SUPPLEMENTAL DATA
Supplemental Table 1. Clinicopathological characteristics of patients included in RPPA comparison of NSCLC tumors with paired normal lung tissue
Specimen Number / Histololgy / Age at surgery / Gender / Race / Smoking Status / T stage / N stage / M stage / Overall Stage / Recurrence Yes/No700 / SQ / 79 / M / Caucasian / Former / T2 / N1 / M0 / IIB / No
708 / SQ / 61 / F / African American / Never / T2 / N1 / M0 / IIB / No
719 / SQ / 76 / M / Caucasian / Former / T2 / N0 / M0 / IB / Yes
720 / SQ / 67 / F / Caucasian / Current / T1 / N1 / M0 / IIA / No
739 / AD / 76 / F / Caucasian / Former / T2 / N2 / M1 / IV / Yes
746 / AD / 67 / F / Caucasian / Former / T4 / N0 / M0 / IIIB / No
759 / AD / 60 / M / Caucasian / Current / T2 / N2 / M0 / IIIB / Yes
763 / AD / 60 / F / Caucasian / Current / T2 / N2 / M0 / IIIA / No
764 / AD / 67 / F / Caucasian / Current / T2 / N0 / M0 / IB / No
767 / AD / 53 / F / African American / Current / T1 / N2 / M0 / IIIA / No
771 / SQ / 67 / M / Caucasian / Former / T2 / N1 / M0 / IIB / No
773 / AD / 77 / F / Caucasian / Former / T4 / N2 / M1 / IV / Yes
774 / SQ / 67 / M / African American / Former / T4 / N2 / M0 / IIIB / Yes
781 / SQ / 80 / F / Caucasian / Former / T1 / N0 / M0 / IA / No
782 / AD / 67 / M / Caucasian / Former / T4 / N0 / M0 / IIIB / Yes
786 / SQ / 81 / M / Caucasian / Former / T2 / N1 / M0 / IIB / No
795 / AD / 64 / M / Caucasian / Never / T1 / N0 / M0 / IA / No
799 / SQ / 61 / F / Caucasian / Current / T2 / N0 / M0 / IB / Yes
801 / AD / 63 / F / Caucasian / Current / T2 / N1 / M0 / IIB / No
803 / AD / 65 / F / African American / Current / T2 / N1 / M0 / IIB / Yes
804 / SQ / 77 / M / Caucasian / Former / T2 / N0 / M0 / IB / No
811 / SQ / 62 / M / Caucasian / Current / T2 / N1 / M0 / IIB / No
813 / SQ / 70 / M / Caucasian / Current / T4 / N0 / M0 / IIIB / Yes
816 / AD / 73 / M / Caucasian / Former / T2 / N0 / M0 / IB / No
833 / AD / 72 / M / Caucasian / Current / T1 / N0 / M0 / IA / Yes
844 / SQ / 67 / M / Caucasian / Former / T2 / N1 / M0 / IB / No
847 / AD / 60 / F / Caucasian / Current / T2 / N0 / M0 / IB / No
848 / AD / 48 / F / Caucasian / Current / T2 / N0 / M0 / IB / Yes
849 / AD / 57 / M / Caucasian / Current / T1 / N1 / M0 / IIA / No
852 / SQ / 67 / M / Caucasian / Current / T2 / N0 / M0 / IB / No
857 / SQ / 71 / M / Caucasian / Current / T2 / N0 / M0 / IB / No
870 / SQ / 53 / M / Caucasian / Current / T2 / N1 / M0 / IIB / No
877 / AD / 68 / M / Caucasian / Former / T2 / N1 / M0 / IIB / Yes
879 / SQ / 67 / M / Caucasian / Current / T2 / N1 / M0 / IIB / No
883 / AD / 58 / F / Caucasian / Former / T2 / N1 / M0 / IIB / No
884 / AD / 70 / F / Caucasian / Former / T1 / N0 / M0 / IA / No
890 / AD / 68 / M / Caucasian / Former / T2 / N0 / M0 / IB / Yes
896 / AD / 49 / F / Caucasian / Current / T1 / N0 / M0 / IA / Yes
899 / AD / 65 / F / Caucasian / Current / T1 / N0 / M0 / IA / No
905 / SQ / 80 / M / Caucasian / Former / T2 / N1 / M0 / IIB / Yes
910 / AD / 74 / F / Caucasian / Former / T2 / N0 / M0 / IB / Yes
911 / SQ / 65 / F / Caucasian / Former / T2 / N0 / M0 / IB / No
913 / SQ / 61 / M / Caucasian / Former / T2 / N2 / M0 / IIIA / Yes
920 / AD / 54 / F / Caucasian / Current / T2 / N0 / M0 / IB / Yes
930 / SQ / 66 / M / Caucasian / Former / T2 / N1 / M0 / IIB / Yes
931 / SQ / 71 / F / Caucasian / Current / T4 / N0 / M0 / IIIB / No
Stages listed are pathological stage
(AD=adenocarcinoma, SQ=squamous cell carcinoma)
Supplemental Table 2. Primary Antibodies used for RPPA analysis.
phospho-Acetyl Coenzyme A / PI3K pathway / CS 36615 / 1/250 / Rb / CS = Cell Signaling
AKT TOTAL / PI3K pathway / CS 9272 / 1/250 / Rb / Up = Upstate
phospho-AKT (308) / PI3K pathway / CS 9275 / 1/200 / Rb / SC = Santa Cruz
phospho-AKT (473) / PI3K pathway / CS 9271 / 1/250 / Rb / Epi = Epitomics
AMP activated protein kinase / LKB pathway / CS 2532 / 1/250 / Rb / Ab = Abcam
phospho-AMP activated kinase / LKB pathway / CS 2535L / 1/200 / Rb / Neo= Neomarkers
b-catenin / Cell Polarity / CS 9562L / 1/1500 / Rb / Rb = Rabbit
cleaved caspase 7 / Apoptosis / CS 9491 / 1/150 / Rb / Ms = Mouse Monoclonal
caveolin-1 / Tumor Suppressor / CS 3238 / 1/1000 / Rb
cyclin B1 / Cell Cycle Regulator / Epi 1495 / 1/500 / Rb
cyclin D1 / Cell Cycle Regulator / SC 718 / 1/1000 / Rb
cyclin E1 / Cell Cycle Regulator / Epi CO41512 / 1/200 / Rb
cleaved PARP / Apoptosis / CS 9541L / 1/100 / Rb
c-myc / Oncogene / CS 9401 / 1/150 / Rb
E-cadherin / Cell Polarity / CS 4065 / 1/200 / Rb
EGFR / Tyrosine Kinase Mediated Pathways / SC 03 / 1/200 / Rb
ERK2 (TOTAL MAP kinase) / MAPK pathway / SC 154 / 1/2500 / Rb
FAK / Integrin Signaling / Epi 1700 / 1/200 / Rb
phospho-FAK (Y576) / Integrin Signaling / CS 3281 / 1/125 / Rb
pFAK (Y397) / Integrin Signaling / BD 611723 / 1/125 / Ms
GSK3 / PI3K Pathway / SC 7291 / 1/1000 / Ms
phospho-GSK3 (Ser21/9) / PI3K Pathway / CS 9331 / 1/250 / Rb
phospho-LKB1 (STK11) (Ser428) / LKB pathway / CS 3051s / 1/250 / Rb
phospho-ERK1/2 (Thr202/Tyr204) / PI3K Pathway / CS 9101L / 1/1200 / Rb
MEK1 / MAPK pathway / Epi 1235 / 1/3000 / Rb
mTOR / PI3K Pathway / CS 2983 / 1/800 / Rb
p130-CAS Y410) / Integrin Signaling / CS 4014 / 1/125 / Rb
phospho-p130 Cas (Y249) / Tyrosine Kinase Mediated Pathways / CS 7104 / 1/125 / Rb
p21 / Cell Cycle Regulator / SC 397 / 1/100 / Rb
p27 / Cell Cycle Regulator / SC 528 / 1/1000 / Rb
p38 / MAPK pathway / CS 9212 / 1/300 / Rb
phospho-p38 (thr180/Tyr182) / MAPK pathway / CS 9211 / 1/200 / Rb
p53 / Cell Cycle Regulator / CS 9282 / 1/200 / Rb
p70S6K / PI3K pathway / Epi 1494 / 1/1000 / Rb
phospho-p70S6K (Thr389) / PI3K pathway / CS 9205L / 1/250 / Rb
Paxillin / Integrin Signaling / Epi 1500 / 1/1500 / Rb
phospho-Paxillin (Y118) / Integrin Signaling / CS 2541 / 1/100 / Rb
plasminogen activator inhibitor-1 (PAI-1) / Inhibitor of Fibrinolysis / BD 612024 / 1/1000 / Ms
proliferating cell nuclear antigen / Cell Cycle Regulator / Ab 29100 / 1/1000 / Ms
p110alpha-phosphatidylinositol 3 kinase / PI3K pathway / Epi 1683-1 / 1/500 / Rb
PKC alpha / Other / Up 05-154 / 1/2000 / Ms
phospho-PKC alpha (Ser657) / Other / Up 06-822 / 1/2000 / Rb
phospho-mTOR / PI3K pathway / CS 2971L / 1/200 / Rb
phospho-STAT6 / JAK/STAT Pathway / CS 9361L / 1/100 / Rb
PTEN / PI3K pathway / CS 9552 / 1/1000 / Rb
RAB25 (small GTPase, member of RAS family) / Other / KW Cheng / 1/4000 / Rb
Retinoblastoma / Cell Cycle Regulator / CS 9309 / 1/6000 / Ms
phospho-RB (Ser807/811) / Cell Cycle Regulator / CS 9308 / 1/250 / Rb
ribosomal protein S6 / PI3K pathway / CS 2212 / 1/200 / Rb
phospho-S6 (235/236) / PI3K pathway / CS 2211 / 1/20000 / Rb
phospho-S6 (240) / PI3K pathway / CS 2115 / 1/5000 / Rb
Src / Tyrosine Kinase Mediated Pathways / Up 05184 / 1/200 / Ms
phospho-Src (416) / Tyrosine Kinase Mediated Pathways / CS 2101L / 1/100 / Rb
phospho-Src (527) / Tyrosine Kinase Mediated Pathways / CS 2105L / 1/400 / Rb
STAT3 / JAK/STAT Pathway / Up 06596 / 1/500 / Rb
phospho-STAT3 (Tyr705) / JAK/STAT Pathway / CS 9131 / 1/250 / Rb
TSC2 / LKB pathway / Epi 1613-1 / 1/500 / Rb
phospho-TSC2 (Thr1462) / LKB pathway / CS 3617 / 1/200 / Rb
Survival of motor neuron 1 / RNA Splicing pathway / SC 15320 / 1/1000 / Rb
Gemin3 / RNA Splicing pathway / SC 50405 / 1/1000 / Rb
estrogen receptor-alpha / Nuclear Receptor pathway / Neo SP1 / 1/250 / Rb
progesterone receptor / Nuclear Receptor pathway / Epi SP2 / 1/250 / Rb
Steroid receptor co-activator / Nuclear Receptor pathway / BD / 1/1000 / Ms
Supplemental Table 3. Predicted performance of multi-marker signatures to separate NSCLC tumor from normal lung using the Top 2 to Top 10 protein markers.
Predicted accuracy / 0.810 / 0.833 / 0.833 / 0.833 / 0.810 / 0.833 / 0.833 / 0.833 / 0.833
Sensitivity / 0.619 / 0.714 / 0.667 / 0.667 / 0.667 / 0.667 / 0.667 / 0.667 / 0.667
Specificity / 1.000 / 0.952 / 1.000 / 1.000 / 0.952 / 1.000 / 1.000 / 1.000 / 1.000
PPV / 1.000 / 0.938 / 1.000 / 1.000 / 0.933 / 1.000 / 1.000 / 1.000 / 1.000
NPV / 0.724 / 0.769 / 0.750 / 0.750 / 0.741 / 0.750 / 0.750 / 0.750 / 0.750
Supplemental Table 4. IHC scores for caveolin and p70S6K
Specimen Number / Tumor Cytoplasm / Tumor Membrane / Alveoli Cytoplasm / Alveoli Membrane / Alveoli Stroma / Bronchial epithelium Cytoplasm / Bronchial epithelium Membrane / Tumor Cytoplasm / Alveoli Cytoplasm / Bronchial epithelium Cytoplasm
700 / 10 / 30 / 40 / 50 / 300 / - / - / 90 / 0 / -
708 / 5 / 5 / 50 / 70 / 300 / 5 / 10 / 80 / 0 / 0
719 / 50 / 40 / 50 / 70 / 300 / 20 / 20 / 50 / 0 / 60
720 / 40 / 90 / 30 / 90 / 300 / - / - / 90 / 0 / -
739 / 5 / 10 / 10 / 70 / 300 / - / - / 50 / 0 / -
746 / 20 / 0 / 10 / 60 / 300 / - / - / 10 / 0 / -
759 / 150 / 180 / 50 / 90 / 300 / 0 / 5 / 80 / 0 / 50
763 / 30 / 20 / 20 / 90 / 300 / 5 / 5 / 100 / 0 / 90
764 / 50 / 50 / 50 / 50 / 300 / 5 / 3 / 150 / 0 / 50
767 / 50 / 0 / 30 / 80 / 300 / - / - / 90 / 0 / 40
771 / 200 / 200 / 30 / 70 / 300 / 5 / 10 / 70 / 0 / 50
773 / 10 / 10 / 30 / 70 / 300 / - / - / 150 / 0 / -
782 / 30 / 30 / 50 / 90 / 300 / 30 / 20 / 100 / 0 / 100
786 / 150 / 100 / 10 / 80 / 300 / 10 / 10 / 90 / 0 / 70
795 / 5 / - / 30 / 90 / 300 / - / - / 60 / 0 / -
799 / 0 / 0 / 50 / 90 / 300 / 0 / 0 / 60 / 0 / 40
801 / 0 / 0 / - / - / 300 / - / - / 5 / - / -
803 / 170 / 200 / 30 / 70 / 300 / 2 / 10 / 60 / 0 / 80
804 / 0 / 0 / 20 / 60 / 300 / 0 / 5 / 50 / 0 / 70
811 / 20 / 10 / 50 / 90 / 300 / - / - / 40 / 0 / -
816 / 30 / 70 / 10 / 80 / 300 / 0 / 5 / 50 / 0 / -
833 / 50 / 100 / 10 / 70 / 300 / 0 / 5 / 100 / 0 / -
847 / 30 / 50 / 10 / 80 / 300 / 0 / 5 / 90 / 0 / 60
849 / 20 / 10 / 30 / 90 / 300 / 5 / 5 / 10 / 0 / 30
857 / 0 / 0 / 10 / 50 / 300 / - / - / 20 / 0 / -
870 / 200 / 300 / 10 / 80 / 300 / 5 / 10 / 60 / 0 / 30
877 / 0 / 0 / 20 / 80 / 300 / 20 / 10 / 80 / 0 / 5
883 / 0 / 0 / 20 / 90 / 300 / 0 / 5 / 10 / 0 / 30
884 / 10 / 0 / 20 / 80 / 300 / 10 / 0 / 50 / 0 / 60
890 / 10 / 0 / 30 / 90 / 300 / 0 / 5 / 20 / 0 / 50
896 / 50 / 0 / 10 / 90 / 300 / - / - / 20 / 0 / -
899 / 0 / 0 / 5 / 80 / 300 / - / - / 30 / 0 / 30
905 / 40 / 30 / 20 / 90 / 300 / 10 / 10 / 100 / 0 / -
910 / 0 / 0 / 10 / 90 / 300 / 5 / 5 / 10 / 0 / 20
910 / 100 / 20 / 10 / 70 / 300 / 2 / 10 / 30 / 0 / 30
911 / 0 / 0 / 20 / 90 / 300 / 20 / 20 / 50 / 0 / 60
913 / 0 / 0 / 10 / 90 / 300 / 0 / 2 / 200 / 0 / 20
920 / 0 / 0 / 10 / 90 / 300 / - / - / 40 / 0 / -
930 / 40 / 150 / 20 / 90 / 300 / 10 / 10 / 80 / 0 / 80
931 / 150 / 140 / 10 / 80 / 300 / 10 / 10 / 20 / 0 / 50