Supplemental Table 1 Specimen Specimen Initial Clinical Clinical Clinical Treatment Pathologic Pathologic Pathologic Number type Age Sex Smoker WT(Kg) Resectability T Stage N Stage M Grade NACT received Effect T Stage N Stage M Stage % tumor % necrosis Inflammation Fibrosis 1 Surgical 80 Male Former 70.7 LAPC 3 1 0 Not Assessed Gem/Abraxane Not Assessed 3 1 1 n/a n/a n/a n/a 2 Surgical 54 Male Unknown 96.3 LAPC 3 0 0 Not Assessed Gemcitabine Not Assessed 3 0 1 80 0 moderate moderate 3 Surgical 57 Male Unknown 50.1 LAPC 4 1 1 2 FOLFIRINOX Moderate 3 0 0 90 0 moderate present 4 Surgical 59 Female Unknown 49.9 BRPC 2 0 1 Not Assessed FOLFIRINOX Not Assessed 2 0 1 n/a n/a n/a n/a 5 Surgical 56 Female Unknown 63.5 BRPC 3 1 0 1 FOLFIRINOX Poor 3 1 1 80 0 mild present 6 Surgical 60 Male No 90.7 BRPC 3 0 0 2 Gem/Abraxane Not Assessed 4 0 0 1 0 mild moderate 7 Surgical 75 Female No 49.9 BRPC 4 0 0 2 FOLFIRINOX Poor 3 1 0 10 0 moderate moderate 8 Surgical 74 Male Former 54.4 BRPC 3 0 0 2 FOLFIRINOX Moderate 1 0 0 5 0 moderate mild 9 Surgical 63 Female Former 63.5 BRPC 3 1 0 2 Gemcitabine Moderate 3 1 0 80 0 moderate present 10 Surgical 67 Male Former 88.0 BRPC 3 0 0 2 FOLFIRINOX Poor 3 1 0 40 0 moderate moderate 11 Surgical 62 Female Former 53.1 BRPC 3 0 0 3 FOLFIRINOX Moderate 3 1 0 20 0 moderate moderate 12 Surgical 70 Male No 59.0 BRPC 4 0 0 2 Gem/Abraxane Moderate 3 0 0 10 0 mild present 13 Surgical 67 Female No 56.7 LAPC 2 0 0 2 FOLFIRINOX Moderate 2 0 0 5% 0 moderate moderate 14 Surgical 55 Male No 83.9 BRPC 3 0 0 3 FOLFIRINOX Moderate 3 0 0 15 0 moderate moderate 15 Surgical 53 Female Former 50.3 BRPC 3 1 0 1 FOLFIRINOX Poor 3 0 0 35 0 mild moderate 16 Surgical 68 Female No 53.1 BRPC 4 0 0 3 FOLFIRINOX Moderate 3 1 0 n/a n/a n/a n/a 17 Surgical 62 Male No 85.7 BRPC 3 1 0 2 Gem/Paclitaxel Moderate 3 1 0 10 0 mild mild 18 Surgical 82 Female No 63.5 BRPC 4 0 0 2 Gem/Abraxane Poor 4 0 0 30 0 moderate moderate 19 Surgical 66 Male Former 85.7 BRPC 4 0 0 2 FOLFIRINOX Moderate 2 0 0 <1% 0 moderate moderate 20 Surgical 69 Female Former 56.7 BRPC 3 0 0 Not Assessed FOLFIRINOX Marked 1 0 0 <1% 0 mild moderate 21 Surgical 75 Male Former 78.9 BRPC 3 0 0 3 Gem/Abraxane Moderate 3 1 0 <1% 0 moderate mild 22 Surgical 59 Female No 65.8 BRPC 4 1 0 Not Assessed Gem/Abraxane Moderate 3 1 0 n/a n/a n/a n/a 23 Surgical 56 Male No 89.3 BRPC 2 1 0 Not Assessed Gem/Abraxane Not Assessed 3 1 1 50 0 moderate mild 24 Surgical 61 Female No 43.5 BRPC 2 0 0 2 FOLFIRINOX Poor 3 1 0 40 0 moderate mild 25 Surgical 76 Female No 60.3 BRPC 3 1 0 2 FOLFIRINOX Marked 1 0 0 5 0 moderate severe 26 Surgical 49 Male No 89.8 BRPC 2 1 0 2 FOLFIRINOX Moderate 2 1 0 5 0 mild mild 27 Surgical 67 Female No 52.5 BRPC 1 0 0 3 FOLFIRINOX Moderate 1 0 0 10 0 mild present 28 Surgical 71 Female Former 64.4 BRPC 2 0 0 2 Gem/Abraxane Moderate 2 0 0 <1% 0 moderate moderate 29 Surgical 86 Female Unknown 74.4 BRPC 3 0 0 2 Gem/Abraxane Moderate 2 1 0 10 0 mild severe 30 FNA 59 Male No 88.4 BRPC 3 0 0 Not Assessed FOLFIRINOX Not Assessed 3 0 1 31 FNA 60 Male No 54.3 LAPC 4 0 0 Not Assessed FOLFIRINOX Not Assessed 4 0 0 32 FNA 61 Female No 77.7 LAPC 3 0 0 Not Assessed FOLFIRINOX Not Assessed 3 0 0 33 FNA 80 Male Former 70.7 LAPC 3 1 0 Not Assessed Gem/Abraxane Not Assessed 3 1 1 34 FNA 57 Male Unknown 50.1 LAPC 4 1 1 2 FOLFIRINOX Moderate 3 0 0 35 FNA 59 Female Unknown 49.9 BRPC 2 0 1 Not Assessed FOLFIRINOX Not Assessed 2 0 1 36 FNA 60 Male No 90.7 BRPC 3 0 0 2 Gem/Abraxane Not Assessed 4 0 0 37 FNA 75 Male Former 80.3 BRPC 2 0 0 2 Gem/Abraxane Moderate 3 1 0 38 FNA 75 Female No 49.9 BRPC 4 0 0 3 FOLFIRINOX Poor 3 1 0 39 FNA 63 Female Former 63.5 BRPC 3 1 0 2 Gemcitabine Moderate 3 1 0 40 FNA 51 Male No 82.1 BRPC 2 1 0 2 FOLFIRINOX Moderate 3 1 0 41 FNA 67 Female No 56.7 LAPC 2 0 0 2 FOLFIRINOX Moderate 2 0 0 42 FNA 53 Female Former 50.3 BRPC 3 1 0 3 FOLFIRINOX Poor 3 0 0 43 FNA 67 Male No 71.7 BRPC 3 0 0 3 FOLFIRINOX Poor 3 1 0 44 FNA 68 Female No 53.1 BRPC 4 0 0 2 FOLFIRINOX Moderate 3 1 0 45 FNA 62 Male No 85.7 BRPC 3 1 0 2 Gem/Paclitaxel Moderate 3 1 0 46 FNA 71 Female Former 45.8 BRPC 2 0 0 Not Assessed FOLFIRINOX Complete 2 0 0 47 FNA 66 Male Former 85.7 BRPC 4 0 0 2 FOLFIRINOX Moderate 2 0 0 48 FNA 69 Female Former 56.7 BRPC 3 0 0 1 FOLFIRINOX Marked 1 0 0 49 FNA 51 Male Current 70.3 BRPC 3 0 0 2 FOLFIRINOX Moderate 3 1 0 50 FNA 62 Female Former 62.6 BRPC 3 0 0 2 FOLFIRINOX Moderate 1 1 51 FNA 56 Male No 89.3 BRPC 2 1 0 Not Assessed Gem/Abraxane Not Assessed 3 1 1 52 FNA 61 Female No 43.5 BRPC 2 0 0 3 FOLFIRINOX Poor 3 1 0 53 FNA 76 Female No 60.3 BRPC 3 1 0 1 FOLFIRINOX Marked 1 0 0 54 FNA 67 Female No 52.5 BRPC 1 0 0 3 FOLFIRINOX Moderate 1 0 0 Supplemental Table 2.

Specimen Ini�al Clinical T Clinical N Clinical M Treatment Pathologic T Pathologic N Pathologic Specimen Number type RT Age Sex Smoker WT(Kg) Resectabilit Stage Stage stage Grade NACT received Effect Stage Stage M Stage % tumor % necrosis Inflamma�on Fibrosis 1 Surgical Yes 60 Male No 90.7 Borderline 3 0 0 2 Gem/Abraxane Not Assessed 4 0 0 1 0 Mild Moderate 2 Surgical Yes 75 Female No 49.9 Borderline 4 0 0 2 FOLFIRINOX Poor 3 1 0 10 0 Moderate Moderate 4 Surgical Yes 74 Male Former 54.4 Borderline 3 0 0 2 FOLFIRINOX Moderate 1 0 0 5 0 Moderate Mild 8 Surgical Yes 53 Female Former 50.3 Borderline 3 1 0 1 FOLFIRINOX Poor 3 0 0 35 0 Mild Moderate 9 Surgical Yes 69 Female Former 56.7 Borderline 3 0 0 Not AssessedFOLFIRINOX Marked 1 0 0 <1 0 Mild Moderate

3 Surgical No 56 Male No 75.5 Resectable 3 0 0 3 None Not present 3 1 0 80 5 Moderate Mild 5 Surgical No 71 Female No 68.0 Resectable 3 0 0 2 None Not present 3 1 0 50 0 Moderate Mild 6 Surgical No 55 Male No 77.1 Resectable 3 0 0 2 None Not present 3 0 0 15 0 Moderate Moderate 7 Surgical No 66 Male No 88.0 Resectable 3 0 0 2-3 None Not present 3 1 0 10 0 Mild Moderate 10 Surgical No 65 Male Former 62.6 Resectable 3 0 0 2-3 FOLFIRINOX Absent 3 1 0 15 0 Severe Moderate 11 Surgical No 65 Female Former 61.7 Resectable 3 0 0 2-3 FOLFIRINOX Absent 1 2 0 70 15 Severe Severe Supplementary Table 3

A. Evidence for pro/an name Gene Process invasion/metastasis Proteasome subunit beta 4 PSMB4 Proteasome component pro Adhesion G -coupled receptor E5 ADGRE5 G-protein coupled receptor, cell cell interacons pro Proteasome acvator subunit 3+B48:F48 PSME3 Proteasome component pro Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 PLOD3 Rough ER Protein, collagen hydroxylaon pro ABRA C-terminal like ABRACL pro RAB7A, member RAS family RAB7a Ras-like GTPase pro EH domain containing 1 EHD1 EPS15 homology (EH) domain-containing pro Capping acn protein, gelsolin like CAPG gelsolin/villin family of acn-regulatory proteins pro AHNAK nucleoprotein 2 AHNAK2 Large nucleoprotein, calcium signaling pro ULubmiqiucainnol-cytochrome c reductase complex III LUM small leucine-rich proteoglycan (SLRP) family pro subunit VII UQCRQ Cytochrome C related pro Hexosaminidase subunit beta HEXB Lysosomal enzyme pro COP9 signalosome subunit 3 COPS3 Signaling kinase pro

Keran 6A KRT6A Type II Intermediate filament pro Glutathione peroxidase 3 GPX3 glutathione peroxidase family pro Ras related protein 2c RAP2C Ras-like GTPase pro ATPase H+ transporng V0 subunit a1 ATP6V0A1 Vacuolar proton pump ATPase pro Aminopepdase puromycin sensive NPEPPS zinc metallopepdase Voltage dependent anion channel 2 VDAC2 Mitochondrial anion channel ATPase H+ transporng V1 subunit B2 ATP6V1B2 ATPase, acidificaon of organelles Ankyrin repeat and FYVE domain containing 1 ANKFY1 Intracellular signaling V-type proton ATPase subunit D Atp6v1d vacuolar ATPase ATPase H+ transporng V1 subunit F ATP6V1F vacuolar ATPase Mannosidase alpha class 2B member 1 MAN2B1 Glycoprotein turnover Pepdylprolyl isomerase C PPIC pepdyl-prolyl cis-trans isomerase (PPIase)) family Glucosidase alpha, acid GAA Lysosomal enzyme Amidohydrolase domain containing 2 AMDHD2 Keran 33b KRT33B Type II Intermediate filament Immunoglobulin kappa light chain IGKV4-61 immunoglobulin light chain Phospholipase D family member 3 PLD3 phospholipase D (PLD) family of enzymes

B.

Evidence for Pro/an Gene name Gene Process invasion/metastasis Protein FAM107B Fam107b Migraon an Carbonyl reductase [NADPH] 3 CBr3 Migraon, proliferaon an GATA binding protein 6 GATA6 Transcripon factor an MHeetmerborgaennee-aosusso rciibaotendu cplreoogpersotteerionn pea rreccelep tFor HNRNPF Pre-mRNA processing/alternave splicingan component 2 PGRMC2 Migraon an

B-Spectrin SPTBN1 Invasion/migraon an minichromosome maintenance 6 MCM6 DNA Replicaon pro Probable ATP-dependent RNA helicase DDX46 DDX46 Invasion pro RAN binding protein 2 RANBP2 Nuclear membrane protein, GTPase, nuclepar iomport Acdevnaytlors uocf c9i0n aktDea L hyeasaet shock protein ATPase ADSL purine synthesis pro homolog 1 Ahsa1 Migraon pro Pumilio RNA binding family member 1 PUM1 RNA binding protein pro Calpain small subunit 1 CAPNS1 invasion/migraon pro Proteasome 26s subunit, non-ATPase 8 PSMD8 Proteasome 26s subunit, non-ATPase 8

Sialophorin SPN(CD43) cell surface protein on leukocytes Mitochondrial anviral-signaling protein MAVS Innate immunity UDP-N-acetylglucosamine pyrophosphorylase 1 UAP1 hexosamine biosynthesis

Topoisomerase 1 TOP1 DNA Topoisomerase

Kinecn 1 KTN1 Endoplasmic reculum processing NADH:ubiquinone oxidoreductase subunit A12 NDUFA12 Mitochondrial metabolism Eukaryoc iniaon factor S1 EIF1S1 Translaon iniaon factor Heterogeneous ribonucleoprotein parcle K HNRNPK Pre-mRNA processing/alternave splicing Sideroflexin-1 SFXN1 Serine transporter Heat Shock Protein 8 HSPA8 Heat shock protein Valyl-tRNA synthetase VARS Aminoacyl t-rna synthetase 40S ribosomal protein S6 RPS6 DNA repair,