Matrix Biology Plus

Background and aimsAtherosclerotic plaques form preferentially at vascular sites exposed to disturbed blood flow, yet the protein changes underlying this site-specific plaque development remain unclear. Mouse models are widely used to study atherosclerosis but yield only limited amounts of tissue, previously restricting proteomic studies. However, recent advances in mass spectrometry now enable proteomic profiling of very small tissue samples. We aimed to utilise this to uncover site-specific protein changes in aortic regions prone or resistant to plaque formation. MethodsAortic arches from apolipoprotein E-deficient (ApoE-/-) mice fed a Western diet (WD) for 16 weeks were dissected into plaques from the major branches and inner curvature and visibly healthy regions. Proteins were extracted, enzymatically digested, and analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). ResultsMore than 4000 proteins were identified per sample despite their small size (< 1 mg tissue). Principal component analysis showed clustering by both disease status and anatomical location within the aortic arch, indicating distinct proteomes. Proteins known to drive atherosclerosis - including vascular cell adhesion molecule 1 (Vcam1), apolipoprotein B (Apob), lipoprotein lipase (Lpl), and galectin 3 (Lgals3) - were most abundant in advanced plaques and decreased progressively across anatomical regions, reaching their lowest levels in healthy regions furthest from the plaques. Enrichment analysis highlighted pathways related to the extracellular matrix, immune system, hemostasis, and lipoprotein transport as central to disease progression. ConclusionsThis study demonstrates the feasibility of region-resolved proteomics in individual murine aortas and provide new molecular insights into the site-specific nature of atherosclerotic plaque development.

The axolotl salamander can fully regenerate amputated limbs, yet the systemic consequences underlying this process remain largely understudied. Cerebrospinal fluid is an emerging signaling medium capable of communicating with both the central and peripheral nervous systems, but its composition and potential role in salamander limb regeneration have not yet been examined using modern multi-omics techniques. Here, we developed a protocol for extracting mixed perilymph-cerebrospinal fluid (P-CSF) from axolotl and provided the first proteomic and metabolomic characterization of this biological fluid. We identified 2,626 unique proteins and 173 high-confidence metabolites and quantified them across four time points of early limb regeneration. We demonstrated that limb amputation drives progressive shifts in P-CSF proteins, including an elevation of sarcomeric muscle proteins, regeneration-associated factors, and protease/extracellular matrix proteins. We observed shifts in metabolites involved in oxidative stress, polyunsaturated fatty acid oxidation, and histamine metabolism. Injury-comparison experiments revealed that the observed proteomic changes as a result of limb amputation are different than crush injury, denervation, or tail amputation. This study proposes axolotl P-CSF as a reservoir for limb amputation-associated systemic signaling and as a potential conduit of signals involved in limb regeneration.

The sperm surface glycocalyx undergoes extensive remodeling during epididymal maturation, required for sperm to reach and bind the oviductal epithelium. N-acetylglucosamine (GlcNAc)-containing glycans are candidate mediators of these events, however, how these residues are regulated across the reproductive tract, and whether their changes depend on specific epididymal enzymes or functionally contribute to sperm-oviduct epithelial adhesion, remains poorly defined. Here, we addressed this gap by examining how surface GlcNAc changes as sperm mature and become functionally competent, from epididymal maturation through capacitation and the acrosome reaction. We further asked whether these changes relate to the ability of spermatozoa to bind the oviductal epithelium. Surface GlcNAc, assessed by WGA reactivity, increased progressively from caput to cauda epididymal spermatozoa, with a corresponding shift in GlcNAc-bearing protein profiles, while remaining predominantly localized to the acrosomal region throughout maturation. Incubation of caput spermatozoa with cauda epididymal fluid reduced WGA labeling, an effect blocked by the selective {beta}-N-acetylglucosaminidase ({beta}-NAG) thiourea derived hydroxy pyrrolidine inhibitor VP150, identifying luminal {beta}-NAG as an active contributor to GlcNAc remodeling in the epididymis. In ejaculated spermatozoa, capacitation induced minor changes in surface GlcNAc, whereas the calcium ionophore-induced acrosome reaction produced a marked reduction in WGA reactivity and acrosomal labeling, consistent with glycoprotein loss during acrosomal exocytosis. Functionally, spermatozoa that bound to BOEC monolayers were preferentially WGA-positive, and pre-incubation of BOECs with WGA significantly reduced sperm adhesion, implicating surface GlcNAc in sperm-oviduct epithelial recognition. Together, these findings define surface GlcNAc as a dynamically regulated glycan that is progressively established during epididymal transit, partly through luminal {beta}-NAG activity, redistributed during capacitation and acrosomal exocytosis, and functionally engaged during sperm-BOEC adhesion, providing a mechanistic framework for glycocalyx-mediated sperm selection in cattle.

Chondrosarcoma is a hyper-vascularised, chemoresistant cartilage malignancy driven by VEGF-centred angiogenesis, and local adipose depots are increasingly recognised as paracrine drivers of tumour angiogenesis via adipokines and extracellular vesicles (EVs). The infrapatellar fat pad (IFP), an inflammatory adipose depot within the articular joint in direct cartilage contact, is a key local source of adipose-derived EVs, and thus a candidate driver of angiogenesis in chondrosarcoma. The aim of this study was to determine whether the IFP is a productive source of EVs, and whether IFP-derived EVs induce angiogenesis in articular chondrocytes. The IFP released significantly more EVs than subcutaneous fat (n = 8 per depot; p = 0.027). Treating primary human articular chondrocytes with IFP EVs for 24 h upregulated VEGFA (+1.6-fold, p = 0.036) and downregulated BMP4 (-2.4-fold, p = 0.011), engaging the VEGF/eNOS/ERK axis that drives chondrosarcoma angiogenesis. Re-analysis of a previously published phospho-kinase dataset from the same donor EVs, corroborated by a pooled donor-group analysis (n = 3), supported activation of eNOS, ERK1/2, PLC-{gamma}1 and HSP27. These findings identify the IFP as a dominant source of EVs within the articular joint, which can induce a pro-angiogenic, VEGF-axis switch in articular cartilage cells, supporting a signalling model relevant to chondrosarcoma angiogenesis.

At the onset of intervertebral disc degeneration, within the disc core, the pH and osmolarity decrease, and the residing notochordal cells (NCs) gradually transition towards nucleus pulposus cells (NPCs). How these microenvironmental cues shape the NCs extracellular vesicles (EV)-enriched secretome, and thus EV-mediated communication with NPCs during this transition, remains poorly understood. To study this, we collected the secretome from pig NC-rich tissue cultured for 4 days in either healthy or degenerate disc media to mimic these changes. In both conditions, NC-rich tissues were largely comparable at the histological and biochemical levels. Despite, tissues released glycosaminoglycans (GAGs), depleting the extracellular matrix. Surprisingly, degenerative media did not differentially release inflammatory regulators, though it reduced PGE2 release. We asked whether this extended to EV-enriched secretome media (SM_EV+), and found that the degenerative media reduced the number of EVs without altering their morphology or size. We then determined NC-EV association of inflammatory and matrix regulators. NC-EV isolation enriched MMP1, IL6 and IL10 and depleted soluble GAGs. Conversely, EV-depletion (SM_EV-) removed most GAGs without affecting MMP1, IL6, and IL10, suggesting that they contribute to the NC-EV soft corona. Functionally, healthy SM_EV+ improved GAG production by NPCs, but attenuated TBXT expression. Degenerate SM_EV+ did not elicit detectable EV-specific effects. These findings suggest that, in health, secretome-mediated communication from NCs to NPCs is only partially EV-mediated. At the onset of IVD degeneration, low pH and osmolarity impair the release of NC-EVs and negate the EV-specific beneficial matrix-anabolic effects on NPCs, contributing to the NC-to-NPC transition.

Decellularized extracellular matrix (dECM) scaffolds are increasingly used in regenerative medicine, yet the extent to which processed placental dECM retains properties capable of influencing cellular responses remains unclear. This study combines functional cell assays with deep learning-enabled quantitative imaging to determine how dehydrated placental ECM regulates cellular behavior across multiple human cell lineages. Human dermal fibroblasts, cardiac fibroblasts, and osteoblasts were cultured on dehydrated placental ECM or standard cell culture surfaces and assessed for cell attachment, viability, extracellular matrix production, and nuclear morphology. Placental dECM supported attachment and survival across all three cell types, while Pro-Collagen I Alpha 1 secretion varied by cell lineage relative to negative controls. To identify structural responses associated with scaffold culture, an automated imaging pipeline combining Cellpose-based nuclear segmentation with nuclear morphometric analysis was used to quantify nuclear area, eccentricity, and circularity. Quantitative profiling of hundreds of nuclei revealed scaffold-dependent remodeling of nuclear morphology that was not apparent by conventional microscopy. Cells cultured on placental dECM exhibited reduced nuclear area and increased nuclear eccentricity, while cardiac fibroblasts and osteoblasts showed alterations in nuclear circularity. These lineage-dependent morphological responses demonstrate that placental dECM provides more than a permissive substrate for cell attachment and is associated with measurable changes in cellular architecture following processing. Together, these findings support the biological relevance of processed placental dECM as a regenerative biomaterial and demonstrate the utility of quantitative single-cell morphometric analysis for detecting cell-material interactions that may not be apparent through qualitative imaging alone, guiding the rational design of regenerative therapies.

ObjectiveThe repair response to focal osteochondral injuries frequently fails to truly restore native osteochondral tissue, predisposing the joint to the likelihood of progressive degeneration and post-traumatic osteoarthritis. The biological mechanisms governing the earliest stages of repair in these tissues remain poorly understood, limiting the development of effective regenerative therapies. We therefore aimed to define the early cellular and spatial organisation of repair in a reproducible murine osteochondral injury model by integrating single cell spatial transcriptomics across the whole joint with longitudinal structural imaging and histological analyses. DesignA reproducible, non-critical osteochondral injury was created in the trochlear groove of female C57BL/6 mice. Structural repair was assessed using a multimodal approaching comprising quantitative histology, immunophenotyping, longitudinal magnetic resonance imaging (MRI) and micro-computed tomography ({micro}CT), while whole-joint Xenium spatial transcriptomics at days 3 and 7 defined the cellular and molecular organisation of the early repair response. ResultsSpatial transcriptomics demonstrated that the first week after injury is characterised by the emergence of anatomically distinct immune, vascular and stromal microenvironments across the synovial joint. Resolution of the early inflammatory response was accompanied by regional organisation of repair-associated stromal populations by day 7 after injury. The synovium preferentially supported matrix-associated fibro-chondrocyte-like cells, whereas the osteochondral injury itself retained stress-responsive stromal states with comparatively limited representation of matrix-associated populations. These findings indicate that distinct anatomical niches within the joint are associated with transcriptionally distinct stromal cell phenotypes during early repair. Longitudinal MRI and {micro}CT and histological analysis, demonstrated that these early spatial differences in cell phenotype were associated with progressive restoration of osteochondral architecture, with more effective regeneration of subchondral bone and limited restoration of native articular cartilage. ConclusionsThis study provides, to our knowledge, the first spatially resolved transcriptomic analysis of the early osteochondral repair response to injury across the whole synovial joint. Our findings demonstrate that the first week after injury establishes spatially organised immune, vascular and stromal cell microenvironments. Furthermore, these data suggest that incomplete cartilage repair may reflect an initial failure to establish and sustain matrix-associated stromal cellular states within the injury niche. These findings identify the early repair microenvironment as a critical determinant of tissue regeneration and provide a rationale for regenerative strategies that target repair with spatial and temporal precision.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent liver disorder worldwide, yet therapeutic options remain limited. TMPRSS6, a liver serine protease best known for its role in iron homeostasis, has recently emerged as a potential therapeutic target for MASLD. However, the molecular mechanisms linking TMPRSS6 to hepatic lipid metabolism remain incompletely understood. To identify novel TMPRSS6 substrates, we performed extracellular proteomic analyses of TMPRSS6-overexpressing cells. Among the proteins identified, {beta}-klotho (KLB), a co-receptor required for FGF19 and FGF21 signaling, emerged as a compelling candidate substrate. We demonstrate that TMPRSS6 interacts with KLB and promotes its proteolytic shedding in a catalytic activity-dependent manner. Functionally, TMPRSS6 reduced full-length KLB abundance at the cell surface and attenuated FGF19-dependent FGFR4 signaling in a heterologous expression system. Together, these findings identify KLB as a novel functional substrate of TMPRSS6, providing a mechanistic framework through which this protease may influence hepatic lipid metabolism. These results provide a rationale for investigating the regulation of KLB and other candidate substrates by TMPRSS6 in physiological models and further support its evaluation as a therapeutic target for MASLD.

Uterine fibroids (leiomyomas) are highly prevalent benign tumors defined by excessive extracellular matrix (ECM) deposition, altered vascular structure, and progressive tissue stiffening, yet the cellular programs that coordinate these features remain poorly understood. Cellular senescence has been implicated in fibroid biology, but whether senescence represents a uniform state or distinct, functionally specialized cell identities within fibroids is unknown. Here, we identify the distinct heterogeneous populations of senescent cells ("senotypes") present in human fibroids and characterize their role in shaping the fibroid microenvironment. Using single-cell RNA sequencing (scRNA-seq) integrated with a senescence gene signature and protein-level validation, we identify senescent cells (SnC) distributed across fibroblast, mural, and endothelial compartments, each exhibiting distinct transcriptional programs. SnC endothelial cells (ECs) are enriched in fibroids relative to matched myometrium and activate TEAD4-associated mechanosensing, angiogenic, and immune signaling pathways, despite being associated with impaired vessel maturation in situ. In parallel, SnC fibroblast and mural populations in fibroids upregulated SRF-associated cytoskeletal and ECM programs, accompanied by increased COL6A3 expression and collagen VI deposition, consistent with tissue stiffening. Ligand-receptor and spatial analyses reveal that these SnC populations function as interconnected signaling hubs, coordinating immune cell recruitment and stromal remodeling. Importantly, analysis of human fibroids treated with collagenase demonstrated a reduction in both ECM density and SnC burden, supporting a reinforcing relationship between matrix mechanics and senescence. Together, these findings establish senescence in fibroids as a heterogeneous, mechanically reinforced, and network-driven process that links vascular dysfunction, immune signaling, and fibrosis, highlighting distinct SnC states as potential translational targets for non-surgical therapies.

ObjectiveCellular senescence has been shown to underlie many age-related diseases, including osteoarthritis (OA). In addition to age, biological sex is an OA risk factor with females at greater risk of hand and knee OA. We profiled the senescence burden in OA human synovial fibroblasts while accounting for these factors to understand how senescence may contribute to the increased burden of OA in females. MethodsSynovial fibroblasts were isolated from tissue obtained at knee arthroplasty for OA from 10 male and 10 female donors. Single cell multiplexed immunofluorescence imaging was used to profile the senescence burden in samples age-matched to account for the differences in chronological age. Clustering was performed using stability and generalizability scoring. ResultsIndependent of chronological age, OA synovial fibroblasts from female donors showed higher levels of senescence associated proteins p16, p21, p53, phospho-p65, IL-6, and IL-8. Assessment of oxidative stress associated proteins NRF2, SEPP1, NQO1 and TXNIP indicated a lower capacity for female cells to respond to oxidative stress. Clustering analysis revealed male and female enriched clusters. The female-enriched clusters showed higher levels of senescence-associated proteins and an increased oxidative stress response. ConclusionsOA synovial fibroblasts from female donors demonstrated higher levels of senescence associated markers, lower ability to respond to oxidative stress, and increased senescence with increasing age. These findings indicate that female synovial fibroblasts are more likely to show markers of senescence and oxidative stress, suggesting senescence can contribute to the increased incidence of osteoarthritis in women.

Ovarian cancer is among the deadliest gynecologic malignancies, and its molecular heterogeneity limits accurate prognostic stratification. Although multi-omics approaches have improved predictive modeling, many prioritize predictive performance over biological interpretability, limiting their clinical translation. We developed an interpretable three-stage machine learning framework integrating mRNA, microRNA, DNA methylation, copy number variation, and protein expression data from The Cancer Genome Atlas. Hierarchical feature selection was combined with a weighted ensemble of ElasticNet, ridge regression, support vector regression, XGBoost, and random forest models to estimate overall survival time in patients with ovarian cancer. Multi-omics integration outperformed every single-modality model, achieving a Pearson correlation of 0.752, a concordance index of 0.779, and a mean absolute error of 8.57 months between estimated and observed survival time, compared with 0.48 for the best single modality. The framework identified a 20-biomarker signature dominated by tumor-associated macrophage and complement genes. In an independent survival analysis, VSIG4 and CD163 remained significant after false discovery rate correction, and the signature raised the concordance index over clinical covariates alone from 0.615 to 0.686Enrichment analysis implicated PI3K-Akt, MAPK, focal adhesion, hypoxia, apoptosis, and p53 signaling pathways. This framework couples improved prognostic estimation with biological interpretability supporting multi-omics biomarker discovery in ovarian cancer.

Matrix metalloproteinase 13 (MMP13) is a zinc-dependent protease that plays key roles in extracellular matrix remodeling. Like several other MMPs, MMP13 has been shown to interact with heparan sulfate (HS), a highly sulfated glycosaminoglycan found at the cell surface and in the extracellular matrix, but the significance of the interaction remains unknown. Here we report that while zymogen and mature forms of MMP13 both bind HS with high affinity, their interactions with HS display markedly different characteristics in terms of preferred HS structure and binding kinetics. By structure-guided mutagenesis, we identified a large HS-binding site of MMP13 consists of 10 residues in the hemopexin domain, 3 residues in the catalytic domain, and 2 residues in the linker region. While these basic residues participate in binding to both zymogen and mature forms of MMP13, the relative contribution of many residues differs substantially between the two forms, which likely contributes to their distinct HS-binding characteristics. Binding of HS to mature MMP13 resulted in selective inhibition of the collagenase activity of MMP13 in a length- and sulfation-dependent manner, but the binding had no effect on degradation of non-collagen substrates. Mechanistically, the inhibitory effect of HS likely results from reduced interdomain flexibility after binding of HS, and/or HS-induced dimerization of MMP13. In sum, our study establishes HS as a multifaceted regulator of MMP13 activity, and discovers that the HS-binding site of MMP13 is a novel exosite that can be targeted to inhibits its collagenase activity.

Successful cartilage repair remains one of the most significant challenges in the musculoskeletal field. Microfracture (MFx), a form of marrow stimulation, remains the predominant repair technique, but it exhibits routine failure due to inadequate defect fill and inferior fibrotic tissue formation. Whereas current strategies focus on augmenting MFx with scaffolds and bioactive factors, the potential to target the MFx clot itself and use the capabilities of this dynamic environment to guide MFx repair remains largely unexplored. We verified that MFx contraction and fibrosis hinder repair success in minipigs and become evident as early as one week in multiple animal models. Therefore, our objective was to investigate and direct microenvironmental interactions in the MFx clot to promote volumetric maintenance and reprogram cells from a fibrotic to more chondrogenic phenotype. Extracellular control of cell-environment interactions, through fibrinogen augmentation or anti-fibrinolytic treatment, limited contraction but had no effect on or even exacerbated the fibrotic susceptibility of marrow-derived cells (MDCs). Intracellular control of microenvironmental interactions, through modulation of the Rho-ROCK pathway, drove TGF-{beta}3 activity of MDCs along a "chondro-fibro axis". In particular, treatment with the ROCK inhibitor Fasudil drove TGF-{beta}3-treated cells away from a myofibroblast phenotype and towards chondrogenesis. Short-term Fasudil treatment prevented TGF-{beta}3-driven macroscale clot contraction and enhanced cartilage-specific matrix deposition in vitro. In a pilot rat study, this combination treatment improved GAG deposition and better protected surrounding cartilage. These findings suggest that Rho-ROCK modulates TGF-{beta} signaling along this chondro-fibro axis and its precise control could be the key to promoting precise and volumetric cartilage repair through microenvironmental interactions.

Oxygen is essential for all terrestrial animals, but there is dramatic variability in how well different animals and even different cell types can adapt to reduced oxygen availability. We used a meta-analysis of the literature, with a focus on mouse studies, to identify pathways that might act to protect animals in low oxygen environments. We identified 108 genes whose mRNA levels change under hypoxia, and 55 genes critical for mounting a response to hypoxia. With this data, we developed a list of conserved genes, and we tested three C.elegans genes previously uncharacterized in hypoxia, mxl-3, yap-1, and ador-1, and found that loss of function altered egg-laying during and after hypoxia. Our method provides a more targeted approach of how to screen for hypoxic phenotypes and study in more genetically tractable organisms to show mechanisms.

The foreign body response (FBR) is an immune mediated event that occurs with every material implant. The extent of the fibrosis is dependent on many factors including the biomaterial design, tissue location, and host factors such as age, sex, ancestry, diet. There are known clinical outcomes of implants dependent on age and sex, including increased fibrosis and implant failure in aged and female patients. As the population ages, there is a growing need to understand how aging affects the FBR, and how preclinical models can capture this to guide biomaterial design. Here, we investigated how chronic fibrosis in a murine model of the FBR is altered by two biological factors: age and sex. We investigated changes in fibrosis using a volumetric muscle loss (VML) injury model coupled with polycaprolactone (PCL) or polyethylene (PE) microparticle implants. Fibrosis was quantified through gene expression, microscopic analysis of histologic sections, and the corresponding immune response measured via gene expression and flow cytometry data. We found gene expression differences with immune pathways enriched in female mice, and microscopy revealed collagen birefringence area increased in young male mice. Both the innate and adaptive immune response were altered by age and sex via T cell and macrophage phenotype, and the effects of aging differed between sexes. These results reveal both variables contribute to discrepant outcomes in both fibrosis and the local immune response to synthetic material implants. This demonstrates a clear need to understand and account for the influence of biological factors in biomaterial design.

Macrovascular invasion (MVI) and extrahepatic spread (EHS) define the most aggressive, treatment-refractory hepatocellular carcinoma (HCC), yet blood-based markers that report the underlying protein-network biology are lacking. Conventional proteomics measures protein abundance but not the conformational and protein-protein-interaction (PPI) states that govern function. We applied covalent proteome painting (CPP)--a dimethylation-based accessibility assay that reads out binding-site openness--to matched tumor and serum, reasoning that intravascular tumor dissemination remodels plasma protein complexes in a manner detectable as changes in accessibility. Eight treatment-native HCC patients were profiled by CPP using matched FFPE tumor and top-14- depleted serum on a Q Exactive Orbitrap HF. The 85 tumor-serum common proteins defined an 81-protein targeted panel, validated by multiple-reaction-monitoring (MRM) mass spectrometry with heavy stable-isotope-standard peptides (296 peptides; 3,717 light/heavy transition pairs) in 22 FFPE tumors and 22 matched sera. Accessibility was the light/heavy ratio (high, open; low, closed). We assessed differential accessibility, serum-tissue translatability, pathway enrichment, and biomarker/survival performance. Aggressive disease showed broadly decreased protein accessibility. MVI-associated changes were directionally concordant between tumor and serum (Spearman {rho}=0.21; 59% concordant), driven by coagulation and complement proteins (FGG, CTSD, LBP, C4BPA); the EHS axis did not translate. Decreased-accessibility proteins were enriched for complement-coagulation cascades and IGF/IGFBP transport. A six-protein serum accessibility signature discriminated MVI (leave-one-out cross-validated AUC 0.80; best single markers ceruloplasmin 0.83 and haemoglobin- 0.77), and MVI status trended with shorter overall survival (log-rank p=0.06). Accessibility-based serum proteomics captures MVI-associated protein-complex remodeling that abundance assays miss, nominating a coagulation/complement-anchored serum signature for vascular-invasive HCC that warrants prospective validation.

Breast cancer (BC) shows greatest sexual diversity. Increased diagnosis and poorer outcomes in men highlights the need to better understand its biology. We hypothesised that cancer-associated fibroblasts (CAFs), the most abundant cell type in the tumour microenvironment, might define sex-related differences. Using phenotypically matched male and female CAFs generated from breast cancer tissues, we demonstrate distinct transcriptional programmes and functional behaviours associated with extracellular matrix remodelling, cell adhesion, migration and vascular development. Compared to CAFs generated from females BC, those from males generated denser, more complex matrices promoting stronger tumour and endothelial cell adhesion, vascular growth, but less organised capillary network formation. Findings reveal fundamental sex-related variations in CAF phenotype and biology in BC. These findings highlight the need to integrate biological sex into precision oncology to identify opportunities for sex-specific therapeutic strategies in BC.

Endothelial-to-mesenchymal transition (EndMT) has become a central mechanism in developmental biology, fibrosis, vascular disease, and cancer. We previously reported on an integrated signaling model in which TGF-{beta}2 induces EndMT through coordinated activation of Smad-dependent and Smad-independent signaling pathways converging on Snail, while GSK-3{beta} regulates Snail activity. We performed a systematic figure-by-figure reproducibility analysis of the original publication. Independent studies published between 2011 and 2026 were identified and curated according to predefined inclusion criteria. Each original experimental conclusion was evaluated for independent confirmation. In parallel, selected biochemical experiments were independently reproduced using newly acquired reagents and contemporary Western blot methodologies. Independent publications consistently reproduced each major mechanistic conclusion of the original study, including activation of Smad, ERK, PI3K/AKT, and p38 MAPK signaling, regulation of Snail expression, EndMT-associated marker switching, and GSK-3{beta}-dependent control of Snail activity. Independent laboratory experiments reproduced the principal biochemical findings using contemporary reagents and experimental workflows. The combined literature analysis and independent laboratory replication demonstrate that the mechanistic framework in our previous study has remained reproducible across multiple laboratories, endothelial cell types, disease models, and fifteen years of investigation. This work illustrates a complementary framework for assessing reproducibility that integrates direct experimental replication with cumulative independent validation.

Under homeostatic conditions, the cornea is avascular and contains few immune cells, but this changes rapidly following injury. Although the long-term consequences of corneal damage are well characterized, the earliest vascular and immune responses remain poorly understood. Here, we used a murine corneal alkali-burn model to examine limbal vascular activation and leukocyte recruitment immediately and at 2, 6, and 24 hours after injury. Limbal blood vessels underwent immediate dilation; however, vascular leakage into the corneal stroma occurred only in males. Lymphatic capillaries rapidly formed directed extensions toward the injury without significantly increasing their total vascular area, with males exhibiting longer extensions than females. Fluorescent dextran uptake provided evidence that these lymphatic vessels were functionally engaged in early tracer drainage. Despite pronounced vascular activation, early recruitment of neutrophils, monocytes, dendritic cells, macrophages, T cells, B cells, and natural killer cells remained limited. Thus, limbal blood and lymphatic vessels initiate the earliest response to corneal alkali injury before substantial leukocyte infiltration. These findings reveal sex-dependent differences in vascular permeability and lymphatic remodeling and identify the limbal vasculature as an early regulator of corneal inflammation and tissue repair.

The mammary gland relies on reciprocal interactions between epithelial cells and their surrounding extracellular matrix (ECM) to form and maintain milk-producing tissue structures. Yet these processes remain difficult to study in human model systems. Mammary epithelial cells (MECs) can be isolated noninvasively from breast milk, but whether they generate three-dimensional organoids and respond to matrix cues has been unclear. Here, human milk-derived MECs (milk MECs) spontaneously form complex organoids, including polarized acinar and terminal duct lobular unit-like structures after isolation. To investigate how matrix composition shapes these organoids, milk MECs were cultured in decellularized mammary ECM (dECM), Matrigel, and collagen I. In dECM, milk MECs formed polarized branched networks with aligned actin organization along collagen fibrils, whereas in Matrigel they adopted a more lactation-associated state, marked by {beta}-casein expression and milk fat globules. Together, these findings establish breast milk-derived MEC organoids as a human model to study how ECM context regulates mammary morphogenesis and lactation biology.