Biology subjects

Li, Q.

Publications and source records attributed to Li, Q..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Invasion status stratifies the composition of the human pancreatic cancer perineural niche

The peripheral nervous system innervates the pancreatic ductal adenocarcinoma (PDAC) microenvironment, and perineural invasion (PNI), the invasion of cancer cells in and around nerves, correlates with metastatic burden and poor outcomes. Though PDAC innervation is near universal and the majority of PDAC patients harbor PNI, the cellular and molecular composition of the heterocellular perineural niche is largely unknown, obscuring functional significance. Here we provide a deeply phenotyped spatial and single-cell atlas of the human PDAC perineural niche, enabling a high-resolution comparison of invaded versus non-invaded nerve neighborhoods. This atlas leverages a novel vision-centric artificial intelligence model for imaging-based spatial transcriptomics, coupled with pathology-guided single-nucleus RNA-seq. These analyses revealed that invaded nerve neighborhoods harbor cancer cells of the classical subtype, together with myofibroblastic cancer-associated fibroblasts (CAFs) and lipid-associated macrophages. Non-invaded nerve neighborhoods, in contrast, harbor inflammatory CAFs and infiltration of B and T lymphocytes. These findings raise the possibility that PNI and not innervation itself is immune-suppressive in this setting, motivating functional studies. Statement of SignificanceHuman PDAC is innervated and almost invariably harbors PNI, but the composition and functions of perineural niches remain unclear. Here we provide a spatial and single-cell atlas of the human PDAC perineural niche, defining cancer and stromal cell states in the context of PNI and nominating this process as potentially immune-suppressive.

cancer biology↗

bioRxiv2026

Evolutionary Origins and Synthetic Reconstruction of Gingerols

How new enzymatic activities become integrated with existing metabolic networks to generate lineage-restricted plant chemistry remains a central question in metabolic evolution, exemplified by gingerol biosynthesis in Zingiberaceae, whose complete enzymatic basis has remained elusive. Here, we resolve this problem by elucidating the evolutionary origins and the full biosynthetic pathway of gingerol through single-cell transcriptomics, functional screening, structural biology, comparative genomics and pathway reconstruction. A coordinated metabolic program operates in ginger oil cells, thereby guiding the identification of diketide-CoA synthases, gingerol synthases (GS) and gingerol reductases that together constitute the complete pathway. GS remodels the conserved type III polyketide synthase scaffold to organize a fatty acyl-CoA and a phenylpropanoid-derived intermediate for gingerol formation. Furthermore, GS arose through duplication and limited active-site remodeling of a curcumin synthase-like enzyme, accompanied by coordinated recruitment of precursor-supply and reduction pathways. Translating these principles into yeast achieves the first de novo microbial production of 6-gingerol from glucose at 12.4 mg/L. These findings reveal the evolutionary logic by which plants recruit and coordinate novel enzymatic activities to establish lineage-restricted metabolic program, providing a framework for understanding and engineering specialized metabolism across the plant kingdom.

synthetic biology↗

bioRxiv2026

Nicotinamide N-methyltransferase couples inflammation and epigenetic remodelling to hepatic fibrosis

Background & aimsChronic inflammation is a key driver of progression from benign steatosis to metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis. The molecular mechanisms coupling inflammatory cytokine signaling to altered hepatocyte remodeling remain incompletely understood. Here, we report that nicotinamide N-methyltransferase (NNMT) is induced by specific inflammatory cytokines in hepatocytes and acts as a key hub to connect inflammation with fibrotic liver remodeling. Approach & resultsTranscriptomic profiling of primary human hepatocytes and human hepatoma cell lines identified NNMT as a selective downstream target of IL-1{beta} and IL-6, but not of TNF. Genetic silencing of NNMT markedly attenuated cytokine-induced inflammatory and fibrotic gene expression programs and partially reversed IL-6-mediated sensitization of IL-1{beta} responses. Integration of RNA-seq with ChIP-seq, CUT&Tag, and ATAC-seq revealed that inflammatory cytokines remodel the hepatocyte epigenome through coordinated changes in histone modifications. NNMT overexpression promoted selective remodeling of H3K4me2 chromatin landscapes, accompanied by activation of fibrosis-associated transcriptional programs. Nicotinamide supplementation partially suppressed inflammatory gene expression, supporting a role of NNMT-dependent NAD+ metabolism in this process. Importantly, cytokine-induced NNMT expression and its associated transcriptional program were conserved in primary human hepatocytes and 3D liver microtissues. ConclusionsNNMT functions as an inflammatory cytokine-inducible metabolic- epigenetic integrator that links IL-1{beta} and IL-6 signaling to chromatin remodeling and inflammatory transcriptional reprogramming in hepatocytes. These findings identify NNMT as a key regulator of inflammatory and profibrotic responses during MASLD progression and highlight NNMT as a potential therapeutic target for limiting liver inflammation and fibrosis. Impact and ImplicationsThis study identifies NNMT as a previously unrecognized metabolic-epigenetic integrator that selectively links IL-1{beta} and IL-6 signaling to chromatin remodeling and inflammatory transcriptional reprogramming in hepatocytes. Our findings establish a non-canonical mechanistic framework by which inflammatory cytokines drive profibrotic gene expression during MASLD progression through. By uncovering NNMT as a critical mediator of inflammatory-epigenetic crosstalk, this work broadens our understanding of hepatocyte-intrinsic mechanisms underlying liver fibrosis and highlights NNMT as a promising therapeutic target for preventing the transition from steatosis to progressive MASH and fibrosis. HighlightsO_LINNMT is selectively induced by IL-1{beta} and IL-6 in hepatocytes. C_LIO_LINNMT controls fibrogenic gene expression modules. C_LIO_LIIL-6 amplifies IL-1{beta} responses through an NNMT-dependent mechanism. C_LIO_LINNMT links inflammatory signaling to epigenetic remodeling in MASLD. C_LI

molecular biology↗

bioRxiv2026

Brassinosteroid-auxin crosstalk shapes rice flag leaf angle to boost dense planting yield

Flag leaf angle (FLA) critically determines rice yield potential under dense planting conditions. As two pivotal phytohormones determine rice FLA, the antagonistic interaction between brassinosteroid (BR) and auxin remains largely uncharacterized. We here demonstrate that BR signaling reduces auxin biosynthesis to control FLA via regulating the biosynthesis of secondary cell wall (SCW). Genetic evidence demonstrates OsYUC8 mutants disrupt SCW formation, leading to increased FLA. At the molecular level, the BR-related transcription factor OsBZR1 directly binds to and represses OsYUC8 promoter activity, thereby fine-tuning auxin-mediated SCW biosynthesis. Field evaluations reveal that osbzr1 mutants display optimized flag leaf architecture and improved yield performance under high-density cultivation. Our study not only delineates the antagonistic BR-auxin interaction governing FLA but also establishes a genetic strategy for manipulating crop architecture to maximize yield in dense planting conditions. One-sentence summaryOsBZR1-mediated repression of OsYUC8-driven auxin biosynthesis modulates secondary cell wall formation to optimize flag leaf architecture, providing a genetic strategy for maximizing yield under high-density cultivation.

plant biology↗

bioRxiv2026

Deep nanoparticle protein corona plasma proteomics resolves a stage-specific peripheral signature of Alzheimer's disease

Structured AbstractO_ST_ABSINTRODUCTIONC_ST_ABSAlzheimers disease (AD) progresses over decades, yet plasma biomarkers that resolve disease stage rather than simply detect disease remain scarce. This distinction is clinically consequential because effective AD intervention depends on identifying patients before disease biology has progressed beyond a therapeutically responsive stage. METHODSWe used small-molecule-modulated protein corona proteomics to profile plasma from 90 individuals in the Australian Imaging, Biomarker and Lifestyle cohort, stratified by Centiloid (CL) A{beta}-amyloid burden (30 amyloid- negative, CL < 15; 30 moderate-to-high, CL 26 to 100; 30 very high, CL > 100). We quantified 3,176 proteins and applied differential abundance and actual causality analyses to identify stage-specific and candidate causal proteins. RESULTSDifferential protein abundance was exclusively captured during the moderate-to-high AD transition, revealing a discrete proteomic "switch." The switch was marked by accumulation of the autophagy receptor CALCOCO1, together with coordinated depletion of the S100A8/S100A9 calprotectin complex and core erythroid-cytoskeletal network structural markers (e.g., SPTA1, SPTB, ANK1). Adhesion G protein-coupled receptor G6 (ADGRG6) showed a significant moderate positive monotonic association with absolute CL burden, providing a proportional molecular anchor for cumulative disease burden. Actual causality analysis identified COL6A2, FOXRED2, P3H1, PRR4, and GOLGA5 as candidate upstream drivers linking matrix remodeling, Golgi trafficking, and collagen processing to AD progression. DISCUSSIONThese findings suggest a candidate blood-accessible framework for staging AD by active disease biology, which, if replicated in independent cohorts, may have implications for therapeutic selection and mechanism-guided clinical trials. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/740710v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1ead718org.highwire.dtl.DTLVardef@cfa523org.highwire.dtl.DTLVardef@62a367org.highwire.dtl.DTLVardef@1d5c9a5_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

Comparing Nonlinear Trajectories Across Brain Networks: A Key to Understanding Complex Brain Dynamics

This study explores the nonlinear developmental trajectories of brain networks in neurotypically developing infants during their first six months. Using a longitudinal dataset of 137 resting-state functional MRI scans from 74 infants, we analyzed five spatial metrics across 13 intrinsic connectivity networks, including motor, visual, subcortical, and prefrontal networks. A cubic model was specifically employed to capture distinct linear and non-linear trends in the networks developmental patterns, allowing for the identification of significant differences in cubic, quadratic, and linear slope parameters across networks. This model choice was driven by the need to examine how specific non-linear components (e.g., inflection points and acceleration rates) uniquely characterize each networks trajectory, which a generalized approach might smooth out without pinpointing such network-specific features. Notably, the subcortical network exhibited a distinct cubic growth pattern, while secondary motor and visual networks showed pronounced quadratic variations, suggesting network-specific shifts in spatial organization and connectivity. These findings highlight the unique maturation timelines and interactions between functional systems, such as early sensory-motor coordination and later cognitive integration. The results underscore the importance of network-specific growth patterns, providing deeper insights into how infant brain networks evolve and interact to support emerging cognitive and behavioral functions.

neuroscience↗

bioRxiv2026

Transcriptomic analysis of cecal mucosal immunity in SPF White Leghorn chicks infected with precocious and parent strains of Eimeria tenella

Eimeria tenella (E. tenella) preferentially invades the cecum of young chickens and causes enormous economic losses to the global poultry industry. In this study, chick infection models of virulent parent strain and precocious attenuated line were established with schizogony (2 dpi) and gametogony (6 dpi) as two critical sampling time points. Combined with pathogenicity detection, transcriptome sequencing, mucosal immune index measurement and homologous challenge protection assays, we systematically deciphered the differential molecular mechanisms underlying pathogenicity and immune regulation between the two strains. Pathogenicity results showed that increased infection dosages suppressed weight gain and aggravated bloody diarrhea and oocyst shedding in both strains. In particular, infection with 1 x 105 sporulated oocysts of the parent strain caused massive chick mortality, while the precocious line exhibited markedly lower virulence. Transcriptomic data revealed that gametogony (6 dpi) represented the peak of host immune response. The parent strain persistently overactivated the NF- {kappa}B - mediated positive feedback cascade of coagulation and complement as well as ECM remodeling, triggering steroid metabolic disorder and antioxidant exhaustion, which ultimately induced severe hemorrhagic necrosis of the cecum. By contrast, the precocious line specifically activated the PPAR - {gamma} signaling pathway to negatively restrain excessive inflammation, accompanied by enriched TLR signaling and leukocyte transendothelial migration pathways, thereby forming an immune cascade of "lipid anti - inflammation - pathogen elimination - mucosal repair". Immunoprotection trials verified that priming with 1 x 104 sporulated oocysts of the precocious line significantly alleviated cecal lesions and reduced oocyst output upon secondary challenge, conferring stable mucosal immune protection. The expression trends of seven hub genes (PPARG, PLIN1, CYP1A1, THBS1, FMO4, CYP2C18, CYP14) detected via qRT - PCR were consistent with RNA - seq data. This study identified a dual regulatory paradigm consisting of NF - {kappa}B - mediated tissue injury and PPAR - {gamma} - dependent anti - inflammatory responses, refined the mucosal immune theoretical framework for commercially available precocious attenuated strains, and provided candidate molecular targets for targeted anti - coccidial intervention in chickens.

microbiology↗

bioRxiv2026

Chemokine-Dependent Natural Killer Cells Prevent Pulmonary Metastasis in a Newly Established Mouse Osteosarcoma Model

Rampant genomic instability of osteosarcoma (OS) and associated inter- and intratumoral heterogeneity convey a high risk of metastasis despite contemporary multimodal therapy. A mouse primary OS tumor model, originating from Myc-overexpressing Trp53-null mesenchymal progenitor cells, closely mimics cardinal genetic features and gene expression patterns of human OS samples. Subcutaneous injection of OS cells into immunocompromised NSG mice produced extensive metastases, whereas many fewer metastases occurred in T cell-deficient nude mice, suggesting a principal role for innate immunity in controlling OS dissemination. Depletion of natural killer (NK) cells in nude mice facilitated OS metastasis. OS cells released a suite of chemokines, with CCL2 the most prominent. A genome-wide CRISPR/Cas9 screen in OS cells identified 11 genes, including Ccl2, whose loss facilitated pulmonary metastasis in nude mice. Disruption of CCL2 in OS cells partially phenocopied the effects of antibody-dependent NK cell depletion, underscoring a plausible OS-NK signaling pathway that limits OS metastasis. SignificanceOsteosarcoma exhibits complex genomic instability and a propensity for pulmonary metastasis that limit chemotherapeutic response and patient survival. Despite the plethora of heterogeneous genetic alterations that connote poor prognosis, a novel preclinical in vivo model for studying metastasis highlights potentially targetable signaling between osteosarcoma cell-derived chemokines and pulmonary NK cells.

cancer biology↗

bioRxiv2026

Massively parallel characterization and predictive modelling of neuronal regulatory variation

Disease-associated variants reside frequently in noncoding cis-regulatory elements (CREs), yet their functional consequences remain poorly understood. We performed a large-scale lentiMPRA in human excitatory neurons, quantifying the impact of >46,000 naturally occurring variants across >27,000 candidate CREs near 524 disease-associated genes. These data improved regulatory variant effect predictions beyond state-of-the-art models. Significant allelic effects occurred at comparable rates across common, rare, and singleton variants, demonstrating that, within MPRA-measurable effects, population frequency carries limited information about per-variant regulatory impact. Variant effect detectability and magnitude were governed primarily by baseline activity of the enclosing regulatory element and local sequence context. Regulatory effects were distributed across numerous transcription factors rather than concentrated in master regulators, consistent with a combinatorial enhancer architecture. We establish a large-scale functional variant catalog and provide a complementary benchmark and resource for developing and evaluating models of noncoding regulatory variation.

genetics↗

bioRxiv2026

Systematic Development of a Compact Genome-Editing Tool Leveraging the TAM-Independent DNA Nuclease TasR in Bacillus subtilis

Bacillus subtilis is a core microbial chassis in biomanufacturing, and establishing efficient gene editing technologies is key to engineering this strain. In conventional CRISPR gene editing technologies, the large size of DNA nucleases leads to difficulties in plasmid construction, low transformation efficiency, and cumbersome multi-round editing operations; therefore, developing miniature gene editing tools can effectively address these issues. Although our group previously established a miniature gene editing tool based on IscB in B. subtilis SCK6, IscB relies on the 5'-CAGGAA-3' TAM recognition sequence, and 83.36% of the genes in the SCK6 genome harbor no or only one TAM sequence, indicating a bottleneck of restricted editing for IscB in this strain. The novel miniature DNA nuclease TasR does not require a TAM sequence and can thus compensate for the limitation of IscB; however, the applicability of TasR in B. subtilis remains unknown. Therefore, this study first constructed a single plasmid, pBsuTasR, capable of expressing TasR and its guide RNA (tigRNA), which enabled gene deletion of regular-sized fragments in SCK6 with editing efficiencies of 21.7%- 78.3%. Subsequently, the capacity of TasR to delete a long DNA fragment (169.9 kb) was evaluated, and it was found that under the guidance of a single tigRNA, the deletion efficiency was 21.73%, whereas after optimizing to two tigRNAs, the efficiency increased to 39.13%. Furthermore, the gene integration capability of pBsuTasR was further tested, and TasR was able to integrate the aprN gene into the amyE locus at an efficiency of 13.3% under the guidance of a single tigRNA, and after increasing to two tigRNAs, the integration efficiency increased to 91.3%. In terms of iterative genome editing, this study developed the pBsu-SRP (Scissors-Rock-Paper) iterative editing system, which automatically cures the editing plasmid from the previous round while performing a new round of gene editing, with sequential gene deletion efficiencies of 4.34%-26.08%, and using this system, the editing cycle can be shortened from 4N days by the conventional method to 3N+1 days. Subsequently, the pBsu-SRP system was successfully used to achieve the integration of two and three copies of the mCherry fluorescent reporter gene in SCK6, and it was found that the fluorescence intensity increased with the copy number. Finally, this study also explored the escape of SCK6 from TasR cleavage and found that mutations in the tigRNA sequence are the cause of the escape. In summary, this study constructed a novel miniature genome editing system in B. subtilis using the TAM-independent nuclease TasR as the core component. This system can not only provide an efficient technical tool for genetic manipulation of industrial microorganisms, but also offer new instrumental support for the iterative engineering and functional optimization of chassis cells in biomanufacturing.

molecular biology↗

bioRxiv2026

CXCR6 marks polyfunctional effector CD4 T cells required for anti-Chlamydia immunity in the female reproductive tract

CD4 T cells are essential for protective immunity against Chlamydia in the female reproductive tract (FRT), yet the characteristics of protective mucosal effector CD4 T cells remain poorly defined. We previously identified the transcription factor BHLHE40 as a key regulator of polyfunctional effector CD4 T cell differentiation during Chlamydia infection. Here, we identify the chemokine receptor CXCR6 as a marker of these protective T cells. Following intravaginal Chlamydia muridarum infection, Bhlhe40-deficient mice exhibited reduced frequencies of CXCR6 CD4 T cells that correlated with impaired bacterial control. CXCR6 expression on T cells was associated with loss of stem-like features and acquisition of an effector phenotype. Compared with CXCR6- cells, CXCR6 CD4 T cells displayed enhanced proliferation and polyfunctionality by co-producing cytokines IFN-{gamma}, IL-17A, and GM-CSF. Although CXCR6 was dispensable for CD4 T cell homing to the FRT, it promoted localization to the infected epithelium and the emerging memory lymphoid clusters. Importantly, depletion of CXCR6 CD4 T cells reduced polyfunctional effectors and impaired bacterial clearance. Collectively, these findings identify CXCR6 as a marker of protective polyfunctional CD4 T cells and implicate CXCR6-dependent tissue positioning as a key component of effective mucosal immunity, highlighting CXCR6 as a potential biomarker for Chlamydia vaccine development.

immunology↗

bioRxiv2026

IgGM2: An All-Atom Foundation Model for Adaptive Immune Receptor Design

Accurate immune receptor design requires modeling the coupled variation of aminoacid sequence, full-atom conformation, and target-binding geometry across antibodies, nanobodies, and T-cell receptors (TCRs). Existing methods often address only part of this problem, either by separating structure generation from sequence design, relying on fixed-backbone inverse folding, or focusing on a single receptor class. We introduce IgGM2, a unified all-atom generative framework for immune receptor structure prediction and CDR sequence-structure co-design. IgGM2 follows a structure-to-design strategy: it first learns how immune receptors are positioned around fixed target structures, and then transfers this target-conditioned structural prior to CDR design. Unlike modular design pipelines, IgGM2 jointly generates CDR residue identities and full-atom receptor structures, allowing frame-work geometry to adapt to designed CDRs without separate inverse folding or external sidechain packing. Unlike continuous residue encodings based on virtualatom geometry, IgGM2 keeps sequence prediction explicit while using atom14 placeholders only for full-atom representation. On structure prediction benchmarks, IgGM2 better captures receptor-target spatial relationships than AlphaFold3 on FoldBench and achieves strong performance on TCR-pMHC modeling. On sequence design benchmarks, IgGM2 achieves competitive amino-acid recovery and improves Rosetta-based interface preference metrics, suggesting more favorable generated binding interfaces. These results support IgGM2 as a unified all-atom framework for adaptive immune receptor structure prediction and design.

bioinformatics↗

bioRxiv2026

Endothelial Baf60c in BPD-Associated Pulmonary Hypertension

BACKGROUNDBronchopulmonary dysplasia-associated pulmonary hypertension (BPD-PH) complicates prematurity and carries substantial morbidity in extremely preterm infants. Pulmonary microvascular endothelial cell (PMVEC) dysfunction promotes capillary rarefaction and vascular remodeling, but epigenetic mechanisms after neonatal hyperoxia are poorly defined. Baf60c (SMARCD3), a SWI/SNF subunit supporting vascular homeostasis, and Smarcc2 (BAF170), a PBAF scaffold subunit linked to proliferative signaling, have not been studied together in BPD-PH. METHODSNeonatal C57BL/6 mice were exposed to 85% oxygen for 14 days. Right ventricular systolic pressure (RVSP), right ventricular hypertrophy, lung weight index, and pulmonary histopathology were assessed; PMVEC proliferation, migration, and invasion were measured. Transcriptome sequencing with GO/KEGG analyses, siRNA knockdown, LY294002 inhibition, coimmunoprecipitation, and Western blotting mapped the Baf60c-Smarcc2-PI3K-Akt-mTOR axis. A Tie1-driven, lung-tropic adeno-associated virus delivered by superficial facial vein injection at postnatal day 1 enabled PMVEC-specific Baf60c overexpression. RESULTSHyperoxia increased RVSP, right ventricular hypertrophy, and lung weight index, impaired alveolarization, reduced capillary density, and promoted arteriolar remodeling. PMVEC function was impaired, with PI3K-Akt pathway enrichment and suppressed signaling. Hyperoxia decreased Baf60c and increased Smarcc2. Baf60c knockdown upregulated Smarcc2, suppressed PI3K-Akt-mTOR, and phenocopied hyperoxia; Smarcc2 knockdown had opposite effects. Baf60c bound Smarcc2 but not PI3K. PMVEC-specific Baf60c overexpression attenuated pulmonary hypertension and right ventricular hypertrophy and partially improved alveolar and microvascular injury. CONCLUSIONSHyperoxia-induced BPD-PH is associated with reduced Baf60c, increased Smarcc2, and suppressed PI3K-Akt-mTOR signaling in PMVECs. Baf60c may indirectly regulate this pathway through Smarcc2. Endothelial Baf60c is a potential therapeutic target in BPD-PH. Novelty and RelevanceO_ST_ABSWhat Is New?C_ST_ABSA neonatal hyperoxia BPD-PH model was characterized with adverse hemodynamic and pulmonary vascular endpoints together with PMVEC functional impairment. Hyperoxia downregulates Baf60c, upregulates Smarcc2, and suppresses PI3K-Akt-mTOR signaling in PMVECs. Baf60c interacts with Smarcc2 without direct PI3K binding. PMVEC-specific Baf60c overexpression via superficial facial vein AAV delivery ameliorates pulmonary hypertension. What Is Relevant?BPD-PH is a developmental pulmonary hypertension phenotype in which pulmonary vascular resistance and right ventricular load are measurable with RVSP and Fulton index, consistent with Group 3 PH biology. SWI/SNF-mediated chromatin remodeling in pulmonary endothelium may link neonatal oxygen injury to impaired angiogenic endothelial function. Clinical/Pathophysiological Implications?Endothelial Baf60c deficiency may contribute to pulmonary vascular rarefaction after neonatal hyperoxia. Restoring endothelial Baf60c may improve pulmonary hemodynamics in BPD-PH, although structural lung injury may be only partially reversible.

physiology↗

bioRxiv2026

Family Conflict and Parent-Child Similarity in Affective Valuation

How children come to evaluate social-affective cues is shaped within the family, yet the neural expression of this process and its dependence on family relationships remain unclear. We tested whether parent-child similarity in the neural coding of affective judgment varies with family environment, and whether it relates to youth affective distress. Twenty-five parent-child dyads (youth, mean age 11.8; parents mean age 42 years) judged faces morphed along an angry-to-happy continuum as positive or negative during fMRI. For each participant, we defined an evaluative choice axis distinguishing faces judged positive from negative, independent of expression intensity. Using searchlight-based parent-child cross-decoding, we tested whether one dyad members evaluative coding predicted the other members judgments, indexing shared evaluative coding rather than shared sensitivity to expression intensity. Inference focused a priori on medial prefrontal cortex. There was no reliable average parent-child neural similarity across the sample. Instead, higher family conflict was associated with lower parent-child neural similarity in ventromedial prefrontal cortex (vmPFC). Demonstrating specificity to negative relational strain, this effect was not observed for complementary dimensions of family cohesion or identity. Moreover, the effect was specific to true dyads rather than random pairings and to vmPFC rather than a face-selective network or other medial prefrontal regions. Lower vmPFC similarity showed a preliminary association with higher youth affective distress. These findings indicate that affective valuation, rather than sensory encoding, may be a representational level at which perceived family conflict is reflected in parent-child neural similarity.

neuroscience↗

bioRxiv2026

Basal Internalization and Subcellular Localization of XCR1

Chemokines orchestrate immune cell trafficking through receptor-mediated signaling and are implicated in inflammatory, autoimmune, and neuropathic disorders. The XCL1-XCR1 axis is of particular interest because XCR1 is selectively expressed on mature conventional type 1 dendritic cells (cDC1s), where it supports communication with activated CD8+ T cells and NK cells and promotes antigen cross-presentation. This selectivity has made XCR1 an attractive target for dendritic cell-based cancer vaccines, while emerging evidence also links XCL1-XCR1 signaling to neuroinflammation and pain. Despite its therapeutic potential, the mechanisms governing XCR1 activation and trafficking remain understudied. Here, we characterize XCR1 expression, membrane trafficking, and basal internalization to define mechanisms that may influence therapeutic targeting. We show that XCR1 undergoes constitutive internalization through a {beta}-arrestin-independent but adaptor protein 2 (AP2)-dependent pathway, distinguishing it from other chemokine receptors with constitutive endocytosis. Furthermore, we identify specific sequence motifs critical for its subcellular localization and intracellular trafficking. These findings provide new mechanistic insights into XCR1 regulation and may inform the development of targeted therapeutics and antigen-delivery strategies in cancer and inflammation.

pharmacology and toxicology↗

bioRxiv2026

Endothelial KRAS G12V signaling drives aberrant morphogenesis and establishes an AVM transcriptional identity in primary human endothelial cells

Somatic activating mutations in KRAS are found in the endothelium of the majority of sporadic brain arteriovenous malformations (bAVMs), yet the consequences of oncogenic KRAS signaling in endothelial cells during active vessel morphogenesis remain incompletely characterized. We expressed KRASG12V in primary human umbilical vein endothelial cells using a doxycycline-inducible lentiviral system and examined morphogenic behavior, proliferation, migration, and transcriptional output in a three-dimensional planar co-culture angiogenesis assay. KRASG12V-expressing cells failed to organize into vessel-like networks, instead forming compact sheet-like structures that persisted through day 12. A transient proliferative phase at days 3-5 resolved to control levels by day 12, consistent with preserved sensitivity to contact inhibition rather than unrestricted growth. Enhanced migration at day 5 was accompanied by upregulation of a focal adhesion and matrix remodeling program centered on ITGB3, PLAU, PLAUR, and PIK3CG. Translating ribosome-affinity purification sequencing (TRAP-seq) of the EC-specific translatome across four independent donor pools revealed progressive acquisition of an AVM-associated transcriptional identity by day 12, including upregulation of ACVRL1, ENG, JAG1, NOTCH1, ANGPT2, and TEK, with concordance to human bAVM nidus endothelium at both the gene and pathway level. Pharmacological inhibition with Alpelisib (PI3K), Trametinib (MEK), and Pazopanib (VEGFR2) demonstrated that PI3K is the principal organizer of the morphogenic phenotype. These findings characterize a KRASG12V-driven program in endothelial cells that recapitulates core transcriptional features of bAVM endothelium in a primary cell model.

Cell Biology↗

bioRxiv2026

Defining biologically directed therapy target signatures in urothelial carcinoma: A transcriptomic framework for precision therapy

IntroductionNectin-4 targeting antibody-drug conjugate (ADC) enfortumab vedotin (EV), in combination with pembrolizumab, is the first-line treatment for patients with locally advanced or metastatic urothelial carcinoma (UC). Optimal treatment strategies for patients who are non-responders or progress on EV with pembrolizumab remain an unmet clinical need. We sought to characterize ADC and immunotherapy (IO)-associated target expression profiles to identify candidate therapeutic vulnerabilities beyond EV. MethodsWe conducted a literature review to identify ADC and IO targets with approved or investigational relevance in UC. Unsupervised hierarchical clustering was used to identify clusters of target gene expression in RNA-seq data. Transcriptomic clustering analyses were performed in 434 patients from The Cancer Genome Atlas Bladder Urothelial Carcinoma cohort (TCGA-BLCA) and validated in an independent cohort of 478 patients from the Oncology Research Information Exchange Network (ORIEN) consortium. Proteomic interrogation of these targets was performed using mass spectrometry data from additional cohort of 116 patients. Differential gene expression analyses evaluated associations between target expression patterns, histologic variants, and consensus molecular subtypes of muscle-invasive bladder cancer (CMIBC). ResultsWe identified 13 ADC and 10 IO-associated targets with translational relevance in UC. Transcriptomic analyses revealed three reproducible clusters of overexpressed target genes across independent cohorts: 1) a luminal/epithelial-associated cluster enriched for VTCN1, SLITRK6, FGFR3, NECTIN4, TACSTD2, ERBB2, and ERBB3; 2) an immune target predominant cluster enriched for BTLA, LAG3, PDCD1, TIGIT, CTLA4, TNFRSF9, TNFRSF18, TNFRSF4; and 3) a basal/neuroendocrine-associated cluster characterized by CD274, F3, NT5E, EGFR, MET and DLL3. Similar clusters were largely conserved at the proteomic level. Adenocarcinomas overexpressed ERBB3 compared to neuroendocrine and squamous cell carcinomas. Pure squamous cell carcinomas overexpressed TACSTD2 compared to adenocarcinomas. In CMIBC subtypes, basal/squamous tumors expressed higher levels of CD274, EGFR, F3, LAG3, NT5E, and TNFRSF18, whereas luminal tumors demonstrated higher ERBB2 and ERBB3 expression. Neuroendocrine-like tumors showed higher DLL3 expression compared to all other subtypes. Tumors with low expression of NECTIN4, TACSTD2, and FGFR3 were enriched for alternative targets including DLL3, CD274, and CD276. Our findings provide a framework for hypothesis-driven therapeutic prioritization in advanced UC. Conclusions: UC is characterized by reproducible, biologically distinct patterns of ADC and IO target expressions. The degree of expression of NECTIN4 was positively associated with TACSTD2, FGFR3 and inversely associated with DLL3, CD276, and CD274, supporting alternative biologically informed treatment strategies besides EV . Histologic variants and molecular subtypes of UC also display distinct patterns of target expression. This study provides the first integrated transcriptomic framework linking ADC and IO target co-expression patterns for hypothesis-driven therapeutic prioritization. These findings provide a basis for rational ADC and immunotherapy development in advanced UC and support prospective proteomic validation in treatment stratified cohorts. Statement of Translational RelevanceEnfortumab vedotin plus pembrolizumab has redefined first-line therapy for advanced urothelial carcinoma, yet treatment selection following resistance or progression remains undefined. In this study, we integrate transcriptomic and proteomic analyses across independent cohorts to define reproducible patterns of antibody-drug conjugate (ADC) and immunotherapy target co-expression in urothelial carcinoma. We identify biologically distinct target-expression patterns that are associated with histologic and molecular subtypes and demonstrate coordinated and, in some cases, mutually exclusive relationships among therapeutically actionable targets. These findings have direct translational implications. First, they provide biologic rationale for rational sequencing and combination strategies based on co-expressed targets in NECTIN4-enriched tumors. Second, they identify alternative therapeutic vulnerabilities, including DLL3- and CD274-associated pathways, in tumors with low NECTIN4 expression, a population potentially enriched for resistance to EV-based therapy. Finally, this framework establishes a foundation for biomarker-driven clinical trials in urothelial carcinoma and supports the development of precision therapeutic approaches beyond current standards.

cancer biology↗