Biology subjects

Suzuki, Y.

Publications and source records attributed to Suzuki, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

SPATNIC enables H&E-grounded cancer-cell identification across spatial and single-cell transcriptomic modalities in colorectal cancer

Tumors contain diverse non-cancer cells that constitute the tumor microenvironment; thus, identifying which cells are cancerous is a foundational and critical first step in cancer research. However, to our knowledge, no transcriptome-based classifier has been trained using pathologist-defined annotations from matched H&E images at single-cell resolution. Moreover, few tools can be shared across diverse platforms. Here, we present SPATNIC, a variational autoencoder that classifies individual cells as cancer or normal, trained on Xenium cells labeled by a pathologist review of matched H&E images. It matches or exceeds the performance of existing tools in primary colorectal tumors and liver and lung metastases. SPATNIC generalizes zero-shot across Visium, Visium HD, CosMx, Xenium, MERSCOPE, and single-cell RNA sequencing. In public single-cell atlases, it identified a rare POU2F3 tuft-like cancer stem cell population missed by existing annotations and associated with worse survival. In rectal cancer profiled before and after chemoradiotherapy, it separated cancer from normal epithelium in tissue, thus enabling per-patient screening of antibody-drug conjugate (ADC) targets.

cancer biology↗

bioRxiv2026

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

NECTIN4 is the target of enfortumab vedotin (EV), but its biological role in bladder cancer (BC) and its relationship to EV plus PD-1 blockade remain unclear. Integrating clinical multi-omics, spatial and single-cell immune profiling, and experimental models, we identify NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity. In basal BC cells, NECTIN4 suppressed inflammatory and mesenchymal programs. Consistently, NECTIN4-high basal/squamous muscle-invasive BCs showed favorable survival, higher checkpoint inhibitor response rates, and a coordinated CD8+ T cell-inflamed microenvironment with no comparable associations in luminal papillary tumors. In orthotopic models, murine Nectin4 promoted CD8+ T cell-dependent tumor control, whereas human NECTIN4 conferred EV sensitivity. EV also attenuated NECTIN4-dependent TIGIT binding. Conversely, NECTIN4-low models were preferentially sensitive to HDAC inhibition. NECTIN4 therefore couples antibody-drug conjugate targetability to a subtype-specific tumor-immune state permissive for checkpoint blockade, whereas the NECTIN4-low state defines a distinct inflammatory-mesenchymal state with an alternative therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Non-retroviral Endogenous Viral Element Acts as a Stable Antiviral Regulator Across Mosquito Life Stages and Generations

Endogenous viral elements (EVEs) from non-retroviral RNA viruses are widespread in host genomes, yet their functional significance in vivo remains poorly understood. In mosquitoes, EVEs have been shown to suppress cognate viral replication through the PIWI-interacting RNA (piRNA) pathway. However, how this antiviral activity shapes virus-host dynamics beyond reducing viral replication remains unclear. Here, we established Aedes aegypti mosquito lines naturally infected with cell-fusing agent virus (CFAV) that differ in the presence or absence of a CFAV-derived EVE (CFAV-EVE1). Using this natural virus-host system, we showed that CFAV-EVE1 suppressed viral replication across sexes, tissues, developmental stages, and generations. This antiviral effect is initiated by EVE-derived primary piRNAs, as demonstrated in ovaries and heads. Despite reducing viral load, CFAV-EVE1 conferred no measurable benefits on mosquito survival or reproduction, nor did it eliminate CFAV from the naturally infected population under standard laboratory conditions. However, vertical transmission rates were reduced in EVE-containing mosquitoes and prolonged egg storage further reduced viral prevalence, suggesting that environmental stress may reveal EVE-mediated viral suppression. Together, these findings demonstrate that EVEs function as stable, heritable regulators of persistent virus-host interactions and highlight that ecological context may be critical for fully appreciating their functional significance.

microbiology↗

bioRxiv2026

TGM2-mediated histone serotonylation is an epigenetic cardioprotective mechanism in HFpEF

Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome with incompletely understood molecular mechanisms. Histone serotonylation is a recently identified epigenetic modification in which serotonin is covalently conjugated to glutamine 5 of histone H3 in H3K4me3-marked nucleosomes. Here, we investigated the role of transglutaminase 2 (TGM2)-mediated histone serotonylation in HFpEF. In a mouse model of HFpEF induced by salty drinking water, unilateral nephrectomy and aldosterone infusion (SAUNA), cardiac H3K4me3Q5ser and nuclear TGM2 levels were increased. Cardiomyocyte-specific TGM2-deficient mice developed aggravated HFpEF phenotypes after SAUNA exposure, including worsened diastolic dysfunction, reduced exercise capacity, pulmonary congestion and delayed cardiomyocyte relaxation. CUT&RUN sequencing identified H3K4me3Q5ser-enriched regions predominantly around transcription start sites after SAUNA exposure, with notable enrichment at genes associated with G2/M checkpoint-related stress-response signaling. RNA sequencing further showed that activation of this pathway was impaired in SAUNA-exposed TGM2-deficient hearts. In cardiac myocytes, calcium-binding sites and nuclear localization of TGM2 support checkpoint-related stress-response gene activation in cardiac myocytes. Pharmacological WEE1 inhibition, which activates downstream CDK1-associated checkpoint signaling, partially rescued the aggravated HFpEF phenotype in TGM2-deficient mice. Finally, in patients with HFpEF, lower circulating serotonin levels were associated with adverse cardiac outcomes, and cardiomyocyte H3K4me3Q5ser levels correlated with serum serotonin concentrations. These findings suggest that cardiomyocyte TGM2-mediated histone serotonylation represents a stress-adaptive, cardioprotective epigenetic mechanism in HFpEF.

pathology↗

bioRxiv2026

Antiviral activity of anisomycin against chikungunya virus

Chikungunya virus (CHIKV) is a globally prevalent arbovirus transmitted by Aedes mosquitoes, which causes acute fever accompanied by debilitating joint pain that can persist for extended periods. Despite the significant public health impact and an increasing incidence worldwide, antiviral treatment targeting CHIKV has not been clinically approved. In this study, we screened compounds using a newly developed In-Cell ELISA-based assay and CHIKV Indian Ocean Lineage (IOL) and found that an antibiotic derived from Streptomyces bacteria, anisomycin, potentially inhibited CHIKV. The selectivity index of anisomycin was favorable for anti-CHIKV activity, with 50% effective concentration (EC50) of 200 pM and 50% cytotoxic concentration (CC50) of 390 nM in Vero cells. This robust inhibitory activity against CHIKV was confirmed in a human cell line and against a CHIKV East/Central/South African (ECSA) lineage. These effects of anisomycin were apparently independent of its functions as a translation inhibitor and mitogen-activated protein kinase (MAPK) pathway stimulator. These findings, together with the finding that anisomycin suppressed the production of infectious CHIKV virions, suggested that anisomycin inhibits CHIKV via a distinct mechanism. Further mechanistic insights were gained through genetic analyses of anisomycin-resistant mutants, which revealed that a single amino acid substitution (G117R) in the macrodomain of CHIKV nsP3 confers resistance to anisomycin. Importantly, anisomycin reduced footpad swelling and viremia in mice during the early days of CHIKV infection, indicating its therapeutic potential. Given its inhibitory activity against other arboviruses, our study positions anisomycin as a promising lead inhibitor for the future development of broad-spectrum antiviral drugs, including CHIKV. Author summaryChikungunya fever (CHIKF) is a mosquito-borne disease caused by the chikungunya virus (CHIKV) and is characterized by fever, rash, and arthralgia. Although most persons infected with CHIKV recover within days, joint pain and severe complications can persist. However, the management of CHIKF is limited to symptom relief, and specific antiviral treatments are not available. Our study focused on identifying potential inhibitors of CHIKV infection. We found that the natural alkaloid, anisomycin, inhibited CHIKV replication in cultured cells in vitro using a novel screening assay and a chemical compound library. Interestingly, the mechanism by which anisomycin blocks CHIKV infection likely differs from its currently known effects, suggesting a distinct mode of inhibition. We also identified an amino acid change in a nonstructural protein that conferred resistance to anisomycin, providing insights into a viral target of anisomycin. Importantly, anisomycin reduced disease symptoms and viremia in mouse models of CHIKV in vivo. Because anisomycin inhibits other mosquito-borne viruses, our findings suggest that it could serve as a basis for developing broad-acting antiviral drugs.

microbiology↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2026

Calmodulin controls the tempo of HSV-1 gene-expression cascade to reshape infection heterogeneity

Viral replication exhibits substantial heterogeneity among individual cells. Although temporally ordered gene-expression cascades are thought to contribute to such heterogeneity in DNA viruses, whether and how their tempo is regulated, and how cell-to-cell variability shapes population-level infection outcomes, remain unknown. Here, we developed a high-throughput live-cell imaging platform to track HSV-1 gene-expression dynamics in individual cells and, in combination with single-cell RNA sequencing, identified calmodulin (CaM) as a host regulator of HSV-1 gene-expression tempo. CaM accelerates progression from immediate-early to early and late phases at the single-cell level by advancing their onset. By increasing the fraction of virus-producing cells without altering burst size, CaM reshapes the distribution of infection outcomes, thereby promoting population-level viral replication. Pharmacological inhibition of CaM protects mice from lethal infection, exceeding acyclovir. These findings establish CaM-mediated temporal control as a key determinant of population-level viral output and a regulator of infection heterogeneity.

microbiology↗

bioRxiv2026

Interleukin-11 promotes the colonic epithelial organoid regeneration from mechanical disruption

The intestinal epithelium relies on rapid repair to maintain homeostasis after injury, and dysregulation of this process contributes to the pathogenesis of inflammatory bowel disease and colorectal cancer. Interleukin-11 (IL-11), a fibroblast-derived cytokine elevated in these diseases, has well-documented effects on stromal cells, but its direct action on intestinal epithelial cells remains poorly characterized. Here, we used mouse colon organoids as an isolated epithelial system to directly examine the effects of IL-11 on epithelial cells. IL-11 stimulation activated the canonical JAK/STAT3 pathway, as evidenced by increased STAT3 phosphorylation and Socs3 induction in a concentration-dependent manner. In a pipetting-based mechanical disruption model, IL-11 significantly increased the number of organoids recovered. Although mechanical disruption dominated the overall transcriptional landscape, RNA-seq analysis identified coordinated upregulation of STAT3 target genes and proliferation-related pathways specifically in response to IL-11. Pharmacological inhibition of STAT3 attenuated the IL-11-induced promotion of organoid recovery, indicating that STAT3 signaling mediates the epithelial response to IL-11 and maintains organoid size under basal conditions. Together, these findings demonstrate that IL-11 directly promotes intestinal epithelial repair after mechanical disruption through STAT3-dependent signaling, providing a mechanistic basis for its protective role in acute colonic injury.

cell biology↗

bioRxiv2026

Osmotic-stress-inducible nuclear condensates restrict gene inducibility

Plants, as sessile organisms, have developed various mechanisms to respond to environmental stress conditions. The plant hormone abscisic acid (ABA) is necessary for the plant to adapt to osmotic stress conditions. However, the molecular mechanisms preceding ABA accumulation remain largely unknown. To isolate transcriptional complexes on the promoter region of NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) encoding a rate-limiting enzyme in the ABA biosynthetic pathway in planta, we developed the insertional chromatin immunoprecipitation (iChIP) screen method. The identified ALBA proteins formed condensates through liquid-liquid phase separation (LLPS) in response to osmotic stress conditions. ALBA4 directly binds to stress-inducible genes, including NCED3, and suppresses their stress inducibility. Our results demonstrate how plants respond to osmotic stress at early timepoints before ABA biosynthesis through condensate formation as osmo-sensors.

plant biology↗

bioRxiv2026

DNA Double-decker Ring Scaffolded Nanodisc for Self-assembly of Membrane Protein into Lipid Bilayer

Membrane models of scaffolded discoidal lipid bilayers called nanodiscs have proven to be a valuable tool for the study of membrane proteins in a native environment. DNA-scaffolded membrane model has emerged as an alternative tool for membrane protein studies. Taking advantage of the designability of DNA nanostructure, we created a double-decker double-stranded DNA ring (DDring) to self-assemble DNA-based nanodiscs (DNA-ND). The DDring is 17 nm wide and 4 nm high, and equipped with 28 alkyl chains on the inside that can interact with each hydrophobic leaflet of the lipid bilayer. We further demonstrate the functionality of DNA-ND membrane model with the assembly of membrane proteins. DDrings are suited to neutral or cationic charged phospholipids and detergents. This study provides more insights into the potential use of DNA- assisted nanodiscs for membrane protein characterization.

bioengineering↗

bioRxiv2026

Real-time tracking of pupil-phase fluctuations reveals state-dependent modulation of temporal attentional capacity

Pupil diameter is widely used as an index of arousal and brain state, yet it remains unclear whether slow pupil-linked state fluctuations systematically modulate the effective capacity of temporal attention. Here, we tested this question using an auditory attentional blink paradigm, in which participants were required to detect the first (T1) and second (T2) targets. In Experiment 1, trial-by-trial analyses revealed that successful T2 detection, given correct T1 detection (T2|T1), was associated with smaller baseline pupil size. Furthermore, analyses focusing on slow pupil fluctuations (< 0.2 Hz) revealed that the T2|T1 detection accuracy increased during the pupil dilation phase occurring 0-2 seconds after pupil constriction. In Experiment 2, we used real-time pupillometry to trigger stimulus presentation during predefined phases of ongoing slow pupil dynamics. This closed-loop manipulation produced reliable phase-dependent differences in T2|T1 detection accuracy. Critically, the effect of pupil phase remained significant in a linear mixed-effects model that included baseline pupil size as a covariate, indicating that it cannot be explained by baseline pupil size alone. Together, these findings demonstrate that temporal attentional capacity is shaped not only by arousal level but also by the phase of slow pupil-linked brain-state fluctuations. Our results suggest that the attentional blink reflects a dynamically regulated, state-dependent limitation rather than a fixed processing bottleneck.

neuroscience↗

bioRxiv2026

Aqp1aa and Aqp4a mediate collecting duct water permeability in a marine teleost

Regulation of water permeability in the collecting duct is important for osmoregulatory acclimation in teleost fish. In hyperosmotic environments such as seawater (SW), the teleost kidney functions as a site of divalent ion excretion. The collecting ducts reabsorb Na+, Cl-, and water, thereby reducing urine volume and producing small amounts of isotonic urine with high concentrations of divalent ions. In hypoosmotic environments such as freshwater (FW) or low-salinity brackish water (BW), the kidney produces large volumes of hypotonic urine and serves as a site of water excretion; under these conditions, the collecting ducts reabsorb Na+ and Cl- but not water. To identify aquaporins (Aqps) involved in regulating water permeability in the collecting ducts of teleosts, we analyzed renal Aqp expression in a euryhaline marine fish, the Japanese pufferfish (Takifugu rubripes), which possesses 16 Aqp genes in its genome, seven of which (Aqp1aa, 1ab, 3a, 4a, 7, 8bb, and 11a) are expressed in the kidney. Quantitative RT-PCR analysis showed that Aqp1aa and Aqp4a were highly expressed in collecting duct tissues, and that Aqp1aa expression was markedly reduced in fish acclimated to BW. Immunohistochemistry revealed apical localization of Aqp1aa and basolateral localization of Aqp4 in collecting duct cells, with apical Aqp1aa downregulated in BW. These results suggest that Aqp1aa and Aqp4 mediate water reabsorption in SW and that downregulation of Aqp1aa contributes to hypotonic urine production in BW. NEW & NOTEWORTHYRegulation of water permeability in the collecting duct is important for osmoregulation in teleost fish. Expression analyses of aquaporins (Aqps) in the marine pufferfish Takifugu rubripes showed that Aqp1aa and Aqp4a are highly expressed in the collecting duct and localized to the apical and basolateral membranes, respectively. Renal Aqp1aa expression was markedly reduced in fish acclimated to hypoosmotic brackish water. These results indicate that collecting duct water permeability is regulated by Aqp1aa expression.

physiology↗

bioRxiv2026

Pathway-Centric Integration of CRISPR Fitness with Molecular Features Draws Cancer State Maps

Cancer cells display heterogeneous pathway activity that shapes therapeutic vulnerability, but mapping it remains challenging. Transcriptomic scores do not directly measure functional activity, and CRISPR knockout data alone lack molecular interpretability. We introduce StateMap, a pathway-centric framework integrating gene expression and genome-wide CRISPR knockout fitness data from the Cancer Dependency Map. For a given pathway, StateMap selects features by co-dependency and mutual information, then projects cell lines into a low-dimensional space reflecting pathway activity and molecular state. Applied to the Hippo pathway, it resolved five functional states refining the YAP-on/YAP-off dichotomy. Notably, the Hippo-strong state showed selective dependence on integrin V{beta}5; ITGAV depletion triggered Hippo-dependent cell aggregation and G1 arrest via enhanced cell-cell adhesion. Machine learning transfer to TCGA identified a matching subtype with poor prognosis, nominated NNMT as a biomarker, and predicted sensitivity to the V inhibitor Cilengitide. StateMap enables pathway-specific state mapping and discovery of state-selective therapeutic vulnerabilities.

cancer biology↗

bioRxiv2026

Single-cell spatial multiomics identifies POSTN+ CAFs mediating chemoradiotherapy resistance in rectal cancer

Neoadjuvant chemoradiotherapy (CRT) is standard for locally advanced rectal cancer (LARC), yet many patients retain residual disease. To resolve CRT-associated remodeling of the tumor microenvironment, we generated a multimodal spatial atlas from serial sections of paired pretreatment and post-treatment specimens from 24 patients using Xenium single-cell spatial transcriptomics and PhenoCycler multiplex proteomics, profiling 2.8 million cells; matched Visium HD datasets were generated on adjacent serial sections. Resistance was most strongly associated with fibroblast and myeloid programs adjacent to residual tumor. We identify a periostin (POSTN)-expressing CAF subset selectively enriched around residual tumor cells in non-responders, displaying a myofibroblastic phenotype and activating extracellular matrix remodeling, noncanonical WNT signaling, and immunosuppressive pathways. Tumor cells neighboring POSTN+ CAFs show consistent epithelial-mesenchymal transition signatures. Together, this atlas enables interrogation of CRT-induced spatial remodeling and nominates POSTN+ CAFs as key mediators and targets of CRT resistance, with direct relevance to CRT-based combination strategies.

cancer biology↗

bioRxiv2026

Microbe-dependent inter-organ communication regulates germline stem cell proliferation in Drosophila

Animals integrate environmental cues with internal physiological states through inter-organ communication to regulate reproduction. However, how environmental microbes are incorporated into these systemic pathways to control reproductive stem cell proliferation remains poorly understood. Here, we demonstrate that environmental microbes colonizing the gut promote stem cell-mediated oogenesis in Drosophila melanogaster by increasing germline stem cell (GSC) number. This process requires microbial activation of gut metabolic pathways, including glycolysis and the pentose phosphate pathway (PPP), linking microbial cues to organismal physiology. We further show that microbial cues modulate circadian clock gene expression in both the gut and brain, and that circadian gene activity in these tissues is required for microbe-induced increases in GSCs. These metabolic changes promote ecdysone and juvenile hormone signaling in ovarian somatic cells, and single-cell transcriptomic analyses further reveal cell type-specific metabolic and hormonal responses across germline and follicle cell populations. Together, our findings establish that microbe-dependent gut-mediated inter-organ communication integrates metabolism, circadian gene expression, and endocrine signaling to regulate stem cell-mediated reproduction in Drosophila.

developmental biology↗

bioRxiv2026

Global-scale microbiome analyses identify an ancestral gut cyanobacterial lineage enriched in African populations

Industrialization has profoundly reshaped the structure and function of the human gut microbiome, yet our current knowledge of its diversity remains heavily biased toward industrialized populations. Here, we performed an integrated analysis of a large-scale metagenomic dataset (n = 41,471) to systematically characterize the gut microbiome across the African continent. We show that sub-Saharan African populations harbor gut microbiome structures that are distinct not only from industrialized populations but also from other non-industrialized populations. Notably, we identify a strong enrichment of Gastranaerophilales, a poorly characterized lineage of non-photosynthetic Cyanobacteria, in sub-Saharan African populations. Comparative genomic analyses reveal that this lineage encodes distinctive functional features, including motility-related genes, vitamin biosynthesis pathways, and specialized carbohydrate transport systems. Furthermore, we show that this lineage is widely distributed across non-human primates, supporting an evolutionarily conserved host association predating modern humans. Together, our findings identify Gastranaerophilales as a potential ancestral gut symbiont that has been markedly reduced in industrialized societies but retained within African populations, highlighting a major but previously underappreciated component of the human gut microbiome.

microbiology↗

bioRxiv2026

Spatial profiling of CAR protein organization reveals in vivo remodeling during CAR-T therapy

Chimeric antigen receptor (CAR) T cell therapy utilizes genetically engineered patient-derived T cells to target cancer cells. Despite its clinical successes in multiple cancer types, the underlying molecular mechanisms by which molecules on CAR-T cells and surrounding cells interact with other proteins and collectively determine treatment efficacy remain elusive. Most previous studies have relied on transcriptome profiling, which does not fully reflect protein-level organization and interactions. In this study, we developed an antibody-oligonucleotide conjugate targeting the FMC63 region of CAR and integrated it into molecular pixelation (MPX). This approach enabled profiling of the dynamics of CAR molecules on cell surfaces as well as their colocalization with other proteins at the single-cell level. By applying MPX to longitudinal samples from three patients undergoing CAR-T cell therapy, we characterized the dynamic changes in CAR-associated protein organization in both pre-infusion CAR products and post-infusion peripheral blood. While CAR protein abundance and polarization showed limited variation across clinical courses, remodeling of a CAR-centered co-localization network was observed over time, including different retentions of specific molecular associations between patients with different clinical outcomes. Although derived from a limited cohort, our study identifies insights from this methodological framework beyond those gained by conventional omics analyses and offers results of a systematic investigation to predict and enhance CAR therapeutic outcomes. Key pointsO_LIMolecular pixelation was applied for chimeric antigen receptor (CAR) profiling at single-molecule and single-cell resolutions. C_LIO_LIProtein and transcriptome analyses of the CAR molecule showed dynamic remodeling during CAR-T therapy in patients with non-Hodgkin lymphoma. C_LI

genomics↗

bioRxiv2026

A senescent iCAF-like fibroblast state governs therapy resistance in rheumatoid arthritis

ObjectivesRheumatoid arthritis (RA) synovitis frequently persists despite cytokine-targeted therapies, suggesting the existence of pathogenic stromal programs that sustain chronic inflammation independently of canonical immune pathways. Although synovial fibroblasts (SF) are increasingly implicated in treatment resistance, the pathogenic fibroblast states driving refractory disease and their therapeutic vulnerabilities remain poorly defined. MethodsWe integrated multimodal single-cell and spatial profiling of synovial tissue from 54 patients with RA with prospective treatment-response data and functional studies in human fibroblasts and experimental arthritis models. ResultsWe identified a C-X-C motif chemokine 12 (CXCL12)hi Apolipoprotein C1 (APOC1)+ fibroblast population selectively enriched in treatment-refractory synovitis. Spatial analyses demonstrated that these fibroblasts establish CXCL12-dependent plasmablast niches within inflamed synovium, resembling inflammatory cancer-associated fibroblasts (iCAF) that orchestrate immune cell recruitment in the tumor microenvironment. CXCL12hi APOC1+ fibroblasts exhibited a senescence-associated iCAF-like transcriptional program characterized by STAT3-C/EBP activation and APOC1 expression and were associated with poor response to TNF and IL-6 pathway inhibition. Mechanistically, APOC1 knockdown in RA-SF attenuated invasive mesenchymal behavior and disrupted senescence-associated inflammatory programs, identifying APOC1 as a central regulator of pathogenic fibroblast reprogramming. Importantly, genetic or pharmacological elimination of senescent cells ameliorated experimental arthritis and enhanced the efficacy of TNF blockade. ConclusionsThese findings implicate iCAF-like fibroblasts with senescent properties as a mechanistic driver of refractory RA synovitis and highlight stromal senescence programs as preclinically actionable therapeutic targets beyond cytokine inhibition.

immunology↗