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Supplementary Table 1

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Protein Associated Description NC miR1 NC miR-1 Base 2 Log Name Gene Name Peptides Peptides PepHits PepHits of NC/miR-1 ENSP00000338413 UBA1 ubiquitin-like modifier activating enzyme 1 14 0 59 0 5.9 ENSP00000304592 FASN fatty acid synthase 33 1 99 1 5.6 ENSP00000296122 PPP1CB protein phosphatase 1, catalytic subunit, beta isozyme 6 0 36 0 5.2 ENSP00000220849 EIF3E eukaryotic translation initiation factor 3, subunit E 9 0 35 0 5.2 ENSP00000346037 RPLP1 ribosomal protein, large, P1 1 0 32 0 5.0 ENSP00000262982 CSE1L CSE1 chromosome segregation 1-like 12 0 32 0 5.0 ENSP00000353157 septin 2 septin 2 5 0 28 0 4.9 ENSP00000326031 PPP1CA protein phosphatase 1, catalytic subunit, alpha isozyme 8 0 28 0 4.9 ENSP00000401802 PSMC6 proteasome (prosome, macropain) 26S subunit, ATPase, 6 8 0 28 0 4.9 ENSP00000327539 HNRNPH1 heterogeneous nuclear ribonucleoprotein H1 5 0 28 0 4.9 ENSP00000335084 PPP1CC protein phosphatase 1, catalytic subunit, gamma isozyme 6 0 27 0 4.8 ENSP00000300648 GCN1L1 GCN1 general control of amino-acid synthesis 1-like 1 13 0 27 0 4.8 (yeast) ENSP00000358765 4 0 27 0 4.8 ENSP00000325002 COPG1 coatomer protein complex, subunit gamma 1 9 0 26 0 4.8 ENSP00000298852 PSMC3 proteasome (prosome, macropain) 26S subunit, ATPase, 3 5 0 24 0 4.6 ENSP00000322419 RPLP2 ribosomal protein, large, P2 4 1 47 1 4.6 ENSP00000307288 MCM7 minichromosome maintenance complex component 7 9 0 23 0 4.6 ENSP00000309474 PSMD1 proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 0 22 0 4.5 1 ENSP00000358921 ACTR1A ARP1 actin-related protein 1 homolog A, centractin alpha 5 0 22 0 4.5 ENSP00000320309 FARSA phenylalanyl-tRNA synthetase, alpha subunit 3 0 21 0 4.5 ENSP00000317788 HNRNPK heterogeneous nuclear ribonucleoprotein K 5 0 21 0 4.5 ENSP00000249923 COPB1 coatomer protein complex, subunit beta 1 9 0 21 0 4.5 ENSP00000299218 11 0 21 0 4.5 ENSP00000369042 IPO7 importin 7 [Source:HGNC Symbol;Acc:9852] 5 0 20 0 4.4 ENSP00000352288 PLXNB2 plexin B2 [Source:HGNC Symbol;Acc:9104] 5 0 19 0 4.3 ENSP00000262832 ACSL4 acyl-CoA synthetase long-chain family member 4 7 0 19 0 4.3 ENSP00000269349 EIF4A3 eukaryotic translation initiation factor 4A3 7 1 38 1 4.3 ENSP00000361927 HNRNPH2 heterogeneous nuclear ribonucleoprotein H2 5 0 18 0 4.2 ENSP00000226253 ALDOC aldolase C, fructose-bisphosphate 6 1 37 1 4.2 ENSP00000313454 UBA6 ubiquitin-like modifier activating enzyme 6 7 0 17 0 4.2 ENSP00000418447 PPP2CA protein phosphatase 2, catalytic subunit, alpha isozyme 8 0 17 0 4.2 ENSP00000332256 ALDH1A3 aldehyde dehydrogenase 1 family, member A3 10 1 35 1 4.2 ENSP00000289316 HIST1H2BD histone cluster 1, H2bd 5 2 68 3 4.1 ENSP00000264705 CAD carbamoyl-phosphate synthetase 2, aspartate 4 0 16 0 4.1 transcarbamylase, and dihydroorotase ENSP00000345156 RPL14 ribosomal protein L14 3 2 48 2 4.0 ENSP00000246957 TRAP1 TNF receptor-associated protein 1 1 1 31 1 4.0 ENSP00000256689 SLC38A2 solute carrier family 38, member 2 3 0 15 0 4.0 ENSP00000264170 KYNU kynureninase 2 0 15 0 4.0 ENSP00000382840 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 6 0 15 0 4.0 ENSP00000373918 GARS glycyl-tRNA synthetase 8 2 46 2 4.0 ENSP00000367336 RPL23 ribosomal protein L23 3 1 30 1 4.0 ENSP00000295901 PSMD6 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 1 30 1 4.0 6 ENSP00000317334 TCP1 t-complex 1 14 2 60 3 3.9 ENSP00000290158 KPNB1 karyopherin (importin) beta 1 12 4 75 4 3.9 ENSP00000310040 EIF3F eukaryotic translation initiation factor 3, subunit F 5 0 14 0 3.9 ENSP00000367992 ESD esterase D 4 0 14 0 3.9 ENSP00000241704 COPA coatomer protein complex, subunit alpha 16 2 43 2 3.9 ENSP00000358140 EIF3A eukaryotic translation initiation factor 3, subunit A 9 1 28 1 3.9 ENSP00000054666 VAMP3 vesicle-associated membrane protein 3 3 0 13 0 3.8 ENSP00000261182 NAP1L1 nucleosome assembly protein 1-like 1 8 1 27 1 3.8 ENSP00000332455 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 3 0 13 0 3.8 ENSP00000356481 FAM129A family with sequence similarity 129, member A 3 0 13 0 3.8 ENSP00000384863 XPO1 exportin 1 (CRM1 homolog, yeast) 5 0 13 0 3.8 ENSP00000338481 EPB41L2 erythrocyte membrane protein band 4.1-like 2 6 0 13 0 3.8 ENSP00000264028 ARCN1 archain 1 1 0 13 0 3.8 ENSP00000309477 ACO1 aconitase 1, soluble 6 0 13 0 3.8 ENSP00000329528 7 0 13 0 3.8 ENSP00000196551 RPS5 ribosomal protein S5 ] 4 1 53 3 3.8 ENSP00000262325 AP2B1 adaptor-related protein complex 2, beta 1 subunit 8 1 26 1 3.8 ENSP00000426909 GNB2L1 guanine nucleotide binding protein (G protein), beta 17 6 156 11 3.7 polypeptide 2-like 1 ENSP00000324804 PPP2R1A protein phosphatase 2, regulatory subunit A, alpha 12 2 38 2 3.7 ENSP00000261712 PSMD11 proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 0 12 0 3.7 11 ENSP00000229854 MCM3 minichromosome maintenance complex component 3 6 0 12 0 3.7 ENSP00000365024 LY6G5B lymphocyte antigen 6 complex, locus G5B 1 0 12 0 3.7 ENSP00000260985 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 8 1 25 1 3.7 ENSP00000310749 HPCAL1 hippocalcin-like 1 3 0 12 0 3.7 ENSP00000356787 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide 3 0 12 0 3.7 ENSP00000175506 ASNS asparagine synthetase (glutamine-hydrolyzing) 4 0 12 0 3.7 ENSP00000265112 TARS threonyl-tRNA synthetase 5 0 11 0 3.6 ENSP00000295736 SLC4A7 solute carrier family 4, sodium bicarbonate cotransporter, 2 0 11 0 3.6 member 7 ENSP00000348442 PSMD12 proteasome (prosome, macropain) 26S subunit, non-ATPase, 5 0 11 0 3.6 12 ENSP00000311713 OXSR1 oxidative-stress responsive 1 [Source:HGNC 2 0 11 0 3.6 Symbol;Acc:8508] ENSP00000252172 MYH13 myosin, heavy chain 13, skeletal muscle 2 1 35 2 3.6 ENSP00000305860 HNRNPD heterogeneous nuclear ribonucleoprotein D (AU-rich element 4 0 11 0 3.6 RNA binding protein 1, 37kDa) ENSP00000318687 HSPH1 heat shock 105kDa/110kDa protein 3 0 11 0 3.6 ENSP00000275603 CCT6A chaperonin containing TCP1, subunit 6A (zeta 1) 8 1 23 1 3.6 ENSP00000346067 RPSA ribosomal protein SA 11 4 79 6 3.5 ENSP00000328808 13 5 156 13 3.5 ENSP00000348965 DYNC1H1 dynein, cytoplasmic 1, heavy chain 84 16 279 24 3.5 ENSP00000253792 ACLY ATP citrate lyase 23 5 110 9 3.5 ENSP00000025399 STRAP serine/threonine kinase receptor associated protein 6 0 10 0 3.5 ENSP00000227638 PANX1 pannexin 1 2 0 10 0 3.5 ENSP00000302961 HSPA4 heat shock 70kDa protein 4 3 0 10 0 3.5 ENSP00000229314 GOLT1B golgi transport 1B 3 0 10 0 3.5 ENSP00000349053 GANAB glucosidase, alpha; neutral AB 17 2 32 2 3.5 ENSP00000267113 ESYT1 extended synaptotagmin-like protein 1 4 0 10 0 3.5 ENSP00000317399 EEF1D eukaryotic translation elongation factor 1 delta (guanine 2 0 10 0 3.5 nucleotide exchange protein) ENSP00000253413 ATP6V1E1 ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 1 0 10 0 3.5 ENSP00000318697 TUBB6 tubulin, beta 6 class V 25 9 286 26 3.4 ENSP00000264639 PSMD3 proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 1 20 1 3.4 3 ENSP00000329419 COPB2 coatomer protein complex, subunit beta 2 (beta prime) 9 1 20 1 3.4 ENSP00000231572 RARS arginyl-tRNA synthetase 9 1 20 1 3.4 ENSP00000376174 RAN RAN, member RAS oncogene family 9 3 61 5 3.4 ENSP00000286371 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide 7 2 50 4 3.4 ENSP00000211402 VARS valyl-tRNA synthetase 3 0 9 0 3.3 ENSP00000262803 UPF1 UPF1 regulator of nonsense transcripts homolog (yeast) 5 0 9 0 3.3 ENSP00000270792 SH3BGRL3 SH3 domain binding glutamic acid-rich protein like 3 2 0 9 0 3.3 ENSP00000237530 RPN2 ribophorin II 2 0 9 0 3.3 ENSP00000054950 RCN1 reticulocalbin 1, EF-hand calcium binding domain 3 0 9 0 3.3 ENSP00000325074 PPP2R2A protein phosphatase 2, regulatory subunit B, alpha 3 0 9 0 3.3 ENSP00000351410 PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha 3 0 9 0 3.3 ENSP00000283179 HNRNPU heterogeneous nuclear ribonucleoprotein U (scaffold 4 0 9 0 3.3 attachment factor A) ENSP00000221419 HNRNPL heterogeneous nuclear ribonucleoprotein L 4 0 9 0 3.3 ENSP00000340391 FERMT2 fermitin family member 2 6 0 9 0 3.3 ENSP00000362409 FAM129B family with sequence similarity 129, member B 9 2 39 3 3.3 ENSP00000327821 XPOT exportin, tRNA 6 0 9 0 3.3 ENSP00000260818 DNAJC13 DnaJ (Hsp40) homolog, subfamily C, member 13 4 0 9 0 3.3 ENSP00000290776 CPNE2 copine II 2 0 9 0 3.3 ENSP00000256854 NARS asparaginyl-tRNA synthetase 4 0 9 0 3.3 ENSP00000263270 AP2S1 adaptor-related protein complex 2, sigma 1 subunit 1 0 9 0 3.3 ENSP00000261733 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) 9 3 67 6 3.3 ENSP00000331901 EEF1G eukaryotic translation elongation factor 1 gamma 11 3 76 7 3.3 ENSP00000313420 PRKDC protein kinase, DNA-activated, catalytic polypeptide 10 1 18 1 3.2 ENSP00000290349 CBR1 carbonyl reductase 1 6 1 18 1 3.2 ENSP00000233072 CPS1 carbamoyl-phosphate synthase 1, mitochondrial 15 2 36 3 3.2 ENSP00000326381 EIF4A2 eukaryotic translation initiation factor 4A2 10 4 82 8 3.2 ENSP00000339485 WARS tryptophanyl-tRNA synthetase 6 0 8 0 3.2 ENSP00000303145 TMED10 transmembrane emp24-like trafficking protein 10 (yeast) 3 1 17 1 3.2 ENSP00000316029 TLN1 talin 1 28 7 80 8 3.2 ENSP00000350708 RAD23B RAD23 homolog B (S.
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  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant

    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
  • Knock-Out Validated Antibodies from Cloud-Clone Cat.No

    Knock-Out Validated Antibodies from Cloud-Clone Cat.No

    Knock-out validated antibodies from Cloud-Clone Cat.No. Target PAA778Hu01 B-Cell Leukemia/Lymphoma 2 (Bcl2) PAL763Hu01 Myxovirus Resistance 1 (MX1) PAB698Hu01 Lactate Dehydrogenase B (LDHB) PAA009Hu01 Angiopoietin 2 (ANGPT2) PAA849Ra01 Glycogen Phosphorylase, Liver (PYGL) PAA153Hu01 Alpha-Fetoprotein (aFP) PAF460Hu01 Folate Receptor 1, Adult (FOLR1) PAB233Hu01 Cyclin Dependent Kinase 4 (CDK4) PAA150Hu04 Carcinoembryonic Antigen (CEA) PAB905Hu01 Interleukin 7 Receptor (IL7R) PAC823Hu01 Thymidine Kinase 1, Soluble (TK1) PAH838Hu01 Isocitrate Dehydrogenase 2, mitochondrial (IDH2) PAK078Mu01 Fas Associating Death Domain Containing Protein (FADD) PAA537Hu01 Enolase, Neuron Specific (NSE) PAA651Hu01 Hyaluronan Binding Protein 1 (HABP1) PAB215Hu02 Fibrinogen Beta (FGb) PAB769Hu01 S100 Calcium Binding Protein A6 (S100A6) PAB231Hu01 Keratin 18 (KRT18) PAH839Hu01 Isocitrate Dehydrogenase 1, Soluble (IDH1) PAE748Hu01 Karyopherin Alpha 2 (KPNa2) PAB081Hu02 Heat Shock 70kDa Protein 1A (HSPA1A) PAA778Mu01 B-Cell Leukemia/Lymphoma 2 (Bcl2) PAA853Hu03 Caspase 8 (CASP8) PAA399Mu01 High Mobility Group Protein 1 (HMG1) PAA303Mu01 Galectin 3 (GAL3) PAA537Mu02 Enolase, Neuron Specific (NSE) PAA994Ra01 Acid Phosphatase 1 (ACP1) PAB083Ra01 Superoxide Dismutase 2, Mitochondrial (SOD2) PAB449Mu01 Enolase, Non Neuronal (NNE) PAA376Mu01 Actinin Alpha 2 (ACTN2) PAA553Ra01 Matrix Metalloproteinase 9 (MMP9) PAA929Bo01 Retinol Binding Protein 4, Plasma (RBP4) PAA491Ra02 Keratin 2 (KRT2) PAC025Hu01 Keratin 8 (KRT8) PAB231Mu01 Keratin 18 (KRT18) PAC598Hu03 Vanin 1 (VNN1)
  • Supplementary Methods

    Supplementary Methods

    Supplementary methods Human lung tissues and tissue microarray (TMA) All human tissues were obtained from the Lung Cancer Specialized Program of Research Excellence (SPORE) Tissue Bank at the M.D. Anderson Cancer Center (Houston, TX). A collection of 26 lung adenocarcinomas and 24 non-tumoral paired tissues were snap-frozen and preserved in liquid nitrogen for total RNA extraction. For each tissue sample, the percentage of malignant tissue was calculated and the cellular composition of specimens was determined by histological examination (I.I.W.) following Hematoxylin-Eosin (H&E) staining. All malignant samples retained contained more than 50% tumor cells. Specimens resected from NSCLC stages I-IV patients who had no prior chemotherapy or radiotherapy were used for TMA analysis by immunohistochemistry. Patients who had smoked at least 100 cigarettes in their lifetime were defined as smokers. Samples were fixed in formalin, embedded in paraffin, stained with H&E, and reviewed by an experienced pathologist (I.I.W.). The 413 tissue specimens collected from 283 patients included 62 normal bronchial epithelia, 61 bronchial hyperplasias (Hyp), 15 squamous metaplasias (SqM), 9 squamous dysplasias (Dys), 26 carcinomas in situ (CIS), as well as 98 squamous cell carcinomas (SCC) and 141 adenocarcinomas. Normal bronchial epithelia, hyperplasia, squamous metaplasia, dysplasia, CIS, and SCC were considered to represent different steps in the development of SCCs. All tumors and lesions were classified according to the World Health Organization (WHO) 2004 criteria. The TMAs were prepared with a manual tissue arrayer (Advanced Tissue Arrayer ATA100, Chemicon International, Temecula, CA) using 1-mm-diameter cores in triplicate for tumors and 1.5 to 2-mm cores for normal epithelial and premalignant lesions.
  • MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test

    MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test

    MALE t-test t-test Accession Molecular H PDAC PDAC vs. PDAC vs. Protein Name Number Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean Mean Mean H CP PDAC/H PDAC/CP - 22 kDa protein IPI00219910 22 kDa 7 5 4 8 1 0 6 6 1 0.1126 0.0456 0.1 0.1 - Cold agglutinin FS-1 L-chain (Fragment) IPI00827773 12 kDa 32 39 34 26 53 57 36 30 55 0.0309 0.0388 1.8 1.5 - HRV Fab 027-VL (Fragment) IPI00827643 12 kDa 4 6 0 0 0 0 5 0 0 - 0.0574 - 0.0 - REV25-2 (Fragment) IPI00816794 15 kDa 8 12 5 7 8 9 10 6 8 0.2225 0.3844 1.3 0.8 A1BG Alpha-1B-glycoprotein precursor IPI00022895 54 kDa 115 109 106 112 111 100 112 109 105 0.6497 0.4138 1.0 0.9 A2M Alpha-2-macroglobulin precursor IPI00478003 163 kDa 62 63 86 72 14 18 63 79 16 0.0120 0.0019 0.2 0.3 ABCB1 Multidrug resistance protein 1 IPI00027481 141 kDa 41 46 23 26 52 64 43 25 58 0.0355 0.1660 2.4 1.3 ABHD14B Isoform 1 of Abhydrolase domain-containing proteinIPI00063827 14B 22 kDa 19 15 19 17 15 9 17 18 12 0.2502 0.3306 0.7 0.7 ABP1 Isoform 1 of Amiloride-sensitive amine oxidase [copper-containing]IPI00020982 precursor85 kDa 1 5 8 8 0 0 3 8 0 0.0001 0.2445 0.0 0.0 ACAN aggrecan isoform 2 precursor IPI00027377 250 kDa 38 30 17 28 34 24 34 22 29 0.4877 0.5109 1.3 0.8 ACE Isoform Somatic-1 of Angiotensin-converting enzyme, somaticIPI00437751 isoform precursor150 kDa 48 34 67 56 28 38 41 61 33 0.0600 0.4301 0.5 0.8 ACE2 Isoform 1 of Angiotensin-converting enzyme 2 precursorIPI00465187 92 kDa 11 16 20 30 4 5 13 25 5 0.0557 0.0847 0.2 0.4 ACO1 Cytoplasmic aconitate hydratase IPI00008485 98 kDa 2 2 0 0 0 0 2 0 0 - 0.0081 - 0.0