Search Results (1,160)

Renal cell carcinoma (RCC) is a biologically heterogeneous malignancy characterized by variable clinical behavior and diverse molecular phenotypes. Although immune checkpoint inhibitors and targeted therapies have transformed the treatment landscape of advanced RCC, clinically validated biomarkers capable of improving risk stratification, therapeutic-decision making and disease monitoring remain lacking. Kidney injury molecule-1 (KIM-1), also known as hepatitis A virus cellular receptor-1 (HAVCR1) or T-cell immunoglobulin and mucin domain-containing protein-1 (TIM-1), has emerged as a biologically compelling investigational biomarker e because of its close relationship to proximal tubular epithelial injury and renal carcinogenesis. KIM-1 is a transmembrane glycoprotein minimally expressed in normal kidney tissue but markedly upregulated in dedifferentiated proximal tubular epithelial cells following injury, and in clear cell RCC, where its extracellular domain can be shed into plasma and urine. Beyond its role as a marker of tubular injury, KIM-1 participates in immune regulation, phagocytosis, inflammatory signaling and tissue remodeling, supporting its potential relevance to tumor biology. Clinical studies have demonstrated associations between elevated circulating KIM-1 levels and RCC diagnosis, recurrence risk, and survival outcomes, particularly in localized and postoperative disease settings. KIM-1 has additionally been investigated as a therapeutic target through antibody–drug conjugate approaches. Despite promising translational data, important limitations yet remain. Current evidence is predominantly prognostic rather than predictive, and substantial analytical and biological challenges continue to limit implementation. Assay standardization, clinically meaningful cutoffs, specimen selection, timing of sampling, and confounding by chronic kidney disease or nonmalignant renal injury remain incompletely resolved. Furthermore, evidence supporting incremental value beyond established clinicopathologic models remains limited. This review critically evaluates the biological rationale, analytical considerations and clinical evidence supporting KIM-1 in RCC. Particular emphasis is placed on distinguishing prognostic, predictive, pharmacodynamic, and therapeutic applications, as well as defining the evidentiary gaps that must be addressed before clinical implementation. Current evidence is derived predominantly from retrospective and exploratory analyses, and important limitations remain regarding assay standardization, biological specificity, chronic kidney disease-related confounding, and prospective validation. The review concludes with a summary of the evolving landscape of KIM-1-directed biomarker strategies in RCC, which may ultimately contribute to improved biologic risk stratification and biomarker-driven clinical investigation in RCC. Full article

Background: The mucosal barrier presents a significant challenge for non-invasive delivery of macromolecular therapeutics, often requiring administration with poor bioavailability and increased toxicity risks. The polymeric immunoglobulin receptor (pIgR) contains an extracellular secretory component (SC) for immunoglobulin binding and a membrane-anchored stem domain capable of apical-to-basolateral transcytosis. We hypothesized that targeting the stem domain could enable active drug transport across mucosal barriers. Methods: Using phage display, we identified four high-affinity nanobodies against human and murine pIgR. Two lead candidates (3LTHMP-4 and 3LTHMP-5) demonstrated efficient apical-to-basolateral transport in vitro (Transwell assays) and in vivo (fluorescence imaging). Engineered bispecific antibodies fusing these nanobodies with anti-IL-5 mAb reslizumab were administered via inhalation in a murine asthma model at one-tenth the intraperitoneal reslizumab dose. Resluts: The bispecific antibodies showed significant therapeutic efficacy, while reslizumab alone at equivalent concentrations failed to demonstrate efficacy. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) revealed that both 3LTHMP-4 and 3LTHMP-5 specifically bind to the pIgR stem domain (residues 578–612), a region distinct from the dimeric IgA binding site. Conclusions: These findings suggest that stem domain-specific binding may facilitate transport across the mucosal barrier while preserving native receptor physiology, offering a potential strategy for effective transmucosal delivery of biologics. Full article

Alzheimer’s disease and related dementias (ADRD) are neurodegenerative conditions characterized by progressive cognitive and functional decline. AD pathology is associated with extracellular amyloid-β plaques, intracellular tau neurofibrillary tangles, synaptic dysfunction, and neuronal loss. AD accounts for approximately 60–80% of dementia cases globally. In 2022, AD was the seventh leading cause of death in the United States, and the number of Americans aged 65 and older living with Alzheimer’s dementia is projected to increase substantially by 2060. Despite decades of research, AD/ADRD data resources remain fragmented across clinical, imaging, genetic, genomic, and therapeutic domains. This paper addresses that gap by providing a centralized review of widely used AD/ADRD databases and computational methods. We first summarize computational approaches used to analyze these datasets, including machine learning (ML), natural language processing (NLP), and biomedical imaging. We then review eight databases classified into three categories: Clinical and Population Data, Genetics and Genomics, and Drug Discovery and Therapeutics. Finally, we discuss real-world applications, including early diagnosis, clinical decision support, personalized medicine, and drug-mechanism analysis. This review identifies opportunities for future work in data harmonization, cross-database compatibility, and robust, generalizable AI models for AD/ADRD research. Full article

Discoidin domain receptor 1 (DDR1) has been implicated in fibrotic progression in multiple organs, including the kidney. However, its role in regulating cytoskeletal organization and matrix remodeling in renal fibroblasts remains unclear. Here, we investigated how DDR1 expression is regulated by profibrotic stimulation and extracellular matrix stiffness, and how DDR1 influences cytoskeletal organization and collagen remodeling. Single-cell RNA sequencing of murine kidneys subjected to unilateral ureteral obstruction (UUO) revealed enrichment of Ddr1 expression in transitional fibroblast populations during early activation. In vitro, transforming growth factor-β1 (TGF-β1) increased DDR1 expression, but DDR1 depletion did not affect canonical myofibroblast marker expression. Instead, DDR1 depletion suppressed stress fiber assembly while promoting actin-rich podosome formation associated with matrix degradation. Functionally, DDR1-deficient cells exhibited impaired focal adhesion maturation, enhanced collagen degradation, reduced gel contraction, and decreased collagen matrix stiffness as measured by atomic force microscopy. Furthermore, extracellular matrix stiffness dynamically regulated DDR1 expression, suggesting a bidirectional relationship between DDR1 expression and matrix mechanics. Together, these findings identify DDR1 as a modulator of cytoskeletal remodeling that governs the balance between matrix-degradation and contractile remodeling programs in renal fibroblasts. Full article

Liver fibrosis is the excessive accumulation of extracellular matrix (ECM) that occurs in most types of chronic liver diseases (CLDs) as a response to sustained liver injury. While the ECM comprises different proteins, collagen being the most abundant, the term matrisome refers to a plethora of ECM-related molecules, including collagen-associated proteins, growth factors, cytokines, enzymes and their endogenous inhibitors. The hepatic matrisome undergoes significant qualitative and quantitative changes during liver fibrosis. Despite intense research over recent years, our understanding of the matrisome in the liver—both in health and disease—and particularly of its function beyond its conventional structural role, remains poor. This review highlights how comprehending hepatic matrisome responses to liver injury can yield novel insights into disease progression and regression and could be exploited as a potential antifibrotic strategy. The antifibrotic potency of drugs that interfere with the matrisome at different levels has been demonstrated in preclinical studies, but translation to clinical trials remains still limited. So far, simtuzumab (LOXL2 inhibitor antibody), imatinib (small-molecule inhibitor against discoidin domain receptors—DDRs), bexotegrast (integrin inhibitor), GR-MD-02 (galectin 3 inhibitor), and BMS-986263 (siRNA-targeting HSP47) have been or are being evaluated in clinical trials related to CLD, and some of them have shown promising results. Full article

Glioblastoma (GBM) is one of the most aggressive human cancers, with therapeutic failure driven by pronounced intratumoral heterogeneity, microenvironmental plasticity, immune suppression, blood–brain barrier (BBB)-related pharmacological constraints, and adaptive resistance mechanisms. A major limitation in GBM research is the lack of a human-relevant experimental system able to reproduce these dynamic features while generating interpretable, multimodal datasets. In this context, we propose a testable organ-on-chip (OoC)-extracellular vesicle (EV)-deep learning (DL) framework in which patient-derived GBM cells, endothelial cells, astrocytes, pericytes, stromal cells, and immune components are organized within perfused microphysiological systems. EVs are selectively and temporally harvested from defined compartments, and imaging, barrier-function, sensor, and EV-cargo data are integrated through modality-specific and multimodal DL architectures. This framework is intended not as an immediately validated clinical tool but as an experimental roadmap for linking EV-mediated communication to measurable phenotypes such as BBB disruption, invasion, immune reprogramming, and drug response. We critically discuss the technical requirements of BBB-on-chip systems, EV source attribution, immune-component integration, DL model selection, data scarcity, overfitting, batch effects, domain shift, regulatory barriers, cost, throughput, and reproducibility. By repositioning OoC-EV-DL integration as a staged translational strategy rather than a clinically established solution, this work aims to define a realistic and biologically grounded route for advancing precision oncology in GBM. Full article

Magnetic targeting of drug carriers is commonly studied at macroscopic scales, while its impact on drug transport across individual cell membranes remains poorly quantified. Here, we present a theoretical and numerical model of magnetically assisted drug transport across the membrane of a single tumor cell exposed to magnetic field gradients. Extracellular transport is described by an advection–diffusion equation that couples passive diffusion with magnetophoretic drift, whereas intracellular transport is governed by diffusion and first-order uptake kinetics. The cell membrane is modeled as a semi-permeable interface with finite permeability, providing explicit coupling between extracellular and intracellular domains. Assuming spherical symmetry, the coupled transport equations are solved using finite-difference schemes, with magnetic forcing represented through an effective drift velocity $v_{\mathrm{m}\mathrm{a}\mathrm{g}}$ and interpreted using the magnetic Peclet number. To enable a controlled comparison between healthy and tumor cells, identical geometric, diffusive, and magnetic parameters are used, while biological differences are introduced solely through membrane permeability and intracellular uptake rates. By separating cumulative membrane delivery from cumulative intracellular uptake, the model resolves ambiguities arising from heterogeneous uptake kinetics. The results show that magnetophoretic drift enhances near-membrane drug accumulation and effective transmembrane flux without modifying intrinsic membrane properties. Magnetic targeting therefore acts as a transport amplifier, magnifying pre-existing biological differences and producing a larger model-predicted delivery advantage in tumor cells. Overall, the framework identifies the magnetic Peclet number as the key parameter governing the transition from diffusion-dominated to drift-enhanced cellular drug transport. Full article

Chitin synthase (CHS) catalyzes the final polymerization step in chitin biosynthesis and is therefore central to cuticle formation in arthropods. In this study, a chitin synthase gene from the swimming crab Portunus trituberculatus (PtCHS) was identified and functionally characterized in relation to epidermal formation and molting. The open reading frame of PtCHS was 4731 bp and encoded a predicted protein of 1576 amino acids belonging to glycosyltransferase family 2. Domain prediction revealed multiple transmembrane helices, a conserved chitin-synthase catalytic region, a coiled-coil region, and the diagnostic EDR, QRRRW, and SWGTRE motifs. Phylogenetic analysis assigned PtCHS to the class A/CHS1 chitin synthase lineage, and two alternative splice variants, designated PtCHS1a and PtCHS1b were detected. PtCHS transcripts were broadly distributed across examined tissues, with comparatively high abundance in the Y-organ, midgut, ovary, and epidermis. During the molting cycle, epidermal PtCHS expression increased during premolt, reached its highest level in postmolt stages, and declined during intermolt. During embryonic development, PtCHS expression remained relatively stable until late embryogenesis and then increased sharply before hatching. RNA interference-mediated knockdown of PtCHS reduced the expression of key chitin-biosynthesis genes, decreased epidermal chitin content, prolonged the molting interval, and was associated with molting failure and increased mortality. Conversely, unilateral eyestalk ablation induced PtCHS and molting-related genes, increased epidermal chitin content, shortened the molting interval, and promoted histological features consistent with enhanced extracellular matrix deposition and epidermal biosynthesis. These findings indicate that PtCHS is indispensable for epidermal chitin deposition and successful molting in P. trituberculatus, and provide a molecular basis for understanding molting regulation in economically important portunid crabs. Full article

Toll-like receptors (TLRs) are conserved pattern recognition receptors essential to insect innate immunity. However, the functions of TLRs in Loxostege sticticalis, a destructive agricultural pest, remain poorly characterized. In this study, the full-length coding sequence of the L. sticticalis Toll receptor (LsToll) was identified and characterized to analyze its molecular features. Structural analysis showed that LsToll possesses typical Toll family features, including an extracellular domain containing 19 leucine-rich repeats (LRRs), a transmembrane helix, and a highly conserved intracellular Toll/interleukin-1 receptor (TIR) domain. LsToll transcript levels were significantly upregulated after bacterial challenge. RNAi-mediated silencing of LsToll significantly reduced larval tolerance to bacterial infection and increased mortality. Notably, LsToll suppression also induced severe developmental abnormalities, including molting obstruction, pupation failure, and defects in wing expansion in newly emerged adults. Transcriptome analysis after RNAi identified 5230 differentially expressed genes (DEGs), which were significantly enriched in insect hormone biosynthesis and metabolic pathways. Biochemical assays further confirmed that LsToll knockdown decreased 20-hydroxyecdysone (20E) titers and increased juvenile hormone III (JH III) titers. These results suggest that LsToll contributes to antibacterial defense and normal development in L. sticticalis. Its involvement in both survival and development indicates that LsToll may serve as a promising molecular target for sustainable pest management strategies. Full article

Endometriosis affects an estimated 5–10% of women of reproductive age and presents with substantial clinical and biological heterogeneity. Recent clinical guidelines have shifted toward symptom-guided diagnosis supported by expert imaging, moving away from mandatory diagnostic laparoscopy and redefining the evidentiary standards for evaluating new diagnostic technologies. Advances across omics domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, extracellular vesicle profiling, microbiome research, and multi-omics integration, have deepened understanding of lesion biology, immune dysregulation, metabolic alterations, and progesterone resistance. However, translation of these molecular insights into clinically actionable tools remains limited. Most candidate biomarkers remain at discovery or internal/developer-led validation stages, constrained by small sample sizes, heterogeneous analytical platforms, incomplete control of confounding variables, and limited independent multicenter validation. In this review, we apply a four-tier evidence-maturity framework, spanning discovery, internal or developer-led validation, independent external validation, and demonstrated clinical utility, to classify omics-based diagnostic, prognostic, and treatment-response applications in endometriosis. We also distinguish potential clinical roles, including triage, adjunctive testing, and replacement-test evaluation, each requiring different validation standards and performance thresholds. Salivary microRNA currently represents the most clinically advanced diagnostic omics candidate, but the available evidence remains developer-led and is best classified as advanced Tier 2/Tier 2+ rather than independent Tier 3 validation. Prognostic and treatment-response applications are less mature and remain discovery-stage because prospective patient-level longitudinal validation and biomarker-stratified treatment trials are lacking. Overall, no omics-derived biomarker has yet achieved independent Tier 3 validation or Tier 4 readiness for routine clinical implementation. At present, omics approaches should be regarded primarily as research and translational prioritization tools rather than determinants of routine clinical decision-making. Full article

Objectives: Membrane-enveloped virus-like particles (VLPs) constitute a versatile vaccine platform allowing for the display of heterologous viral surface antigens. The density of displayed antigens is paramount for the efficient elicitation of a strong cellular and humoral immune response. SARS-CoV-2 spike protein variants with engineered cytoplasmic tails (CTs) were generated to enhance decoration efficiency on the surface of VLPs formed by the HIV core protein Gag. These HIV (SARS-CoV-2) chimeric particles serve as a vaccine component prototype. Methods: Spike variants were first analyzed for cellular and surface expression as well as incorporation into extracellular vesicles (EVs) and VLPs using flow cytometric analysis and Western blot analysis. Receptor binding, fusogenicity, i.e., mediating the fusion of spike-positive with receptor-containing membranes, and the proteins’ potential to mediate lentiviral vector gene transduction into susceptible target cells was examined by employing syncytia-formation assays and vector titration experiments. The display of a neutralization-sensitive epitope was examined utilizing immuno-precipitation using a neutralizing antibody. Results: All four variants were shown to be cell-surface expressed, to recruit the cognate receptor, to mediate membrane fusion and cell entry of lentiviral pseudotype vector particles and to decorate VLPs and EVs. However, the spike variant encompassing a truncated CT derived from the gibbon ape leukemia virus (GaLV) transmembrane (TM) envelope protein was most efficiently incorporated into HIV Gag-formed VLPs. All variants exposed a neutralization-sensitive epitope in the receptor binding domain. Conclusions: Engineering of the CTs of viral surface antigens can enhance VLP decoration, while required functionality of the ecto-domain such as receptor recognition, fusogenicity and neutralization-sensitive epitope presentation are not abrogated. This indicates the preservation of the structural integrity of the antigen required to elicit a neutralizing humoral immunity upon vaccination. The identified truncated CT of GaLV TM may be of utility to improve the incorporation of other viral surface antigens into a variety of membrane-enveloped VLPs derived from a range of different parental viruses. Full article

Resistance to systemic therapy remains the defining challenge in the management of gastric cancer (GC) and esophageal adenocarcinoma (EAC). While genomic drivers of resistance are well characterized, traditional bulk profiling has failed to capture the physical rules governing tumor survival within the complex tissue ecosystem. Emerging data from 2024–2025, leveraging high-resolution spatial transcriptomics and multi-omics, have recontextualized resistance as a phenomenon of “spatial privilege” rather than solely an intrinsic cellular fate. This review summarizes recent evidence to define “architectural refuges”: distinct spatial niches that physically shield malignant clones from cytotoxic and targeted agents. We delineate three critical resistance domains common to upper gastrointestinal adenocarcinomas: (1) The “Excluded” Niche, where specific cancer-associated fibroblast (CAF) subpopulations (iCAFs vs. myCAFs) and stiffened extracellular matrix create hypovascular zones that limit drug delivery; (2) the “Immune-Tolerant” Niche, characterized by the spatial exclusion of CD8+ T cells and the recruitment of suppressive myeloid populations via the MIF/CD74 and USP14 axes; and (3) the “Metabolic” Niche, where mitochondrial heterogeneity and lipid metabolic symbiosis establish nutrient-deprived niches that select for stem-like, dormant states. By mapping these conserved spatial determinants from primary GEJ tumors to peritoneal and distant metastases, we argue that overcoming resistance requires an advancement: moving beyond targeting individual mutations to dismantling the multicellular architecture that sustains malignancy. Full article

Primary aldosteronism (PA) is the most common cause of secondary hypertension and accounts for 5–15% of hypertensive patients. Familial hyperaldosteronism, a monogenic cause of PA, accounts for ~1–5% of cases. Familial hyperaldosteronism type III results from mutations in the KCNJ5 gene, which lead to excessive aldosterone production and hypertension due to dysfunction of the GIRK4 channel in the adrenal gland. Despite the importance of KCNJ5 in PA pathogenesis, little is known about the molecular mechanisms underlying germline KCNJ5 mutations and their functional consequences. This study explored the structural changes in KCNJ5 pathogenic variant c.452G>A (p.Gly151Glu or GIRK4^G151E). Homology modeling and molecular dynamics simulations of the mutant GIRK4 channel showed that structural rearrangements occur in GIRK4^G151E when compared to GIRK4^WT, displaying higher RMSD and SASA, which may be attributed to differences in residue fluctuations in the cytosolic and extracellular domains, and ligands may bind with a stronger affinity to GIRK4^G151E. Given that the mutation is located within or proximal to the selectivity filter of GIRK4, we expect that the primary mechanism of dysfunction involves altered ion selectivity, leading to membrane depolarization. Our novel findings highlight the importance of understanding the molecular mechanisms underlying KCNJ5 mutations in PA and hypertension pathogenesis. This knowledge could inform the development of more targeted and effective treatments for this condition. Full article

The proton-activated chloride channel PAC/TMEM206 is broadly expressed in mammalian tissues and contributes to acid-induced cell injury in pathological settings such as ischemia, inflammation, and tumor acidosis. In addition to its established proton sensitivity, PAC is strongly modulated by temperature: heating potentiates proton-evoked currents and shifts activation toward less acidic pH yet does not open the channel at neutral pH. How proton and thermal inputs are structurally integrated remains unclear. Here, we combined site-specific incorporation of the environmentally sensitive fluorescent amino acid ANAP with automated patch-clamp electrophysiology and molecular dynamics simulations to identify structural elements underlying PAC thermal modulation. ANAP reporters introduced across the extracellular domain and vestibule–pore coupling region revealed residue-specific thermal- and proton-dependent spectral shifts, showing that heating and acidification remodel overlapping but non-identical local environments. The strongest ANAP-reported temperature-dependent changes were observed at R93, Y111, F196, R237, and F282, whereas proton-dependent changes prominently involved R93, Y111, H130, and R237. Several temperature-sensitive ANAP reporters mapped to an intersubunit region also highlighted by dynamic correlation analysis. Together, our results identify structural correlates of PAC thermal modulation consistent with a model in which protonation creates an activation-permissive landscape while heating reweights coupling across an intersubunit scaffold; this model generates testable predictions that should be addressed by targeted mutagenesis and thermodynamic characterization. Full article

Lectin receptor-like kinases (LecRLKs) are a large subfamily of receptor-like kinases (RLKs), and their N-terminal lectin domain is predicted to reversibly bind to carbohydrates. Within this family, G-type LecRLKs represent a distinct subclass defined by an extracellular S-locus glycoprotein (SLG) domain, which was originally identified for its role in governing self-incompatibility in Brassica species. Emerging evidence suggests that G-type LecRLKs are involved in plant immunity; however, only a small fraction have been functionally characterized, leaving the roles of most family members largely unknown. In this study, we identified RK3 (Receptor Kinase 3) as the most strongly induced gene within the G-type LecRLK clade VI upon infection with Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Through both gain- and loss-of-function analyses, we demonstrated that RK3 positively regulates flg22-induced immune signaling events, including oxidative burst and mitogen-activated protein kinase (MAPK) activation, as well as downstream responses such as defense gene expression and ethylene production. Remarkably, the immune-enhancing activity of RK3 does not require its kinase domain. Critically, both full-length RK3 and a kinase-deleted variant (RK3-ΔK) constitutively interact with FLS2 (Flagellin-Sensing 2) and BAK1 (BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1). This provides direct evidence that RK3 functions primarily as a co-regulatory component within the PRR complex, independent of its kinase activity. Moreover, ectopic expression of RK3 in tomato enhanced resistance to Pst DC3000, highlighting its potential utility in engineering disease resistance in crops. Thus, RK3 reveals a non-canonical, kinase-independent mechanism by which a G-type LecRLK potentiates plant immunity, expanding our understanding of RLK signaling complexity. Full article