Traditional fermented products of the Indian Himalayas are gaining attention due to their health benefits. Ladakh hard chhurpi (LHC) collected from different altitudes (2784-4523 m) was assessed for antioxidant and ACE inhibitory activities. The activity of LHC generally increased upon GI digestion. Peptidome analysis of GI-digested LHCs revealed varying peptide profiles and the presence of bioactive and multifunctional peptides. Comparative peptidome analysis of Ladakh (Western Himalaya) and Sikkim (Eastern Himalaya) cheese revealed 5 common peptides. Amino acid composition analysis revealed proline and leucine to be the most abundant in Ladakh and Sikkim cheese, respectively. The MPO and ACE inhibitory potential of several novel peptides were predicted. VYPFPGPI demonstrated high MPO binding affinity. GGVSLPE was predicted to have the best ACE inhibition potential. In vitro activity assessment revealed VYPFPGPI as a more potent ACE inhibitor (IC50 of 215.5 ± 7.87 μM), while GGVSLPE showed higher MPO inhibitory activity (IC50 of 0.84 ± 0.05 mM) between the two peptides. This is the first report on the LHC peptidome profile and comparative peptidome analysis of the hard cheese of Ladakh and Sikkim. The present study proposes bioactive peptides-enriched LHCs as a functional food of Ladakh with nutraceutical potential.

Oral squamous cell carcinoma (OSCC) develops through a continuum of tissue states from chronic inflammation and potentially malignant lesions to invasive cancer, yet the dynamic remodeling of the oral immune microenvironment and its relevance to immunotherapy-associated inflammation remain poorly understood. Here, we integrated single-cell RNA sequencing, spatial transcriptomics, murine immunotherapy datasets, and experimental validation to characterize immune and stromal alterations across healthy mucosa, periodontitis, leukoplakia, and OSCC. This integrated analysis revealed distinct oral immune microenvironment states and identified condition-associated neutrophil programs, including an S100A12-enriched inflammatory state, an S100A14-associated metabolic state in leukoplakia, and tumor-associated neutrophil states in OSCC. Spatial analyses and cell-cell communication modeling further nominated immune-stromal interaction networks involving S100A12[+] neutrophils and fibroblast-associated inflammatory signaling. A machine-learning framework identified a nine-gene Neu_S100A12-associated signature that discriminated periodontitis-associated inflammatory states across two retrospective cohorts, with seven concordantly upregulated genes prioritized for biological validation. Multiplex immunofluorescence and an IFN-γ-primed OSCC inflammatory model provided experimental support for a TNF-associated inflammatory phenotype linked to the S100A12 program. Together, these findings establish a cross-sectional multi-omics framework for defining oral immune states and identify S100A12-associated neutrophil programs as candidate mediators of oral inflammation and immunotherapy-related immune perturbation, providing a foundation for future prospective and mechanistic studies.

Marine-derived collagen (MDC) represents a sustainable source of bioactive biomolecules derived from marine processing by-products, with emerging applications in molecular nutrition and healthy aging. Compared with mammalian collagen, MDC exhibits distinctive structural characteristics, including variable imino acid composition, reduced thermal stability, and enhanced enzymatic accessibility, which determine its physicochemical properties, processing behavior, and biological potential. These structural features also underpin the distinct functional roles of native collagen and collagen-derived peptides: intact MDC retains triple-helical architectures and extracellular matrix-interactive motifs that support cellular responses and tissue homeostasis, whereas hydrolyzed marine collagen peptides (MCPs) are orally administered bioactive peptides that can undergo gastrointestinal absorption and have been investigated for potential systemic health effects. This review summarizes current advances in the molecular characteristics, sustainable production, structural modification, and biological functions of MDC and MCPs, emphasizing the structure-function relationships that govern their nutritional and physiological effects. We discuss how extraction and processing strategies regulate collagen architecture, peptide generation, and bioactivity, and further examine the molecular mechanisms that have been proposed to underlie the antioxidant, anti-inflammatory, metabolic regulatory, and musculoskeletal protective effects of MCPs. Particular attention is given to aging-associated physiological decline, in which oxidative stress, chronic inflammation, and extracellular matrix deterioration contribute to impaired tissue homeostasis. Emerging experimental evidence suggests that marine collagen-derived bioactive peptides may modulate key signaling pathways, including Nrf2-mediated antioxidant responses, NF-κB-related inflammatory regulation, and pathways involved in connective tissue remodeling and metabolic balance. Finally, we highlight current challenges limiting the broader application of MDC-derived biofactors, including source variability, structural and compositional standardization, bioavailability characterization, and the need for well-designed human studies. By integrating marine sustainability, molecular structure, and biological function, MDC and its derived peptides may serve as promising food-derived biofactors with potential applications in supporting healthy aging and age-related health maintenance.

Mitochondrial metabolism and oxidative stress (OS) play critical roles in the progression of hepatocellular carcinoma (HCC). However, reliable prognostic biomarkers for these processes remain unidentified. This study integrated bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) to identify OS&mitochondrial metabolism-related genes (OMRGs). A prognostic model was constructed using LASSO regression, followed by external validation. Associations of the model with clinicopathological features, tumor microenvironment (TME), immune functions, therapeutic response, and drug sensitivity were systematically explored. Finally, the relationships between key OMRGs and mitochondrial metabolism as well as OS were validated. A risk score based on five key OMRGs (LPCAT1, IMPDH1, RAMP3, FZD7, and B4GALT5) was established. Low OMRS was significantly associated with improved overall survival and identified as an independent prognostic factor. Two subtypes (C1/C2) were characterized based on the OMRGs: the C1 subtype exhibited poorer survival and epithelial-mesenchymal transition (EMT) enrichment, whereas the C2 subtype showed greater immune infiltration and sensitivity to immunotherapy. High OMRS was associated with higher predicted IC50 values to oxaliplatin and cisplatin, while low OMRS indicated favorable responses to TACE, sorafenib, and immunotherapy. FZD7 knockdown increased reactive oxygen species (ROS) levels and reduced mitochondrial membrane potential in HCC cells. FZD7, a key gene among OMRGs, represent promising prognostic biomarkers and therapeutic targets in HCC.

Skin aging is characterized by impaired extracellular matrix (ECM) synthesis and increased inflammatory signaling in dermal fibroblasts. Notably, ubiquinol-10 (UqH-10), the reduced form of coenzyme Q10 (ubiquinone-10, Uq-10), supports mitochondrial function and reduces oxidative stress, but its dermal levels decrease with aging. The topical efficacy of UqH-10 is limited by its physicochemical properties, including oxidative instability, photo instability, and phototoxicity. This study aimed to evaluate the anti-aging potential of esterified UqH-10 derivatives-UqH 1,4-bis-hemi-succinate (UqH-SUC) and UqH 1,4-bis-hemi-glutarate (UqH-GLUT)-in human dermal fibroblasts. Normal human dermal fibroblasts (NHDFs) were treated with Uq-10, UqH-10, or their derivatives (100 μM) for 48 h. Intracellular Uq-10 and UqH-derivatives were quantified by LC-MS/MS, while ATP levels and viability were measured using luminescence- and fluorescence-based assays. Gene and protein expression of ECM components, matrix metalloproteinases (MMP1, MMP3), and SASP markers (IL6, IL8, p21) were analyzed by qPCR, ELISA, western blotting, and immunofluorescence. Additional experiments were conducted in the presence of an ascorbic acid derivative to evaluate pro-COL1A1 production. We found that UqH-SUC markedly increased intracellular Uq-10 and UqH-10 (2.1-fold vs. Uq-10; 8.3-fold vs. UqH-10), enhanced ATP production, suppressed SASP factors, and upregulated ECM components including COL1A1, elastin, and hyaluronic acid. Despite its minimal conversion to UqH-10, UqH-GLUT accumulated intracellularly, reduced SASP expression, and downregulated MMPs. Co-treatment with UqH-SUC and phosphorylated ascorbic acid derivatives significantly enhanced extracellular COL1A1 secretion while lowering intracellular retention. Moreover, esterified UqH-10 derivatives, particularly UqH-SUC, enhance mitochondrial function, modulate fibroblast senescence, and stimulate ECM synthesis. Moreover, their combination with ascorbic acid derivatives provides a promising strategy for skin anti-aging intervention.

Hepatocellular carcinoma (HCC) remains a major challenge threatening global health. It has a high incidence with poor prognosis, and its response to current conventional therapies is not satisfactory, so we need to explore new effective therapies to address this problem. Targeted therapy represents a promising approach, but the therapeutic efficacy of targeting ion transporters and nuclear transport proteins, such as Na+/K+/2Cl- cotransporter 1 (NKCC1) and Karyopherin β1 (KPNβ1), remains poorly investigated. This study aims to assess the therapeutic efficacy of targeting NKCC1 and KPNβ1 individually and in combination. We also explored the roles of these transporters in tumor cell proliferation and HCC progression. To achieve this aim, an HCC rat model was used, induced by diethylnitrosamine and phenobarbital. The evaluation included histopathological examination and assessment of liver function biomarkers (alanine aminotransferase and aspartate aminotransferase), cell cycle regulators (Cyclin D1, p21, E2F1), proliferation (Ki-67), apoptosis (Caspase-3), and expression of NKCC1 and KPNβ1. This study revealed that NKCC1 and KPNβ1 were upregulated in the HCC group. This increase was associated with increased proliferation and suppressed apoptosis. Targeting these proteins, particularly in combination, significantly improved liver function. It also induced cell cycle arrest, reduced proliferative markers, and enhanced apoptosis. These findings indicate that NKCC1 and KPNβ1 could serve as possible therapeutic targets in HCC treatment.

PTTG1 has been implicated in tumor progression and drug resistance, but its role in acquired anlotinib resistance in non-small cell lung cancer (NSCLC) remains unclear. This study investigated whether PTTG1 contributes to resistance and immune remodeling in NSCLC. We analyzed peripheral blood from NSCLC patients collected before treatment, during response, and after acquired resistance to define clinical changes associated with anlotinib failure. Anlotinib-resistant A549/AL and NCI-H1975/AL cell models were established and subjected to lentiviral shRNA-mediated PTTG1 silencing to assess tumor-intrinsic functions and drug sensitivity. Tumor cell proliferation, migration, invasion, and molecular changes were evaluated using CCK-8, EdU, Transwell, reverse transcription quantitative polymerase chain reaction, Western blotting, immunofluorescence, immunohistochemistry, co-immunoprecipitation, STRING analysis, and humanized mouse models. Immune remodeling was assessed by flow cytometry in PBMC co-culture and tumor samples to examine T-cell subsets and cytotoxic effector activity. PTTG1 was upregulated in resistant clinical samples and resistant NSCLC cell models. Silencing PTTG1 suppressed proliferation, migration, invasion, epithelial-mesenchymal transition, tumor growth and metastasis in vivo, with enhanced anlotinib efficacy observed in subcutaneous xenografts. PTTG1 knockdown reprogrammed the tumor immune microenvironment (experimental models) toward an activated cytotoxic state, characterized by increased CD8+ T-cell infiltration and enhanced cytotoxic effector activity, with reduction of immune checkpoint-associated suppression. Mechanistically, STRING analysis and co-immunoprecipitation identified AURKA as a direct PTTG1-interacting protein, and AURKA overexpression reversed the immune-activating effects of PTTG1 depletion. In conclusion, PTTG1 promotes acquired anlotinib resistance in NSCLC by coupling malignant progression with immune suppression via the PTTG1-AURKA axis. Targeting PTTG1 may be a strategy to overcome resistance and restore anti-tumor immunity.

Clear cell carcinoma with enteroblastic differentiation arising in the female genital tract is exceptionally rare, and its pathogenesis, diagnostic features, and therapeutic implications remain poorly understood. We report a rare case in a 67-year-old woman with tumor involvement of the cervix, uterine cavity, fallopian tubes, and ovaries, and highlight the value of multi-site sequencing for resolving tumor origin and biological heterogeneity. Histologically, the tumor exhibited a fetal intestinal-like morphology with glycogen-rich clear cytoplasm. Immunohistochemistry revealed positive staining for HNF1β, with variable immunoreactivity for Glypican-3 and SALL4. Multi-site whole-exome sequencing revealed marked inter-lesional genomic heterogeneity, divergent clonal evolution, and a molecular phylogenetic pattern supporting the fallopian tube as the most likely primary site. RNA sequencing further demonstrated a more immunogenic microenvironment in the fallopian tube lesion, characterized by increased infiltration of CD4[+] T cells and B cells and a higher immunophenoscore, suggesting potential sensitivity to immunotherapy. Comparison with previously reported cases also helped define immunophenotypic features of diagnostic relevance. Collectively, this case underscores the value of integrating clinicopathologic evaluation with multi-site whole-exome and transcriptomic sequencing to refine diagnosis, infer tumor origin, and identify potential therapeutic opportunities in this rare gynecologic tumor subtype.

Keratinocytes coordinate re-epithelialization, barrier restoration, inflammatory control, and matrix remodeling during cutaneous repair. Although betanin has reported cytoprotective and antioxidant properties, its wound-relevant transcriptional program in keratinocytes remains incompletely defined. This study therefore asked whether betanin engages barrier, inflammatory, and remodeling-related keratinocyte programs under inflammatory conditions, and whether existing wound-healing databases can account for the resulting transcriptional pattern. Scratch closure was quantified by ImageJ measurement and by an independent rule-based automated image-analysis pipeline with first-order kinetic modeling; transcriptional responses in IFN-γ/TNF-α-stimulated HaCaT cells were interpreted through database-weighted evidence scoring and machine learning-based stress testing. Betanin (20 μg/mL) significantly reduced residual wound area at 24 h (p = 0.020) and 48 h (p = 0.035) by ImageJ quantification, and automated image analysis with kinetic modeling yielded an approximately 1.5-fold higher first-order closure rate constant relative to the vehicle-treated wounded control. Betanin partially restored FLG, reduced KRT14, and selectively attenuated inflammatory mediators including IL1B, ICAM1, CCL22, and CXCL8. Among remodeling-associated genes, TGFB1, COL1A1, and VEGFA were suppressed while COL3A1 was partially restored. NFE2L2 and HMOX1 were only modestly affected, indicating a dominant anti-inflammatory and barrier-modulating response rather than canonical antioxidant axis activation. Database-weighted evidence scoring stably prioritized FLG, COL3A1, COL1A1, and ICAM1, corroborated by betanin-specific experimental responses. Three architecturally distinct machine learning models showed no evidence that database-derived wound-healing features predict betanin-induced transcriptional responses, indicating that the selected prior-knowledge annotations were insufficient to account for the observed pattern in this 15-gene, single-context dataset.

Gastrointestinal malignancies, including gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic ductal adenocarcinoma, remain major causes of cancer-related morbidity and mortality worldwide. Although chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the treatment of hematologic malignancies, its efficacy in gastrointestinal solid tumors remains limited by antigen heterogeneity, insufficient trafficking and infiltration, immunosuppressive tumor microenvironments, on-target off-tumor toxicity, and adaptive resistance. In this review, we summarize the current landscape of CAR-T therapy in gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic cancer, with a focus on representative target antigens and emerging biomarker strategies. We further discuss two major categories of biomarkers: target antigen-related biomarkers and conventional dynamic biomarkers, including serum tumor markers, cytokine changes, CAR-T expansion kinetics, and antigen-loss monitoring. In addition, we highlight how single-cell ribonucleic acid sequencing and spatial transcriptomics provide complementary insights into cellular states, immune exhaustion, stromal barriers, and spatially restricted immune exclusion. By integrating these multi-omics approaches with biomarker-guided patient stratification and next-generation CAR-T engineering, gastrointestinal solid tumor CAR-T therapy may evolve from empirical optimization toward mechanism-driven and precision-guided clinical translation.

Lung adenocarcinoma (LUAD) is characterized by marked cellular heterogeneity, yet how malignant epithelial states contribute to immune regulation and clinical outcomes remains incompletely defined. We integrated single-cell RNA-sequencing data to map the cellular landscape of LUAD and identify malignant epithelial cells based on inferred copy-number alterations. Epithelial states were further examined through trajectory inference, transcription factor analysis, and cell-cell communication profiling. Single-cell-derived genes were subsequently integrated with TCGA and independent GEO cohorts to construct and validate a machine learning-based prognostic signature. Malignant epithelial cells displayed distinct functional programs, including an immune-like state associated with genomic instability, immune-related transcriptional activity, tumor-immune communication, and patient outcomes. The resulting immune-like malignant epithelial cell signature (IMEC-Sig) consistently stratified survival across multiple cohorts. Low IMEC-Sig scores were accompanied by greater immune infiltration, higher immune checkpoint expression, and increased immunophenoscore, whereas high scores were linked to a comparatively immunosuppressive phenotype. Pan-cancer analyses further identified KRT8 as a gene associated with unfavorable prognosis, and functional experiments showed that KRT8 silencing suppressed proliferation, migration, invasion, and colony formation in LUAD cells. Together, these findings connect malignant epithelial heterogeneity with the immune context and clinical outcomes, support IMEC-Sig as a biologically informed prognostic tool, and nominate KRT8 as a potential therapeutic target in LUAD.

Macrophage heterogeneity is increasingly recognized as an important feature of the gastric cancer tumor microenvironment, yet the macrophage states linked to poor outcome and the molecules connecting them to stromal remodeling remain incompletely defined. Here, we integrated single-cell RNA sequencing data from GSE183904, spatial transcriptomic data from GSE251950, and TCGA-STAD bulk transcriptomic data to characterize macrophage diversity and identify clinically relevant macrophage-associated genes. Cell-cell communication analysis revealed intensified intercellular signaling in tumors, with prominent changes in MIF, COLLAGEN, FN1, LAMININ, and SPP1 pathways. Five macrophage subclusters were resolved. Among them, macro_SPP1 and macro_IL1B signatures were associated with shorter overall survival, whereas macro_C3_CX3CR1 was linked to a more favorable outcome. By integrating macro_SPP1 markers with tumor-associated differentially expressed genes and applying Cox regression together with multiple machine learning approaches, SERPINE1 emerged as the most consistent prognostic candidate. High SERPINE1 expression was associated with poor survival and with stromal, myeloid, and vascular features. Spatial analysis further localized SERPINE1-high regions to microenvironments enriched for fibroblast- and endothelial-related components and for TGF-β, hypoxia, inflammatory, and extracellular matrix remodeling programs. Virtual perturbation suggested that SERPINE1 may influence myeloid and matrix-related transcriptional networks. Functionally, SERPINE1 knockdown reduced proliferation, colony formation, migration, and invasion in gastric cancer cells. Together, these findings identify SERPINE1 as a macro_SPP1-associated molecule with prognostic and functional relevance and suggest a potential link between macrophage-associated programs, stromal remodeling, and malignant behavior in gastric cancer.

Primary liver cancer (PLC) is a biologically heterogeneous group of malignancies dominated by hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), and a smaller subset of combined hepatocellular-cholangiocarcinoma (cHCC-CCA), and its clinical burden remains high because current diagnostic and prognostic tools do not adequately capture molecular diversity. Conventional imaging, serum markers, and histopathological assessment remain insufficient for precise early diagnosis, subtype-resolved classification, and outcome stratification, while tissue and liquid biopsy approaches have expanded the range of analytes available for clinical assessment. Recent studies have identified candidate biomarker signatures across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and circulating layers, suggesting that integrated multi-omics profiling may better represent tumor lineage, clonal evolution, immune context, and therapeutic vulnerability than isolated molecular readouts. However, these layers are not equally mature for clinical use: genomic testing is closest to routine therapeutic application in iCCA, plasma methylation assays are advancing for HCC surveillance augmentation, and many proteomic or metabolomic panels remain validation-stage tools. Their clinical value remains constrained by sampling bias, biospecimen-dependent signal loss, assay standardization, cost, and the need for prospective validation across clinically diverse populations. This narrative review critically synthesizes current evidence on multi-omics biomarker signatures for precision diagnosis and prognosis in primary liver cancer and argues that clinically useful signatures should be question-specific, stage-aware, and specimen-aware rather than universal multi-analyte panels.

Remodeling of the immune microenvironment is a critical determinant of tissue regeneration, yet the molecular programs associated with the enhanced therapeutic activity of hypoxia-preconditioned extracellular vesicles remain incompletely defined. In this study, we investigated the regenerative and immunomodulatory effects of hypoxia-preconditioned tendon stem cell-derived extracellular vesicles (Hypo-EVs) and employed transcriptomic profiling to identify molecular signatures associated with their biological activity. The therapeutic effects of Hypo-EVs were evaluated using a rat patellar tendon defect model and lipopolysaccharide-stimulated RAW 264.7 macrophages. Histological analysis, immunostaining, biomechanical testing, and reverse transcription-quantitative polymerase chain reaction were performed to assess tendon healing and macrophage polarization, while RNA sequencing was conducted in macrophages treated with Hypo-EVs or normoxia-derived EVs, followed by Gene Set Enrichment Analysis, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes pathway analyses. Hypo-EVs significantly alleviated local inflammatory responses, improved collagen organization and biomechanical properties of repaired tendons, and promoted macrophage polarization toward a reparative M2 phenotype both in vivo and in vitro. Consistent with these biological effects, transcriptomic profiling revealed extensive remodeling of inflammation-related gene expression programs, including significant suppression of NF-κB, TNF, IL-17, and cytokine-cytokine receptor interaction pathways. Integrative bioinformatic analyses identified an NF-κB-associated immune-regulatory signature that distinguished Hypo-EV-treated macrophages from those receiving normoxic EVs. Mechanistically, Hypo-EVs attenuated NF-κB activation, as evidenced by reduced phosphorylation of p65 and IκBα, whereas TNF-α-mediated NF-κB activation partially diminished their macrophage-repolarizing effects. Collectively, these findings demonstrate that hypoxic preconditioning enhances the immunomodulatory and regenerative functions of tendon stem cell-derived EVs. Transcriptomic analyses identified an NF-κB-associated immune-regulatory signature linked to the biological activity of Hypo-EVs, providing a molecular framework for understanding EV-mediated immune modulation and supporting the development of transcriptome-guided molecular signatures for regenerative therapies targeting tendon immune homeostasis.