Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

lncRNAs contribute to caste differentiation as a regulatory layer in ants

Caste differentiation in ants represents one of the major evolutionary transitions and provides a unique model for studying developmental mechanisms underlying division of labor. Genetically identical individuals follow divergent epigenetically-regulated developmental trajectories that give rise to morphologically distinct phenotypes and specialized roles. While long non-coding RNAs (lncRNAs) are emerging as key epigenetic regulators across diverse biological systems, their specific contributions to caste development in social insects remain largely unexplored. Here, we conducted comprehensive transcriptomic analyses across major developmental stages of two evolutionarily and ecologically distinct ants Monomorium pharaonis and Acromyrmex echinatior, identifying over 10,000 lncRNAs. We demonstrated that lncRNAs exhibit dynamic, caste-specific expression patterns throughout development. We also identified a subset of lncRNAs displaying canalized expression patterns, characterized by progressively increasing caste bias and decreasing within-caste variation as development proceeds. Co-expression analyses revealed that canalized lncRNAs are functionally linked to canalized protein-coding genes, which are crucial regulators for caste differentiation. These canalized lncRNAs show striking tissue-specific enrichment consistent with canalized protein-coding genes. Functional validation through RNA interference revealed that canalized lncRNAs directly regulate caste-specific traits. Furthermore, juvenile hormone treatment capable of redirecting worker lncRNA expression profiles toward gyne-like patterns, with similar expression changes and tissue specificity to JH-responsive protein-coding genes, linking lncRNA regulation to established hormonal pathways controlling caste fate. Our findings establish lncRNAs as active architects of caste differentiation in social insects, demonstrating that these rapidly-evolving regulatory molecules contribute to the evolution and maintenance of social phenotypes through tissue-specific regulation of caste-associated developmental programs.

developmental biology↗

bioRxiv2025

Multimodal AI for Single cfDNA Profiling and Cancer Screening

Cell-free DNA (cfDNA) serves as a non-invasive biomarker for cancer detection, but conventional methods face challenges due to the ultra-low abundance of tumor-derived cfDNA (ctDNA) among normal cfDNA. Though nucleosome-bound cfDNA harbors rich epigenomic features that could enable ctDNA identification by single-molecule multi-omics cross-validation, this remains unexplored due to methodological limits. Here, we developed a cfDNA sequencing approach integrating methylation, fragmentomics, and histone modifications at the single-molecule level; together with gene semantics and epigenomic annotations, these modalities were vectorized and fused to represent each cfDNA molecule. We trained a Transformer-based model (cfAI) to profile and evaluate ctDNA likelihood at molecule, gene, and sample levels. cfAI achieved [~]10-fold enrichment of cancer-derived signals over noise and reached 72.6% sensitivity at 93.1% specificity for multi-cancer detection. Our study establishes an innovative framework that overcomes the inherent signal-to-noise limitations of conventional assays and reveals biological features at molecular resolution for cancer detection.

bioinformatics↗

bioRxiv2025

MusTer: A Generalizable Microfluidic Platform Combining Multi-Parametric Droplet Sorting and Multi-Droplet Merging in Single-Cell Sequencing

Droplet microfluidics is a core technology that powers high-throughput single cell sequencing. However, the current generation of single-cell microfluidics faces notable limitations, including cell aggregation, suboptimal on-chip reactions that compromise experimental outcomes and elevate background noise, as well as a dependence on costly commercial barcode beads. To address these challenges, we present MusTer, an integrated next-generation platform with multi-parametric singlet droplet sorting and triple-droplet merging capability. MusTers multi-parametric singlet sorting module enables in-line droplet analysis of intrinsic fluorescence peak amplitude, width and interval from single-nucleus- (singlet) or multiple-nuclei (multiplet)-encapsulating droplets, subsequently allowing an effective separation of the singlet droplets from multiplet droplets and empty droplets. MusTers triple-droplet merging module enables precise multi-step reactions, with each step performed under its own optimal conditions, thereby significantly enhancing experimental flexibility and efficiency. We validated MusTers performance by performing single-cell ATAC-seq on maize leaves. The results demonstrate that MusTer significantly reduces the doublet rate, enhances the signal-to-noise ratio, and yields improved cell clustering compared with traditional methods. These results validate MusTers capability to overcome key limitations in droplet-based single-cell analysis, effectively enhancing data quality and reliability, and also paves the way for its use in other challenging sample types and multi-step single-cell assays.

bioengineering↗

bioRxiv2025

Comparative Study of BBB-Targeting AAV Capsids on Central Nervous System Delivery Efficiency

The efficacy of adeno-associated virus (AAV)-mediated systemic gene therapy for central nervous system (CNS) diseases is often limited by the blood-brain barrier (BBB). This study systematically evaluated the tissue distribution of three BBB-crossing AAV capsid variants (PHP.eB, CNSRCV300, and BI-hTFR1) following intravenous injection in mice, using either a constitutive promoter (CAG) or a neuron-specific promoter (hSyn) to drive EGFP reporter expression. Compared with AAV9, both PHP.eB and CNSRCV300 demonstrated significantly enhanced BBB penetration and brain transduction efficiency. While the use of the hSyn promoter led to reduced transgene expression in the brain compared with the CAG promoter, and substantially decreased visible reporter expression in peripheral organs, viral deposition in the liver could still be detected via immunohistochemistry. Overall, CNSRCV300 exhibited the most favorable balance between brain-targeting efficiency and biosafety, highlighting its potential as a promising delivery vector. In summary, both the capsid and promoter jointly influence AAV-mediated expression in vivo, and although cell type-specific promoters can reduce off-target expression, residual viral deposition in non-target tissues remains a potential safety concern.

neuroscience↗

bioRxiv2025

Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology

Sporotrichosis is a globally distributed subcutaneous mycosis caused mainly by Sporothrix brasiliensis, S. schenckii, and S. globosa. Cat-transmitted sporotrichosis, primarily caused by S. brasiliensis in South America and to a lesser extent by S. schenckii in Southeast Asia, is emerging as a significant public health concern, due its outbreak potential. Itraconazole is the first-choice drug for treatment of human and cats, but reduced susceptibility has been reported based on previously proposed epidemiological cut-off values (ECVs). To support resistance surveillance, we aimed to establish CLSI-endorsed ECVs for these clinically relevant Sporothrix species. A total of 3,588 minimum inhibitory concentration (MIC) values for seven antifungal agents (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, olorofim, and terbinafine) were obtained from 19 international laboratories. Four of seven antifungals met the CLSI M57 guidelines criteria to determine the ECV. Established ECVs for amphotericin B were found to be high with 8 {micro}g/mL for S. brasiliensis and S. globosa, and 4 {micro}g/mL for S. schenckii. Itraconazole ECVs were 4 {micro}g/mL for S. brasiliensis and S. schenckii. Posaconazole ECVs were 4 {micro}g/mL for all three species (tentative for S. globosa), while the terbinafine ECV for S. brasiliensis was 0.12 {micro}g/mL. Olorofim demonstrated good in vitro activity, particularly against S. brasiliensis. Overall, this study establishes validated ECVs for key antifungals against Sporothrix species and identifies a low prevalence of non-wild type (NWT) isolates, supporting ongoing antifungal resistance monitoring.

microbiology↗

bioRxiv2025

Adipocyte-related genes analysis contributes to the prognosis of atrial fibrillation

BackgroundPatients with mild left atrial appendage fibrosis have a significantly lower rate of atrial fibrillation (AF) recurrence after 5 years compared to those with moderate or severe fibrosis, which presented a significantly increased positive area of cellular senescence. MethodsGSE135445, a RNA-sequencing dataset between epicardial adipose tissue (EAT) from patients with persistent non-valvular AF and sinus rhythm (SR), was downloaded and analyzed and hub genes were obtained. To obtain the abundance of immune cells, the CIBERSORT algorithm with 100 permutations was applied. The senescent hub genes were obtained and validated using human blood samples. ResultsA total of 164 up-regulated and 317 down-regulated DEGs was obtained between EAT from subjects with AF and SR. Using immune infiltration analysis in whole PAT related DEGs, the abundance of M0 macrophages was significantly different between PAT and SAT and 22 M0 macrophages-related DEGs were also obtained, such as MMP7, APOE, CCND1, MMP12 and APOC1. Venn diagram was utilized to obtain the same transcripts between senescence datasets and DEGs and PPI network was used to 94 overlapping genes. The top15-degree senescence adipicytes hub genes were explored. To investigate senescence-related hub genes effects on AF progression, we collected the blood samples of patients with paroxysmal atrial fibrillation and persistent atrial fibrillation. There were no significant differences at baseline characteristics and laboratory examinations at 1d after admission except heart failure history and function examinations, for instance, ALT, LDL, LVEF and LA diameters. Using univariate analysis and multivariate analysis, heart failure history, ALT and LA diameters can be prognostic factors for AF progression. BMP7, COL4A3, COL4A4, CHRD, IRX1, SPON1, ALPL, TCF19 and SIX2 were validated to be highly expressed in persistent atrial fibrillation compared to paroxysmal atrial fibrillation. ConclusionBased on our current study, BMP7, COL4A3, COL4A4, CHRD, IRX1, SPON1, ALPL, TCF19 and SIX2 were validated to be highly expressed in persistent atrial fibrillation compared to paroxysmal atrial fibrillation, which may be potential therapeutic targets to treat AF progression and improve patients prognosis.

genetics↗

bioRxiv2025

Temporal Dynamics of High-Frequency Oscillations in Alzheimer's Disease: A Longitudinal Study in hAPP-J20 Mice

Alzheimers disease (AD) is characterized by progressive cognitive decline and increased seizure susceptibility; yet both the mechanistic and temporal links between AD and epileptogenesis remain poorly defined. In this study, we conducted a longitudinal analysis of epileptogenesis in relation to AD pathology using hAPP-J20 transgenic mice aged 9 to 27 weeks, encompassing the AD conversion phase. Wireless electroencephalography (EEG) was employed to monitor hippocampal high-frequency oscillations (HFOs), including ripples (80-200 Hz) and fast ripples (250-600 Hz), in conjunction with histological, behavioral, and neurophysiological assessments to characterize underlying neural circuit alterations. We identified three distinct epileptogenic stages in transgenic mice: (1) 9-15 weeks: emerging memory deficits, increased excitatory/inhibitory (E/I) neuron ratio, mossy fiber sprouting, and peak seizure-related mortality, alongside the initial emergence of pathological HFOs; (2) 15-21 weeks: a pronounced escalation of pathological HFO activity and persistent network hyperexcitability preceding detectable amyloid plaque deposition, indicating rapid epileptogenic progression; (3) 21-27 weeks: stabilization of HFO activity despite continued progression of amyloid accumulation, suggesting a plateau in epileptogenic remodeling amid advancing Alzheimers pathology. These findings indicate that neuronal hyperexcitability precedes amyloid plaque deposition and likely contributes to disease progression, highlighting a critical early window for therapeutic intervention in AD. Moreover, pathological HFOs hold promise as electrophysiological biomarkers of early circuit dysfunction and represent a promising target for modifying the course of AD. O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/693578v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@2e4a24org.highwire.dtl.DTLVardef@1059f53org.highwire.dtl.DTLVardef@1f1d57org.highwire.dtl.DTLVardef@bf3cde_HPS_FORMAT_FIGEXP M_FIG C_FIG Figure abstractThis study examines the temporal dynamics of epileptogenic activity and amyloid pathology in hAPP-J20 transgenic mice, a model of Alzheimers disease (AD). Top: Illustration of pre-plaque and post-plaque stages in hAPP-J20 mice, depicting neural network alterations, amyloid plaque deposition, and electrophysiological changes. The top panel shows the transition from a pre-plaque to a post-plaque state, where early hippocampal activity is stable and amyloid plaques are absent. As pathology advances, the network exhibits progressive hyperexcitability, characterized by increased pathological HFOs (ripple-IEDs, fast ripples), neuronal loss, NPY sprouting, and amyloid plaque formation. Bottom: The progression of key biomarkers and disease hallmarks, comparing hAPP-J20 transgenic (Tg) mice with non-transgenic (nTg) controls. The bottom panel quantifies biomarker progression over time, revealing that CaMK2+/PV (C/P) imbalance emerges first, followed by a peak in pathological HFOs incident rate (patho-ripple, fast ripple rate), and finally, amyloid beta plaque (A{beta} plaque). These findings establish a temporal relationship between early network hyperactivity and amyloid accumulation, underscoring the importance of targeting neural hyperexcitability as a therapeutic strategy to mitigate AD progression.

neuroscience↗

bioRxiv2025

Stimuli-Expressed Protein Qubits for Quantum Quantification of Heavy Metals in Natural Water

Environmental heavy metal pollution poses a severe threat to ecological security and human health, necessitating the development of highly sensitive, specific, and rapid detection technologies. Traditional fluorescent biosensors are often constrained by high background interference and limited sensitivity, while single-target detection systems struggle to meet the demands of complex environmental monitoring. This study constructs a novel magnetically modulated photonic quantum biosensing system based on the CadC-T7 gene circuit, replacing the traditional fluorescent reporter gene EGFP with the magnetically modulated fluorescent protein MagLOV - a quantum biomaterial. To enhance its magnetic modulation performance, the mutant with the highest lock-in amplitude during the directed evolution (R10, MagLOV 2) was selected; Simultaneously, systematic parameter optimization was conducted to determine the optimal magnetic modulation frequency (0.05 Hz), the heavy metal stimulation duration (the 2-hour group exhibited the most significant intra-group variation), and the bacterial concentration at the onset of the heavy metal stimulation (controlled at OD600 = 1 to prevent fluorescence quenching due to culture turbidity). The system demonstrates excellent multi-analyte detection capabilities for lead chloride, lead nitrate, and cadmium chloride across a concentration range of 10-8 to 10-4 M. Compared to conventional steady-state photometric methods based on EGFP and MagLOV 2, the lock-in analysis of MagLOV 2 achieves detection sensitivities enhanced by 1[~]2 orders of magnitude, with detection limits as low as 2.4 nM for cadmium chloride, 4.8 nM for lead nitrate, and 9.9 nM for lead chloride. Langmuir isotherm fitting results demonstrate high quantitative accuracy (R2 > 0.950), with particularly outstanding fitting performance for cadmium chloride (R2 = 0.999) and lead nitrate (R2 = 0.995).

synthetic biology↗

bioRxiv2025

Epitope and functional classification of human neutralizing antibodies against SFTSV Gn

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a lethal bunyavirus lacking approved countermeasures. From SFTS survivors, we isolate 84 human monoclonal antibodies (mAbs) against the viral glycoproteins Gn and Gc. Gn-specific mAbs demonstrate superior neutralization breadth and potency compared to the restricted neutralizing activity observed with Gc. Using a high-throughput yeast display deep mutational scanning (DMS) platform, we classify Gn-head mAbs into eight epitope groups, among which four groups (IA, ID, IIIA, IIIB) conferring neutralization. Notably, mAbs BD70-4003 (group IA) and BD70-4017 (group IIIA) exhibit broad neutralization and provide 100% protection in a lethal mouse model. Cryo-EM structural analysis of these mAbs in complex with the Gn-head reveal their binding interfaces, directly validating the epitope residues identified by DMS. Our study delineates the antigenic landscape of SFTSV Gn, identifies potent therapeutic candidates, and establishes DMS coupled with structural validation as a powerful framework for antibody discovery against bunyavirus.

immunology↗

bioRxiv2025

Characterization of hippocampal subfields using histology-based annotated postmortem MRI: Lessons for in vivo segmentation II

High-resolution in vivo magnetic resonance imaging (MRI) of hippocampal subfields is a rapidly advancing field due to their implication in cognition, disorder, and disease. Hippocampal subfield segmentation on in vivo MRI is generally guided by postmortem reference material, which has been limited by small sample sizes that preclude comprehensive characterization of subfield border locations and their variability. Addressing this, we characterized hippocampal subfield border variability in two ultra-high-resolution postmortem MRI datasets with combined annotated histological sections, including cases with and without dementia. We examined: 1) the order of appearance and disappearance of subfields along the long axis of the hippocampus; 2) the order of appearance and disappearance of subicular subregions; 3) the medial-lateral position of subicular subregional boundaries along the hippocampal body; 4) the location of the CA3 relative to hippocampal head digitations; 5) the subfield borders in the hippocampal body relative to a volume proportion of the dark band; and 6) the association of hippocampal length and subiculum-CA1 border location with diagnosis, demographic factors, and factors related to postmortem imaging. Our findings reaffirmed that there is a consistent order of appearance and disappearance of subfields in the hippocampal head and tail, respectively. The subicular subregions exhibited a first in, last out order of appearance and disappearance, and pre/parasubiculum consistently occupied half of the subicular complex in coronal slices throughout the hippocampal body. Hippocampal head digitations were not a reliable landmark for CA3 appearance, but SRLM proportionality did offer a potentially consistent approach for estimating CA2 and CA3 subfield borders in relation to the hippocampal border. No clear relationship was found between the anatomical features and diagnosis, demographic factors, and factors related to postmortem imaging. These findings have implications for the development and harmonization of hippocampal subfield segmentation protocols and interpretation of high-resolution functional MRI studies of the human hippocampus.

neuroscience↗

bioRxiv2025

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

Immunosenescence, a major hallmark of systemic aging, refers to the progressive functional decline of the immune system. This decline not only compromises host defense and immunological memory but also fuels chronic inflammation and tissue degeneration (collectively known as inflammaging). While single-cell RNA sequencing (scRNA-seq) has revealed transcriptomic alterations in immune aging, analyses restricted to transcript abundance fail to capture deeper regulatory layers, such as transcript isoform diversity and the remodeling of immune receptor repertoires. To address this, we present the human peripheral immune single-cell multi-omics atlas that integrates gene expression, transcript isoforms diversity, and immune receptor repertoires. By combining single-cell full-length transcriptome sequencing (scCycloneSEQ), short-read scRNA-seq, and single-cell immune receptor sequencing (scTCR/BCR-seq), we systematically profiled peripheral blood mononuclear cells (PBMCs) from healthy young and elderly donors. Our analyses uncovered extensive age-related remodeling of immune cell composition, functional states, and TCR/BCR diversity. Notably, we identified in CD4 effector memory T cells exhibited widespread differential isoform usage (DIU), 3'UTR length variation, and a marked reshaping of cytotoxic T lymphocyte (CTL) clonotypes--all closely associated with aging-related inflammation and cellular senescence. This multi-omics atlas delineates key molecular features of immunosenescence and provides a high-resolution resource for deciphering the regulatory architecture underlying immune aging.

immunology↗

bioRxiv2025

Brain endothelial PRMT5-ANGPTL4 axis regulates cerebellar inhibitory synaptogenesis and motor coordination

Brain vasculature is essential for central nervous system function, but its specific roles in synaptic development and motor function regulation are poorly understood. In this study, we identify a cerebrovascular signaling axis wherein endothelial PRMT5 critically regulates inhibitory synaptogenesis and motor coordination. Cerebrovascular-specific deletion of Prmt5 gene leads to excessive inhibitory synaptic input onto Purkinje cells and progressive motor deficits in mice. Mechanistically, PRMT5 deficiency epigenetically upregulates the expression of the secreted factor ANGPTL4 through reduced symmetric dimethylation of H3R8 and H4R3, along with increased H3K9 acetylation at the Angptl4 promoter, thereby driving excessive inhibitory synaptogenesis onto Purkinje cells. Importantly, Angptl4 deletion in brain endothelium normalizes inhibitory synaptic input onto Purkinje cells and restores motor coordination in PRMT5-deficient mice. Together, these findings define the endothelial PRMT5-ANGPTL4 axis as a key regulator of cerebellar inhibitory circuitry and motor function, highlighting cerebrovascular mechanisms as potential therapeutic targets for motor coordination disorders. Teaser Cerebrovascular PRMT5 prevents excessive inhibitory synaptogenesis via epigenetic repression of Angptl4.

neuroscience↗

bioRxiv2025

Structure basis for distinct protective mechanisms of IGHV3-23 antibodies targeting influenza hemagglutinin stem

Characterization of antibodies targeting the conserved stem domain of influenza hemagglutinin (HA) is critical for developing broadly protective countermeasures against influenza virus. From a phage display human antibody library, this study discovers three group 1 HA-specific stem antibodies, namely HB31, HB34, and HB315, all of which are encoded by IGHV3-23. While HB31 and HB34 have minimal neutralization activity in vitro, their Fc-mediated effector functions lead to better in vivo protection than the potently neutralizing HB315. Consistently, cryo-EM analysis suggests that HB31 and HB34 have a higher Fc accessibility than HB315, based on their epitopes and approaching angles. HB31 and HB34 engage a pocket in the upper HA stem that is rarely targeted by known HA stem antibodies, whereas the epitope of HB315 involves the lower stem. Overall, our findings provide insights not only into the structure-function relationship of HA stem antibodies, but also into the design of next-generation influenza therapeutics.

immunology↗

bioRxiv2025

Plateau potentials are instructive signals for behavioral timescale synaptic plasticity in the neocortex

Learning occurs via the adjustment of synaptic weights across a variety of timescales. The mechanisms supporting these processes, from single-shot to iterative learning, are unclear. The prevailing model in the neocortex, spike-timing dependent plasticity (STDP), requires many pairings of precisely coordinated activity. This is difficult to reconcile with single-shot learning in behaving animals. In hippocampus, an alternative form of plasticity driven by plateau potentials (behavioral timescale synaptic plasticity; BTSP) alters synaptic weights in a single trial to reorganize spatial representations. Here we show that layer 5 pyramidal neurons (L5 PNs) of mouse primary visual cortex (V1) exhibit highly prevalent plateau potentials that drive single-shot changes in sensory representations. Spontaneously occurring and experimentally induced plateaus rapidly and persistently modified L5 PN responses to visual stimuli. In acute slices, plateau potentials drove synapse-specific plasticity with few repetitions across seconds-long pairing intervals. Our results demonstrate that plateau potentials in the neocortex rapidly reshape neuronal representations through BTSP. This instructive form of plasticity provides a mechanism for dynamic adjustment of neocortical synaptic weights to support rapid learning.

neuroscience↗

bioRxiv2025

A Reference Atlas of the Human Dorsal Root Ganglion

Somatosensory perception largely emerges from diverse peripheral sensory neurons whose cell bodies reside in dorsal root ganglia (DRG). Damage or dysfunction of DRG neurons is a major cause of chronic pain and sensory loss. In mice, deep single-cell transcriptomic profiling and genetically defined models have offered important clues into DRG function, but in humans, the cellular and molecular landscape of DRG neurons remains less understood. Here, we constructed a reference cell atlas of the human DRG by profiling transcriptomes of cells and nuclei from 126 donors sampled across cervical, thoracic, and lumbar DRGs. This atlas resolves 22 neuronal subtypes, including known and previously unrecognized subtypes linked to nociception, mechanosensation, thermosensation, and proprioception, as well as 10 types of non-neuronal cells. Cross-species integration, spatial transcriptomics, and microneurography enabled cell-type-specific comparisons of soma size and conduction velocity between species. Human DRG somata are larger across all cell types than their mouse counterparts, and the conduction velocities of human hair follicle innervating A-fibers are faster than in mice, suggesting a functional shift in rapid mechanical detection in humans. This integrated human DRG reference cell atlas provides a resource for exploring new molecular and physiological features of human DRG, which could help identify new strategies for treating chronic pain and other diseases of the peripheral nervous system.

neuroscience↗

bioRxiv2025

FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data

Integrating single-cell and spatial omics data remains challenging due to strong batch effects across experiments and platforms. Existing methods focus on minimizing these effects but cannot disentangle technical variation from true biological signals. Here, we present FADVI, a variational autoencoder framework partitioning the latent space into batch-specific, label-related, and residual subspaces. By combining supervised classification, adversarial training, and cross-covariance penalty, FADVI disentangles batch from biological representations, preserving biological variation while correcting batch effects. Benchmarking across scRNA-seq, scATAC-seq, and high-resolution spatial transcriptomics datasets, FADVI consistently outperforms state-of-the-art integration methods. FADVI also enables feature attribution for revealing genes associated with cell type identity and batch variation. Together, these results demonstrate that FADVI provides robust, interpretable integration for large-scale single-cell and spatial omics data, offering a powerful framework for downstream analysis and discovery.

bioinformatics↗

bioRxiv2025

Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis

BackgroundMacrophages are key players in the pathogenesis of atherosclerosis. They trigger immune responses through their cell-surface receptors. However, how macrophages regulate those receptors in response to pro-inflammatory stimuli is not completely understood. Endocytic membrane trafficking involving receptor internalization, followed by endosomal transport and recycling of the internalized receptors, plays essential roles in balancing cell-surface receptors to meet cellular needs. Here, we explored the role of the endocytic regulator EHD1 in immune responses in macrophages and determined its contribution to atherosclerosis progression. MethodsEHD1 expression profiles in mouse and human plaques were determined by single-cell RNA sequencing (scRNA-seq) and immunofluorescence staining. Bone marrow transplantation (BMT) by transplanting bone marrow cells from Ehd1-/- or littermate wild-type mice to irradiated Ldlr-/- mice was performed to determine the effect of EHD1 deletion on atherosclerosis progression. In vitro mechanistic studies including inflammation signaling and endocytosis assays were performed in bone marrow-derived macrophages. ResultsEHD1 expression in macrophages is enhanced as atherosclerosis progresses in both mice and humans. Histological analysis of aortic root sections from BMT mice showed that EHD1 deletion reduces lesion size. ScRNA-seq of aortic CD45+ cells demonstrated that EHD1 deletion attenuates pro-inflammatory responses and cell-cell interactions. Mechanistic studies revealed that EHD1 accelerates the endocytic recycling of TNFR2 and activates NF-kB, leading to increased expression of inflammatory cytokines. Moreover, EHD1 interacts with retromer and stabilizes sortilin, a retrograde cargo of retromer and a risk factor for atherosclerosis. ConclusionsEHD1 promotes inflammation by enhancing TNFR2-NF-kB signaling and stabilizing sortilin, leading to accelerated atherosclerosis. Our study reveals novel roles for EHD1-mediated membrane trafficking in macrophage function and paves the way to innovative therapeutic strategies that aim to address dysregulated membrane trafficking in atherosclerosis.

cell biology↗

bioRxiv2025

APOBEC3A-Induced DNA Damage Drives Polymerase Theta Dependency and Synthetic Lethality in Cancer

APOBEC3 cytidine deaminases drive cancer evolution. There is an unmet need to target cancer cells with APOBEC3 activity. Here, we identify error-prone theta-mediated end joining (TMEJ) as the main pathway for repairing APOBEC3-induced double-strand breaks (DSBs). Using fluorescent DSB repair reporters and a novel biochemical assay, we demonstrate that APOBEC3A competes with replication protein A (RPA) for single-stranded DNA overhangs, exposing microhomologous sequences to shift DSB repair towards error-prone TMEJ. Genomic analysis of clinical tumor samples confirmed the co-occurrence and proximity between APOBEC3-induced mutational footprints, microhomology-mediated deletions (MMDs), and TMEJ-associated chromosomal instability signatures. Crucially, inhibition of DNA polymerase theta (Pol{theta}) synergizes with APOBEC3A-induced DSBs to induce synthetic lethality in vitro and in vivo. Collectively, our findings identify TMEJ as the preferred mechanism for repairing APOBEC3A-induced DSBs and establish Pol{theta} inhibition as a novel promising strategy to eliminate cancer cells with APOBEC3A activity.

cancer biology↗