Biology subjects

Xiao, M.

Publications and source records attributed to Xiao, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Low-temperature HILIC provides enhanced separations and stability for LC-MS-based metabolomics

AbstractLiquid chromatography-mass spectrometry is a potent and robust tool for studying metabolism. However, conventional workflows can suffer from poor peak shapes, limited pressure tolerance, co-elution of polar metabolites, and unstable retention times. Here, we describe the development of a more stable HILIC method for LC-MS metabolomics of human plasma and cell extracts, optimizing a zwitterionic HILIC (Z-HILIC) column for improved untargeted performance. We found that using high-pH ammonium bicarbonate with 90% acetonitrile in mobile phase B (ABC B) can greatly improve peak shapes of select metabolites when compared to 100% acetonitrile (ACN B), but at the cost of poor retention time stability. We therefore focused on optimizing chromatography for the ACN B method and observed that cooling the column to 5 {degrees}C substantially enhanced peak shape. This low-temperature Z-HILIC (LT-ZHILIC) method provides high-resolution separation of metabolites from both cellular extracts and human plasma, is stable over days, and generally outperformed a standard method using the widely described ZIC-pHILIC column. Application of the untargeted LT-ZHILIC method to characterize the metabolic consequences of glutamine and pyruvate deficiency in human cells revealed a striking change in nucleotide phosphates; a perturbation that was not observed in the ZIC-pHILIC analysis of the same samples likely due to inadequate elution profiles. In sum, the LT-ZHILIC workflow offers a robust platform to advance untargeted metabolomics by improving metabolite coverage, resolution, and retention time stability, making it a promising technique for providing novel insights into cellular metabolic rewiring and the human plasma metabolome.

bioinformatics↗

bioRxiv2025

Persistence of vestibular function in the absence of glutamatergic transmission from hair cells

Quantal synaptic transmission in vestibular end-organs is glutamatergic. Although genetic deletion of Slc17a8 (termed Vglut3) leads to deafness in mice, the dependence of vestibular function on VGLUT3-mediated quantal transmission is unknown. Here, we investigated the vestibular phenotype of Vglut3-/- mice at the cellular, systems, and behavioral levels. The type-II vestibular hair cells (VHCs) in Vglut3+/+mice were strongly immunoreactive for VGLUT3, while type-I VHCs showed poor immunoreactivity. In Vglut3-/- mice quantal synaptic transmission in utricular calyces was reduced in rate and amplitude by > 95%. In vivo recordings of spontaneous activity in the vestibular nerve revealed similar action potential rates and regularity in Vglut3+/+and Vglut3-/- mice, suggesting a divergent underlying mechanism compared to the silent Vglut3-/- auditory nerve. In behavioral studies, Vglut3-/- mice did not exhibit considerable sensorimotor or balance deficits. Collectively, these data support the view that non-quantal transmission is the predominant mode of neurotransmission between type I VHCs and vestibular calyceal afferent neurons. We propose that non-quantal transmission alone underlies the apparently normal vestibular nerve physiology and behavioral function in Vglut3-/- mice.

neuroscience↗

bioRxiv2025

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.

cancer biology↗

bioRxiv2025

Altered NPTX2 dynamics associated with impaired cognitive aging

Changes in synaptic integrity and neural activity homeostasis are hallmarks of brain aging and are closely tied to cognitive outcomes. Yet, defining their relationship across the continuum from normal aging to neurodegenerative disease has proven challenging. Recent research investigating the dynamic changes of neuronal pentraxin 2 (NPTX2, or Narp, neuronal activity-related pentraxin) in cerebrospinal fluid (CSF) of Alzheimers disease (AD) subjects supports its promise as a prognostic marker of disease progression, possibly as an expression of synaptic damage related to cognitive impairment. However, studies in human subjects are unable to clearly differentiate age-related and disease-related processes. Here we took advantage of a well-characterized rat model that displays substantial individual differences in hippocampal memory during aging, uncontaminated by slowly progressive, spontaneous neurodegenerative disease. Through this approach, we aimed to interrogate the underlying neural substrates that mediate aging as a uniquely permissive condition and the primary risk for neurodegeneration. We found that successful cognitive aging is associated with an elevation of NPTX2 levels above that found in young or cognitively impaired subjects. Pharmacological engagement of neural activity was sufficient to increase NPTX2 levels in all subjects, but cognitively-impaired aged subjects failed to recruit NPTX2 in response to a hippocampus-dependent memory task. Together the findings demonstrate that changes in NPTX2 are coupled to differential cognitive outcomes of aging, and that successful neurocognitive aging is associated with adaptive upregulation of NPTX2, not simply the persistence of youthful synaptic dynamics. Significance StatementAlthough aging is the most prominent risk factor for Alzheimer Disease (AD), the age-dependent processes that disrupt neurophysiological homeostasis leading to neurodegenerative disease remain poorly defined. Alterations in NPTX2, a synaptic protein biomarker for AD, may elucidate aging processes underlying pathological trajectories. We examined NPTX2 in an aging context and identified circuit specific alterations of NPTX2 that are coupled with distinct memory outcomes in aging in the absence of potential confounds of neurodegenerative disease. Greater NPTX2, associated with successful cognitive aging, may reflect coordinated molecular and circuit-level adaptations that sustain memory-relevant hippocampal activity. Development of targets and interventions that promote neuroadaptive network homeostasis, bending the trajectory of aging away from neurodegeneration, are a potentially valuable alternative to current therapeutic strategies.

neuroscience↗

bioRxiv2025

BIN1 deficiency leads to DNA damage and neuronal insulin resistance through ATM dysregulation

The major neuronal isoform of the AD risk gene BIN1 is specifically reduced in patients. In the present work, we demonstrate that BIN1 is necessary for intact insulin signaling and its loss leads to cellular-level insulin resistance. Persistently activated mTORC1 feedback inhibits the insulin signaling; meanwhile, ATM-dependent DNA Damage Response decreases the expression of multiple insulin signaling pathway members. Unexpectedly, nuclear ATM activation is accompanied by autophagic degradation of the cytoplasmic ATM, rendering neurons susceptible to oxidative stress, which predisposes oxidative DNA damage, DNA strand breaks, and ATM-dependent DNA Damage Response. Treating BIN1-deficient mice with rapamycin or liraglutide to improve the insulin response, or with the natural antioxidant alpha-lipoic acid to attenuate oxidative stress, both effectively preserved the spatial cognitive ability. Lastly, we reanalyzed a single-cell transcriptomic dataset from human neurons and identified positive correlations between levels of BIN1 and the insulin signaling, as well as neuronal activity. Together, this work revealed an ATM-centered mechanism that globally damages neuronal health in BIN1-deficient pyramidal neurons, which could be a driving force in the AD disease course.

cell biology↗

bioRxiv2025

A Reproducible Supermicrosurgical Model of Cervical Lymphatic-Venous Anastomosis in a Transgenic Alzheimer's Mouse: Technical Translation, Proficiency, and a Validated Learning Curve

BackgroundCervical Lymphatic-Venous Anastomosis(LVA) holds therapeutic potential for Alzheimer disease (AD). However, a validated AD animal model for preclinical investigation remains lacking. This study aimed to establish and standardize LNVA, as a form of lymphatic-venous Anastomosis, in a murine AD model; to quantitatively assess its surgical learning curve; and to create a platform for mechanistic exploration and translational research. MethodsWe established and standardized a deep cervical lymph node-to-vein anastomosis (DC-LNVA), a specific type of lymphatic-venous anastomosis (LVA), in rodents. A two-stage training program was applied to a junior surgeon: 60 DC-LNVA procedures were performed in 30 small Sprague-Dawley rats (50-60g), followed by 20 bilateral anastomoses in 10 male 5XFAD mice. Surgical proficiency was evaluated using procedure time, UWOMSA scoring, and CUSUM analysis. Anatomical parameters were assessed with ImageJ. Anastomotic patency was confirmed via ICG lymphangiography. Intranasal Evans Blue was used to trace cranial distribution pathways. ResultsSD rats had significantly larger external jugular veins (0.376 {+/-} 0.013 mm vs. 0.228 {+/-} 0.011 mm) and DCLNs (1.359 {+/-} 0.084 mm2 vs. 0.333 {+/-} 0.022 mm2) than mice (P < 0.0001). Proficiency was achieved after 27 anastomoses in rats and 10 in mice. ICG confirmed 100% patency in 9 surviving 5XFAD mice. Evans Blue suggested a nasal-cranial pathway for tracer distribution. ConclusionWe developed and validated a cervical lymphatic-venous bypass (LVA) in transgenic AD mice. This platform complements existing loss-of-function approaches and offers a foundation for mechanistic and translational research into brain lymphatic clearance.

animal behavior and cognition↗

bioRxiv2025

Enhancing Strain-level Phage-Host Prediction through Experimentally Vali-dated Negatives and Feature Optimization Strategies

BackgroundAccurate prediction of phage-host interactions at the strain level is critical for understanding microbial ecology and for developing phage-based therapeutics. However, existing models are limited by the lack of experimentally validated negative interactions and inconsistencies in data construction strategies. ResultsIn this study, we present a large-scale phage-host interaction dataset comprising 13,000 experimentally verified links between 125 Klebsiella pneumoniae((K. pneumoniae) phages and 104 K. pneumoniae strains. Using this unique resource, we systematically evaluate the impact of negative data construction methods, feature extraction strategies, and machine learning algorithms on predictive performance. We show that randomly generated negatives significantly inflate model accuracy, while models trained on experimental negatives yield more realistic and robust results. Furthermore, protein-derived features outperform DNA-based features across various data conditions. Notably, models using only tail protein sequences achieve performance comparable to those using full-genome sequences, offering a time-efficient alternative without compromising accuracy. Finally, interpretable machine learning reveals amino acid preferences in both phages and hosts that align with known infection mechanisms and suggest novel determinants such as anti-transcriptional proteins. ConclusionsOur findings highlight best practices for constructing high-fidelity strain-level phage-host prediction models. The dataset and insights presented here provide a valuable benchmark for future studies and lay the foundation for more biologically grounded, interpretable modeling frameworks in viromics and microbiome research.

bioinformatics↗

bioRxiv2025

DNA2 and FANCM function in two distinctive pathways in disrupting TERRA R-loops and suppressing replication stress at ALT telomeres

Cancers maintain their telomeres through two main telomere maintenance mechanisms (TMMs): 85-90% of cancers rely on telomerase, while 10-15% of cancers adopt the Alternative Lengthening of Telomere (ALT) pathway. Previously, we and others reported that FANCM, one of the Fanconi Anemia proteins, plays a critical role in suppressing replication stress and DNA damage at ALT telomeres by actively disrupting TERRA R-loops [1-4]. Here, we showed that inactivation of DNA2 in ALT-positive (ALT+) cells, but not in telomerase-positive (TEL+) cells, induces a robust increase of replication stress and DNA damage at telomeres, which leads to a pronounced increase of many ALT properties, including telomere dysfunction-induced foci (TIFs), ALT-associated PML bodies (APBs), and C-circles. We further demonstrated that depletion of DNA2 induces a pronounced increase of TERRA R-loops and a decrease in replication efficiency at ALT telomeres. Most importantly, we uncovered a strong additive genetic interaction between DNA2 and FANCM in the ALT pathway. Furthermore, co-depletion of DNA2 and FANCM causes synthetic lethality in ALT+ cells, but not in TEL+ cells, suggesting that targeting DNA2 and FANCM could be a viable strategy to treat ALT+ cancers. Finally, utilizing the single-molecule telomere assay via optical mapping (SMTA-OM) technology, we thoroughly characterized genome-wide changes in DNA2 deficient cells and FANCM deficient cells and found that most chromosome arms manifested increased telomere length. Unexpectedly, we uncovered many chromosome arm-specific telomere changes in those cells, suggesting that telomeres at different chromosome arms may regulate and respond to replication stress differently. Collectively, our study not only shed new light on the molecular mechanisms of the ALT pathway, but also discovered a new strategy for targeting ALT+ cancer.

cancer biology↗

bioRxiv2025

Multi ligand sensing by a bacterial histidine kinase through inhibition of dimerization

Two component systems (TCS) mediate bacterial signal transduction in response to specific environmental conditions. The two components are the sensor kinase (SK), which senses the signal and autophosphorylates on a histidine residue, and a response regulator (RR), which is phosphorylated by the kinase and modifies gene expression. Despite intensive study, the mechanisms of signal sensing by sensor kinases are incompletely defined and the mechanisms by which SKs can sense multiple ligands are unclear. Mycobacterium tuberculosis PdtaS/PdtaR is a soluble TCS pair that participates in the Rip1 signal transduction cascade to control virulence by responding to copper and nitric oxide (NO). In contrast to paradigmatic ligand activated SKs, PdtaS is constitutively active without ligand and directly inhibited by Cu or NO, yet it remains unclear how such chemically diverse ligands are sensed. Here we show that PdtaS is a dimeric kinase that constitutively autophosphorylates in trans. Cu and NO both inhibit PdtaS phosphorylation by inhibiting dimerization. Phylogenetic analysis of the PdtaS family reveals conservation of the GAF/PAS dimer interface rather than the ligand binding pockets and mutations in the GAF dimer interface that alter dimerization impair multi-ligand sensing both in vitro and in M. tuberculosis cells. These results indicate that a single bacterial kinase can sense chemically diverse inputs through inhibition of dimerization dependent phosphorylation.

microbiology↗

bioRxiv2024

scCompass: An integrated cross-species scRNA-seq database for AI-ready

Emerging single-cell sequencing technology has generated large amounts of data, allowing analysis of cellular dynamics and gene regulation at the single-cell resolution. Advances in artificial intelligence enhance life sciences research by delivering critical insights and optimizing data analysis processes. However, inconsistent data processing quality and standards remain to be a major challenge. Here we propose scCompass, which provides a data quality solution to build a large-scale, cross-species and model-friendly single-cell data collection. By applying standardized data pre-processing, scCompass integrates and curates transcriptomic data from 13 species and nearly 105 million single cells. Using this extensive dataset, we are able to archieve stable expression genes (SEGs) and organ-specific expression genes (OSGs) in human and mouse. We provide different scalable datasets that can be easily adapted for AI model training and the pretrained checkpoints with state-of-the-art (SOTA) single-cell foundataion models. In summary, the AI-readiness of scCompass, which combined with user-friendly data sharing, visualization and online analysis, greatly simplifies data access and exploitation for researchers in single cell biology(http://www.bdbe.cn/kun).

bioinformatics↗

bioRxiv2024

Detecting Special Genes in Marine Symbionts: A Phylogeny-Deviation Approach Identifies Recombination-Enhancing Variants

Different microbes possess special traits that enable adaptation to their specific niches, often through specialized genes. Identifying such species-special genes provides insights into microbial physiology and offers new tools for bioengineering. However, beyond the search for orphan genes, there are few methods for detecting genes that are homologous to those in other species yet contain unusual functional regions. In investigating the extreme recombination frequency of the marine symbiont bacterium Ca. E. kahalalidifaciens, we developed a computational approach to identify vairants that substantially deviate from phylogenetic expectations. This unbiased strategy successfully identified multiple Holliday junctions-related genes in Ca. E. kahalalidifaciens as candidates responsible for its exceptional recombination capacity. Heterologous expression of these gene variants in Escherichia coli significantly enhanced recombination efficiency. These high-efficient variants offer insights into improving tools for genetic manipulations, and our gene-identification approach can be applied broadly for microbial genome mining.

bioinformatics↗

bioRxiv2024

In Vivo Expression of an SCA27A-linked FGF14 Mutation Results in Haploinsufficiency and Impaired Firing of Cerebellar Purkinje Neurons

Autosomal dominant mutations in FGF14, which encodes intracellular fibroblast growth factor 14 (iFGF14), underlie spinocerebellar ataxia type 27A (SCA27A), a devastating multisystem disorder resulting in progressive deficits in motor coordination and cognitive function. Mice lacking iFGF14 (Fgf14-/-) exhibit similar phenotypes, which have been linked to iFGF14-mediated modulation of the voltage-gated sodium (Nav) channels that control the high frequency repetitive firing of Purkinje neurons, the main output neurons of the cerebellar cortex. To investigate the pathophysiological mechanisms underlying SCA27A, we developed a targeted knock-in strategy to introduce the first point mutation identified in FGF14 into the mouse Fgf14 locus (Fgf14F145S), we determined the impact of in vivo expression of the mutant Fgf14F145S allele on the motor performance of adult animals and on the firing properties of mature Purkinje neurons in acute cerebellar slices. Electrophysiological experiments revealed that repetitive firing rates are attenuated in adult Fgf14F145S/+ cerebellar Purkinje neurons, attributed to a hyperpolarizing shift in the voltage-dependence of steady-state inactivation of Nav channels. More severe effects on firing properties and Nav channel inactivation were observed in homozygous Fgf14F145S/F145S Purkinje neurons. Interestingly, the electrophysiological phenotypes identified in adult Fgf14F145S/+and Fgf14F145S/F145S cerebellar Purkinje neurons mirror those observed in heterozygous Fgf14+/- and homozygous Fgf14-/-Purkinje neurons, respectively, suggesting that the mutation results in the loss of the iFGF14 protein. Western blot analysis of lysates from adult heterozygous Fgf14F145S/+ and homozygous Fgf14F145S/F145Sanimals revealed reduced or undetectable, respectively, iFGF14 expression, supporting the hypothesis that the mutant allele results in loss of the iFGF14 protein and that haploinsufficiency underlies SCA27A neurological phenotypes.

neuroscience↗

bioRxiv2024

Nutrient Signaling-Dependent Quaternary Structure Remodeling Drives the Catalytic Activation of metazoan PASK

The Per-Arnt-Sim (PAS) domains are characterized by diverse sequences and feature tandemly arranged PAS and PAS-associated C-terminal (PAC) motifs that fold seamlessly to generate the metabolite-sensing PAS domain. Here, using evolutionary scale sequence, domain mapping, and deep learning-based protein structure analysis, we deconstructed the sequence-structure relationship to unearth a novel example of signal-regulated assembly of PAS and PAC subdomains in metazoan PAS domain-regulated kinase (PASK). By comparing protein sequence, domain architecture, and computational protein models between fish, bird, and mammalian PASK orthologs, we propose the existence of previously unrecognized third PAS domain of PASK (PAS-C) formed through long-range intramolecular interactions between the N-terminal PAS fold and the C-terminal PAC fold. We experimentally validated this novel structural design using residue-level cross-linking assays and showed that the PAS-C domain assembly is nutrient-responsive. Furthermore, by combining structural phylogeny approaches with residue-level cross-linking, we revealed that the PAS-C domain assembly links nutrient sensing with quaternary structure reorganization in PASK, stabilizing the kinase catalytic core of PASK. Thus, PAS-C domain assembly likely integrates environmental signals, thereby relaying sensory information for catalytic control of the PASK kinase domain. In conclusion, we theorize that during their horizontal transfer from bacteria to multicellular organisms, PAS domains gained the capacity to integrate environmental signals through dynamic modulation of PAS and PAC motif interaction, adding a new regulatory layer suited for multicellular systems. We propose that metazoan PAS domains are likely to be more dynamic in integrating sensory information than previously considered, and their structural assembly could be targeted by regulatory signals and exploited to develop therapeutic strategies.

biochemistry↗

bioRxiv2024

Graph Contrastive Learning as a Versatile Foundation for Advanced scRNA-seq Data Analysis

Single-cell RNA sequencing (scRNA-seq) offers unprecedented insights into transcriptome-wide gene expression at the single-cell level. Cell clustering has been long established in the analysis of scRNA-seq data to identify the groups of cells with similar expression profiles. However, cell clustering is technically challenging, as raw scRNA-seq data have various analytical issues, including high dimensionality and dropout values. Existing research has developed deep learning models, such as graph machine learning models and contrastive learning-based models, for cell clustering using scRNA-seq data and has summarized the unsupervised learning of cell clustering into a human-interpretable format. While advances in cell clustering have been profound, we are no closer to finding a simple yet effective framework for learning high-quality representations necessary for robust clustering. In this study, we propose scSimGCL, a novel framework based on the graph contrastive learning paradigm for self-supervised pretraining of graph neural networks. This framework facilitates the generation of high-quality representations crucial for cell clustering. Our scSimGCL incorporates cell-cell graph structure and contrastive learning to enhance the performance of cell clustering. Extensive experimental results on simulated and real scRNA-seq datasets suggest the superiority of the proposed scSimGCL. Moreover, clustering assignment analysis confirms the general applicability of scSimGCL, including state-of-the-art clustering algorithms. Further, ablation study and hyperparameter analysis suggest the efficacy of our network architecture with the robustness of decisions in the self-supervised learning setting. The proposed scSimGCL can serve as a robust framework for practitioners developing tools for cell clustering. The source code of scSimGCL is publicly available at https://github.com/zhangzh1328/scSimGCL.

bioinformatics↗

bioRxiv2024

Targeting the Atypical Chemokine Receptor 2 (ACKR2) improves the benefit of anti-PD-1 immunotherapy in melanoma

Immune checkpoint blockade (ICB) therapies, targeting PD-1 or PD-L1, have transformed cancer treatment, particularly for aggressive cancers. However, many patients fail to benefit from ICBs due to tumor characteristics, including a non-inflammatory tumor microenvironment (TME) that impedes immune cell infiltration. This study investigated the potential of targeting the Atypical Chemokine Receptor 2 (ACKR2), known for scavenging CXCR3-related chemokines crucial for lymphocyte recruitment to tumors. Genetic targeting of ACKR2 in melanoma cells increased the release of essential chemokines associated with the inflamed TME. In mouse models, ACKR2 inhibition suppressed tumor growth, improved survival, and enhanced activated immune cell infiltration into the TME. Moreover, ACKR2 targeting synergized with anti-PD-1 therapy, overcoming resistance to anti-PD-1 and improving its efficacy. Analysis of melanoma patient data from The Cancer Genome Atlas (TCGA) revealed that patients with high levels of chemokines scavenged by ACKR2 had significantly better survival rates, with increased expression of NK cell and CD8 T cell markers indicating their presence in the TME. Notably, even in patients with high CD8 expression, those expressing low ACKR2 survived better than those expressing high ACKR2. This study emphasizes the clinical importance of targeting ACKR2 as an attractive strategy for the development of combination immunotherapies to treat cold tumors, which are clinically stratified to not be eligible for ICB-based therapy.

cancer biology↗

bioRxiv2024

Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model

Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during tumorigenesis and tumor evolution. However, the detailed mechanisms for the individual steps of the BFB cycle warrants further investigation. Here, we demonstrated that a nuclease-dead Cas9 (dCas9) coupled with a telomere-specific single-guide RNA (sgTelo) can be used to model the BFB cycle. First, we showed that targeting dCas9 to telomeres using sgTelo impeded DNA replication at telomeres and induced a pronounced increase of replication stress and DNA damage. Using Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM), we investigated the genome-wide features of telomeres in the dCas9/sgTelo cells and observed a dramatic increase of chromosome end fusions, including fusion/ITS+ and fusion/ITS-.Consistently, we also observed an increase in the formation of dicentric chromosomes, anaphase bridges, and intercellular telomeric chromosome bridges (ITCBs). Utilizing the dCas9/sgTelo system, we uncovered many novel molecular and structural features of the ITCB and demonstrated that multiple DNA repair pathways are implicated in the formation of ITCBs. Our studies shed new light on the molecular mechanisms of the BFB cycle, which will advance our understanding of tumorigenesis, tumor evolution, and drug resistance.

cancer biology↗

bioRxiv2024

Female mice lacking GluA3 show early onset of hearing loss, synaptopathy, and afferent swellings in ambient sound levels

AMPA-type glutamate receptors (AMPAR) mediate excitatory cochlear transmission. However, the unique roles of AMPAR subunits are unresolved. Lack of subunit GluA3 (Gria3KO) in male mice reduced cochlear output by 8-weeks of age. Since Gria3 is X-linked and considering sex differences in hearing vulnerability, we hypothesized accelerated presbycusis in Gria3KO females. Here, auditory brainstem responses (ABR) were similar in 3-week-old female Gria3WTand Gria3KO mice. However, when raised in ambient sound, ABR thresholds were elevated and wave-1 amplitudes were diminished at 5-weeks and older in Gria3KO. In contrast, these metrics were similar between genotypes when raised in quiet. Paired synapses were similar in number, but lone ribbons and ribbonless synapses were increased in female Gria3KOmice in ambient sound compared to Gria3WT or to either genotype raised in quiet. Synaptic GluA4:GluA2 ratios increased relative to Gria3WT, particularly in ambient sound, suggesting an activity-dependent increase in calcium-permeable AMPARs in Gria3KO. Swollen afferent terminals were observed by 5-weeks only in Gria3KO females reared in ambient sound. We propose that lack of GluA3 induces sex-dependent vulnerability to AMPAR-mediated excitotoxicity.

neuroscience↗

bioRxiv2023

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

Precisely defining and mapping all cytosine positions and their clusters, known as CpG islands (CGIs), as well as their methylation status are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG site coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also show more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

bioinformatics↗