Search Results (8,794)

Background: Quiescent cancer cells (QCCs) evade conventional therapies and contribute to minimal residual disease (MRD) and relapse, yet the signaling pathways governing their survival remain poorly understood. Methods: Here, we performed integrative proteomic and phosphoproteomic profiling of triple-negative breast cancer (TNBC) cells transitioning between proliferation and serum removal-induced quiescence, followed by re-stimulation. Results: We identified dynamic remodeling of both proteome and phosphoproteome, with quiescent cells showing downregulation of mitotic drivers and upregulation of extracellular matrix components. Notably, phosphorylation of CK2 substrates was increased during quiescence, and CK2 inhibition using CX-4945 impaired cell survival under nutrient and genotoxic stress, disrupted autophagy, microtubule dynamics, and protein synthesis. Phospho-enrichment and functional assays identified death-associated protein kinase 3 (DAPK3) as a CK2-regulated effector mediating stress-induced apoptosis. In silico analysis confirms a link between high CK2 expression and poor chemotherapy response in basal breast cancer. Conclusions: These findings establish CK2 as a critical survival kinase in QCCs and a potential therapeutic target for MRD eradication in breast cancer. Full article

Copy number variations (CNVs) are a major source of structural genomic diversity that influence adaptation, reproduction, and production traits in livestock. The Black Bengal goat, an economically important Indian breed known for its high fecundity, superior skin quality, and resilience to humid tropical climates, was studied to uncover its structural genomic landscape. We performed whole-genome CNV analysis using high-depth (10×) sequencing data from eight individuals. A total of 31,816 copy number variants (CNVs) were identified, predominantly duplications, with an average length of approximately 45 kb. These CNVs were combined into 8910 copy number variation regions (CNVRs) covering approximately 0.15 Gb (about 5.3% of the autosomal genome). CNVR hotspots were mainly located on chromosomes 1. Gene annotation showed that regions overlapping with CNVs and CNVRs contained over 1987 protein-coding genes that are involved in pathways related to immunity, reproduction, metabolism, and extracellular matrix (ECM) organization. The presence of copy number variations involving genes such as GDF9 and BMPR1B on chromosome 7 & 6, respectively, are important because it indicates that the breed has a high reproductive capacity due to dosage-sensitive duplications. Changes in the extracellular matrix and increased dermal strength have been linked to duplications of genes such as COL6A1, LAMC2, LAMB3, FMN1, and CLDN1. This helps explain the superior hide quality of the breed. This research offers a comprehensive map of CNVs and CNVRs within the genome of the Black Bengal goat. It demonstrates how these duplications lead to structural changes that enhance both reproductive performance and skin resilience. These findings provide a valuable genomic resource for future marker-assisted selection, comparative genomics, and conservation breeding programs aimed at preserving indigenous goat populations. Full article

Background: Modern oncology views immune system dysfunction as a key factor in carcinogenesis. The induction of immunogenic cell death (ICD), a form of regulated cell death capable of activating adaptive immunity, represents a promising therapeutic strategy. Damage-associated molecular patterns (DAMPs) play a central role in this process. This review aims to summarize current knowledge of DAMPs, their release mechanisms during ICD, their classification, and their prognostic and therapeutic significance in antitumor immunity. Methods: We systematically reviewed and synthesized literature published in Pubmed and Google Scholar on ICD and DAMPs, focusing on distinct forms of DAMPs which were categorized based on recognition mechanisms (five classes) and cellular origin (extracellular, mitochondrial, nuclear, and cytosolic). Key molecules, their receptors, downstream signaling pathways, and clinical associations were analyzed. Results: The spatiotemporally coordinated release of the pattern of DAMPs promotes dendritic cell maturation, antigen presentation, activation of cytotoxic T lymphocytes, and elimination of tumor cells. DAMPs can exhibit a dual role: they are able to induce sterile inflammation essential for antitumor immunity, but may also contribute to metastasis and chronic inflammation. Among all DAMPs, high-mobility group box 1 (HMGB1, a nuclear DAMP) and calreticulin (CRT, a cytosolic protein) demonstrate the greatest prognostic value. Other DAMPs (e.g., extracellular matrix components, uric acid) act as signal amplifiers during various forms of cell death. Conclusions: Understanding the spatiotemporal dynamics of DAMP release is critical for activating immune responses against malignant cells. Monitoring DAMPs may improve patient stratification, predict therapeutic responses, and enable personalized immunotherapeutic strategies. Further investigation of ICD mechanisms and DAMP release represents a fundamental basis for developing novel anticancer therapies. Full article

Background: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease marked by excessive extracellular matrix (ECM) deposition. Current FDA-approved therapies, such as pirfenidone and nintedanib, offer limited efficacy in halting disease progression. Lysyl oxidase-like 2 (LOXL2) is a key enzyme involved in ECM remodeling and fibrosis. This study investigates Compound #765, a novel indolizine derivative, as a potential LOXL2 inhibitor for IPF treatment. Methods: Compound #765 was synthesized and characterized using spectroscopic methods. Its inhibitory effect on LOXL2 activity was evaluated using LOXL2 enzymatic assays, in vitro fibrosis models with human lung fibroblasts, and in vivo models of pulmonary fibrosis, including bleomycin-treated and TGF-β1-overexpressing transgenic mice. In silico docking studies predicted the binding affinity of Compound #765 to LOXL2. Results: Compound #765 targeted LOXL2 activity and reduced collagen production in lung fibroblasts. In both bleomycin-induced pulmonary fibrosis and TGF-β1-overexpressing murine models, Compound #765 significantly alleviated fibrosis, as indicated by reduced collagen accumulation and inflammatory cell infiltration. The in silico docking studies predicted favorable binding affinity to LOXL2, which was confirmed through in vitro experiments. Importantly, Compound #765 suppressed fibrosis-associated markers in fibroblasts derived from IPF patients, suggesting translational potential. Conclusions: These results demonstrate that Compound #765 functions as a LOXL2 inhibitor with significant anti-fibrotic effects in vitro and in vivo, offering a promising therapeutic approach for IPF and other fibrotic lung diseases. Full article

Objective: Gastric cancer (GC) is characterized by molecular heterogeneity, yet current classifications are largely based on cross-sectional molecular profiles and do not account for the temporal order of mutation accumulation. This study aimed to reconstruct somatic mutation trajectories to identify prognostically distinct subtypes and to examine transcriptomic and microenvironmental features associated with these inferred trajectories. Methods: We applied the Subtype and Stage Inference (SuStaIn) algorithm to TCGA-STAD somatic mutation data to infer the temporal sequence of mutation accumulation. Stage-correlated gene expression analysis was performed to identify genes whose expression levels changed with evolutionary stage. The tumor microenvironment (TME) was characterized using EcoTyper and single-cell RNA sequencing deconvolution, while drug sensitivity was estimated through transcriptome-based IC₅₀ prediction. The clinical relevance of the inferred trajectories was further evaluated in three independent external transcriptomic cohorts. Results: We identified two distinct evolutionary trajectories: the Accelerated Path (AP, 65%) and the Gradual Path (GP, 35%). In the AP, TP53 mutations were positioned at an earlier evolutionary stage (Stage 3) compared to the GP (Stage 8). AP patients had significantly worse overall survival (Hazard Ratio = 1.437, p = 0.044, adjusted for clinical stage and molecular subtypes). The AP was associated with stage-correlated downregulation of the sodium channel gene SCN4A (ρ = −0.36, p < 0.001) and an increase in a squamous-associated gene expression score, while the GP showed stage-correlated expression changes in the mitochondrial gene SDHD (ρ = −0.35, p < 0.001). The AP was further characterized by higher inferred abundance of extracellular matrix CAFs (eCAFs) and lower inferred immune cell scores, whereas the GP was associated with higher inferred signatures of activated B cells and effector memory T cells. Computational drug sensitivity modeling predicted a negative correlation between AP stage and IC₅₀ values for 5-Fluorouracil and Docetaxel. Conclusions: Two distinct mutational ordering patterns identified by SuStaIn are associated with divergent transcriptomic features, TME compositions, and clinical outcomes in gastric cancer. The AP subtype is characterized by early TP53 mutations, SCN4A downregulation, and a stromal-enriched microenvironment, while the GP subtype is associated with later TP53 mutations, SDHD-correlated expression, and higher inferred immune cell scores. The reproducibility of these associations was confirmed in independent cohorts. The computational drug sensitivity predictions and the proposed mechanistic links between gene expression patterns and clinical outcomes should be viewed as hypothesis-generating findings that require prospective and functional validation. Full article

The modulation of the tumour microenvironment represents a pivotal step in tumorigenesis and metastasis and results from direct and paracrine cellular interactions. The innate immune Toll-like receptor 4 (TLR4) controls immune and inflammatory signalling in the tumour microenvironment. A growing body of evidence shows that TLR4 activation in cancer, immune and stromal cells upregulate gelatinase expression and activity, linking innate immune responses to extracellular matrix (ECM) remodelling. Gelatinases, or matrix metalloproteinases (MMP2) and (MMP9) play a pivotal role in tumour matrix degradation, thereby facilitating invasion, angiogenesis and metastasis. Interestingly, although TLR4 signalling in cancer cells and tumour-associated macrophages leads to different activation outputs, they can both induce gelatinases through NF-κB, MAPK, and Akt pathways. Evidence from clinical tumour tissues, co-culture models, in vivo and in vitro studies supports the crucial interplay between TLR4 signalling and gelatinases production in tumour growth and metastasis. An in-depth understanding of this crosstalk may reveal new therapeutic opportunities in targeted strategies. Full article

Background/Objectives: Phillygenin (PHI), a natural lignan derived from Forsythia suspensa, has garnered attention for its potential to alleviate chronic diseases, including chronic colitis, pulmonary fibrosis, and diabetes. Chronic kidney disease (CKD) poses a global health challenge, characterized by high morbidity and mortality rates and associated with a spectrum of secondary complications. In this study, we aim to investigate the therapeutic effectiveness of PHI on CKD and also identify molecular signals by using a unilateral ureteral obstruction (UUO) mouse model and in vitro experiments. Methods: C57BL/6 mice were administered PHI at 50 mg/kg/day to assess its therapeutic effectiveness. In vitro, lipopolysaccharide (LPS) and adenosine triphosphate (ATP) were used to induce pyroptosis, also known as pyroptosis, in renal proximal tubular cells (NRK52E). Results: After PHI treatment for 14 consecutive days, the collagen deposition and extracellular matrix (ECM) accumulation, the expression of oxidative stress response proteins (catalase, superoxide dismutase 2, NADPH oxidase 4, and thioredoxin reductase 1), pro-inflammatory markers (TNF-α and Cyclooxygenase-2(COX-2), and infiltration of neutrophils and macrophages were significantly ameliorated in the UUO mice. Interestingly, the pyroptosis-related proteins (NLRP3/Caspase-1/GSDMD/IL-1β) and cell apoptotic death were also conspicuously relieved after treatment with PHI. Furthermore, PHI administration significantly attenuated the ATP/LPS-induced NF-κB/NLRP3/Caspase-1/GSDMD pyroptosis signal pathway in NRK52E cells. Conclusions: These results demonstrate, for the first time, that PHI treatment ameliorates inflammation and the related pyroptosis via inhibitory regulation of the NF-κB/NLRP3/Caspase-1/GSDMD axis, leading to attenuated renal fibrosis and progressive CKD in UUO mice and in vitro. Our findings suggest that PHI could be a nutraceutical candidate for attenuating CKD progression. Full article

Tendinopathy involves a dysregulated inflammatory microenvironment in which cytokines, growth factors (GF) and extracellular matrix components interact dynamically. Platelet-rich plasma (PRP) is widely used as a regenerative therapy, but its mechanisms of action in inflamed tendon remain unclear. This study evaluated whether platelet-rich gel supernatant (PRGS) reprograms the inflammatory–anabolic mediator network in an equine in vitro tendon explant system stimulated with lipopolysaccharide (LPS). Tendon explants were cultured under six experimental conditions, including non-stimulated control, LPS-stimulated control, and LPS combined with 25% or 50% PRGS or platelet-poor gel supernatant (PPGS). Cytokines, GF, and hyaluronic acid (HA) were quantified at 1 h and 48 h and analyzed using linear mixed-effects models, mediator ratios, correlation networks, and principal component analysis. PRGS contained higher concentrations of PDGF-BB (2044 pg/mL, 95% CI 1382–2706) and IL-1ra (1196 pg/mL, 95% CI 424–1967) compared with PPGS. In LPS-stimulated explants, PRGS significantly increased IL-1ra and PDGF-BB, while IL-1β and HA exhibited significant time-dependent changes (F = 8.675 and F = 10.752, respectively). The PDGF-BB:HA ratio remained consistently higher in PRGS-treated groups (F = 46.100, p < 0.001). Multivariate analysis showed that the first two principal components explained 62% of the total variance and revealed coordinated shifts in mediator organization over time. These findings indicate that PRGS does not simply suppress inflammation but actively reprograms the tendon microenvironment toward a regulatory and reparative phenotype within this experimental system. Full article

The production of cultivated meat relies on in vitro animal cell growth and requires the use of scaffolds that structurally resemble key features of the extracellular matrix (ECM), providing mechanical support and biochemical cues for cell adhesion, proliferation, and differentiation. Electrospinning has emerged as a promising technique for manufacturing three-dimensional edible scaffolds because it is robust, versatile, and capable of producing nanofibers with a high surface area-to-volume ratio, tunable porosity, and ECM-like fibrous architectures. Natural biopolymers are promising candidates for the fabrication of electrospun scaffolds, combining biocompatibility, biodegradability, and processing compatibility with food-grade requirements. However, the absence of fully food-grade electrospinning systems, coupled with limited scalable green-processing strategies, remains a critical barrier to industrial translation. In this context, this review presents recent advances in the food-grade electrospinning of natural biopolymers focused on cultivated meat production. Furthermore, scientific gaps in the development of fully edible scaffolds are discussed, along with the need for alternatives to animal-derived materials and synthetic carrier polymers, considering sustainability, consumer acceptance, and the translation from laboratory-scale studies to industrial systems. Finally, this review outlines a strategic roadmap to accelerate the transition from proof-of-concept studies toward scalable, regulatory-compliant, and industrially viable electrospinning technologies for cultivated meat production. Full article

Fetal skeletal muscle development involves coordinated interactions among myogenic, stromal, vascular, and immune compartments, yet the cellular and molecular programs guiding tissue maturation remain incompletely understood. To address this, we generated a high-resolution single-cell atlas of fetal female goat skeletal muscle and performed trajectory analysis, transcription factor activity profiling, and intercellular communication mapping. Unsupervised clustering identified RUNX2 mesenchymal progenitors, fibro-adipogenic progenitors (FAPs), myofibroblasts, endothelial cells, macrophages, differentiating myocytes, and mature skeletal muscle fibers, revealing a heterogeneous ecosystem in which stromal populations support myogenic progression and vascular and immune cells contribute to tissue organization. Pseudotime analysis traced a maturation continuum from differentiation-competent myocytes to contractile fibers, marked by sequential activation of extracellular matrix remodeling, cytoskeletal stabilization, and sarcomere assembly. KEGG and GO enrichment highlighted stage-specific engagement of ErbB, Hedgehog, and Hippo signaling, as well as cell cycle and ubiquitin-mediated proteolysis pathways, linking proliferation, differentiation, and structural maturation. Transcription factor profiling revealed early-stage proliferative and morphogenetically permissive states driven by E2F4/5, HMGA2, and HAND2, transitioning to late-stage differentiation, ECM remodeling, and tissue stabilization orchestrated by CEBPB, CREB3L1, ELK1, and E2F2. Cell–cell communication analysis showed a developmental redistribution of signaling authority, from ECM-driven, progenitor-centered networks to modular, structurally stabilized interactions. These findings define the cellular, transcriptional, and signaling framework orchestrating fetal skeletal muscle maturation. Full article

Background: Anterior cruciate ligament (ACL) injuries are increasing in young athletes and many are related to non-contact, spontaneous mechanical fatigue-related ruptures. The objective of this narrative review is to identify and synthesize the anatomical, histological, physiological, and biomechanical basis of extracellular matrix (ECM) factors that contribute to ACL injuries and suggest ways to decrease their occurrence. Methods: The primary investigator searched PubMed, Web of Science, and Google Scholar database titles and abstracts using search phrases with Boolean operators: “anterior cruciate ligament” OR “ACL”, OR “cranial cruciate ligament” AND “disease”; “anterior cruciate ligament” OR “ACL”, OR “cranial cruciate ligament” AND “spontaneous rupture” OR “non-contact injury”; and “anterior cruciate ligament” OR ACL, OR cranial cruciate ligament” AND “crosslink”, “collagen” OR “extracellular matrix”; and “anterior cruciate ligament” OR “ACL”, OR “cranial cruciate ligament” AND “microtrauma”, OR “sudden” OR “fatigue failure”. The primary investigator and a sports orthopedic surgeon reviewed titles and abstracts of diverse evidence sources. From these identified sources, the study team performed full text reviews, selected contributing articles, performed Strength of Recommendation Taxonomy (SORT) grading, and synthesized the following themes: A Hostile Environment, ACL Strain, and Poor Nutrient Delivery; Accumulative ACL Microtrauma and Mechanical Failure; The ACL Differs From Other Ligaments; Collagen, the ECM, and ACL Mechanobiology; Crimps and ACL ECM Stretch; Crosslinks Improve ECM Mechanical Properties; The Delicate Collagen Synthesis and Degradation Balance; Exercise Training and the ACL; Can Nutraceuticals Help Restore the Balance?; Training Induced ACL Hypoxia; Estrogen and the Female Athlete; Counting Pitches or Counting Collagen Fiber Ruptures; and Restoring A Positive Anabolic–Catabolic Collagen Balance. Results: Regular exercise training within a physiologically safe loading range is vital to ACL ECM health. However, low or moderate evidence suggested that poor blood supply, slow metabolism, and a hypoxic environment may unbalance anabolic and catabolic homeostasis. Active rest and recovery concepts that prevent youth baseball shoulder and elbow injuries may help prevent non-contact ACL injuries. Conclusions: More prescriptive active rest and recovery intervals and neuromuscular control training may restore the anabolic–catabolic balance that increases mature crosslink density and improves ACL ECM strength. Confirmatory studies are needed to better establish therapeutic intervention mode(s), timing, dosage, and frequency optimization. Full article

Background: Corneal organoids derived from pluripotent stem cells have emerged as powerful tools for studying corneal development, disease modeling, and regenerative medicine applications. While previous protocols have successfully generated corneal tissue structures, there remains a need for three-dimensional models that recapitulate the complex cellular architecture and diversity of native human cornea. Methods: We developed a modified spontaneous three-dimensional corneal organoid model using human embryonic stem cells (hESCs) through an adapted Self-formed Ectoderm Autonomous Multi-zone (SEAM) protocol. hESCs were cultured as spheroids in ultra-low-binding plates under normoxic conditions and differentiated over 7–8 weeks. Organoids were characterized using immunofluorescence staining for corneal-specific markers and single-cell RNA sequencing to assess cellular composition and gene expression patterns. Results: Approximately 20% of organoids developed transparent regions characteristic of corneal tissue by day 30 of differentiation. Immunofluorescence analysis revealed spatially organized expression of corneal markers, including ZO-1 and E-cadherin in the outermost epithelial layers, P63α-positive putative limbal stem cells at the epithelial–stromal interface, vimentin-positive stromal cells in the interior, and laminin-1 deposition that suggests Bowman’s membrane formation. The organoids expressed cornea-specific keratins (K3, K12, and K15) and the master regulator PAX6 in appropriate cellular compartments. Single-cell RNA sequencing identified 18 distinct cell clusters, including three corneal epithelium subclusters with differential expression of MUC16, KRT12, and ΔNp63α, two stromal populations with distinct inflammatory profiles, and a corneal endothelium cluster. Transcriptomic analysis confirmed expression of key corneal genes, including AQP3, CDH1, multiple keratins, mucins, and extracellular matrix components (HAS2, CD34, CD44, COL8A1, and KERA). Conclusions: This three-dimensional spheroid-based putative corneal organoid model successfully recapitulates the multilayered architecture and cellular diversity of human cornea, including stratified epithelium, putative limbal stem cells, stroma, and endothelium in spatially appropriate arrangements. The model demonstrates molecular signatures consistent with native corneal tissue and provides a valuable platform for studying corneal development, disease mechanisms, and potential therapeutic applications. Future optimization to improve organoid formation efficiency and functional maturation will enhance the utility of this system for both basic research and translational medicine. Full article

Purpose: A high-salt extracellular environment promotes fibrosis in multiple organs by inducing oxidative stress, fibroblast activation, and extracellular matrix remodeling. In the lung, sodium accumulation may result from impaired epithelial ion transport. Transforming growth factor-β1 (TGF-β1), a key profibrotic cytokine, downregulates epithelial sodium and chloride channels, promoting sodium retention and fibrotic remodeling. This study investigated whether antifibrotic drugs can prevent TGF-β1-induced suppression of sodium channel expression in the lung epithelium. Methods: Human A549 alveolar epithelial cells and primary alveolar epithelial cells were cultured with or without TGF-β1 in the presence or absence of nintedanib or pirfenidone. Expression of epithelial sodium channel (ENaC) subunits (SCNN1A, SCNN1B, SCNN1G, SCNN1D) and CFTR was analyzed. In vivo, lung tissues from TGF-β1 transgenic mice and wild-type controls were examined following intranasal administration of pirfenidone. Results: TGF-β1 markedly reduced the expression of all ENaC subunits and CFTR in vitro. Nintedanib prevented suppression of SCNN1A, SCNN1D, and SCNN1G, whereas pirfenidone prevented suppression of SCNN1A, SCNN1B, and SCNN1G. In TGF-β1 transgenic mice, Scnn1a, Scnn1b, and Scnn1g expression was significantly decreased compared with wild-type controls. Pirfenidone administration dose-dependently restored expression of these ENaC subunits in vivo. Conclusions: Antifibrotic drugs partially prevent TGF-β1-induced suppression of epithelial sodium channels, preserving epithelial ion homeostasis. Restoration of ENaC expression may represent a novel mechanism by which antifibrotic therapy mitigates sodium-associated lung fibrosis. Full article

Bone is a hierarchically organized composite material with unique mechanical properties and an intrinsic regenerative capacity that conventional repair strategies, including autografts, allografts, xenografts, and metallic or ceramic implants, fail to fully replicate due to donor scarcity, immunogenicity, mechanical mismatch, and poor long-term integration. Bone tissue engineering (TE) offers a biologically informed alternative by integrating osteoconductive scaffolds, osteogenic progenitor cells, and osteoinductive signaling molecules into a unified regenerative framework. Unlike existing reviews that evaluate these components in isolation, this review provides a mechanistically integrated analysis that repositions scaffold design as a biologically instructive platform whose topography, stiffness, porosity, and surface chemistry collectively govern cell adhesion, mechanotransduction, osteogenic differentiation, and extracellular matrix remodeling. Critically, it moves beyond cataloging materials and fabrication approaches to evaluate how specific scaffold features drive biological outcomes and to identify frequently understated limitations, including polymer-ceramic degradation kinetics and the inadequacy of small-animal models for clinical translation. By synthesizing advances in biomaterials, additive manufacturing, and smart scaffold technologies within this integrative framework, this review provides researchers and clinicians with a structured framework for evaluating emerging strategies and prioritizing future directions in functional bone regeneration. Full article

The dipeptidyl peptidase (DPP) family comprises enzymes with important metabolic and immunomodulatory properties. This narrative review summarizes recent clinical and experimental evidence on the role of DPP-1, DPP-4, DPP-9, and DPP-10 in pulmonary diseases. The strongest translational evidence currently supports DPP-1 inhibition in non-cystic fibrosis bronchiectasis, where brensocatib reduces exacerbations and prolongs time to first exacerbation, with additional DPP-1 inhibitors in development. By contrast, the roles of DPP-4, DPP-9, and DPP-10 are supported mainly by preclinical studies in pulmonary hypertension, acute lung injury (ALI)/acute respiratory distress syndrome (ARDS), pulmonary fibrosis, asthma, non-small cell lung cancer (NSCLC), and nonsteroidal anti-inflammatory drugs (NSAIDs)/aspirin-exacerbated respiratory disease. Across these models, DPP inhibition modulates inflammation, protease activation, epithelial or endothelial mesenchymal transition, extracellular matrix (ECM) remodeling, and related signaling pathways. Overall, DPP-targeted interventions are promising in pulmonary medicine, but broader clinical translation will require well-designed prospective trials. Full article