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Label-Free Urinary Proteomics Uncovers Immune-Related Non-Invasive Biomarkers for Primary Biliary Cholangitis.

Diagnosis of primary biliary cholangitis (PBC) currently depends on invasive liver biopsy or serum markers with inadequate diagnostic performance. This study aimed to identify non-invasive urinary protein biomarkers for PBC detection. Urine specimens from biopsy-verified PBC patients and healthy controls were processed through ultracentrifugation-based protein extraction, enzymatic digestion, and HPLC-ESI-IT/MS proteomic profiling; protein quantification was completed using Spectronaut v14.8. We identified 194 differentially expressed urinary proteins (109 upregulated, 85 downregulated) and screened 10 immune-related candidates through GO and KEGG enrichment. Pearson correlation further filtered three core proteins, osteopontin (SPP1/OPN), RAMP3 and S100A8, that correlated significantly with key PBC biochemical indices (ALP, GGT, AST, ALT, IgM, p < 0.05). Elevated urinary concentrations of OPN, RAMP3 and S100A8 were validated by ELISA in an independent cohort containing 30 PBC patients and 20 healthy volunteers. In summary, urinary OPN, RAMP3 and S100A8 are markedly increased in PBC patients and hold promise as non-invasive diagnostic biomarkers for PBC; however, their diagnostic specificity against other cholestatic and autoimmune liver diseases remains to be evaluated, and further confirmation in larger multicenter cohorts with disease control groups is warranted.

Humans

Uncovering hidden protein modifications with native top-down mass spectrometry.

Protein modifications drive dynamic cellular processes by modulating biomolecular interactions, yet capturing these modifications within their native structural context remains a significant challenge. Native top-down mass spectrometry promises to preserve the critical link between modifications and interactions. However, current methods often fail to detect uncharacterized or low-abundance modifications, limiting insights into proteoform diversity. To address this gap, we introduce precise and accurate Identification Of Native proteoforms (precisION), an interactive end-to-end software package that leverages a robust, data-driven fragment-level open search to detect, localize and quantify 'hidden' modifications within intact protein complexes. Applying precisION to four therapeutically relevant targets-PDE6, ACE2, osteopontin (SPP1) and a GABA transporter (GAT1)-we discover undocumented phosphorylation, glycosylation and lipidation, and resolve previously uninterpretable density in an electron cryo-microscopy map of GAT1. As an open-source software package, precisION offers an intuitive means for interpreting complex protein fragmentation data. This tool will empower the community to unlock the potential of native top-down mass spectrometry, advancing integrative structural biology, molecular pathology and drug development.

Mass Spectrometry

Biological requirements for material integration.

The recognition that synthetic devices can provide functional replacements for failed teeth, or for previously edentulous areas, has resulted in increased emphasis being placed on understanding of the interactions between synthetic materials and host tissues in order for the success of these devices to be optimized. A key to achievement of an optimal biological interface between the implant and the surrounding tissue is through an understanding of host response to materials. This article reviews the biological requirements for implant-tissue integration, with specific focus on the role of adhesion molecules and cytokines (growth factors) in this process. Adhesion molecule/cytokine interactions are discussed, and in particular the possible role for osteopontin, an adhesion molecule as well as a cytokine, is considered in wound healing. Finally, the causes of peri-implantitis are discussed, and methods of decontamination are presented. The decontamination methods focus on enhancement of cell adhesion and integration to the altered implant surface.

Cell Adhesion Molecules

Development and characterization of a rapidly proliferating, well-differentiated cell line derived from normal adult human osteoblast-like cells transfected with SV40 large T antigen.

A new bone cell line was established by transfecting normal adult human osteoblast-like (hOB) cells, derived from a 68-year-old woman, with the plasmid pSV3 neo. The plasmid included coding sequences and promotors for the large and small T antigens of the SV40 virus as well as resistance to the antibiotics neomycin and G418. A single antibiotic-resistant colony was located and cloned. Large tumor antigen production in the clonal cell line was confirmed by indirect immunofluorescence study. Treatment with 1,25-dihydroxy-vitamin D3 increased steady-state concentrations of protein and mRNA for osteocalcin and for alkaline phosphatase. Northern blot analyses also demonstrated the presence of mRNAs for alpha(I)-procollagen, osteopontin 1a, transforming growth factor beta, and interleukin-1 beta. The plasma membrane calcium pump and osteonectin were identified by immunocytochemical analysis. These cells produced a matrix that mineralized when beta-glycerophosphate was added to their cultures. As assessed by functional receptor assays, both estrogen and androgen receptors were present and functional, although at low concentrations. Treatment with parathyroid hormone did not stimulate adenylate cyclase activity. Thus, these cells are a well-differentiated, steroid-responsive clonal cell line that closely approximates the phenotype of the mature osteoblast. They should serve as an excellent model for the study of osteoblast biology.

Aged

Contact hypersensitivity promotes hair regeneration through SPP1-secreting macrophages.

Allergic contact dermatitis, or contact hypersensitivity (CHS), is a pathological adaptive immune response that paradoxically induces hair regeneration, yet its underlying mechanisms remain unclear. We integrated high-resolution spatial transcriptomics and single-cell RNA sequencing to map the intricate interactions between immune cells, stroma, and hair follicles during CHS-induced hair growth in mice. Among all immunocytes, macrophages underwent the most prominent compositional and functional remodeling. We resolved five transcriptionally distinct macrophage subsets, with contact hypersensitivity driving a shift from homeostatic antigen-presenting cells toward a pro-inflammatory CD14+SPP1+ population. Trajectory analysis revealed divergent differentiation paths under homeostatic versus allergic conditions, highlighting the plasticity of skin macrophages. Mechanistically, CD14+SPP1+ macrophages secreted SPP1 (osteopontin), which engaged CD44 on hair follicle stem cells to activate PI3K-AKT signaling and trigger their proliferation. Notably, canonical pro-inflammatory cytokine signaling through TNF-&#x3b1; and IL-1 was dispensable for this process, underscoring the specificity of the SPP1-CD44 axis in immune-mediated hair regeneration. These findings reveal a macrophage-dependent mechanism of immune-mediated hair regeneration, offering therapeutic insights into immune-stem cell crosstalk.

Journal Article

Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis.

Immune checkpoint inhibition (ICI) has emerged as a critical treatment strategy for squamous cell carcinoma of the head and neck (HNSCC) that halts the immune escape of the tumor cells. Increasing evidence suggests that the onset, progression, and lack of/no response of HNSCC to ICI are emergent properties arising from the interactions within the tumor microenvironment (TME). Deciphering how the diversity of cellular and molecular interactions leads to distinct HNSCC TME subtypes subsequently governing the ICI response remains largely unexplored. We developed a cellular-molecular model of the HNSCC TME that incorporates multiple cell types, cellular states, and transitions, and molecularly mediated paracrine interactions. Simulation across the selected parameter space of the HNSCC TME network shows that distinct mechanistic balances within the TME give rise to the five clinically observed TME subtypes such as immune/non-fibrotic, immune/fibrotic, fibrotic only and immune/fibrotic desert. We predict that the cancer-associated fibroblast, beyond a critical proliferation rate, drastically worsens the ICI response by hampering the accessibility of the CD8&#x2009;+&#x2009;killer T cells to the tumor cells. Our analysis reveals that while an Interleukin-2 (IL-2) + ICI combination therapy may improve response in the immune desert scenario, Osteopontin (OPN) and Leukemia Inhibition Factor (LIF) knockout with ICI yields the best response in a fibro-dominated scenario. Further, we predict Interleukin-8 (IL-8), and lactate can serve as crucial biomarkers for ICI-resistant HNSCC phenotypes. Overall, we provide an integrated quantitative framework that explains a wide range of TME-mediated resistance mechanisms for HNSCC and predicts TME subtype-specific targets that can lead to an improved ICI outcome.

Tumor Microenvironment

Generation and validation of a Myh11Dre-Spp1Cre intersectional mouse model for lineage tracing of disease-associated smooth muscle cell states.

BACKGROUND: Phenotypic modulation of vascular smooth muscle cells (VSMCs) is a hallmark of vascular remodeling and cardiovascular disease. Recent lineage-tracing and single-cell transcriptomic studies have identified secreted phosphoprotein 1 (SPP1) as a prominent marker associated with disease-associated VSMC states, particularly those linked to fibrotic remodeling and vascular calcification. However, the cellular origins and fate of SPP1-associated VSMC populations remain incompletely understood. METHODS AND RESULTS: We generated a novel Spp1-rSTOPr-Cre (Spp1Cre) knock-in mouse line in which Cre recombinase is expressed from the endogenous Spp1 locus following Dre-mediated excision of a rox-flanked transcriptional STOP cassette. Correct targeting of the knock-in allele was validated by internal, 5' junction, 3' junction, and long-range PCR analyses, as well as Sanger sequencing. To establish an intersectional lineage-tracing strategy, Spp1Cre mice were crossed with Myh11DreERT2 and Rosa26-RSR-LSL-tdTomato-LSL-eGFP reporter mice, enabling permanent labeling of VSMC-derived populations following activation of the endogenous Spp1 locus. Under physiological conditions, eGFP-positive cells were detected at low frequency within the vascular wall and were predominantly negative for the contractile markers ACTA2 and MYH11. As a proof-of-principle application, eGFP-positive cells markedly expanded within atherosclerotic lesions induced by AAV-PCSK9D377Y and high-fat diet feeding. These lineage-traced cells remained largely ACTA2- and MYH11-negative, consistent with a modulated phenotype. Notably, only a minority of eGFP-positive cells expressed SPP1 or fibronectin at the time of analysis, demonstrating the utility of permanent lineage tracing for tracking cells with a history of endogenous Spp1 activation during vascular remodeling. CONCLUSION: We report the generation and validation of a novel Myh11Dre-Spp1Cre intersectional mouse model for lineage tracing of VSMC-derived populations that have activated the endogenous Spp1 locus. This genetic resource provides a valuable platform for investigating the origin, fate, and phenotypic evolution of Spp1-associated VSMC populations during vascular remodeling and cardiovascular disease.

Animals

New concepts of vitamin D functions.

Besides its classical actions in calcium metabolism, it is clear that the hormonal form of vitamin D has many new functions, which have only been discovered as a result of following the appearance of its receptor. Furthermore, because of the vitamin D-based endocrine system, the use of vitamin D compounds in treating a variety of diseases has been expanded. We now know that 1.25-(OH)2D3 not only stimulates the intestine to absorb calcium and phosphorus, the bones to mobilize calcium and phosphorus, and the kidney to cause increased renal reabsorption of calcium, but also directly suppresses the parathyroid hormone and is a developmental hormone necessary for the recruitment of cells for osteoclast formation, for female reproduction, for development of skin, and for the treatment of certain malignant conditions.

Animals

Discovery and validation of a prognostic SPP1/PLAU signature in HPV-negative oropharyngeal squamous cell carcinoma.

BACKGROUND: This study aimed to identify and validate robust prognostic biomarkers for oropharyngeal squamous cell carcinoma (OPSCC), with a specific focus on the high-risk HPV-negative subtype. METHODS: Integrated bioinformatics analysis was performed on transcriptomic data from four GEO datasets (n&#x2009;=&#x2009;418 samples). Differentially expressed genes (DEGs) were identified, and a protein-protein interaction (PPI) network was constructed for the most dysregulated genes. Key modules were analyzed via survival analysis and multivariate Cox regression. The top candidate genes were validated at the protein level using immunohistochemistry (IHC) in an independent cohort of 304 OPSCC patients. RESULTS: A 33-gene module related to extracellular matrix organization showed significant prognostic association. It stratified patients into high- and low-risk groups with markedly different overall survival (HR&#x2009;=&#x2009;2.71, p&#x2009;<&#x2009;0.001). From this module, SPP1 and PLAU were identified as independent prognostic factors through multi-step screening. Both genes were significantly overexpressed in tumors (approximately 20-fold and 10-fold, respectively, p&#x2009;<&#x2009;0.001), with high expression strongly correlated with advanced tumor stage (p&#x2009;<&#x2009;0.01) and, notably, the HPV-negative subtype (p&#x2009;<&#x2009;0.001). In survival analysis, high expression of either SPP1 or PLAU was associated with poorer overall survival (SPP1: p&#x2009;<&#x2009;0.001; PLAU: p&#x2009;<&#x2009;0.001) and progression-free survival (p&#x2009;<&#x2009;0.001). IHC validation confirmed high protein expression in 69.7% (SPP1) and 54.8% (PLAU) of cancer tissues. A prognostic nomogram integrating the SPP1/PLAU signature with clinical variables was constructed with strong predictive accuracy (C-index&#x2009;=&#x2009;0.75). CONCLUSION: The SPP1/PLAU dual-gene signature is a robust and independent prognostic biomarker for OPSCC, with particular clinical utility for stratifying high-risk HPV-negative patients.

Humans