Search Results (152)

Direct antibody labeling is essential for immunoassays, multiplexed imaging, and biosensing; however, current methods are often time-consuming, restricted by antibody source, risk compromising protein performance, or vary with multiple steps. We introduce multiplex in situ tagging (MIST) Linker, a rapid and Fc-site-specific labeling tool that conjugates fluorophores or DNA oligonucleotides to antibodies from diverse commercial sources in as fast as 10 min using minimal starting material. MIST Linker achieves >90% cleavage upon UV exposure, facilitating rapid cyclic imaging on a single specimen. Validated across multiple species and sources, the platform outperforms conventional two-step immunofluorescence and immunohistochemistry in various tissues and cell lines. By enabling the rapid, cost-effective customization of antibody panels, MIST Linker significantly lowers the barrier to accessing antibody–DNA conjugates for spatial biology. When integrated with the spatial MIST platform and MIST-Explorer, it enables high-plex, single-cell spatial proteomics at high signal-to-noise ratios in human clinical biopsies, mouse specimens and cell lines. This toolkit provides an efficient, accessible solution for high-resolution spatial mapping, allowing for the in-depth analysis of cell subpopulations, biomarker distributions, and signaling events in complex biological specimens. Thus, MIST Linker offers a versatile, accessible, and scalable solution for antibody-labeling-based research and clinical diagnosis. Full article

Background and Aims: Accurate pre-operative identification of high-risk intraductal papillary mucinous neoplasms (IPMNs) remains a major clinical challenge, particularly for branch-duct (BD) lesions where guideline-based criteria incompletely capture biologic aggressiveness. We investigated whether tumoral mucin expression identifies high-risk IPMN pathology (i.e., high-grade dysplasia or invasive carcinoma) and whether computed tomography (CT)-derived radiomic features can serve as non-invasive biomarkers to enhance pre-operative risk assessment beyond international consensus guidelines (ICG) criteria. Methods: Multiplex immunofluorescence quantified MUC1, MUC2, MUC5AC, and MUC6 expression in tissue microarrays from 101 surgically resected IPMNs classified as low-risk (low-grade dysplasia) or high-risk (high-grade dysplasia or invasive carcinoma). Associations were evaluated using Wilcoxon rank-sum tests, and their discriminatory capability evaluated using receiver operating characteristic curves. For mucins predictive of high-risk pathology, a CT-based ‘radiomic’ signature was developed. Incremental value beyond ICG criteria was evaluated using discrimination metrics and decision curve analysis. Results: Reduced MUC6 expression was significantly associated with high-risk pathology (p = 0.001) and had the highest discriminatory performance (AUC = 0.72). A CT-derived radiomic signature predictive of low MUC6 expression achieved an AUC of 0.75 and, when integrated with ICG high-risk stigmata (HRS), demonstrated improved discrimination and favorable decision-curve characteristics compared with HRS alone, including among BD-IPMNs. Conclusions: Loss of tumoral MUC6 expression is associated with high-risk IPMN pathology and may be approximated using CT-derived radiomic features, supporting the feasibility of non-invasive molecular phenotyping. These findings suggest that integration of molecular and imaging biomarkers with guideline-based criteria may enhance pre-operative IPMN risk stratification; however, prospective external validation in broader surveillance populations and multi-institutional cohorts is warranted prior to clinical implementation. Full article

Background: Tertiary lymphoid structures (TLSs) are spatial immune niches in solid tumors, but their relationship to mature regulatory dendritic-cell (mregDC) states in ovarian cancer remains incompletely resolved. Methods: We integrated public gynecological-tumor single-cell RNA sequencing, representative CD11C/HLA-DRA/LAMP3/CCR7 multiplex immunofluorescence, public Xenium and multi-sample spatial transcriptomics, TCGA-OV immune deconvolution and exploratory prognostic modeling, scTenifoldKnk and CellOracle perturbation analyses, and supplementary computational drug prioritization. Results: A $LAMP{3}^{+}CCR{7}^{+}$ dendritic-cell state showed mature migratory, antigen-presentation, checkpoint, and NF-$\kappa$B/TNF-associated programs. Spatial analyses linked TLS-score-defined regions to mregDC, antigen-presentation/MHC-II proxy, and interferon-associated signals, with distance-gradient analyses supporting TLS-proximal enrichment. Immune deconvolution associated the TLS/mregDC axis with an immune-infiltrated TCGA-OV contexture, whereas adjusted analyses emphasized dependence on broader immune-program richness. Perturbation analyses nominated candidate regulatory axes for experimental testing, and the supplementary drug-prioritization layer was retained only as target-class hypothesis support. Conclusions: These data support a hypothesis-generating model of a TLS-associated $LAMP{3}^{+}CCR{7}^{+}$ mregDC antigen-presentation program in ovarian cancer, while requiring raw-channel tissue validation, functional perturbation, and independent clinical testing. Full article

Immunohistochemistry (IHC) is a widely used method for detecting specific proteins in tissue samples, helping diagnose diseases such as cancer. Traditional analysis methods rely heavily on human interpretation, which can lead to inconsistencies. In this study, we propose DeepFlare, a weakly supervised deep learning framework for cross-modality translation and segmentation of immunofluorescence and immunohistochemistry images. The proposed method utilizes multiplex immunofluorescence (mpIF) and co-registered IHC images, combined with preprocessing techniques such as affine transformation, stain normalization, noise reduction, and artifact removal. Multiple imaging channels, including hematoxylin, DAPI, Lap2, and nuclear envelope signals, are leveraged to generate segmentation masks using a U-Net++ architecture. The final segmentation mask is obtained through weighted fusion of modality-specific outputs. A generative adversarial network (GAN) is employed to measure translation fidelity between generated and real images. Weakly supervised learning techniques, including image-level supervision and consistency constraints, are applied to enhance performance under limited annotation scenarios. Pretrained pathology foundation encoders such as UNI and Virchow are integrated to extract multi-scale morphological and contextual features. Explainable AI techniques are incorporated to highlight critical regions and refine model attention. Experimental results demonstrate strong performance, achieving an SSIM of 0.7077 for image translation and a Dice score of 0.7424 for segmentation. The integration of the UNI encoder provides marginal improvement over the baseline (0.72 Dice score), indicating limited domain adaptation without fine-tuning on the dataset of 1264 training samples. Full article

The introduction of immune checkpoint inhibitors (ICIs) into the treatment of melanoma has significantly reduced mortality over the past decade. However, therapeutic benefit is not observed in all patients, and treatment may be associated with severe adverse events. Therefore, identifying patients who are most likely to benefit from immunotherapy remains of critical importance. Currently used biomarkers, such as programmed death-ligand 1 (PD-L1) expression and manual assessment of tumour-infiltrating lymphocytes (TILs), have limited predictive value. This narrative review provides a critical appraisal of studies employing digital pathology tools, multiplex and spatial techniques (including multiplex immunofluorescence, imaging mass cytometry, and digital spatial profiling), as well as machine learning algorithms for predicting response to ICIs in patients with melanoma. Available evidence suggests that the highest predictive value may be achieved by approaches integrating quantitative assessment of immune infiltration with information on its spatial distribution, functional state, and interactions within the tumour microenvironment. Particular relevance may be attributed to features associated with the “immune-inflamed”, “immune-excluded”, and “immune-desert” phenotypes, the presence of tertiary lymphoid structures, and the organisation of local immune niches. In addition, this review highlights key limitations in the interpretation of current data, including lack of methodological standardisation, data heterogeneity, and insufficient validation. Directions for future research necessary for the implementation of these approaches into routine clinical practice are also discussed. Full article

Intrahepatic cholangiocarcinoma (ICC) is an aggressive liver malignancy with a rising global incidence and limited therapeutic options. Vascular invasion (VI) is a hallmark of advanced disease, correlating with early recurrence and dismal prognosis, yet its tumor microenvironment (TME) drivers remain elusive. We analyzed single-cell RNA sequencing (scRNA-seq) data from 25 ICC samples to systematically characterize the cellular composition and molecular features related to VI. By integrating bulk RNA-seq data, spatial transcriptomics, and multiplex immunofluorescence, we identified a distinct subset of tumor-like cancer-associated fibroblasts (CAFs), termed tCAFs, enriched in VI-positive tumors. Functional enrichment analyses revealed that tCAFs were prominently associated with hypoxia and angiogenesis pathways, findings corroborated by the significant upregulation of tCAF markers (MME and NT5E) in ICC-derived CAFs under hypoxic conditions in vitro. Cell–cell communication analysis and spatial mapping uncovered that tCAFs might promote VI primarily through VEGF signaling interactions with endothelial cells. Integrative bioinformatics and RT-qPCR validation identified three key functional genes in tCAFs: SLC2A1, PTGS2, and PLOD2. In endothelial sprouting assays, pharmacological inhibition of SLC2A1 exerted a pronounced suppressive effect. Consistently, sprouting assays using ICC-derived CAFs with SLC2A1 knockdown confirmed that its downregulation significantly reduced endothelial sprouting capacity. Importantly, administration of the SLC2A1 inhibitor BAY-876 effectively suppressed tumor progression and intrahepatic metastasis in the orthotopic ICC mouse model. Our findings define a VI-associated cellular ecosystem and molecular landscape in ICC, unveiling a novel hypoxia–tCAFs–endothelial cells axis. Furthermore, we identify SLC2A1 as a clinically relevant therapeutic target, offering new insights into tumor VI. Full article

Background: Recruitment and activation of monocyte-derived macrophages (MoMFs) sustain cholangitis in primary biliary cholangitis (PBC), but whether MoMFs amplify inflammation through ferroptosis remains unclear. We defined ferroptotic programs in MoMFs and evaluated the calpain/ACSL4 axis as a regulatory and therapeutic node. Methods: We analysed a public human liver single-cell RNA sequencing (scRNA-seq) dataset and examined MoMF-associated ACSL4 and 4-hydroxynonenal (4-HNE) signals in CD11b⁺CD68⁺ cells by multiplex immunofluorescence. We used a 2OA–BSA-induced PBC-like mouse model to assess liver injury, inflammation and ferroptosis-related markers and tested Liproxstatin-1 (Lip-1), rosiglitazone (ROSI) or the calpain inhibitor PD150606. Bone marrow-derived macrophages (BMDMs) from control and PBC mice were profiled and challenged with RSL3, with or without Ferrostatin-1 (Fer-1), ROSI or PD150606. Results: MoMFs were expanded in PBC livers and showed the strongest induction of ferroptosis signatures, centered on ACSL4, with enhanced inflammatory crosstalk with cholangiocytes. Human PBC tissues showed increased CD11b⁺CD68⁺ cells positive for ACSL4 or 4-HNE. In PBC-like mice, malondialdehyde (MDA) increased and glutathione (GSH) decreased, and macrophages showed greater colocalization with ferroptosis markers; Lip-1, ROSI or PD150606 improved liver biochemistry, reduced inflammation scores and limited macrophage infiltration. PBC-derived BMDMs upregulated ACSL4 and CAPN1/2 and were more sensitive to RSL3; Fer-1, ROSI or PD150606 attenuated ferroptosis-associated molecular changes. Conclusions: MoMF ferroptosis is prominently engaged in PBC, and our findings implicate a pharmacologically tractable calpain/ACSL4 axis that may contribute to macrophage ferroptotic susceptibility and inflammatory liver injury. Full article

Background/Objectives: Chronic glomerulonephritis (CGN) is a progressive chronic kidney disease that can ultimately advance to end-stage renal disease (ESRD). Zhuangyang Bushen Pill (ZYBSW) is a traditional Chinese herbal formulation derived from the Yi ethnic medicine of Yunnan Province, and it has been widely employed in folk practice for the amelioration of chronic nephritis and renal dysfunction. This study was designed to evaluate the therapeutic efficacy of ZYBSW against CGN and to provide preliminary insights into its underlying mechanisms of action. Methods: The nephropathy model was induced in mice by tail vein injection of ADR (10 mg/kg). Renal function was evaluated by measuring relevant biochemical parameters, and renal histopathological alterations were examined using HE staining. Chemical constituents of ZYBSW were analyzed by LC-MS/MS. Its mechanisms of action were investigated using network pharmacology, WGCNA, molecular docking, multiplex immunofluorescence, and Western blotting. Results: ZYBSW significantly reduced ACR by 88.9%, SCr by 56.4%, and BUN by 30.4%, increased ALB by 32.4%, and alleviated renal histopathological damage (all p < 0.01). LC-MS/MS analysis identified 419 chemical constituents in ZYBSW. Network pharmacology, WGCNA, and molecular docking experiments identified EGFR and DUSP1 as potential targets, and indicated the MAPK pathway as a key pathway. Mechanistic studies revealed that ZYBSW significantly inhibited EGFR expression in renal tissue, enhanced DUSP1 expression, and reduced the phosphorylation levels of ERK, JNK, and p38. Conclusions: This study reveals ZYBSW can effectively alleviate CGN, with EGFR and DUSP1 as likely therapeutic targets, and its mechanism of action primarily involves regulating the MAPK signaling pathway. Full article

Formalin-fixed paraffin-embedded (FFPE) tissues represent an invaluable resource for both basic and clinical research due to their stable preservation of tissue architecture and molecular integrity. Multiplex immunofluorescence (mIF) using tyramide signal amplification (TSA) enables the simultaneous detection of multiple antigens within a single FFPE section. Here, we describe a kit-independent and customizable TSA-based mIF protocol that utilizes commercially available horseradish peroxidase (HRP)-conjugated secondary antibodies and tyramide–fluorophore reagents. The method was applied using FFPE endometriosis tissue, targeting estrogen receptor alpha (ERα), progesterone receptor (PR), α-smooth muscle actin (αSMA), CD20 and CD31. Each staining round was followed by heat-induced epitope removal (HIER) of the bound antibodies while preserving covalently deposited signals. Fluorescence imaging was performed using a multi-channel slide scanner with carefully selected fluorophores to enable optical separation between detection channels. Under the conditions described, the protocol enabled clear visualization of maker-specific staining patterns with preserved tissue morphology. This study provides a practical and flexible TSA-based mIF protocol as a qualitative proof of concept, offering an accessible alternative to commercial kit-based approaches. Further studies will be required to establish quantitative performance and a broader applicability across tissue types. Full article

The life sciences are currently undergoing a serious transition from the reductive biochemical analysis of dissociated tissues to non-destructive “spatial forensics”. In addition to discovering new molecules, we are moving towards finding out their precise tissue localization and performing in situ interrogation to uncover a biological logic within preserved cellular “neighborhoods”. Our perspective is focused on exploring the spatial imperative, including the structural logic and “neighborhood effects” of the tissue microenvironment, which is a prerequisite to understanding cellular function in normal and in pathological conditions. Beginning with a historical foundation of the origins of histochemistry, dating back to the 19th century with pioneer botanist François-Vincent Raspail, we emphasize the technological metamorphosis, transitioning from classical immunohistochemistry to modern multi- and high-plex spatial multi-omics. A critical evaluation of the current operational landscape has been made, addressing the engineering strategies behind multiplexed immunofluorescence (mIF), the challenges of experimental design in spatial transcriptomics, and the functional symbiosis between targeted and unbiased spatial proteomics. There are many layers of genomic and proteomic information we have to consider in order to unravel the mechanisms underlying body function. If we learn how to combine all this information together, we will be able to better understand how cells communicate with each other and what disrupts their communication, leading to cancer and many other pathologies. It is obvious that by implementing spatial biology tools, it becomes possible to develop new medicines and treat diseases in the most efficient ways. At the same time, we realize that there is an urgent need to learn how to put data pieces together so that they blend seamlessly into a meaningful output, further transitioning spatial biology over time into a routine tool to cure for both common and rare diseases and improve our lives and health. Full article

Dermal papilla (DP) cells orchestrate hair follicle growth and cycling by secreting signaling molecules that stimulate follicular epithelial stem cells. The signal peptide CUB-EGF-like domain-containing protein 3 (SCUBE3) was recently identified as a potent anagen stimulator secreted by DP cells. Ageratum houstonianum ethanolic extract (AHE) and its active constituent agerarin exhibit anti-inflammatory properties; however, their effects on hair follicle growth remain unclear. This study aimed to investigate the effects of AHE and agerarin on SCUBE3 expression in primary human DP cells and to elucidate the underlying molecular signaling pathway. Cell viability was assessed by measuring cell confluency. Ex vivo hair growth was analyzed using organ cultures of human hair follicles. Gene and protein expression were determined using reverse transcription-PCR, immunoblot analysis, immunofluorescent staining, tyramide signal amplification-based multiplex immunohistochemistry, and gene promoter-reporter assay in primary human follicle DP cells. In a hair follicle organ culture model, both AHE and agerarin increased the population of the anagen phase and promoted hair shaft elongation. AHE and agerarin significantly upregulated SCUBE3 expression at both the mRNA and protein levels. Mechanistically, AHE and agerarin induced activator protein-1 (AP-1) expression by activating mitogen-activated protein kinase signaling pathways, thereby increasing SCUBE3 gene promoter activity. AHE and agerarin promoted hair follicle growth by upregulating SCUBE3 expression via activation of the MAPK–AP-1 signaling axis. In conclusion, AHE and agerarin may serve as potential therapeutic agents for the prevention and treatment of alopecia (hair loss). Full article

Background: Pemphigus diseases are rare autoimmune blistering disorders mediated by pathogenic autoantibodies directed mainly against desmoglein 1 and desmoglein 3. Although most cases are considered idiopathic, external triggers that can disrupt immune tolerance have been described. Vaccination has been discussed as a potential precipitating factor in autoimmune skin diseases. However, the relationship between vaccination and the induction of pemphigus-related autoantibodies has not been comprehensively summarized. Methods: We conducted a narrative review of all available studies published in the last 25 years identified through medical databases, excluding studies on COVID-19 vaccinations. Reports describing either new-onset pemphigus or exacerbation of preexisting pemphigus with a temporal association to vaccination were included. Clinical characteristics, vaccine type, latency period, direct immunofluorescence findings, and ELISA results for desmoglein autoantibodies were analyzed. In addition, we present our own clinical-laboratory experience illustrating this issue. Results: The current evidence consists predominantly of case reports and small case series. Published cases describe pemphigus vulgaris and pemphigus foliaceus occurring after vaccinations against influenza, hepatitis B, tetanus, diphtheria, pertussis, rabies, and other routinely administered immunizations. The latency period most often ranged from several days to a few weeks. Immunopathological findings were consistent with classical pemphigus diseases, including intercellular IgG deposits in the epidermis and circulating autoantibodies against desmoglein 1 and/or desmoglein 3. Our patient was a 78-year-old woman who developed cutaneous form of pemphigus vulgaris, diagnosed with direct immunofluorescence (DIF) and multiplex ELISA, 10 days after diphtheria–tetanus–pertussis vaccination. The patient had a positive family history of autoimmune blistering disease, namely mucous membrane pemphigoid. Conclusions: Based on the currently available evidence, a direct causal relationship between vaccination and pemphigus diseases cannot be established. Nevertheless, accumulated clinical and serological observations suggest that vaccination may act as a triggering factor in genetically or immunologically predisposed individuals, possibly by amplifying pre-existing subclinical autoreactive immune responses. Further population-based and mechanistic studies are required to clarify this association, while the overall benefits of vaccination remain substantial. Full article

Background: The progression of idiopathic pulmonary fibrosis (IPF) involves distal airway remodeling and bronchiolization; however, the mechanisms driving these changes, particularly the contributions of epithelial stem cells, are not fully understood. K13⁺ hillock cells, normally quiescent in proximal airways, were examined for their potential contribution to IPF pathogenesis. Methods: Spatial immunofluorescence was used to profile K13 expression along the airway axes in IPF and control lungs. Multiplex staining complemented by ex vivo culture assays was used to test expression stability. Single-cell RNA-sequencing (scRNA-seq) data were re-analyzed to identify cell subclusters and pathway enrichments. Meanwhile, cell–cell communication was inferred by using CellChat. Results: K13 was ectopically upregulated in IPF honeycomb cysts, triggering a proximal-like pseudostratified phenotype. This shift was marked by surges in K13⁺ regionally overlapping expression patterns (K5⁺, ~9%; CC10⁺, ~53%; ACE-TUB⁺, ~44%; MUC5AC⁺, ~23%) and a decline in SOX2 expression (~95% to ~64%), with ~70% of residual SOX2^low cells exhibiting elevated K13. Accompanying the expansion of K13⁺ subclusters (basal: 1.8% to 41.5%; club: 10.7% to 31.5%), it was observed that the profibrotic markers (K17, S100A2, LGALS7, IGFBP6) and ontologies related to RNA processing, stress response, and senescence were also enriched. These subclusters also amplified pro-fibrotic signaling (e.g., TGF-β, SEMA3, and GALECTIN-9) associated with epithelial subtypes and HAS1^high fibroblasts. Conclusions: Here, we demonstrate that K13⁺ cell activation is a pivotal event, driving the dysregulated proximalization of distal airways in IPF through fate reprogramming and epithelial-mesenchymal crosstalk. Thus, elucidating these K13-mediated fate dynamics provides a critical framework for understanding IPF pathogenesis. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) and its consequences represent a growing global health burden that urgently requires physiologically relevant in vitro models beyond conventional 2D culture systems. In this study, we report the successful establishment of 45 patient-derived liver organoid lines. These organoids were generated from healthy, steatotic and cirrhotic tissues collected from 207 liver surgeries at RWTH University Hospital Aachen, with an initiation success rate of 82%. The organoids were propagated for at least six passages using an optimized protocol. Multiplex immunofluorescence analysis revealed highly proliferative structures with approximately 40% Ki-67-positive cells expressing hepatocyte (Albumin and HNF4α) and cholangiocyte (CK19) markers. Intermittent LGR5 staining suggested the presence of liver progenitor cell features. Quantitative PCR results confirmed variable HNF4α expression, indicating inter-patient heterogeneity in differentiation status. Time-lapse imaging combined with mathematical modeling uncovered a biphasic growth dynamic with an initial linear expansion in the first 15 h, followed by exponential growth (doubling time ≈ 20.6 h) between 30 and 72 h. Overall, our workflow produced genetically and phenotypically stable liver organoids that recapitulate essential features of various hepatic conditions. This provides a solid foundation for disease modeling, potential drug testing, and quantitative systems biology. Full article

Clear-cell renal cell carcinoma (ccRCC) accounts for the majority of kidney cancer diagnoses and exhibits widely variable clinical behaviour. The dataset described here was generated to support the discovery of robust biomarkers of tumour cell-cycle arrest and to inform the risk-stratified management of ccRCC. We assembled four independent cohorts including 480 patients from the UK arm of the SORCE adjuvant trial, 300 patients from a surgically treated series in Korea, 120 patients from a retrospective Scottish cohort, and a paired primary–metastatic cohort comprising 62 patients. Formalin-fixed paraffin-embedded nephrectomy specimens were processed for routine hematoxylin and eosin (H&E) histology, and for multiplex immunofluorescence (mIF). The mIF panels detect the cyclin-dependent kinase inhibitor p21^CDKN1a, the DNA replication licencing factor MCM2, endoglin/CD105, Lamin B1 and nuclear DNA (Hoechst). Whole-slide images (WSIs) were acquired at high resolution, and artificial-intelligence pipelines were used to segment nuclei, classify individual cells into arrested phenotypes, and calculate the fraction of cells. Accompanying metadata include demographics, tumour stage, grade, Leibovich score, treatment arm (sorafenib/placebo), relapse events, and disease-free survival. All images and derived tables are released under a CC0 licence via the BioImage Archive, ensuring unrestricted reuse. This multi-cohort dataset provides a rich resource for studying cell-cycle arrest and proliferation markers, training image-analysis algorithms, and developing prognostic signatures in RCC. Full article