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Systematic Reviews
Copyright: ©Author(s) 2026.
World J Transl Med. Nov 28, 2026; 12(4): 126295
Published online Nov 28, 2026. doi: 10.5528/wjtm.126295
Table 1 Population, intervention, comparison, outcome, and study design framework for study eligibility
Criteria
Review stage
Inclusion
Exclusion
Study designAbstract/full article reviewOriginal human studies evaluating the prognostic significance of tumor-derived transcriptomic and/or proteomic biomarkers in PDAC. Eligible designs include prospective or retrospective cohort studies, nested biomarker studies, translational correlative studies embedded within clinical trials, and secondary analyses of publicly available human molecular datasets (e.g., TCGA, ICGC, CPTAC). Eligible only if the study demonstrated an independent prognostic biomarker, i.e. the tumor transcriptomic/proteomic biomarker remained significantly associated with the survival outcome in an adjusted multivariable time-to-event model including clinicopathological covariatesIn vitro studies, cell line studies, animal studies, narrative reviews, systematic reviews, meta-analyses, editorials, letters, commentaries, protocols, case reports, case series with insufficient outcome data, and conference abstracts without full-text data
PopulationAbstract/full article reviewAdults (≥ 18 years) with histologically confirmed PDAC, including resectable, locally advanced unresectable, and metastatic disease, provided that survival or other prognostic outcome data were availableStudies focused exclusively on non-PDAC malignancies, including pancreatic neuroendocrine neoplasms, periampullary cancers, ampullary cancers, cholangiocarcinoma, acinar cell carcinoma, or mixed pancreatic tumor populations where PDAC-specific results cannot be disaggregated
Treatment/interventionAbstract/full article reviewTumor molecular profiling using transcriptomic or proteomic methods, including RNA sequencing, gene expression microarrays, qPCR-based tumor expression profiling, mass spectrometry-based proteomics, RPPA, or molecular signatures derived from transcriptomic/proteomic datasetsStudies based solely on clinical variables, histopathology without molecular profiling, circulating biomarkers only, imaging biomarkers only, radiomics without molecular tumor data, genomic/DNA-only biomarkers without transcriptomic or proteomic readout, or studies lacking explicit biomarker assessment
ComparatorAbstract/full article reviewComparisons across biomarker-defined strata, such as high vs low expression, biomarker-positive vs biomarker-negative status, molecular subtype classification, or low- vs high-risk prognostic groups derived from transcriptomic/proteomic signaturesStudies with no biomarker-based stratification or no analysable comparison across molecular groups
OutcomesAbstract/full article reviewPrimary outcome: OS. Secondary outcomes: PFS, DFS, RFS, CSS, PFI, and other clinically relevant time-to-event prognostic outcomesStudies not reporting survival, recurrence, or other prognostic time-to-event outcomes; studies reporting only treatment response without survival correlation
Biomarker modality and sample typeAbstract/full article reviewEligible only if the biomarker was a transcriptomic (RNA) or proteomic readout measured in PDAC tumor tissue (resection specimen, biopsy, or FFPE/fresh-frozen archival tissue), including tumor tissue profiled by RNA-seq, microarray, qPCR, NanoString, mass spectrometry, RPPA, or IHC-validated protein expression where the protein readout was the tested prognostic marker. Multimodal studies are eligible if tumor transcriptomic/proteomic results are reported separately and can be disaggregatedNot eligible: (1) Liquid biopsy/circulating analytes as the sole readout (ctDNA, cfDNA, CTCs, circulating or exosomal miRNA/mRNA, plasma or serum proteomics, CA19-9 and other serum markers); (2) Histopathology alone (grade, stage, margin status, lymphovascular or perineural invasion, tumor budding, stroma scoring) without a molecular readout; (3) Genomic/DNA-only markers (KRAS, TP53, SMAD4, or CDKN2A mutations; copy number; methylation; TMB; MSI) with no transcript- or protein-level measurement; (4) Imaging/radiomics markers; and (5) Germline variants. These modalities were recorded at screening but excluded from data extraction unless accompanied by a tumor transcriptomic or proteomic result
Table 2 Prognostic strength of biomarkers in pancreatic ductal adenocarcinoma (57 biomarker studies; 14 interventional trials are presented separately in Table 3)
Biomarker
Type
Outcome
Multivariable analysis
Independent prognostic association
Validation
Internal descriptive category
Ref.
UFM1Single proteinOS/PFSYesYesLimitedBWang et al[14]
9-gene signatureMulti-geneOSYesYesExternalA-Wang et al[15]
3-gene MRSMulti-geneOSYesYesExternalALi et al[16]
LMRGSMulti-gene MLOSYesYesMulti-cohortAGe et al[17]
PCLM-BM signatureMulti-geneOSYesYesExternalA-Zhou et al[18]
MCMBPSingle geneOSYesYesExternalAZhang et al[19]
APOBEC scoreGenomicOSYesYesExternalAYu et al[20]
JUPSingle geneOSYesLikelyLimitedBYang et al[21]
Manganese metabolism signatureMulti-geneOSYesYesExternalAXiong et al[22]
ALDH familyMulti-geneOSYesLikelyLimitedBWu et al[23]
EFFscore/P2RY6Multi-geneOSYesYesExternalAWang et al[24]
mCAF signatureMulti-geneOSYesYesMulti-cohortAWang et al[25]
18-gene immune signatureMulti-geneOSYesYesExternalAWang et al[26]
PCD signatureMulti-geneOSYesYesMulti-cohortAWang et al[27]
ICD signature (AJM1)Multi-geneOSYesYesExternalAMa et al[28]
MDRG/CITED4Multi-geneOSYesLikelyLimitedBLiu et al[29]
IGFBP signatureMulti-geneOSYesYesExternalAGuan et al[30]
A2ML1 subtype modelMulti-geneOSYesYesMulti-cohortAGe et al[31]
BM-related signature (LAMA3/ITGA3/ITGB6)Multi-geneOSYesYesExternalAGe et al[32]
ER stress-related TF signatureMulti-geneOSYesYesExternalAGao et al[33]
PLAAT2Single geneOSYesYesExternalAChen et al[34]
LY6D (stem-like, gastric-like cell-state marker)Single geneOSYesYesLimitedBShi et al[35]
Disulfidptosis-related gene signature; key genes: RPN1, PML; Model genes: NDUFA11, MYH14, TRIP6, ACTN1, ANP32E, PML, CD2AP, RPN1Multi-gene signatureOSYesYesExternalA-Pei et al[36]
Palmitoylation-related gene signature (7 genes: DCBLD2, CXCL5, ASPH, LAMC2, KRT6A, TOP2A, NPNT); Upstream regulators: ZDHHC family (palmitoyl transferases)Multi-gene signatureOSYesYesExternalA-Lu et al[37]
7-gene SASP prognostic signature: ANGPTL4, DKK1, EREG, IGFBP3, IL18, MMP13, PLAU; Plus SASP molecular subtypesMulti-gene signatureOSYesYesMulti-cohortAKuang et al[38]
SEMA3 family genes; 9-gene prognostic signature derived from SEMA3-related DEGs; key driver: SEMA3CMulti-gene signatureOSYesYesExternalA-Jin et al[39]
Six-gene mitophagy-related signature (PAPPA, NBPF12, CXCL11, CKLF-CMTM1, CCDC6, AHNAK)Multi-gene signatureOSYesYesMulti-cohortACai et al[40]
Six ICD-associated lncRNA prognostic signature: ZEB2-AS1, AC099792.1, LINC01091, LINC02613, AC005304.3, LINC00705Multi-gene signatureOSYesYesExternalA-Zhu et al[41]
11-gene ITH-related prognostic signatureMulti-gene signatureOSYesYesMulti-cohortAZhao et al[42]
Ferroptosis-related 3-gene signature (NOTCH2, KRT18, H1-2); key single biomarker: NOTCH2Multi-gene signatureOSYesYesMulti-cohortAZhang et al[43]
16-gene DNA damage and repair-related prognostic risk score model; key experimental gene: LY6DMulti-gene signatureOSYesYesMulti-cohortAZhang et al[44]
STING signalling pathway-derived 6-gene prognostic signature: DTX4, IFI16, MAVS, PRKDC, ZDHHC1, IFIT2Multi-gene signatureOSYesYesExternalAYu et al[45]
SERPINE1Single geneOSYesYesExternalAWang et al[46]
KRAS protein level, KRAS mRNA expression, KRAS mutation status/subtypeSingle geneOSYesYesLimitedBStålberg et al[47]
RAD51AP1 (DNA repair-associated protein)Single geneOSYesYesExternalA-Rezagholizadeh et al[48]
Mitochondrial 12-gene prognostic signature; mechanistic emphasis on CAMK2A and THEM4Multi-gene signatureOSYesYesMulti-cohortANie et al[49]
Innate immune barrier gene signature (84 genes); key genes: UBASH3B, ITGB6, COL17A1, MMP28, DIAPH3 (focus on UBASH3B)Multi-gene signatureOSYesYesMulti-cohortALuo et al[50]
P4HA1, CCDC148, UCA1, TMPRSS11E + tumour stageMulti-gene signatureOSYesYesMulti-cohortALin et al[51]
KRAS mutational status as key biomarker; integrated molecular classifier of KRAS wild-type vs KRAS-mutant classical vs KRAS-mutant basal-like; exploratory HRD and other somatic mutationsMulti-gene signatureOSYesYesInternalB+Lansbergen et al[52]
PAUF (ZG16B-related protein product)Single geneOSYesYesLimitedBKim et al[53]
Six BA-related prognostic genes: SERPINB5, CALU, TFRC, LY6D, SFRP1, GBP2Multi-gene signatureOSYesYesExternalA-Kang et al[54]
TIPARP (PARP7) expressionSingle geneOSYesYesLimitedBJiang et al[55]
Microenvironmental, stromal, and immune markers, including MFAP4, EGR3, KRT8, monocyte infiltration, CD68+ macrophages, CD3/CD4/CD8 T-cell infiltrationMulti-gene signatureOSYesYesLimitedBHan et al[56]
Hypoxia score; 13-gene signature (including LYZ, PLAU, INSIG2, and KRTCAP2)Multi-gene signatureOS/PFSYesYesExternalAGe et al[57]
CSCLPI genes (SHCBP1, CEP55, GMNN, CDCA5, FAM111B)Multi-gene signatureOSYesYesLimitedBFang et al[58]
23 ISGS-based features in risk score modelMulti-gene signatureOSYesYesExternalAFang et al[59]
Cuproptosis-related lncRNA prognostic model; key lncRNAs: LINC00900 and AC078820.1Multi-gene signatureOSYesYesPartialB+Duo et al[60]
ST3GAL2, SLCO1B3, PTGES, PRKACAMulti-gene signatureOS/PFSYesYesExternalA-Deng et al[61]
DCBLD2, OCIAD2, SAMD9Multi-gene signatureOSYesYesExternalACui et al[62]
Disulfidptosis-related prognostic signature (8-gene signature: SLC3A2, HMGA1, S100A2, DUSP5, SPRR1B, MET, CREB5, MACROD2)Multi-gene signatureOSYesYesMulti-cohortACui et al[63]
M2 macrophage-related 6-gene prognostic signature: CCL2, CD9, FBP1, LIMS1, LYZ, TGFBI; M2/TAM biology and TNFRSF12A also highlightedMulti-gene signatureOSYesYesPartialB+Chen et al[64]
20-protein diagnostic panel; 4 proteomic prognostic subtypes; 18-protein prognostic risk score (PURB, SDCBP2, CD2BP2, GALM, SERPINA3, OAS3, FAN1, ZPR1, KRT2, NUDT2, SMNDC1, SERPINA4, CUTA, WDR36, POSTN, CLEC11A, PEX14, PI4KA)Multi-protein signatureOSYesYesExternalAAref et al[65]
Complement pathway genes (C1R, C1S, C3, C4B, C7) in tumour microenvironmentMulti-gene signatureOSYesYesPartialB+Zhang et al[66]
13-gene autophagy-related signature (EIF4EBP1, HDAC6, GABARAP, CASP4, ATG16 L2, BCL2 L1, BAG3, ATG4B, TNFSF10, PTK6, ITGA3, BIRC5, BAK1)Multi-gene signatureOSYesYesExternalA-Wang et al[67]
Fibroblast-related 14-gene prognostic signatureMulti-gene signatureOSYesYesMulti-cohortAWang et al[68]
ANP32ESingle geneOSYesYesExternalA-Liu et al[69]
Cuproptosis-related signature score (MIR3677, AC068620.2, UPK2, LDHAP7, FAM83A)Multi-gene signatureOSYesYesExternalA-Ge et al[70]
Table 3 Characteristics and reported outcomes of interventional trials included for clinical context in pancreatic ductal adenocarcinoma
NCT
Study design
n
Intervention
Stage
Primary outcome
Result
Secondary outcomes
Key finding
Ref.
NCT01726582Single-arm130Personalised perioperative treatment (chemo/CRT/surgery)Resectable/borderline resectableCompletion of surgery (feasibility)108/130 (83.1%)OS: 45 months vs 11 months; PFS: 36/130 (27.7%); Biomarker: 93/130 (71.5%); CR: 0/107; Near CR: 17/107; PR: 44/107; Poor: 42/107The study demonstrated a high rate of completion of surgery (83.1%)Tsai et al[71]
NCT00536874Single-arm35Gem + oxaliplatin (neoadjuvant)Resectable18-month OS rate63% (95%CI: 45-76)OS: 39.6 months; PR: 4/35; SD: 28/35; PD: 3/35; CEA Δ: -5.1%; CA19-9 Δ: -25.6%The 18-month OS rate was 63% (95%CI: 45%-76%)O’Reilly et al[72]
NCT01926197Randomised13/12mFOLFIRINOX vs mFOLFIRINOX + SBRTLocally advanced (unresectable)PFS (median)6.5 months vs 8.4 monthsLocal PFS: 6.5 vs 8.4; PFS 1 year: 5/13 vs 2/12; MFS: 12.9 vs 10.8; OS: 12.9 vs 13.4; GI toxicity events: 16 vs 19Median PFS was numerically higher in the SBRT arm (8.4 months vs 6.5 months)Vitzthum[73]
NCT00810719Single-arm30Gem + erlotinibAdvanced/metastaticPFS (median)2.07 months (1.87-5.50)ORR: 11%; OS: 5.67 months (2.83-11.87)The observed median PFS of 2.07 months indicated limited disease controlSemrad et al[74]
NCT00769483Phase I/II, non-randomised, multi-armApproximately 15/armMK-0646 + Gem ± erlotinibStage IV (metastatic)MTD + PFS (time to progression/death)MTD: 10 mg/kg (Gem), 5 mg/kg (Gem + erlotinib); PFS: Approximately 1.8-2.0 monthsOS: 5.7-10.4 months; ORR: Approximately 13%-17%; Toxicity: HighThe study achieved its dose-escalation objective (MTD), but showed limited efficacy with median PFS of approximately 2 monthsAbdel-Wahab et al[75]
NCT00365144Single-arm36Bevacizumab + erlotinibMetastatic, Gem-refractoryOS rate (6 months) + safety8/36 (22.2%)ORR: 1/36 (2.8%); TTP: 40 days (35-41); CA19-9 decline ≥ 25%: 4/26 (15.4%)Low 6-month OS rate (22.2%)Ko et al[76]
NCT00550836Randomised46/46Gem + erlotinib vs + panitumumabMetastaticOS (median; arm A vs arm B)4.2 months vs 8.3 months; P = 0.36ORR: 8.7% vs 6.5%; PFS: 2.0 months vs 3.6 months, P = 0.419; TTF: 2.0 months vs 3.8 months, P = 0.36; G3+ AE: 41/46 vs 41/46; G4+ AE: 15/46 vs 14/46Primary endpoint was not metHalfdanarson et al[77]
NCT03941093Randomised, double-blind143/141Pamrevlumab + G/nab-P or FOLFIRINOX vs placebo + G/nab-P or FOLFIRINOXLocally advanced, unresectableOS17.25 months vs 17.94 months; HR 1.08 (0.83-1.41); P = 0.5487EFS: 5.72 months vs 5.78 months; PFS: 9.36 months vs 9.40 months; ORR: 43/143 (30.1%) vs 64/141 (45.4%)Primary endpoint not metPicozzi et al[78]
NCT00408564Single-arm38-39Gem + oxaliplatin + cetuximab, reassessment, surgery or RT/capecitabineLocally advanced, unresectable, nonmetastatic6-month PFS rate82% (70%-95%)G3-4 AE: 9/39 (23.1%); OS rate: 49% (36%-68%); ORR: 5/38 (13.2%)High 6-month PFS rateMedical University of South Carolina[79]
NCT00521404Single-arm61CS-1008 (anti-DR5) + GemUnresectable/metastatic (chemo-naive)16-week PFS rate52.5% (39.3%-64.1%)PFS: 3 months 59%, 6 months 34.4%; OS: 6 months 55.7%, 12 months 24.6%; ORR: 5/61 (8.2%); SD: 28/61 (45.9%)Modest activitySankyo[80]
NCT00417976Single-arm39-40Bevacizumab + Gem + infusional 5-FUStage III-IV6-month PFS rate49%ORR: 12/40 (30%); SD: 18/40 (45%); PD: 10/40 (25%)Moderate activityBekaii-Saab[81]
NCT00499486Single-arm31Sirolimus monotherapyAdvanced PDAC, post-Gem (refractory)6-month OS rate26%CR + PR: 0%. SD: 4 patients (approximately 13%). ORR = 0%mTOR inhibition alone is insufficient in PDACGarrido-Laguna et al[82]
NCT01560949Single-arm33mFOLFIRINOX, Gem-based CRT, surgeryBorderline resectable/high-risk resectableResectability rate15/33 (45.5%)R0: 10/15 (66.7%); DFS: 11.1 months (5.8-NA); OS: 24.0 months (16.2-29.6); SMAD4+ pre: 4/15 (26.7%); SMAD4+ post: 4/15 (26.7%); Local recurrence: 0/15; Distant recurrence: 10/15 (66.7%)Moderate conversion to surgery; distant failure predominatesM.D. Anderson Cancer Center[83]
NCT01146054Single-arm49SBRT + GemLocally advanced, unresectable, nonmetastaticLate GI toxicity ≥ grade 2 at 1 year5/49 (10.2%)Acute GI toxicity: 14/49 (28.6%); PFS: 7.8 months (5.8-10.2); OS: 13.9 months (10.2-16.7); FFLP: 0.78 (0.60-0.89)Low late GI toxicity; local control > systemic controlKoong[84]
Table 4 Comparison of prognostic performance between the initial biologically derived signature and the least absolute shrinkage and selection operator-derived 5-gene signature in The Cancer Genome Atlas pancreatic adenocarcinoma cohort
Prognostic model
Cox model
Hazard ratio
P value
Harrell’s C-index
95%CI
Initial biologically derived signatureUnivariable1.130.2390.5220.472-0.579
Multivariable1.080.4800.5630.498-0.626
LASSO-derived 5-gene signatureUnivariable6.41< 0.0010.5870.526-0.634
Multivariable6.13< 0.0010.5990.534-0.653
Table 5 Calibration, overall prediction accuracy and baseline survival for the initial biologically derived signature and the least absolute shrinkage and selection operator-derived 5-gene signature in The Cancer Genome Atlas pancreatic adenocarcinoma derivation cohort and the Gene Expression Omnibus dataset GSE71729 validation cohort
Cohort
Model
Calibration slope
Brier score at 1/2/3 year
Integrated Brier score, 0-3 years
Baseline survival at 1/2/3 years (%)
TCGA-PAAD derivation cohort (n = 177, 93 events)LASSO-derived 5-gene signature, univariable1.8610.183/0.203/0.1710.16876.9/42.0/35.4
LASSO-derived 5-gene signature, multivariable1.8170.163
Initial biologically derived signature, univariable0.1240.185/0.240/0.2250.18675.5/40.5/35.2
Initial biologically derived signature, multivariable0.173
GSE71729 validation cohort (n = 125, 84 events)LASSO-derived 5-gene signature, univariable0.1540.234/0.213/0.1630.18964.0/33.3/22.2
LASSO-derived 5-gene signature, subtype-adjusted0.2230.177


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