Pancreatic ductal adenocarcinoma (PDAC) is a highly heterogeneous cancer with poor prognosis and limited therapeutic options. Bulk transcriptomic profiling has identified two major gene expression-based molecular subtypes: classical/progenitor and basal-like/squamous/quasimesenchymal. These subtypes differ in biological characteristics, differentiation status, drug sensitivity, and clinical outcomes. Advances in single-cell and spatial transcriptomics have further revealed intermediate/hybrid states, as well as distinct subtypes within the tumor microenvironment. These technologies have also uncovered intratumoral heterogeneity, tumor-stroma interactions, and spatially organized transcriptional programs that further shape subtype identity and plasticity, which can shift over time or under therapeutic pressure. In parallel, metabolomic analyses have revealed distinct metabolic subtypes that align with molecular subtypes and highlight subtype-specific metabolic rewiring and vulnerabilities. Furthermore, recent deep learning approaches applied to histopathology allow for high-resolution, morphology-based subtype prediction using Hematoxylin & Eosin-stained slides, providing practical and potentially scalable diagnostic tools. These multi-layered insights are reshaping PDAC taxonomy and enhancing our understanding of how transcriptional, metabolic, and spatial features together define tumor behavior and therapeutic response. This review discusses molecular (transcriptomic), metabolic, and histological subtyping approaches for PDAC, with the aim of enabling practical, cost-effective diagnosis and personalized medicine. By integrating data from recent experimental and clinical studies, we aim to provide a comprehensive and accessible overview of PDAC subtype heterogeneity, which may help guide future subtype-informed therapeutic strategies.

Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous disease with distinct molecular subtypes described as classical/progenitor and basal-like/squamous PDAC. We hypothesized that integrative transcriptome and metabolome approaches can identify candidate genes whose inactivation contributes to the development of the aggressive basal-like/squamous subtype. Using our integrated approach, we identified endosome-lysosome associated apoptosis and autophagy regulator 1 (ELAPOR1/KIAA1324) as a candidate tumor suppressor in both our NCI-UMD-German cohort and additional validation cohorts. Diminished ELAPOR1 expression was linked to high histological grade, advanced disease stage, the basal-like/squamous subtype, and reduced patient survival in PDAC. In vitro experiments demonstrated that ELAPOR1 transgene expression not only inhibited the migration and invasion of PDAC cells but also induced gene expression characteristics associated with the classical/progenitor subtype. Metabolome analysis of patient tumors and PDAC cells revealed a metabolic program associated with both upregulated ELAPOR1 and the classical/progenitor subtype, encompassing upregulated lipogenesis and downregulated amino acid metabolism. 1-Methylnicotinamide, a known oncometabolite derived from S-adenosylmethionine, was inversely associated with ELAPOR1 expression and promoted migration and invasion of PDAC cells in vitro. Taken together, our data suggest that enhanced ELAPOR1 expression promotes transcriptome and metabolome characteristics that are indicative of the classical/progenitor subtype, whereas its reduction associates with basal-like/squamous tumors with increased disease aggressiveness in PDAC patients. These findings position ELAPOR1 as a promising candidate for diagnostic and therapeutic targeting in PDAC.

Pancreatic ductal adenocarcinoma (PDAC) manifests diverse molecular subtypes, including the classical/progenitor and basal-like/squamous subtypes, with the latter known for its aggressiveness. We employed integrative transcriptome and metabolome analyses to identify potential genes contributing to the molecular subtype differentiation and its metabolic features. Transcriptome analysis in PDAC patient cohorts revealed downregulation of adrenoceptor alpha 2A (ADRA2A) in the basal-like/squamous subtype, suggesting its potential role as a candidate suppressor of this subtype. Reduced ADRA2A expression was significantly associated with a high frequency of lymph node metastasis, higher pathological grade, advanced disease stage, and decreased survival among PDAC patients.In vitroexperiments demonstrated thatADRA2Atransgene expression and ADRA2A agonist inhibited PDAC cell invasion. Additionally, ADRA2A-high condition downregulated the basal-like/squamous gene expression signature, while upregulating the classical/progenitor gene expression signature in our PDAC patient cohort and PDAC cell lines. Metabolome analysis conducted on the PDAC cohort and cell lines revealed that elevated ADRA2A levels were associated with suppressed amino acid and carnitine/acylcarnitine metabolism, which are characteristic metabolic profiles of the classical/progenitor subtype. Collectively, our findings suggest that heightened ADRA2A expression induces transcriptome and metabolome characteristics indicative of classical/progenitor subtype with decreased disease aggressiveness in PDAC patients. These observations introduce ADRA2A as a candidate for diagnostic and therapeutic targeting in PDAC.

Pancreatic ductal adenocarcinoma (PDAC) encompasses diverse molecular subtypes, including the classical/progenitor and basal-like/squamous subtypes, each exhibiting distinct characteristics, with the latter known for its aggressiveness. We employed an integrative approach combining transcriptome and metabolome analyses to pinpoint potential genes contributing to the basal-like/squamous subtype differentiation. Applying this approach to our NCI-UMD-German and a validation cohort, we identified LIM Domain Only 3 (LMO3), a transcription co-factor, as a candidate suppressor of the basal-like/squamous subtype. Reduced LMO3 expression was significantly associated with higher pathological grade, advanced disease stage, induction of the basal-like/squamous subtype and decreased survival among PDAC patients. In vitro experiments demonstrated that LMO3 transgene expression inhibited PDAC cell proliferation and migration/invasion, concurrently downregulating the basal-like/squamous gene signature. Metabolome analysis of patient tumors and PDAC cells revealed a metabolic program linked to elevated LMO3 and the classical/progenitor subtype, characterized by enhanced lipogenesis and suppressed amino acid metabolism. Notably, glycerol 3-phosphate (G3P) levels positively correlated with LMO3 expression and associated with improved patient survival. Furthermore, glycerol-3-phosphate dehydrogenase 1 (GPD1), a crucial enzyme in G3P synthesis, showed upregulation in LMO3-high and classical/progenitor PDAC, suggesting its potential role in mitigating disease aggressiveness. Collectively, our findings suggest that heightened LMO3 expression reduces transcriptome and metabolome characteristics indicative of basal-like/squamous tumors with decreased disease aggressiveness in PDAC patients. The observations describe LMO3 as a candidate for diagnostic and therapeutic targeting in PDAC.

Inflammation and aberrant cellular metabolism are widely recognized as hallmarks of cancer. In pancreatic ductal adenocarcinoma (PDAC), inflammatory signaling and metabolic reprogramming are tightly interwoven, playing pivotal roles in the pathogenesis and progression of the disease. However, the regulatory functions of inflammatory mediators in metabolic reprogramming in pancreatic cancer have not been fully explored. Earlier, we demonstrated that pro-inflammatory mediator macrophage migration inhibitory factor (MIF) enhances disease progression by inhibiting its downstream transcriptional factor nuclear receptor subfamily 3 group C member 2 (NR3C2). Here, we provide evidence that MIF and NR3C2 interactively regulate metabolic reprogramming, resulting in MIF-induced cancer growth and progression in PDAC. MIF positively correlates with the HK1 (hexokinase 1), HK2 (hexokinase 2) and LDHA (lactate dehydrogenase) expression and increased pyruvate and lactate production in PDAC patients. Additionally, MIF augments glucose uptake and lactate efflux by upregulating HK1, HK2 and LDHA expression in pancreatic cancer cells in vitro and in mouse models of PDAC. Conversely, a reduction in HK1, HK2 and LDHA expression is observed in tumors with high NR3C2 expression in PDAC patients. NR3C2 suppresses HK1, HK2 and LDHA expression, thereby inhibiting glucose uptake and lactate efflux in pancreatic cancer. Mechanistically, MIF-mediated regulation of glycolytic metabolism involves the activation of the mitogen-activated protein kinase-ERK signaling pathway, whereas NR3C2 interacts with the activator protein 1 to regulate glycolysis. Our findings reveal an interactive role of the MIF/NR3C2 axis in regulating glucose metabolism supporting tumor growth and progression and may be a potential target for designing novel approaches for improving disease outcome.

Supplementary Figures 7-8 from Regulation of Human Nitric Oxide Synthase 2 Expression by Wnt β-Catenin Signaling

Supplementary Figure 6 from The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress

Table S3: List of 1820 differentially expressed genes between short and long survival groups

Supplementary Figure 2 from The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress

Figure S1: Representative pictures of immunohistochemical staining, showing NOSTRIN expression largely in the tumor cells in the patient with long survival. Figure S2: NOSTRIN overexpression sensitizes the Panc1 pancreatic cancer cells to gemcitabine. Figure S3: (a) A negative correlation existed between miR-222 and NOSTRIN expression in tumors from PDAC cases (N=37). (b) miR-222 expression does not show any significant association with survival. (ns=non significant).

Supplementary Figure 4 from Nitric Oxide, a Mediator of Inflammation, Suppresses Tumorigenesis

Supplementary Tables S1-S5 from The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress

Supplementary Figure S3 - PDF file 112K, Immunohistochemical staining of PNLIP in pancreatic tumors and adjacent nontumor tissue

Supplementary Figure 5 from Nitric Oxide, a Mediator of Inflammation, Suppresses Tumorigenesis

Supplementary Table S1 - PDF file 67K, Characteristics of Patients

Supplementary Figure Legends from Quantitative Detection of p53 Mutations in Plasma DNA from Tobacco Smokers

Table S1: Clinical characteristics of long and short survival groups of PDAC patients in test cohort. Table S2: Clinical Characteristics of test and validation cohorts.

Abstract Inflammation influences the development of cancer. The nitric oxide synthase (NOS2) is induced by inflammatory cytokines, e.g., tumor necrosis factor α and interleukin 1β, and produces nitric oxide (NO·), a critical mediator of the inflammatory response. Because p53 governs NO· production by transcriptionally transrepressing NOS2, we used a genetic strategy to determine whether NO· and p53 cooperatively regulate tumorigenesis. Lymphomas developed more rapidly in p53−/−NOS2−/− or p53−/−NOS2+/− mice than in p53−/−NOS2+/+ mice that were cross-bred into a >95% C57BL6 background and maintained in a pathogen-free condition. Likewise, sarcomas and lymphomas developed faster in p53+/−NOS2−/− or p53+/−NOS2+/− than in p53+/−NOS2+/+ mice. When compared with the double knockout mice, p53−/−NOS2+/+ mice showed a higher apoptotic index and a decreased proliferation index with an increased expression of death receptor ligands, CD95-L and tumor necrosis factor-related apoptosis-inducing ligand, and the cell cycle checkpoint protein, p21waf1, in the spleen and thymus before tumor development. Furthermore, mice deficient in both p53 and NOS2 produced a high level of anti-inflammatory interleukin 10 when compared with p53-deficient mice. These studies provide genetic and mechanistic evidence that NO· can suppress tumorigenesis.

Supplementary Figure 1 from The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress