Biology subjects

Zhou, L.

Publications and source records attributed to Zhou, L..

At least 19 recordsLinked to original sources

bioRxiv2026

p53 activity links chromosomal instability to pro-migratory extracellular vesicles

Chromosomal instability (CIN) promotes tumor evolution and metastasis while imposing cellular stress that can limit cell proliferation via activation of p53 and its downstream effector p21. However, how cells recover from this p53-mediated proliferation block while adopting a more malignant fate remains poorly understood. Here, using a p21-RFP reporter in p53-proficient NIH/3T3 cells, we show that acute CIN gives rise to two phenotypically distinct p21 cell populations with divergent recovery trajectories. p21-RFPLOW cells re-enter the cell cycle following a short cell-cycle arrest, while p21-RFPHIGH cells display a more persistent arrest that coincides with a senescence-like state. Longitudinal transcriptomic and extracellular vesicle (EV) proteomic analyses reveal that extracellular-matrix (ECM)- and adhesion-associated programs are initially suppressed following CIN but specifically reactivated in p21-RFPHIGH cells. The content of late-stage p21-RFPHIGH-derived EVs is enriched for ECM-, adhesion-, and cytoskeleton-associated proteins compared with that of p21-RFPLOW-derived EVs. Consequently, EVs derived from p21-RFPHIGH cells confer increased migration. Together, these findings reveal that CIN can yield distinct p21-expressing cell populations that display different cell-cycle recovery trajectories, EV makeup, and migration-associated paracrine activity.

cancer biology↗

bioRxiv2026

Efficacy of Tumor Treating Fields (TTFields) in triple negative breast cancer cells and synergy with PARP inhibitor talazoparib

Breast cancer is the most diagnosed cancer worldwide. Triple-negative breast cancer (TNBC) is a subtype with a poor prognosis because of its aggressiveness and high likelihood of relapse, making its treatment particularly challenging. We explored the effect of Tumor Treating Fields (TTFields) as a novel treatment option for breast cancer, which can be used together with other therapies, such as PARP inhibitors. TTFields use alternating electric fields to inhibit cell growth and induce cellular damage. Our findings indicate that TTFields increase expression of the universal cell cycle CDK inhibitory protein p21(WAF1)/CDKN1A independently of TP53 mutational status. Moreover, when used together with the PARP inhibitor talazoparib, the combination further upregulates p21 protein. Both TTFields alone and together with talazoparib induce cell death as documented by PARP cleavage while reducing markers of cell growth and anti-apoptotic proteins, including p-STAT3, STAT3, and MCL-1. Additionally, TTFields together with talazoparib induce DNA damage, as indicated by increased {gamma}H2AX expression. The combination of talazoparib plus TTFields treatment decrease PDL-1 levels and given its utility in predicting response to PD-1/PD-L1 by mediating immune evasion, this raises the possibility of future combination for immune modulation in cancer therapy. Our preclinical results suggest TTFields alone or together with PARP inhibitors such as talazoparib as a promising therapeutic approach for further development for the treatment of breast cancer.

cancer biology↗

bioRxiv2026

BMP6 coordinates dermal papilla and epithelial cell states for hair follicle engineering and regeneration

Human hair follicle engineering is hindered by the rapid loss of inductive competence in culture-expanded dermal papilla (DP) fibroblasts. Here we show that bone morphogenetic protein 6 (BMP6) maintains and restores DP-associated characteristics while promoting follicular epithelial differentiation by restricting keratinocyte (KC) proliferation and inducing hair follicle-associated marker expression. Human follicle transcriptomics further linked BMP activity to DP identity and follicular epithelial differentiation. Genetic mouse studies demonstrate that BMP6 in Sox2-positive DP cells contributes to normal anagen onset, progression, and maintenance. Gain- and loss-of-function studies in KC-DP organoids show that BMP6 promotes epithelial-mesenchymal organization and spatially patterned follicular structures. In vivo, topical BMP6 promotes anagen onset, whereas BMP6 overexpression restores the hair follicle-generating capacity of late-passage human DP fibroblasts. Together, these findings identify BMP6 as a compartment-dependent regulator that enhances human DP competence and promotes epithelial differentiation, supporting regenerative hair follicle formation and engineering with culture-expanded DP cells.

developmental biology↗

bioRxiv2026

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

Edible waxy maize is a unique domesticated cereal valued for its superior sensory and nutritional properties, yet high quality gap free genomes remain lacking, hindering the exploration of structural variations (SVs) and domestication related divergence. Here, we assembled two chromosome level, gap free genomes of the elite waxy maize inbred lines Tongxi 5 and Hengbai 522, the parents of the widely cultivated hybrid Suyunuo 1. Comparative genomic analysis revealed substantial genome size variation, prominent megabase scale SVs, and extensive knob repeat expansion in Tongxi 5. We identified widespread gene presence absence variation and hyperdivergent regions enriched in transposable elements, which largely underpin genomic differentiation between waxy and field maize. Population genomic analyses further demonstrated asymmetric introgression from field maize into the two parents, whereas the conserved waxy haplotype supports a shared ancestral origin. Integrative GWAS based on SNPs, InDels and SVs revealed that SVs substantially contribute to phenotypic diversity and mediate the co-regulation of yield traits and flavor-related metabolites. Our results uncover key genomic events underlying post-domestication divergence and highlight the essential roles of SVs in heterosis and flavor-yield balance, providing valuable genomic resources for waxy maize improvement.

plant biology↗

bioRxiv2026

TFAM Dependent Mitochondrial Fitness Limits CD8⁺ T Cell Immunopathology and Sustains Protective Immunity during Viral Pneumonia

During respiratory virus infection, CD8 T cells kill infected cells and establish antigen-specific memory, but mechanisms regulating these functions remain incompletely understood. Here, we identify mitochondrial transcription factor A (TFAM)-dependent mitochondrial fitness as a regulator of CD8 T cell function during influenza infection. Human CD8 T cells exhibited an age-associated decline in TFAM expression and mitochondrial function. To model this physiologically relevant decline and determine its consequences for antiviral immunity, we generated CD8 T cell-specific TFAM-haploinsufficient mice. TFAM insufficiency disrupted mitochondrial integrity and bioenergetics and increased mitochondrial DNA and oxidative stress. During influenza infection, TFAM-insufficient CD8 T cells exhibited increased cytotoxic and inflammatory activity associated with lung immunopathology without improved viral control. This early phenotype was followed by loss of effector function, diminished antigen-specific responses, reduced protection following adoptive transfer, and impaired heterosubtypic recall immunity. Thus, TFAM-dependent mitochondrial fitness is a cell-intrinsic regulator that limits immunopathology while sustaining recall immunity.

immunology↗

bioRxiv2026

Inflammatory burning pain depends on a specific line of nociceptors

The development and persistence of burning pain and heat hyperalgesia following tissue injury and the subsequent inflammatory response, depend on the nuclear enzyme mitogen- and stress-activated kinase 1 (MSK1) expressed in a specific subset of transient receptor potential subfamily V member 1 (TRPV1)-expressing primary sensory neurons termed nociceptors, which are specialised for detecting harmful stimuli. Inflammation up-regulates and activates MSK1, and MSK1 governs TRPV1 expression in the MSK1 and TRPV1 co-expressing mouse and human nociceptors. Importantly, inhibition of inflammatory MSK1-mediated TRPV1 upregulation protects from heat hypersensitivity without affecting other relevant TRPV1 functions, such as the sensation of acute painful heat stimuli or the maintenance of the body core temperature. The newly discovered importance of the interaction between MSK1 and TRPV1 in a specific line of nociceptors provides mechanistic understanding of inflammatory pain and heat hyperalgesia pathogenesis.

neuroscience↗

bioRxiv2026

HDA6-mediated histone deacetylation restricts premature tapetal PCD to maintain male fertility during early flowering in Arabidopsis

Histone deacetylation regulates plant development, yet its role in male gametophyte development and fertility remains unclear. Here, we show that histone deacetylase 6 (HDA6), an RPD3-like histone deacetylase, epigenetically regulates timely tapetal programmed cell death (PCD) and male fertility, predominantly during early flowering in Arabidopsis. Loss of HDA6 in axe1-4 causes early-stage male sterility followed by fertility recovery, accompanied by premature tapetal PCD, impaired pollen development and defective pollen wall formation. HDA6 interacts with squamosa promoter binding protein-like 8 (SPL8) to repress Arabidopsis NAC domain containing protein 087 (ANAC087) through H3K9/K14 deacetylation. In axe1-4, ANAC087 derepression activates cysteine endopeptidase 1 (CEP1), triggering precocious tapetal PCD. Genetic suppression of ANAC087 or CEP1 restores male fertility. Thus, HDA6-SPL8 establishes a stage-dependent epigenetic checkpoint that restrains the ANAC087-CEP1 cell death pathway and ensures timely tapetal PCD. Our study reveals how chromatin regulation integrates with developmental timing to safeguard plant male fertility.

plant biology↗

bioRxiv2026

Comparative Genomic and Epigenetic Landscape of Histone H3.3 G34R and K27M-Mutated Pediatric High-Grade Glioma Suggests Divergent Precision Oncology Strategies

Histone H3-G34R and H3-K27M mutations define distinct diffuse high-grade glioma subtypes diffuse hemispheric glioma (DHG), midline (DMG), and pontine gliomas (DIPG). We characterized pathway-architectures using cBioPortal and pedcBioPortal for H3-G34R (n=112) and H3-K27M (n=727) mutated-gliomas, co-mutations, copy numbers (CNA), and variant data (n=112/727, n=86/578, n=51/313). We evaluated altered-genes as oncogenic by OncoKB, Gene-Ontology (GO) heatmaps and process-enrichment using clusterProfiler (Benjamini-Hochberg-adjusted p<0.05). H3-G34R-gliomas harbored near-universal TP53 (94.1%), ATRX (81.4%) co-mutations and PDGFRA alteration (54.9% mutation; 17.1% amplification) within 4q12 amplicon that includes KIT and KDR. Pathway-enrichment converged on G1/S cell-cycle checkpoints, and epigenetic regulation, driven principally by TP53, ATRX, PTEN, BCOR, TERT, FBXW7, and PPM1D. CDK6 amplification was rare (2.6%), despite H3-G34R association with CDK6-dependency including benefit from CDK4/6 inhibition. H3-K27M-gliomas displayed PI3K/AKT pathway activation (PIK3CA, 14.9%; NF1, 13.3%; PDGFRA, 10.8%, PIK3R1, 7.8%; PTEN, 5.7%) and developmental signatures through NF1, PTEN, and SOX10 (4.95%) mutations. TP53 (62.2%) and ATRX (21.2%) co-mutations were less frequent in H3-K27M versus H3-G34R, while PPM1D was H3-K27M-enriched (19.3%). MGMT promoter methylation occurred frequently in H3-G34R (65.2%, 15/23) versus H3-K27M-gliomas (5.4%, 4/74), despite genome-hypomethylation of H3-G34R. H3-G34R-gliomas, unlike H3-K27M, upregulated ganglionic GSX2, DLX1, DLX2, and FOXG1. SOX10 was upregulated in H3-K27M-gliomas, versus H3-G34R. Lack of MGMT methylation in H3-K27M-gliomas correlates with temozolomide resistance; we previously reported imipridones ONC201/ONC206 reduce MGMT, EZH1 and EZH2 expression in H3-K27M-glioma cells. Divergent PDGFRA-mutations among MGMT-methylated versus unmethylated H3-G34R-gliomas warrants investigation of PDGFRA-signaling and epigenetic regulation. Our findings suggest divergent precision oncology therapeutic strategies to exploit unique vulnerabilities in H3-K27M and H3-G34R-gliomas.

cancer biology↗

bioRxiv2026

Accounting for pseudo-replication of Linkage Disequilibrium for contemporary Ne estimation

The Linkage Disequilibrium (LD) of unlinked loci can be used to estimate contemporary effective population size (Ne) of one to a few generations ago. In genomic datasets loci on different chromosomes are considered unlinked, but there are many more pairs of unlinked loci than there are independent pairs of chromosomes, resulting to confidence intervals (C.I.) being too narrow if the non-independence is not taken into account. Simulations were run to investigate the correlation structure among LD of unlinked loci, which can be expressed by the LD of loci along the same chromosomes, based on a discovery of a novel Random Probe LD estimator. We classify the correlation into two categories: overlapping of loci and disjoint pairs. The former is induced from the same locus being considered twice and is the stronger form of correlation. These correlations feed into {rho}, a parameter to quantify the degree of pseudo-replication in a dataset, and further a correction formula from which C.I. can be properly inferred. We demonstrate the use of our method via an analysis of genomic data from the malaria-transmitting Anopheles gambiae s.s mosquitoes. Apart from the point and C.I. estimates, we find that Var((r^2 ) ) is inflated by about 550 times due to pseudo-replication, highlighting the danger of not handling genetic correlation properly.

bioinformatics↗

bioRxiv2026

Loss of Mitochondrial Respiratory Capacity Reshapes Myeloid Cell Function during Mycobacterium tuberculosis infection

Myeloid cells are essential mediators of host defense against Mycobacterium tuberculosis (Mtb), yet the metabolic programs that sustain their function during chronic infection remain poorly defined. Here, using scRNA-seq we identified a striking, coordinated decline in mitochondrial electron transport chain gene expression across diverse myeloid populations as Mtb disease progressed in mice. This transcriptional remodeling was associated with broad changes in immune and metabolic pathways, including reduced antigen presentation, interferon responses, protein synthesis, and glycolysis. Accordingly, loss of Complex I in macrophages (Ndufs4 knockdown) reduced MHC-II surface expression, dysregulated inflammatory gene expression, and limited control of Mtb replication. Finally, analysis of single-cell transcriptomic data from Mtb-exposed human household contacts identified an almost identical transcriptional program enriched in IGRA+ individuals, supporting a role for mitochondrial respiratory remodeling in human TB. Together, these findings demonstrate that mitochondrial bioenergetic competence is required to sustain macrophage effector function during chronic Mtb infection and suggest that mitochondrial restoration may boost protective responses in TB patients.

immunology↗

bioRxiv2026

RECON infers regions of interest from H&E images and reconstructs whole-slide molecular profiles at single-cell resolution

Spatial omics technologies resolve molecular expression and spatial architecture at single-cell resolution, but profiling whole slides remains costly. In practice, only a few regions of interest (ROIs) are profiled, leaving the rest of the tissue unmeasured. S2-omics was the first framework to unify ROI selection with out-of-ROI prediction, but it operates on superpixels rather than individual cells and predicts discrete cell types rather than continuous molecular profiles. Superpixel-based representations do not explicitly preserve cell boundaries, while categorical cell-type labels cannot quantify molecular expression within cells. Here we present RECON, a two-stage framework that performs ROI inference and whole-slide molecular reconstruction at single-cell resolution, predicting both continuous molecular profiles and discrete cell-type labels. In the first stage, RECON extracts morphological and microenvironmental features from individual cells to identify a representative ROI for spatially resolved single-cell molecular profiling. In the second stage, RECON trains deep learning models on molecular measurements acquired within the selected ROI and reconstructs transcriptomic or proteomic profiles for all remaining cells on the slide. Benchmarked against pathologist annotations, RECONs ROI selection outperforms the superpixel-based S2-omics approaches (IoU: 0.75 versus 0.64). For transcriptomics, refining the modeling unit from superpixels to single cells improves per-gene Pearson correlation by 22%. For proteomics, RECON surpasses the current state-of-the-art method, ROSIE, across all 16 markers, with a median per-cell Pearson correlation of 0.91 versus 0.84. Moreover, RECON delineates tumour boundaries and regions with distinct immune-cell densities, and highlights candidate tertiary lymphoid structures. Together, these results demonstrate that RECON enables informative ROI selection and whole-slide molecular reconstruction at single-cell resolution for both spatial transcriptomics and spatial proteomics.

bioinformatics↗

bioRxiv2026

Endocrine-Adapted Pituitary Macrophages Regulate Gonadotropin Secretion through CXCL5-CXCR2-MAPK Signaling

Chronic inflammation disrupts hormonal balance in the Hypothalamic-Pituitary-Gonadal (HPG) axis, contributing to reproductive disorders. While immune cells in the hypothalamus and ovaries have been extensively studied, their impact on the pituitary remains largely unexplored. Our research identifies pituitary macrophages (PitMacs) as the dominant pituitary immune cell population with a role in regulating reproductive gonadotropin secretion both in vitro and in vivo. Using a targeted AAV-based depletion strategy, we demonstrate that a reduction of PitMacs decreases serum gonadotropins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH), in female mice. PitMacs are transcriptomically distinct from other tissue-resident macrophages and harbor a unique translational program that reflects the pituitarys endocrine identity, including active translation of growth hormone (Gh) and prolactin (Prl). Cytokine profiling identified CXCL5 and IFN-{gamma} as key PitMac-derived mediators of gonadotropin regulation. Mechanistically, CXCL5 signals through CXCR2 to activate the MAPK pathway, converging with Gonadotropin-Releasing Hormone (GnRH) signaling in a time-dependent manner to regulate LH secretion and GnRH receptor surface expression. These findings establish PitMacs as essential endocrine-immune integrators, opening new avenues for understanding inflammation-driven reproductive disorders. One Sentence SummaryPituitary macrophages are unique hormone-producing immune cells that regulate hormone secretion via cytokine signaling.

immunology↗

bioRxiv2026

ACCREDIT: A Quality-Aware Agentic Engine for Cell-resolved Cross-modal Image Registration with Dynamic Iterative Tuning

Spatial omics across complementary modalities is transforming our understanding of tissue architecture. Realizing this potential requires accurate and robust registration of cross-platform molecular images with hematoxylin-and-eosin (H&E) sections, the primary morphological reference for pathology. Existing methods, however, often fail silently when image orientation is unknown, image contrast is inverted, or tissue overlap is incomplete, producing erroneous registrations without alerting users or attempting recovery. Here, we present ACCREDIT, a quality-aware agentic framework that redefines cross-modal registration as an adaptive decision-making process rather than a one-shot computation. ACCREDIT combines deterministic registration pipelines with a reference-free composite quality score that automatically evaluates registration quality and rejects plausible but biologically incorrect registrations. When registration quality is insufficient, a large language model (LLM)-based rescue agent autonomously diagnoses failure modes and selects targeted recovery strategies, while an optional strategy-learning module captures expert-validated corrections for future reuse. Across Xenium, CODEX, cell-boundary, and IHC-to-H&E registration tasks, ACCREDIT outperformed competing methods by detecting registration failures and improving alignment quality through automated recovery and rescue. Ultimately, ACCREDIT enables robust integration of histology and spatial molecular profiling, providing a foundation for translating spatial omics into routine H&E-based pathology workflows.

bioinformatics↗

bioRxiv2026

Multifaceted and evolutionarily dynamic interactions between Caenorhabditis elegans SPO-11 and its cofactors ensure proper formation of meiotic DNA double-strand breaks

DNA double-strand breaks (DSBs) generated during meiotic prophase by the topoisomerase-like protein SPO11 are essential to create crossovers between homologous chromosomes. Since crossovers are required to biorient chromosomes at the first meiotic division, DSB formation is essential for meiosis in most sexually-reproducing organisms. Since excess DSBs have the potential to destabilize the genome, SPO-11 activity must be strictly regulated by many cofactors. Recent studies have established that SPO11 must dimerize to cut DNA, whereas soluble SPO11 and SPO11-TOPOVIBL complexes are predominantly monomeric (1-3). This contrast suggested that a major role of SPO11 cofactors could be to promote SPO11 dimerization, through means such as increasing local concentration or co-orienting SPO11 protomers. However, the mechanism of this regulation is not well-understood. Here, by taking advantage of phylogenomic analysis in the nematode genus Caenorhabditis, we show that the conserved cofactor DSB-1Rec114 evolved to replace TOPOVIBL function in C. elegans. We provide genetic and biochemical evidence that multiple interactions between SPO-11 and DSB-1 stabilize protein complex formation and promote SPO-11 dimerization. Our results shed light on the regulatory mechanism of programmed DSB formation, which ensures crossover formation and meiotic chromosome segregation while protecting genomic stability. Significance StatementProgrammed DNA double-strand breaks catalyzed by SPO11 are essential for meiosis, but how SPO11 and its cofactors cooperate to cut DNA is not understood. SPO11 only cuts DNA as a homodimer, but soluble SPO11, with or without its core component TOPOVIBL, is predominantly monomeric. We show here that DSB-1, a conserved cofactor of C. elegans SPO-11, has evolved to replace TOPOVIBL to make direct, multifaceted interactions with SPO-11. We provide evidence that DSB-1 simultaneously binds both SPO-11 protomers, and this binding is critical for DNA cleavage, implying a major role of DSB-1 in promoting SPO-11 dimerization. Our phylogenetic analysis also highlights the evolutionary flexibility of a conserved, essential protein complex after the loss of one of its members, TOPOVIBL.

cell biology↗

bioRxiv2026

Boldine inhibits SARM1 NADase Activity and Preserves Axonal Integrity After Nerve Injury

Wallerian degeneration of anucleated axonal segments is driven by SARM1, which depletes axonal NAD+, disrupting energy metabolism and triggering self-destruction. SARM1 inhibition is an emerging therapeutic target for traumatic nerve injuries. Boldine, a natural aporphine alkaloid from Peumus boldus, modulates connexin hemichannels, oxidative stress, and inflammation. Building on our published work showing boldines neuroprotective effects in nerve injury models, we hypothesized that boldine also inhibits SARM1 directly. A fluorescence polarization assay revealed that boldine inhibits SARM1 NADase activity with an IC50 of approximately 7.5 uM. AI-assisted structural modeling (AlphaFold3-based Boltz-1 with GNINA docking) predicted two boldine binding sites on SARM1: the TIR catalytic site (Kd [~] 13.5 uM) and the ARM-TIR regulatory interface (Kd [~] 12 uM). In a sciatic nerve explant model, boldine preserved the integrity of anucleated axonal segments at 3 and 7 days post-transection relative to vehicle controls. These findings suggest boldine may act as a dual-site SARM1 inhibitor and support its development as a neuroprotective therapy after traumatic axonal injury.

neuroscience↗

bioRxiv2026

Structure-function studies of HRIKD-{triangleup}KI, a Minimal Kinase Domain of Human Heme-Regulated Inhibitor Kinase

EIF2 kinase heme-regulated inhibitor (HRI) is a novel target for haematological malignancies with modulators reported to trigger cell death via the HRI-eIF2-ATF4 pathway. We report a protocol for producing the minimal kinase domain of full-length human HRI, termed HRIKD-{Delta}KI, where the unstructured 140 amino acid (aa) kinase insert (KI) within HRI kinase domain (HRIKD) is replaced with a 2aa glycine/serine (GS) linker. X-ray crystal structures were determined of apo-HRIKD-{Delta}KI and of its complex with ATP at 2.1 & 2.5 [A] resolution respectively. Both structures display a canonical bi-lobal kinase fold. However, they remain in a non-productive state with a displaced C-helix, disassembled R-spine, and a disordered activation segment hindering the substrate site. Biophysical assays (fluorescence based thermal shift & Synchrotron Radiation Circular Dichroism) demonstrate HRIKD-{Delta}KI retains its functional ligand-binding conformation. All together, these findings define structural and ligand-binding features of HRI to support ongoing drug discovery efforts in blood cancer.

biochemistry↗

bioRxiv2026

NR4A3 knockdown ameliorates metabolic dysfunction-associated steatotic liver disease through ATF3 transcriptional repression

ObjectivesThe role of nuclear receptor subfamily 4, group A, member 3 (NR4A3) in hepatic steatosis, inflammation, and insulin resistance (IR) within the context of metabolic dysfunction-associated steatotic liver disease (MASLD) remains largely underexplored. Consequently, this study aimed to examine NR4A3s impact on MASLD and the potential underlying mechanisms. MethodsWe aimed to elucidate the functional role of NR4A3 in MASLD through its knockdown in cell culture and animal models. To establish the cell culture model of MASLD, LO2 cells were treated with free fatty acids (FFAs), while male C57BL/6 mice were fed a high-fat diet (HFD) to create the animal model. NR4A3 knockdown was achieved using specific short hairpin RNA (NR4A3-shRNA) in the mice model and three small interfering RNAs (NR4A3-siRNAs) in the cell culture model. The lipids content, fatty acid synthesis, inflammatory factors, and IR were then assessed with and without NR4A3 knockdown. Furthermore, the underlying mechanism through which NR4A3 exerts its influence was explored by analyzing the interaction between NR4A3 and activating transcription factor 3 (ATF3). ResultsIn the cell culture experiments, the knockdown of NR4A3 significantly decreased the lipids content, fatty acid synthesis, and inflammatory factors in the LO2 cells treated with FFAs in the NR4A3-shRNA group compared with those in the NC-shRNA control group. In the animal model experiments, NR4A3 knockdown in the HFD male C57BL/6 mice significantly ameliorated HFD-induced hepatic steatosis, inflammation, and IR. Mechanistically, the knockdown of NR4A3 downregulated the expression and transcriptional activity of ATF3, resulting in an impaired ATF3 function. ATF3 overexpression significantly reversed lipid accumulation decline and reduced inflammation after NR4A3 knockdown. ConclusionThe downregulation of NR4A3 alleviates MASLD by modulating ATF3, suggesting this may be a promising therapeutic target.

pathology↗

bioRxiv2026

Depleting prion protein using splice-switching small molecules

Prion diseases are fatal neurodegenerative disorders driven by prion protein (PrP) misfolding, and lowering cellular PrP represents a promising therapeutic strategy. Here we report a small-molecule approach that reduces PrP by modulating pre-mRNA splicing of the PRNP gene. Through chemical modification of the clinically approved splicing modulator risdiplam, we generated CP3, the first class of compounds that selectively activate a cryptic exon in PRNP and routes its mRNA product for degradation, reducing PrP by [~]70% in cells. We demonstrate that CP3 activity critically depends on alternative splicing factor Luc7L, revealing a novel requirement for alternative splicing factors in small molecule splicing modulation. Strikingly, co-administration of CP3 with a Luc7L activator PTC258 significantly lowers PrP levels in the brains of transgenic mice. These results establish splicing modulation as a powerful strategy for PrP reduction and highlight the potential of small-molecule cooperativity for therapeutic RNA targeting.

biochemistry↗