Background: Hilar cholangiocarcinoma (HC) is a highly aggressive malignancy with a poor prognosis, highlighting the urgent need to elucidate its molecular drivers. This study aimed to systematically identify and functionally validate key genes and pathways driving HC pathogenesis. Methods: RNA sequencing (RNA-seq) was performed on paired primary HC tumors and matched adjacent non-tumorous tissues to identify differentially expressed genes (DEGs). Subsequent bioinformatic analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction, were conducted to characterize the functional landscape and identify hub genes. Transwell assays and orthotopic metastatic models were used to investigate the functions of Contactin-1 (CNTN1) in HC invasion in vitro and metastasis in vivo. Results: RNA-seq analysis identified 35 DEGs in HC, mainly involved in cell adhesion, cytoskeletal regulation, and axon development. PPI network analysis identified six hub genes, including CNTN1, NCAM1, PLP1, GPM6B, SLC1A3, and PMP2. Furthermore, we demonstrated that CNTN1, a neuronal membrane glycoprotein, was markedly up-regulated in HC at both mRNA and protein levels, and its elevated expression correlated with poor prognosis. Gain- and loss-of-function studies demonstrated that CNTN1 promotes HC cell invasion in vitro and metastasis in vivo. Mechanistically, CNTN1 exerts its pro-invasive effects by activating the PI3K-AKT signaling pathway and inducing epithelial-mesenchymal transition (EMT). Conclusions: Our integrated analysis identifies CNTN1 as a critical oncogenic driver in HC, promoting metastasis through PI3K-AKT-mediated EMT. These findings nominate CNTN1 as a potential prognostic biomarker and therapeutic target in HC.

Risk stratification in hepatocellular carcinoma (HCC) is limited by the lack of robust biomarkers reflecting tumor biology. The antioxidant enzyme Paraoxonase-1 (PON1) shows prognostic potential, yet its role in tumor tissues and the feasibility of non-invasive assessment remain unclear. Senescence-related pathways and prognostic candidates were screened using transcriptomic data from TCGA-LIHC and GTEx. PON1 expression was validated in multicenter cohorts through qPCR, immunohistochemistry, and Western blotting. Functional assays in PON1 knockdown and overexpression models evaluated oxidative stress, glutathione balance, mitochondrial dysfunction, and senescence markers. We developed a radiomics model based on contrast-enhanced CT scans with super-resolution reconstruction to predict tumoral PON1 expression. This radiomics signature was then integrated with clinical variables to build a combined model, which was evaluated across training, validation, test, and external cohorts. PON1 was identified as a downregulated senescence-related prognostic gene. Low PON1 expression was associated with poorer overall and progression-free survival across independent clinical cohorts. PON1 depletion increased intracellular and mitochondrial ROS, lowered the GSH/GSSG ratio, impaired mitochondrial membrane potential, and induced senescence phenotypes, while its restoration mitigated these effects. SR-enhanced radiomics improved prediction of tumoral PON1 expression across all cohorts. Integration of radiomics signatures with clinical variables further improved discrimination, achieving the highest accuracy and net clinical benefit. PON1 downregulation contributes to oxidative stress–driven senescence and unfavorable clinical outcomes in HCC. SR-enhanced radiomics provides an accurate, non-invasive method for estimating tumoral PON1 expression, demonstrating potential value for radiogenomic profiling and preoperative risk stratification.

Background and Objective:Microtubules (MTs) are essential components of the cytoskeleton and regulate fundamental cellular processes, including cell division, maintenance of cell shape, and intracellular transport. Post-translational modifications (PTMs) of tubulin, such as acetylation, detyrosination, methylation, and polyglutamylation, diversify microtubule functions and constitute the "tubulin code". Increasing evidence suggests that dysregulated microtubule PTMs contribute to tumor progression. This review summarizes the clinical relevance, molecular mechanisms, and therapeutic potential of microtubule PTMs in gastrointestinal tumors. Methods:A narrative review was conducted using PubMed, EMBASE, Web of Science, and Google Scholar to identify relevant studies on microtubule PTMs in gastrointestinal tumors. Search terms included "microtubule", "tubulin", "post-translational modification", "acetylation", "detyrosination", "tyrosination", "polyglutamylation", "polyglycylation", "methylation", and "phosphorylation", together with terms related to gastrointestinal malignancies. Reference lists of relevant articles were also screened. Peer-reviewed original studies, relevant reviews, and representative translational reports were narratively synthesized according to clinical associations, molecular mechanisms, regulatory enzymes, and therapeutic implications. Key Content and Findings:Current evidence indicates that microtubule PTMs are closely involved in the progression of gastrointestinal tumors. Acetylation, detyrosination, methylation, and polyglutamylation regulate microtubule stability, intracellular transport, mitosis, migration, invasion, angiogenesis, mechanotransduction, and tumor microenvironment remodeling. Key regulatory enzymes, including HDAC6, αTAT1, TTL, TTLLs, and VASH1/2, have emerged as potential biomarkers and therapeutic targets in gastrointestinal malignancies. Conclusions:Microtubule PTMs represent an important regulatory layer in gastrointestinal tumor biology and may provide new opportunities for biomarker development and targeted therapy. However, their clinical application remains limited by insufficient tumor-specific validation and incomplete understanding of PTM crosstalk. Further studies integrating mechanistic investigation, large clinical cohorts, and multi-omics approaches are needed to promote translation of the tubulin code into precision oncology.

Genetic deficiency of dystrophin leads to disability and premature death in Duchenne muscular dystrophy (DMD), affecting the heart as well as skeletal muscle. Here, we report that clinical-stage cardiac progenitor cells, known as cardiosphere-derived cells (CDCs), improve cardiac and skeletal myopathy in the mdx mouse model of DMD. Injection of CDCs into the hearts of mdx mice augments cardiac function, ambulatory capacity, and survival. Exosomes secreted by human CDCs reproduce the benefits of CDCs in mdx mice and in human induced pluripotent stem cell-derived Duchenne cardiomyocytes. Surprisingly, CDCs and their exosomes also transiently restored partial expression of full-length dystrophin in mdx mice. The findings further motivate the testing of CDCs in Duchenne patients, while identifying exosomes as next-generation therapeutic candidates.

Microtubule minus-end binding proteins (−TIPs) are critical regulators of microtubule dynamics and stability, whose dysfunctions are increasingly associated with tumorigenesis and cancer progression. This review systematically consolidates current research advances on the molecular characteristics, oncogenic mechanisms, and therapeutic potential of −TIPs in cancer. By integrating preclinical studies, multi-omics data, and clinical evidence, it was found that calmodulin-regulated spectrin-associated proteins (CAMSAPs) and abnormal spindle microtubule assembly (ASPM) primarily exhibit oncogenic properties, whereas CAMSAP3 acts as a tumor suppressor by negatively regulating tumor cell migration. Studies also demonstrate that pharmacological inhibition of the γ-tubulin ring complex (γ-TuRC) effectively attenuates the centrosomal hyper-clustering capacity of malignant cells, thereby suppressing invasive phenotypes. This result underscores the therapeutic value of targeting −TIPs. In summary, −TIPs play critical and complex roles in cancer progression and hold significant potential as prognostic biomarkers and therapeutic targets. Intervention strategies focusing on specific −TIPs, such as γ-TuRC, offer promising strategies for precision cancer therapy; however, the context-dependent functions of these proteins require further investigation to facilitate clinical translation.

Supplemental Figure S1 Outcome by Chromosome 5 Status. (A) EFS and (B) OS by Chromosome 5 status

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, with hepatitis B virus (HBV) as a major driver. Despite the pivotal role of viral infections in shaping the tumor microenvironment (TME), the mechanistic differences among HBV-, hepatitis C virus (HCV)-, and non-B non-C (NBNC)-associated HCC remain poorly understood. By integrating the largest publicly available single-cell RNA sequencing (scRNA-seq) dataset of HCC (160 samples from 124 patients) with multi-scale protein-level validation using multiplex immunofluorescence and tissue microarrays (198 HCC specimens), HLA-DR⁺ tumor cells are identified as a distinctive feature of HBV+HCC. These tumor cells uniquely express MHC class II molecules, typically restricted to antigen-presenting cells, and correlate with immune checkpoint activation and PD-L1 expression, potentially contributing to an immunosuppressive microenvironment specific to HBV+HCC. Trajectory analysis revealed distinct CD8⁺ T-cell differentiation pathways in HBV+HCC, characterized by enhanced exhaustion and stem-like phenotypes. HLA-DR⁺ tumor cells are associated with increased recruitment of CD8⁺ T cells and correlated with T-cell exhaustion, potentially contributing to a suppressive TME. Clinically, high proportions of HLA-DR⁺ tumor cells are linked to poor survival outcomes, especially when accompanied by elevated PD-L1 expression, suggesting that HLA-DR⁺ tumor cells may serve as a potential predictive biomarker for immunotherapy efficacy in HCC. Collectively, the findings highlight HLA-DR⁺ tumor cells as a distinctive feature of HBV-associated HCC (HBV+HCC), providing novel insights into possible immunosuppressive mechanisms and therapeutic targets for immunotherapy in this disease context.

Supplemental Figure S3 Non-negative Matrix Factorization (NMF) Clustering of Tumor Specimens. (A) Clustering similarity matrix and (B) Silhouette plot of samples by cluster id. (C) Enrichment score for adrenergic (ADRN), mesenchymal (MES), and Schwann cell profile (SCP) gene signatures.