Biology subjects

Mao, Y.

Publications and source records attributed to Mao, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

Oncogenesis involves widespread genetic and epigenetic alterations, yet the full spectrum of somatic variation genome-wide remains unresolved. We generated a near-telomere-to-telomere (T2T) diploid assembly of a donor paired with deep short- and long-read sequencing of their melanoma. This revealed that 16% of somatic variants occur in sequences absent from GRCh38, with satellite repeats acting as hotspots for UV-induced damage due to sequence-intrinsic mutability and inefficient repair. Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation, leading to remodeling of centromere kinetochore binding domains during tumor evolution. Single-molecule telomere reconstructions uncovered cycles of attrition, deletion, and telomerase-mediated extension that shape cancer telomeres. Finally, diploid chromatin maps exposed that copy number alterations and epimutations, rather than point mutations, predominate in rewiring cancer regulatory programs. These findings define the full landscape of a cancers somatic variation and their functional impact, establishing a blueprint for T2T studies of mosaicism.

genomics↗

bioRxiv2025

Early menopause is associated with reduced global brain activity

Menopause affects the aging process in women through significant ovarian hormone production decline in midlife. Women who experience early menopause face an accelerated physiological aging rate, along with impaired memory and increased risks of neurodegenerative diseases. However, it remains elusive how the timing of menopause affects brain activity, which could be crucial for understanding menopause-related acceleration of aging and increased risk of dementia. Recent studies have revealed a highly structured infra-slow (< 0.1 Hz) global brain activity across species and linked it to arousal and memory functions, as well as waste clearance in Alzheimers diseases (AD). In this study, we examined how this global brain activity relates to age of menopause using resting-state fMRI data from the Human Connectome Project-Aging dataset. We found that women who experienced earlier menopause (mean menopausal age 45{+/-}3.5 yr) exhibited weaker global brain activity (p = 5.0x10-4) with reduced coupling to cerebrospinal fluid (CSF) flow (p = 0.017) compared to age-matched later-menopausal women (mean menopausal age 54{+/-}1.2 yr). Differences appeared mainly in higher-order brain regions, where activation levels correlated with memory performance in earlier but not in intermediate or later menopausal women. These findings highlight brain activity changes linked to early menopause, suggesting a potential mechanism underlying memory decline and the increased risk of AD and dementias in early-onset menopausal women.

neuroscience↗

bioRxiv2025

Profiling of terminating ribosomes reveals translational control at stop codons

Accurate termination of protein synthesis is paramount for the integrity of cellular proteome, yet the dynamics and fidelity of ribosome termination remain poorly understood. Here, we establish a profiling strategy to capture terminating ribosomes in mammalian cells and reveal a substantial heterogeneity in ribosome pausing at individual stop codons. We identify a sequence motif upstream of the stop codon that promotes termination pausing, a finding validated by massively paralleled reporter assays. Unexpectedly, reduced termination pausing increases the likelihood of stop codon slippage, giving rise to proteins with heterogenous C-terminal extensions. Mechanistically, we show that sequence-dependent termination pausing arises from post-decoding mRNA scanning by the 3 end of 18S rRNA. We further uncover tissue-specific patterns of termination pausing that correlates with the stoichiometry of Rps26, which modulates mRNA:rRNA interactions. Together, these results establish termination pausing as a distinct translational signature shaped by mRNA sequence contexts, ribosome heterogeneity, and cell type-specific translational control.

biochemistry↗

bioRxiv2025

Sleep deprivation exhibits age-dependent effect on infra-slow global brain activity

Infra-slow (< 0.1 Hz) global brain activity, quantified by the global mean BOLD (gBOLD) signal in resting-state fMRI, is elevated during sleep and closely associated with cerebrospinal fluid (CSF) dynamics, a key mechanism for the brain waste clearance implicated in neurodegenerative disorders such as Alzheimers disease (AD). However, the effect of sleep deprivation on gBOLD activity and its interaction with aging remain poorly understood. Using a rigorously controlled in-laboratory total sleep deprivation (TSD) protocol, we demonstrate that TSD significantly increases both the amplitude of the gBOLD signal and its coupling with CSF flow, suggesting a compensatory mechanism that may enhance glymphatic clearance following acute sleep loss. Notably, these TSD-induced enhancements exhibit robust age dependency, with diminished responses in individuals at midlife (40-50 yrs). The absence of this compensatory mechanism in these midlife participants may exacerbate age-related impairments in neurotoxic clearance and increase dementia susceptibility, thereby offering mechanistic insights into the nexus between sleep disruption, aging, and neurodegeneration.

neuroscience↗

bioRxiv2025

Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability

Polysaccharides are known to be synthesized by enzymes in the endoplasmic reticulum and Golgi apparatus and transported through the secretory pathway to the cell surface or extracellular space1, where they mediate essential biological processes2-6. While classical localization and functions of polysaccharides are well established, their presence and potential roles in the nucleus remain unclear. Here, we demonstrate that N-glycans, a type of polysaccharides, are present in the cell nucleus and modify inner nuclear membrane (INM) proteins across diverse cell types--a modification referred to as N-linked glycosylation (N-glycosylation). N-glycosylation is enriched in chromatin regions marked by H3K9me3 and long interspersed nuclear element-1 (LINE-1) retrotransposons. N-glycosylation inhibition and INM protein N-glycosylation site mutation both downregulate H3K9me3 within lamina-associated domains (LADs) and lead to genomic instability. Mechanistically, N-glycosylation regulates the interaction between the histone H3K9 methyltransferase SETDB1 and INM proteins, promotes the association of SETDB1 with the INM, and maintains H3K9me3. Moreover, we reveal that canonical N-glycan biosynthetic machinery in ER contributes to the N-glycosylation of INM proteins. These findings uncover a previously unrecognized nuclear role for polysaccharides, broadening our understanding beyond their traditional subcellular distributions and functional profiles.

molecular biology↗

bioRxiv2025

3D epithelial cell topology tunes signalling range to promote precise patterning

Cell behaviours in multicellular organisms are coordinated via both diffusible molecules and by signals based on direct cell-cell contacts. The mode of cell communication used influences the signalling range. In many developing epithelia, contact-based Notch-Delta lateral inhibition signalling is used to pattern cell fates. While previous work revealed that cells can use protrusions to extend the range of Notch-Delta signalling to alter these patterns, this is not a general feature of epithelia. In addition, it is not known how the complex three-dimensional (3D) shapes of epithelial cells influence cell communication. In exploring this question, we show that epithelial cells at the Drosophila wing margin, which lack basal protrusions, contact different neighbours at different heights along their apico-basal axis, effectively increasing the number of neighbours each cell touches. To quantitatively assess this behaviour, we develop a novel mathematical modelling framework (Multi-layer Signalling Model) to simulate Notch-Delta signalling over data-derived 3D cell topologies. The model predicts that lateral cell surface signalling is essential to tune the spacing between SOPs. In agreement, we show that perturbing cortical stiffness and cell tortuosity in vivo modifies SOP spacing. These results emphasise the importance of 3D cell geometry and topology in fine-tuning signalling range.

developmental biology↗

bioRxiv2025

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias

A truly complete, telomere-to-telomere (T2T), and error-free reference genome remains a foundational resource--and long-standing goal--for unbiased comparative and functional genomics. While recent T2T assemblies of humans and other primates have made substantial progress, most still contain thousands of base-level errors, particularly within highly repetitive regions. Here, we present T2T-MMU8v2.0, a near-perfect T2T assembly of the rhesus macaque (Macaca mulatta), representing the highest base-level accuracy reported in a primate genome to date. By employing an optimized ONT-only assembly strategy, we identify subtelomeric satellite-rich regions as the principal bottleneck to improving assembly quality, owing to technological biases in long-read platforms and limitations in current hybrid assembly frameworks. We discover 268 previously unannotated repeat families and resolve [~]8 Mbp of SATR satellite arrays, with over 99-fold enrichment in historically misassembled subtelomeric regions. These satellites form four distinct genomic architectures, each with unique SATR satellite composition, segmental duplication organization, and epigenetic signatures, distinct from the subtelomeric architectures observed in hominid genomes. Notably, in contrast to the largely gene-poor subtelomeric regions in African hominids, the SATR architectures in macaques harbor 58 actively transcribed genes, supported by open chromatin and expression data, suggesting gene innovation within these repetitive regions. Functionally, T2T-MMU8v2.0 improves read mappability and accuracy across sequencing platforms, and results in a 19% improvement of transcription start site enrichment scores and 5,821 additional chromatin accessibility peaks on average, thereby enhancing variant detection, regulatory annotation, and transcriptomic resolution in population genetics or single-nucleus studies. Together, this work establishes a new benchmark for genomics, offers a roadmap for resolving complex repetitive regions, and reveals previously unrecognized features of subtelomeric genome structure and evolution.

genomics↗

bioRxiv2025

The DDIT4L-TOM40-ATP5A pathway suppresses glioblastoma oncogenesis

The characteristics of glioblastoma (GBM), including resistance to cell death and aberrant energy metabolism, are associated with the function of mitochondria. To date, the inherent suppressors that couple mitochondrial function with cell death remain unclear. DNA damage-inducible transcript 4-like (DDIT4L) expression in human gliomas and its association with patient survival was determined by public databases, western-blot and immunostaining. The role of DDIT4L in regulating tumor growth was analyzed using lentivirus and PDX model. The mechanism of DDIT4L on GBM mitochondrial function was determined by different assays. Here, we show that DDIT4L is an endogenous inhibitor of GBM via suppressing mitochondrial function. DDIT4L was expressed at high levels in GBM and transported into mitochondria via single import channel TOM40 other than the import receptors TOM22, TOM20 or TOM70. Then, DDIT4L interacted with the subunit of ATP synthase, inhibited mitochondrial function and induced tumor cell apoptosis. Furthermore, the synthetic peptide DDIT4LV125-P132 suppressed GBM oncogenesis. Based on these results, DDIT4L suppresses GBM oncogenesis through both TOM40- and ATP5A-dependent mechanisms to curb mitochondrial dynamics and induce cell apoptosis, and the DDIT4LV125-P132 peptide is a potential therapy for GBM.

cancer biology↗

bioRxiv2025

Three-Dimensional Mechanical Cooperativity Optimises Epithelial Wound Healing

Epithelial tissues serve as critical physical barriers that protect organs, making efficient repair essential upon damage. To achieve this, tissues must quickly react, forcing cells to rearrange and accommodate. Therefore, cells must cope with forces that will deform their shape to achieve these sudden but necessary changes. In the Drosophila wing disc, we showed how tissue fluidisation accelerated wound healing in 2D. However, the 3D aspect of tissue repair remains poorly understood. Here, we uncover a new mechanism aiding the tissue in repairing itself by changing cell height. We find actomyosin contractile cables at the wound edge connecting the apical and basal cell surface, which indent the apical side of the tissue and deform the basement membrane (BM), respectively. To understand the role of the different repair mechanisms, we developed a 3D vertex model allowing apico-basal intercalations. The model predicts that lateral cables play a role in regulating cell-cell intercalations, confirmed by Drosophila mutations affecting cell deformations. Our results demonstrate that lateral cables cooperate with the apical purse string to drive 3D cell shape changes and intercalations to promote more efficient wound repair.

developmental biology↗

bioRxiv2025

Target-enriched metagenomics-informed qPCR detects rare, potentially dangerous β-lactamase genes in wastewater

The rapid emergence of novel antibiotic resistance genes (ARGs) decreases the effectiveness of empirical antibiotic treatment for pathogen infections. Environmental ARG surveillance is an early-warning approach that can better inform antibiotic usage. Quantitative polymerase chain reaction (qPCR) is widely used for ARG surveillance because qPCR is easy, fast, and highly sensitive. However, it can only identify DNA targeted by pre-selected primers. In contrast, metagenomic sequencing can identify ARGs agnostically. However, sequencing is more expensive, less sensitive, and requires lengthy analysis of complex data sets. Target-enrichment metagenomic sequencing (TEMS), a method we developed previously, can mitigate the disadvantage of low sensitivity of traditional metagenomic sequencing. In this study, we propose a hybrid ARG surveillance pipeline for wastewater that capitalizes on both TEMS and qPCR. It uses a large-scale target determination of ARGs by using TEMS, followed by fine-scale routine surveillance of ARGs using qPCR. To connect the two steps, we developed a primer design tool, MSEDAP, which automatically analyzes metagenomic sequencing data and designs qPCR primers for ARG surveillance. This new workflow was ground-truthed using wastewater samples. TEMS identified seventeen {beta}-lactamase gene targets of potential clinical importance. qPCR validated their presence and abundance using primers generated by MSEDAP. SynopsisA metagenomics-qPCR hybrid scheme can be used for environmental surveillance of antibiotic resistance genes (ARGs) to discover emerging ARGs originating from communities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/665820v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@625e06org.highwire.dtl.DTLVardef@ae34aorg.highwire.dtl.DTLVardef@d03e7borg.highwire.dtl.DTLVardef@1b625a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Copper-Containing ROS-Scavenging Nanozyme Paradoxically Drives Alpha-Synucleinopathy by Amplifying Nitrosative Stress

Reactive oxygen and nitrogen species (RONS) are implicated in neurodegeneration, but their specific pathogenic roles remain unclear. Here, we developed a pair of iridium-based nanozymes with opposing functionalities to dissect these pathways. We show that a copper-tuned iridium nanozyme (Ir{square}Cu), despite being a superior ROS scavenger, paradoxically and dramatically exacerbated -synuclein (Syn) pathology in vivo. This pathology was causally linked to its ability to amplify RNS, as pharmacological inhibition of nitric oxide synthase (NOS) with L-NAME completely abrogated the pathology and reversed a human Parkinsons disease (PD)-like transcriptomic signature. In contrast, a copper-free, broad-spectrum RONS-scavenging iridium (Ir) nanozyme demonstrated substantial therapeutic efficacy across diverse brain-first, body-first, and Alzheimers disease with Lewy body co-pathology models. Our findings uncover the importance of the RNS pathway in driving -synucleinopathies and establish a critical design principle for nanomedicine, mandating caution in the use of redox-active copper for neuroprotective applications.

pathology↗

bioRxiv2025

A Compact Two-Photon Module for Simultaneous Dual-Depth, Multi-Region in vivo Brain Imaging

Understanding how distributed brain regions interact across cortical depths is crucial for uncovering the neural basis of behavior and cognition. Two-photon microscopy (2PM) excels at imaging the superficial layer, while three-photon microscopy (3PM) penetrates deep tissues but lacks sufficient speed for capturing fast superficial dynamics. Here, we present a compact two-photon imaging module (2PIM) that seamlessly integrates with existing 3PM to achieve simultaneous, high-speed imaging of superficial and deep brain regions, while preserving the deep tissue penetration of 3PM. This dual-modality system allows for remote and independent control of imaging planes in both axial and lateral dimensions. Leveraging this technology, we discovered context-dependent modulation of hippocampal CA1 and visual cortex responses to identical tactile stimuli, layer-specific temporal dynamics in sensory cortex during air puff stimulation, and depth-divergent neuronal activity patterns in motor cortex across acute-to-chronic pain. These results highlight the systems potential for dissecting the spatiotemporal coordination of distributed brain circuits.

bioengineering↗

bioRxiv2025

Cortex-Wide, Cellular-Resolution Volumetric Imaging with a Modular Two-Photon Imaging Platform

Mapping cortex-wide neuronal activity at single-cell resolution has been limited by the physical trade-off between numerical aperture and field-of-view (FOV) in two-photon microscopes. We present Meso2P, a modular two-photon platform that decouples excitation and detection by introducing a lateral paraboloid fluorescence collector. The design sustains an effective NA 0.87 over a contiguous 6 x 6 mm2 FOV at high speed (2,048 x 2,048 pixels at 7.67 Hz). The modular platform can be upgraded with optional modules for simultaneous multi-plane imaging (1-4 planes at full resolution and speed), volumetric imaging (6 x 6 x 0.5 mm3, 2,048 x 2,048 x 28 voxels at 1 Hz capturing> 210,000 neurons), and holographic two-photon optogenetic stimulation for targeted perturbations. To handle the resulting large-scale data, we provide an open-source deep-learning pipeline that automates motion correction, segmentation, and spike inference. We demonstrate cortex-wide sensory responses, layer-specific network synchrony during anaesthesia, and in-vivo tracking of micro and nanoplastic distribution. Meso2P therefore provides a reproducible route to high-throughput volumetric imaging across almost the entire cortex with high detection efficiency.

neuroscience↗

bioRxiv2025

AdSI-MIMO: Adaptive stain imputation with multi-input and multi-output learning for multiplex immunofluorescence imaging

Multiplex immunofluorescence (mIF) imaging plays a crucial role in studying multiple biomarkers and their interactions within the tumour microenvironment. However, acquiring mIF images that include all desired biomarkers presents significant challenges due to the need for specialised equipment and costly reagents, which increase technical complexity, time and expense. Stain imputation offers a promising solution by synthesising target biomarker images using generative models, thereby eliminating the need for additional staining procedures. Existing deep learning-based stain imputation methods lack flexibility in generating multiple biomarker images from various input combinations. To overcome this limitation, we propose AdSI-MIMO, a novel stain imputation framework for mIF images. Our method features a multibranch deep learning architecture capable of generating multiple outputs and incorporates an adaptive progressive masking strategy to accommodate the varying combinations of input biomarkers. This approach not only improves the quality of the generated biomarker images, but also eliminates the need to train separate models for each target biomarker. We evaluated AdSI-MIMO using two datasets, including a local dataset comprising mIF images from 257 melanoma patients and a public dataset of 55 urothelial carcinoma samples. Our method achieved substantial improvements over state-of-the-art methods, particularly in the imputation of key T-cell and activation biomarkers, such as CD8 and PD-L1. Specifically, across both public and proprietary datasets, our model achieved a 18.4% improvement in Pearson Correlation Coefficient (Pearson-r) for CD8 imputation and a 48.1% improvement for PD-L1 imputation under various input biomarker configurations on the external test set.

bioinformatics↗

bioRxiv2025

VAMPIRE: Analyzing variation and motif pattern in tandem repeats

Tandem repeats (TRs) are pervasive in eukaryotic genomes and play key roles in genome organization, evolution, and function, particularly in complex regions such as centromeres and subtelomeres. Although long-read sequencing technologies have improved the resolution of these regions, existing methods remain limited in their ability to systematically and accurately characterize large-scale TRs. Here, we introduce VAMPIRE, a k-mer-based computational tool for comprehensive TR discovery, annotation, and quantification. Unlike previous methods, VAMPIRE enables reference-free, fine-grained decomposition of both simple and complex TRs, capturing motif variation in sequence, length, and structure with high sensitivity and scalability. Applied to complete telomere-to-telomere (T2T) human and nonhuman primate (NHP) genome assemblies, VAMPIRE reveals previously unrecognized high-order repeat inversions within human centromeres--an underappreciated evolutionary mechanism contributing to centromere diversity. Additionally, the tool identifies lineage-specific and expanded TRs, including human-specific STR/VNTR expansions and NHP-specific subtelomeric heterochromatin (e.g., pCht/StSat), underscoring their dynamic turnover and structural complexity. VAMPIRE provides a robust and scalable framework for TR analysis in the era of long-read sequencing, with broad utility across human genetics, evolutionary biology, and the study of complex TRs in non-model organisms.

genomics↗

bioRxiv2025

Metabolic basis of the astrocyte-synapse interaction governs dopaminergic-motor connection

Perisynaptic astrocyte processes are constitutive attachments of synapses in the central nervous system. However, the molecular mechanisms that control perisynaptic astrocyte ensheathment and their implications in the wiring of neural circuits remain unclear. Here, we report that glycolysis controls astrocyte-synapse contact. In the Drosophila larval dopaminergic (DAergic) circuit, blocking astrocyte glycolysis stimulated perisynaptic ensheathment by attenuating astrocyte-to-DAergic neuron neuroligin 2-neurexin 1 signaling. As a result, the larvae executed more reorientation actions during locomotion. At the circuit level, behavioral alterations were found to arise from increased DAergic neuronal synaptogenesis and DAergic-motor connection. Our research uncovers an ancient metabolic basis that determines perisynaptic astrocyte ensheathment abundance through a conserved neuroligin-neurexin signaling pathway and demonstrates the role of astrocyte glycolysis in controlling DAergic-motor circuit assembly and function.

neuroscience↗

bioRxiv2025

Control of leaflet movement pattern by a novel PP2C phosphatase DLM1 in Medicago truncatula

Sessile plants exhibit diverse movement behaviors that have long intrigued the scientists. The legume plants display a rhythmic leaflet movement pattern characterized by horizontal opening during the day and vertical closure at night. However, the underlying mechanisms remain largely enigmatic. Here, we isolated a mutant designated as dlm1 (downward leaflet movement1) from Medicago truncatula that displays leaflets downward opening during daytime while upward closure at night. Cellular analyses reveal that this aberrant phenotype correlates with abnormal volume changes of motor cells within the pulvinus. DLM1 exhibits high expression level in the motor organ pulvinus and encodes an unreported nuclear-localized PP2C phosphatase. Notably, phylogenetic analysis demonstrates that species exhibiting rhythmic leaflet movements consistently retain DLM1 homologs, suggesting the possibility of its functionally conserved role in regulating leaflets movement pattern. Structural characterization reveals that DLM1 possesses both phosphatase and kinase domains. Functional complementation assays demonstrate that the phosphatase domain is necessary and sufficient for maintaining the leaflet movement pattern. Collectively, our work uncovers a novel PP2C protein that governs the leaflet movement, providing mechanistic insights into this intriguing plant behavior.

plant biology↗

bioRxiv2025

Cryo-EM structure revealed a novel F-actin binding motif in a Legionella pneumophila lysine fatty-acyltransferase

Legionella pneumophila is an opportunistic bacterial pathogen that causes Legionnaires disease. To establish an intracellular niche conducive to replication, L. pneumophila translocates a diverse array of effector proteins that manipulate various host cellular processes, including the actin cytoskeleton. In a screen for effectors that alter actin dynamics, we identified a Legionella effector, Lfat1 (lpg1387), which colocalizes with the actin cytoskeleton in eukaryotic cells. Lfat1 specifically binds F-actin through a novel actin-binding domain (ABD). High-resolution cryo-electron microscopy (cryoEM) analysis revealed that this ABD forms a long -helix hairpin, with its tip interacting with subdomains I and II of two adjacent actin molecules within the F-actin filament. Interestingly, while individual -helices of the hairpin fail to bind F-actin, co-expression as separate fusion proteins restores binding activity. Furthermore, we demonstrated that Lfat1 exhibits lysine fatty-acyltransferase (KFAT) activity, targeting host small GTPases. These findings establish a foundation for studying the KFAT family of bacterial toxins and uncover a novel F-actin binding motif, providing an alternative F-actin marker with notable flexibility.

biochemistry↗