Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Novel bile salt analogs reduce lipid accumulation in liver cells with potential to treat both metabolic dysfunction-associated steatotic liver disease and Clostridioides difficile infection

Metabolic dysfunction-associated steatotic liver disease (MASLD) and Clostridioides difficile (C. difficile) infection (CDI) are clinically associated, yet there is limited effective treatment for both diseases. Bile salt analogs (BSAs) have demonstrated potential in treating either MASLD or CDI. We screened a library of BSAs (n=112) previously synthesized as potential inhibitors of C. difficile spore germination, for their therapeutic potential in reducing intracellular accumulation of fatty acids in HepG2 cells as candidates for prevention and treatment of both MASLD and CDI. The screening was based on an in vitro model established by incubating HepG2 cells with free fatty acids, with obeticholic acid (OCA), a known BSA with anti-MASLD activity as a control. Gene and protein expressions were quantified to validate the treatment effect. We found that compounds C13, C24, C25, C74, C98, and C101 demonstrated significant effectiveness in both preventing the intracellular accumulation of lipids and removing pre-loaded cellular lipids. Gene expression analysis showed that C24, C25, and C74 produced a similar pattern characterized by a robust induction of FGF21 expression, while C13, C98, and C101 produced a transcription pattern that mirrors the effect of OCA. Structurally, while C13, C24, and C25 do not display drug-like properties, C74, C98, and C101 are drug-like and share a similar structure. Interestingly, C101 is a potent inhibitor of C. difficile spore germination. OCA shows a weak anti-gemination effect. Our study identified lead compound candidates for the development of novel therapeutics capable of treating both MASLD and CDI. Significance statementThe clinical association between MASLD and CDI remains an unmet need for dual acting therapeutic strategies. Given the reported potential of BSA, we screened 112 previously synthesized as potential inhibitors of C. difficile spore germination, for their therapeutic potential in reducing intracellular accumulation of fatty acids in HepG2 cells. Our study identified compounds that effectively reduce intracellular lipid accumulation and inhibit C. difficile spore germination. These results nominate lead candidates for developing dual-acting therapeutics targeting both MASLD and CDI.

pharmacology and toxicology↗

bioRxiv2026

Homeobox transcription factor MSX2 down-regulates ERα action to facilitate anti-estrogensensitivity in ERα+ breast cancer

Breast cancer is the most common malignancy among women worldwide. Estrogen receptor (ER)-positive breast cancer is about 70% in the total breast cancer. It has variable prognosis and high recurrent risk, frequently developing resistance to endocrine therapies. Herein, we have identified that a homeobox transcription factor MSX2 downregulated in ER-positive breast cancer is correlated with the advanced grade and poor survival outcomes. Our results have demonstrated that MSX2 interacts with ER to inhibit ER-mediated transactivation. Mechanistically, MSX2 associates with HDAC1/HDAC2 to form a protein complex. MSX2 is required for recruitment of HDAC1/HDAC2 complex to estrogen response elements (EREs) region on ER downstream target genes, reducing histone H3K9ac and H3K27ac levels to inactivate gene transcription. Functionally, ectopic expression of MSX2 suppresses cell growth and enhances the sensitivity to anti-estrogen treatment in ER-positive breast cancer cells. Our results indicate that MSX2 as a novel co-repressor of ER is involved in suppression of ER-positive breast cancer progression. Restoring MSX2 protein may provide a promising strategy to overcome endocrine resistance in ER-positive breast cancer.

Molecular Biology↗

bioRxiv2026

Cardiomyocytes Undergo a Mesenchymal-Like Fate Transition in Myocardial Fibrosis

BACKGROUNDMyocardial fibrosis, a pathological hallmark of adverse cardiac remodeling and heart failure, has been conventionally attributed to the activation of resident fibroblasts. Although recent studies suggest contributions from non-fibroblast lineages, direct in vivo genetic evidence that cardiomyocytes can undergo a mesenchymal-like fate transition during myocardial fibrosis remains absent. This study aims to investigate whether such a transition occurs and to elucidate the underlying regulatory mechanisms. METHODSHuman myocardial infarction (MI) tissues were analyzed by immunohistochemistry and integrated with public single-nucleus RNA sequencing (snRNA-seq) data to detect mesenchymal-like signatures in cardiomyocytes. Genetic lineage-tracing was performed in MI mice, and in cardiomyocyte-specific Hgs (hepatocyte growth factor-regulated tyrosine kinase substrate) gene knockout mice, to map the fate of cardiomyocyte-derived cells. Mechanistic insights were obtained through proteomic and snRNA-seq analysis of Hgs knockout hearts and validated through gain- and loss-of-function experiments targeting Aldh1a2 (aldehyde dehydrogenase 1 family member A2). RESULTSIn human MI samples, a subset of cardiomyocytes showed reduced expression of cardiomyocyte markers concurrent with acquisition of mesenchymal-associated markers. Genetic lineage tracing demonstrated that adult cardiomyocytes can adopt a mesenchymal-like cell fate during post-MI remodeling. We identify HGS as a factor constraining this transition. Hgs knockout in adult cardiomyocytes upregulated Aldh1a2, triggered the mesenchymal-like fate transition, and gave rise to cells expressing markers of activated fibroblasts or osteoblasts, accompanied by pronounced myocardial fibrosis and calcification. Forced Aldh1a2 overexpression in cardiomyocytes drove the mesenchymal-like fate transition in vitro and in vivo, whereas Aldh1a2 deletion in cardiomyocytes mitigated MI-induced myocardial fibrosis. CONCLUSIONSThis study provides in vivo genetic evidence that adult cardiomyocytes possess the capacity to undergo a mesenchymal-like fate transition under pathological conditions. Our data suggest that HGS and ALDH1A2 serve as regulators of the transition, offering a new basis for understanding cellular and molecular mechanisms of myocardial fibrosis. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIMyocardial fibrosis is primarily driven by resident fibroblast activation, with additional contributions from cardiac CD34+ cells, pericytes, and macrophages. C_LIO_LIAdult cardiomyocytes exhibit phenotypic plasticity and transdifferentiate into epicardial-like or pacemaker cells under specific conditions. C_LI What New Information Does This Article Contribute?O_LIA subset of cardiomyocytes adopts a mesenchymal-like cell fate during myocardial fibrosis, marked by downregulation of cardiomyocyte identity markers and loss of aligned cell-cell contacts. C_LIO_LIThese cells acquire mesenchymal morphology and markers, ECM components, migratory gene signatures, and proliferative capacity. C_LIO_LIHGS and ALDH1A2 act as regulators of this mesenchymal-like fate transition. C_LI Myocardial fibrosis drives heart failure progression, yet the cellular sources of pathological fibroblasts remain incompletely defined. Here, we demonstrate that a subset of cardiomyocytes adopts a mesenchymal-like cell fate during myocardial fibrosis by using an integrated approach combining human MI samples, murine genetic lineage tracing, and snRNA-seq. Mechanistically, we identify HGS and ALDH1A2 as regulators of this transition. Cardiomyocyte-specific Hgs deletion upregulates Aldh1a2, triggering the mesenchymal-like fate transition. Furthermore, Aldh1a2 overexpression drives this transition, while its deletion attenuates MI-induced fibrosis. These findings reveal a previously unrecognized plasticity of adult cardiomyocytes and identify potential therapeutic targets for fibrotic heart disease.

genetics↗

bioRxiv2026

MZF1-mediated GAPDH overexpression drives glycolytic reprogramming and neuroendocrine progression in advanced prostate cancer

Drug resistance to the androgen receptor (AR) antagonist is a critical obstacle in the clinic for advanced prostate cancers. Especially, AR antagonist treatment-induced neuroendocrine progression represents a lethal and therapy-resistant subtype. Although transcriptional and epigenetic lineage plasticity have been extensively implicated in treatment-induced neuroendocrine progression, the contribution of metabolic adaptation remains incompletely understood. Here, we identified a previously unrecognized metabolic reprogramming mechanism induced by AR antagonists in castration-resistant prostate cancer (CRPC) models. AR antagonist treatment markedly enhanced glycolytic activity and induced glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression. Genetic depletion of GAPDH suppressed AR antagonist-induced glycolytic activation, altered transcriptomic and metabolic programs, reduced neuroendocrine-associated marker expression, and inhibited xenograft tumor growth. Mechanistically, GAPDH promoter pulldown coupled with mass spectrometry, siRNA screening, and chromatin immunoprecipitation assays identified myeloid zinc finger-1 (MZF1) as a key transcription factor for Enzalutamide-induced GAPDH gene expression. Pharmacological inhibition of GAPDH using koningic acid (KA) or penta-O-galloyl-{beta}-D-glucopyranose (PGG) significantly suppressed tumor growth and attenuated neuroendocrine-associated molecular programs in CRPC cell-derived xenograft and patient-derived t-NEPC xenograft models. Collectively, our findings identify an AR antagonist-induced MZF1-GAPDH signaling axis that promotes glycolytic activation and neuroendocrine-associated metabolic adaptation during treatment resistance. These results support targeting GAPDH-dependent metabolic reprogramming as a potential therapeutic strategy for treatment-resistant prostate cancer. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/729867v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@10480b2org.highwire.dtl.DTLVardef@9d2ed8org.highwire.dtl.DTLVardef@16e8705org.highwire.dtl.DTLVardef@1627ad2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Aβ Aggregates Bind the U1 Spliceosomal Ribonucleoprotein in Alzheimer Disease Brain

Missplicing due to U1 small nuclear ribonucleoprotein (U1 snRNP) insolubilization and dysfunction has been identified in Alzheimer disease (AD) brain. Cytoplasmic aggregation and mislocalization of the U1 snRNP partly co-localizes with tau neurofibrillary tangles, and some evidence for tau-U1 binding has been identified. However, tau-U1 co-localization by immunohistochemistry is only partial, and insoluble U1 small nuclear RNA (snRNA) binding proteins correlate better with A{beta} than with tau in unbiased proteomics. While investigating the sedimentation characteristics of A{beta} aggregates capable of diffusing out of AD brain tissue, we unexpectedly found that some were bound to small RNA. A{beta} immunoprecipitation and deep sequencing revealed the U1 snRNA, with specific binding confirmed through reverse immunoprecipitation and oligonucleotide hybridization. Double immunoelectron microscopy revealed decoration of A{beta} fibrils, more than tau fibrils, with the U1-70k protein, a component of the U1 snRNP. Immunofluorescence of unfixed cryostat sections but not formalin fixed paraffin embedded sections of AD brain revealed labeling of a subset of amyloid plaques with anti-U1-70k antibodies, confirmed by RNA in situ hybridization of the U1 snRNA. We conclude that a subset of AD brain A{beta} aggregates are bound to the U1 snRNP at the edges of some amyloid plaques, explaining prior proteomics findings. These data provide a potential link between A{beta} aggregation and spliceosome dysfunction and unite A{beta} with other fibril-forming proteins across the neurodegenerative diseases whose aggregation is affected by RNA binding.

neuroscience↗

bioRxiv2026

Interstitium-mimicking porous alveolar membranes enable physiologic aerosol transport and distinct acute-chronic lung injury responses

Barrier membranes govern transport and mechanochemical coupling in lung-on-chip systems but typically exhibit low open porosity, limited pore interconnectivity, and diffusion distances exceeding native thin septal regions. An interstitium-mimicking, alveolus-shaped poly({varepsilon}-caprolactone) membrane is developed using dual-templated nonsolvent-induced phase separation followed by controlled enzymatic pore enlargement. The resulting architecture achieves [~]40% total porosity with 97% pore interconnectivity and incorporates a locally thinned dome region ([~]2.5 {micro}m). This structure sustains cyclic deformation while increasing oxygen diffusivity fivefold compared with conventional Transwell(R) membranes under both acellular and epithelial-endothelial co-culture conditions. Integrated into an air-liquid interface platform, the membrane enables direct aerosol deposition and quantitative interrogation of cross-barrier mass transfer. Using carbonaceous nanoscale particulate matter as a model inhaled aerosol, controlled exposure induces dose-dependent oxidative, inflammatory, and genotoxic responses. Matched cumulative dose studies reveal distinct biological trajectories: acute high-dose exposure produces rapid cytotoxic stress and barrier disruption, whereas chronic low-dose exposure preserves viability yet promotes sustained DNA repair and genome-maintenance programs. Compartment-resolved analysis and therapeutic intervention further demonstrate the platforms utility for spatial and translational interrogation of lung injury. By restoring physiologically relevant diffusion distance, interconnectivity, and strain responsiveness, the interstitium-mimicking membrane advances lung-on-chip design toward functional replication of alveolar transport dynamics for studying lung injury and barrier dysfunction.

bioengineering↗

bioRxiv2026

Chronic Mild Stress Impairs Hippocampal Myelination through SOX6-Dependent Dysfunction of Oligodendrocyte Lineage Cells

Chronic stress induces structural and functional changes in the brain, increasing susceptibility to major depressive disorder and other mental illnesses. Myelination deficits are a key pathological feature of stress-related disorders, yet the molecular mechanisms linking chronic stress to oligodendrocyte dysfunction remain poorly understood. Here, we used single-nucleus multiome sequencing to map gene expression and chromatin-accessibility remodeling in the hippocampus of mice exposed to chronic unpredictable mild stress (CUMS), a model that simulates key features of human daily stressors. CUMS induced broad molecular reprogramming across hippocampal cell populations, with stress-responsive gene networks significantly enriched for depression-associated genes. The oligodendrocyte lineage showed heightened vulnerability, with CUMS preferentially disrupting immature OPC/intermediate states and impairing OPC migration, OPC-to-ODC lineage progression, intercellular communication, and myelination. Integrated multiomic analysis identified stage-specific cis-regulatory elements and stress-sensitive gene regulatory networks, converging on SOXD transcription factors, particularly SOX5 and SOX6, as key regulators of OPC dysfunction. SOX6 ChIP-seq confirmed direct SOX6 binding at regulatory elements associated with genes controlling OPC morphogenesis, migration, and glutamatergic signaling. CUMS reduced SOX6 protein levels and SOX6-associated regulatory network activity in OPCs, whereas OPC-specific enhancer-driven restoration of SOX6 rescued stress-induced defects in OPC migration and myelination. Together, these findings define a stress-sensitive SOXD/SOX6 regulatory mechanism linking chronic stress to oligodendrocyte lineage dysfunction and myelination deficits, identifying SOX6 as a functional regulatory node with therapeutic potential for stress-related brain pathology.

neuroscience↗

bioRxiv2026

Glucocorticoid Programming of Erythrocyte Hypoxic Memory Enables Rapid High-Altitude Acclimatization

BackgroundRapid ascent to high altitude causes acute mountain sickness (AMS) and life-threatening pulmonary/cerebral edema, yet no prophylaxis enables immediate acclimatization. Intermittent hypoxia training (IHT) establishes a "hypoxic memory" that accelerates adaptation, to high altitude, but its cellular and molecular basis remains undefined, precluding effective pharmacological strategies. MethodsA human cohort of 18 sea-level inhibitants was equally divided into two groups, one group received IHT prior to ascent to 3,500 meters, the other group did not. Multi-omics profiling of erythrocytes and plasma, along with isotopic glucose tracing, was employed to examine the metabolic effects of IHT upon high altitude acclimatization. Preclinical studies with genetically engineered mice were used to further define the molecular and metabolic basis of IHT-induced hypoxic memory allowing rapid acclimatization to high altitude. ResultsMetabolomics revealed glucocorticoids as previously unrecognized endogenous erythroid hypoxic memory orchestrators induced by IHT that negatively correlated with AMS severity. Lipidomics and isotopic glucose tracing demonstrated that glucocorticoid signaling via the glucocorticoid receptor (GR) coordinately enhanced glucose metabolism and activated sphingosine kinase-1 (SPHK1)-driven sphingosine-1-phosphate (S1P) synthesis, pre-conditioning erythrocyte oxygen unloading and antioxidant capacity. Glucocorticoid supplementation enhanced erythrocyte SPHK1 activation and oxygen delivery, counteracting multi-tissue hypoxia and pulmonary and renal neutrophil infiltration. Conversely, erythrocyte-specific Sphk1 ablation abolished glucocorticoid-induced S1P production causing severe tissue hypoxia and exaggerated pulmonary neutrophil infiltration. ConclusionsWe establish a new function of glucocorticoids in erythrocyte metabolic plasticity to enhance oxygen delivery as a hypoxic memory mechanism for rapid adaptation to high altitude. This previously unrecognized GR-mediated reprograming of glucose and sphingolipid metabolism offers a transformative precision pharmacologic strategy for high altitude preconditioning, high altitude emergencies and hypoxia-driven diseases.

cell biology↗

bioRxiv2026

SpatialDataAgent: Autonomous Spatial Omics Data Curation at Decade Scale

Fragmented metadata in spatial omics archives has rendered large volumes of multimodal molecular-histological data inaccessible as dark data. Here, we introduce SpatialDataAgent, an agentic workflow for autonomous spatial omics data curation, combining schema-constrained evidence evaluation with a self-refining standardization agent. Applied to a decade of GEO records, SpatialDataAgent identified 769 paired H&E-spatial transcriptomics (ST) datasets, representing a 6.4-fold scale expansion over existing manually curated baselines. Within the benchmarking window, the framework achieved a 141% increase in high-confidence Class A paired datasets. We further assembled a recent high-confidence subset into HESRT, a standardized datalake containing 29.2 million spots/cells, establishing a blueprint for evidence-grounded autonomous curation of multimodal biomedical archives.

bioinformatics↗

bioRxiv2026

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

bioRxiv2026

The HOG MAPK - Transcription Factor CsAtf1 - CsErg5B Regulatory Module Mediates Conidial Germination and Fludioxonil Sensitivity in Colletotrichum siamense

Colletotrichum siamense is a predominant causal agent of anthracnose in rubber tree and numerous economically important crops, causing severe yield losses worldwide. Conidial germination represents a critical early step for successful infection, while the high-osmolarity glycerol (HOG) MAPK pathway and ergosterol biosynthesis individually govern fungal development, stress adaptation and fungicide responses. However, the molecular crosstalk between these two modules remains largely elusive in phytopathogenic fungi. Here, we identified CsErg5B, a sterol C-22 desaturase homolog, as a direct target of the HOG- regulated transcription factor CsAtf1 in C. siamense. CsErg5B was indispensable for ergosterol biosynthesis, conidial germination, appressorium formation, and full virulence. The {Delta}CsErg5B mutant showed increased conidiation but severely impaired germination, and exhibited elevated resistance to fludioxonil while hypersensitivity to azole fungicides. Epistasis analysis using the {Delta}CsErg5B/{Delta}CsCyp51G1 double mutant - where CsCyp51G1 serves as another downstream target of CsAtf1 - revealed that CsErg5B functions as the predominant downstream effector of CsAtf1 in modulating conidial development and fludioxonil sensitivity. Furthermore, overexpression of CsErg5B significantly rescued the defects in conidial germination and fludioxonil sensitivity in both {Delta}CsAtf1 and {Delta}CsPbs2 mutants. Taken together, our findings uncover a HOG MAPK - CsAtf1 - CsErg5B regulatory axis that connects HOG MAPK signaling to ergosterol homeostasis, thereby governing conidial germination and fungicide sensitivity in C. siamense. This study provides novel insights into the regulatory network underlying fungal development and fungicide response, and offers promising molecular targets for the integrated management of plant anthracnose.

microbiology↗

bioRxiv2026

A Synthetic Platform for Antibody Junctional Diversification Beyond Natural Constraints

Antibody junctional diversity in jawed vertebrates arose from RAG transposon domestication, generating CDR3-focused V(D)J recombination with lymphocyte specificity--a constrained system limiting engineered antibody diversity. To overcome these limitations, we developed ARESEC (Antibody Reprogram and Expression System in Engineered Cells), a synthetic platform that enables programmable V(D)J recombination in non-lymphoid HEK293T cells. Through engineered recombination signal sequences (RSS) and optimized RAG1/2 expression, ARESEC enables RSS-guided DNA recombination across all three complementarity-determining regions (CDR1/2/3). Co-expression of terminal deoxynucleotidyl transferase (TdT) enhanced junctional sequence diversity by 41.5-86.3% across 3 CDRs. The platform enables native IgG production by coupling mammalian surface display with FACS-based functional screening. Using clinical-grade antibodies (Nivolumab and Durvalumab) as high-affinity starting scaffolds, we achieved further efficient affinity maturation through focused CDR diversification (library complexity >103). From these diversification libraries, we identified optimized variants including the anti-PD-L1 Dur1 with 2.01-fold enhanced binding, demonstrating the systems capacity for rapid antibody optimization from minimal diversity sampling. Collectively, ARESEC establishes a synthetic paradigm that transcends natural V(D)J constraints, generating multi-CDR diversification in non-lymphoid cells to enable rapid discovery of affinity-matured antibodies, effectively bridging immune evolution with modern antibody engineering demands.

synthetic biology↗

bioRxiv2026

Receptor-Anchored Olfaction Representation through Perception-Consistent Metric Learning

Olfactory perception arises from distributed activation across hundreds of olfactory receptors (ORs), yet our understanding of this landscape remains constrained by the scarcity of OR affinity measurements. Here, we present Receptor-Anchored Metric Supervision (RAMS), a transfer learning framework using perceptual consistency as weak supervision to predict OR activation spectra. RAMS fine-tunes a pretrained drug-target affinity model by imposing constraints derived from olfactory perception, where similar odorants are encouraged to exhibit similar OR activations. It transfers protein-ligand interaction knowledge learned from large-scale pharmacological data into the olfactory domain and reshapes it toward OR activation prediction. Evaluations against experimental measurements show that RAMS improves the accuracy of receptor-spectrum prediction and yields biologically plausible activation patterns. The predicted spectra show concordance between receptor discriminative capacity and expression level, and highlight the understudied OR52 family as a potential contributor to primary odor recognition. Together, RAMS provides a scalable framework for reconstructing receptor-anchored olfactory representations.

bioinformatics↗

bioRxiv2026

A shared neural code for gender across faces, bodies, and objects in the human brain

Humans can readily infer gender from diverse visual categories, including faces, bodies, and objects, yet it remains unclear whether the brain constructs a shared, category-general representation of gender. To fill the gap, we measured neural responses using fMRI while participants viewed female and male stimuli across these three categories. Multivoxel pattern analyses revealed that gender information was encoded throughout distributed occipitotemporal regions for all categories. Critically, cross-category decoding and regression-based representational similarity analyses converged on a region of the right middle temporal gyrus (rMTG) that encoded gender independently of stimulus category. This region also carried category information, indicating mixed selectivity. Comparisons between neural representational dissimilarity matrices and those from a fine-tuned convolutional neural network (CNN) showed that rMTG activity most closely resembled intermediate CNN layers, suggesting that shared gender representations rely on mid-level visual features. Finally, functional connectivity analyses revealed that gender-related interactions among occipitotemporal regions were similar for faces and bodies but not for objects. Together, these findings identify a category-general neural hub for gender perception and illuminate how mid-level visual features and distributed networks support the abstraction of gender across heterogeneous visual inputs.

neuroscience↗

bioRxiv2026

Fibroblast-encoded inflammatory memory orchestrates recurrent skin inflammation via NNMT-dependent metabolic remodeling

Chronic skin inflammation frequently recurs at the same anatomical sites after therapy withdrawal, implying stromal cells may encode local inflammatory memory. Here, we identified nicotinamide N-methyltransferase (NNMT) as a central metabolic-epigenetic regulator of fibroblast inflammatory memory enabling psoriasis relapse. Single-cell and spatial transcriptomics revealed that dermal fibroblasts acquire a persistent senescence-associated secretory phenotype (SASP) during inflammation, maintaining pro-inflammatory niche in resolved skin that supports CD 8+CD 103+ tissue-resident memory T cell (Trm) differentiation. Multi-omics profiling demonstrated that NNMT depletes S-adenosylmethionine (SAM), reduces H 3K 27me3 deposition, and permits sustained AP-1 occupancy at SASP gene promoters. Fibroblast-specific NNMT ablation or pharmacologic inhibition suppressed SASP activity, limited Trm accumulation, and prevented both initiation and relapse of skin inflammation in mice. These findings establish NNMT as a stromal regulator linking fibroblast metabolism to durable epigenetic memory and propose its targeting to erase inflammatory memory and achieve long-term remission in psoriasis and related immune-mediated diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/721223v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@34b2f4org.highwire.dtl.DTLVardef@1d0bb89org.highwire.dtl.DTLVardef@c8277borg.highwire.dtl.DTLVardef@9825ac_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic Abstract:C_FLOATNO Proposed mechanism through which NNMT-driven fibroblast SASP facilitates the initiation and recurrence of psoriasis C_FIG

immunology↗

bioRxiv2026

Systems Pharmacology Reveals Type I Interferon and Myeloid-Like B Cell Reprogramming as Druggable Axes in Antiphospholipid Syndrome

Antiphospholipid syndrome (APS) lacks targeted therapies beyond anticoagulation, and its molecular heterogeneity remains poorly characterized. We employed an integrative systems pharmacology approach combining weighted gene co-expression network analysis (WGCNA), single-cell RNA sequencing, Connectivity Map (CMap) screening, and molecular docking to identify druggable targets in APS. WGCNA of bulk RNA-seq data from neutrophils (n = 18) and whole blood (n = 88) identified two disease-associated modules: ME10 (176 genes, r = 0.77, interferon-I signaling) and ME2 (3409 genes, r = 0.79, degranulation/innate activation). Single-cell analysis of 26,936 B cells revealed transitional B cells with elevated ME2 scores and aberrant SPI1 expression, suggesting myeloid-like transcriptional reprogramming. CMap analysis ranked chloroquine, a first-line APS therapy, among top ME2 candidates (NCS = -2.07), validating the computational approach. DrugBank mapping identified 14 FDA-approved drugs targeting module genes, and a 3-gene machine learning signature (CORO1A, ANKRD22, IFITM1) achieved cross-tissue validation AUC of 0.802. External validation confirmed ME2 pathway modulation by NAPc2 intervention and cross-tissue module conservation in platelets. Patient-level ME10 x ME2 stratification revealed four molecular subtypes with distinct pathway activation profiles. This framework nominates druggable targets across both IFN-I and degranulation pathways, providing a foundation for pathway-guided precision medicine in APS.

bioinformatics↗

bioRxiv2026

Turep: Detecting cross-cancer tumor-reactive T cells in single-cell and spatial transcriptomics data

Tumor-infiltrating lymphocytes are essential for anti-tumor immunity, yet distinguishing tumor-reactive T cells from non-reactive bystander cells remains a significant challenge. Existing signatures, often derived from single cohorts, lack robustness in cross-cancer prediction. We present Turep, a deep learning method designed for robust, cross-cancer prediction of tumor-reactive T cells using single-cell or spatial transcriptomics data. By integrating paired single-cell RNA and T cell receptor sequencing data from seven human malignancies, we identified a pan-cancer tumor-reactive gene signature and leveraged generative data augmentation to address data imbalance. Turep consistently outperformed existing biomarkers, achieving a mean area under the receiver operating characteristic curve of 0.870 across cancer types. In validation across diverse cohorts, we found that Turep-predicted tumor-reactive T cell proportions could predict clinical response to immunotherapy. Furthermore, extending Turep to spatial transcriptomics revealed that tumor-reactive T cells preferentially resided in spatial niches where target cells exhibited elevated antigen presentation. Overall, Turep provides a powerful, generalizable tool for identifying tumor-reactive T cells and their spatial architectures, facilitating personalized cancer immunotherapy strategies.

bioinformatics↗

bioRxiv2026

Acquired resistance to the PRMT5 inhibitor confers collateral sensitivity to MEK inhibition in MTAP-null non-small cell lung cancer

Protein arginine methyltransferase 5 (PRMT5) is a synthetic lethal target in methylthioadenosine phosphorylase-deleted (MTAP-null) cancers. Second-generation MTA-cooperative PRMT5 inhibitors preferentially target MTAP-null cells while largely sparing MTAP-wildtype (MTAP-WT) cells, thereby improving tumor selectivity over first-generation PRMT5 inhibitors. Despite encouraging efficacy and safety signals in early clinical studies, the modest objective response rates (ORRs) observed with these inhibitors suggest that intrinsic or acquired resistance may limit their clinical benefit. Here, we investigated mechanisms of acquired resistance to the MTA-cooperative PRMT5 inhibitor BMS-986504/MRTX1719 in MTAP-null non-small cell lung cancer (NSCLC) cells and sought to identify therapeutic vulnerabilities that emerge upon resistance. Using multiple in vitro-derived resistant models, we found that acquired resistance was not fully explained by alterations in PRMT5 activity or reduced MTA levels. Instead, resistance was associated with collateral sensitivity to MEK inhibition and enrichment of MAPK-related transcriptional programs. Together, these findings identify MEK inhibition as an actionable collateral vulnerability in MTAP-null NSCLC cells that acquire resistance to PRMT5 inhibition.

cancer biology↗