Biology subjects

Yang, M.

Publications and source records attributed to Yang, M..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗

bioRxiv2025

GPX4 Promotes Optic Nerve Regeneration and RGC Neuroprotection

Preventing retinal ganglion cells (RGCs)s soma and axon degeneration and promoting optic nerve (ON) regeneration holds great promise for effective glaucoma treatment. To explore potential neural repair strategies, we focused on glutathione peroxidase 4 (GPX4), a key regulator of lipid peroxidation. GPX4 is upregulated in surviving RGCs after acute ON crush or chronic ocular hypertension insult, and also in regenerating RGCs. AAV-mediated RGC-specific overexpression of GPX4 promotes significant ON regeneration and RGC survival, along with visual functional preservation, demonstrating the detrimental role of lipid peroxidation in glaucoma and the therapeutic potential of modulating lipid peroxidation through GPX4 in optic neuropathies.

neuroscience↗

bioRxiv2025

Cryo-EM structure of DNA-unbound human MCM2-7 complex reveals new disease-relevant regulation

Chromatin loading of the hexameric replicative helicase MCM2-7 complex requires coordinated interactions with the origin recognition complex (ORC), CDC6, and CDT1. MCM2-7 not bound to DNA forms a single hexamer (SH) with an open DNA entry gate. Two MCM2-7 SHs are loaded sequentially to form the double hexamer (DH) that encircles the DNA duplex. Activated MCM2-7 then unwinds DNA and initiates DNA replication. Our cryo-electron microscopy analyses show that a fraction of human MCM2-7 without DNA exists as DH. Unexpectedly, we find that the MCM3 winged helix domain (WHD) docks on MCM2 in both DNA-free DH and SH, creating a safety latch across the DNA entry gate to block DNA entry into the central channel. The safety latch can be opened by ORC-CDC6 binding. Disrupting this latch by designed or human disease-related mutations of MCM3 causes replication defects and DNA damage checkpoint activation. Our findings uncover a new regulated step in MCM2-7 loading with implications for human diseases.

biophysics↗

bioRxiv2025

An Adipose mTORC1 Effector Links Nutrient-induced Ribosomal Protein Translation to Lifespan in Drosophila

Mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to orchestrate metabolic processes critical for physiological homeostasis and organismal ageing1. While mTORC1 preferentially regulates the translation of 5'-terminal oligopyrimidine (TOP) motif-containing mRNAs that predominantly encode ribosomal proteins (RPs) via the translational repressor 4E-BP 2, this mTORC1 function is resistant to rapamycin inhibition 3. TOP mRNAs are exceptionally abundant, thus imposing a major translational burden on cells; yet how their translation is physiologically tuned and linked to longevity remain unexplored. Here we identify Lsp2, originally known as a storage protein 4, as an adipose effector of mTORC1 that modulates lifespan in Drosophila. Lsp2 is induced by essential amino acids (EAAs) via mTORC1. Genetic ablation of Lsp2 to blunt organismal response to protein diets drives robust lifespan extension without compromising key life-history traits such as reproduction. Translatomic profiling reveals that loss of Lsp2 selectively reduces global TOP mRNA translation in a 4E-BP-dependent manner, thereby extending lifespan via a mechanism distinct from rapamycin inhibition that fails to reduce 4E-BP phosphorylation in vivo. Finally, Lsp2 adipokine promotes 4E-BP phosphorylation and acts systemically across tissues to shape the lifespan responses to dietary protein. Collectively, our findings establish Lsp2 as a novel translational regulator of TOP genes that mechanistically couples physiological ribosomal protein synthesis with organismal longevity.

physiology↗

bioRxiv2025

Dual roles of Drosophila reward-encoding dopamine neurons in regulating innate and learned behaviors

Dopaminergic neurons (DANs) play a key role in learning the value of cues that predict reward. The fruit fly Drosophila has provided a powerful model to dissect the mechanisms by which reward-encoding DANs mediate reward learning. However, the role of these DANs in regulating innate behaviors is less clear. Here, we show that activating the entire population of reward-encoding DANs in Drosophila drives innate aversion in multiple behavioral assays, including feeding, locomotion, and spatial preference, even as these neurons confer a positive value onto associated cues to drive future learned attraction. Activating subsets of DANs reveals that the effects on innate and learned behaviors are dissociable. Based on known circuitry, it is likely that innate aversion and learned attraction elicited by DANs arise from distinct effects - direct activation versus synaptic plasticity - on the same target neurons. These results reveal distinct roles for reward-encoding DANs in guiding immediate and future behavior.

neuroscience↗

bioRxiv2025

Spatial epigenomic niches underlie glioblastoma cell state plasticity

IDH-wildtype glioblastoma (GBM) is an aggressive brain tumor with poor survival and few therapeutic options. Transcriptionally-defined cell states coexist in GBM and occupy defined regions of the tumor. Evidence indicates that GBM cell states are plastic, but it remains unclear if they are determined by the underlying epigenetic state and/or by microenvironmental factors. Here, we present spatially-resolved epigenomic profiling of human GBM tissues that implicate chromatin structure as a key enabler of cell plasticity. We report two epigenetically-defined and spatially-nested tumor niches. Each niche activates short-range molecular signals to maintain its own state and, surprisingly, long-range signals to reinforce the state of the neighboring niche. The position of a cell along this gradient-like system of opposing signals determines its likelihood to be in one state or the other. Our results reveal an intrinsic system for cell plasticity that is encoded in the chromatin profiles of two adjacent niches that dot the topological architecture of GBM in cartesian space.

genomics↗

bioRxiv2025

Transcriptomic comparison of early onset preeclampsia and placenta accreta identifies inverse trophoblast and decidua functions at the maternal-fetal interface

Early onset preeclampsia is a placental disorder characterized by shallow implantation, whereas placenta accreta spectrum is a placental disorder of deep placental attachment. This study compares the transcriptome of these two obstetric syndromes. By integrating available microarray and single-cell placenta/decidua transcriptomic datasets, we demonstrated that early onset preeclampsia genes are inversely expressed in placenta accreta, with the most marked differences noted in cell types of decidua, endothelial, and extravillous trophoblasts. Our findings highlight the key functions of trophoblast cell migration and invasion, decidua cell signaling, hypoxia pathways, and global growth factor and collagen contributions to these pregnancy disorders. This research provides new insights into the mechanisms of placentation and unifies these clinical siloes of disease by focusing on the fundamental biology of placental development at the maternal-fetal interface.

molecular biology↗

bioRxiv2025

Uev1A counteracts oncogenic Ras stimuli in both polyploid and diploid cells

Oncogenic Ras is known to induce DNA replication stress, leading to cellular senescence or death. In contrast, we found that it can also trigger polyploid Drosophila ovarian nurse cells to die by inducing aberrant division stress. To explore intrinsic protective mechanisms against this specific form of cellular stress, here we conducted a genome-wide genetic screen and identified the E2 enzyme Uev1A as a key protector. Reducing its expression levels exacerbates the nurse cell death induced by oncogenic Ras, while overexpressing it or its human homologs, UBE2V1 and UBE2V2, mitigates this effect. Although Uev1A is primarily known for its non-proteolytic functions, our studies demonstrate that it collaborates with the E3 APC/C complex to mediate the proteasomal degradation of Cyclin A, a key cyclin that drives cell division. Furthermore, Uev1A and UBE2V1/2 also counteract oncogenic Ras-driven tumorigenesis in diploid cells, suppressing the overgrowth of germline tumors in Drosophila and human colorectal tumor xenografts in nude mice, respectively. Remarkably, elevated expression levels of UBE2V1/2 correlate with improved survival rates in human colorectal cancer patients harboring oncogenic KRAS mutations, indicating that their upregulation could represent a promising therapeutic strategy.

cell biology↗

bioRxiv2025

The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis

E3 ubiquitin ligases mediating turnover of proteins engaged in cancer progression point to key regulatory nodes. To uncover modifiers of metastatic competency, we conducted an in vivo genome-wide CRISPR-inactivation screen using cultured breast circulating tumor cells, following intravascular seeding and lung colonization. We identified HECTD4, a previously uncharacterized gene encoding a conserved potential HECT domain-containing ubiquitin transferase, as a potent tumor and metastasis suppressor. We show that purified HECTD4 mediates ubiquitin conjugation in vitro, and proteomic studies combined with ubiquitin remnant profiling identify a major degradation target as the prostaglandin synthetic enzyme cyclooxygenase-2 (COX-2; PTGS2). In addition to COX-2 itself, HECTD4 targets its regulatory kinase MKK7. In breast cancer models, HECTD4 expression is induced as cells lose adherence to the matrix, and its depletion massively increases COX-2 expression, enhancing anchorage-independent proliferation and tumorigenesis. Genetic or pharmacologic suppression of COX-2 reverses the pro-tumorigenic and pro-metastatic phenotype of HECTD4-depleted cells. Thus, HECTD4 encodes an E3 ubiquitin ligase that downregulates COX-2 suppressing anchorage-independence in epithelial cancer cells. Significance StatementA genome-wide CRISPR-inactivation screen identified the previously uncharacterized E3 ubiquitin ligase HECTD4, as a tumor and metastasis suppressor, with COX-2 as its major degradation target. The pro-tumorigenic and pro-metastatic effect of HECTD4 suppression depends on COX-2 stabilization, which is critical for anchorage-independent growth, providing a basis for investigating COX-2 inhibition to prevent metastatic recurrence.

cancer biology↗

bioRxiv2025

Presence of Hepatitis B virus infection in colon cancer

Hepatitis B virus (HBV) infection affects [~]300 million people worldwide, which population is at an elevated risk of various cancers, such as gastrointestinal cancer, while the matter behind is largely unclear. In this study, we analyzed 10 colonic specimens from 6 colon cancer patients who were also chronic HBV carriers through Fluorescence-activated Cell Sorting and Immunofluorescence assay to inspect the expression of HBsAg (HBV surface antigen), NTCP (current known cellular receptor of HBV) and CD45 (common marker for immune cells) proteins in single-cell resolution. We found that presence of HBsAg in colonic cells was observed in specimens from all patients, and the proportions of HBV-infected cells were higher in tumors than normal tissues. Strikingly, HBsAg in both immune cells and NTCP-negative cells were also observed in all the patients. In vitro experiments further demonstrated that colonic cells expressing NTCP were indeed highly suspectable to HBV infection. Hence, HBV could infect colonic cells (including immune ones) and may play roles during tumorigenesis in colon cancer.

cancer biology↗

bioRxiv2025

A biofilm activator MmtA1 modulates multi-drug resistance in mycobacteria

When exposed to the antibiotic-induced stress, Mycobacterium species have the ability to survive by forming protective multicellular structures known as biofilms. However, the underlying mechanism of biofilm formation in response to antibiotics is not fully understood. In this study, we identified a transcriptional factor, MmtA1, which responds to the first-line anti-tuberculosis drug isoniazid and regulates genes involved in sugar and lipid transportation. This leads to increased biofilm formation and multi-drug resistance in M. smegmatis. These findings suggest that isoniazid may act as a molecular messenger, working in coordination with transcriptional regulatory factors to induce multidrug resistance under chemotherapy. ImportanceThis study elucidates a novel transcriptional regulatory mechanism by which Mycobacterium smegmatis develops multidrug resistance in response to the anti-tuberculosis drug isoniazid. By linking antibiotic stress to transcriptional regulation and metabolic adaptation, this work provides new insights into drug-induced tolerance in mycobacteria, suggesting antibiotic functional as inducer of biofilm formation, triggering a coordinated transcriptional response to enhance bacterial survival under antibiotic pressure.

microbiology↗

bioRxiv2025

The Neurocognitive Mechanisms Underlying Narrative Schematic and Paraphrastic Transmission

Narrative transmission serves multiple crucial functions, such as cultural preservation, knowledge accumulation, and consensus building, in human society. However, our understanding of its neurocognitive mechanisms remains limited. In this study, we combined a social transmission chain design with fMRI to investigate the dynamic changes of different narrative components occurring throughout transmission chains and to uncover the factors driving fidelity and distortion. A total of 58 participants were scanned as they listened to and subsequently recalled a story within a social transmission chain. We distinguished two types of transmission modes: schematic transmission, which prioritizes preserving the structural framework of the information, and paraphrastic transmission, which entails rephrasing the content while conveying its meaning. Behavioral results revealed a pattern in which paraphrastic transmission led to distortion and divergence, whereas schematic transmission remained more stable and convergent. Neural findings indicated that the transmission of story structure and content involved subsystems of the Default Mode Network (DMN) and specific subregions of the Hippocampus (HPC). While neural reinstatement between narrative listening and speaking failed to predict across-generation fidelity of content and structure, functional connectivity pattern similarity analysis showed that the DMN and HPC work as an episodic memory system supporting transmission performance. These findings highlight that narrative transmission is supported by distinct neurocognitive representations within episodic memory subsystems, which work collaboratively to sustain the transmission of narratives.

neuroscience↗

bioRxiv2025

A foundation model for protein-ligand affinity prediction through jointly optimizing virtual screening and hit-to-lead optimization

The structure of the protein binding pocket governs the ligand binding affinity by providing crucial intermolecular interactions and spatial compatibility. While existing methods have leveraged these structural insights to advance affinity prediction, they often treat virtual screening and hit-to-lead optimization separately, mainly due to incompatible speed-accuracy requirements. However, these two tasks complement each other, and their integration enables broader chemical exploration while preserving focus on affinity-determining substructures. Here, we present LigUnity, a foundation model for affinity prediction that jointly embeds ligands and pockets into a shared space. In particular, LigUnity learns coarse-grained active/inactive distinction through scaffold discrimination and fine-grained pocket-specific ligand preference through pharmacophore ranking. We demonstrate the effectiveness and versatility of LigUnity on eight benchmarks across six settings. In virtual screening, LigUnity outperforms 24 methods with >50% improvement and demonstrates robust generalization to novel targets. In hit-to-lead optimization, it achieves state-of-the-art performance across split-by-time, split-by-scaffold, and split-by-unit settings, emerging as a cost-efficient alternative to free energy perturbation. We further showcase how LigUnity can be employed in an active learning framework for TYK2 to efficiently find optimal ligands. Collectively, these results establish LigUnity as a versatile foundation model for affinity prediction, offering broad applicability across the drug discovery pipeline.

bioinformatics↗

bioRxiv2025

Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity

Genome editing enzymes can introduce targeted changes to DNA in living cells1-4, transforming biological research and enabling the first approved gene editing therapy for sickle cell disease5. However, their activity can be altered by genetic variation at on- or off-target sites6-8, potentially impacting both their precision and therapeutic safety. Due to a lack of scalable methods to measure genome-wide editing activity in cells from large populations and diverse target libraries, the frequency and extent of these variant effects on editing remain unknown. Here, we present the first systematic, population-scale study of how genetic variation affects the cellular genome-wide activity of CRISPR-Cas9, enabled by a novel, sensitive, and unbiased cellular assay, GUIDE-seq-2, with improved scalability and accuracy compared to the original broadly adopted method9. Analyzing Cas9 genome-wide activity at 1,115 on- and off-target sites across six guide RNAs in cells from 95 individuals spanning four genetically diverse populations, we found that genetic variants frequently overlap off-target sites, with 14% significantly altering Cas9 editing activity. To understand the effect of mismatches in more diverse sequence contexts, we developed a novel method, combinatorial high-throughput analysis of nuclease cleavage effects (CHANCE-seq), the first massively parallel biochemical approach that can quantify Cas9 activity across millions of mismatched target sites. We leveraged this large-scale CHANCE-seq dataset to train a context-aware deep neural network model, CHANCE-net, to accurately predict and interpret the effects of single-nucleotide variants on off-targets with up to six mismatches. Our deep combinatorial profiling of Cas9 off-target activity revealed frequent, context-dependent synergistic effects of mismatches. Taken together, our findings illuminate an approach to accounting for genetic variation when designing genome-editing strategies for research and therapeutics.

genomics↗

bioRxiv2025

Predicting Mutation-Induced Relative Protein-Ligand Binding Affinity Changes via Conformational Sampling and Diversity Integration with Subsampled Alphafold2 in Few-Shot Learning

Predicting the impact of mutations on protein-ligand binding affinity is crucial in drug discovery, particularly in addressing drug resistance and repurposing existing drugs. Current structure-based methods are constrained by their dependence on known protein-ligand complex structures. The absence of structural data for mutated proteins, along with the potential of mutations to modify protein conformational states, brings challenges for reliable predictions. The downstream application of conformational sampling of Alphafold, such as the prediction of binding free energy changes induced by mutation, has not been fully explored. To tackle the challenge, we propose a few-shot learning approach that integrates AlphaFold2 subsampling, ensemble docking, and Siamese learning to predict the relative binding affinity changes induced by mutations. We validate our approach for predicting binding affinity changes in 31 variants of the mutated Abelson tyrosine kinase (ABL). The conformation ensembles for each ABL variant are generated using AlphaFold2 subsampling. The most likely conformational states are selected by Gaussian fitting to construct the pairwise structural inputs and compute relative binding energies. Then the relative binding affinities are derived by averaging the values predicted by the Siamese learning model across the constructed conformational pairs. By benchmarking on the Tyrosine kinase inhibitors (TKI) dataset and the direct binding affinity using the refined set of PDBbind database, our proposed approach achieves an increased Spearman correlation coefficient for five out of six TKI molecules across 31 mutants when estimating relative binding affinities. Although the proposed method is validated on the ABL, it can be transferred and applied to other drug-target interaction predictions when the conformational flexibility of proteins needs to be considered. We anticipate the approach will be valuable for predicting binding energy changes induced by mutations in proteins or ligands, facilitating drug discovery efforts.

bioinformatics↗

bioRxiv2025

TRPV4 Dominates High Shear-Induced Initial Traction Response and Long-Term Relaxation Over Piezo1

Modulation of endothelial traction is critical for the responses of endothelial cells to fluid shear stress (FSS), which has profound implications for vascular health and atherosclerosis. Previously, we demonstrated that under high FSS, endothelial cells rapidly increase traction forces, followed by relaxation, with traction aligning in the flow direction. In contrast, low shear preconditioning induces a modest short-term increase in traction (<30 min), followed by a secondary long-term (>14 hr) rise, with traction/cells aligning perpendicular to the flow. The upstream mechanosensors driving these responses, however, remain unknown. Here, we sought the roles of Piezo1 and TRPV4 ion channels in shear-induced traction modulation. We report that HUVECs with Piezo1 silencing reduced the initial traction rise in half under high FSS compared to those by WT cells, while not affecting the traction modulation in response to low FSS or traction/cell alignment to the flow direction. Conversely, cells with siTRPV4 fully abrogated the initial traction rise, as well as alignment of traction and cells, in response to both high and low FSS conditions. Dual inhibition of Piezo1 and TRPV4 further impaired both initial and long-term traction under high FSS. Interestingly, dual-inhibited cells displayed larger initial traction responses to low FSS compared to control cells, suggesting the involvement of alternative calcium-independent pathways that become dominant when both ion channels are nonfunctional. Additionally, either ion channel inhibition led to secondary long-term traction increase even under high FSS condition. These findings suggest that while both Piezo1 and TRPV4 channels contribute to shear mechanotransduction, TRPV4 plays more dominant role than Piezo1 in mediating the initial traction rise and sustaining long-term relaxation under high or low shear stress, highlighting their critical and distinct contributions to endothelial mechanotransduction and remodeling.

cell biology↗

bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

bioRxiv2025

Spatial profiling of central nervous system cellular markers in murine breast cancer to brain metastases

BackgroundBrain metastasis occurs in approximately 16% of metastatic breast cancer patients, and incidence is increasing. Patients with breast cancer brain metastases frequently develop neurological problems including cognitive impairments and seizures. We previously demonstrated accumulation of activated microglia around the tumour site in a breast cancer brain metastasis model, which co-localised with spontaneously occurring local field potential events that resembled interictal epileptic discharges. However, the mechanisms underlying these spatially restricted effects on neuronal excitability are poorly understood. MethodsTo better understand the underlying cellular changes and potential mechanisms, we used digital spatial profiling of brain cell subtype-specific markers to chart the spatial organisation of neurons, oligodendrocytes, astrocytes, and microglia in relation to metastatic lesion site. We developed a novel chordline-based approach to analyse these spatial changes in biomarker distribution. ResultsSeveral protein markers associated with proliferation (Ki67), astrocytes (GFAP) and microglia (CD11b, IBA1, CD45, MSR1) were upregulated in the tumour compared to healthy contralateral brain parenchyma. In contrast, some neuroglial markers (MAP2, Neurofilament light, NeuN, S100B and TMEM119) were lower in the lesion compared to normal tissue. ConclusionsOverall, the protein marker changes in the lesion are indicative of neuronal cell loss and changes in the immune microenvironment of the metastatic lesion involving activated microglia, astrocytes and recruitment of peripheral immune cells. Such cellular changes may contribute to the changes in electrical activity resulting from brain metastases observed in mice and patients.

neuroscience↗