Biology subjects

Tran, T.

Publications and source records attributed to Tran, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease

Single-cell studies have defined immune states in inflammatory bowel disease (IBD), but how adaptive receptor histories organize circulating immunity remains unclear. We generated a single-cell transcriptomic atlas of peripheral blood from 249 participants with Crohn's disease, ulcerative colitis, or non-IBD control status, including 182 with productive TCR and BCR recovery. Expanded TCR clonotypes marked inflammatory-memory and cytotoxic states, while distinct but similar paired TCRs shared inflammatory programs across participants. BCR lineage maturation linked IgA-associated mucosal and plasma B cell programs to somatic mutation and class switching, distinguishing maturation-associated biology from clonal expansion. Helper, regulatory, and cytotoxic T-cell programs covaried with B-cell states, and inferred interactions nominated reciprocal antigen-presentation and helper pathways. Repertoire-based machine learning distinguished diagnosis, inflammation, and contemporaneous six-month treatment-response status. Together, this atlas connects receptor architecture to coordinated systemic immune remodeling, establishes a foundation for repertoire-informed patient stratification, and prioritizes candidate mechanisms of IBD pathogenesis.

immunology↗

bioRxiv2026

A beneficial bacteria influences myo-inositol homeostasis to protect plants during drought

Exposure to abiotic stress is one of the primary factors limiting crop productivity with drought stress is the most prevalent. Under drought, plants can produce osmolytes that increase water retention and prevent severe drought symptoms. Plant responses by extension also impact their associated root microbiomes through altered root metabolite concentrations and exudation. For example, myo-inositol (MI) serves as a precursor to osmolytes and also serves as a mediator for plant-microbe interactions in Arabidopsis thaliana (Arabidopsis). Here, we inoculated plants with Pantoea sp. R4 (R4), an isolate that can catabolize MI, and subjected them to drought. We observed that R4 colonized plants experiencing drought maintained their leaf relative water content while uninoculated planted did not, and that this colonization coincided with enrichment of MI in the shoots and depletion of MI in the roots. Interestingly, exogenous MI alone rescued water retention in wild-type Col-0, but not in int1 mutants, which lack the tonoplast MI transporter. Together, our results show that R4 colonization under drought conditions increases MI in the shoots, that this accumulation is associated with increased leaf water retention, and that INT1-mediated MI transport is required for this protection. Our results suggest that microbial colonization can alter how MI is localized in plants, which can inform future development of treatments to protect plants from drought.

microbiology↗

bioRxiv2026

Spatial immune ecosystems govern therapeutic response in HER2-low breast cancer

HER2 low breast cancer represents a clinically important but biologically heterogeneous disease state, and the spatial immune programs underlying therapeutic response remain poorly understood. Here, we used single-cell spatial transcriptomics to characterize HER2 low and HER2 high breast tumors and define microenvironmental features associated with treatment sensitivity and resistance. We identified diverse malignant, stromal, and immune compartments, with dendritic cells emerging as a highly remodeled population in HER2 low tumors. Focused analysis resolved distinct dendritic cell states, including homeostatic cDC2, IFN activated mature cDC, classical functional cDC2, plasmacytoid DC, and ITGAX positive monocyte derived DC populations. Spatial proximity analysis further revealed that resistant HER2 low tumors exhibited increased segregation of tumor epithelial cells from effector immune populations and enrichment of myeloid-rich immune niches, consistent with an immune-restricted spatial architecture. Independent TCGA BRCA validation confirmed the clinical relevance of these dendritic-cell states, with elevated homeostatic cDC2 signatures predicting poor survival, whereas inflammatory dendritic cell signatures were associated with favorable outcomes. Resistant HER2 low tumors were characterized by enrichment of homeostatic and classical cDCs, depletion of IFN-activated cDCs and pDCs, altered tumor myeloid T cell communication, and expansion of spatially organized resistant niches, whereas sensitive tumors retained immune-intermixed niches enriched for antigen presentation and effector immune interactions. Together, these findings demonstrate that therapeutic resistance in HER2 low breast cancer is driven by coordinated spatial remodeling of dendritic-cell states and immune architecture, identifying dendritic cell myeloid niche organization as a potential biomarker and therapeutic vulnerability.

cancer biology↗

bioRxiv2026

A NON-CANONICAL ROLE FOR NOTCH3 IN BUILDING THE INTESTINAL LYMPHATIC NICHE

Lymphatic dysfunction drives severe and often intractable human diseases, yet the cellular mechanisms that establish functional lymphatic vasculature remain poorly understood. In the intestine, lacteals are specialized lymphatic vessels that absorb dietary lipids and rely on surrounding villus smooth muscle to propel lymph, forming the muscular-lacteal complex (MLC). How distinct mesenchymal populations coordinate assembly of this functional lymphatic unit remains unknown. By integrating developmental single-cell profiling, genetic lineage tracing, conditional mouse genetics, and functional assays of lipid absorption, we identify Notch3 as a central organizer of MLC development that coordinates communication between distinct mesenchymal lineages. While Notch3 promotes smooth muscle differentiation within the PDGFR lineage, PDGFR{beta} lineage cells do not directly contribute to villus smooth muscle. Instead, they function as Notch3-dependent signaling hubs that instruct expansion and differentiation of neighboring PDGFR smooth muscle progenitors via paracrine TGF{beta} signaling. Loss of Notch3 in PDGFR{beta} cells disrupts MLC development, impairs intestinal lipid absorption, and causes postnatal growth failure and lethality. Restoration of TGF{beta} signaling rescues the structural, functional, and survival defects caused by Notch3 loss, identifying TGF{beta} as a critical downstream effector of the Notch3 pathway. Furthermore, selective inhibition of canonical Notch signaling in the PDGFR{beta} lineage fails to phenocopy Notch3 deletion, revealing a non-canonical mechanism of Notch3 function in intestinal mesenchymal development. Together, these findings establish PDGFR{beta} cells as essential mesenchymal signaling organizers and define a new paradigm in which lineage-specific, non-canonical Notch3 signaling coordinates villus stromal communication to build a functional intestinal lymphatic niche.

developmental biology↗

bioRxiv2026

Phenotypic CRISPR screening identifies ZBTB10 as a novel regulator of human trophoblast differentiation

The human placenta is built by trophoblast cells that fuse together, secrete hormones, and invade the uterus, and defects in these processes contribute to pregnancy disorders such as preeclampsia. Because cell-cell fusion and hormone secretion are inherently non-cell-autonomous processes, their regulators have remained inaccessible to conventional pooled CRISPR screens. Here, we developed an arrayed CRISPR screen in fusogenic BeWo trophoblasts that simultaneously quantifies fusion and hCG secretion across 412 gene perturbations. The screen revealed that these two hallmark functions of trophoblast differentiation are genetically separable. We characterized the strongest novel hit, ZBTB10, in trophoblast stem cells, organoids, and placental tissue and find that ZBTB10 is an essential regulator of human trophoblast differentiation. ZBTB10 is required for invasive extravillous trophoblast differentiation and supports syncytiotrophoblast maturation, establishing it as a cross-lineage regulator that both activates and represses distinct trophoblast fate programs. Together, these findings provide a genetic platform and phenotypic dissection of how regulatory networks control human placental development.

cell biology↗

bioRxiv2026

Chitinase-3-like protein 1 decodes chitosan acetylation patterns into toll-like receptor 2 signaling through heparan sulfate

Chitinase-3-like protein 1 (CHI3L1), which is associated with a wide range of inflammatory diseases, lacks chitinase activity but retains the ability to bind chitin and chitosan. Chitin is a major component of fungal cell walls, whereas chitosan is used in biomedicine. In addition to chitosan, CHI3L1 has been proposed to interact with heparan sulfate (HS), a highly sulfated glycosaminoglycan on mammalian cell surfaces. Here, we investigated how interactions with chitosan and HS regulate the pro-inflammatory activity of CHI3L1. Mapping of the chitin-binding cleft revealed preferential binding of CHI3L1 to chitosans with a regular acetylation pattern that, together with CHI3L1, promoted toll-like receptor 2 signaling. We further identified a dominant HS-binding site that recognizes a distinct HS sulfation code containing a coherent motif of N- and 6-O-sulfations. Mutation of this HS-binding site or impaired HS biosynthesis prevented CHI3L1 accumulation at the cell surface and abolished CHI3L1-mediated cell activation. Together, our findings establish HS as a critical co-receptor for CHI3L1 and reveal a pro-inflammatory cross-talk between HS, CHI3L1, and chitosan that may contribute to host defense against fungal pathogens and responses to chitosan-based biomaterials. These findings identify HS- and chitosan-dependent CHI3L1 signaling as a potential target for modulating inflammatory responses.

Molecular Biology↗

bioRxiv2026

FOXP3-engineered regulatory T cells restore intestinal barrier integrity in Crohn's disease enteroids via PDGF-AA

Epithelial regeneration and barrier integrity are impaired in inflammatory bowel diseases, including Crohns disease (CD), yet current therapies largely target immune inflammation without directly promoting mucosal repair. While regulatory T cells are classically immunomodulatory, their capacity to directly support human intestinal stem cells (ISCs) and barrier function remains unclear. In this study, we tested the hypothesis that FOXP3-expressing regulatory T cells--engineered CD4LVFOXP3 and thymic-derived Treg (tTreg)--directly support human ISC maintenance and restore epithelial barrier function independent of their immunomodulatory function. Using CD patient ISCs-derived enteroids that display disease-associated damage, we established co-culture with FOXP3-engineered Treg cell-CD4LVFOXP3 or thymic-derived Treg (tTreg). The presence of either CD4LVFOXP3 or tTreg cells enhanced enteroid growth, improved epithelial barrier function, and restored apical-basal polarity of ISCs, indicating reparative capacity. Conversely, activated conventional CD4+ T cells reduced barrier function and abrogated apical-basal polarity. Integrating secretome profiling with ligand add-back and receptor or ligand blockade, we identify the PDGF-AA-PDGFR axis as a key regulator of Treg-mediated intestinal epithelial barrier integrity, but dispensable for Treg suppressive capacity. Collectively, our data delineate a direct, human tissue-intrinsic role of FOXP3-driven Treg in the interaction with ISCs via PDGF-AA-PDGFR, enhancing epithelial barrier function and positioning CD4LVFOXP3 as a treatment approach coupling immunoregulation with epithelial repair. One Sentence SummaryRegulatory T cells improve the intestinal epithelial barrier function, primarily, through the PDGF-AA-PDGFR axis

immunology↗

bioRxiv2026

Fasting disrupts the InsP6 HDAC3 axis to drive ER stress-mediated clearance of DNA-damaged cells and enforce tissue quality control.

Fasting drives metabolic adaptation but also elicits acute cellular stress. How this stress shapes tissue integrity is unknown. Here, we show that in the intestine, fasting depletes growth factor signaling, which triggers cellular stress. This response functions as a tissue quality-control checkpoint that selectively eliminates pre-existing DNA-damaged cells while sparing healthy counterparts. A short-term fast diminishes TGF-{beta} signaling and elicits endoplasmic reticulum (ER) stress, driving DNA-damaged intestinal cells beyond an apoptotic threshold, thereby reducing the inflammatory burden. Mechanistically, loss of TGF-{beta} signaling triggers FBXO22-Cullin1-mediated degradation of the inositol kinase IPMK, leading to depletion of inositol hexaphosphate (InsP). InsP loss attenuates HDAC3 activity and initiates coordinated epigenetic and post-translational reprogramming, thereby increasing CDK5RAP3 abundance. Elevated CDK5RAP3 inhibits ribosomal RPL26 UFMylation, thereby amplifying ER stress and selectively licensing apoptosis in DNA-damaged cells. Collectively, fasting disrupts a TGF-{beta}-InsP6-HDAC3 axis to drive ER stress-dependent clearance of DNA-damaged cells, enforcing tissue quality control.

cell biology↗

bioRxiv2026

Chronic TGFβ1 Signaling Drives Aberrant Alveolar-Basaloid Metaplasia through a KRT17-Stratifin migratory complex

Chronic fibrotic disorders like idiopathic pulmonary fibrosis (IPF) are characterized by aberrant alveolar regeneration and severely limited treatment options. Identification of the mechanisms driving aberrant epithelial repair can lead to new viable therapeutic targets. Using integrated single nucleus ATAC- and RNA-sequencing on human lungs and an in vitro model of dysplastic repair, we identify two distinct regenerative trajectories for alveolar type 2 (AT2) cells: a resolvable euplastic repair trajectory and a persistent, non-resolving dysplastic repair trajectory. The latter is governed by a spatially restricted ITGB6/TGF {beta} 1/SMAD3 signaling axis in fibrotic regions of IPF lungs and in murine lungs characterized by chronic epithelial remodeling. Mechanistically, SMAD3 directly regulates dysplastic transitional cell (DTC) markers, including KRT17 and Stratifin. We show that TGF {beta} 1-induced physical interaction between KRT17 and Stratifin at the leading edge of migrating DTCs is essential for their migration. These findings collectively define the molecular regulation of AT2-driven dysplastic regeneration and identify TGF {beta} 1-induced KRT17-Stratifin axis as a central driver of AT2 remodeling and their migration in chronic fibrosis, highlighting a therapeutically targetable signaling axis.

cell biology↗

bioRxiv2026

Magnetogenetic control of endogenous calcium signaling via ROS-sensitive ion channels reveals astrocytic regulation of neural circuit activity

Astrocytes exhibit complex calcium signaling proposed to detect, integrate, and modulate neuronal activity; however, their causal contribution to neural circuit function remains unresolved. This is partly due to the lack of tools that recapitulate physiological astrocyte calcium signaling. Here, we show that experimental magnetic control of endogenous calcium signaling in astrocytes is sufficient to modulate neural circuit dynamics. Using pmFeRIC, a magnetogenetic tool for remote, noninvasive, and on-demand activation of endogenous calcium pathways, we demonstrate that selective activation of astrocyte calcium signaling drives neuronal activity. pmFeRIC uses magnetic fields and endogenous ferritin to generate localized reactive oxygen species (ROS) at the plasma membrane, activating native ROS-sensitive ion channels, inducing calcium influx. In hippocampal circuits in vitro, magnetic activation of endogenous astrocytic calcium signaling produced robust, state-dependent changes in neuronal circuit activity, in part by increasing presynaptic release probability, postsynaptic burst firing, and glutamatergic transmission. These effects were mediated by transient receptor potential channels, amplified by intracellular calcium stores, and abolished when astrocyte calcium signaling was disrupted, establishing a causal role in neural circuit dynamics. In vivo, pmFeRIC activates endogenous calcium signaling in astrocytes with kinetics comparable to locomotion-induced activity, enabling control of astrocyte calcium dynamics that resemble physiological behavioral responses. Together, these findings establish that endogenous astrocytic calcium signaling is sufficient to modulate neural circuit function and introduce a broadly applicable platform for cell-specific, wireless, on-demand control of endogenous calcium signaling through magnetic activation of ROS-sensitive ion channels.

neuroscience↗

bioRxiv2026

AI-2 Production in Fusobacterium nucleatum Is Subspecies-Specific and Uncoupled from Quorum Sensing

Autoinducer-2 (AI-2) is a LuxS-dependent product of the activated methyl cycle (AMC) that functions as a quorum-sensing signal in diverse bacteria. Fusobacterium nucleatum is a genetically heterogeneous oral anaerobe comprising four subspecies: nucleatum (FNN), vincentii (FNV), polymorphum (FNP), and animalis (FNA). Previous studies have reported that FNN and FNP strains produce AI-2 and have proposed that AI-2-mediated quorum sensing contributes to biofilm formation and virulence. However, the distribution and functional relevance of AI-2 across all subspecies have not been systematically examined. Here, we show that AI-2 production is restricted to FNA strains. Genomic analysis revealed that FNN and FNV lack luxS, whereas FNP carries a disrupted luxS homolog. Consistent with these findings, AI-2 bioassays using the Vibrio harveyi BB170 reporter detected AI-2 exclusively in FNA strains. Deletion of luxS in FNA abolished AI-2 production but resulted in minimal transcriptional changes, and exogenous AI-2 failed to elicit global gene expression responses in non-producing subspecies. These results demonstrate that AI-2 production in F. nucleatum is subspecies-specific and uncoupled from quorum sensing. Our findings revise current assumptions regarding AI-2-mediated communication in F. nucleatum and reveal previously unrecognized metabolic divergence within the species complex. IMPORTANCEPeriodontitis affects nearly half of adults in the United States and remains a leading cause of tooth loss worldwide. Fusobacterium nucleatum is a central member of oral biofilms and has also been linked to adverse pregnancy outcomes and colorectal cancer. Although AI-2-mediated quorum sensing has been proposed to contribute to its biofilm formation and virulence, our study demonstrates that AI-2 production is confined to subsp. animalis and is absent in other subspecies. Moreover, AI-2 does not function as a conserved quorum-sensing regulator in this species. These findings fundamentally revise prevailing assumptions about AI-2 signaling in F. nucleatum and suggest that subspecies-specific metabolic traits, rather than universal quorum sensing, may underlie ecological adaptation and host association.

microbiology↗

bioRxiv2026

STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics

Sequencing-based spatial transcriptomics technologies, including Visium HD and Stereo-seq, now enable transcriptome-wide profiling at subcellular resolution. However, these platforms generate measurements over spatially barcoded units rather than biologically segmented cells, creating a fundamental bottleneck for cell-centric analysis and interpretation. Robust recon-struction of coherent single-cell transcriptomes from high-density spatial bins remains an unresolved computational challenge. Here we present STCS (Spatial Transcriptomics Cell Segmentation), a platform-agnostic framework that reconstructs cell-level gene expression profiles by integrating nuclei segmentation with a joint transcriptomic-spatial distance model. STCS is governed by two interpretable parameters and incorporates a reference-free parameter selection strategy based on internal stability and spatial coherence metrics, enabling adaptable deployment across tissue types and technologies without requiring matched ground-truth annotations. We benchmark STCS on a Visium HD human lung cancer dataset with matched Xenium-derived cell segmentation, enabling direct cell-level validation, and on high-resolution Stereo-seq mouse brain data to assess cross-platform generalizability. Across multiple evaluation dimensions--including cell-type agreement, spatial organization, gene-expression fidelity, and compositional accuracy--STCS achieves consistent improvements over existing methods while preserving biologically coherent spatial structure. As sequencing-based spatial transcriptomics is rapidly adopted across biomedical research, STCS provides a broadly applicable and open-source solution for reconstructing cell-resolved transcriptomes, facilitating more reliable downstream analyses and cross-platform integration.

bioinformatics↗

bioRxiv2026

Proteogenomic Profiling Reveals a Distinct Endogenous p16INK4a-Associated Senescence Signature in the Human Ovary.

The tumor suppressor and cell cycle regulator, p16INK4a (p16), has been extensively linked to cellular senescence, and its accumulation can reflect endogenous senescence within ovarian tissue. However, gene and protein signatures associated with p16 have not been well defined in human tissue. We utilized immunohistochemical (IHC) staining for P16 to identify distinct positive (P16+) and negative (P16-) regions within the ovarian cortex and employed the GeoMx Digital Spatial Profiler for simultaneous proteomic and transcriptomic analyses on cortical tissue cores. Differential expression and translation between p16-positive and p16-negative cores identified genes and proteins that are cellular senescence related (e.g., CDKN1A, GADD45B, GADD45G, and MYC) or key regulators of the extracellular matrix (e.g., collagen I, ADAMTS4, and MMP11). Additionally, the transcriptomic signature identified here was significantly enriched for the spatially derived ovarian p16-associated signature, BuckSenOvary, but not for other senescence gene sets. Lastly, given the association between changes to the extracellular matrix in aged ovaries and ovarian cancer, we compared genes upregulated and downregulated in p16-positive regions relative to p16-negative regions against multiple ovarian cancer transcriptomic datasets. These findings provide new insight into the molecular landscape of naturally occurring ovarian senescence and its possible relationship to age-associated disease processes, including cancer development.

cell biology↗

bioRxiv2026

Developmental dysregulation of chandelier cell excitability in a mouse model of Dravet Syndrome

Chandelier cells (ChCs) are a rare and highly specialized sub-type of inhibitory neuron in the cerebral cortex that specifically and exclusively form synapses onto the axon initial segment of excitatory neurons and thereby exert powerful control of excitability. We applied a newly developed, cell type-specific enhancer element to label ChCs and assess their electrophysiological and morphological properties across development in Dravet Syndrome (Scn1a+/- mice), a prominent neurodevelopmental disorder defined by epilepsy and features of autism spectrum disorder. Dravet Syndrome is known to predominantly impact GABAergic interneurons. We found that ChCs from juvenile Scn1a+/- mice (postnatal day, P18-21) exhibit impaired excitability, and that deficits largely persist in young adulthood (P35-56). These findings are distinct from prior observations in the more common subtype of parvalbumin-positive interneurons, basket cells. We found no differences in the axonal or dendritic morphology of ChCs at either time point. Our results suggest a role for ChCs in the pathogenesis of Dravet Syndrome and constitute the first targeted study of ChC function in a specific genetically-defined neurodevelopmental disorder.

neuroscience↗

bioRxiv2026

antigen-prime: Simulating coupled genetic and antigenic evolution of influenza virus

Seasonal influenza virus undergoes rapid antigenic drift to escape population immunity. Computational methods can be used to organize viral genetic diversity into antigenically similar variants and estimate variantspecific growth rates. However, benchmarking these methods is challenging because it can be difficult to accurately quantify antigenicity and growth rates in nature. Simulating viral evolution using defined selective pressures can provide ground-truth data for benchmarking. But, existing simulators do not link genetic sequences to antigenic phenotypes under selection from host populations. Here, we present a forward-time epidemic simulator called antigen-prime that links these factors. We use it to simulate viral evolution over 30 years and validate the simulation recapitulates genetic and antigenic patterns observed in natural influenza evolution. We then use the simulated data to benchmark methods for assigning variants and estimating their growth rates. We evaluated a sequencebased and a phylogenetics-based method for variant assignment, finding the former was slightly more effective at separating viruses into antigenically distinct groups. We also evaluated methods for estimating variant growth rates in one-year sliding windows. Estimates were accurate in most windows, but highly inaccurate in several others. Examining higherror windows revealed several examples of a previously unreported failure mode. In all, antigen-prime provides a simulation framework to benchmark models of influenza evolution, and could be used to help guide future development of these models. The source code is openly available at https://github.com/matsengrp/antigen-prime.

bioinformatics↗

bioRxiv2025

Identification and Regulation of a Hepatic Lipogenic Metabolon

De novo lipogenesis (DNL) plays a key role in the excessive fat accumulation present in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). Most mechanistic studies and experimental strategies for improving hepatic steatosis in MASLD have focused on the transcriptional regulation of enzymes involved in DNL and triglyceride (TG) synthesis. Here, we provide evidence for a post-translational mechanism that enhances fatty acid (FA) and TG synthesis through the assembly of a multi-protein lipogenic metabolon in liver. Under anabolic conditions, acetyl-CoA carboxylase 1 (ACC1) interacts with additional key enzymes in the DNL and TG synthesis pathway. Immunofluorescence and electron microscopy reveal that this lipogenic metabolon localizes around lipid droplets (LDs) and in proximity to mitochondria and LD interfaces in the anabolic state. The formation of the lipogenic metabolon facilitates the efficient transfer of FA synthesis intermediates to enhance lipogenic flux. These findings uncover a new nutrient-responsive, post-translational regulatory mechanism for hepatic lipogenesis and highlight the lipogenic metabolon as a potential therapeutic target for metabolic liver diseases.

cell biology↗

bioRxiv2025

Glucocorticoids regulate the human non-coding genome

Glucocorticoids (GCs) are widely used anti-inflammatory and immunosuppressive agents known to induce dramatic changes in gene expression, yet their effects on non-coding RNAs such as long non-coding RNAs (lncRNAs) or microRNAs (miRNAs) remain poorly characterized. We present the first comprehensive and systematic analysis of GC regulation of the non-coding genome across nine human primary cell types from both hematopoietic and non-hematopoietic lineages. In vitro GC treatment was applied to each cell type, with transcriptomic profiling (total RNA-seq and small RNA-seq) at 2 and 6 hours post-treatment. We identified over 2,000 GC-responsive non-coding transcripts, including 654 annotated lncRNAs, 1,376 novel lncRNAs, and 39 miRNAs. The non-coding RNA response to GCs was highly cell type-dependent: 80% of GC-responsive lncRNAs and 97% of miRNAs were unique to a single cell type. Hematopoietic cells exhibited a greater magnitude of lncRNA induction than non-hematopoietic cells. Notably, dozens of facultative lncRNAs (undetectable at baseline) were induced de novo by GC. GC-responsive transcripts spanned diverse lncRNA classes, with enrichment of host lncRNAs. By contrast, only a limited number of miRNAs were GC-responsive. GC regulation of transcript abundance for miRNAs and their host lncRNAs appears to be independent. Our results, which are accessible through an interactive web application, establish a framework for studying how non-coding transcription contributes to physiological and clinical heterogeneity in GC responses. The newly identified GC-responsive non-coding transcripts could represent biomarkers of GC exposure, determinants of GC sensitivity or resistance, or candidate regulators of tissue-specific GC effects.

genomics↗

bioRxiv2025

Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics

Cellular senescence is implicated as a driver of ovarian aging, but senescent cells in the human postmenopausal ovary remain poorly defined. Using spatially resolved p16INK4a protein expression, a canonical senescence marker, we identified and mapped senescent cells in postmenopausal ovaries. We integrated p16 immunohistochemistry, multiplexed immunofluorescence, spatial transcriptomics, and AI-guided digital pathology to map senescent microenvironments. p16-positive cells formed discrete stromal, vascular, and cyst-associated clusters that increased with age and were enriched for macrophages and myofibroblast-like cells. Wholetranscriptome profiling of 92 spatial regions uncovered a 32-gene p16-associated signature, BuckSenOvary, that distinguished p16-positive regions across cortex and medulla. BuckSenOvary is characterized by suppression of cell-cycle regulators and activation of inflammatory and extracellular-matrix remodelling genes. AI-based collagen matrix analysis confirmed that p16-positive regions exhibit more architecturally complex collagen, demonstrating that focal senescent microenvironments are fibro-inflammatory. These findings position senescent ovarian niches as therapeutic targets to preserve ovarian function.

cell biology↗