Biology subjects

Wang, Q.

Publications and source records attributed to Wang, Q..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

A Novel Therapeutic Approach: Notch Inhibition Enhances Radiotherapy and Checkpoint Blockade Therapy via Reprogramming of the Tumor Microenvironment

BackgroundHigh-dose radiotherapy (RT) in cancer is immunogenic but also induces an immunosuppressive tumor microenvironment (TME) that limits the efficacy of immune checkpoint inhibitors (ICIs). Overcoming this immunosuppressive barrier is therefore critical to unlocking the full potential of RT-ICI combinations. As Notch signaling regulates tumor microenvironment, we hypothesized that the {gamma}-secretase inhibitor (GSI), AL101, would suppress radiation-induced immunosuppression and enhance antitumor efficacy when combined with RT and anti-PD-1 (aPD-1) therapy. MethodsSyngeneic neuroblastoma (9464D) and triple-negative breast cancer (EO771) tumors were established in C57BL/6, macrophage-depleted C57BL/6 mice, or athymic mice. Mice received 12 Gy RT (day 3), AL101 (6.5 mg/kg daily, day 0-9), and aPD-1 (days 0, 3, 6). Tumors were analyzed by spectral flow cytometry and single-cell RNA sequencing (scRNA-seq), and lung metastases were evaluated histologically. ResultsThe triple combination of RT, aPD-1, and GSI produced durable tumor growth inhibition and significantly prolonged survival in both models, with median survival more than doubled compared to all other treatment groups. Triple therapy also markedly reduced lung metastases in EO771 mice. These effects were abrogated in athymic nude mice and macrophage-depleted immunocompetent mice, consistent with an immune-dependent mechanism. Based on scRNA-seq and spectral flow cytometry analysis, RT alone increased exhausted T cells and immunosuppressive macrophages, while triple therapy reversed these effects, including expansion of activated CD8 T cells, reduction of Tregs and exhausted T cells, restoration of cross-presenting CD103 dendritic cells, and reprogramming of myeloid cells toward a proinflammatory state. ConclusionsGSI remodels the RT-induced immunosuppressive TME and potentiates the efficacy of RT + ICI. GSI combined with RT+aPD-1 reprograms the TME toward an immunostimulatory state and supports GSI as a promising immuno-radiotherapeutic strategy with strong translational potential.

cancer biology↗

bioRxiv2025

Connections of early visual areas with posterior parietal and temporal cortex in galagos, a strepsirrhine primate

To better understand the cortical connections and organization of visual areas in galagos, we examined the interconnections among cortical visual fields and their relationships with posterior parietal cortex (PPC) and temporal regions associated with dorsal and ventral streams of visual processing. In five galagos, two to four distinguishable tracers were injected into different visual areas, allowing direct comparison of connection patterns within the same cases. To reveal distributions of labeled neurons for each injection, labeled cells were plotted from serial brain sections cut parallel to the flattened cortical surface and summed across sections to generate surface reconstructions. Alternate sections processed for cytoarchitectonic features were used to identify cortical borders, especially those of V1 and middle temporal visual area (MT). Overall, our results support the conclusion that regions of V2 and V3 represent the contralateral visual hemifield in parallel with V1 and with each other. However, dorsal V3, representing the lower visual hemifield, includes at least one discontinuity where representations of the upper visual field extend to the dorsal border of V2. This portion of V3 appears to belong to the dorsomedial visual area (DM), which extends rostrally from V2 into PPC. The dorsal part of the DL-V4 region receives projections from other parts of dorsolateral visual area (DL), central V1, V2 and V3, inferotemporal (IT) cortex, the MT complex, and PPC regions surrounding the intraparietal sulcus (IPS). More central portions of DL-V4 receive inputs from central representations of V1, V2, and V3, as well as from PPC regions lateral to the IPS, the MT complex, and upper IT cortex. The ventral part of DL receives projections from central V2, caudal PPC adjoining DM and ventral PPC, and from IT cortex. These patterns indicate that the DL-V4 region serves as a major node linking dorsal and ventral streams and likely includes more than one functionally distinct visual area. In addition, areas MT and DM show strong reciprocal connections with PPC, while the connections of IT cortex indicate that much of this region is visual in nature having strong connections with higher order visual areas and it is composed of multiple functionally specialized visual domains. Key pointsO_LIOrganization of the visual cortex in galagos is much like that in New World and Old Word monkeys. C_LIO_LIPatterns of cortical connections of early visual areas V1 and V2 support the view that dorsal V3 has a gap in the representation of the lower visual field that is occupied by the proposed dorsomedial visual area (DM). C_LIO_LIVisual areas DM and middle temporal visual area (MT) provide the major visual inputs to posterior parietal cortex (PPC) of the dorsal stream of visual processing for actions. C_LI

neuroscience↗

bioRxiv2025

Structural Insights into Single-Stranded DNA Recognition and Modified Substrate Tolerance in an Engineered Terminal Deoxynucleotidyl Transferase

Terminal deoxynucleotidyl transferase (TdT) is the cornerstone enzyme for de novo enzymatic DNA synthesis (EDS), promising to overcome the length and sustainability limitations of traditional phosphoramidite chemistry. We previously identified a highly active TdT ortholog from Zonotrichia albicollis (ZaTdT) and engineered a variant (R335L/K337G) capable of efficiently incorporating 3-aminooxy (3-ONH2) reversible terminators. However, the atomic-level mechanism by which these engineered mutations alter substrate specificity has remained elusive. Here, we present the high-resolution (2.20 [A]) crystal structure of the engineered ZaTdT in complex with a single-stranded DNA primer. Structural analysis reveals a conserved catalytic core anchored by a hydrophobic platform (Phe110/Phe257/Trp308) that stabilizes the primer. Crucially, comparative modeling with the homologous murine TdT ternary complex demonstrates that the engineered mutations (corresponding to L190/G192 in the crystal structure) disrupt a rigid salt-bridge network at the active site entrance. This electrostatic remodeling not only reduces local positive charge but also expands the catalytic pocket depth from 3.8 [A] to 5.8 [A]. This specific spatial expansion provides the structural rationale for the accommodation of bulky 3-blocking groups, validating our rational design strategy and paving the way for next-generation long-read DNA synthesis.

biochemistry↗

bioRxiv2025

Structural Mechanism of Specific Nucleobase Recognition by a Monoclonal Antibody in CoolMPSTM Sequencing

Massively parallel sequencing (MPS) has revolutionized genomics, yet traditional methods utilizing fluorescently labeled nucleotides suffer from "scarring" effects that limit read accuracy. The CoolMPS technology overcomes this by using unlabeled reversible terminators (RTs) with a 3-O-azidomethyl blocking group, detected by highly specific fluorescent antibodies. However, the atomic-level mechanism by which these antibodies discriminate between modified and natural nucleotides within a DNA strand remains unclear. Here, we report the crystal structures of the "A-fab" antibody fragment in complex with the monomeric antigen 3-O-azidomethyl-dATP (dATP-N3) at 2.50 [A] resolution, and with an one strand of the duplex carries an azide-modified deoxyadenosine nucleotide at its 3' terminus (dsDNA-dATP-N3) at 1.99 [A] resolution. Isothermal titration calorimetry (ITC) revealed that A-fab binds dATP-N3 with nanomolar affinity (KD{approx}17.14 nM), while binding to natural dATP is negligible (KD{approx}7.51{micro}M), representing a [~]440-fold specificity. Structural analysis reveals a conserved hydrophobic pocket formed by CDR residues (e.g., Trp79, Tyr53, Leu67) that specifically accommodates the 3-azidomethyl group. This interaction is critical for affinity and is maintained in the dsDNA-ATP-N3 complex, validating the antibodys function in a sequencing context. These findings provide the structural rationale for the high fidelity of the CoolMPS platform.

biochemistry↗

bioRxiv2025

Exudate-Guided Janus Trilayer Bioelectronic Dressing for Multimodal Sensing and Therapy of Chronic Wounds

Chronic wound treatment remains challenging because conventional dressings and systemic therapies typically lack real-time adaptability to the dynamic changes in the wound microenvironment. Here, we report a breathable self-adhesive multifunctional wound dressing based on a gradient-wettable Janus trilayer fibrous membrane, which integrates real-time biochemical sensing, on-demand drug release, and low-voltage electrical stimulation therapy simultaneously. The dressing features a vertically integrated trilayer architecture with hierarchical partitioning, where the three vertically stacked layers integrate a multiplex electrochemical sensor array (glucose, lactate, pH), a silver-sulfadiazine drug reservoir, and stimulation electrodes. Specifically, a hydrophilic sensing layer, intermediate drug-storage layer, and hydrophobic adhesivelayer are assembled to achieve spatially resolved functionalities. The membranes gradient wettability and asymmetric porous structure enable directional exudate transport, thereby triggering stepwise activation of sensing, drug release, and electrical stimulation in a spatiotemporally controlled manner. The dressing is thin, breathable, stretchable, self-adhesive and biocompatible, enabling conformal contact and stable signal acquisition on deformable skin without tapes. This design ensures continuous bio-signal monitoring while maintaining a favorable wound healing microenvironment. Preclinical tests demonstrate its effectiveness in promoting wound closure, reducing infection, and providing continuous wound status monitoring. This integrated system offers a promising approach for next-generation wound care and regenerative medicine.

bioengineering↗

bioRxiv2025

An Expectation and Maximization Algorithm for Multivariate Genome-wide Association Studies (EMmvGWAS)

Genome-wide association studies (GWAS) commonly focus on one quantitative trait at a time, even when multiple traits are collected. However, joint analysis of multiple traits can increase the power to detect genetic associations by leveraging trait correlations. Multivariate GWAS is particularly important for identifying pleiotropic effects and uncovering shared genetic architecture underlying complex traits. Despite its great potential, multivariate GWAS methods face substantial computational challenges due to the high dimensionality of polygenic covariance structures and the cost of scanning genome-wide markers. We present EMmvGWAS, an efficient computational framework implemented as an R, which dramatically reduces computation time for multivariate GWAS involving a moderate number of traits. The algorithm estimates the genetic and environmental covariance matrices from a pure polygenic model using an Expectation-Maximization (EM) algorithm. To improve computational efficiency during genome-wide scanning, we use a semi-exact method that fixes the estimated covariance matrices and treats their ratio, defined as the genetic covariance matrix multiplied by the inverse of the environmental covariance matrix, as a known constant across all markers. This approach enables closed-form solutions for marker effects at each locus, dramatically reducing the computation time without compromising statistical power. We demonstrate the scalability and performance of our method through both simulation studies and real dataset analyses from rice, mouse and human populations. The method is implemented in R and is designed to support multivariate GWAS involving a moderate number of traits, while also accommodating univariate analyses as a special case. The R package is available at https://github.com/Jason-Teng/EMmvGWAS.

genomics↗

bioRxiv2025

AAV vectors with enhancer-controlled ITR promoters

Adeno-associated virus (AAV) is limited by its packaging capacity and the unwanted promoter activity of inverted terminal repeats (ITRs). Here we utilized mini-enhancers to regulate ITR promoters and drive AAV cargo expression in the absence of the canonical promoters, which not only solved the ITR issue but also released more payload for the cargo. As an example, this new design successfully enabled robust, tissue-specific SpCas9 gene editing via a single AAV, which otherwise requires a dual-AAV system due to the large size of SpCas9.

bioengineering↗

bioRxiv2025

Characterizing and mitigating confounding by unreplicated evolutionary events in phylogenetic regression

When researchers want to test for a direct effect of one attribute on another using interspecific data, they need to account for the confounding influence of other attributes that have phylogenetic structure. Accordingly, a suite of approaches have been developed for this purpose, mostly notably the use of phylogenetic regression. However, it has been shown that such methods can be misled by evolutionary events with large effects. We suggest that one widely-applicable solution to this problem can be found by borrowing both from the statistical genetics literature and by digging into the past of phylogenetic comparative methods. In conventional phylogenetic regression, the phylogenetic variance-covariance matrix is included as a random-effect term; here, we argue that it can be advantageous to also include the leading eigenvectors of this matrix as fixed effects. Building on the recent results of Schraiber et al. (2024), we use mathematical analysis and simulations to show under which scenarios this hybrid strategy is effective. We develop a novel approach for visualizing the contributions of different branches of the phylogeny to the eigenvectors of the variance-covariance matrix. We also illustrate how quantile-quantile plots can be used to assess whether the phylogenetic structure has been effectively controlled. We then apply the mixed approach to investigate the co-evolution of gene expression levels of different genes across the phylogeny of cichlid fishes; we show that including the leading eigenvectors likely reduces the false positive rate. To facilitate the use of our visualization approach and of including eigenvectors in phylogenetic regression models, we present a new R package called EIGER. We argue that the approaches we explore here can both help address the statistical problems that arise from large, historical events and more generally, provide richer insights into the nature of phylogenetic confounding.

evolutionary biology↗

bioRxiv2025

Spatial Flavonoid Accumulation in Soybean Pericycle Restricts Phytophthora sojae Invasion

Root immunity relies on coordinated defenses across distinct tissues, yet the underlying cellular mechanisms remain unclear. Here, we integrated single-cell transcriptomics, spatial metabolomics, and genetic manipulation to dissect soybean (Glycine max) interactions with Phytophthora sojae. In resistant Williams82 (Wm82) roots, P. sojae hyphae were excluded from the stele, exhibiting negative tropism toward the pericycle. scRNA-seq revealed that this resistance is mediated by infection-induced pericycle cells expressing high levels of flavonoid biosynthetic genes, including GmCHS7 and GmCHI4A. CRISPR-Cas9 knockout of these genes compromised resistance, whereas overexpression enhanced immunity in susceptible cultivars. Metabolomic and spatial metabolic analyses identified naringenin, a flavonoid phytoalexin, as a key antimicrobial compound that specifically accumulates in pericycle-adjacent tissues of Wm82 during infection. Naringenin directly inhibited hyphal growth in vitro and enhanced resistance when applied exogenously. These findings uncover a spatially targeted immune strategy where pericycle-localized activation of flavonoid synthesis forms a chemical barrier to safeguard vascular integrity, highlighting pericycle-centered metabolic immunity as a target for engineering durable resistance.

plant biology↗

bioRxiv2025

Preserved Neural Dynamics across Arm- and Brain-controlled Movements

The neural activity for motor control is complex and dynamic; it has been found to dramatically transit from planning to executing movements. As brain-machine interfaces (BMIs) can directly connect the brain and the external world by yielding comparable motor outcomes with artificial apparatus, a central question is whether the BMI-controlled movements share neural dynamics or underlying mechanism with natural movements. To enable a systematic comparison, we developed a feedforward BMI framework with distinct planning and executing epochs that enables ballistic cursor control to intercept moving targets. This BMI allowed monkeys to voluntarily initiate neural states which controlled the direction and timing to launch a ballistic movement, like skeet shooting. Based on this, we found similar neural representations and computational structures across arm- and brain-controlled conditions. Notably, in addition to resembling the rotational structure in natural reaching, the neural population dynamics during open-loop BMI also shared preserved manifolds with those during reaching arm movements. These findings suggest a fundamental principle, and reveal a set of basic computational motifs for the neural control of movement in an abstract hierarchy in the absence of constraints from actuators. This study thus has the potential to reshape the consideration of how BMIs assist paralyzed patients in interacting with dynamic environments, and to promote next-generation BMI systems.

neuroscience↗

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

Homotypic endoplasmic reticulum membrane tethering is critical for flavivirus replication

Flaviviruses (genus Orthoflavivirus) are arthropod-borne viruses which cause approximately 400 million annual global infections in humans. Flavivirus infection requires cellular machinery to facilitate replication and spread. All known flaviviruses replicate in association with the host endoplasmic reticulum (ER), where genome replication is confined within virus-induced ER invaginations called viral replication organelles (vROs). Despite the central role of these structures during flavivirus infection, the mechanisms underlying vRO biogenesis remain undefined - particularly the membrane rearrangements required for their formation. In this work, we report a conserved role for a cellular ER remodeling protein, atlastin-2 (ATL2), in the organization of vROs within infected cells. Using confocal and electron microscopy, we show that ATL2 depletion leads to a reduction in vRO spatial distribution in flavivirus-infected cells. Changes in vRO distribution corresponded with a decrease in virus production and robust induction of innate immune responses. We also demonstrate that ATL2 accumulates in areas of vRO formation during flavivirus infection. Critically, mutational analysis showed that a tethering-competent but fusion-defective ATL2 mutant was sufficient to rescue DENV and ZIKV replication in ATL2-knockout cells. Finally, inhibition of ATL2 activity using synthetic peptides significantly reduced DENV replication in both immortalized and human primary cells, suggesting a possible avenue for targeting host ER functions to limit flavivirus replication. Taken together, these results show that membrane tethering plays a critical and conserved role in flavivirus infection, functioning to organize membranes for vRO biogenesis and limit cellular immune activation. Importantly, we provide evidence that ATL2-mediated membrane organization can be targeted to inhibit viral replication.

microbiology↗

bioRxiv2025

Multi-stem-loop constrained library enables accelerated SELEX for aptamers with superior kinetics and affinity

AbstractAptamers are single-stranded nucleic acids with ligand-binding capacity as cost-effective alternatives to antibodies. However, their utility is often undermined by the inherent conformational instability of single-stranded nucleic acids, which can compromise binding kinetics and final affinity. To overcome this critical limitation, we synthesized a novel primary library incorporating multiple inlaid stem-loop structures to enhance molecular stability and rigidity. This structural constraint dramatically accelerated the selection process, allowing us to isolate aptamer candidates with superior affinity in just three rounds of SELEX (Systematic Evolution of Ligands by EXponential enrichment), a significant reduction compared to conventional methodologies. Critically, the resulting aptamer demonstrated higher affinity and faster binding kinetics compared to previously reported sequences, which directly validate our hypothesis that structural stabilization leads to high-performance aptamers. This methodology, which integrated rational conformational constraint with a high-throughput selection process, offered a generalizable strategy to efficiently select aptamers with excellent kinetic and thermodynamic performance for demanding applications such as continuous, real-time ligand detection.

biochemistry↗

bioRxiv2025

Sustained Humoral Activation through self-amplifying mRNA Vaccination Enhances Longitudinal Antibody Function in a Phase III Trial

Sustained and functional antibody responses to respiratory pathogens through vaccination is critical for global public health. The development and deployment of mRNA vaccines during the coronavirus disease 2019 (COVID19) pandemic was a landmark achievement in modern medicine and ushered in a new age of vaccine innovation. The mRNA-based vaccines elicited strong antibody responses, both neutralizing and extra-neutralizing, against the viral Spike protein. The antibody levels waned with time since vaccination, and that coupled with the antigenic drift of the virus prompted updates to the mRNA vaccine composition and evaluation of other mRNA modalities. Self-amplifying mRNA (sa-mRNA) vaccines such as ARCT-154 can prolong antigen production and durability of humoral immune response post-immunization, and can thus be administered at a lower dose. How this translates into the overall humoral architecture compared to that shaped by conventional mRNA vaccinations, however, is unclear. Here, we analyze serum-based antibody responses from a recent Phase III trial comparing humoral responses elicited by ARCT-154 and mRNA BNT162B2. All participants had received three doses of mRNA COVID-19 vaccines and were randomized to receive a booster dose of ARCT-154 or BNT162B2. Primary outcomes were to quantify waning responses against ancestral/wild type SARS-CoV-2 Spike (WT Spike) and a panel of antigenically SARS-CoV-2 variants Spikes. Through a systems serology approach, we identified that the sa-mRNA vaccine ARCT-154 elicited a unique antibody response compared to BNT162B2 defined by a sustained, activating profile to the vaccine-encoded Spike protein and a broad spectrum of drifted Spikes. Notably, potently activating Fc{gamma}RIIIA-binding antibodies showed a sustained stimulation in the ARCT-154-treatment arm, and this translated to an enhanced natural killer (NK) cell activation. The NK-activation through ARCT-154 was present for both target WT Spike and the antigenically drifted BA.5 Spike, which was the predominant form of SARS-CoV-2 during the observation period. Our results support a model whereby prolonged antigen expression and presentation moves immune profiles towards activating phenotypes with broad antigenic coverage.

immunology↗

bioRxiv2025

Predictive Neural Signals during Natural Mandarin Speech Comprehension

Language comprehension requires the continuous transformation of speech into a hierarchy of linguistic units, from phonemes to syllables to words. Because speech unfolds rapidly, listeners are thought to predict upcoming content to keep pace. Previous research has provided empirical evidence for predictive processes operating at multiple linguistic levels during naturalistic listening, including words and phonemes. However, it remains unclear whether prediction also operates concurrently at other levels, such as syllabic and phrasal representation. Here we use Mandarin Chinese to examine the neural signatures of predictive processing across multiple levels of linguistic granularity during natural speech comprehension. Mandarin comprises four representational levels: phoneme, sub-syllabic, character and word, and its lexical identity is largely constrained at the sub-syllabic level, potentially redistributing predictive weight across linguistic representations. We recorded magnetoencephalography (MEG) data while 34 native Mandarin speakers (21 females) listened to a naturalistic audiobook and applied linear regression modeling to examine how linguistic features modulated neural activity. We found that the brain activity of listeners segmented speech into hierarchical units, and that surprisal modulated responses simultaneously across sub-syllabic, character and word levels. In contrast to findings from Indo-European languages, however, we did not observe unique surprisal effects at the lowest, phonemic level. Furthermore, the surprisal of lexical tone in Mandarin modulated brain activity only when integrated with its phonological components. These findings suggest that predictive processing during Mandarin speech comprehension operates concurrently across multiple (though not necessarily all) levels of linguistic granularity, with its implementation shaped by language-specific structural properties. Significance statementLanguage comprehension involves segmenting a continuous acoustic stream into multiple linguistic units, from phonemes to words, and generating predictions at these levels. However, direct neural evidence remains limited regarding how segmentation and prediction operate simultaneously across levels of linguistic granularity, particularly outside Indo-European languages. Using temporal response function analysis of magnetoencephalography data recorded during naturalistic Mandarin listening, we show that predictive processing occurs across multiple levels of linguistic granularity. Specifically, we find evidence for prediction-related neural responses at sub-syllabic, character, and word levels, but not a reliable unique effect at the phonemic level. These results indicate that predictive processing also operates during Mandarin speech comprehension, and its neural implementation is shaped by language-specific structural properties.

neuroscience↗

bioRxiv2025

OPUS-ET: Resolving Compositional and Conformational Heterogeneities of Biomolecules in Cryo-Electron Tomography

Structural heterogeneity in biomolecules, arising from both compositional and conformational variability, limits resolution and interpretability of cryo-electron tomography (cryo-ET). Here, we present OPUS-ET, a deep learning framework that resolves multiscale heterogeneity throughout the cryo-ET workflow. OPUS-ET combines a composition decoder that captures compositional differences with a conformation decoder that models large-scale motions, thereby providing a hierarchical representation of structural heterogeneity. Starting from noisy template-matching candidates with templates of varying similarity or quality, OPUS-ET efficiently enriches target particle populations and delivers sub-nanometer in situ reconstructions in a single round. It leads to improved resolutions by up to 4.5 [A] over expert annotations or existing deep-learning approaches in four benchmark systems, and reveals continuous conformational landscapes capturing F-F flexible coupling in mitochondrial ATP synthase and tRNA-translocation intermediates in eukaryotic and bacterial ribosomes. Together, these results establish OPUS-ET as a powerful computational tool for linking particle purification, high-resolution reconstruction, and analysis of structural heterogeneity in cryo-ET, with demonstrated robustness to template quality, initial pose noise, and clustering parameters.

molecular biology↗

bioRxiv2025

Dysregulation of transcription networks regulating oligodendrogenesis in age-related decline in CNS remyelination

In demyelinating diseases like multiple sclerosis (MS), efficient remyelination is critical for functional recovery. Remyelination efficiency declines with age, and is linked to progressive disability. The gene regulatory network underlying remyelination, and how it is altered with aging, remains unclear. Here we present a comparative single-nucleus RNA and ATAC sequencing analysis of remyelination in young and aged mice. We identified gene modules dynamically expressed throughout oligodendrocyte differentiation, revealing age-dependent changes in key processes related to myelination. Multi-omic analysis allowed us to map the regulatory network driving efficient remyelination within oligodendrocyte lineage cells in young mice. We highlight key transcription factors in the network dysregulated with age, and we describe similar dysregulations in MS lesions. Modifying the expression of these transcription factors in primary oligodendrocyte progenitor cells impacts differentiation. These findings provide a foundational understanding of this regenerative process in the context of aging and in chronic demyelinating diseases.

neuroscience↗

bioRxiv2025

MitoEM 2.0 - A Benchmark for Challenging 3D MitochondriaInstance Segmentation from EM Images

We present MitoEM 2.0, a curated data resource for training and evaluating three-dimensional (3D) mitochondria instance segmentation in volume electron microscopy. The collection assembles multiscale vEM datasets (FIB-SEM, SBF-SEM, ssSEM) spanning diverse tissues and species, with expert-verified instance labels emphasizing biologically difficult scenarios, including dense mitochondrial packing, hyperfused networks, and thin filamentous connections with ambiguous boundaries. All releases include native-resolution volumes and standardized processed versions, per-volume metadata (voxel size, modality, tissue, splits), and official train/validation/test partitions to enable reproducible benchmarking. Annotations follow a consistent protocol with quality checks and instance reindexing. Data are provided in NIfTI with nnU-Net-compatible layout, alongside machine-readable split files and checksums. Baseline scripts support common training pipelines and size-stratified evaluation. By consolidating challenging volumes and harmonized labels, MitoEM 2.0 facilitates robust model development and fair comparison across methods while supporting reuse in bioimage analysis, algorithm benchmarking, and teaching.

neuroscience↗