Trastuzumab Pertuzumab Combination0
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Control Trastuzumab Pertuzumab Combination0.0
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Supplementary Figure 1A
R2 = 0.9694 p < 0.0001
qRT-PCR
Illu
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Supplementary Figure 1B
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Trastuzumab Pertuzumab Combination PCNA(ILMN_1706958) 1.03 1.03 -1.03 DNA ReplicationUBE2C(ILMN_1742958) -1.04 -1.07 1.04 Cell cycle, mitosisCKS2(ILMN_1756326) -1.13 1.07 -1.08 Cell cycleCKS2(ILMN_2072296) -1.07 1.02 1.05 Cell cycleTYMS(ILMN_1806040) -1.22* 1.00 -1.04 DNA replicationFEN1(ILMN_2160929) -1.21* -1.05 -1.09 DNA repair and synthesisFEN1(ILMN_1755834) -1.16* 1.01 -1.13* DNA repair and synthesisZWINT(ILMN_1653209) -1.13* -1.08 -1.06 Cell cycle, spindleRFC4(ILMN_2370365) -1.17* -1.03 -1.08 DNA replication and repairUBE2C(ILMN_2265654) -1.17* -1.06 1.01 Cell cycle, mitosisTOP2A(ILMN_1686097) -1.12 -1.04 1.06 DNA replicationAURKA(ILMN_2357438 STK6) -1.20* -1.13 1.00 Cell cycle, spindleAURKA(ILMN_1680955 STK5) -1.18 -1.06 -1.02 Cell cycle, spindleZWINT(ILMN_2362549) -1.09 -1.07 1.05 Cell cycle, spindleHMGB2(ILMN_1654268) -1.14 -1.14* 1.05 ChromatinHMGB2(ILMN_2219712) -1.21 -1.13 1.09 ChromatinSPAG5(ILMN_2141259 DEEPEST) -1.21* -1.08 -1.03 Cell cyclePCNA(ILMN_1694177) -1.13 -1.05 -1.11 DNA ReplicationBUB1B(ILMN_1797307 MAD3L) -1.19* -1.13* -1.14* Cell cycle, mitosisRFC4(ILMN_1724489) -1.17* -1.10* -1.10* DNA replication and repairNDC80(ILMN_1664511 HEC) -1.17 -1.10 -1.05 Cell cycle spindleUBE2C(ILMN_1714730) -1.16 1.03 1.05 Cell cycle, mitosisUBE2C(ILMN_2301083) -1.12 1.02 1.09 Cell cycle, mitosisZWINT(ILMN_2362545) -1.10 -1.07 1.08 Cell cycle, spindleGINS1(ILMN_1697751 KIAA0186) -1.07 1.01 -1.12 UnknownZWINT(ILMN_1673117) -1.00 -1.01 -1.02 Cell cycle, spindlePCNA(ILMN_1685682) 1.05 -1.01 -1.05 DNA ReplicationPHLDA2(ILMN_1671557) 1.08 1.13 1.40* Fas expressionHIST1H4C(ILMN_2075334 H4FG) 1.01 1.08 -1.00 Chromatin
CCNG2(ILMN_1747244) 1.15* -1.08 1.05CCNG2(ILMN_2228732) 1.05 -1.22* -1.01
Trastuzumab Pertuzumab Combined
Supplementary Figure 2A
Trastuzumab Pertuzumab Combination HER2+ breast
cancer patients KIAA1549(ILMN_1728060) -1.02 1.01 -1.01 Higher in pCRPSMD11(ILMN_1800952) -1.21 1.03 -1.03 Higher in non-pCRSYNCRIP(ILMN_1727740) -1.11* -1.00 -1.11 Higher in pCRLAMA3(ILMN_2293594) -1.07* -1.03 -1.04 Higher in non-pCRGRHL2(ILMN_2060145) -1.03 -1.01 1.02 Higher in pCRP2RX1(ILMN_1758529) -1.04 -1.03 -1.03 Higher in non-pCRSENP7(ILMN_1778294) -1.03 -1.06 -1.00 Higher in pCRPRKACA(ILMN_1786195) -1.07 -1.05 -1.02 Higher in non-pCRDERL1(ILMN_2209748) -1.01 -1.01 -1.02 Higher in non-pCRPPP2CA(ILMN_2196097) 1.02 -1.01 1.01 Higher in non-pCRSENP7(ILMN_2382354) 1.05 -1.25* 1.03 Higher in pCRCDC14A(ILMN_1774930) -1.06 -1.05 1.01 Higher in non-pCRSENP8(ILMN_1767690) -1.01 -1.01 -1.08 Higher in non-pCRWEE1(ILMN_1778561) -1.06* -1.04 1.00 Higher in pCRCDC14A(ILMN_2244653) -1.09* -1.08 -1.06 Higher in non-pCRPEX19(ILMN_1658759) -1.05 -1.05 -1.10 Higher in non-pCRZNF146(ILMN_2054442) -1.02 -1.19* -1.19* Higher in pCRCCDC123(ILMN_1679971) -1.11* -1.10* -1.14* Higher in pCRC5orf3(ILMN_1675701) -1.10* -1.08 -1.11 Higher in non-pCRPPP2CA(ILMN_1722858) -1.05 -1.03 -1.03 Higher in non-pCRSLC30A6(ILMN_1699365) -1.08 -1.05 -1.10 Higher in non-pCRCDC14A(ILMN_1655983) -1.02 -1.03 -1.02 Higher in non-pCRLAMA3(ILMN_1704247) 1.00 1.17* -1.18* Higher in non-pCRLAMA3(ILMN_2406035) 1.31 1.47* -1.54* Higher in non-pCRLAMA3(ILMN_1688892) 1.16 1.34* -1.44* Higher in non-pCRSTX1A(ILMN_1760160) 1.04 -1.00 -1.04 Higher in pCRCDC14A(ILMN_2324537) -1.01 1.02 -1.01 Higher in non-pCRFLJ20160(ILMN_1710209) 1.01 1.03 1.24* Higher in non-pCRCDC14A(ILMN_1774557) 1.02 1.09* 1.01 Higher in non-pCRPITPNA(ILMN_1715804) 1.02 1.03 1.05 Higher in non-pCRCTNS(ILMN_1807719) -1.02 1.09 1.12 Higher in non-pCRSLC35A4(ILMN_2105966) 1.02 1.13 1.14 Higher in non-pCRNFE2L1(ILMN_1739450) 1.05 1.03 1.19 Higher in non-pCRZNF146(ILMN_1699423) 1.04 1.01 1.02 Higher in pCRGPR22(ILMN_1684865) 1.12 1.16* 1.11* Higher in pCRCDC14A(ILMN_1739164) 1.11* 1.04 1.03 Higher in non-pCRCTNS(ILMN_1738010) -1.02 1.04 1.05 Higher in non-pCRPRKACA(ILMN_2395314) 1.03 -1.03 1.02 Higher in non-pCRCTNS(ILMN_1776132) 1.02 -1.03 1.03 Higher in non-pCRSLC30A6(ILMN_2151168) 1.02 1.00 1.06 Higher in pCR
Trastuzumab Pertuzumab Combined
Supplementary Figure 2B
Either HER2-inhibitor alone
Trastuzumab alone AND combination
Combination only
Trastuzumab alone
Pertuzumab alone
Control Trastuzumab Pertuzumab Combined
JUN, JUP
DST, CDKN1A, CLIC6
JUN, SERPIN-A1/B5, MMP13, KRT-6A/16/7, ANXA8, PAK6
KRT5, ERBB3, CDH1, FOXO1LCN2, KLK11
CD9, KRT14
CD36, CD36, CASP1
NRG4
PAK1
LAMA3FOS, DUSP1, SNAI2
IL4R, CCL26, GADD45
CAV2, JAG1
IL8, IL8
TGFBI, SPARCCDH6, CAV1, CXCL1LAMC2, LAMC2
IL6, IL15
GSTA1, GSTA2ESR1
CDH17
TFF2, TFF3
Supplementary Figure 2C
Pertuzumab alone AND combination
Data from Ghosh et al. (2010) Cancer Research 71:1871-1882
Both HER2 inhibitors AND combination
Co
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1C
on
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Co
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2A
P15
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AP
1510
.2A
P15
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Her
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.1H
ereg
uli
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Her
egu
lin
.3T
GF
alp
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1T
GF
alp
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2T
GF
alp
ha.
3
Control Trastuzumab Pertuzumab Combined
HE
R2-
HE
R2
HE
R3-
HE
R2
HE
R1-
HE
R2
Homo- or Heterodimers
Control Trastuzumab Pertuzumab Combined
Supplementary Figure 2D
Heatmap from Ghosh et al. (2010) Cancer Research 71:1871-1882
Co
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1C
on
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Co
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P15
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AP
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.2A
P15
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Her
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.1H
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uli
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Her
egu
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.3T
GF
alp
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1T
GF
alp
ha.
2T
GF
alp
ha.
3
HE
R2-
HE
R2
HE
R3-
HE
R2
HE
R1-
HE
R2
Homo- or Heterodimers
SKOV3 (2.15) HOX486 (0.89) HOX516 (1.2)
HOX424 (7.75) OV1002 (0.94) HOX493 (0.575)
Supplementary Figure 3