Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 451 records · Page 25Linked to original sources

bioRxiv2025

Nitrogen deposition reshapes plant nutrient acquisition strategies: a meta-analysis within the root economics space

Global nitrogen (N) deposition has fundamentally reshaped plant nutrient acquisition by altering mechanistic trade-offs between root exploration-exploitation strategies and mycorrhizal symbiosis. Through a meta-analysis of 135 studies spanning 153 sites, we demonstrate that N deposition stimulates root exploration (+84.6% root length density) and exploitation (+13.2% nitrogen content and +8.5% root biomass) while suppressing mycorrhizal dependence (-32.8% biomass, -18.73% colonized root length, -7.55% hyphal length), indicating a systemic shift toward root-autonomous nutrient acquisition. Divergent responses emerged between plant lifeforms: woody plants prioritize exploitation (+13.2% nitrogen content) over exploration capacity (-7.9% root length density), whereas herbaceous species exhibit synergistic enhancement of both strategies (+88% root length density, +13.2% nitrogen content and +71.3% root biomass). In contrast to N-only effects, Combined nitrogen and phosphorus additions reversed mycorrhizal suppression (+41.9% biomass), highlighting their persistent role in phosphorus acquisition under elevated nutrient conditions. The root economics space framework demonstrates predictive power, with plants possessing lower specific root length (SRL) and higher nitrogen content exhibiting stronger positive responses to N deposition, while those possessing higher SRL and lower nitrogen content showed reduced investment in root systems. These trait-mediated thresholds in carbon-nutrient tradeoffs refine our capacity to model belowground ecological responses to anthropogenic nitrogen perturbation, establishing a mechanistic basis for projecting ecosystem trajectories under global change.

plant biology↗

bioRxiv2025

Characterisation of guided entry of tail-anchored proteins in Magnaporthe oryzae

Rice (Oryza sativa L.) is one of the most important staple foods for human population worldwide. However, rice production continues to be severely threatened by rice blast disease caused by an ascomycete fungus Magnaporthe oryzae. Tail-anchored (TA) proteins are conserved across diverse organisms, and belongs to a class of polypeptides that are inserted into the membrane by a hydrophobic sequence located at the C- terminal region. The Guided Entry of Tail-anchored (GET) complex is responsible for the post-translational insertion of nascent TA proteins into the ER lipid bilayer. In Saccharomyces cerevisiae, the GET pathway comprises of six known associated components Get1, Get2, Get3, Get4, Get5, Sgt2 and Ssa1 that have been identified and extensively studied. However, the role of the GET complex in rice blast fungus has not been elucidated. Here in, we identified five proteins of the GET Complex in M. oryzae namely MoGet1, MoGet2, MoGet3, MoGet4 and MoSgt2 and generated the gene knock-out mutants. Deletion of MoGET1 and MoGET2 revealed that they are required for vegetative growth, asexual reproduction and pathogenesis, while MoGet3 negatively regulates hyphal growth, asexual development and pathogenesis of M. oryzae. In contrast, loss of MoGet4 and MoSgt2 had no effect on the normal development of the rice blast fungus. We demonstrated that the MoGet2 is important in osmotic stress response while MoGet2 and MoGet3 positively and negatively regulate cell wall integrity, respectively. The MoGet1 and MoGet2 were ER-localised and indispensable for DTT-induced ER stress response. In vitro and in vivo interaction assay revealed MoGet3 has physical interaction with both MoGet1 and MoGet2 indicating the existence of possible synergistic function amongst the Get components in rice blast fungus. In summary, this finding indicates the GET Components offers an excellent target for the development of antifungal components against recalcitrant plant fungal pathogens.

genetics↗

bioRxiv2025

Restoration of excitation/inhibition balance enhances neuronal signal-to-noise ratio and rescues social deficits in autism-associated Scn2a-deficiency

Social behavior is critical for survival and adaptation, which is profoundly disrupted in autism spectrum disorders (ASD). Social withdrawal due to information overload was often described in ASD, and it was suspected that increased basal noise, i.e., excessive background neuronal activities in the brain could be a disease mechanism. However, experimental test of this hypothesis is limited. Loss-of-function mutations (deficiency) in SCN2A, which encodes the voltage-gated sodium channel NaV1.2, have been revealed as a leading monogenic cause of profound ASD. Here, we revealed that Scn2a deficiency results in robust and multifaceted social impairments in mice. Scn2a-deficient neurons displayed an increased excitation-inhibition (E/I) ratio, contributing to elevated basal neuronal noise and diminished signal-to-noise ratio (SNR) during social interactions. Notably, the restoration of Scn2a expression in adulthood is able to rescue both SNR and social deficits. By balancing the E/I ratio and reducing basal neuronal firing, an FDA-approved GABAA receptor-positive allosteric modulator improves sociability in Scn2a-deficient mice and normalizes neuronal activities in translationally relevant human brain organoids carrying autism-associated SCN2A nonsense mutation. Collectively, our findings revealed a critical role of the NaV1.2 channel in the regulation of social behaviors, and identified molecular, cellular, and circuitry mechanisms underlying SCN2A-associated disorders. HIGHLIGHTSO_LINaV1.2 deficiency leads to pronounced social deficits in mice. C_LIO_LINaV1.2 deficiency results in an overall enhanced E/I ratio, elevated basal neuronal activity, and impaired signal-to-noise ratio. C_LIO_LIBoth the enhanced E/I ratio and impaired sociability are reversible through the restoration of NaV1.2 expression in adulthood. C_LIO_LITargeted restoration of NaV1.2 in striatum-projecting neurons rescues social impairments. C_LIO_LIGABA transmission is reduced in both mouse and human organoid models of SCN2A deficiency, and acute systemic administration of GABAA receptor-positive allosteric modulators restores sociability. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/641498v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@154a323org.highwire.dtl.DTLVardef@1a27fbaorg.highwire.dtl.DTLVardef@16fa3beorg.highwire.dtl.DTLVardef@6712c2_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract: Severe Scn2a deficiency leads to a predominate decrease in GABA transmission with an overall enhanced E/I ratio, elevated basal neuronal activity, impaired SNR, and social deficits in adult NaV1.2-deficient mice.

neuroscience↗

bioRxiv2025

Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells

The olfactory epithelium (OE) possesses an adult stem cell population, the horizontal basal cells (HBCs), to permit lifelong tissue regeneration. Here we show that HBCs exhibit asymmetric inheritance of histone H4 but not H2A-H2B during OE regeneration in mice. Primary HBC cultures further revealed asymmetric histone inheritance for H3 and H3.3. Upon mitotic exit, asymmetric histone inheritance correlates with asynchronous transcription re-initiation and differential enrichment of p63, a key transcription factor for HBC cell fate. Disruption of asymmetric histone inheritance abolished these asymmetric cellular features and attenuated OE regeneration and smell behavior recovery. Single-cell RNA sequencing of paired HBC daughters in culture further supported asymmetric multilineage cell fate priming. Together, these findings reveal asymmetric histone inheritance in a mammalian adult stem cell lineage and highlight its biological significance in neural tissue regeneration and animal behavior.

developmental biology↗

bioRxiv2025

Predicting PROTAC-targeted Degradation and Designing Androgen Receptor Degraders with AiPROTAC

Proteolysis-targeting chimeras (PROTACs), a pioneering class of heterobifunctional ligands, have emerged as transformative tools in combating cancer and immune-related diseases due to their ability to target previously undruggable proteins and overcome drug resistance. Accurate assessment of the degradation potential of PROTACs is essential for advancing their therapeutic applications. However, the development of robust predictive models is hindered by the scarcity of large-scale datasets and domain-specific tools, as well as the underutilization of existing unlabeled data. To address these challenges, we developed an innovative method called AiPROTAC to predict the degradation capacity of PROTACs. In particular, AiPROTAC integrates graph augmentation, message-passing enhanced encoders and cross-attention mechanisms within a contrastive learning framework. Moreover, AiPROTAC leverages a curated specialized dataset combined with the PROTAC-DB dataset to enhance prediction accuracy. Experimental results across two datasets and six evaluation metrics demonstrate that AiPROTAC consistently outperforms state-of-the-art models. Further case studies underline its superior sensitivity and reliability. Notably, AiPROTAC facilitated the design of a novel androgen receptor (AR) degrader, PROTAC GT19, which achieved enhanced in vitro degradation compared to Bavdegalutamide (ARV-110). This advancement highlights our AiPROTACs potential to accelerate PROTAC-based therapeutic development and optimization.

bioinformatics↗

bioRxiv2025

Potency and selectivity of a novel pan-RAS inhibitor in 3D bioprinted organoid tumor models

BackgroundColorectal cancer (CRC) remains a significant global health burden, with KRAS mutations driving [~]40% of cases. Efficacy of recently approved, mutant-specific KRAS inhibitors is limited by intrinsic and adaptive resistance mechanisms. Pan-RAS inhibitors, such as ADT-007, offer broader therapeutic potential by targeting multiple RAS isoforms. Here, we evaluate ADT-007 in 3D bioprinted organoid tumors (BOTs) generated from KRAS-mutant and RAS wild-type (WT) CRC cell lines. MethodsPotency and selectivity of ADT-007 were compared to bortezomib, a proteasome inhibitor, and YM155, a survivin inhibitor, using high-content imaging and ATP-based luminescence assays. Mechanistic studies assessed impact on RAS activation and downstream signaling. ResultsADT-007 exhibited high potency and selectivity in KRAS-mutant BOTs, reducing tumor burdens >30% at nanomolar concentrations, and demonstrated superior selectivity over bortezomib and YM155 with minimal cytotoxicity in RAS-WT BOTs. Mechanistic analysis confirmed ADT-007 inhibited RAS activation and downstream signaling, leading to selective apoptosis induction in KRAS-mutant CRC cells. ConclusionsThe selective potency and specificity of ADT-007 warrants further investigation of pan-RAS inhibitors for treating RAS-driven cancers. This study also underscores the translational utility of 3D BOT models for preclinical drug response assessment. Further validation in patient-derived BOTs is necessary to evaluate potential of ADT-007 in clinical settings.

bioengineering↗

bioRxiv2025

Kinetic control of mammalian transcription elongation

Transcription elongation by RNA polymerase II is an integral step in eukaryotic gene expression. The speed of Pol II is controlled by a multitude of elongation factors, but the regulatory mechanisms remain incompletely understood, especially for higher eukaryotes. In this work, we developed a single-molecule platform to visualize the dynamics of individual mammalian transcription elongation complexes (ECs) reconstituted from purified proteins. This platform enabled us to follow the elongation and pausing behavior of EC in real time and dissect the role of each elongation factor in the kinetic control of Pol II. We found that the mammalian EC harbors multiple gears dictated by its associated factors and phosphorylation status. Moreover, the elongation factors are not functionally redundant but act hierarchically and synergistically to achieve optimal elongation activity. Such exquisite kinetic regulation may underline the major speed-changing events during the transcription cycle and enable cells to adapt to a changing environment.

molecular biology↗

bioRxiv2025

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice

Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In this paper, we extend this capability to achieve optical transparency across the entire visible spectrum by employing molecules with strong absorption in the ultraviolet spectrum and sharp absorption edges that rapidly decline upon entering the visible spectrum. This new color-neutral and reversible tissue transparency method enables optical transparency for imaging commonly used fluorophores in the green and yellow spectra. Notably, this approach facilitates tissue transparency for structural and functional imaging of the live mouse brain labeled with yellow fluorescent protein and GCaMP through the scalp and skull. We show that this method enables longitudinal imaging of the same brain regions in awake mice over multiple days during development. Histological analyses of the skin and systemic toxicology studies indicate minimal acute or chronic damage to the skin or body using this approach. This color-neutral and reversible tissue transparency technique opens new opportunities for noninvasive deep-tissue optical imaging, enabling long-term visualization of cellular structures and dynamic activity with high spatiotemporal resolution and chronic tracking capabilities. Significance StatementTissue scattering represents a major barrier to deep tissue imaging in vivo. We recently showed that tissue can be rendered transparent in the red spectrum using intensely absorbing dye molecules. Here, we introduce a new, color-neutral and reversible tissue transparency approach. We demonstrate longitudinal structural and functional imaging in the deep tissue of awake mice.

bioengineering↗

bioRxiv2025

Staining-free Visualization of Cell Boundaries in Sliced Tissues for Accurate Binning of Gene Expression in Spatial Transcriptomics

Overcoming the limitations of sparse expression data in high-resolution spatial transcriptomics remains a major challenge for dimensionality reduction and clustering analysis. Visualizing or inferring tissue cell boundaries using dye staining on the same slice can help assign capture spots on the chip to corresponding unit cells and enhance UMI counts and the number of detected genes. However, the staining process may disrupt tissue structures or degrade mRNA, leading to inaccurate spot assignment and cell annotation. In this study, we employed LysM-Cre mT/mG transgenic mice for spatial transcriptomic analysis, where cell boundaries were delineated by tdTomato signals, and myeloid cells were labeled with enhanced green fluorescent protein (EGFP). With the aid of these fluorescent markers, UMI counts and the number of detected genes per cell exceeded those obtained through naive binning with a square matrix. This staining-free approach for visualizing cell boundaries and landmark proteins provides a valuable framework for the studies of single-cell spatial transcriptomics.

bioengineering↗

bioRxiv2025

Dynamic fingerprinting of the human functional connectome

Resting-state functional connectivity (FC) have distinct, personalized patterns that could serve as a unique fingerprint of each individuals brain. While previous brain fingerprinting methods have used functional connectivity maps over a scanning session (static method), it has been shown that the brain is a dynamic system that switches between several metastable states, each of which having a different FC map. Taking the dynamic nature of brain connectivity into account will likely lead to more subject-specific information and better individual identification. In this paper, we derived the state-specific FCs using sliding window correlation and clustering and evaluated their performance in individual identification and cognitive score prediction. The resultant dynamic fingerprints outperformed the static fingerprints in identification accuracy. Furthermore, some of the brain states were more accurate in predicting cognitive scores, indicating that connectivity in some brain states is informative of cognition abilities, possibly useful as biomarkers for brain disorders. Impact StatementOur findings suggest that state-specific functional connectivity patterns of the brain are unique for each individual. These brain states predicted participants cognitive performance, suggesting that they have the potential to be used as biomarkers for cognitive function or neurological disorders. Integrating state-based functional connectivity into clinical frameworks could potentially enhance early diagnosis and patient stratification, and lead to targeted interventions for neuropsychiatric and neurodegenerative conditions.

neuroscience↗

bioRxiv2025

MsyB-HU Interaction Modulates a Two-Tiered Bacterial Stress Response by Regulating DNA Supercoiling

Bacteria respond to stressful conditions through multiple pathways, including changes in gene expression patterns and mutations for adaptation. DNA supercoiling is a fundamental regulatory principle of bacterial gene expression, controlled antagonistically by DNA gyrase and topoisomerase I. Nucleoid-associated proteins, such as HU, also regulate supercoiling through interactions with DNA. Here, we identify Escherichia coli protein MsyB as a HU inhibitor and a {beta}-clamp binder. MsyB is fine-tuned under various stressful conditions, where it modulates the population of DNA-bound HU by forming a HU-MsyB complex. Consequently, the balance between DNA-bound HU and MsyB-bound HU adjusts the DNA supercoiling state, thereby influencing transcription for adaptation. Additionally, under prolonged starvation during the stationary phase, sustained high level of MsyB increases DNA exposure to damaging factors, acting as a damage inducer. The HU/MsyB/{beta}-clamp interaction suggests a model in which MsyB coordinates with HU and the {beta}-clamp to facilitate damage acquisition and error-prone DNA repair. Thus, MsyB-dependent supercoiling regulation represents a novel two-tiered bacterial stress response mechanism in gene expression and adaptive mutation. Our findings reveal a previously unrecognized regulatory mechanism of bacterial supercoiling, positioning HU as a promising antibiotic target.

microbiology↗

bioRxiv2025

The fetal hydrops-associated single-residue mutation L322P abolishes mechanical but not chemical activation of the PIEZO1 ion channel

The mechanically activated PIEZO1 ion channel is genetically linked to numerous physiological and pathophysiological processes. For example, deleting PIEZO1 in mice leads to defective lymphatic vessel development, while nonsense mutations in humans are associated with autosomal recessive generalized lymphatic dysplasia (GLD) and non-immune hydrops fetalis. However, it remains unclear whether PIEZO1-dependent biological processes are directly mediated by its intrinsic mechanosensitivity. Here we identified a human fetal hydrops-associated single-residue mutation, L322P (corresponding to L329P in mouse PIEZO1), which completely abolishes PIEZO1s response to mechanical stimuli while maintaining normal plasma membrane expression and responsiveness to its chemical activators, Yoda1 and Jedi1. Remarkably, the mechanical response of the mutant can be restored by Yoda1. These findings demonstrate a direct link between the loss of PIEZO1s mechanosensitivity and the pathophysiological phenotype of fetal hydrops, and raise the therapeutic potential of using PIEZO1 chemical activators to restore the mechanosensitivity of PIEZO1 missense mutants that are associated with genetic diseases such as GLD and hydrops fetalis. Significance StatementGenetic deletion studies have revealed the diverse cellular, physiological, and pathophysiological roles of the mechanically activated PIEZO1 ion channel. However, whether these functions are directly mediated by its mechanosensitivity has remained experimentally unaddressed. In this study, we identified a novel fetal hydrops-associated single-residue mutation, hPIEZO1-L322P, which specifically abolishes PIEZO1s mechanical response while retaining its chemical activation. Remarkably, the mechanical response of the mutant can be fully restored by the PIEZO1 chemical activator Yoda1. These findings address the long-standing question of whether PIEZO1 relies on its mechanosensitivity to mediate in vivo functions, provide critical insights into the mechanosensing mechanism of PIEZO1, and highlight the therapeutic potential of using PIEZO1 chemical activators to rescue the loss of mechanosensitivity caused by missense mutations.

physiology↗

bioRxiv2025

Highly accurate prediction of broad-spectrum antiviral compounds with DeepAVC

Lethal viruses, such as HIV, pose a significant threat to human life, with each pandemic causing millions of fatalities globally. Small-molecule antiviral drugs provide an efficient and convenient approach to antiviral therapy by either inhibiting viral activity or activating the host immune system. However, conventional antiviral drug discovery is often labor-intensive and time-consuming due to the vast chemical space. Although some existing computational models mitigate this problem, there remains a lack of rapid and accurate method specifically designed for antiviral drug discovery. Here, we propose DeepAVC, a universal framework based on pre-trained large language models, for highly accurate broad-spectrum antiviral compounds discovery, including two models, DeepPAVC for phenotype-based prediction and DeepTAVC for target-based prediction. As a result, DeepAVC greatly outperforms other in silico methods. More importantly, in the top predictions, MNS and NVP-BVU972 were identified as novel compounds with promising broad-spectrum antiviral activities by in vitro experiments. Finally, DeepAVC demonstrates high interpretability, one of the bottlenecks of current AI methods, due to its ability of analyzing key functional groups of antiviral compounds and important binding sites on targets.

bioinformatics↗

bioRxiv2025

Dynamic regulation of NeuroD1 expression level by a novel viral construct during astrocyte-to-neuron reprogramming

Astrocyte-to-neuron reprogramming presents a viable approach for regenerative medicine. The reprogramming factor NeuroD1 has demonstrated capability of neuronal reprogramming with high efficiency both in culture and in the injured central nervous system. High level of NeuroD1 expression is required to break down the cellular identity barrier for a successful reprogramming, and yet persistence of this high level drives the reprogrammed neurons primarily to glutamatergic subtype. This is consistent with the critical role of NeuroD1 in determination of glutamatergic neuronal lineage during development. However, diversified neuronal subtypes are needed to establish appropriate neuronal connectivity in disease/injury conditions. We reason that continuously high level of NeuroD1 expression forces the reprogrammed neurons into glutamatergic subtype, and that reducing NeuroD1 level after reprogramming may allow generation of neurons with diversified subtypes. For this purpose, we engineered a novel viral expression vector by which NeuroD1 expression can be dynamically regulated during the reprogramming process. Specifically, the target site of a neuron-specific microRNA (miR-124) is incorporated in the expression system. Therefore, this novel construct would still achieve a high NeuroD1 expression level in astrocytes for reprogramming to occur and yet reduce its level in the reprogrammed neurons by suppression of endogenous miR-124. In this study, we demonstrated that this construct elicits a dynamic gene expression pattern with much reduced level of NeuroD1 at later stages of neuronal reprogramming. We also showed that this construct still retains relatively high reprogramming efficiency and can generate mature neurons with an enhanced GABAergic neuronal phenotype.

neuroscience↗

bioRxiv2025

Integrative Analysis of Single-cell and Bulk RNA Sequencing Reveals Macrophage Heterogeneity in Lyme Arthritis

IntroductionLyme arthritis (LA) is a common late-stage manifestation of Lyme disease caused by Borrelia burgdorferi (Bb) infection. Macrophages play a crucial role in LA pathogenesis, yet their heterogeneity and functional states within the arthritic microenvironment remain poorly understood. MethodsWe integrated single-cell RNA sequencing data from ankle joint tissues of Bb-infected C57BL/6 mice with bulk RNA sequencing data from both infected ankle joints and bone marrow-derived macrophages. We developed a LA mouse model and validated key findings through histopathological examination and RT-qPCR analysis. ResultsWe identified nine distinct cell types in the joint microenvironment with significant compositional shifts during disease progression. Analysis of 16,617 Macrophages/Monocytes revealed seven functionally distinct subpopulations with differential responses to infection. Pseudo-time trajectory analysis demonstrated three principal differentiation pathways from monocyte-derived macrophages toward anti-inflammatory, TNF+, and IL1b+ inflammatory phenotypes. Cell-cell communication analysis revealed significantly altered TGF-{beta} signaling networks in LA, with the Tgfb1-(Tglbr1+TgIbr2) axis playing a critical role. GSVA and pathway analyses showed metabolic reprogramming from oxidative phosphorylation toward glycolysis in macrophages during infection. Through integrated analysis and LASSO regression, we identified four characteristic genes (SIRPB1C, FABP5, MMP14, and EGR1) as potential LA biomarkers and developed a diagnostic nomogram with high predictive accuracy. ConclusionOur integrative analysis provides comprehensive insights into macrophage heterogeneity and functional plasticity in LA, identifying characteristic biomarkers and potential therapeutic targets. The metabolic reprogramming and altered TGF-{beta} signaling networks we identified may contribute to disease pathogenesis and offer new avenues for intervention strategies.

genomics↗

bioRxiv2025

Pyrimethamine and a potent analogue WCDD115 inhibit NRF2 by suppressing DHFR and one-carbon metabolism

Nuclear factor erythroid 2-related factor 2 (NFE2L2/NRF2) is a critical mediator of the cellular oxidative stress response. Aberrant activation of NRF2 is common in lung and upper aerodigestive cancers, where it promotes tumor initiation and progression and confers resistance to chemotherapy, radiation therapy, and immune checkpoint inhibitors. As such, NRF2 therapeutic inhibitors are actively being sought. We previously reported that the antiparasitic drug Pyrimethamine (PYR) inhibits NRF2 in cell lines and in a NRF2-inducible genetically engineered mouse model. Here we design, synthesize, and define structure-activity relationships across a series of 25 PYR-based derivatives to reveal WCDD115 as a 22-fold more potent inhibitor of NRF2 (57nM versus 1.2{micro}M). PYR is known to inhibit plasmodial and human dihydrofolate reductase (DHFR). We found that WCDD115 inhibits hDHFR with 31-fold greater potency than PYR (144nM versus 4.49{micro}M). Metabolomics showed strong similarities between PYR, WCDD115 and methotrexate. Genetic, pharmacological and metabolic epistasis studies reveal that DHFR inactivation is required for NRF2 suppression by WCDD115 and PYR. Global and targeted proteomics revealed overlapping profiles for WCDD115, PYR and methotrexate, including suppression of NRF2 oxidative stress response and activation of TP53 and the DNA damage response. Therefore, PYR and a novel potent derivative WCDD115 are effective, indirect inhibitors of NRF2 and its antioxidant functions. These data underscore the importance of one- carbon metabolism for the NRF2 signaling pathway and support a new therapeutic strategy to suppress NRF2-driven cancer biology.

cancer biology↗

bioRxiv2025

Improved Microbubble Tracking for Super-Resolution Ultrasound Localization Microscopy using a Bi-Directional Long Short-term Memory Neural Network

Ultrasound localization microscopy (ULM) enabled high-accuracy measurements of microvessel flow beyond the resolution limit of conventional ultrasound imaging by utilizing contrast microbubbles (MBs) as point targets. Robust tracking of MBs is an essential task for fast and high-quality ULM image reconstruction. Existing MB tracking methods suffer from challenging imaging scenarios such as high-density MB distributions, fast blood flow, and complex flow dynamics. Here we present a deep learning-based MB pairing and tracking method based on a bi-directional long short-term memory neural network for ULM. The proposed method integrates multiparametric MB characteristics to facilitate more robust and accurate MB pairing and tracking. The method was validated on a simulation data set, a tissue-mimicking flow phantom, and in vivo on a mouse and rat brain.

bioengineering↗

bioRxiv2025

DNA G-quadruplex Profiling Reveals Functional and Mechanistic Role of G-quadruplexes in Skeletal Muscle Stem Cells

DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling permits global mapping of endogenous G4 formation. Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs) which are essential for injury induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs from quiescent to activated and further differentiated cells, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs. Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.

molecular biology↗