Complete list of LC-MS myc interating protiens in the MCF7 cells, proteins highlighted in red are those differentially expressed from the LCC1 and LCC1 EGF treated cells.

Supplemental Table S1

MCF7 Identifier Uniprot Acc code Mr No. of pepides Log (e)

Band No.

4F2 cell-surface antigen heavy chain (4F2hc) ENSP00000367124 P08195 71.1 1 -2.3 1

78 kDa glucose-regulated protein precursor (GRP 78) ENSP00000324173 P11021 72.3 3 -15.2 1

Actin-like protein (Fragment) ENSP00000306469 Q562S9 42.0 1 -1.7 1

actin-like protein Source: RefSeq_peptide NP_001017421 ENSP00000365045 n/a 42.0 1 -6.5 1

Alpha enulase   ENSP00000234590 P06733 47.1 1 -3.3 1

Alpha-actinin 4 (F-actin cross linking protein)   ENSP00000252699 O43707 104.8 4 -22.1 1

Annexin A2 (Annexin II)   ENSP00000348640 n/a 38.6 1 -1.9 2

Antileukoproteinase 1 precursor (ALP) ENSP00000342082 P03973 14.3 1 -4.5 2

Apolipoprotein E precursor (Apo-E).   ENSP00000252486 P02649 36.1 1 -1.4 3

BA13B9.3 (NOVEL PROTEIN SIMILAR TO KRT8) ENSP00000334513 n/a 55.1 2 -7.4 1

Beta-catenin (PRO2286)  ENSP00000344456 P35222 85.4 1 -1.6 8

Clathrin heavy chain 1 ENSP00000269122 Q00610 191.5 1 -2.8 1

Cytokeratin type II.   ENSP00000252245 O95678 59.5 3 -17.8 1

Desmoplakin ENSP00000369129 P15924 331.6 1 -1.3 6

Fatty acid synthase ENSP00000363777 P49327 277.3 3 -28.1 1

Filamin B (FLN-B) (Beta-filamin)   ENSP00000349819 O75369 230.7 2 -11.9 1

Filamin-A (Alpha-filamin) (Filamin-1) ENSP00000353467 P21333 279.8 1 -5.3 1

Fructose-bisphospate aldolasea ENSP00000336927 P04075 39.4 1 -7.4 1

Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH)   ENSP00000229239 P04406 36.0 3 -24.1 1

Heat shock 70 kDa ENSP00000364805 P34931 70.3 5 -36.6 1

Heat shock 70 kDa protein 1 ENSP00000364802 P08107 70.0 8 -62.6 2

Heat shock cognate 71 kDa protein   ENSP00000227378 P11142 70.0 5 -40.3 1

Heat shock protein HSP 90beta   ENSP00000325875 P08238 83.2 3 -22.7 6

Histone H2B.f (H2B/f) (H2B.1).   ENSP00000350580 P33778 13.9 1 -7.7 4

Histone H4 ENSP00000352980 P62805 11.4 1 -3.3 4

Ig alpha-1 chain C region ENSP00000372520 P01876 59.0 1 -3.5 2

Junction plakoglobin (Desmoplakin III).   ENSP00000311113 P14923 16.5 1 -5.7 2

K0256 Isoform 2 ENSP00000261847 Q93073 116.5 1 -1.6 8

Keratinocyte proline-rich protein (hKPRP) ENSP00000357762 Q5T749 64.1 1 -2.7 8

Lipin-3 (Lipin 3-like) ENSP00000362356 Q9BQK8 38.0 1 -1.2 8

L-lactate dehydrogenase B chain  ENSP00000229319 P07195 36.6 1 -4.9 6

Lysozyme C precursor  ENSP00000261267 P61626 16.5 1 -5.7 2

Malate dehydrogenase, mitochondrial precursor ENSP00000327070 P40926 35.5 2 -10.0 1

Nuclear receptor corepressor 2 (N-CoR2) (SMRT) (SMRTe) ENSP00000348551 Q9Y618 274.4 1 -2.6 7

Predicted: similar to 60S ribosomal protein ENSP00000349185 n/a 29.6 1 -4.0 2

Protein disulfide-isomerase A3 precursor ENSP00000300289 P30101 56.7 1 -2.1 2

Puromycin-sensitive aminopeptidase(PSA) ENSP00000320324 P55786 103.2 1 -4.3 1

Pyruvate kinase, isozymes M1/M2 ENSP00000320171 P14618 58.0 2 -9.1 1

Receptor tyrosine-protein kinase erbB-4 precursor   ENSP00000342235 Q15303 146.7 1 -1.1 1

Stress-70protein, mitochondrial precursor  ENSP00000297185 P38646 73.6 2 -9.8 1

Transkeltolase   ENSP00000296289 B4E022 67.8 1 -4.0 1

type I hair keratin KA35   ENSP00000347823 Q6A163 55.6 1 -5.6 4

Ubiquitin-activating enzyme E1 ENSP00000366568 P22314 117.8 1 -1.3 1

Supplemental Table S2

Complete list of LC-MS myc interating protiens in the LCC1 cells, proteins highlighted in red are those differentially expressed from the LCC1 EGF and MCF7 cells

LCC1 Identifier Uniprot Acc code Mr No. of pepides Log (e) Band No.26 kDa protein ENSP00000342026 P30041 25.0 1 -11.0 7

Actin,(alpha-actin 2) ENSP00000224784 P62736 42.0 2 -11.9 5Actin-like protein (Fragment) ENSP00000306469 Q562S9 42.0 2 -16.6 5Alpha enulase ENSP00000234590 P06733 47.1 1 -5.1 1Apolipoprotein E precursor (Apo-E). ENSP00000252486 P02649 36.1 1 -1.3 3BA13B9.3 (novel protein similar to KRT8). ENSP00000334513 n/a 55.1 2 -8.5 1Dermcidin precursor (Preproteolysin) ENSP00000293371 P81605 11.3 1 -1.6 3Fatty acid synthase ENSP00000363777 P49327 277.3 2 -16.7 1Filamin B (FLN-B) (Beta-filamin) ENSP00000349819 O75369 230.7 1 -6.5 1Filamin-A (Alpha-filamin) (Filamin-1) ENSP00000353467 P21333 279.8 2 -8.6 1Fructose-bisphospate aldolasea ENSP00000336927 P04075 39.4 1 -2.6 1Glutathione S-transferase Mu 3 ENSP00000256594 P21266 26.5 1 -2.0 7

Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH). ENSP00000229239 P04406 36.0 1 -4.1 1Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2) ENSP00000364802 P08107 70.0 4 -30.3 1Heat shock 70 kDa protein 1L ENSP00000364805 P34931 70.3 1 -3.2 2Heat shock cognate 71 kDa protein ENSP00000227378 P11142 70.9 4 -27.0 1Heat shock protein HSP 90beta ENSP00000335153 P07900 98.1 1 -11.6 7

Heterogeneous nuclear ribonucleoproteins A2/B1 ENSP00000349101 P22626 28.4 1 -3.6 7

Histone H2B.f (H2B/f) (H2B.1). ENSP00000350580 P33778 13.9 1 -1.5 6

Junction plakoglobin (Desmoplakin III). ENSP00000311113 P14923 81.7 1 -3.9 7

L-lactate dehydrogenase B chain ENSP00000229319 P07195 36.6 1 -4.3 7

Malate dehydrogenase, mitochondrial precursor ENSP00000327070 P40926 35.5 1 -3.0 1Nesprin 2 (Nuclear envelope spectrin repeat protein 2) (Syne-2) ENSP00000350719 Q8WXH0 798.4 1 -1.6 7

Peptidyl-prolyl cis-trans isomerase A ENSP00000358255 P62937 17.9 1 -1.3 7

Peroxiredoxin 2 ENSP00000301522 P32119 21.9 1 -3.0 7

Phosphatidylethanolamine-binding proteinPEBP) ENSP00000261313 P30086 21.0 1 -1.5 5

Poly [ADP-ribose] polymerase 4 ENSP00000371419 Q9UKK3 192.5 1 -1.2 4Predicted: similar to 60S ribosomal protein L7 ENSP00000349185 n/a 29.6 1 -1.2 1

Probable ATP-dependent RNA helicase DDX4 ENSP00000334167 Q9NQI0 75.8 1 -1.1 6

Pyruvate kinase, isozymes M1/M2 ENSP00000320171 P14618 58.0 1 -4.2 1Ras-related protein Rab-10 ENSP00000370062 P61026 22.5 1 -2.4 7

Ras-related protein Rab-1A (YPT1-related protein). ENSP00000260638 E7ETK2 22.4 1 -2.4 7

rhomboid, veinlet-like 6 isoform 2 ENSP00000322775 Q6PJF5 96.5 2 -6.1 1Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) ENSP00000361824 Q13813 284.9 2 -2.5 1Stress-70protein, mitochondrial precursor ENSP00000297185 P38646 73.6 1 -1.6 3

Transkeltolase ENSP00000321259 P37837 37.5 1 -1.4 5

Triosephosphate isomerase ENSP00000229270 P60174 26.7 5 -49.6 7

Tubulin--tyrosine ligase-like protein 3 ENSP00000373339 Q9Y4R7 17.1 1 -2.0 7

Supplemental Table S3

Complete list of LC-MS myc interating protiens in the LCC1 EGF treated cells, proteins highlighted in red are those differentially expressed from the LCC1 and MCF7 cells

LCC1 EGF Identifier Uniprot Acc code Mr No. of pepides Log (e) Band No.60S ribosomal protein L18. ENSP00000084795 Q07020 21.6 1 -7.4 1Actin, cytoplasmic 1 (Beta-actin). ENSP00000349960 P60709 41.7 1 -3.7 1ALPHA ENOLASE ENSP00000234590 P06733 47.1 1 -4.4 1Alpha-actinin 4 (F-actin cross linking protein) ENSP00000252699 O43707 104.8 1 -1.5 1Beta-catenin ENSP00000344456 P35222 85.4 1 -1.5 2Dermcidin precursor (Preproteolysin) ENSP00000293371 P81605 11.3 1 -1.2 1Desmocollin 1A/1B precursor (Desmosomal glycoprotein 2/3) ENSP00000257197 Q08554 93.8 1 -1.4 4DJ14N1.2 (Novel S-100/ICaBP type calcium binding domain protein ENSP00000271816 n/a 247.9 1 -3.7 5E3 ubiquitin-protein ligase ENSP00000361994 Q8IWV8 49.9 1 -1.3 2Fatty acid synthase (EC 2.3.1.85) ENSP00000363777 P49327 277.3 2 -12.3 1Fatty acid synthase (EC 2.3.1.85) ENSP00000363777 P49327 277.3 2 -8.3 2Filamin B (FLN-B) (Beta-filamin) ENSP00000349819 O75369 230.7 6 -53.4 1Filamin-A (Alpha-filamin) (Filamin-1) ENSP00000353467 P21333 279.8 5 -40.3 1Fructose-1,6-bisphosphatase ENSP00000253266 P09467 36.8 1 -2.7 1Fructose-bisphospate aldolasea ENSP00000336927 P04075 39.4 1 -7.1 1Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH). ENSP00000229239 P04406 36.0 1 -3.3 5Glycogen phosphorylase, muscle form ENSP00000366663 P11217 97.0 5 -37.6 2Glycogen phosphorylase, muscle form ENSP00000366663 P11217 97.0 4 -24.8 1Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2) ENSP00000364802 P08107 70.0 3 -20.0 1Histone H2B.f ENSP00000350580 P33778 13.9 1 -3.3 3Histone H4. ENSP00000352980 P62805 11.4 1 -1.8 3Junction plakoglobin (Desmoplakin III). ENSP00000311113 P14923 81.7 1 -1.3 5

Keratin type II cytoskeletal cytokeratin ENSP00000257935 n/a 38.5 10 -67.1 4Keratinocyte proline-rich protein (hKPRP). ENSP00000357762 Q5T749 64.1 3 -9.1 5Myosin heavy chain, skeletal muscle, adult 1 ENSP00000226207 P12882 223.0 1 -3.4 1

Poly [ADP-ribose] polymerase 4 ENSP00000371419 Q9UKK3 192.5 1 -1.4 1predicted: similar to 60S ribosomal protein L7 ENSP00000349185 n/a 29.6 1 -2.8 1Probable RNA-dependent helicase P72 (DEAD-BOX PROTEIN 17) ENSP00000216019 Q92841 80.2 1 -1.3 3Pyruvate kinase, isozymes M1/M2 ENSP00000320171 P14618 58.0 1 -1.5 1

similar to ribosomal protein S2; 40S ribosomal protein S2 ENSP00000317418 n/a 31.5 1 -1.9 1Stress-70 protein, mitochondrial precursor ENSP00000297185 P38646 73.6 2 -7.9 1

Triosephosphate isomerase ENSP00000334713 P00938 26.9 1 -3.7 4

WD repeat protein 60 ENSP00000309252 Q8WVS4 122.3 1 -1.3 1

Supplemental Table S4

Clinical trials examining the potential benefit of trastuzumab in Her2 low/Her2 negative breast cancer patients

Trial Number Trial Name Traget Group of Patients Agents End Point Result

NCT01275677

Chemotherapy With or Without Trastuzumab After Surgery in Treating Women With Invasive Breast Cancer

Her2 Low (1+, 2+ not FISH ratio <2)trastuzumab, doxorubicin, doxitaxel, cyclophosphamide, pacitaxel ongoing n/a

NCT00944047

Abraxane and Trastuzumab Followed by Dose Dense Doxorubicin and Cyclophosphamide as Neoadjuvant Therapy in Invasive Breast Cancer With Low HER2 Expression (1+ or 2+ by IHC)

T2-4, N1,N0. Her2 Low (1+, 2+ FISH ratio <2.2)

trastuzumab, Nab-paclitaxel, doxorubicin, cyclophosphamide ongoing n/a

NCT01570036

Combination Immunotherapy With Herceptin and the HER2 Vaccine NeuVax

T2-4, N1,N0. Her2 Low (1+, 2+ FISH ratio <2.2) trastuzumab, NeuVax, GM-CSF ongoing n/a

NCT01779050

A Phase II Randomized Trial Evaluating the Effect of Trastuzumab on Disease Free Survival in Early Stage HER2-Negative Breast Cancer Patients With ERBB2 Expressing Bone Marrow Disseminated Tumor Cells Her2 0, 1+ or 2+ (FISH not amplified)

trastuzumab, doxorubicin, cyclophosphamide, paclitaxel Not yet started n/a

NCT00351858

Phase II Study of the Trifunctional Anti-HER-2/Neu x Anti-CD3 Antibody Ertumaxomab for Hormone Therapy Refractory Patients With Her-2/Neu 1+ or 2+ Expressing Advanced or Metastatic Breast Cancer Her2 0, 1+ or 2+ (FISH not amplified) ertumaxomab terminated n/a

LPS study

An open-label study of lapatinib in women with HER-2-negative early breast cancer: the lapatinib pre-surgical study (LPS study). Her2 0, 1+ or 2+ lapatinib completed

Primary end point showed no signi?cant reduction in Ki67 with treatment. Lapatinib monotherapy had little effect on this cohort of patients (R. C. Coombes et al )