Transcript Supplementary Tables 1–4 (ppt 528K)

Supplemental Table S1
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.
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
26 kDa protein
Actin,(alpha-actin 2)
Actin-like protein (Fragment)
Alpha enulase
Apolipoprotein E precursor (Apo-E).
BA13B9.3 (novel protein similar to KRT8).
Dermcidin precursor (Preproteolysin)
Fatty acid synthase
Filamin B (FLN-B) (Beta-filamin)
Filamin-A (Alpha-filamin) (Filamin-1)
Fructose-bisphospate aldolasea
Glutathione S-transferase Mu 3
Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH).
Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2)
Heat shock 70 kDa protein 1L
Heat shock cognate 71 kDa protein
Heat shock protein HSP 90beta
Heterogeneous nuclear ribonucleoproteins A2/B1
Histone H2B.f (H2B/f) (H2B.1).
Junction plakoglobin (Desmoplakin III).
L-lactate dehydrogenase B chain
Malate dehydrogenase, mitochondrial precursor
Nesprin 2 (Nuclear envelope spectrin repeat protein 2) (Syne-2)
Peptidyl-prolyl cis-trans isomerase A
Peroxiredoxin 2
Phosphatidylethanolamine-binding proteinPEBP)
Poly [ADP-ribose] polymerase 4
Predicted: similar to 60S ribosomal protein L7
Probable ATP-dependent RNA helicase DDX4
Pyruvate kinase, isozymes M1/M2
Ras-related protein Rab-10
Ras-related protein Rab-1A (YPT1-related protein).
rhomboid, veinlet-like 6 isoform 2
Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain)
Stress-70protein, mitochondrial precursor
Transkeltolase
Triosephosphate isomerase
Tubulin--tyrosine ligase-like protein 3
Identifier
Uniprot Acc code
ENSP00000342026
P30041
ENSP00000224784
P62736
ENSP00000306469
Q562S9
ENSP00000234590
P06733
ENSP00000252486
P02649
ENSP00000334513
n/a
ENSP00000293371
P81605
ENSP00000363777
P49327
ENSP00000349819
O75369
ENSP00000353467
P21333
ENSP00000336927
P04075
ENSP00000256594
P21266
ENSP00000229239
P04406
ENSP00000364802
P08107
ENSP00000364805
P34931
ENSP00000227378
P11142
ENSP00000335153
P07900
ENSP00000349101
ENSP00000350580
ENSP00000311113
ENSP00000229319
P22626
P33778
P14923
P07195
ENSP00000327070
P40926
ENSP00000350719
Q8WXH0
ENSP00000358255
ENSP00000301522
P62937
P32119
ENSP00000261313
P30086
ENSP00000371419
Q9UKK3
ENSP00000349185
n/a
ENSP00000334167
Q9NQI0
ENSP00000320171
P14618
ENSP00000370062
P61026
ENSP00000260638
E7ETK2
ENSP00000322775
Q6PJF5
ENSP00000361824
Q13813
ENSP00000297185
P38646
ENSP00000321259
P37837
ENSP00000229270
P60174
ENSP00000373339
Q9Y4R7
Mr
No. of pepides
Log (e)
Band No.
25.0
1
-11.0
7
42.0
2
-11.9
42.0
2
-16.6
47.1
1
-5.1
36.1
1
-1.3
55.1
2
-8.5
11.3
1
-1.6
277.3
2
-16.7
230.7
1
-6.5
279.8
2
-8.6
39.4
1
-2.6
26.5
1
-2.0
36.0
1
-4.1
70.0
4
-30.3
70.3
1
-3.2
70.9
4
-27.0
98.1
1
-11.6
7
28.4
1
-3.6
7
13.9
1
-1.5
6
81.7
1
-3.9
7
36.6
1
-4.3
7
35.5
1
-3.0
798.4
1
-1.6
7
17.9
1
-1.3
7
21.9
1
-3.0
7
21.0
1
-1.5
192.5
1
-1.2
29.6
1
-1.2
75.8
1
-1.1
58.0
1
-4.2
22.5
1
-2.4
7
22.4
1
-2.4
7
96.5
2
-6.1
284.9
2
-2.5
73.6
1
-1.6
37.5
1
-1.4
5
26.7
5
-49.6
7
17.1
1
-2.0
7
5
5
1
3
1
3
1
1
1
1
7
1
1
2
1
1
5
4
1
6
1
1
1
3
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
60S ribosomal protein L18.
ENSP00000084795
Actin, cytoplasmic 1 (Beta-actin).
ENSP00000349960
ALPHA ENOLASE
ENSP00000234590
Alpha-actinin 4 (F-actin cross linking protein)
ENSP00000252699
Beta-catenin
ENSP00000344456
Dermcidin precursor (Preproteolysin)
ENSP00000293371
Desmocollin 1A/1B precursor (Desmosomal glycoprotein 2/3)
ENSP00000257197
DJ14N1.2 (Novel S-100/ICaBP type calcium binding domain protein
ENSP00000271816
E3 ubiquitin-protein ligase
ENSP00000361994
Fatty acid synthase (EC 2.3.1.85)
ENSP00000363777
Fatty acid synthase (EC 2.3.1.85)
ENSP00000363777
Filamin B (FLN-B) (Beta-filamin)
ENSP00000349819
Filamin-A (Alpha-filamin) (Filamin-1)
ENSP00000353467
Fructose-1,6-bisphosphatase
ENSP00000253266
Fructose-bisphospate aldolasea
ENSP00000336927
Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH).
ENSP00000229239
Glycogen phosphorylase, muscle form
ENSP00000366663
Glycogen phosphorylase, muscle form
ENSP00000366663
Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2)
ENSP00000364802
Histone H2B.f
ENSP00000350580
Histone H4.
ENSP00000352980
Junction plakoglobin (Desmoplakin III).
ENSP00000311113
Keratin type II cytoskeletal cytokeratin
ENSP00000257935
Keratinocyte proline-rich protein (hKPRP).
ENSP00000357762
Myosin heavy chain, skeletal muscle, adult 1
ENSP00000226207
Poly [ADP-ribose] polymerase 4
ENSP00000371419
predicted: similar to 60S ribosomal protein L7
ENSP00000349185
Probable RNA-dependent helicase P72 (DEAD-BOX PROTEIN 17)
ENSP00000216019
Pyruvate kinase, isozymes M1/M2
ENSP00000320171
similar to ribosomal protein S2; 40S ribosomal protein S2
Stress-70 protein, mitochondrial precursor
Triosephosphate isomerase
WD repeat protein 60
ENSP00000317418
ENSP00000297185
ENSP00000334713
ENSP00000309252
Uniprot Acc code
Q07020
P60709
P06733
O43707
P35222
P81605
Q08554
n/a
Q8IWV8
P49327
P49327
O75369
P21333
P09467
P04075
P04406
P11217
P11217
P08107
P33778
P62805
P14923
n/a
Q5T749
P12882
Q9UKK3
n/a
Q92841
P14618
n/a
P38646
P00938
Q8WVS4
Mr
No. of pepides
Log (e)
21.6
1
-7.4
41.7
1
-3.7
47.1
1
-4.4
104.8
1
-1.5
85.4
1
-1.5
11.3
1
-1.2
93.8
1
-1.4
247.9
1
-3.7
49.9
1
-1.3
277.3
2
-12.3
277.3
2
-8.3
230.7
6
-53.4
279.8
5
-40.3
36.8
1
-2.7
39.4
1
-7.1
36.0
1
-3.3
97.0
5
-37.6
97.0
4
-24.8
70.0
3
-20.0
13.9
1
-3.3
11.4
1
-1.8
81.7
1
-1.3
38.5
10
-67.1
64.1
3
-9.1
223.0
1
-3.4
192.5
1
-1.4
29.6
1
-2.8
80.2
1
-1.3
58.0
1
-1.5
31.5
1
-1.9
73.6
2
-7.9
26.9
1
-3.7
122.3
1
-1.3
Band No.
1
1
1
1
2
1
4
5
2
1
2
1
1
1
1
5
2
1
1
3
3
5
4
5
1
1
1
3
1
1
1
4
1
Supplemental Table S4
Clinical trials examining the potential benefit of trastuzumab in Her2 low/Her2 negative breast cancer patients
Trial Number Trial Name
NCT01275677
Chemotherapy With or Without
Trastuzumab After Surgery in Treating
Women With Invasive Breast Cancer
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
NCT00944047 IHC)
Traget Group of Patients
Her2 Low (1+, 2+ not FISH ratio <2)
T2-4, N1,N0. Her2 Low (1+, 2+ FISH
ratio <2.2)
Combination Immunotherapy With
T2-4, N1,N0. Her2 Low (1+, 2+ FISH
Herceptin and the HER2 Vaccine NeuVax
ratio <2.2)
NCT01570036
A Phase II Randomized Trial Evaluating
the Effect of Trastuzumab on Disease
Free Survival in Early Stage HER2Negative Breast Cancer Patients With
ERBB2 Expressing Bone Marrow
Her2 0, 1+ or 2+ (FISH not amplified)
NCT01779050 Disseminated Tumor Cells
Phase II Study of the Trifunctional AntiHER-2/Neu x Anti-CD3 Antibody
Ertumaxomab for Hormone Therapy
Refractory Patients With Her-2/Neu 1+
or 2+ Expressing Advanced or Metastatic
Her2 0, 1+ or 2+ (FISH not amplified)
NCT00351858 Breast Cancer
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+
Agents
End Point
Result
trastuzumab, doxorubicin,
doxitaxel, cyclophosphamide,
pacitaxel
ongoing
n/a
trastuzumab, Nab-paclitaxel,
doxorubicin, cyclophosphamide
ongoing
n/a
trastuzumab, NeuVax, GM-CSF
ongoing
n/a
trastuzumab, doxorubicin,
cyclophosphamide, paclitaxel
Not yet started
n/a
ertumaxomab
terminated
lapatinib
completed
n/a
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 )