Biology subjects

Suzuki, K.

Publications and source records attributed to Suzuki, K..

At least 19 recordsLinked to original sources

bioRxiv2026

A cascade of attentional and default mode network dynamics following the resolution of perceptual ambiguity

The neural mechanisms underlying spontaneous perceptual switches during bistable perception, particularly the dynamic interplay between large-scale brain networks, remain incompletely understood. Here, using functional magnetic resonance imaging (fMRI) in six participants and a bistable kinetic depth effect (KDE) stimulus, we investigated the spatiotemporal dynamics of brain activity associated with spontaneous perceptual reversals compared to physically induced (replayed) switches. Leveraging a fine-grained functional brain parcellation (MD758) and time-resolved analysis including noise correlations, we identified a distributed network encompassing occipital (MT/MST, LOC), parietal (IPS), and frontal (FEF, IFC, DLPFC) regions showing differential activity during spontaneous versus replayed switches. This network topography qualitatively overlapped a prior review-derived synthesis of perceptual-switching regions. Temporal decomposition of the differential fMRI signal further revealed a characteristic network cascade after the perceptual report: positive dorsal attention (DAN) and visual (VIS) network contrasts peaked approximately 4 s after the report alongside a negative default mode network (DMN) contrast; a slower, more modest ventral attention (VAN)-frontoparietal (FPN) component was observed around 10 s post-report but was weak and is treated as preliminary. The early 4 s profile was recovered across raw-signal, PCA-denoised, and noise-correlation analyses (three related, not fully independent analyses), with the noise-correlation analysis indicating that it is not fully attributable to shared motor-report signals. These findings delineate the temporal sequence of network recruitment following spontaneous perceptual transitions and suggest that interplay between attentional control and default mode networks accompanies the resolution of perceptual ambiguity.

neuroscience↗

bioRxiv2026

TET loss of function selects for aneuploidies that confer a proliferative advantage

Mutations in the Ten-Eleven Translocation (TET) family of DNA dioxygenases are among the most common epigenetic alterations in clonal hematopoiesis and hematologic malignancies, yet how TET loss of function reshapes genome evolution during cellular expansion remains to be fully understood. Here we show that loss of Tet2/3 in invariant natural killer T (iNKT) cells drives aggressive lymphoid expansion that is consistently associated with recurrent chromosome 17 trisomy, a dominant aneuploid state observed across more than ten independently derived tumors following transplantation into immunocompetent recipient mice. Single-cell whole-genome sequencing of TET-deficient iNKT cells induced to proliferate in culture with antigen and IL-2 stimulation revealed that rare pre-existing cells with chromosome 17 trisomy appeared soon after Tet gene deletion in the thymus, together with cells harboring other copy number alterations, but only the cells with chromosome 17 trisomy were progressively enriched during further expansion. Similarly, inducibly Tet-deficient mouse embryonic stem cells (mESCs) showed selection for aneuploid states that were present prior to Tet gene deletion, including trisomy of chromosome 6. Reanalysis of independent datasets from Dnmt3a-deficient mouse lymphomas identified recurrent chromosome gains, including chromosome 17 trisomy. Our results establish TET and DNMT3A deficiency as drivers of karyotypic evolution, and suggest that disruption of DNA methylation/ demethylation pathways through either TET or DNMT3A deletion promotes chromosomal instability, in part by facilitating the emergence and selection of cryptic aneuploid subclones during clonal expansion.

genetics↗

bioRxiv2026

Early origin of sugar sensing in jawed vertebrates

Sweet taste guides animals to consume carbohydrate-rich foods, and many different vertebrate groups, from fish to mammals, rely on sugar-rich fruits or nectar produced by flowering plants (angiosperms). Although the genes encoding T1R2-T1R3, the receptor pair that mammals use to sense sugars, exist in the genomes of many vertebrates, their functions are unclear--and whether sugar sensing arose once early in vertebrate evolution or independently in different lineages after angiosperms evolved is currently unknown. Here, we combined ancestral reconstruction and receptor functional profiling to examine the evolutionary history of T1R taste receptors--including recently-described non-canonical receptors--across all major vertebrate clades. Our results pinpoint the origin of sugar sensing to before the emergence of angiosperms and uncover a myriad of alternative T1R-based sugar-sensing mechanisms, suggesting multiple independent T1R trajectories and revealing uncharted sensory diversity across vertebrates.

evolutionary biology↗

bioRxiv2026

ELAplus: Fast and accurate analysis platform for energy landscape analysis facilitated by fine-tuning optimization algorithm.

1. Large-scale community-composition datasets, especially from microbiome studies, increasingly provide opportunities to identify major community compositional types (e.g., enterotypes in human microbiomes) and potential transitions depending on environmental factors. Energy landscape analysis based on maximum entropy models has emerged as a promising framework for characterizing such multi-stability in ecological communities. However, its application to diverse, high-dimensional compositional datasets remains limited by computational inefficiency, insufficient evaluation of predictability, and lack of systematic assessment of uncertainty. 2. Here, we present a computationally tractable inference framework for energy landscape analysis of multispecies communities, implemented in the R package ELAplus. We introduce a framework combining cross-validation-based selection of optimization settings, enabling accurate and computationally efficient model fitting across a wide range of simulated community datasets. In addition, we incorporate a bootstrap-based approach to quantify the reliability of inferred stable states, providing a systematic measure of uncertainty in landscape structures. 3. Simulation analyses demonstrate improved predictive performance and robustness compared to existing implementations. Applications to empirical datasets further illustrate how the framework can reveal stable states, basins of attraction, and potential tipping points under varying environmental conditions. The package also provides visualization tools, including disconnectivity graphs and energy surface plots, to facilitate intuitive interpretation of complex ecological landscapes. 4. Our framework enables robust and computationally efficient inference of ecological stability from compositional and environmental data, expanding the applicability of energy landscape approaches in diverse natural communities.

ecology↗

bioRxiv2026

Major microbiota transitions across liver disease progression are mediated by key taxa linking host environments and microbial communities

The gut microbiome plays a critical role in chronic liver disease, yet quantitative methods that integrate microbial community structure with clinical indices remain limited. Here, we applied an energy landscape analysis (ELA)-based framework to characterize transitions in gut microbiota along a clinical gradient of liver disease severity, as measured by the FibroScan-AST (FAST) score. The analysis revealed characteristic community states corresponding to low, intermediate, and high FAST scores, indicating that liver disease progression is associated with structured transitions in microbial community organization rather than simple changes in overall diversity. To further dissect community-level organization, we developed the community shaping index (CSI), which quantifies how strongly individual taxa are associated with specific community structures. Integrating CSI with species-environment association parameters identified key taxa with distinct ecological roles, including unclassified Subdoligranulum taxon, an unclassified Ruminococcus gnavus group taxon, and Streptococcus salivarius, that link host environmental conditions with community composition. Exploratory causal discovery suggested that Streptococcus salivarius and the unclassified Subdoligranulum may play distinct, potentially active roles in linking liver health with gut microbial organization, but with contrasting associations: S. salivarius was linked to disease-related liver deterioration and dysbiotic states, whereas the unclassified Subdoligranulum was associated with healthier liver function and coherent community organization. Overall, this ecologically grounded framework provides a unified and mechanistic foundation for analyzing microbiome structure and disease-associated transitions.

ecology↗

bioRxiv2026

Complexity-multistability relationships: How does species diversity shape the number of alternative stable states?

Ecologists have long investigated how community complexity affects ecological stability, yet how community complexity influences multistability, defined as the presence of alternative stable states, remains poorly understood. We developed a novel framework integrating stochastic community assembly with stability landscape analysis to quantify multistability from species interaction matrices. Using this framework, we systematically explored how species interaction properties shape the relationship between species diversity (species pool size) and the number of alternative stable states. Mean interaction strength was the primary determinant: competitive interactions amplified the positive relationship between species diversity and the number of alternative stable states. In competitive communities, a greater number of alternative stable states was associated with lower community uncertainty, a measure of the long-term unpredictability of community assembly dynamics. These results highlight the importance of characterizing the entire stability landscape. Our framework provides a general approach for understanding and quantifying multistability in complex ecological communities.

ecology↗

bioRxiv2026

Animal model of leprous neuritis using transfer of sensitized lymphocytes into M. leprae-inoculated nude mice

BackgroundLeprosy is curable with multidrug therapy, but preventing peripheral neuropathy remains challenging. In leprosy, reversal reactions (Type 1 reactions) are characterized by sudden enhanced cell-mediated immunity against Mycobacterium leprae (M. leprae), leading to acute neuritis that may cause irreversible nerve damage, paralysis, sensory impairment, and muscle atrophy. Armadillo and nude mouse models are used to study M. leprae infection, but detailed neuropathological models for immune-mediated reactions in leprosy are lacking. This study aimed to establish a reproducible animal model to analyze leprous neuritis pathogenesis. Methodology/Principal FindingsBALB/c nude mice were inoculated with M. leprae and six months later received transfers of naive CD4+ cells, sensitized CD4+ cells, or sensitized whole spleen cells from BALB/c mice. Histological and quantitative analyses were performed four weeks post-transfer. Mice that received transfer of sensitized CD4+ cells or sensitized spleen cells exhibited footpad swelling up to 88% greater than in animals with no cell transfer. Mice that received the sensitized cells also had massive inflammatory cell infiltration into nerve fascicles. Quantitative imaging confirmed a significant reduction in the percentage of myelinated area in mice that received transfer of sensitized CD4+ (p < 0.05) or whole spleen cells (p < 0.01) compared to control mice with no transfer. Furthermore, bacterial fragmentation within the endoneurium coincided with myelinated axon destruction, indicating that the immune response targeted bacilli but simultaneously damaged nerve structures. Conclusions/SignificanceThis study successfully reproduced leprous peripheral neuritis that resembles the reversal reaction in humans. The findings indicate that CD4+ cells are primary drivers of inflammation, whereas interactions between multiple immune cell populations in whole spleen cell transfers further exacerbate disease pathology. This model confirms that host immune responses are crucial for nerve injury progression. This model provides a valuable tool for investigating neuroprotective therapies to prevent permanent disability in patients with leprosy. Author SummaryAlthough leprosy can be treated as an infectious disease, many patients still suffer from permanent peripheral nerve damage, known as leprous neuritis. A particularly dangerous condition called the "reversal reaction" occurs when the immune system of an infected individual suddenly overreacts, causing severe acute inflammation in the nerves. Without prompt treatment, this inflammatory response can result in irreversible nerve damage, paralysis, and muscle atrophy. In this study, we developed a new animal model using "nude mice", which lack their own T-cells, to understand how this damage happens. We infected these mice with leprosy bacteria and then transferred specific immune cells, specifically sensitized CD4+ T cells, isolated from M. leprae-immunized mice. The results showed that this transfer triggered significant footpad swelling and caused inflammatory cells to invade the nerve fascicles. Most importantly, we observed a significant reduction in myelin, the protective coating that promotes nerve signaling. These findings confirm that nerve damage is largely driven by the hosts own immune response attempting to clear the bacteria. By successfully recreating this reaction, our research provides a vital tool for developing new therapies aimed at preventing permanent disability and protecting the physical functions of patients.

immunology↗

bioRxiv2026

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Arterial Inflammation

Despite suppressive antiretroviral therapy (ART), people with HIV (PWH) remain at increased risk of cardiovascular disease (CVD), likely driven, at least in part, by persistent immune activation and vascular inflammation. Mechanistic pathways may include ongoing low-level HIV transcription within immune cells, particularly peripheral blood mononuclear cells (PBMCs), which may contribute to chronic inflammatory signaling. Persistent viral transcription and inflammatory signaling may also be associated with an interferon-responsive cellular environment conducive to APOBEC3 activation and mutational editing of viral transcripts. APOBEC3 enzymes, which are interferon (IFN)-inducible cytidine deaminases, generate characteristic premature stop codons (PSCs) within retroviral genomes and may reflect interferon-associated inflammatory states relevant to vascular pathology. We investigated whether APOBEC3-associated PSC signatures and reservoir-associated drug resistance mutations (RA-DRMs) in viral reservoirs, as markers of persistent reservoir transcriptional activity, are associated with vascular inflammation in ART-suppressed individuals. PBMCs from ART-suppressed PWH (n=36) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb) and PSCs as a surrogate marker of APOBEC3 activity, with RA-DRMs assessed by Oxford Nanopore sequencing. Arterial inflammation was quantified using PET imaging of the aorta and carotid arteries. Additionally, an exploratory panel of >60 cardiometabolic, clinical, and inflammatory biomarkers was profiled to identify host immune signatures associated with reservoir PSC burden, with focused analyses on circulating inflammatory biomarkers sCD14, sCD163, and IP-10. Long HIV-1 transcripts were detected in 67% (24/36) despite ART. Higher PSC frequency within these transcripts was significantly associated with increased aortic inflammation, but not carotid inflammation, in univariable analysis ({beta} = 0.00834, p = 0.013). RA-DRMs were detected in 50% (12/24), including triple-class resistance, but were not associated with vascular inflammation or soluble biomarkers. In multivariable models, PSCs remained independently associated with aortic inflammation after adjustment for sCD14 and sCD163 ({beta} = 0.0075, p = 0.023), and remained the only significant predictor when IP-10 was included ({beta} = 0.0073, p = 0.036). These findings suggest that APOBEC3-associated PSC signatures in long HIV transcripts identify transcriptionally active HIV reservoir states associated with aortic inflammation during suppressive ART. Rather than reflecting ongoing mutational accumulation or direct pathogenic effects of PSCs themselves, these signatures may serve as biomarkers of an interferon-associated inflammatory reservoir state related to cardiovascular risk. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/729898v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@531cb9org.highwire.dtl.DTLVardef@82c53corg.highwire.dtl.DTLVardef@16318aaorg.highwire.dtl.DTLVardef@e87e22_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights: Interferon-inducible APOBEC3-associated PSC signatures in HIV reservoirs and vascular inflammationO_LIAPOBEC3-associated premature stop codon (PSC) signatures were identified in transcriptionally active HIV reservoir-derived RNA despite suppressive ART. C_LIO_LIHigher PSC burden was significantly associated with increased aortic vascular inflammation measured by FDG-PET. C_LIO_LIReservoir-associated drug resistance mutations (RA-DRMs) showed no association with arterial inflammation. C_LIO_LIPSC burden remained independently associated with aortic vascular inflammation in multivariable analyses. C_LIO_LIPSC-enriched reservoir states were associated with inflammatory biomarker patterns consistent with monocyte-macrophage activation and vascular immune activation. C_LIO_LIThese findings are consistent with an interferon-inducible APOBEC3-edited reservoir state associated with persistent arterial inflammation during suppressive ART. C_LIO_LIAPOBEC3-associated mutational signatures may represent a candidate biomarker of vascular inflammation and cardiovascular risk in people with HIV. C_LI

molecular biology↗

bioRxiv2026

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Reduced Neuroaxonal Integrity

Despite sustained viral suppression with effective antiretroviral therapy (ART), impaired neuroaxonal integrity persist in a subset of people with HIV-1 (PWH). We investigated whether interferon (IFN)-inducible APOBEC3-associated mutational signatures, reflected by premature stop codons (PSCs), and reservoir-associated drug resistance mutations (RS-DRMs) within transcriptionally active HIV-1 reservoirs influence neuroaxonal integrity in fully virally suppressed individuals. Peripheral CD4 T cells from individuals with undetectable plasma HIV-1 RNA (n = 27) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb), and frontal white matter (FWM) neuroaxonal integrity was assessed using proton magnetic resonance spectroscopy ({superscript 1}H-MRS) measurement of N-acetylaspartate (NAA). Short HIV-1 RNA transcripts, reflecting promoter-associated transcriptional activity, were detected in all participants and were associated with reduced NAA levels in FWM, consistent with a relationship between ongoing reservoir activity and impaired neuroaxonal integrity despite virological suppression. Long gag/pol transcripts (>4.2 kb) were detected in 78% of participants and exhibited marked heterogeneity in APOBEC3-associated PSC burden. PSC-containing long transcripts were associated with higher NAA, whereas long transcripts lacking such inactivating mutations were associated with reduced NAA, suggesting that APOBEC3-associated restriction of viral translational competence may contribute to differences in the downstream neurobiological effects of transcriptionally active reservoir states. RA-DRMs were detected in 43% of participants, including triple-class resistance consistent with archived treatment exposure over more than a decade. Matching gag/pol sequences from reactivated virions confirmed latent reservoir origin; however, RS-DRMs showed no independent association with neuroaxonal outcomes. Across systemic inflammatory markers, vascular risk factors, cerebrospinal fluid immune activation measures, and clinical neurocognitive outcomes (including HAND status), no consistent associations with NAA were observed. Overall, reduced neuroaxonal integrity in the FWM was associated with the interplay between short HIV-1 RNA transcriptional activity and APOBEC3-edited translational states of long HIV-1 RNA transcripts within peripheral reservoirs, suggesting that interferon-inducible APOBEC3-associated mutational signatures may reflect biologically distinct reservoir states that correspond to neurobiological effects during suppressive antiretroviral therapy. Graphical AbstractInterferon-Inducible APOBEC3-Associated Premature Stop Codon Signatures in HIV-1 Reservoirs and Preservation of Neuroaxonal Integrity O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/729658v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@19c98d8org.highwire.dtl.DTLVardef@1f6c627org.highwire.dtl.DTLVardef@4b33a7org.highwire.dtl.DTLVardef@12c4a54_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIShort HIV-1 RNA transcription within peripheral CD4 T-cell reservoirs was associated with reduced frontal white matter N-acetylaspartate during suppressive ART. C_LIO_LILong HIV-1 gag/pol RNA transcripts exhibited marked heterogeneity in interferon-inducible APOBEC3-associated G-to-A hypermutation, including premature stop codon signatures. C_LIO_LIArchived reservoir-associated drug resistance mutations were identified within transcriptionally active long HIV-1 reservoir-derived RNA during suppressive ART. C_LIO_LIReduced neuroaxonal integrity was associated with the interplay between short HIV-1 transcriptional activity and interferon-inducible APOBEC3-associated editing of long HIV-1 transcripts with reduced predicted translational competence. C_LI

molecular biology↗

bioRxiv2026

Dysregulated flow responses drive pathogenesis in a cellular model of Sturge-Weber syndrome

Vascular diseases comprise a broad spectrum of conditions associated with organ dysfunction, yet how endothelial responses to mechanical forces drive their pathogenesis remains unclear. Sturge-Weber syndrome (SWS), a flow-associated vascular malformation caused by somatic GNAQ mutations, provides a model to investigate this question. Here, using isogenic induced pluripotent stem cell-derived endothelial cells (ECs), perfusable vascular models, and simplified systems under defined flow conditions, we show that SWS ECs exhibited maladaptive responses to laminar flow, including impaired flow alignment, reduced CLDN5 expression, and decreased transendothelial electrical resistance. Importantly, three-dimensional acoustic microscopy uncovered disturbed surface changes in SWS ECs, potentially contributing to changes in mechanosensing signaling. Transcriptomic and chromatin accessibility analyses revealed dysregulated flow-responsive gene programs, some of which were validated in human SWS samples. These findings provide insights into flow-dependent endothelial dysfunction and a framework for therapeutic modulation in SWS and other vascular disorders.

cell biology↗

bioRxiv2026

Impaired Motor Awareness of Balance Control is Associated with Postural Instability in Parkinson's Disease

BackgroundBalance instability is a major contributor to disability and falls in people with Parkinsons disease (PwP) and is often insufficiently explained by motor impairment alone. Altered awareness of motor control has been suggested to contribute to sensorimotor dysfunction in PwP, but its relationship with balance performance is poorly understood. ObjectiveTo determine whether awareness of balance control, assessed using a control detection task (CDT), differs between healthy controls (HC) and PwP, and whether CDT performance is associated with balance-related measures. MethodsHealthy older adults (n=20) and PwP (n=22) performed a standing version of the CDT based on center-of-pressure (COP) control, using a force plate. CDT accuracy was used as the primary outcome measure. Static balance during quiet standing was assessed using the COP trajectory length and rectangular area. Dynamic standing balance was assessed using the Index of Postural Stability (IPS). Group differences were examined by independent-samples t-tests. Correlations between CDT accuracy and balance measures were analyzed. ResultsThe PwP group showed significantly lower CDT accuracy. Higher CDT accuracy was associated with better static balance in the HC group and the combined sample, and with higher IPS primarily in the PwP group. ConclusionsMotor awareness during postural tasks is altered in PwP and is associated with balance control. These findings suggest that balance instability in Parkinsons disease may involve altered balance-related action-outcome monitoring in addition to motor dysfunction.

neuroscience↗

bioRxiv2026

Schlafen 11 (SLFN11) overexpression and nucleolar localization in response to bortezomib in multiple myeloma

Proteins belonging to the Schlafen family are interferon-inducible and participate in the regulation of antiviral responses, immune signaling and proteotoxic stress. SLFN11 also kills cells with replicative damage, serving as a predictive biomarker for chemotherapeutic response. Here we examined SLFN11 expression and significance in multiple myeloma (MM). The TCGA and MMRF CoMMpass datasets were analyzed for SLFN11 expression. Bone marrow and cell lines samples were analyzed for SLFN11 protein. SLFN11-knockout MM cell lines were used to explore how SLFN11 affects bortezomib response. Retrospective analysis of the HOVON-65/GMMG-HD4 phase III trial (n=327) assessed clinical relevance. SLFN11 is consistently highly expressed across MM subtypes (except CD1 and MAF/MAFB) and in normal plasma cells, and its expression strongly correlates with super-enhancer-driven plasma cell transcriptional programs. CD138-positive normal and myeloma plasma cells retain SLFN11 expression even when proliferative activity (MKI67/Ki-67) increases with disease progression. Bortezomib, a first-line MM treatment, induces SLFN11 nucleolar translocation with suppression of ribosomal RNA synthesis. Knocking out SLFN11 in MM cells enhances bortezomib sensitivity and exatecan resistance, supporting SLFN11s protective role in proteotoxic stress and sensitizing role in replication stress. In the HOVON-65/GMMG-HD4 trial, SLFN11-low patients showed selective benefit from bortezomib-based therapy, suggesting that SLFN11 expression may guide therapeutic stratification in MM. SignificanceSLFN11 is highly expressed in normal and malignant plasma cells. Bortezomib induces SLFN11 nucleolar translocation, suppressing ribosomal RNA synthesis and global translation. SLFN11 confers bortezomib resistance while sensitizing to topoisomerase I inhibitors. Clinical analysis supports that low SLFN11 expression predicts bortezomib benefit, providing a mechanistic basis for SLFN11-guided therapeutic stratification.

cancer biology↗

bioRxiv2026

Combining evolution and machine learning-guided pathway optimization to engineer a novel methylsuccinate module for synthetic C1 metabolism in vivo

De novo metabolic pathways open possibilities for sustainable biotransformations in microbes. However, the in vivo-implementation of such new-to-nature pathways is highly challenging and heavily relies on adaptive laboratory evolution (ALE) of the hosts native metabolic network. Here, we assess how much this need for host-centric ALE can be overcome and/or complemented through the informed design of the newly introduced pathway. Exemplifying for a synthetic CO2-fixation module via methyl-succinate, we established methylsuccinate-dependent growth of Escherichia coli over six months by ALE of E. colis native metabolism. In parallel, we developed a machine-learning guided workflow (MEVIS) for the automated engineering of the synthetic pathway, resulting in methylsuccinate-dependent growth within three weeks. Critically, performing MEVIS in the background of the ALE-evolved strain is necessary to further approach wild-type like growth, demonstrating how ALE in combination with machine-learning-guided lab automation holds great potential to accelerate and improve design-build-test-learn cycles in contemporary metabolic engineering.

bioengineering↗

bioRxiv2026

Heterogeneous Nuclear Ribonucleoprotein A1 as a Key Regulator in Pulmonary Arterial Hypertension Development

BackgroundAlthough plexiform lesion (PL) formation in severe pulmonary arterial hypertension (PAH) is a therapeutic target, the mechanisms underlying their formation have not been fully elucidated. This study aimed to identify candidate proteins involved in PL formation by examining differentially expressed proteins (DEPs) in PAH lesions. MethodsProteomic remodeling was assessed before and after the formation of PLs in a SU5416 combined with hypoxia (SuHx) rat model of severe PAH using laser-capture microdissection coupled with mass spectrometry. Unobstructed pulmonary arteries with medial hypertrophy (UMHPAs) and PLs from SuHx rats were subjected to qualitative and quantitative proteomics, revealing DEPs between these structures. ResultsWe identified 718 proteins with 58 DEPs, of which 31 were upregulated in UMHPAs and 27 were upregulated in PLs. Immunostaining confirmed that DEPs detected in our proteomic analysis were differentially expressed between UMHPAs and PLs. Among them, we focused on heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) as a candidate protein that may be strongly associated with PL formation because of its strong association with cell proliferation. siRNA knockdown of hnRNPA1 in hypoxia-treated pulmonary artery smooth muscle cells reduced pyruvate kinase M2 expression and significantly decreased proliferative capacity. Treatment of SuHx rats with hnRNPA1 inhibitors also suppressed pulmonary artery remodeling in PAH and PL formation. ConclusionsSeveral DEPs associated with PL formation but with unclear relevance to pulmonary artery remodeling in PAH were discovered. Among these, hnRNPA1, which was not detected in transcriptome analysis, may be important in PL formation. What are the Clinical Implications?The prognosis for pulmonary arterial hypertension (PAH) with plexiform lesions (PLs) is poor. Although PLs are therapeutic targets, the mechanisms of PL formation have not been fully elucidated, and there have been no direct examinations of proteomic remodeling before and after their formation. We identified several differentially expressed proteins (DEPs) that may be strongly associated with PL formation. Of these, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) was examined as a candidate protein involved in PA remodeling in PAH and PLs. Inhibition of hnRNPA1 in a severe PAH model not only suppressed pulmonary artery remodeling in PAH but also reduced PL formation. Several DEPs involved in pulmonary artery remodeling in PAH may be of significant value in the search for new therapeutic targets.

cell biology↗

bioRxiv2026

CAR-T-drug conjugate against solid tumor

Chimeric antigen receptor (CAR)-T cell therapy has been clinically successful in hematologic cancers but faces challenges in solid tumors, primarily due to limited tumor infiltration, immunosuppressive tumor microenvironments (TME), and antigen heterogeneity. While combining CAR-T cell therapy with chemotherapy can enhance antitumor activity, this often leads to substantial systemic toxicity. In this study, we introduce CAR-T-drug conjugate (CAR-T-D-C), a new class of dual-functional therapeutics that effectively addresses these obstacles by integrating click chemistry for precise conjugation of cytotoxic agents onto antigen-specific CAR-T cells. By transforming the hostile TME into an ally, this approach facilitates localized delivery of cytotoxic payload directly to the tumor site, enhancing the overall effectiveness of CAR-T therapy in solid tumors. CAR-T-D-Cs with different CAR-T cell binders exhibit robust antitumor activity across diverse solid tumor models, including both human tumor xenografts and syngeneic models. Spatial transcriptomic studies reveals that CAR-T-D-C achieves improved CAR-T tumor infiltration and functional activation within the TME. Compared to conventional CAR-T therapy, CAR-T-D-C markedly enhances immune cell infiltration, augments effector functions, promotes antigen spreading, amplifies systemic immune responses, and improves overall anti-tumor immunity. CAR-T-D-C represents a versatile therapeutic concept that combines the potency of small molecule drugs and the specificity of CAR-T cells as a 2-in-1 immunochemotherapy for treatment of solid tumors.

immunology↗

bioRxiv2025

Sox4 in Treg Cells Suppresses IL-10 Production via c-Maf Degradation and Exacerbates Type 2 Inflammation

The anti-inflammatory cytokine interleukin-10 (IL-10) produced by regulatory T (Treg) cells plays a crucial role in regulating allergic airway inflammation. However, the mechanisms governing IL-10 production in Treg cells remain unclear. In this study, we first identified Sox4 as a gene whose expression is down-regulated in IL-10-producing Treg cells. Comprehensive gene expression profiling of Sox4-deficient Treg cells and Sox4-overexpressing Treg cells revealed specific downregulation of Il10 and Ctla4 by Sox4. Sox4-deficient Treg cells exhibited increased IL-10 production and CTLA-4 expression both in vitro and in vivo and strongly suppressed Th2 cell proliferation compared with Sox4-expressing Treg cells. In a house dust mite (HDM)-induced asthma model, Treg-specific Sox4-deficient (Sox4-cKO) mice exhibited IL-10-dependent reductions in eosinophilic inflammation and Th2 cell infiltration in the airways. A comparison of Sox4-cKO and wild-type Treg cells in the same inflamed environment in mixed bone marrow chimeric mice with HDM-induced asthma revealed that Sox4-mediated suppression of c-Maf is cell-intrinsic. In addition, overexpression of Sox4 in Treg cells repressed the activation of c-Maf-regulated chromatin regions, including those around the Il10 and Ctla4 loci. Moreover, Sox4-induced suppression of IL-10 and CTLA-4 in Treg cells was rescued by forced expression of c-Maf. While Sox4 did not significantly affect Maf mRNA levels, Sox4 degraded c-Maf proteins in Treg cells through its 33 C-terminal residues. Via a domain distinct from its C-terminus, Sox4 physically interacted with c-Maf, subsequently facilitating its degradation through a ubiquitin-proteasome pathway. These findings elucidate a mechanism by which Sox4 influences the asthmatic responses by regulating the c-Maf/IL-10 axis in lung Treg cells.

immunology↗

bioRxiv2025

Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causingautoimmune diseases through autoantibody production

T regulatory cells (Treg cells) express the transcription factor FOXP3 and maintain immune homeostasis by attenuating effector responses. Treg cells are prone to lose FOXP3 and convert to pathological ex-Treg cells under conditions of strong or chronic inflammation. One mechanism for loss of FOXP3 expression involves increased DNA methylation of intronic enhancers CNS1 and CNS2 in the Foxp3 locus; these enhancers are maintained in a demethylated state by TET enzymes, 5-methylcytosine (5mC) dioxygenases that generate 5-hydroxymethylcytosine (5hmC) and other oxidized methylcytosines that are essential intermediates in all pathways of DNA demethylation. We previously showed that FOXP3+ Treg cells from Tet2/3-deficient (Tet2/3 DKO) mice displayed increased methylation of CNS1 and CNS2 and converted to FOXP3-negative ex-Treg cells considerably more efficiently than WT Treg cells. Here we extend our previous analysis of Foxp3-Cre Tet2/3fl/fl mice. We classified the mice as DKO- moderate or DKO-severe based on the total number of leukocytes in the spleen and peripheral lymph nodes and investigated the phenotypic and molecular basis for the progressive inflammation occurring in these mice. RNA-seq as well as histological and immunocytochemical analyses showed a striking expansion of T follicular helper (Tfh) cells and plasma cells in Tet2/3 DKO-severe mice. RNA-seq analyses also revealed increased induction of interferon-stimulated genes (ISGs) in CD4+ FOXP3- T cells from these mice, and single-cell (sc) RNA-seq analyses suggested strongly that this was due to skewed differentiation of both Tet2/3 DKO FOXP3+ Treg cells and Tet2/3 DKO FOXP3- ex-Treg cells into Tfh-like cells. Base-resolution "6-base" sequencing showed the expected loss of 5hmC and increased 5mC in Tfh cells purified from Tet2/3 DKO-severe mice, and suggested that the observed bias in gene expression patterns could arise both from a direct increase in methylation of essential enhancers stemming from TET deficiency, or because methylation interfered with binding of methylation-sensitive transcriptional regulators including CTCF.

immunology↗

bioRxiv2025

Dietary soy shapes murine microbiota to consolidate the mucosal IgA response through T follicular helper cells

The commensal microbiota plays a crucial role in shaping mucosal immunity, particularly in the induction of T follicular helper (Tfh) cells and IgA production. Here, we demonstrate that dietary soy elicits a robust Tfh cell and IgA response in Peyers patches of weaning mice. Soy feeding promotes the expansion of two principal commensal bacterial species, Limosilactobacillus reuteri and Muribaculum intestinale. Mechanistically, L. reuteri provides cognate antigens for Tfh cell activation, while M. intestinale functions as an adjuvant by promoting IL-1{beta} production from myeloid cells. The resulting IgA exhibits polyreactivity and enhances protection against Salmonella infection. These findings highlight the specific interplay among dietary components, intestinal microbiota, and mucosal immunity, thereby establishing a diet-microbe-immune axis that shapes host defense in early life. This axis represents a promising therapeutic target for developing novel strategies to enhance resistance to enteric pathogens. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/669459v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1ae8277org.highwire.dtl.DTLVardef@1f787ceorg.highwire.dtl.DTLVardef@1f51fd6org.highwire.dtl.DTLVardef@1fd3439_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDietary soy promotes T follicular helper (Tfh) cell and IgA responses in the Peyers patches of weaning mice. C_LIO_LISoy enhances the colonization of two key commensals, Limosilactobacillus reuteri and Muribaculum intestinale, in the small intestine. C_LIO_LIThese two bacteria synergize to drive mucosal immunity: L. reuteri provides cognate antigens, while M. intestinale provides an adjuvant signal by promoting IL-1{beta} production from myeloid cells. C_LIO_LISoy-induced IgA is polyreactive and protects against Salmonella infection. C_LI

immunology↗