Biology subjects

Zhang, N.

Publications and source records attributed to Zhang, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Glioblastoma Hijacks Astrocyte Ribosomes to Feul Malignancy through Translatome Reprogramming

Cancer cells demand elevated protein synthesis, yet whether they directly requisition ribosomes from microenvironmental host cells remains unknown. Here, utilizing in vivo and in vitro ribosome tracing, we show that glioblastoma (GBM) cells hijack ribosomes from surrounding astrocytes via tunneling nanotube-like structures. This transfer supports GBM malignancy in both murine and patient derived models. Single cell RNA sequencing along with whole cell and cell source traceable ribosome profiling reveal that transferred ribosomes are translationally active and selectively reprogram the tumor translatome, prioritizing cell-cycle genes and driving interferon-response-mediated immune evasion. Through a genome wide CRISPR screen, we identify INTS12 as a critical mediator of ribosome transfer. Genetic inactivation or AAV-mediated knockdown of INTS12 impairs ribosome uptake, curbs translation and proliferation, remodels the immunosuppressive landscape, and extends survival in orthotopic models. Our study uncovers a parasitic translation-support mechanism in GBM, establishing INTS12 as a therapeutic vulnerability to disrupt ribosome transfer.

cancer biology↗

bioRxiv2026

A KaiA Conformational Switch Links Day-Night Transitions to Clock Robustness

Biological clocks require mechanisms that enable transition between temporal phases and buffer against environmental fluctuations. In the cyanobacterial KaiABC-based circadian oscillator, KaiA has been regarded as a daytime activator that is passively sequestered at night. Here we define KaiA as a conformationally regulated activator and an active catalyst of the night-to-dawn transition. We identify a single linker helix, 5, that acts as a structural switch, mediating a domain-driven "tug-of-war" that sets the open-closed equilibrium in KaiA. Structure-guided mutations that shift this balance in either direction abolish stable rhythmicity both in vitro and in cells. Also, we show that substoichiometric KaiA dismantles nighttime KaiB-KaiC complexes through interactions with the KaiC C-terminal tails and likely initiates an autocatalytic feedback loop that resets the phosphorylation cycle at dawn. Furthermore, we present two independent kinetic models that offer distinct, deterministic explanations for the clock's low-temperature amplitude decline and failure at 20 {degrees} C.

biochemistry↗

bioRxiv2026

Apoptotic Cells Promote Tim4+ Macrophage Differentiation Through Direct and Indirect Signaling Pathways

Tissue macrophages are the primary cells responsible for efficiently clearing apoptotic cells, yet how professional efferocyte populations are established remains unclear. Tim4 marks a subset of macrophages across multiple tissues that are highly efferocytic, but the mechanisms governing Tim4 acquisition are poorly understood. Here, we show that monocyte-derived macrophages progressively differentiate into Tim4 macrophages in homeostatic and pathological settings. We identify a cell-autonomous pathway in which efficient apoptotic cell clearance promotes Tim4 acquisition in macrophages, as combined deficiency of CD11b and MerTK impairs both efferocytosis and Tim4 acquisition. Surprisingly, excessive apoptotic cell burden enhanced Tim4 acquisition independently of these receptors. We demonstrate that serial exposure to apoptotic cells induces a type 2 immune response characterized by expansion of IL-4-producing populations and that IL-4R-STAT6 signaling is sufficient and required to drive Tim4 acquisition. These findings support a model in which Tim4 acquisition in macrophages integrates direct signals associated with apoptotic cell clearance and indirect signals generated by apoptotic cell burden. We propose that these complementary mechanisms enable tissues to dynamically adjust the size and function of the professional efferocyte compartment to meet changing demands for apoptotic cell clearance.

immunology↗

bioRxiv2026

In situ identification of pre-hematopoietic stem cells and their niche

Definitive hematopoietic stem cells (HSCs) emerge predominantly along the ventral surface of the dorsal aorta in the embryonic aorta-gonad-mesonephros (AGM) region, yet the spatial organization of the niche underlying this developmental asymmetry remains poorly understood. Defining the native niche of pre-HSCs has also been hindered by their rarity, transient nature and lack of a single definitive marker for their identification in situ. Here, we integrated single-cell and spatial transcriptomics to construct a spatiotemporal atlas of the niche in the AGM. Neural cells and chondrogenic mesenchyme predominated dorsally, whereas N-cadherin mesenchymal stromal cells (N-cad+ MSCs) formed a ventral layer between the aortic endothelium and mesonephric cells. BMP and SHH signaling showed overall dorsal enrichment, whereas WNT, NOTCH and KIT signaling were enriched ventrally, with these cellular and signaling patterns dynamically remodeled across HSC ontogeny. Imaging-based spatial transcriptomics validated the findings and further enabled the identification of individual pre-HSCs in situ and revealed a multicellular niche comprising endothelial cells, N-cad+ MSCs, intra-aortic hematopoietic cluster cells and macrophages. TGF{beta} and NOTCH signals were primarily supplied locally, whereas major sources of BMP and WNT were more distant. Functional perturbation identified niche-derived CD200 as an immune-regulatory signal promoting HSC development, validating a spatially predicted niche interaction. Together, our findings link tissue-scale spatial organization with the local multicellular niche supporting the preferential development of HSCs along the ventral aorta.

developmental biology↗

bioRxiv2026

Metabolic engineering of Salmonella enterica for coupled kynurenine sensing and depletion enhances antitumor efficacy

Immunosuppressive tumor metabolic microenvironment remains a major barrier to effective cancer therapy. Tumor-targeting Salmonella enterica strains were engineered to deplete the intratumoral immunosuppressive kynurenine, triggering metabolic rewiring and fostering an active antitumor immune microenvironment. Equipping S. enterica VNP20009 with bacterial kynureninase enzyme (KynU) and a kynurenine transporter enabled efficient intratumoral kynurenine degradation. We then developed a next-generation strain, AD51, combining quorum-sensing controlled KynU expression with kynurenine-dependent growth and tumor targeting. AD51 induced robust immune activation and exhibited better anti-tumor efficacy. The addition of intratumoral exogenous IFN{gamma} to AD51 synergistically enhanced immune activation and antitumor efficacy in murine ovarian cancer and melanoma models, reducing tumor burden by 75% and 84%, respectively, compared with untreated controls (p<0.0001 for both). Our data establishes a framework for engineering bacteria to target and degrade tumor immunosuppressive metabolites while coupling bacterial growth to metabolite availability, paving the way for more precise and programmable microbial therapies.

cancer biology↗

bioRxiv2026

Discriminating rare disease cases from their controls based on observed and excluded phenotypes

Rare diseases are individually uncommon but collectively prevalent. Their primary clinical challenge lies not in treatment but in diagnosis. In the early stages of clinical management, it is frequently unclear whether the observed phenotypes are associated with a rare disease. Leveraging machine learning methods to mine latent associations between these phenotypes and rare diseases for early diagnosis offers a viable strategy to alleviate this diagnostic dilemma. In the present study, we demonstrated that machine learning can effectively discriminate rare disease cases from their controls using observed and excluded phenotypes as features. Among them, the Random Forest model achieved the best classification performance with a certain degree of generalizability. Based on further analysis of the feature selection results, we conclude that the two factors, specificity and occurrence count, are important for phenotype selection in rare disease discrimination, and comparable importance should be attached to both observed and excluded phenotypes, during feature construction.

bioinformatics↗

bioRxiv2026

Measurement reliability bounds functional benchmarks and relocates where variant effect prediction fails

Background. Variant effect predictors are increasingly benchmarked against multiplexed assays of variant effect (MAVEs) rather than clinical labels, which removes label circularity but introduces a new problem: a correlation against a measurement cannot exceed the measurement's own reproducibility, and precision varies sharply across the territories compared. Results. We scored nineteen predictors across sixteen strata of a frozen atlas of 64,178 saturation genome editing variants in seven cancer-susceptibility genes. From published replicate scores and standard errors we estimated each territory's reliability ceiling, and showed by simulation that the correction reduces error above a ceiling of about 0.45 and amplifies it below. Ceilings vary more across territory than predictors do, and correcting for them redraws the map at the splice extremes. The collapse at canonical splice sites is largely a property of the assay: the median shortfall relative to coding narrows from 1.7- to 1.4-fold; this convergence survives dropping BARD1 or PALB2 but inverts when BRCA1 is dropped, so we report all three leave-one-gene-out folds rather than claim gene independence, and the frontier parity rests on one deposit. Genuine failure lies 11-50 bp into the intron, which the uncorrected map presents as modest. Across MaveDB, 2,452 of 2,803 score sets carry, at the upper bound, what a reliability estimate needs, though a conventional column-name search finds only a tenth; among 674 human deposits with a computable ceiling, 29.9-51.8% fall below 0.90. Scored as classification against the assays' own functional calls in three genes, the same predictors separate damaging from tolerated better than their correlations suggest, though none reaches the strongest evidence band at the 95%-specificity operating point. Conclusions. Territory-resolved benchmarks should report a per-stratum reliability estimate, or state that the assay permits none. It asks nothing of depositors and applies today, at the upper bound, to most (87%) of MaveDB.

bioinformatics↗

bioRxiv2026

3D Spatial Interactomics Maps the Dynamics of NF-κB Multiprotein Signalosomes in Single Cells

NF{kappa}B signaling drives inflammatory responses by rapidly assembling membrane-proximal multiprotein supercomplexes, yet how these assemblies are organized in space and time within the 3D interior of a single cell has remained uncharacterized. We addressed this by profiling endogenous NF{kappa}B protein-protein interactions with an intelligent sequential proximity ligation assay (iseqPLA), read out by spinning disk confocal microscopy and 3D reconstruction. Each detected protein-protein proximity event is represented by a rolling-circle amplification product, and we treat clusters of co-localized puncta as a measure of supercomplex spatial organization. Across NIH-3T3 mouse fibroblasts, cystic fibrosis (CF) patient-derived macrophage co-cultures with IMR-90 human fibroblasts, and an independent set of healthy- and CF-donor monocyte-fibroblast co-cultures profiled by 3D iseqPLA, we tracked supercomplex dissociation, p65 nuclear translocation, and negative-feedback engagement across cytokine time courses. Three findings emerge: 3D volumetric quantification reduces the variance in nuclear-to-cytoplasmic ratio measurements relative to 2D projections, the choice of extracellular matrix coating shapes the fraction of NF{kappa}B-responsive cells, and CF airway-conditioned macrophages amplify paracrine NF{kappa}B signaling in neighboring fibroblasts in a CF model. A single-cell Generative Pretrained Transformer (scGPT) foundation model, fine-tuned on curated transcriptomic datasets, further places our NF{kappa}B gene panel within an inflammation-relevant feature space. Together, these results establish a 3D spatial interactomics workflow for dissecting supercomplex dynamics in health and disease.

bioengineering↗

bioRxiv2026

Cardiomyocytes upregulated PD-L1 expression to alleviate cardiac injury induced by irradiation combined with anti-PD-1 antibody: an in vitro and in vivo study

Objective: Preclinical studies suggest that irradiation combined with anti-PD-1 antibody (iRT) exacerbates cardiac injury in mice, partly through CD8 T-cell-mediated mechanisms. We investigated radiation-induced PD-L1 expression in cardiomyocytes and explored its potential role in iRT-associated cardiac injury. Methods: AC16 cells were exposed to different doses of irradiation. PD-L1 expression was assessed at different time points by flow cytometry, qRT-PCR, western blotting, and immunofluorescence. Cell viability, apoptosis, and cytokine levels were evaluated. PD-L1 was knocked down using siRNA to assess its function. PBMCs or CD8 T cells were co-cultured with irradiated or non-irradiated AC16 cells at different E:T ratios, with or without PD-1 blockade. A C57BL/6J mouse model of iRT-induced myocardial injury was established, and myocardial PD-L1 expression and T-cell infiltration were evaluated. Results: Irradiation upregulated PD-L1 expression in AC16 cells, with increased membrane and cytoplasmic signals at 48 h and prominent nuclear-associated fluorescence at 72 h. Irradiation increased IL-6, MCP-1, CCL5, and CXCL10 release, decreased IL-10, reduced cell viability, and increased apoptosis. PD-L1 knockdown further increased inflammatory cytokine and chemokine release but did not significantly alter apoptosis or further reduce viability in irradiated AC16 cells. In the presence of a high density of activated CD8 T cells, disruption of PD-1/PD-L1 signaling was associated with a further reduction in AC16 cell viability. In vivo, myocardial PD-L1 expression was increased, whereas CD8 T-cell infiltration remained limited and focal. Conclusion: PD-L1 upregulation in cardiomyocytes may exert an adaptive protective and immunoregulatory role during iRT-associated injury, potentially by limiting inflammatory mediator release and modulating susceptibility to activated CD8 T-cell mediated injury. CD8 T-cell density and activation are the key issues.

cancer biology↗

bioRxiv2026

PlantRegMoD: An integrative and AI-driven multi-omics database for plant regeneration research

Plant regeneration underpins plant developmental plasticity, tissue culture, genetic transformation and crop improvement. Although numerous related omics datasets have been generated, specialized multi-omics databases for this field are still scarce. Here, we constructed PlantRegMoD, an AI-powered integrated database dedicated to plant regeneration. This platform hosts 20.54 TB standardized multi-omics data from 147 projects across 32 plant species and 2,593 samples. We established a unified hierarchical classification system covering five major categories and nine regeneration models, and curated 236 regeneration genes as well as their 28,190 homologs across 58 representative plant species. It contains extensive transcriptomic resources across all regeneration models, together with 196,423 single cells and over 8.81 million epigenetic peaks to dissect cellular heterogeneity and multi-layered epigenetic regulation. Equipped with nine online omics-related tools and a RAG-based intelligent Q&A system, PlantRegMoD greatly reduces bioinformatic barriers and serves as a robust resource for mechanistic, functional and evolutionary studies of plant regeneration.

plant biology↗

bioRxiv2026

Cth1 is essential for gametogenesis and fertility in zebrafish

Infertility frequently arises from defects in germ cells and early embryonic transition. Successful fertilization depends on the developmental competence and molecular integrity of mature gametes from both parents, which are established through tightly coordinated programs of RNA regulation, metabolism, and genome maintenance. In our previous work, we identified Cth1 as a maternally regulated RNA decay factor essential for early embryonic development, acting through spatiotemporal control of maternal transcript clearance. Interestingly, Cth1 loss of function in adults also resulted in infertility, suggesting an additional and unexplored role during gametogenesis. Here, we extend these findings by defining the gametogenic function of Cth1 in zebrafish. Through detailed phenotypic, cytological and molecular characterization of Cth1 loss of function mutants, we show that Cth1 is highly enriched in germ cells and early embryos and is spatio-temporally localized across oogenesis and early development. Loss of Cth1 causes severe defects in early oogenesis and spermatogenesis, resulting in complete infertility in males and females. Mutant germ cells display transcriptomic changes consistent with metabolic and translational dysregulation, increased DNA damage, and striking abnormalities in gamete morphology. Together, these findings identify Cth1 as essential for gamete quality and fertility. Our study suggests a link between RNA decay mediated regulation of metabolism and genome integrity during germ cell development and reveals disruption of post-transcriptional control as a potential mechanism underlying infertility.

developmental biology↗

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

Brain dynamics exhibit scale-dependent reversibility during consciousness transitions

Consciousness is a dynamic brain state, yet the systems-level mechanisms underlying transitions into and out of unconsciousness remain poorly understood. It is unclear whether neural dynamics during loss of consciousness (LOC) and recovery of consciousness (ROC) simply retrace the same trajectory or instead follow distinct paths across multiple spatial scales. Here, we simultaneously measured local electrophysiology, whole-brain functional MRI, and pupil dynamics in rats during graded propofol anesthesia to characterize consciousness transitions from local circuits to whole-brain networks. We found that local field potential, regional BOLD responses, and pairwise functional connectivity exhibited largely reversible changes between LOC and ROC. In contrast, the global brain organization showed distinct and asymmetric patterns during the two transitions, as consistently revealed by traveling-wave propagation, low-dimensional network trajectories, and graph-theoretical analyses. Importantly, brain-wide coupling between pupil dynamics and regional BOLD activity remained highly consistent during LOC and ROC, indicating that these distinct global trajectories cannot be simply explained by differences in neuromodulatory tone. Together, our findings identify scale-dependent reversibility as a systems-level organizing principle of consciousness transitions. These results suggest that recovery of consciousness is an active process of large-scale network reorganization rather than merely the reversal of anesthetic suppression.

neuroscience↗

bioRxiv2026

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

The liver is organized into tightly regulated zones with distinct metabolic functions but zonation erodes with age. Cellular senescence contributes to aging and liver diseases, however, its impact on aging biology is ill-defined. As part of The Cellular Senescence Network Consortium, we used multiple spatial transcriptomics approaches (GeoMx, Visium, CosMx) with snRNA-seq to profile senescence signatures, zonation markers, and metabolic pathways in livers from wild-type (WT) mice of multiple ages. We observed a loss of canonical zone signatures in aged mouse livers characterized by "expansion" of midlobular (zone 2) marker gene expression, accompanied by diminished expression of zone 3 marker genes by middle-age (18 months), indicative of loss of cell identity. Multiple analytic approaches identified distinct age-, zone- and sex-specific senescence signatures, which were significantly associated with zonation markers changes. This was recapitulated in Ercc1 mutant models of accelerated senescence, supporting a causal role of senescent cells in liver aging. A "no-zone" hepatocyte-like cluster expanded with age and with the strongest Senescence-Associated Secretory Phenotype (SASP) profile. Gene expression profiles from senescent hepatocytes implicate decreased WNT signaling and increased BMP as contributing to age-related loss of zonation. Together, these data elucidate the role of senescent cells in driving aging biology in non-diseased liver through disruption of cell:cell signaling and the loss of metabolic and cell identity gene expression necessary for hepatocyte function.

cell biology↗

bioRxiv2026

Association of Sleep with Anxiety in Chinese Empty-Nest Older Adults: The Mediating Roles of Physical Exercise and Social Participation

Sleep disturbances are common among older adults and are often closely associated with anxiety symptoms, which together can substantially compromise physical and mental health.A cross-sectional analysis was conducted using data from the 2017/2018 wave of the Chinese Longitudinal Healthy Longevity Survey (CLHLS). The study included 6,106 Chinese older adults (aged [≥]65 years) living in empty-nest households. Physical exercise was measured based on self-reported regular engagement in exercise, and social participation was defined as involvement in organized social activities (e.g., community or group-based events). Associations between sleep quality and duration and anxiety were estimated using multivariable logistic regression, and mediation effects of physical exercise and social participation were tested using bootstrap resampling.Among the 6,106 participants, 593 (9.7%) reported anxiety symptoms. Multivariable logistic regression analysis indicated that poor sleep quality was significantly associated with a higher risk of anxiety (OR = 3.23, 95% CI: 2.62-4.01, P < 0.001). Short sleep duration was also an independent risk factor for anxiety (OR = 1.34, 95% CI: 1.04-1.74, P = 0.025), whereas long sleep duration showed no significant association. Subgroup analyses stratified by sex, marital status, and economic status consistently revealed significant associations between sleep (both quality and duration) and anxiety, with no statistically significant interactions observed. Mediation analyses demonstrated that physical exercise significantly mediated the relationships of both sleep quality and long sleep duration with anxiety (all P < 0.01, with bootstrap confidence intervals excluding zero). Similarly, social participation significantly mediated the relationships of both short and long sleep duration with anxiety (all P < 0.01, with bootstrap confidence intervals excluding zero).In Chinese empty-nest older adults, both poor sleep quality and short sleep duration are independent risk factors for anxiety symptoms, with sleep quality exerting a stronger influence. Physical exercise partially mediated the associations between sleep quality and anxiety and between long sleep duration and anxiety, whereas social participation mediated the association between sleep duration (short and long) and anxiety. Improving sleep quality and ensuring adequate sleep duration may help reduce anxiety risk, and interventions promoting physical exercise and social participation could enhance these protective effects.

immunology↗

bioRxiv2026

High-Specificity Detection of Chromosomal Mosaicism Reveals Cell-Type-Specific Genomic Alteration Patterns in Aging Tissues

Mosaic chromosomal alterations (mCAs) increase with age and are associated with multiple diseases, yet the cell types and states that harbor these alterations remain largely unknown. Because mCAs arise in individual cells prior to clonal expansion, they are typically rare and obscured in bulk data. We develop CHASM, a method for detecting chromosomal copy number alterations (CNA) from single-cell chromatin accessibility (scATAC-seq) data, a scalable modality that captures both cell state and chromosomal alterations. CHASM estimates a CNA-null background for each cell, providing an individualized expectation for chromosomal accessibility, which is critical in non-neoplastic tissues where alteration-carrying cells are not readily distinguishable from normal. By comparing each cell against its expected background, CHASM distinguishes chromosomal alterations from background variation and achieves more stringent control of false positives. We validate CHASM using in silico spike-in experiments, cross-modality comparisons with matched single-cell DNA and RNA data, and established genome-instability contrasts, including p53 deficiency and chromosome Y loss. Applied to multiple aging data sets, CHASM consistently recovers mCA burden in age-susceptible cell populations and reveals aging-associated signatures not detected by existing methods. In a cohort of 99 human kidney samples spanning age and disease conditions, CHASM identifies enrichment of mCAs in injury-associated cell states (VCAM1-high proximal tubule cells). Notably, CHASM detects the age-associated emergence of mCAs in cancer-relevant genomic regions, including chromosomes 3 gains and losses and chromosome 7 gain, in ostensibly normal cell populations. Cells harboring mCAs exhibit activation of injury-response regulatory programs and reduced epithelial identity programs, while elevated mCA burden in specific epithelial populations are associated with increased immune and stromal infiltration. Overall, we develop CHASM for high-specificity detection of CNA at single cell resolution. Applied across tissues, CHASM reveals aging-patterns of genome instability within cell types and implicates mCAs in early, pre-disease cellular states.

bioinformatics↗

bioRxiv2026

Prolonged developmental programming of somatostatin neurons defines adolescent remodeling of the prelimbic, but not barrel, cortex

Higher order association cortices like the prefrontal cortex (PFC) mature over a longer developmental window than sensory cortices, but whether genetically defined interneuron populations follow this region-wide delayed trajectory remains unclear. We compared the postnatal development of somatostatin-expressing interneurons in a higher-order cortical region (prelimbic cortex; PLC) and a sensory cortical region (somatosensory barrel cortex; S1BF) across adolescence using complementary structural, electrophysiological, and circuit analyses. We found that the maturation of SST neurons within these two cortical regions differs across time. S1BF SST neurons exhibited relatively linear maturation, whereas PLC SST neurons underwent continued dendritic remodeling, nonlinear intrinsic maturation, and age-dependent refinement of inhibitory output onto pyramidal neurons. Multivariate analyses likewise supported a more linear developmental trajectory in S1BF and a more prolonged, heterogeneous trajectory in PLC. This suggests divergent maturation of the PLC and S1BF and supports a broader, longer window of critical cellular plasticity in the PLC than in sensory cortices. Together, this reflects an extended developmental program at the level of a genetically defined inhibitory cell type. Because SST neurons are positioned to regulate pyramidal neuron output via control of dendritic integration, their delayed maturation is a crucial reflection of overall circuit function. These findings provide a cellular framework for the prolonged plasticity and developmental vulnerability known to be characteristic of adolescent prelimbic cortex. Significance statementWithin the brain, higher order association cortex remains plastic long after sensory cortex has matured, but the cellular basis for this prolonged developmental window has remained unknown. We find that developmental timing is encoded within genetically defined microcircuits. Prelimbic somatostatin circuits continue to remodel after sensory somatostatin circuits have largely stabilized through changes in cell shape, action potential firing dynamics, and inhibitory signaling. This work points to a specific prelimbic inhibitory cell type that matures more slowly, and less linearly, than its counterparts in other brain regions, and may help explain why prelimbic circuits remain vulnerable during adolescence, representing a biological substrate for extended adolescent remodeling in prelimbic cortex, and potentially the overall extensive flexibility, but also cognitive susceptibility, seen during adolescence.

neuroscience↗

bioRxiv2026

Network-scale disruption of RNA-protein interactions by a bioaccumulating small-molecule drug

Many small-molecule drugs accumulate in both host and gut microbial cells. Yet, the molecular consequences of intracellular drug accumulation are largely unknown. Here we show that the antidepressant duloxetine broadly disrupts RNA-protein interactions revealing a previously unrecognized mode of drug effect. Across phylogenetically diverse bacteria and human intestinal cells, duloxetine consistently reduced RNA-binding capacity, with approximately 80% of RNA-binding proteins responding to duloxetine in bacteria (E. coli IAI1) and human (Caco-2) cells. As a mechanistic example, we show how duloxetine disrupts interactions between the pyrimidine biosynthesis enzyme PyrB and transcripts encoding metabolically linked functions. Biochemical and structural analyses show that duloxetine competes with aspartate, the natural substrate of PyrB, weakening the enzymes binding with 3' UTR-localized stem-loop structures in its RNA partners. Overall, our results uncover the off-target disruption of RNA-protein interactions due to drug accumulation and have implications for understanding molecular basis of variation in drug efficacy and toxicity.

systems biology↗