Biology subjects

Abe, K.

Publications and source records attributed to Abe, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression

Tandem repeats (TRs) and transposable elements (TEs) occupy substantial fractions of eukaryotic genomes, yet how repeat detection programs affect downstream expression analyses remains poorly explored. Here, we present an improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri. The assembly matches experimentally estimated genome size and chromosome number. It resolves highly expanded TRs that occupy up to 28.0% of the whole genome. Using this assembly and other complete vertebrate genome assemblies, we compared TR and TE-derived regions across combinations of TR detection programs and TE consensus library construction workflows under a standardized TE classification scheme. Choices in TR detection reshaped the apparent TE landscape. TE workflows shared a broad core of TE-derived regions but recovered complementary sets of age- and sex-associated TE loci, evaluated with a sex-balanced killifish multi-tissue aging cohort. Together, the combinatorial use of adaptable programs supports robust, locus-aware detection of complex repeats across genome assemblies.

genomics↗

bioRxiv2026

RNA helicase Drs1 gates 25S rRNA domain III incorporation during early nucleolar pre-60S maturation

Assembly of eukaryotic large ribosomal subunits (LSU) requires coordinated structural and compositional transitions within pre-60S particles, yet the underlying mechanisms remain poorly understood. Here, we show that the DEAD-box helicase Drs1 promotes early maturation across distinct regions of the pre-60S particle. Loss of Drs1 function causes accumulation of co-transcriptional intermediates retaining SSU processome components, indicating that Drs1 promotes timely separation of nascent LSU precursors from the small-subunit assembly pathway. Cryo-EM analyses reveal both a redistribution toward early nucleolar maturation states upon loss of Drs1, including Nsa1-deficient intermediates, and a confinement of Drs1-associated particles to states preceding stable incorporation of 25S rRNA domain III. Drs1 directly engages Erb1 through its unstructured N-terminal extension, promoting stable assembly of the Nop7-Erb1-Ytm1 module associated with domain III maturation. CRAC analysis localizes Drs1 to spatially clustered sites spanning the 5.8S and 25S rRNAs, encompassing domains I-IV. Together, these findings support a model in which Drs1 couples stabilization of assembly-factors with pre-rRNA remodeling across the pre-60S particle, thereby driving ordered early LSU maturation and the timed integration of domain III.

biochemistry↗

bioRxiv2026

A universal plug-and-display vaccine platform for mucosal and systemic immunity using Bacillus subtilis membrane vesicles

Many bacterial species naturally secrete membrane vesicles (MVs) that mediate the intercellular transport of biomolecules, including nucleic acids, proteins, and metabolites. Beyond their native physiological roles, MVs hold considerable potential for biomedical applications. Here, we demonstrate that MVs from several Bacillus species exhibit potent intrinsic adjuvant activity, efficaciously eliciting immune responses and facilitating antigen-specific antibody production in mice. Exploiting this adjuvanticity, we engineered a highly adaptable universal vaccine platform that uses B. subtilis MVs as self-adjuvanting carriers. This system employs a modular "plug-and-display" architecture that covalently anchors recombinant antigens to the MV surface through a multi-step bioconjugation cascade. After validation of this methodology using a model antigen, we adapted the platform to target Yersinia pestis, the causative agent of plague. We formulated a Y. pestis vaccine by labeling the MV surface with a modified capsule antigen fraction 1 (mCaf1). Intranasal administration of the mCaf1-MV vaccine effectively elicited both systemic and mucosal immunity. Crucially, this vaccine conferred highly efficacious protection against a lethal Y. pestis infection in a murine model. These findings demonstrate the exceptional protective efficacy of the B. subtilis MV platform and highlight its broad potential for the rapid development of mucosal vaccines against diverse emerging pathogens.

bioengineering↗

bioRxiv2026

N-terminal intrinsically disordered region mediates self-catalytic interfacial nucleation of Aspergillus oryzae hydrophobin RolA

Hydrophobins are biosurfactant proteins that coat the cell surfaces of filamentous fungi. On the conidial surface, hydrophobins self-assemble into rodlets, forming a dense hydrophobic film that promotes air-dispersibility. Although rodlet formation is closely associated with the physiology of filamentous fungi, its underlying molecular mechanisms remain largely unknown. Previously, we revealed that RolA, a hydrophobin derived from Aspergillus oryzae, forms rodlets at the air-water interface. In this study, we focused on the flexible N-terminal region of RolA, which lacks a well-defined tertiary structure, and hypothesized that this intrinsically disordered region regulates rodlet formation. To investigate its role, we used RolA mutants with reduced charges in the N-terminal region and analyzed the rodlet formation process on the surface of a water-in-air sessile droplet using atomic force microscopy. In addition, we quantitatively characterized rodlet formation at the air-water interface by applying a kinetic perspective to the interfacial tension change profiles obtained from dynamic surface tension measurements. The results suggested that RolA first forms a monolayer at the air-water interface, then rodlet formation proceeds through the continuous supply of free RolA monomers from the bulk phase to the interfacial RolA film. Our molecular dynamics simulations of RolA at the interface supported a model in which RolA molecules within the interfacial film interact with free monomers in the bulk phase through their N-terminal regions. These results reveal a previously unidentified role of the N-terminal region in rodlet formation and provide a more comprehensive framework for understanding the molecular mechanism underlying RolA rodlet formation.

biophysics↗

bioRxiv2026

Improved recombinant protein production and scale-up fermentation of Aspergillus oryzae hyphal-dispersion hydrophobin-deficient strain

In liquid fermentation of filamentous fungi such as Aspergillus oryzae, increased broth viscosity and biomass adhesion to bioreactor surfaces remain major challenges. We previously developed a hyphal dispersion mutant lacking two hyphal adhesion factors, namely cell wall -1,3-glucan (AG) and biofilm galactosaminogalactan (GAG) (AG{Delta}-GAG{Delta} strain). The culture broth of the AG{Delta}-GAG{Delta} strain has low viscosity, which improves mixing and enzyme production. However, mycelia still extensively attach to bioreactor walls and downstream equipment, which impairs mixing and reduces product recovery. The hydrophobin RolA, a surface-active protein of A. oryzae, densely coats conidia and hyphae and contributes to cell surface hydrophobicity. In this study, we disrupted the rolA gene in AG{Delta}-GAG{Delta} (AG{Delta}-GAG{Delta}-{Delta}rolA strain) and evaluated the effects of this disruption on hyphal adhesion to the walls of culture vessels, enzyme production, and bioreactor performance. At the flask scale, the adhesion to glass surfaces was significantly reduced and recombinant enzyme activity was increased by 10%. Improved culture recovery at the end of fermentation further increased total enzyme yield. In a lab-scale stirred-tank bioreactor, both growth and enzyme production were increased. Scaling-up to a 200-L bioreactor showed reduced agitation power consumption while improving hydrodynamic properties. Fermentation of AG{Delta}-GAG{Delta}-{Delta}rolA was successfully scaled up to a 3000-L bioreactor; consistent enzyme activity and improved flow circulation in the bioreactors were confirmed by computational fluid dynamics analysis. Overall, the AG{Delta}-GAG{Delta}-{Delta}rolA strain has increased enzyme production and scalability, supporting its suitability for industrial applications.

bioengineering↗

bioRxiv2026

Activation of the NAD⁺-Sirtuin Axis Protects Against Chronic Doxorubicin-Induced Subclinical Renal Tubular Injury Through Restoration of Mitochondrial Homeostasis and Suppression of Inflammation

Background and purposeAnthracyclines, such as doxorubicin (DOX), are associated with late-onset kidney dysfunction; however, the mechanisms underlying chronic tubular injury remain poorly understood. We investigated whether chronic low-dose DOX exposure induces persistent mitochondrial dysfunction in renal tubules and evaluated the therapeutic potential of activating the NAD-Sirtuin axis. Experimental ApproachC57BL/6 mice were repeatedly administered low-dose DOX with or without resveratrol (RSV) or nicotinamide mononucleotide (NMN), a sirtuin activator. Renal injury was assessed using neutrophil gelatinase-associated lipocalin (NGAL) staining. Integrated proteomic and RNA sequencing analyses were performed to identify molecular alterations. Mitochondrial morphology and function were evaluated using structured illumination microscopy (SIM) of Massons trichrome-stained paraffin sections and ex vivo Seahorse analysis of freshly isolated renal tubules. Key ResultsChronic DOX administration induced tubular injury, despite preserving serum creatinine levels. Multi-omics analyses consistently demonstrated the suppression of mitochondrial pathways, including oxidative phosphorylation, fatty acid oxidation, and mitochondrial gene expression. SIM revealed mitochondrial fragmentation in tubular epithelial cells, whereas the Seahorse assay showed impaired mitochondrial respiratory capacity in isolated renal tubules. DOX also increased tubular acetylated superoxide dismutase 2 (SOD2) levels and activated inflammatory pathways. Importantly, both RSV and NMN attenuated tubular injury, restored mitochondrial metabolic pathways, reduced SOD2 acetylation, improved mitochondrial morphology, and suppressed inflammatory responses. Conclusions and ImplicationsChronic low-dose DOX exposure induces subclinical renal tubular injury characterized by mitochondrial dysfunction and inflammation. The pharmacological activation of sirtuins confers reno-protective effects by preserving mitochondrial homeostasis. These findings identify mitochondrial dysfunction as a central therapeutic target in DOX-induced nephrotoxicity and support sirtuin modulation as a potential strategy for preventing chemotherapy-related chronic kidney injury. Bullet point summaryO_ST_ABSWhat is already knownC_ST_ABSO_LIDoxorubicin causes cardiotoxicity through mitochondrial dysfunction and oxidative stress. C_LIO_LIDoxorubicin-induced tubular injury and the associated late-onset kidney dysfunction are clinically proven. C_LI What does this study addO_LIChronic low-dose doxorubicin induces tubular mitochondrial dysfunction, as identified by integrated multi-omics analyses. C_LIO_LIResveratrol and NMN preserve mitochondrial integrity and suppress inflammatory responses in renal tubules. C_LI Clinical significanceO_LIMitochondrial dysfunction may represent an early therapeutic target in doxorubicin-associated nephrotoxicity. C_LIO_LIActivation of the NAD-Sirtuin axis could prevent chronic kidney injury in cancer survivors. C_LI

pharmacology and toxicology↗

bioRxiv2026

Muscle-to-Bone CX3CL1 Signaling Promotes Skeletal Repair Through CX3CR1+ Osteoprogenitors

In the context of muscle loss, bone repair is impaired, suggesting that muscle derived signals contribute to bone regeneration. However, how muscle surrounding the injury site communicates with the bone repair niche remains unclear. Here we found that CX3CL1 expression was induced in endothelial cells in muscle surrounding a femoral bone injury site. Deletion of Cx3cl1 impaired bone healing, demonstrating a functional role for CX3CL1 in bone repair. A CX3CL1 receptor, CX3CR1, was expressed by PDGFR stromal progenitors and lineage tracing showed that CX3CR1 expressing osteoprogenitor lineage cells accumulated at the injury site during repair. PDGFR stromal progenitors showed enhanced osteoblastogenesis in response to recombinant CX3CL1. In older mice, local CX3CL1 delivery increased PDGFRCX3CR1 osteoprogenitor accumulation and improved bone repair. These findings identify a muscle bone signaling pathway in which endothelial CX3CL1 promotes bone repair through CX3CR1 expressing osteoprogenitors.

cell biology↗

bioRxiv2026

Systemic metabolic correlates of environmental sensitivity in group-housed mice

Environmental changes significantly impact the social behaviors of animals, yet individuals exhibit substantial variability in their responsiveness, known as environmental sensitivity. Understanding the biological basis of this individual variability is critical for elucidating vulnerability to stress-related and psychiatric disorders. To investigate the organism-wide physiological states linked to environmental sensitivity, we combined continuous, non-invasive RFID-based behavioral tracking with untargeted plasma metabolomics in group-housed mice undergoing spatial and social environmental restructuring. Following the environmental alteration, we observed heterogeneous behavioral shifts across individuals, enabling their operational classification into high-responsiveness mice (HRM) and low-responsiveness mice (LRM). Untargeted metabolomic profiling revealed distinct systemic metabolic signatures associated with these behavioral phenotypes. Specifically, HRM exhibited elevated levels of circulating essential and non-essential amino acids, as well as metabolites linked to one-carbon and energy metabolism. Exploratory co-variation analysis further identified plasma metabolic modules associated with individual behavioral metrics. These findings suggest that individual differences in behavioral adaptation are not solely neural phenomena but are coupled with coordinated, organism-wide metabolic adjustments. This study provides a framework for identifying candidate peripheral metabolic correlates of behavioral responsiveness to environmental and social change.

systems biology↗

bioRxiv2026

Inhibition of the gut ceramidase Asah2 decelerates the vertebrate ageing rate

The pace of ageing varies markedly among vertebrate species and individuals. However, the mechanisms underlying these differences in ageing rates remain unclear. Here, we show that the activity of the gut ceramidase Asah2 determines species- and strain-specific rates of vertebrate ageing. Comparative genomic analyses of vertebrate species and strains with different ageing rates reveal an association between low Asah2 activity and increased lifespan. Using the ultra-short-lived killifish Nothobranchius furzeri as a model, we demonstrate that knockout of Asah2 (asah2 KO) extends lifespan and attenuates systemic ageing phenotypes, including declines in locomotor activity, abnormal protein accumulation in the brain, and accumulation of senescent cells in the liver. asah2 KO elevates levels of ceramide species with long-chain fatty acids in the intestine, and supplementation with these ceramide species suppresses ageing phenotypes and extends lifespan in wild-type fish. asah2 KO and ceramide supplementation alter gut microbiota composition, and asah2 KO-derived microbiota transplantation attenuates ageing phenotypes, suggesting that reduced Asah2 activity prevents ageing through intestinal ceramide-mediated modulation of the microbiota. Given the evolutionary conservation of the Asah2 gene and its age-dependent upregulation in fish and humans, Asah2 and ceramides may act as ageing accelerators and decelerators, respectively, across animal species.

developmental biology↗

bioRxiv2026

Metabolic reprogramming and partial acquisition of cancer stem cell-like phenotype in human umbilical cord-mesenchymal stem cells under hypoxia

Mesenchymal stem cells (MSCs) cultured in hypoxic conditions have been suggested to have more therapeutic efficacy than those cultured under normoxic conditions, and there is growing interest in using hypoxic MSCs for clinical treatment, particularly human umbilical cord (hUC)-MSCs. We investigated how hUC-MSCs and human bone marrow (hBM)-MSCs change from normoxia to hypoxia (1% O2) for 2 weeks of culture. In the growth speed and population doubling time, hUC-MSCs cultured under hypoxia exhibited a significantly higher proliferation rate beyond cancerous cells, such as human glioblastoma and breast cancer cells, while hBM-MSCs did not show a significant difference between normoxia and hypoxia, and were statistically slower than these cancerous cells. Notably, hypoxic hUC-MSCs showed upregulation of genes related to metabolic reprogramming (cholesterol biosynthesis and fatty acid metabolism pathways) and cancer stem cell-like phenotype (factors related to Wnt and Hedgehog signaling pathways, cell proliferation drivers, and apoptosis-resistance), and lesser migration and homing to the traumatic brain injury than normoxic hUC-MSCs after intravenous injection. Thus, whether hUC-MSCs cultured under hypoxia offer clinical benefits and use are safe, given their extremely accelerated proliferation rate and partial cancer stem cell-like traits, requires comprehensive and careful investigation.

cell biology↗

bioRxiv2026

Skip-Zeros Variational Inference in the Million-Cell Era of Single-Cell Transcriptomics

Combinatorial indexing-based single-cell RNA sequencing methods such as sci-RNA-seq and sci-RNA-seq3 now enable the profiling of millions of cells, producing expression matrices that are both extremely sparse and high-dimensional. Conventional nonnegative matrix factorization (NMF) provides an interpretable framework for uncovering latent biological structures but is computationally prohibitive at this scale, as it requires explicit access to the vast number of zero entries. We introduce UNISON (Unified Sparse-Optimized Nonnegative factorization), a scalable framework for matrix and tensor factorization based on skip-zeros variational inference. By reformulating stochastic variational Bayes updates in terms of sufficient statistics, UNISON performs inference using only nonzero elements, while implicitly accounting for zeros through geometric sampling. This strategy enables efficient parameter estimation without matrix expansion and naturally accommodates multiple experimental contexts. Simulation studies show that UNISON is robust to diverse learning-rate schedules and mini-batch sizes, providing practical guidelines for optimization. Application to the Mouse Organogenesis Cell Atlas demonstrates scalability to over one million cells, yielding latent factors that capture developmental trajectories and lineage-specific signatures with improved interpretability compared to existing methods. Cross-species analysis of aqueous humor outflow pathways across five vertebrate species further highlights UNISONs ability to disentangle conserved from species-specific transcriptional programs and to recover biologically meaningful gene-gene and gene-phenotype relationships relevant to glaucoma. By efficiently exploiting sparsity while preserving interpretability, UNISON establishes a principled and practical solution for integrative, large-scale single-cell transcriptomics. Significance StatementSingle-cell technologies now generate datasets spanning millions of cells, creating massive, sparse matrices that are computationally difficult to analyze. Conventional methods often sacrifice statistical rigor for speed, either by discarding data or employing inappropriate models. We present UNISON, a framework that leverages a mathematical trick to perform exact inference using only nonzero elements. By combining this efficient computation with a probability model tailored for count data, UNISON scales to millions of cells while preserving information on rare cell types. This approach resolves the trade-off between scalability and accuracy, enabling precise integrative analyses of development and evolution across species without requiring massive computational resources.

bioinformatics↗

bioRxiv2026

A novel periplasmic layer formed by an outer membrane lipo-protein governs the cell-envelope integrity and stiffness of Leptospira interrogans

The structural integrity and mechanical properties of the cell envelope are crucial for bacterial physiology and dynamics; however, how specific molecular components govern these properties remains poorly understood. Here, we report the novel structural and mechanical functions of LipL32, the most abundant outer-membrane (OM) lipoprotein in the pathogenic spirochete Leptospira interrogans. LipL32 accounts for approximately 75% of the total OM proteins, yet its functional role has remained enigmatic. Cryo-electron microscopy revealed that the highly dense LipL32 forms a hitherto unappreciated thin layer in the periplasmic space, positioned adjacent to the peptidoglycan (PG) layer. The structural analysis also demonstrates that the disruption of lipL32 by transposon insertion results in irregular deformation of OM and spatial variability in the width of the periplasmic space. Quantitative measurements by optical tweezers confirmed that the lipL32::Tn mutant exhibited a significant reduction in whole-cell stiffness. Consistent with this mechanical impairment, the lipL32::Tn mutant displayed a diminished ability to penetrate a heterogeneous agar mesh model that mimics the hosts extracellular matrix, suggesting an important role for cell rigidity in initial infection via damaged skin. These findings define LipL32 as a critical mechanical stabilizer that maintains the structural integrity of the cell envelope. This work provides a new paradigm for understanding how specialized lipoproteins contribute to bacterial cell mechanics, offering insights into pathogenic invasiveness.

microbiology↗

bioRxiv2026

Amorphous-to-Rodlet Structural Transition Governs the Interfacial Functions of Aspergillus oryzae Hydrophobin RolA

Hydrophobins are low-molecular-weight biosurfactant proteins that coat the cell surface of filamentous fungi, making it hydrophobic and supporting morphogenesis. On conidia, hydrophobins self-assemble to form rod-shaped multimeric structures known as rodlets. Previously, we reported that hydrophobin RolA from the industrial fungus Aspergillus oryzae first forms an amorphous film at the air-water interface and then undergoes structural rearrangement to form a densely packed rodlet film. This raised the question of whether the amorphous or the rodlet film is more important for the biological functions of RolA. In this study, to compare the properties of amorphous films with those of rodlet films, we used RolA mutants that had lost the ability to form rodlets and therefore remained in the amorphous state. We found that the rodlet film was more rigid than the amorphous film and had stronger surface activity and a greater capacity to change surface wettability. RolA altered the properties of A. oryzae conidia only when it was in the rodlet state. These findings highlight the functional versatility of RolA and show that their dynamic structural transitions directly modulate their function.

microbiology↗

bioRxiv2026

scTREND: An annotation-free single-cell time-resolved and condition-dependent hazard model

Prognosis in cancer and other complex diseases is shaped by heterogeneous cell states and clinical or genetic contexts whose effects change over time. Yet most survival analyses assume predefined cell types and time-invariant covariates, and cohorts pairing single-cell transcriptomes with outcomes are limited, obscuring within-type heterogeneity, time-varying risk, and condition-specific effects. We developed scTREND, an annotation-free, time-resolved, condition-dependent hazard model that learns variational single-cell embeddings, deconvolves bulk or spatial samples without labels, and fits a conditional piecewise-constant hazard model to estimate cell-level hazard coefficients across discrete time bins and conditions. scTREND enables cell-level risk attribution without prior cell-type annotations, dynamic risk modeling over time, and mutation- or treatment-specific risk assessment. In simulations, scTREND recovered ground-truth temporal and condition-specific coefficients with strong concordance and improved prediction over an existing method. In melanoma, scTREND identified subpopulations with risk amplified in BRAF-mutant tumors; in COVID-19, cytotoxic T-cell subpopulations with early-to-late risk reversal and pathways associated with prognosis under remdesivir; and in spatial transcriptomics of clear cell renal carcinoma, spatial regions whose prognostic relevance shifts over time. Across diseases and modalities (bulk RNA-seq and spatial transcriptomics), scTREND provides a time-resolved, condition-aware link between single-cell states and clinical outcomes and is implemented in Python (GitHub:https://github.com/R301Carbine/scTREND).

bioinformatics↗

bioRxiv2026

Periodontal pathogen-derived extracellular vesicles promote EGFR-dependent malignant traits in human pancreatic cancer cells

Extracellular vesicles (EVs) produced by periodontopathic bacteria have been implicated in systemic diseases, yet their mechanistic impact on pancreatic cancer (PAC) cell behavior remains poorly defined. Here, we show that EVs derived from Aggregatibacter actinomycetemcomitans (Aa), but not from Porphyromonas gingivalis or Fusobacterium nucleatum, robustly induce epithelial-mesenchymal transition (EMT), migration, and invasion in human PAC cells. These effects require the Aa genotoxin cytolethal distending toxin (Cdt), which is selectively packaged into Aa-derived EVs and efficiently delivered to host cells. EV-associated Cdt induces DNA damage, triggers a senescence-like transcriptional program, increases EGF sensitivity, and activates the EGFR-ERK/Akt signaling axis independently of TGF{beta} signaling, thereby promoting malignant traits in vitro. Notably, these responses occur in human but not murine PAC cells, revealing species-specific susceptibility to bacterial genotoxins. Together, these findings reveal a previously unrecognized cross-kingdom mechanism by which periodontopathic bacterial EVs promote metastatic traits in human pancreatic cancer cells through Cdt-mediated DNA damage and EGFR-ERK/Akt signaling.

microbiology↗

bioRxiv2026

Chemogenetic activation induces persistent transcriptomic remodeling and functional plasticity in cultured astrocytes

Astrocytes are essential regulators of neuronal function and brain homeostasis. Recent methodological advances have increasingly revealed their active roles through precise manipulation of astrocyte function in the brain. While chemogenetic strategies, such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), have been widely used to recapitulate endogenous G-protein-coupled receptors (GPCRs) signaling and selectively modulate astrocyte activity, the molecular mechanisms accompanying DREADD activation remain incompletely understood. Here, we characterized the transcriptional responses of cultured cortical astrocytes and found that DREADD activation induces profound changes in astrocytic gene expression profiles. Activation of Gi-, Gq-, and Gs-coupled DREADDs elicited distinct transcriptomic responses. Transcription factor activity profiling further revealed that each DREADD subtype selectively modulates a distinct set of transcription factors that collectively shape astrocytic transcriptomic responses, thereby indicating subtype-specific transcriptional mechanisms. Importantly, DREADD activation induced persistent changes in the astrocytic transcriptome that remained detectable even three days after stimulation. These transcriptomic alterations were associated with sustained changes in astrocytic calcium responses to extracellular ATP, indicating plastic changes in astrocytic physiological function. Together, these findings provide a molecular framework for interpreting astrocytic DREADD manipulations and reveal a mechanistic basis for functional plasticity and heterogeneity of astrocytes.

neuroscience↗

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

Comprehensive Analysis of Multi-Omics Vaccine Response Data Using MOFA and Stabl Algorithms

FluPRINT is a multi-omics dataset that measures donors protein expression and cell counts across various assays. Donors were also assigned a binary value (0 or 1), being labeled as high responders (1) if they had a fold change [≥] 4 of the antibody titer for hemagglutinin inhibition (HAI) from day 0 to day 28, and low responders otherwise (0). In this project, we used the MOFA and Stabl algorithms to analyze FluPRINT, estimate the population structure from the data, and identify the most important features for predicting response to the vaccine. The preprocessing of the dataset included removing repeat features, scaling by assay, and removing outliers. Since Stabl does not directly address missing values, features with high amounts of missing values were removed and the remaining were ignored. MOFA identified the top feature in structure extraction as IL neg 2 CD4 pos CD45RA neg pSTAT5. MOFA explains well the variance of the data while also choosing features that have good significance, as illustrated by their significant p-values (p < 0.05). Stabl found the top feature for explaining the outcome to be CD33- CD3+ CD4+ CD25hiCD127low CD161+ CD45RA+ Tregs, which matched the top result of previously published analysis. MOFAs features achieved an AUROC of 0.616 (95% CI of 0.426-0.806), and Stabls achieved an AUROC of 0.634 (95% CI of 0.432-0.823). Our research addresses a key knowledge gap: understanding how these fundamentally different analytical approaches perform when analyzing the same complex dataset. Our exploration evaluates their respective strengths, limitations, and biological insights and provides guidance on using MOFA and Stabl to find the best predictive cell subsets and features for understanding large immunological multi-omics data. The code for this project can be found at https://github.com/aanya21gupta/fluprint.

immunology↗