Biology subjects

Wang, K.

Publications and source records attributed to Wang, K..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Senescence and DNA Damage-Induced Inflammation Drive Heart Failure with Preserved Ejection Fraction in Cardiovascular Kidney Metabolic Syndrome

IntroductionHeart failure with preserved ejection fraction (HFpEF) is strongly associated with cardiometabolic comorbidities, including obesity, diabetes, hypertension, chronic kidney disease and aging, yet the mechanistic contribution of cellular senescence to HFpEF pathogenesis remains poorly defined. Methods and ResultsTo model clinically relevant HFpEF, we subjected p16-3MR mice to a novel chronic "four-hit" cardiovascular-kidney-metabolic stress regimen (10 months of a high-fat diet, low-dose streptozotocin, L-NAME, and aging). These mice developed a robust HFpEF phenotype characterized by left ventricular hypertrophy, impaired diastolic function (reduced E'/A' and elevated E/E'), preserved ejection fraction, reduced -dP/dt, exercise intolerance, pulmonary congestion, and increased cardiac CD68 macrophage infiltration. Cardiac proteomics identified 821 proteins significantly altered by four-hit stress. Selective genetic ablation of p16 senescent cells using ganciclovir ameliorated HFpEF phenotypes, reduced cardiac p16 expression and inflammation, and normalized proteomic remodeling, without affecting body weight or glycemic status. Comparative network analysis of mouse and human HFpEF cardiac proteomes revealed highly concordant upstream regulatory networks, prominently involving cell-cycle control, DNA damage responses, and inflammatory signaling. Immunohistochemical analysis of human HFpEF cardiac biopsies confirmed increased p16, {gamma}H2AX, STING, IRF3, NF-{kappa}B p65, and CD68 macrophages, mirroring the murine findings. The 4-Hit mice also developed chronic diabetic kidney disease with increased kidney inflammation, both of which were attenuated by Senolytic therapy. Mechanistically, the cGAS-STING (cyclic GMP-AMP synthase - stimulator of interferon genes) is activated in response to damaged DNA, which in turn activates the downstream immune responses, including NF-{kappa}B and interferons. Cross-species validation further demonstrated that combined metabolic stress impaired cardiac function and nephrocyte function in Drosophila. Cardiac and nephrocyte dysfunctions were independently rescued by cardiomyocyte-specific and nephrocyte-specific inhibition of the cGAS-STING pathway, respectively. In human iPSC-derived cardiomyocytes, irradiation and palmitate induced senescence, DNA damage sensing via ZBP1, and activation of the cGAS-STING-IRF3 signaling axis; ZBP1 knockdown or senolytic treatment suppressed this inflammatory axis. ConclusionsAcross mouse, human, fly, and human iPSC models, our findings identify DNA damage-driven senescence and ZBP1-cGAS-STING signaling as conserved, causal mechanisms linking cardiovascular-kidney-metabolic comorbidities to HFpEF, highlighting senescence and innate immune pathways as promising therapeutic targets.

pathology↗

bioRxiv2026

Single-crypt evolutionary trajectories of human sporadic and hereditary colorectal precancers

Our understanding of the earliest genomic processes and evolutionary trajectories that distinguish sporadic from hereditary human cancers remains limited, impeding early diagnosis and risk stratification. Here, we performed whole-genome sequencing of 319 single crypts dissected from normal colorectal mucosa, premalignant polyps and malignant colorectal cancers (CRCs) from five sporadic patients and three familial adenomatous polyposis (FAP) patients. We found 66% of premalignant crypts from sporadic polyps did not harbor APC mutations, but frequently accumulated non-canonical but positively selected driver mutations including KMT2C, CACNA1A and FBLN2. In contrast, most premalignant crypts (71%) in FAP indeed acquired one or more somatic APC mutations or 5q loss of heterogeneity (LOH). Sporadic polyps were dominated by clock-like mutational processes at single-crypt level. In contrast, FAP crypts evolved more diverse genomics processes, including reactive oxygen species-associated damages, APOBEC-associated mutagenesis and pks+ Escherichia coli-associated mutagenesis. Premalignant crypts in FAP also exhibited a 2-fold higher burden of LINE-1 retrotranspositions than sporadic ones, despite arising at a substantially younger age. Phylogenetic timing estimations showed that the first somatic APC mutation in FAP often occurs prenatally. Phylogeographic analysis further revealed spatial lineage segregation in early polyclonal polyps, followed by Big-Bang lineage intermixing in later monoclonal ones. Together, these data demonstrate that early colorectal tumorigenesis does not obey a universal APC-first model, where sporadic and hereditary precancers follow distinct evolutionary trajectories. Our study also highlights that polyclonal-to-monoclonal transition in premalignant stages represents the Big-Bang growth of colorectal tumors, offering crucial insight into early diagnosis and risk stratification.

cancer biology↗

bioRxiv2026

Mosaic terrestrial diversity dynamics through the Permo-Triassic interval

The end-Permian mass extinction (EPME) represents the most severe biotic crisis of the Phanerozoic Eon on Earth and has been well documented in marine taxa. However, its impact on terrestrial organisms and ecosystems remains incompletely understood. Here we present a high-resolution reconstruction of terrestrial diversification dynamics and spatial reorganization across the Permo-Triassic boundary (PTB) using comprehensive occurrence data of macroplants, sporomorphs and vertebrates. Terrestrial responses to the EPME show highly temporal, regional and taxonomic heterogeneities. Plants experienced a genus-level diversity loss of [~] 6.7%, across the PTB, whilst vertebrates, a lagged decline from the late Permian, peaking at a diversity loss of [~] 66.7%. Global distributions of plant and vertebrate show converging on similar latitudinal gradients post the PTB. Plant diversity loss is disproportionately high in low-latitude and tropical regions and progressively lower toward mid- and high-latitudes. Our study facilitates a fine-grained understanding to terrestrial macroevolution in geologic history through multi-analysis of a large volume of fossil data. Our findings challenge the long-held notion of global terrestrial collapse and mass extinction in plants during the PTB and offer a deep-time analogue for uneven response of extant terrestrial biodiversity to ongoing climate change.

paleontology↗

bioRxiv2026

Detergent-Free Nuclear-Cytoplasmic Fractionation Enables Spatially Resolved PELSA for Enhanced Nuclear Drug Target Identification

Accurate identification of drug target proteins remain major challenges in proteomics-based target discovery, particularly for low-abundance nuclear proteins that are difficult to detect because of the complexity of whole-cell lysates. Here, we developed a detergent-free nuclear-cytoplasmic fractionation strategy compatible with peptide-centric local stability analysis (PELSA), which markedly improves detection of nuclear drug targets. Using K562 cells, we demonstrated that mild detergent-free fractionation enables high-fidelity nuclear-cytoplasmic separation with minimal cross-contamination. When coupled with PELSA, this workflow significantly increases the number of detected nuclear targets relative to whole-cell analysis. Benchmarking with well-characterized nuclear drugs, including the histone deacetylase inhibitor panobinostat and the RNA polymerase II inhibitor -amanitin, our results showed improved identification of canonical nuclear targets. Broad profiling of staurosporine target further revealed expanded kinase target coverage by combining the results of nuclear and cytoplasmic fraction, with the CLK family kinases detected exclusively in the nuclear fractions. Additionally, we showed that PELSA can also be performed on intact nucleus level. Collectively, these findings establish detergent-free nuclear-cytoplasmic fractionation-PELSA as a robust and scalable strategy for spatially resolved drug target identification, improving sensitivity for nuclear and low-abundance proteins.

biochemistry↗

bioRxiv2026

TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration

Network pharmacology has become a widely used approach for deciphering multi-component, multi-target mechanisms of traditional Chinese medicine (TCM). Here we introduce TCMCard, a high-confidence digital infrastructure built on a Multi-Dimensional Evidence Integration (MDEI) framework. The framework integrates experimental activity data from authoritative chemical databases, literature-derived evidence, and structure-based similarity inference. Preprocessing steps include chemical structure normalization, species-specific filtering, and target quality scoring. Applied to conventional interaction datasets, this pipeline leads to the removal of over 60% of low-confidence noise. TCMCard supports network pharmacology exploration through an interactive visualization platform, and module analysis identifies functionally relevant communities that offer insights into the synergistic actions of TCM formulas. Overall, TCMCard may help move the field beyond simple data aggregation toward evidence-informed curation and quality-driven analysis. As an interactive and publicly accessible platform, it reveals an organized backbone within complex interaction networks, offering a more reliable basis for understanding multi-component synergy in TCM.

bioinformatics↗

bioRxiv2026

Fluorescent Protein Photobleaching: From molecular processes to spectromicroscopy

Fluorescent proteins (FPs) are essential tools for biological imaging but are limited by photobleaching, a light-induced loss of fluorescence intensity that reduces spatial and temporal resolution. Despite extensive use, the molecular mechanisms underlying FP photobleaching remain poorly understood due to the diversity of FPs and the complexity of their photochemistry. Existing approaches either monitor fluorescence decay in live cells, reflecting imaging conditions but lacking molecular detail, or rely on in vitro spectroscopy of purified proteins, providing mechanistic insight but often limited to individual FPs. We introduce a quantitative workflow bridging these approaches by combining live-cell measurements with in vitro spectroscopy. In vitro measurements are performed on a dedicated setup that simultaneously monitors absorption, emission, and fluorescence decay during photobleaching. Applied to six FPs spanning different chromophores, emission ranges and sequences, this approach reveals that photobleaching strongly depends on FP. It involves multiple chemical pathways, including oxidation, dimerization, and backbone cleavage. Spectroscopic analysis uncovers a heterogeneous ensemble of photoproducts with distinct photophysical properties that can remain optically active during irradiation, including shortened fluorescence lifetimes or altered absorption spectra. These findings demonstrate that FP photobleaching cannot be described as a simple ON-OFF process but involves complex transformations affecting both fluorescence intensity and lifetime. Such transformations can introduce significant biases in quantitative imaging, particularly in advanced techniques such as FLIM and FRET. Finally, we introduce quantitative indicators enabling robust comparison of FP photostability across experimental conditions. This framework provides a comprehensive approach for understanding and quantifying photobleaching and its implications for fluorescence imaging.

biochemistry↗

bioRxiv2026

A Targeting Parameter Space for Personalized 4x1 HD-tES: Montage Description, Optimization and Application

BackgroundPersonalized optimization of 4x1 high-definition transcranial electrical stimulation (HD-tES) faces inherent trade-offs between montage flexibility, computational efficiency, and implementation accessibility. Conventional 10-10 electrode systems constrain placement to discrete landmark positions, while unconstrained optimization relies on stochastic algorithms that risk converging to local optima and requires neuronavigation equipment often unavailable in rehabilitation settings. Here we introduce a scalp geometry-based parameter space (SGP) that parameterizes 4x1 HD-tES montages using three intuitive scalp-defined parameters--position, radius, and orientation--and characterize parameter-performance regularities through exhaustive electric field simulations across 30 subjects and 624 cortical targets (>3.6 million configurations). ResultsPosition primarily determined proximity to optimal performance, radius governed the intensity-focality trade-off, and orientation served as fine-tuning. Exploiting these regularities, a minimal search space (SGP-MSS) was constructed that reduced computational complexity by over 90% while guaranteeing global optima identification. Compared with standard 10-10 montages, SGP-MSS achieved up to 99% higher targeting intensity and 126% higher focality (all p < 0.0001). Compared with lead-field-free optimization, SGP-MSS achieved comparable performance with greater cross-subject stability. ConclusionsThe SGP framework enables efficient individualized HD-tES optimization without neuronavigation. Its scalp-based parameterization supports electrode positioning via standard cranial landmark measurements, facilitating translation to routine clinical and home-based rehabilitation settings.

biophysics↗

bioRxiv2026

Mitochondrial protein translation is a heightened dependence and therapeutic vulnerability of chemo-refractory triple negative breast cancer

Triple negative breast cancer (TNBC) patients harboring residual cancer burden following completion of conventional neoadjuvant chemo-immunotherapy regimens have poor relapse-free and overall survival rates and limited therapeutic options. We and others have demonstrated that mitochondrial function is required for the survival of chemo-refractory TNBC. Here, we define the mitochondrial translation machinery as a critical and targetable dependency underlying chemo-refractory TNBC. Analyses of human and orthotopic patient-derived xenograft (PDX) mass spectrometry proteomics datasets revealed that mitochondrial protein translation-related signatures were among the top associated with chemoresistance. These signatures included core mitoribosome components and the mitoribosome-associated factor Oxidase (Cytochrome C) Assembly 1-Like (OXA1L), which was consistently enriched in chemoresistant versus chemosensitive TNBC across datasets. OXA1L, a key mediator of mitochondrial translation and electron transport chain (ETC) assembly, has not been functionally characterized in cancer. We therefore tested whether OXA1L-dependent mitochondrial translation sustains mitochondrial function and chemoresistance in TNBC. Knockdown (KD) of OXA1L in human TNBC cells reduced ETC protein levels, mitochondrial respirasome supercomplex levels, ATP production, and oxidative phosphorylation (oxphos), establishing a requirement for OXA1L in maintaining mitochondrial bioenergetics in TNBC. OXA1L was required for the characteristic oxphos elevation induced by carboplatin (CRB), and KD significantly enhanced CRB sensitivity, demonstrating that mitochondrial translation supports adaptive metabolic responses to chemotherapy. To explore the translational potential of targeting the mitoribosome in TNBC, we leveraged the bacterial ancestry of mitochondria to repurpose the FDA-approved antibiotic tigecycline (TIG) as a mitochondrial translation inhibitor. Direct measurement of mitochondrial nascent peptide levels revealed that, while CRB elevated mitochondrial translation, TIG potently suppressed mitochondrial translation as monotherapy and in combination with CRB or docetaxel (DTX). TIG abolished CRB-induced oxphos, decreased oxphos in combination with DTX, and significantly improved chemotherapy sensitivity in human TNBC cell lines, PDX-derived spheroids, and in vivo. TIG sensitivity associated with mitochondrial translation-related proteomic signatures, concordant with PDX and patient-derived signatures associated with chemoresistance. Together, these data identify OXA1L-dependent mitochondrial translation as a targetable dependency that sustains mitochondrial function and chemoresistance in TNBC, demonstrate that its inhibition enhances chemotherapeutic response, and nominate a mitochondrial translation-related protein signature as a candidate predictive biomarker of TIG sensitivity and chemoresistance. These findings support mitochondrial translation inhibition as a potential therapeutic strategy in chemo-refractory disease. DISCLOSURESGVE is co-founder, Chief Scientific Officer, and an equity stakeholder of Nemea Therapeutics, Inc. G.V.E. formerly received sponsored research funding from Chimerix Inc. G.V.E. receives experimental compounds from the Lead Discovery Center of Germany and from Jazz Pharmaceuticals. MLB is a co-inventor at Nemea Therapeutics. MTL is a founder and limited partner in StemMed Ltd. and a manager in StemMed Holdings, its general partner. MTL is a founder and equity stakeholder in Tvardi Therapeutics Inc. The BCM PDX models, are exclusively licensed to StemMed Ltd., resulting in royalty income to MTL when used for commercial purposes. LED is a compensated employee of StemMed Ltd; however, the PDX models resulting in royalty income to LED were not included in this study. All other authors have nothing to disclose.

cancer biology↗

bioRxiv2026

Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas

Gliomas comprise a heterogeneous group of central nervous system tumors in which gene fusions (GFs) are significant oncogenic drivers and emerging diagnostic and therapeutic biomarkers. In cancer diagnosis, GF detection largely relies on targeted short-read sequencing fusion panels, such as the Childrens Hospital of Philadelphia (CHOP) Fusion Panel (FUSIP). While these panels are effective for detecting recurrent, well-characterized GFs, they are limited to predefined gene sets and cannot identify full-length transcripts. Here, we analyzed 49 high-and low-grade gliomas previously classified as fusion-negative by FUSIP using an untargeted whole-transcriptome RNA sequencing approach with Oxford Nanopore Technologies (ONT) long-read sequencing. This enabled transcriptome-wide fusion discovery of additional known and potentially novel oncogenic GFs beyond panel constraints. Long-read sequencing further allowed direct resolution of full-length fusion transcripts and their associated isoform structures. By integrating GF detection with isoform-level transcript analysis, we identified fusion-associated transcript isoforms with alternative splicing patterns that aligned near reported GF breakpoints, including ZNF254::GNAS and PTPRK::NOX3, which have not been reported in literature or existing fusion databases. To assess functional relevance, candidate GFs were evaluated using the Drosophila melanogaster model, with ventral nerve cord (VNC) morphology serving as a quantitative in vivo readout of fusion-induced disruption of glial regulation. VNC enlargement or elongation reflects abnormal glial growth or defects in brain tissue organization. Of the 15 candidate GFs subjected to experimental functional testing, 8 induced significant VNC abnormalities relative to wild-type controls, indicating fusion-specific disruption and oncogenic potential. Notably, CLDND1::WRN and DUSP22::APOE produced the most pronounced VNC phenotypes. Together, these findings demonstrate that untargeted transcriptome-wide GF discovery, coupled with long-read isoform-level analysis and in vivo functional validation, enables the identification and prioritization of potentially novel and clinically relevant GFs that are missed by standard targeted short-read fusion panels in glioma.

cancer biology↗

bioRxiv2026

Integrated single-cell and spatial transcriptomic analysis of T cell exhaustion and immunometabolic remodeling in HPV-positive oropharyngeal squamous cell carcinoma

HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) harbors dense lymphocytic infiltration yet responds poorly to immune checkpoint blockade (ICB), a paradox whose mechanistic basis remains unresolved. Here we constructed an integrated single-cell and spatial transcriptomic atlas of HPV OPSCC (23,119 cells, 24 cell types), complemented by CRISPR-Cas9 functional validation in two HPV cell lines and multiplex immunofluorescence across independent cases. Pseudotime trajectory analysis placed TOXCD8 T cells, rather than canonically defined exhausted cells, at the terminal exhaustion endpoint, and uncovered a previously uncharacterized IEGCD8 effector memory population at a fate-decision juncture between activation and irreversible exhaustion. Actively cycling Tregs with broad co-stimulatory and co-inhibitory receptor expression underwent intratumoral immunosuppressive differentiation. Compartmentalized LDHA/MCT4 expression in cancer cells versus LDHB/MCT1 in T cells established a directional lactate flux model, and spatial deconvolution confirmed peripheral immune exclusion. We identified a KMT2D-KLF7-PD-L1 regulatory axis: KMT2D sustains KLF7 transcription through H3K4me1-dependent enhancer activation; KLF7 concurrently drives neural crest differentiation and upregulates PD-L1, thereby linking epigenetic remodeling to both neural programming and immune checkpoint expression. These findings define converging multi-scale mechanisms underlying ICB resistance in HPV OPSCC and nominate the KMT2D-KLF7-PD-L1 axis as a combinatorial therapeutic target.

cancer biology↗

bioRxiv2026

Ribosome Processing Factor-2 Interacts with RPL10A to Regulate Selective Translation during Plant Immunity and Drought Stress

Processing of ribosomal RNA (rRNA) is essential for ribosome biogenesis, translation, plant development, and stress adaptation. Ribosome processing factor-2 (RPF2), which plays a role in the later stages of rRNA maturation, interacts with ribosomal protein L10A (RPL10A). RPF2 overexpression in Arabidopsis and Nicotiana benthamiana showed enhanced plant growth and trichome development due to increased gibberellic acid (GA) levels. Conversely, RPF2-silenced and mutant plants had a dwarf phenotype, reduced stomatal apertures, and decreased glucosinolate accumulation. RPF2 silenced and mutant plants also showed compromised nonhost disease resistance, whereas RPF2 overexpression lines exhibited enhanced disease resistance to both host and nonhost pathogens. RPL10A and RPF2 overexpression lines were sensitive to abscisic acid (ABA) and tolerant to drought, which is attributed to their unique roles in translation regulation. Despite having larger stomatal apertures, RPF2 overexpression plants displayed low pathogen multiplication rates and reduced water loss, indicating independent resistance mechanisms associated with ribosomal functions in translation regulation. Although both RPL10A and RPF2 proteins interact with each other and are involved in translation regulation, proteomic analysis suggests that they regulate the translation of distinct sets of genes during pathogen or drought stress. These findings indicate that RPF2 and RPL10A play independent roles in the regulation of unique protein translation.

plant biology↗

bioRxiv2026

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

Noncoding genetic variation contributes to brain disorder risk, but the mechanisms through which it acts in specific brain cell types remain unclear. DNA methylation (DNAm), a highly cell type-specific regulatory layer in the brain, may mediate noncoding genetic risk, yet whether methylation at CG (mCG) and neuron-enriched non-CG (mCH) dinucleotides contribute differently to that risk remains unknown. Here we develop a deep learning framework that predicts DNAm from DNA sequence and estimates variant effects across 186 brain cell subtypes in both mCG and mCH, leveraging single-nucleus DNAm profiles from 46 brain regions. The models reveal distinct transcription factor (TF) programs underlying the two methylation contexts, with mCH-associated TFs showing stronger evolutionary constraint. Predicted variant effects agree closely with cell type-matched mQTLs in both direction and magnitude. Common variants predicted to affect mCG, particularly in excitatory neurons, show substantially greater heritability enrichment for brain-related traits than variants affecting mCH. By contrast, noncoding de novo mutations in autism preferentially perturb mCH, but not mCG, at conserved neuronal regulatory regions. This pattern is replicated across two independent cohorts totaling 5,782 probands and 4,053 unaffected siblings. Together, these findings indicate that common and rare noncoding variants contribute to brain disorders through distinct DNA methylation mechanisms.

genetics↗

bioRxiv2026

Platelets promote acute liver injury via extracellular vesicles-mediated Aldolase A

Platelets have emerged as active regulators of acute liver injury (ALI), yet the molecular mechanisms underlying their pathogenic functions remain poorly defined. Here, we demonstrate that platelets contribute to liver injury, in part, by metabolically reprogramming Kupffer cells (KCs). We show that platelets are actively recruited to the injured liver and communicate with KCs through extracellular vesicles (EVs), which deliver the glycolytic enzyme aldolase A (ALDOA) into recipient cells. This EV mediated transfer promotes glycolytic reprogramming in KCs, contributing to their proinflammatory activation and amplification of hepatic injury. Genetic ablation of Aldoa in platelets attenuated liver injury, demonstrating a pathogenic role for platelet derived ALDOA in vivo. Pharmacological inhibition of ALDOA with Aldometanib markedly attenuated liver injury. Circulating ALDOA levels were elevated in patients with ALI and correlated with disease severity. These findings uncover a platelet macrophage metabolic axis that drives ALI and nominate ALDOA as a therapeutic target and biomarker.

pathology↗

bioRxiv2026

TFBSpedia: a comprehensive human and mouse transcription factor binding sites database

Mapping the genomic locations and patterns of transcription factor binding sites (TFBS) is essential for understanding gene regulation and advancing treatments for diseases driven by DNA modifications, including epigenetic changes and sequence variants. Although several TFBS databases exist, no study has systematically benchmarked these databases across different sequencing technologies and computational algorithms. In this study, we addressed this gap by constructing a TFBS database that integrates all available ENCODE cell line ATAC-seq and Cistrome Data Browser ChIP-seq datasets, comprising 11.3 million human and 1.87 million mouse TFBS. We also integrated previously published TFBS resources (Factorbook, Unibind, RegulomeDB, and ENCODE_footprint) and found each contains a substantial fraction of unique TFBS predictions, highlighting significant discrepancies among existing resources. To assess the accuracy of the combined TFBS regions, we assembled ten independent genomic annotation datasets for evaluation and found that TFBS regions predicted by multiple databases are more likely to represent true and biologically meaningful binding sites. For each predicted TFBS region, we define two scores: the confidence score reflects prediction reliability, while the importance score represents biological functional relevance. Finally, we introduce TFBSpedia, a lightweight and efficient search engine that enables rapid retrieval of TFBS regions and comprehensive annotation information across the integrated databases.

bioinformatics↗

bioRxiv2026

High-Precision Pneumatic Induction of Traumatic Brain Injury in Larval Zebrafish

Zebrafish have recently emerged as a cost-effective vertebrate model for Traumatic brain injury (TBI) research. However, current injury paradigms, particularly the weight-drop method, suffer from poor reproducibility due to sensitivity to small variations in materials and setup. Here, we introduce a high-precision pneumatic piston system, the Zebrafish Pneumatic Injury Device (ZePID), which delivers controlled, repeatable pressure pulses to induce TBI in larval zebrafish. ZePID achieves 97% accuracy in applied force and substantially reduces variability compared with weight-drop approaches. Using 6-days-post-fertilization (dpf) larvae, we quantified injury severity by tracking seizure-like locomotor behaviors. Larvae exposed to 150 psi exhibited a significant increase in maximum swimming speed relative to uninjured controls, as well as increased total distance traveled, consistent with TBI-associated hyperactivity. Overall, ZePID provides a standardized, compact, and high-efficiency method for inducing TBI in larval zebrafish.

neuroscience↗

bioRxiv2026

The diversity of lesion network mapping findings

Lesion network mapping (LNM) has emerged as a popular framework to map the network mechanism of brain disorders using lesions and normative brain connectome (NBC)1. It was first demonstrated in neurological symptoms and was rapidly extended to a broad range of brain disorders in the past decade. A recent study by Van den Heuvel et al. questioned the methodological foundations of LNM2. We here raise concerns regarding their errors and biases in the methodology and visualization. The conclusion of that study--LNM maps circumscribed brain changes mostly to one and the same outcome--is not supported by the data presented.

neuroscience↗

bioRxiv2026

CPLfold: Chimeric and Pseudoknot-capable almost Linear-time RNA Secondary Structure Prediction

Motivation RNA structure plays a central role in how transcripts function, but inferring it reliably remains difficult, especially when pseudoknots need to be part of the prediction. Chemical probing experiments provide additional signals, yet these signals do not directly identify base pairing partners. RNA proximity ligation provides direct evidence of base pairing, but balancing this evidence with pseudoknot prediction accuracy and scalability of structure prediction for long sequences remains challenging. Results We present CPLfold, a fast and flexible RNA folding method that combines thermodynamic modeling with chimeric evidence from RNA cross-linking and ligation experiments, while naturally supporting pseudoknots. CPLfold scales to long sequences and recovers more accurate global structures and long-range interactions than existing approaches across multiple benchmarks such as COMRADES and IRIS. By tuning two simple trade-off parameters (, {beta}) the method allows flexibility in the level of incorporating chimeric evidence and asserting pseudoknots. Availability and Implementation Source code and scripts are available at https://github.com/Vicky-0256/CPLfold. ContactK.Wang-72@sms.ed.ac.uk

bioinformatics↗

bioRxiv2026

Lmna deficiency promotes EPHX2 nuclear translocation to ameliorate cardiac dysfunction in mice

BackgroundCardiovascular diseases are often associated with altered protein subcellular localization. As a major cause of inherited cardiomyopathy, LMNA deficiency could trigger nuclear envelope rupture and broadly impair the localization of nuclear and cytoplasmic proteins. Systemic approaches to identify, dissect and manipulate the localization of endogenous proteins are important for mechanistic and therapeutic investigation. MethodProximity proteomics of the nuclear lamina was performed specifically in cardiomyocytes in Lmna-deficient murine models. AAV-mediated Cas9-based gene silencing and subcellular gene upregulation were conducted via the nuclear localization signal (NLS) and nuclear export signal (NES). Cas9-based somatic mutagenesis was supplemented with the single-strand DNA templates of AAV to achieve robust homology-directed repair (HDR) and targeted NLS knock-in, which translocated cytoplasmic proteins into nuclei. ResultIn vivo proximity proteomics detected increased epoxide hydrolase 2 (EPHX2) in cardiomyocyte nuclei in mice carrying germline or cardiac-specific Lmna truncating variants. This phenotype was associated with ruptured nuclear envelope. Cas9-mediated Ephx2 knockout in cardiomyocytes ameliorated cardiac dysfunction in Lmna-deficient mice. Strikingly, overexpression of NLS-EPHX2, but not NES-EPHX2, also mitigated cardiac dysfunction. The cardiac protective EPHX2 substrates, epoxyeicosatrienoic acids (EETs), did not alter upon NLS-EPHX2 overexpression. By contrast, the Lmna-related DNA damage marker {gamma}-H2AX was reduced. The EPHX-D333A mutant lacking hydrolase activity recapitulated the effects of wildtype EPHX2 in nuclei. AAV-Cas9-based HDR achieved efficient NLS knock-in and EPHX2 nuclear translocation in more than 60% cardiomyocytes, which improved cardiac function. ConclusionLmna deficiency leads to the nuclear translocation of EPHX2, which ameliorated cardiac dysfunction in a hydrolase-independent manner. AAV-HDR-mediated somatic gene editing provides an efficient approach to manipulate the subcellular localization of endogenous proteins in cardiomyocytes in vivo. What is Known?O_LICardiovascular diseases are regulated by the changes in protein subcellular localization. In particular, LMNA-related cardiomyopathy is associated with nuclear rupture and impaired separation between nuclear and cytoplasmic proteins. C_LIO_LIEpoxide hydrolase 2 (EPHX2) is a cytoplasmic hydrolase that catalyzes the hydrolysis of cardioprotective epoxyeicosatrienoic acids (EETs) and aggravates an array of heart diseases including myocardial infarction and heart failure. C_LIO_LICRISPR/Cas9-mediated homology-directed repair (HDR) exhibits uniquely high gene editing efficiency in cardiomyocytes with an AAV-based DNA donor, which is suitable for somatic genetic knock-in of small DNA fragments in vivo. C_LI What New Information Does This Article Contribute?O_LILamin-targeted proximity proteomics specifically in cardiomyocytes uncovers novel proteins undergoing subcellular localization changes upon Lmna deficiency. C_LIO_LILmna deficiency leads to EPHX2 nuclear translocation that ameliorates cardiac dysfunction by both mechanisms of cytoplasmic reduction and nuclear induction. C_LIO_LIAAV-HDR-mediated knock-in provides a robust platform to manipulate subcellular localization of endogenous proteins specifically in cardiomyocytes in vivo. C_LI Cardiovascular diseases are often associated with altered protein subcellular localization, but systemic approaches to identify, study and manipulate subcellular localization remain incomplete. This study established an in vivo proximity proteomics approach to identify novel proteins undergoing localization changes relative to the nuclear lamina. In murine models of LMNA-related cardiomyopathy, this approach uncovered EPHX2, a classic cytoplasmic hydrolase that aggravates cardiovascular diseases, as a new protein that translocated into cell nucleus and exerted a cardiac protective effect. CRISPR/Cas9-based cardiomyocyte gene editing with an AAV-based DNA donor efficiently achieved NLS knock-in into the Ephx2 gene, promoted EPHX2 protein nuclear translocation and mitigated cardiac dysfunction with Lmna deficiency. These findings indicated a novel avenue to identify and manipulate the subcellular localization changes of endogenous proteins for basic and translational cardiology.

pathology↗