Background Pancreatic ductal adenocarcinoma (PDAC) has dismal outcomes and is shaped by a fibroblast‐rich tumor microenvironment (TME). A cell type–resolved, module‐level understanding of cancer‐associated fibroblasts (CAFs) and their therapeutic relevance remains incompletely characterized. Methods We integrated single‐cell RNA‐seq data from six treatment‐naïve PDAC resection specimens in GSE212966; individual tumor‐stage information was not available in the public metadata. Standardized preprocessing, clustering, and major‐cell‐type annotation were performed. Contact‐mediated intercellular signaling toward fibroblasts was profiled. High‐dimensional weighted gene co‐expression network analysis (hdWGCNA) was applied to fibroblasts to identify co‐expression modules and hub genes. Associations with overall survival were assessed by univariate Cox models and Kaplan–Meier analysis; immune infiltration was evaluated with CIBERSORT and ESTIMATE; pathway associations were examined by gene set enrichment analysis (GSEA). Candidate compounds were screened via Enrichr/DSigDB and docked to target proteins using a PyMOL–Chem3D–AutoDockTools workflow. SEMA3C was further examined in PDAC cell lines by siRNA‐mediated knockdown followed by qRT–PCR, CCK‐8, wound‐healing, and Transwell invasion assays. Results We resolved 10 cell subpopulations and observed broad contact signals to fibroblasts, including the CD99–CD99 axis. hdWGCNA delineated fibroblast modules, from which four key modules were prioritized. Five genes—SEMA3C, PMP22, CPE, SNX9, and UACA—were significantly associated with overall survival. These biomarkers showed both positive and negative associations with specific immune‐cell fractions but were positively correlated with the StromalScore, ImmuneScore, and ESTIMATEScore. High‐expression groups were enriched for cancer‐relevant programs such as epithelial–mesenchymal transition, inflammatory response, and TNF α –NF‐ κ B signaling, whereas several proliferative and metabolic pathways were enriched in the CPE‐low group. In vitro, siRNA‐mediated SEMA3C knockdown in PANC‐1 and Capan‐2 cells reduced cell viability, wound closure, and invasion, supporting a cell‐intrinsic protumorigenic role of SEMA3C in PDAC cells. Coumestrol emerged as a computationally prioritized compound, and molecular docking predicted a potentially favorable interaction with SNX9 (predicted binding energy −7.5 kcal/mol); this association requires experimental validation. Conclusion An integrative single‐cell and network framework identified fibroblast‐related co‐expression modules and five survival‐associated genes in PDAC. The prognostic relevance of these genes and the predicted coumestrol–SNX9 association require further independent and experimental validation.
Early‐onset colorectal cancer (EOCRC) exhibits distinct clinical and biological features compared with late‐onset CRC (LOCRC), yet its genomic architecture and immune microenvironmental determinants remain incompletely characterized. Here, we integrated multiomics discovery analyses of 69 EOCRC and 461 LOCRC patients from the TCGA cohort, complemented by independent validation, single‐cell RNA sequencing, spatial transcriptomics, and systems‐level network analysis. We identified 10 genes significantly enriched for mutations in EOCRC, including ANXA7, ZNF267, and POLQ, which displayed distinct domain‐specific clustering and were validated in an external cohort. Mutational signature decomposition showed that EOCRC was associated with an SBS87‐like signature, whereas LOCRC was dominated by SBS1; because TCGA lacks detailed treatment history, this SBS87‐like inference should not be interpreted as direct evidence of prior thiopurine exposure. Immunologically, EOCRC displayed an immunosuppressive microenvironment characterized by elevated regulatory T cells, resting NK cells, and tighter immune‐stromal coupling, as further supported by spatial transcriptomic analysis. Single‐cell atlas analysis identified M2‐polarized, SPP1‐expressing macrophage subsets in EOCRC. Weighted gene coexpression network analysis identified a mitochondrial‐ribosomal biogenesis module as the transcriptional hallmark of EOCRC. Finally, random forest analysis identified FAT3 mutations as a genomic correlate of a hot‐like, immune‐activated phenotype in EOCRC. Integrative single‐cell analysis localized FAT3 predominantly to cancer‐associated fibroblasts, especially myofibroblasts, and an in silico FAT3 perturbation analysis suggested potential downstream programs involving extracellular matrix remodeling, inflammatory signaling, chemokine response, and mitotic spindle regulation. These findings delineate age‐stratified genomic and microenvironmental features of EOCRC and generate testable hypotheses for future functional and clinical validation.
Background Genes associated with cardiovascular diseases are strongly linked to idiopathic recurrent pregnancy loss. Because these genetic mutations often involve coagulation factors, anticoagulant therapy, particularly low‐molecular‐weight heparin, is increasingly encountered in obstetric practice in Lebanon for selected maternal and pregnancy‐related indications. However, data describing the prevalence and prescribing patterns of anticoagulant use among Lebanese obstetricians remain limited. In this multicenter retrospective case‐control study, 12 mutations within 10 CVD‐related genes in Lebanese women with a history of recurrent pregnancy loss were assessed to uncover further potential genetic links between these two conditions. Methods Data were collected from a total of 117 women with recurrent pregnancy loss (≥ 2 pregnancy losses with the same partner before the 22nd week of gestation) and 38 women with a history of at least one successful pregnancy. Data were collected from two independent medical centers in Lebanon, Abou Jaoude Hospital and the Lebanese Diagnostic Medical Center, through medical‐record review and participant interviews. Twelve mutations were covered employing polymerase chain reaction and reverse‐hybridization techniques. Because of the variation in genotyping completeness across assays, the effective sample size for individual polymorphisms ranged from 27 to 38 controls and 78 to 117 cases. Results Genetic analysis revealed a significant association between Factor V Leiden (OR = 0.31; p = 0.017), Factor XIII: V34L (OR = 0.3; p = 0.009), plasminogen activator inhibitor‐1: 4G/5G (OR = 0.3; p = 0.034), and lower odds of recurrent pregnancy loss. However, these associations did not remain significant after correction for multiple testing and should therefore be considered exploratory. No significant associations were observed for other evaluated polymorphisms, including methylenetetrahydrofolate reductase C677T and A1298C. Conclusion Repeated pregnancy loss is multifaceted and not necessarily linked to coagulopathy‐related mutations; in the Lebanese population, certain polymorphisms showed nominal associations with lower odds of recurrent pregnancy loss that require confirmation in larger, independent studies, and no statistically significant association was observed between methylenetetrahydrofolate reductase mutations and recurrent pregnancy loss in the present study. These findings suggest that the routine presumption of a thrombophilic etiology in recurrent pregnancy loss may not be universally applicable. Future research should prioritize validating these genetic associations in larger, adequately powered cohorts and exploring the underlying biological mechanisms before any therapeutic implications are considered.
Immune checkpoint inhibitors (ICIs) are first‐line therapies for advanced Nonsmall cell lung cancer (NSCLC), yet managing ICI resistance remains a critical, unavoidable challenge. This study identified genetic markers of anti‐PD‐1 resistance and developed an exploratory predictive model to differentiate responsive and resistant NSCLC patients. The GSE126044 transcriptomic subseries was used as the discovery cohort and included 16 pretreatment NSCLC biopsies (5 responders and 11 nonresponders). The prespecified eight‐gene score was re‐evaluated using repeated stratified out‐of‐fold prediction and was further assessed in two independent checkpoint‐blockade cohorts. The averaged out‐of‐fold AUC in GSE126044 was 0.982 (95% CI 0.931–1.000), although the eight genes had been selected before cross‐validation. External discrimination was limited in GSE135222 (AUC = 0.636, 95% CI 0.363–0.909) and GSE253564 (AUC = 0.567, 95% CI 0.230–0.903). These findings do not support stable generalization of the score across independent treatment settings. The eight‐gene score should be regarded as an exploratory checkpoint‐blockade response‐associated signature. Its potential clinical value requires validation in larger, prospectively collected cohorts with harmonized treatment and response endpoints.
Ciliopathies represent a diverse group of inherited disorders resulting from dysfunctional cilia. A rare subset is associated with biallelic variants in WDR19, with fewer than 100 affected individuals reported worldwide. This study is aimed at reviewing the clinical and molecular spectrum of WDR19-associated ciliopathies, with a particular focus on genotype-phenotype correlations. We report a 32-year-old woman with renal, ocular and hepatic manifestations attributed to compound heterozygous variants in WDR19, and reviewed available data from 93 previously published cases. Missense, truncating, splice-site and copy number variants have all been reported, with renal, ocular, skeletal and hepatic involvement most frequently observed. Genotype-phenotype analyses indicated that the presence of a truncating variant was associated with increased likelihood of skeletal involvement and reduced likelihood of hepatobiliary disease compared with individuals harbouring only missense variants. Amongst individuals with only missense variants, variants located outside repeat protein domains were associated with early symptom onset (before 16 years of age) and with ocular manifestations. Notably, recurrent variants demonstrated considerable phenotypic variability. This study represents the largest review of WDR19 variants to date and contributes to current understanding of WDR19-related disease.
