Biology subjects

Chen, Q.

Publications and source records attributed to Chen, Q..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Role of Alanine Transaminase in Retinal Metabolic Homeostasis: Potential therapeutic target in retinal diseases

PurposeAlanine transaminases (ALT), encoded by the GPT gene, catalyzes the reversible conversion of pyruvate and glutamate to alanine and alpha-ketoglutarate, thereby correlating carbohydrate and amino acid metabolism. However, its role in the human neural retina remains unclear. This study aimed to explore the expression, localization, and metabolic function of ALT in the human neural retina and its potential involvement in retinal diseases. MethodsALT1 and ALT2 expression and localization were examined in the retinas of healthy and diabetic retinopathy (DR) donors via immunoblotting and immunofluorescence. ALT function was assessed in ex vivo human retinal explants using pharmacological inhibition with beta-chloro-L-alanine (BCLA), followed by the analyses of enzyme activity, tissue injury, and transcriptomic responses. Stable-isotope tracing with 13C-and 15N-labelled substrates combined with GC-MS was used to define ALT-dependent carbon and nitrogen fluxes in macular and peripheral retinas. Redox level (NADPH/NADP+) was also evaluated under tert-butyl hydroperoxide-induced oxidative stress. ResultsALT1 and ALT2 were both expressed in the human neural retina, with prominent localization in Muller glia and photoreceptor inner segments. ALT1 displayed a diffuse cytoplasmic distribution, whereas ALT2 demonstrated a punctate pattern consistent with mitochondrial localization. In DR retinas, ALT1 expression was spatially disorganized and heterogeneous, while ALT2 remained comparatively preserved. Inhibition of ALT with BCLA markedly reduced ALT activity without causing overt cytotoxicity or major transcriptional changes. Isotope tracing demonstrated that retinal ALT predominantly channels pyruvate-derived carbon into alanine, whereas alanine was minimally contributed to pyruvate production under basal conditions. ALT inhibition suppressed alanine synthesis and release, redirected nitrogen flux towards glutamate, glutamine, and aspartate, and uncovered distinct metabolic adaptations in macular but not peripheral retinas. Under oxidative stress, ALT inhibition induced the decrease of NADP+/NADPH ratio and LDH release, indicating improved redox balance and reduced tissue injury. ConclusionsALT is previously unrecognized as a regulator of carbon and nitrogen partitioner in the human neural retina, contributing to redox homeostasis under stress. The altered distribution of ALT1 in DR retina and the protective metabolic effects of ALT inhibition suggest ALT as a potential contributor to retinal metabolic vulnerability and a candidate therapeutic target in retinal diseases.

neuroscience↗

bioRxiv2026

Precise Alternation Between Image-Forming Sample Planes Enables Quantitative Monitoring of Receptor-Arrestin Interaction Dynamics at the Plasma Membrane of Live Cells

Investigations of G protein-coupled receptors (GPCRs) interactions with non-visual arrestins in living cells are essential to understanding the complex molecular mechanisms of GPCR-based signaling. Quantitative analysis of these interactions remains challenging in live cells, particularly when attempting to repeatedly image distinct cellular regions with high precision. Here, we describe the implementation of an optical imaging stabilization approach that integrates the recently developed Focal Readjustment for Enhanced Vertical Resolution (FREVR) technology into a multiphoton microscope, enabling high-precision alternation between image-forming sample planes with < 20-nanometer repeatability and stability over time. Using this setup, we monitored the dynamic recruitment of arrestin-2 (Arr2) to the plasma membrane of HEK-293 cells expressing muscarinic acetylcholine M2 receptors (M2R) by alternatively imaging distinct planes of interest, the basolateral membrane and a membrane cross-section. Following stimulation of M2R by agonist ligand, we observed a pronounced redistribution of cytoplasmic arrestin-2 toward the plasma membrane in both cellular cross-sections and at the basolateral membrane. This method enables direct comparison of receptor and arrestin dynamics across regions of individual cells with very high precision, eliminating the need for averaging over numerous cells in order to denoise biologically relevant signals, and thereby capturing physiological cell-to-cell variability.

biophysics↗

bioRxiv2026

Cooperative Control of Arrestin Activation By Membrane Lipids And Phosphorylation Barcodes

Arrestins regulate G protein-coupled receptor (GPCR) signaling by binding phosphorylated receptors embedded in lipid bilayers, yet how receptor phosphorylation and membrane composition cooperate to control arrestin activation remains unclear. Here, we reconstitute this interplay using N-terminally palmitoylated phosphopeptides tethered to nanodiscs of defined lipid composition and quantitatively measure arrestin-2 (Arr2) activation and membrane engagement. We find that both receptor phosphorylation and the lipid environment are essential for robust Arr2 activation, with phosphoinositides (PIPs) and other anionic lipids facilitating Arr2 activation and membrane association through distinct mechanisms. Systematic profiling of phosphorylation barcodes derived from atypical chemokine receptor 3 (ACKR3) and vasopressin receptor 2 (V2R) identifies phospho-motifs that potently activate Arr2. Moreover, the position of these motifs relative to the membrane determines Arr2 engagement, supporting a model of regional phosphorylation barcodes. Genome-wide motif analysis further links the phosphorylation barcode to predicted arrestin coupling strength and classification into Class A or Class B GPCRs. Finally, lipidated phosphopeptides inhibit GPCR-Arr2 interactions in live cells and enable structural characterization of Arr2-phosphopeptide complexes by cryo-electron microscopy, establishing a membrane-integrated framework for decoding arrestin response.

biochemistry↗

bioRxiv2026

Heterogeneous transmission estimation and strategy optimization for Chikungunya: a vector-borne modeling study differentiating age and sex

Against the backdrop of global climate change and accelerating population mobility in 2025, chikungunya fever (CHIKF) exhibited a trend of worldwide spread, significantly increasing the difficulty of controlling tropical mosquito-borne diseases. To enhance the precision of intervention strategies, this study developed an age- and sex-structured human-mosquito interaction dynamic model based on data from the largest CHIKF outbreak ever recorded in China, and conducted a targeted analysis of prevention and control strategies. By decomposing the basic reproduction number and examining population heterogeneity, asymptomatic males aged 15-59 years were identified as the core transmission group. Optimal control analysis revealed that the synergistic implementation of three measures-- reducing the effective human-to-mosquito transmission rate, reducing the effective mosquito-to-human transmission rate, and suppressing mosquito population density--could reduce the overall infection rate by 95.7586%. Among these, mosquito population suppression should be prioritized as a universal core strategy; however, its protective effect on females aged 60 years and above was relatively weak, warranting particular attention. The study further demonstrated that asymmetric intensity combinations targeting these three intervention pathways--such as intensity profiles of "10%, 90%, 90%" or "60%, 80%, 90%"--could achieve effective outbreak control. This research elucidates population-specific transmission patterns and key pathways for intervention intensity, providing a theoretical and strategic foundation for the precise control of mosquito-borne diseases. It also provides actionable operational insights to support rapid response and strategy optimization for future emerging outbreaks. Author summaryCHIKF is a mosquito-borne viral disease that is gradually spreading from tropical regions to other areas. To achieve more precise control of this disease, we developed an age- and sex-structured analytical model based on the largest CHIKF outbreak in China, aiming to provide a scientific basis for responding to potential future outbreaks with inherent uncertainties. The study found that asymptomatic males aged 15-59 years were the primary drivers of transmission and should be prioritized as a key population for reducing viral spread in prevention efforts. When evaluating the effectiveness of different intervention strategies, females aged 60 years and above were the least affected by the implemented measures, indicating that this group should strengthen personal protection to lower their infection risk. Among all control measures, mosquito suppression was the most effective, suggesting that vector control strategies should be prioritized in future outbreak responses.

pathology↗

bioRxiv2026

Transcranial magnetic stimulation to frontal cortex, unlike occipital stimulation, does not disrupt exogenous attention

Orienting covert attention to a target location improves performance across a wide array of visual tasks [1, 2]. Whereas fMRI studies have identified partially overlapping frontoparietal networks underlying endogenous (voluntary) and exogenous (involuntary) covert attention, these correlational methods cannot establish whether a given region is functionally necessary. Prior neurostimulation studies have established that early visual cortex (V1/V2) is critical for exogenous [3, 4] but not endogenous attention [5], whereas the right frontal eye field (rFEF+) is critical for endogenous attention [5]. Here, we used a combined psychophysical-TMS protocol to investigate whether rFEF+ is also required for exogenous attention. Participants performed an orientation discrimination task, in which a peripheral cue (valid, neutral, or invalid) preceded a target and a distractor stimulus. We applied two successive TMS pulses to rFEF+ during stimulus presentation and measured contrast-response functions (CRFs) to quantify perceptual sensitivity (d') across all attention cueing and stimulation conditions. When the distractor was stimulated, exogenous attention yielded a characteristic response gain at the target--with performance benefits for valid cues and costs for invalid cues at high contrast levels. Crucially, this response gain was entirely preserved when the target was stimulated. This pattern contrasts with previous findings demonstrating that TMS to V1/V2 eliminates exogenous attentional effects at the stimulated location. These results indicate that rFEF+ is not necessary for exogenous attention, and together with previous studies [3-5] complete a double dissociation: rFEF+ is critical for endogenous but not exogenous attention, whereas V1/V2 is critical for exogenous but not endogenous attention. These findings reveal a distinct causal cortical architecture for voluntary and involuntary spatial attention, suggesting that they rely on different cortical scaffolds.

neuroscience↗

bioRxiv2026

Learning latent conformational landscapes encoded in cryo-EM

A protein populates a landscape of structural states, abundant snapshots of which are sampled in every cryo-EM experiment. Current analysis averages these snapshots into single density maps or partitions them into discrete classes, discarding the continuous dynamics encoded in the data. Continuous latent-space methods offer a promising alternative, yet whether their learned representations are physically grounded remains unresolved. Here, we realize cryo-EM as structural landscape microscopy, in which latent density directly reflects the probabilistic distribution of molecular states. A central question is whether such a landscape reflects physical reality. For integrin v{beta}8, the learned landscape shows strong agreement with independently derived molecular dynamics simulations, supporting its physical plausibility. We then apply the landscape to structural states that conventional cryo-EM cannot resolve. For LIS1-mediated dynein activation, the landscape reveals a spectrum of states from dominant conformations to low-population intermediates defined by distinct binding modes, including a previously unresolved state. For the KCTD5/CUL3NTD/G{beta}{gamma} complex, the landscape resolves continuous conformational pathways directly from experimental data. Probability-guided particle selection further improves reconstruction quality.

molecular biology↗

bioRxiv2026

Role of Nonneutralizing Antibodies and Fc Effector Functions in Inhibiting SARS-CoV-2 Infection

Neutralizing monoclonal antibodies (mAbs) are a key component of antiviral therapeutics against SARS-CoV-2; however, the contribution of Fc-mediated effector functions remains underexplored. Here, we compare the antiviral activities of the neutralizing and non-neutralizing mAbs CB6 and CR3022, respectively. The Fc regions of both plant-produced mAbs carried nonfucosylated, non-galactosylated complex glycans (pCB6 and pCR3022), and CR3022 was also produced with mammalian-typical galactosylated, fucosylated glycans (mCR3022). pCR3022 exhibited markedly enhanced antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cell-mediated virus inhibition (ADCVI) compared to mCR3022, indicating a significant impact of Fc glycosylation on antiviral activity despite the lack of neutralization. pCB6 exhibited potent neutralization while further enhancing virus clearance through synergistic Fc effector activity. Our findings suggest that Fc-mediated mechanisms, especially ADCC and ADCVI, can contribute substantially to viral control and may be particularly valuable against immune-evasive variants. These results advance our understanding of the functional roles that non-neutralizing antibodies can play in SARS-CoV-2 infection and highlight the potential of Fc glycoengineering to modulate the antiviral efficacy of both neutralizing and non-neutralizing mAbs.

immunology↗

bioRxiv2026

PA-SfM: Tracker-free differentiable acoustic radiation for freehand 3D photoacoustic imaging

Three-dimensional photoacoustic imaging (3D PAI) has shown great potential in preclinical studies and clinical implementations, while it commonly has sparse sensor arrays, limiting both spatial sampling and the field of view (FOV). Freehand scanning could overcome these limitations through anatomy-adaptive scanning that extends spatial coverage and provides complementary views beyond the fixed array aperture, but its flexibility is conventionally constrained by the need for motor feedback or external pose tracking. Here we introduce PA-SfM, a tracker-free structure-from-motion (SfM) framework that recovers multiple poses directly from PA measurements with superior precision, enabling freehand 3D PAI without external pose measurements. PA-SfM integrates a differentiable acoustic radiation model with hierarchical optimization and rigid array constraints, it jointly estimates inter-view transformations and reconstructs 3D volumes. The performance of PA-SfM was demonstrated in numerical simulations, animal studies and human imaging experiments. Compared with motor encoder-based fusion of the mechanically scanned system, PA-SfM produced sharper and more continuous vascular reconstructions with an expanded FOV. In controlled quantitative validations, PA-SfM achieved high reconstruction fidelity, with PSNR values over 40 dB and SSIM values above 0.98 relative to ground truth or known pose reference reconstructions. These results demonstrate that PA-SfM enables robust freehand 3D PAI, with particular potential for clinical implementation of large-scale freehand imaging. The source code is publicly available at https://github.com/JaegerCQ/PA-SfM.

bioengineering↗

bioRxiv2026

SpacerScope: Binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias

The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive off-target assessment remains a bottleneck, particularly in large, complex genomes where existing tools often suffer from prohibitive computational costs, poor search-space convergence, and limited sensitivity toward non-canonical alignments involving insertions and deletions (indels). To address these limitations, we developed SpacerScope, an off-target analysis framework that enables unbiased, genome-wide discovery by leveraging binary vectorization and high-speed bitwise operations. Benchmarking against CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6,142/6,142) within our defined parameter space, achieving zero false negatives while identifying additional high-risk sites with complex edit distances. Unlike conventional tools such as Cas-OFFinder, CHOPCHOP, and CRISPOR, SpacerScope maintains high sensitivity for indel-inclusive off-targets that are otherwise overlooked. Our results establish SpacerScope as a high-speed, high-sensitivity solution for ensuring genome-editing specificity across diverse and complex genomic landscapes. The full source code, documentation, and multi-platform executables are available at https://github.com/charlesqu666/SpacerScope. Graphical TOCSpacerScope is a genome-wide off-target profiling tool for RNA-guided nucleases that combines binary vectorization, bitwise prefiltering, compact 2-bit substitution search, and right-end-anchored indel validation. In the evaluated datasets, it recovered all 6,142 parameter-defined true off-target sites from CIRCLE-seq and showed improved detection of indel-containing candidate sites relative to the previous tools tested here. SpacerScope provides interpretable event-level annotations and empirical risk scores for downstream guide assessment. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/715005v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@bad2ddorg.highwire.dtl.DTLVardef@169b0aborg.highwire.dtl.DTLVardef@1cde3b2org.highwire.dtl.DTLVardef@1fbd11_HPS_FORMAT_FIGEXP M_FIG C_FIG Practitioner Points> SpacerScope enables genome-wide off-target profiling with explicit support for substitutions, insertions, and deletions in a single workflow. > The method combines binary-channel prefiltering with right-end-anchored validation to reduce the search space while preserving sensitivity within the evaluated parameter ranges. > SpacerScope returns event-level match annotations and empirical risk scores, supporting more interpretable downstream guide selection and benchmarking.

bioinformatics↗

bioRxiv2026

ERFMTDA: Predicting tsRNA-disease associations using an enhanced rotative factorization machine

MotivationtRNA-derived small RNAs (tsRNAs) have emerged as a novel class of regulatory molecules implicated in the pathogenesis of many human diseases, making them as promising biomarkers and therapeutic targets. However, existing computational methods for tsRNA-disease association prediction often overlook explicit biological attributes and complex feature interactions, limiting their predictive performance. ResultsWe propose ERFMTDA, an enhanced rotative factorization machine framework for predicting potential tsRNA-disease associations. ERFMTDA explicitly models complex interactions among heterogeneous biological features while integrating latent structural representations derived from the global association matrix. In addition, a biologically informed negative sampling strategy based on motif-level sequence similarity is introduced to improve the reliability of negative samples. Extensive experiments demonstrate that ERFMTDA consistently outperforms eleven state-of-the-art methods. Case studies on diabetic retinopathy and hepatocellular carcinoma further confirm its ability to prioritize biologically meaningful tsRNA-disease associations. Availability and implementationThe source codes and datasets of ERFMTDA are available at https://github.com/lanbiolab/ERFMTDA.

bioinformatics↗

bioRxiv2026

Origin and functional impact of early nonlinearities in primate retina

Receptive fields provide a concise description of the stimulus selectivity of visual neurons. But this stimulus selectivity is neither static nor linear, and these nonlinear effects are not well captured by standard linear or pseudo-linear receptive field models. At the same time, receptive field models incorporating nonlinear effects are largely empirical, and are not easily interpreted in terms of underlying cellular and synaptic mechanisms. Here we show that two nonlinear mechanisms in the primate outer retina shape neural responses and that these contribute significantly to responses to natural stimuli and to the retinal output signals. Incorporating these outer retinal nonlinearities into models for visual function will improve our ability to identify the mechanistic origin of specific features of downstream visual responses.

neuroscience↗

bioRxiv2026

SCALE: Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

Virtual cell models aim to enable in silico experimentation by predicting how cells respond to genetic, chemical, or cytokine perturbations from single-cell measurements. In practice, however, large-scale perturbation prediction remains constrained by three coupled bottlenecks: inefficient training and inference pipelines, unstable modeling in high-dimensional sparse expression space, and evaluation protocols that overemphasize reconstruction-like accuracy while underestimating biological fidelity. In this work we present a specialized large-scale foundation model SCALE for virtual cell perturbation prediction that addresses the above limitations jointly. First, we build a BioNeMo-based training and inference framework that substantially improves data throughput, distributed scalability, and deployment efficiency, yielding 12.51* speedup on pretrain and 1.29* on inference over the prior SOTA pipeline under matched system settings. Second, we formulate perturbation prediction as conditional transport and implement it with a set-aware flow architecture that couples LLaMA-based cellular encoding with endpoint-oriented supervision. This design yields more stable training and stronger recovery of perturbation effects. Third, we evaluate the model on Tahoe-100M using a rigorous cell-level protocol centered on biologically meaningful metrics rather than reconstruction alone. On this benchmark, our model improves PDCorr by 12.02% and DE Overlap by 10.66% over STATE. Together, these results suggest that advancing virtual cells requires not only better generative objectives, but also the co-design of scalable infrastructure, stable transport modeling, and biologically faithful evaluation.

cell biology↗

bioRxiv2026

Grass Expression Atlas: an RNA-seq-based expression resource for grass species.

Grass Expression Atlas (GExA) is an interactive web-based resource for rapid exploration of gene expression across diverse tissues, developmental stages, and conditions in grass species. GExA integrates publicly available RNA sequencing (RNA-seq) datasets for four millets: pearl millet (Cenchrus americanus), foxtail millet (Setaria italica), proso millet (Panicum miliaceum), and finger millet (Eleusine coracana), and includes barley (Hordeum vulgare) and sorghum (Sorghum bicolor) as reference species. Datasets were processed using a unified processing workflow to generate expression values in transcripts per million (TPM). The current release comprises 4,673 samples from 442 BioProjects, including 987 pearl millet samples and 2,216 foxtail millet samples, and is provided through a user-friendly web interface. GExA is designed for scalable expansion to additional species via the pipeline used in this study. GExA is freely available at https://webpark2116.sakura.ne.jp/RNADB.

bioinformatics↗

bioRxiv2026

NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages drive chemoradiotherapy resistance in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is among the most aggressive cancers, with low rates of durable response to chemoradiotherapy and limited therapeutic options for relapsed disease. To uncover mechanisms of treatment resistance and relapse, we performed comprehensive multi-omics profiling of >100 pre-treatment and post-relapse ESCC tumors from a prospective clinical trial (NCT04694391), integrating whole-exome/genome sequencing, bulk RNA-sequencing, single-cell RNA sequencing, and spatial transcriptomics. We identify somatic alterations in NFE2L2/KEAP1 in nearly 40% of relapsed patients, which are associated with upregulation of NRF2 signaling targets in resistant tumors and cell line models. At single-cell and spatial resolution, relapsed tumors are enriched for NRF2-activated epithelial cells that physically co-localize with immunosuppressive SPP1TREM2 macrophages. This co-localization suggests a synergistic interaction between NRF2-driven tumor programs and macrophage-mediated immune suppression that promotes relapse after chemoradiotherapy. Our findings nominate NFE2L2/KEAP1 mutations as predictive biomarkers for patient stratification and highlight therapeutic targeting of NRF2 signaling and SPP1TREM2 macrophages as rational strategies to overcome resistance in ESCC.

cancer biology↗

bioRxiv2026

Geoclimatic oscillations and ancient reciprocal adaptive introgression shape the evolutionary trajectories of threatened Coilia

Geoclimatic oscillations have repeatedly reshaped biodiversity, yet how ancient lineages persist and diversify through profound environmental upheavals remains a central question in evolutionary genomics. By integrating chromosome-level genome assemblies, population genomics, and transcriptomic data across the Coilia species complex, we reconstruct deep evolutionary histories of Coilia along the dynamic East Asian margins. Our analyses reveal divergences dating to the Miocene, coinciding with major tectonic and climatic transitions, including Tibetan Plateau uplift-linked reorganization of the Yangtze drainage toward the East China Sea, and the Middle Miocene Climatic Optimum. Despite long-term separation, we uncover evidence for ancient, reciprocal introgression among Coilia lineages, with gene flow confined to discrete genomic regions rather than distributed genome-wide. These introgressed regions are enriched for loci associated with immune function, vascular development, and osmoregulatory processes, and exhibit population genetic signatures consistent with positive selection. Temporal modelling indicates that this window of adaptive exchange preceded Pleistocene glacial intensification, after which gene flow became effectively restricted. Together, our results suggest that transiently permeable species boundaries historically acted as reservoirs of adaptive variation, shaping evolutionary trajectories and facilitating niche differentiation under repeated geoclimatic oscillations. This study highlights ancient adaptive introgression as an important evolutionary process contributing to the long-term persistence of threatened coastal fishes.

evolutionary biology↗

bioRxiv2026

Z-RNA-ZBP1 axis drives Tau-mediated neurodegeneration

Although the causes of Tau aggregates vary, once Tau aggregates are formed, their neurotoxicity significantly contributes to neuronal death and cognitive decline in tauopathies, with Alzheimers disease (AD) being the most well-known example. Despite its central pathogenic role, however, effective therapeutic strategies targeting neurotoxicity of Tau remain poor. Here we demonstrate the pathogenic role of neuronal cell death in Tau-related neurodegeneration. Tau-expressing neurons undergo cell death through Z-DNA-binding protein 1 (ZBP1) activation triggered by endogenous Z-RNAs. These Z-RNAs are derived from reactivated transposable elements (TEs) that are typically silenced within heterochromatin. Tau aggregates show a strong affinity for H3K9me3-modified chromatin, effectively sequestering these epigenetic marks from Heterochromatin Protein 1 (HP1), thereby disrupting the condensation of constitutive heterochromatin. Clinically, an inverse correlation between ZBP1 expression levels in excitatory neurons and cognitive performance in AD patients was observed. Importantly, Zbp1 haploinsufficiency significantly ameliorated cognitive deficits in aged Tau-transgenic mice (24-month-old), highlighting the therapeutic potential of ZBP1 inhibition to strive against neurodegeneration in tauopathies.

neuroscience↗

bioRxiv2026

Oxidation-Driven mtDNA B-Z Transition Activates ZBP1 to Mediate Acetaminophen Hepatotoxicity

Acetaminophen (APAP) overdose induces mitochondrial damage in hepatocytes, leading to secondary toxicity that resists to N-acetylcysteine (NAC) treatment and culminates in hepatocyte death and acute liver failure (ALF)1. The underlying mechanisms remain poorly understood, often necessitating liver transplantation2. Here, we identify oxidative modification-driven B-to-Z transitions in mtDNA as the central pathological driver of APAP-induced ALF. Upon APAP exposure, oxidized mtDNA fragments leak into the cytosol, activating ZBP1 signaling via its Z domain. Genetic inhibition of ZBP1 mitigates liver damage and improves survival. Using synthetic 12-bp dGdC duplexes, we demonstrate that 8-oxoG substitution, even under physiological salt concentrations, is sufficient to induce Z-DNA formation, enabling specific ZBP1 binding through its Z domain. The 8-oxoG repair enzyme OGG13, activated by TH107854, removes 8-oxoG modifications and reverses Z-DNA to B-DNA conformation. In mice with lethal APAP toxicity, delayed NAC treatment results in 50% mortality. In contrast, TH10785 monotherapy increases survival to 90%, while its combination with NAC achieves 100% survival. These results define the oxidized mt Z-DNA-ZBP1 axis as a critical driver of APAP hepatotoxicity, providing fundamental insights into DNA conformational dynamics and therapeutic opportunities in drug-induced liver failure.

cell biology↗

bioRxiv2026

Chronic Paraventricular OX1R Overexpression Induces Oxidative Stress and Hypertension in Rats

BackgroundHyperactivity of the orexin system has been implicated in hypertension, yet the long-term impact of orexin 1 receptor (OX1R) overexpression in the paraventricular nucleus (PVN), a key brain region involved in arterial blood pressure (ABP) regulation, remains unclear. This study examined whether chronic OX1R overexpression in the PVN alters cardiovascular, neuroendocrine, and oxidative functions. MethodsAdult male Sprague-Dawley rats received bilateral PVN injections of AAV2-OX1R or control virus AAV2-GFP. Their ABP and heart rate (HR) were monitored for eight weeks via radiotelemetry. Renal sympathetic nerve activity (RSNA) and ABP responses to PVN orexin A administration were assessed using in vivo recordings. Reactive oxygen species (ROS) were quantified using MitoProbe, and gene expression was analyzed by qPCR. Primary neuronal cultures were used to explore underlying mechanism involved in increased ROS production and neuronal activity. ResultsPVN OX1R overexpression increased mean ABP ([~]10 mmHg), water intake, and ROS levels in both the PVN and peripheral organs. In addition, orexin A evoked exaggerated RSNA (155% vs. 73%) and pressor responses (27 vs. 16 mmHg) in PVN OX1R overexpression rats compared to control rats, these effects were attenuated by the OX1R antagonist SB408124. Plasma vasopressin levels were elevated, and brain sections confirmed increased ROS in OX1R-positive neurons. In vitro experiments further demonstrated that orexin A upregulated ROS-generating enzymes, suppressed antioxidant genes, and enhanced neuronal excitability. ConclusionChronic PVN OX1R overexpression induces oxidative stress, sympathetic overactivity, and increased plasma vasopressin, contributing to hypertension development. Targeting PVN OX1R signaling may provide therapeutic benefit for hypertension.

physiology↗