Biology subjects

Shi, L.

Publications and source records attributed to Shi, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

CellClick: an interactive platform for adjustable and accurate cell type annotation in single-cell and spatial omics data

Single-cell omics and spatial omics technologies are nowadays widely used in biological and medical research. In both single-cell and spatial omics data analysis, accurate cell type annotation is a key step for downstream analysis and scientific discoveries. However, high-quality cell annotation usually requires multiple rounds of manual analysis for result refinement, which poses great challenges to most researchers. Here, we present CellClick, an interactive platform for convenient and accurate cell type annotation in single-cell and spatial omics data. CellClick provides Data Preprocessing, Data Visualization, Cell Annotation, Annotation Validation, and Cell Reannotation modules, which facilitate automatic or user-guided cell selection and annotation. The feasibility of using CellClick to generate more accurate cell annotation results was exemplified by both scRNA-seq and spatial transcriptomics data.

bioinformatics↗

bioRxiv2026

Engagement-Dependent Neural Entrainment Underlies Dissociable tACS Effects on Item and Sequence Working Memory

A central challenge in neuromodulation research is to elucidate how exogenous electrical stimulation interacts with endogenous neural dynamics to shape cognitive function. Drawing on empirical evidence for dissociable oscillatory mechanisms underpinning item versus sequence working memory (WM), we employed transcranial alternating current stimulation (tACS) and magnetoencephalography (MEG) to establish a causal separation and characterize the underlying neurophysiological basis. We observed a clear behavioral and neural dissociation: prefrontal 6-Hz theta stimulation selectively enhanced item WM, whereas frontoparietal in-phase theta stimulation specifically improved sequence WM. MEG further revealed task-specific modulation effects: during sequence WM, where frontoparietal theta synchrony predicted memory success, in-phase theta stimulation selectively amplified inter-regional synchronization. In contrast, during item WM, where local theta power was indicative of memory success, the identical stimulation overall exerted no significant modulation effect. Critically, across both tasks and oscillatory measures (inter-regional synchronization and theta power), the magnitude of stimulation-induced modulation scaled with each region's or connection's contribution to memory performance, indicating that tACS proportionately amplifies actively engaged oscillatory processes. This engagement-dependent principle explains task- and region-specific neurophysiological effects and the variability in behavioral outcomes, providing a framework for designing precise, functionally aligned stimulation protocols to enhance translational efficacy.

neuroscience↗

bioRxiv2026

An endodermal subpopulation generates neural and mesodermal fates in the posterior chick embryo

Embryogenesis occurs through a progressive narrowing of cell fate potential, initiating with the segregation of three distinct germ layers during gastrulation. Although classically, each germ layer contributes to distinct tissue types as development proceeds, this view has been revised with the discovery of neuromesodermal progenitors (NMPs) -- a bipotent progenitor population in the posterior embryo that gives rise to traditionally ectodermal and mesodermal tissues after gastrulation has concluded. However, until now the notion of lineage restriction of the endoderm to gastrointestinal, respiratory, and endocrine tissues has largely remained intact. Here, we describe a unique subpopulation in the chick endoderm that initially lines the ventral surface of Hensens node (the amniote organizer). As posterior regression of the node ends with termination of the primitive streak, these cells undergo an FGF-dependent epithelial-to-mesenchymal transition, erasing their endodermal identity as they invade the tailbud and subsequently differentiate into a remarkably broad range of cell types including paraxial, lateral plate, and intermediate mesoderm, and to a lesser extent, notochord and neural tube. Disrupting ingression of node endoderm reduced embryonic axis elongation -- a process attributed to mesoderm -- by 50%. Through lineage barcoding, single-cell RNA sequencing, and fate mapping experiments, we conclude that the endodermal compartment of Hensens node harbors a mixed population of fate restricted and multipotent progenitor cells that give rise to clonal populations spanning traditional germ layer boundaries. These findings illustrate a surprising example of germ layer plasticity and fate convergence across distant progenitor populations during amniote development.

developmental biology↗

bioRxiv2026

Visuospatial coding by theta oscillations in human hippocampus

The hippocampus has been proposed to support visual processing and perception, challenging longstanding accounts that emphasize navigation or declarative memory. A key prediction of visual-processing accounts is that the hippocampus should exhibit similar visuospatial coding properties to those of higher-order visual neocortical areas, such as sensitivity to the size of visual stimuli and contralateral visual field biases. We tested for these properties using intracranial EEG to measure hippocampal neural activity during a retinotopic mapping task. The hippocampus exhibited characteristic slow ([~]2 Hz) and fast ([~]8 Hz) theta oscillations throughout the task. Fast theta was responsive to the presence but not the amount of visual stimulation. In contrast, slow theta did not generally respond to stimulus presence but scaled with the size of the visual stimulus, consistent with larger receptive fields. Slow theta also showed a contralateral bias, an effect that was specific to the right hippocampus. None of these effects were attributable to microsaccades or performance of the concurrent vigilance task. These findings provide electrophysiological evidence for visual field coding by human hippocampus, supporting accounts of hippocampal function that emphasize its role atop the visual hierarchy. Visual processing of this kind may combine with self-motion, memory, and other signals to support the broader spatial and mnemonic functions with which hippocampal theta oscillations have long been associated.

neuroscience↗

bioRxiv2026

Identification of non-covalent inhibitors for the atypical peroxiredoxin PRDX5 as a therapeutic strategy in malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is an aggressive asbestos-linked cancer with limited therapeutic options and a dismal 5-year survival rate of [~]5%. While aberrant production of reactive oxygen and nitrogen species (ROS/RNS) is a hallmark of MPM, targeted approaches to exploit these redox vulnerabilities remain scarce. Here, using the MOSAIC multimodal cancer patient atlas, we identify Peroxiredoxin 5 (PRDX5) as being significantly upregulated in the epithelioid subtype of MPM. We show that MPM cells exhibit enhanced resistance to nitrosative and oxidative stress compared to healthy mesothelial cells, a phenotype correlated with basal PRDX5 expression. Next, utilising a machine learning guided discovery pipeline, we identified three putative allosteric pockets in PRDX5 and conducted a virtual screen of 3.6 million compounds. High-throughput biochemical validation of 452 candidates yielded 36 non-covalent hits, including sub-micromolar inhibitors. These findings establish PRDX5 as a novel, subtype specific therapeutic target in MPM and provide a chemical framework for the development of next-generation redox-modulating oncology treatments.

cancer biology↗

bioRxiv2026

Neutrophil migration in the lung is altered by alveolar collapse and stretch

RationaleHeterogeneous alveolar collapse is prevalent in inflammatory lung conditions such as chronic obstructive pulmonary disease, acute respiratory distress syndrome, and pneumonia. Although neutrophil-released proteases contribute to the tissue remodeling that leads to alveolar collapse, how this altered mechanical environment in turn affects neutrophil migration remains largely unexplored. ObjectivesIn this study, we investigate how alveolar collapse and stretch influence neutrophil migration and identify the mechanical and biochemical factors that govern regional migration differences. MethodsWe developed a novel precision-cut lung slice platform that generates collapsed vs non-collapsed regions within the same slice. Neutrophils in both regions were longitudinally imaged for up to 5 hours to quantify motility behavior. Migration mechanisms were probed using migration-related inhibitors, collagenase, and cigarette smoke extract. A crystal ribcage system, which preserves intact alveolar shape and the air-liquid interface, was also used to assess the effects of ventilation on neutrophil migration. ResultsNeutrophil migration was faster in the collapsed region compared to not-collapsed regions. This regional difference was eliminated by Rho-associated protein kinase (ROCK) inhibition, which selectively increased migration speed in the non-collapsed region. The regional difference persisted with the addition of collagenase and cigarette smoke extract, both of which significantly increased the migration speed in both regions. In the crystal ribcage, the preserved air-liquid interface and ventilation together enhanced neutrophil migration compared with a collapsed lung. ConclusionsAlveolar collapse and stretch facilitate neutrophil migration, indicating the role of localized tissue remodeling in driving neutrophil activity and further disease progression.

bioengineering↗

bioRxiv2026

Functional Landscape of Motifs within the Sarbecovirus Spike Cytoplasmic Tail

Sarbecoviruses exhibit extensive diversity in host range and zoonotic potential. Although the ectodomain of the viral spike protein has been well characterized, the functional landscape of the cytoplasmic tail (CT) remains poorly defined. To address this gap, we systematically generated CT truncation variants of representative spike proteins from all major ACE2-utilizing clades to define the roles of conserved host factor-interacting motifs associated with COPI, COPII, FERM, and SNX27. Using vesicular stomatitis virus (VSV)- and lentivirus-based pseudotyping systems, we evaluated viral entry in cells expressing varying levels of ACE2 and TMPRSS2. Our results demonstrate that CT-associated motifs differentially regulate viral infectivity. Specifically, truncation of the COPI- or SNX27-binding motifs markedly reduces entry efficiency, whereas disruption of the COPII-binding motif produces the opposite outcome. By contrast, removal of the FERM-binding motif consistently enhances infectivity across lineages. Mechanistically, truncation of this motif increases spike expression, cell surface localization, incorporation into virions, and particle stability. Importantly, despite these pronounced effects on viral infectivity, deletion of the FERM-binding motif does not affect antigenicity, receptor dependence, or sensitivity to protease inhibitors, as demonstrated by neutralization and inhibition assays. In addition, this approach substantially increases spike protein density on virus-like particles (VLPs). Collectively, by extending the analysis beyond SARS-CoV-1 and SARS-CoV-2, our study reveals a generalizable mechanism in which cytoskeletal anchoring mediated by the FERM-binding motif acts as a limiting determinant of viral assembly. These findings provide a practical framework for optimizing pseudovirus platforms and guiding vaccine development against emerging viral threats.

microbiology↗

bioRxiv2026

Coordinated subpocket engagement underlies nitazene potency at the μ-opioid receptor.

Nitazenes are emerging synthetic opioids that exhibit exceptionally high potency at the {micro}-opioid receptor (MOR) and contribute to rising overdose fatalities worldwide. Despite extensive in vitro profiling, the structural determinants underlying their structure-activity relationships (SARs) remain unresolved. Here, we combine functional profiling with quantum mechanical calculations and molecular dynamics (MD) simulations to establish a MOR structure-based SAR for nitazenes. Across functional assays, systematic variation at the R1, R2, and R3 positions revealed non-additive effects on potency and identified optimal R1 chain length, R2 N-desethylation, and retention of the 5-nitro group as key determinants of high MOR potency. Consistent with this framework, N-desethyl isotonitazene emerged as the most potent analogue. Structural analysis of the cryo-EM MOR-Gi-fluornitrazene complex, together with MD simulations of multiple nitazene analogues, revealed a conserved trivalent binding architecture in which each substituent engages distinct subpockets. N-desethylation at R2 increases the positive electrostatic surface at the protonated amine, reduces steric constraints near transmembrane helix (TM) 7, strengthens R3 interactions, and allosterically modulates R1 engagement in a substituent-dependent manner. Additionally, optimal R1 chain length and shape stabilize the TM5-TM6 interface and influence activation-relevant TM6 dynamics, defining a unified SAR at R1 across nitazene and fentanyl scaffolds. Together, these findings indicate that nitazene potency reflects substituent-dependent coupling among R1, R2, and R3 within the MOR binding pocket, with R3 engagement distinguishing nitazenes from fentanyl. This framework establishes a coherent structural model of nitazene-MOR recognition that accounts for their unusually high potency and efficacy.

molecular biology↗

bioRxiv2026

Label free multimodal optical imaging of metabolic heterogeneity in aging by integrating SRS, MPF, FLIM, and SHG

Cellular metabolism is governed by the coordinated organization of macromolecules, including lipids and proteins, together with redox-active cofactors such as NADH and FAD. However, resolving these biochemical features quantitatively and spatially at subcellular resolution remains challenging because no single imaging modality can capture molecular composition, redox state, and tissue architecture simultaneously without labeling. Here, we present MANIFEST (Multimodal Analysis of Nonlinear Imaging for Functional Endogenous Spatial correlaTion), a label-free imaging platform that integrates stimulated Raman scattering (SRS), second harmonic generation (SHG), multiphoton fluorescence (MPF), and fluorescence lifetime imaging microscopy (FLIM) with their spatial correlation. MANIFEST combines chemical imaging of lipids with autofluorescence- and lifetime-based quantification of NADH and FAD metabolism, enabling spatially resolved analysis of metabolic heterogeneity at organelle and tissue-compartment levels. We apply this framework to four distinct aging or disease models: amyloid-beta-treated tri-cultured brain cells, high-fat diet mouse liver, human non-ischemic cardiomyopathy tissue, and aging mouse retina. Across these systems, MANIFEST reveals disease-associated lipid remodeling, redox imbalance, disrupted metabolic zonation, collagen reorganization, and layer-specific metabolic changes. By integrating complementary nonlinear optical modalities into a single label-free platform, MANIFEST provides an extensible, proof-of-concept platform for high-resolution metabolic phenotyping in complex biological systems and offers new opportunities for studying disease mechanisms, aging biology, and metabolism-driven tissue pathology.

bioengineering↗

bioRxiv2026

Long-lived yeast-derived lipids promote longevity via regional and systemic metabolic remodeling

Aging is marked by a progressive breakdown of intestinal integrity and metabolic homeostasis, which together drives systemic decline in physiology and reduces lifespan. Here, we found that dietary lipids extracted from a genetically engineered long-lived yeast strain robustly extend lifespan in Drosophila and further uncovered the mechanisms using deuterium oxide-probed stimulated Raman scattering microscopy to image metabolic dynamics and single nucleus RNA sequencing (scRNA-seq) to unveil the underlying pathways. These yeast lipids are enriched in shorter, more saturated fatty acids and phospholipids as revealed by Raman spectroscopy and lipidomics, contributing to increased membrane order and reduced lipid storage. Functionally, targeted dietary supplementation with these lipid components synergistically prolongs fly lifespan. We show that these lipids reverse age-related declines in gut lipid droplet abundance, enhance membrane lipid incorporation, and increase de novo lipid synthesis, thereby improving epithelial structural integrity and barrier function. snRNA-seq identifies transcriptional remodeling in metabolically active enterocytes, including upregulation of autophagy and protein turnover genes, alongside reduction of unsaturated fatty acid biosynthesis. In the brain, dietary lipids orchestrate a dual metabolic strategy--promoting energy conservation and enhanced signaling across most neuronal and glial populations, while selectively boosting mitochondrial function in memory-critical Kenyon cells. All these leads to the enhancement of gut-to-glia communication, particularly through EGFR and FGFR pathways. Finally, analysis of our data with the Fly Metabolic Analysis Pipeline (FLY-MAP) reveals that yeast lipids restructure gut metabolic modules to coordinate energy production, redox balance, and nutrient flexibility. Our study uncovers a cross-kingdom mechanism of metabolic longevity regulation, paving the way for leveraging yeast-derived nutritional components to support tissue homeostasis and promote healthy aging.

molecular biology↗

bioRxiv2026

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

Immunosenescence, the age-associated decline in immune function, is a key feature of human aging. In human lymphoid organs, however, the specific immune cell populations that acquire senescence-associated phenotypes during aging and how they influence the surrounding tissue microenvironment remain poorly understood. A spatially resolved map of these senescence-associated immune states in human lymphoid tissues could help clarify their relationship with aging and their potential contributions to the progressive decline of immune function. Here, we integrated single-cell and spatial multi-omics to systematically characterize age-related senescence in human lymph nodes (LNs). Single-cell transcriptomics of lymphoid tissues from donors aged 18 to 100 years old identified 34 immune and stromal cell types and revealed age-associated upregulation of senescence signatures in specific populations. Spatial proteomic profiling of 99 LN sections from 51 donors (18-86 years) using high-plex immunofluorescence ([~]20 million cells) mapped senescence markers (p16, p21, HMGB1, -H2AX) at single-cell resolution, revealing diverse senescent-like cell types ("senotypes") and a stepwise shift from extrafollicular to germinal center (GC) localization with age. Notably, we observed focal clonal-like senescence in GC B cells in older donor LNs. Spatial transcriptomics, epigenomics, and metabolic imaging of selected samples further elucidate the multi-omics signatures and underlying mechanisms of functional impairment, metabolic remodeling, and distinct regulatory programs in senescent-like GC B cells. This study presents a comprehensive spatial atlas of senescence-associated immune states in human lymph nodes, revealing cell-type-specific and spatial heterogeneity that may contribute to immunosenescence and the decline of immune function during aging.

immunology↗

bioRxiv2026

GPLD1 Regulates the Shedding of IZUMO1R to Block Polyspermy in Porcine Oocyte

Mammalian fertilization commences with the essential interaction between sperm IZUMO1 and its oocyte-surface receptor, JUNO. Following gamete fusion, JUNO is rapidly shed from the oocyte to establish a definitive membrane block to polyspermy, a pathological condition that remains a major hurdle in porcine in vitro fertilization (IVF). Despite its biological importance, the molecular networks driving JUNO cleavage has remained elusive. Here, by integrating proteomics, dual-color live-cell imaging, and functional perturbations, we identify the extended existence of JUNO and the GPI-specific phospholipase D1 (GPLD1) as the requisite enzyme mediating JUNO shedding in porcine oocytes. Targeted knockdown or pharmacological inhibition of GPLD1 stabilizes oocyte JUNO, prolongs the window of oocyte receptivity, and significantly exacerbates polyspermy, ultimately compromising embryonic developmental competence. Conversely, GPLD1 overexpression restricts redundant sperm adherence and enhances the efficiency of monospermic zygote formation and blastocyst development. Live-cell imaging reveals that fertilization triggers a transient, pulsed recruitment of GPLD1 in the oocyte, which precisely coincides with the biphasic kinetics of JUNO depletion. Our findings establish that the enzymatic cleavage of the GPI-anchor by GPLD1 is critical for JUNO release, defining a fundamental mechanism for the membrane-level block to polyspermy. This work provides a molecular framework for ensuring sperm-oocyte recognition and improving in vitro fertilization outcomes in mammals.

developmental biology↗

bioRxiv2026

A conserved enhancer cluster regulates efnb2 expression in the vertebrate dorsal retina

The vertebrate retina is patterned along its dorsal-ventral (DV) axis by conserved signaling centers, yet the cis-regulatory architecture maintaining these territories remains unclear. Using the four-eyed fish Anableps anableps, which enables physical separation of dorsal and ventral retina, we integrated RNA-seq, ATAC-seq and Hi-C to map DV regulatory landscapes. We identify a 29-kb dorsal-enriched enhancer cluster within a gene poor region between efnb2a and gtpbp8, embedded in a conserved topologically associating domain spanning efnb2a-gtpbp8-slc10a2. Dorsal-biased chromatin contacts link this cluster to the efnb2a promoter. The orthologous human region contains a genome-wide significant association with retinal thickness (rs2575134; P = 2e-14). Leveraging the compact genome of Tetraodon nigroviridis, we cloned the orthologous interval and show that it drives dorsal retina-specific reporter expression in zebrafish and mouse. Together, these results identify an evolutionarily conserved regulatory domain controlling retinal axial identity and linking enhancer architecture to human ocular variation. Funding, National Science Foundation.

evolutionary biology↗

bioRxiv2026

NetTracer3D Enables User-Friendly Analysis of Diverse Microscopic and Medical 3D Datasets

Recent advances in high-resolution imaging and spatial transcriptomics have enabled reconstruction of complex 3D tissue maps, providing unprecedented insights into cellular connectivity, organization, and tissue architecture. However, standardization challenges hinder integration, sharing, and analysis of these datasets across research communities. We developed NetTracer3D to simplify three-dimensional image analysis across diverse datasets. NetTracer3D is an integrated tool for defining, processing, and sharing 3D tissue maps with standardized data formats and interactive exploration capabilities. It provides three broadly applicable network analysis modalities: Connectivity networks for analyzing functional tissue units or cells connected via secondary structures such as nerves or vasculature; Branch Adjacency and Branchpoint networks for converting branched anatomical structures into analyzable representations; and Proximity networks for grouping structures by spatial relationships to identify cellular organization patterns. We demonstrate several use cases applying NetTracer3D to analyze multidimensional data from CODEX and label free Raman spectroscopy, multiscalar data encompassing subcellular and anatomical scales and a range of modalities. NetTracer3D was able to characterize neural relationships between functional tissue units in human and mouse kidneys and mouse bronchi. Branchpoint networks were used to identify vascular defects in human brain angiogram and define the innervation structure of a lymph node. Finally, we demonstrate how proximity networks characterize the tumor microenvironment in 3D light sheet cancer images and auto-detect cellular neighborhoods in multiplexed 2D CODEX datasets. Beyond network creation, NetTracer3D enables analysis, spatial statistics, and visual analytics tailored for volumetric tissue data. By establishing interoperable formats and analysis workflows, this work provides accessible and reproducible analytical tools for 3D spatial biology, enabling new discoveries of relationships between structure and physiology.

genomics↗

bioRxiv2026

Muscleblind-like proteins dimerize by forming disulfide bonds to regulate alternative splicing and pathogenic RNA foci formation

Muscleblind-like (MBNL) RNA-binding proteins (RBPs) possess modular domains that mediate regulation of alternative splicing and RNA localization. Myotonic Dystrophy Type 1 is a CTG repeat expansion disorder where MBNL is sequestered into intranuclear RNA foci, impairing its function. Previous studies found that MBNL self-associates through its exon 7, but the nature of this interaction is not well understood. We identified a cysteine in MBNL1 exon 7 that enables dimerization through formation of an intermolecular disulfide bond. We likewise demonstrate that MBNL2 dimerizes by forming disulfide bonds between multiple cysteines in its carboxy-terminus. Nucleocytoplasmic fractionation revealed a greater proportion of MBNL1 dimer in the nucleus, suggesting a nuclear function for the MBNL1 dimer. We investigated a connection between MBNL1 dimerization and MBNL1-mediated regulation of alternative splicing. To accomplish this, we mutated the MBNL1 cysteine in question to alanine (C325A) and performed RNAseq. We uncovered novel splicing events sensitive to MBNL1 dimerization. We also found that MBNL1 C325A, when co-expressed with expanded CTG repeats, produces smaller, more numerous foci, suggesting a role for the MBNL1 dimer in maintaining foci integrity. These results provide insight into biological and pathological mechanisms of MBNL1 dimerization and suggest other RBPs might similarly dimerize to regulate function. GRAPHICAL ABSTRACT

molecular biology↗

bioRxiv2026

Stepwise GRN co-option in the evolution of a dipteran respiratory organ

The origin of morphological novelty lies at the heart of evolutionary biology, yet how ecological shifts drive its emergence through rewiring of gene regulatory networks (GRNs) remains poorly understood. Here, we dissect the roles of GRN co-option in the development and evolution of the prothoracic respiratory organ (PROD), a key innovation facilitating aquatic respiration in dipteran pupae. Ancestral-state reconstruction across over 200 species reveals that PROD originated [~]241 Ma in the common ancestor of Diptera, with a major increase in structural complexity in schizophoran flies [~]66-70 Ma. These transitions coincide with the Carnian Pluvial Episode and the K-Pg mass extinction, periods of profound climatic and ecological upheaval that likely imposed selection pressure for efficient pupal gas exchange in flooded or submerged habitats. Using comparative transcriptomics, scRNA-seq, and genetic manipulations in Drosophila melanogaster and Aedes albopictus, we demonstrate that PROD is a prothoracic wing serial homolog, specified by a cut-centered spiracle GRN and arising through heterochronic activation of an appendage GRN. In schizophoran flies, increase in complexity of PROD involved additional co-option of a breathless-centered tracheal GRN. Our findings reveal a stepwise model of hierarchical GRN co-option and provide potential links between geo-climatic events to the origin and escalation of morphological novelty. This eco-evo-devo framework provides a mechanistic and generalizable paradigm for how ecological challenges are translated into morphological innovations over macroevolutionary timescales.

evolutionary biology↗

bioRxiv2026

Convergent effects of neurodevelopmental disorder-associated variants at mitochondria

Investigations into the molecular pathogenesis of clinically defined neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD) and schizophrenia (SCZ) have produced evidence implicating dysfunctional mitochondrial metabolism. However, the functional connection between risk variants and mitochondrial proteins largely remains unclear. We tested the hypothesis that proteins encoded by NDD-associated copy number variants (CNVs) and SCZ risk genes are enriched within the mitochondrial interactome. We found that NDD- and SCZ-associated genes exhibit mitochondrial association comparable to their overlap with synaptic proteins, with interaction networks converging most strongly on mitochondrial translation. Two high-risk CNVs, the 3q29 deletion (3q29Del) and the 22q11.2 deletion (22q11Del), confer similar risks for ASD and SCZ and have independently been linked to mitochondrial phenotypes. To test whether these CNVs produce convergent effects on mitochondrial proteins in developing human neural tissue, we generated an isogenic series of 3q29Del and 22q11Del induced-pluripotent stem cells (iPSCs) and differentiated them into forebrain cortical organoids. Quantitative proteomic analysis showed high similarity in the profiles of dysregulated proteins in 3q29Del and 22q11Del compared to isogenic controls. Enrichment analysis of proteins altered in both variants revealed significant convergence on the mitochondrial ribosome and translation machinery. Furthermore, manipulation of mitochondrial translation elicited similar proteomic and functional responses in organoids and neural progenitor cells across both CNVs. These findings indicate that NDD-associated genes have rich interactions with mitochondrial proteins and that two of the strongest risk factors for NDDs may similarly disrupt neural mitochondrial metabolism through impaired mitochondrial translation.

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↗