Biology subjects

Wu, H.

Publications and source records attributed to Wu, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Trans-generational maintenance of mitochondrial DNA integrity in oocytes during early folliculogenesis

Mutations in mitochondrial DNA (mtDNA) can lead to mitochondrial and cellular dysfunction. However, recent studies suggest that there is purifying selection against mutant mtDNAs during transgenerational transmission. We investigated the mtDNA dynamics during ovarian follicle development. Using base-editing, we generated mice harboring a 3177 G>A mutation corresponding to the human Leber hereditary optic neuropathy (LHON)-related mtDNA mutation and confirmed the transgenerational reduction of mutant mtDNA. Using a mouse follicle culture system in which pathogenic mtDNA mutations were introduced in vitro followed by mtDNA sequencing and digital PCR, we found this germline heteroplasmy shift during early folliculogenesis was induced by the decrease of mutant mtDNA together with compensatory replication of wild-type mtDNA. In contrast, synonymous mtDNA mutations did not impact the mtDNA dynamics. These findings show that mice can eliminate certain pathogenic mtDNA mutations in the germline during early folliculogenesis, maintaining mitochondrial integrity across generations.

genetics↗

bioRxiv2025

Auditory tract maturation in early infancy: Links to speech production

Infants exhibit remarkable language acquisition abilities, supported by highly plastic neural substrates that dynamically interact with early speech experiences. However, the developmental mechanisms of these neural substrates and their specific role in speech acquisition remain incompletely understood. Here, we present NeoAudi Tract (NAT), a robust automated toolbox for extracting the full set of auditory tracts in infants from birth to 24 months using 3T diffusion MRI data. By characterizing the microstructural changes in these tracts, we demonstrate a gradual and continuous maturation process of the auditory system. Additionally, we identify significant correlations between auditory tract maturation and both fine-motor skills and expressive language t-scores from the Mullen Scales of Early Learning tests. Our findings highlight the role of the auditory system in speech production and indicate the intertwined development of auditory and motor systems that underlies speech acquisition, particularly during perceptual reorganization.

neuroscience↗

bioRxiv2024

Spatiotemporal photocatalytic proximity labeling proteomics reveals ligand-activated extracellular and intracellular EGFR neighborhoods

Photo-proximity labeling proteomics (PLP) methods have recently shown that the cell surface receptors can dynamically form lateral interactome networks. Here, we present a paired set of PLP workflows that simultaneously track neighborhood changes for oncogenic epidermal growth factor receptor (EGFR) with temporal resolution, both outside and inside of cells. We achieved this by augmenting the multiscale PLP workflow we call MultiMap, where three photo-probes with different labeling ranges were photo-activated by one photocatalyst, Eosin Y. By anchoring Eosin Y extracellularly and intracellularly on EGFR, we captured hundreds of proteins on both sides of the cell membrane that change in proximity to EGFR upon EGF activation. Neighbors engaged with EGFR within minutes to over an hour, reflecting dynamic interactomes during early, mid- and late-signaling including phosphorylation, internalization, degradation and transcriptional regulation. This rapid "photographic" labeling approach provides snapshots of signaling neighborhoods, revealing their dynamic nature, and potential for drug targeting.

biochemistry↗

bioRxiv2024

Use of Genome Scale Metabolic Reconstructions of Avian Pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways

Avian Pathogenic Escherichia coli (APEC) are a genetically diverse pathotype primarily associated with extra-intestinal infections in birds. APEC lineages are predicted to have unique metabolic capabilities contributing to virulence and survival in the host environment. Here we present a genome-scale metabolic model for the APEC pathotype based on 114 APEC genome sequences, and lineage-specific models for the phylogroups B2, C and G based on a representative isolate for each phylogroup. A total of 1,848 metabolic reactions were predicted in the 114 APEC isolates before gap filling and manual correction. Of these, 89% represented core reactions, whilst the 11% accessory reactions were mostly associated with carbon and nitrogen metabolism. Predictions of auxotrophy were confirmed by inactivation of the conditionally essential lysA and the non-essential potE genes. The APEC metabolic model outperformed the E. coli K-12 iJO1366 model in the Biolog Phenotypic Array platform. Sub-models specific for phylogroups B2, C and G predicted differences in the metabolism of 3-hydroxyphenylacetate (3-HPAA), a phenolic acid derived from the flavonoid quercetin, which is commonly added to poultry feed. Two 3-HPAA associated reactions/genes distinguished APEC phylogroup C from APEC phylogroups B2 and G, and 3-HPAA supported the growth of APEC phylogroup C in minimal media, but not phylogroups B2 and G. In conclusion, we have constructed genome-scale metabolic models for the three major APEC phylogroups B2, C and G, and have identified a metabolic pathway distinguishing phylogroup C APEC. This demonstrates the importance of lineage- and pathotype-specific metabolic models when investigating genetically diverse microbial pathogens. IMPACT STATEMENTAvian Pathogenic Escherichia coli (APEC) are the cause of colibacillosis in poultry, which results in a significant economic burden to the poultry industry, and strongly affects the health and welfare of flocks. APEC isolates show a high level of genetic diversity, which complicates diagnostics, epidemiology and the design of prevention and treatment strategies. In this study we have used genome sequences derived from 114 APEC isolates to investigate their metabolic capabilities, and define the metabolic diversity of APEC within a generalised APEC metabolic model, and lineage-specific metabolic models. These models have been interrogated to find unique pathways that can be targeted for the development of anti-APEC treatments, and one such metabolic pathway was identified as a proof of principle. This approach shows great promise for the design of future strategies to prevent and deal with APEC infections, and can be adapted to other genetically diverse microbial pathogens.

microbiology↗

bioRxiv2024

Single-cell analysis reveals multi-faceted features of B cell development together with age-associated B cell subpopulations

The development and maturation of B lymphocytes involve intricate orchestrated processes, where dedicated gene regulations (GR) take place within specific microenvironments shaped by both extracellular matrix and neighboring cells. Despite extensive investigations aimed at deepening our comprehension of these mechanisms, there remains a dearth of high-dimensional and integrated analysis concerning B cell heterogeneity, gene regulation, and external factors implicated in B cell development. In this study, we scrutinized single-cell transcriptomic data and B cell receptor (BCR) sequencing data obtained from B cells and their surrounding counterparts in the bone marrow, tonsil, and peripheral blood. A full picture of the GR dynamics, the heterogeneity of conventional B cells and cell-cell interactions (CCIs) along B cell development axis was depicted. We found immature B cells represent the most quiescent stage characterized by the least number of expressed genes and low RNA velocity. The homeostatic proliferation and activation of naive B cells is niche-confined and individualized, respectively. Two development models for memory B cell subpopulations seem not mutually exclusive and warrant in-depth investigation. Moreover, CCI analysis reveals a pivotal role of myeloid cells and two dominant and stage-dependent CCI categories, TNF and adhesion signaling, in B cell development. Besides, we unexpectedly identified two age-associated B cell subpopulations that respectively express S100A8/S100A9 and C1q and experimentally confirmed the secretion of S100A8/A9 from human B cells in vitro, suggesting a senescence-associated secretion phenotype. Our integrated analysis provides valuable insights into GR dynamics, the evolution of B cells, and potential intercellular communication networks involved in B cell development and revealed novel phenotypes of age-associated B cell aberrance. This study serves as a valuable resource for in-depth exploration of the intricacies of B cell biology.

cell biology↗

bioRxiv2024

Synapse profiling of identified neurons in the Drosophila brain

Characterization of intracellular synapse heterogeneity aides to understand the intricate computational logic of neuronal circuits. Despite recent advances in connectomics, the spatial patterns of synapses and their inter-individual variability remain largely unknown. Using directed split-GFP reconstitution, we achieved visualization of endogenous Bruchpilot (Brp), a presynaptic active zone (AZ) scaffold protein, in a cell-type-specific manner. By developing a high-throughput quantification pipeline, we profiled AZ structures in identified neurons of the mushroom body circuit, where intracellular synaptic patterns are crucial due to compartmentalized connectivity. Quantitative characterization of the pattern of Brp clusters across multiple individuals revealed cell-type-dependent synapse heterogeneity and stereotypy. Furthermore, we discovered previously unidentified sub-compartmental synapse configuration and its transient structural plasticity triggered by associative learning. These profiles thus uncovered multi-layered spatial configurations of AZs, from stereotyped overall AZ distribution patterns, to local arrangements of neighboring synapses.

neuroscience↗

bioRxiv2024

Octopamine signals coordinate the spatial pattern of presynaptic machineries in the Drosophila mushroom bodies

Neurons need to adjust synaptic output according to the targets. However, the target-specific synaptic structures within individual neurons in the central nervous system remains unresolved. Applying the CRISPR/Cas9-mediated split-GFP tagging, we visualized the endogenous active zone scaffold protein, Bruchpilot (Brp), in specific cells. This technology enabled the spatial characterization of presynaptic machineries only within the Kenyon cells (KCs) of the Drosophila mushroom bodies. We found the patterned accumulation of Brp among the compartments of axon terminals, where a KC synapses onto different postsynaptic neurons. Mechanistically, the localized octopaminergic modulation along {gamma} KC terminals regulate this compartmental Brp heterogeneity via Oct{beta}2R and cAMP signaling. We further found that acute food deprivation reorganizes this spatial pattern in an octopamine-dependent manner. Such coordinated regulation of local synaptic machineries thus explains how the mushroom bodies integrate changing physiological states. This subcellular information processing represents an elegant solution to expand computational capacity of the circuit.

neuroscience↗

bioRxiv2024

Task-induced internal bodily rather than brain states regulate human self-perception

A fundamental ability for us is to identify and distinguish with others, known as the self, whose neural substrate is hard to identify by external self-related stimuli because of possible interference from internal self-related states of both body and brain. Using the same stimuli, we ruled out this dilemma by manipulating human subjects performing own- and celebrity-face discrimination tasks to induce self-related and non-self-related states, respectively. Results showed that stimulus-driven sensory sensory differences among own-, celebrity-, and stranger-faces were independent of task-induced internal states, whereas their perceptual differences were strongly modulated by these states. Intriguingly, we further found that subjects bodily (indexed by heartbeat-evoked potentials) rather than brain (indexed by pre-stimulus -powers) states not only predicated their self-perception but also moderated the relationship between external stimuli and self-perception. Our results reveal for the first time an adaptive self-perception, shaped by not only external stimuli but also internal states, especially the interoception.

neuroscience↗

bioRxiv2024

DNA StairLoop: Achieving High Error-correcting and Parallel-processing Capabilities in DNA-based Data Storage

DNA-based data storage is a promising solution to the challenges of large-scale data storage. However, the low throughput of the mainstream inkjet-based DNA synthesis method has hindered its widespread adoption. In contrast, high-throughput electrochemical synthesis provides higher throughput but with more nucleotide insertion, deletion, and substitution errors. Here, we propose an innovative coding scheme with high error correction capabilities, called DNA StairLoop. This coding scheme features a staircase interleaver and allows for component codes such as the convolutional code and the ow-density Parity-check code, allowing for flexible adaptation of the coding scheme. Both the row and the column decoders are soft input and soft output, enabling further improvement in data recovery accuracy through iterative decoding. The staircase interleaver facilitates extensive parallel decoding capabilities while effectively preserving parallelism across a multitude of nodes. In the in vitro experiment, DNA StairLoop successfully recovered the raw information in a staircase block with a nucleotide error rate of more than 8%. The simulations revealed that the DNA StairLoop can correct 10% nucleotide errors. Moreover, in parallel computing processing, the decoding time of our code continues to decrease dramatically.

synthetic biology↗

bioRxiv2024

Immunologic and Biophysical Features of the BNT162b2 JN.1- and KP.2-Adapted COVID-19 Vaccines

Vaccines remain a vital public health tool to reduce the burden of COVID-19. COVID-19 vaccines that are more closely matched to circulating SARS-CoV-2 lineages elicit more potent and relevant immune responses that translate to improved real-world vaccine effectiveness. The rise in prevalence of the Omicron JN.1 lineage, and subsequent derivative sublineages such as KP.2 and KP.3, coincided with reduced neutralizing activity and effectiveness of Omicron XBB.1.5-adapted vaccines. Here, we characterized the biophysical and immunologic attributes of BNT162b2 JN.1- and KP.2-adapted mRNA vaccine-encoded spike (S) protein immunogens. Biophysical interrogations of S revealed the structural consequences of hallmark amino acid substitutions and a potential molecular mechanism of immune escape employed by JN.1 and KP.2. The vaccine candidates were evaluated for their immunogenicity when administered as fourth or fifth doses in BNT162b2-experienced mice or as a primary series in naive mice. In both vaccine-experienced and naive settings, JN.1- and KP.2-adapted vaccines conferred improved neutralizing responses over the BNT162b2 XBB.1.5 vaccine against a broad panel of emerging JN.1 sublineages, including the predominant KP.3.1.1 and emerging XEC lineages. Antigenic mapping of neutralizing responses indicated greater antigenic overlap of JN.1- and KP.2-adapted vaccine responses with currently circulating sublineages compared to an XBB.1.5-adapted vaccine. CD4+ and CD8+ T cell responses were generally conserved across all three vaccines. Together, the data support the selection of JN.1- or KP.2-adapted vaccines for the 2024-25 COVID-19 vaccine formula. ONE-SENTENCE SUMMARYThe Omicron JN.1- and KP.2-adapted BNT162b2 mRNA vaccines encoding prefusion S proteins elicit similar preclinical neutralizing antibody responses against circulating JN.1 sublineage pseudoviruses that are more potent than those elicited by past iterations of BNT162b2 licensed vaccines, thus demonstrating the importance of annual strain changes to the COVID-19 vaccine.

immunology↗

bioRxiv2024

Reinforced identity confers cells with cancer hallmarks

Genetic alterations trigger tumorigenesis in a cell type-specific manner, but the biological basis for this, remains unclear. Here we define reinforced original cell identity established by interaction between genetic alterations and original cell type is a pivotal determinant of tumor development. Using AML-M5MLL-AF9 as a model system, we demonstrated that MLL-AF9 enhanced key transcriptional factors (TFs) expression of promonocyte and cooperated with them to amplify their downstream programs for AML hallmarks. Interactions between MLL-AF9 and promonocyte endowed cancer cells with a reinforced promonocyte identity. Reinforced intrinsic cell identity also sustained cancer hallmarks across cancer types. Furthermore, we identified narciclasine, as an effective disruptor of reinforced promonocyte identity, effectively treating AML-M5MLL-AF9. This study not only identified reinforced cell identity as a fundamental tumor driver beyond genetic mutations but also offers a proof-of-concept for reinforced identity- targeted cancer therapy.

cancer biology↗

bioRxiv2024

SloR-SRE binding to the S. mutans mntH promoter is cooperative.

Streptococcus mutans is a commensal member of the plaque microbiome. It is especially prevalent when dietary sugars are available for S. mutans fermentation, generating acid byproducts that lower plaque pH and foster tooth decay. S. mutans can survive in the transient conditions of the mouth, in part because it can regulate the uptake of manganese and iron during periods of feast when metal ions are available, and famine when they are limiting. S. mutans depends on a 25kDa metalloregulatory protein, called SloR, to modulate uptake of these cations across the bacterial cell surface. When bound to manganese, SloR, binds to palindromic recognition elements in the promoter of the sloABC genes that encode the major manganese transporter in S. mutans. Reports in the literature describ MntH, an ancillary manganese transporter in S. mutans, that is also subject to SloR control. In the present study, we performed expression profiling experiments that reveal coordinate regulation of the sloABC and mntH genes at the level of transcription. In addition, we describe a role for the mntH gene product that is redundant with that of the sloABC-encoded metal ion uptake machinery. The results of DNA binding studies support direct SloR binding to the mntH promoter region which, like that at the sloABC promoter, harbors three palindromic recognition elements to which SloR binds cooperatively to repress downstream transcription. These findings expand our understanding of the SloR metalloregulome and elucidate SloR-DNA binding that is essential for S. mutans metal ion homeostasis and fitness in the oral cavity.

microbiology↗

bioRxiv2024

Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling

A cells ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

genetics↗

bioRxiv2024

LEGEND: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data

Identifying co-expressed genes across tissue domains and cell types is essential for revealing co-functional genes involved in biological or pathological processes. While both single-cell RNA-sequencing (scRNA-seq) and spatially-resolved transcriptomic (SRT) data offer insights into gene co-expression patterns, current methods typically utilize either data type alone, potentially diluting the co-functionality signals within co-expressed gene groups. To bridge this gap, we introduce LEGEND, a novel computational method that integrates scRNA-seq and SRT data for identifying groups of co-expressed genes at both cell type and tissue domain levels. LEGEND employs an innovative hierarchical clustering algorithm designed to maximize intra-cluster redundancy and inter-cluster complementarity, effectively capturing more nuanced patterns of gene co-expression and spatial coherence. Enrichment and cofunction analyses further showcase the biological relevance of these gene clusters, and their utilities in exploring context-specific novel gene functions. Notably, LEGEND can reveal shifts in gene-gene interactions under different conditions, furnishing insights for disease-associated gene crosstalk. Moreover, LEGEND can be utilized to enhance the annotation accuracy of both spatial spots in SRT and single-cells in scRNA-seq, and pioneers in identifying genes with designated spatial expression patterns. LEGEND is available at https://github.com/ToryDeng/LEGEND.

genomics↗

bioRxiv2024

Abl kinases regulate FGF signaling independent of Crk phosphorylation to prevent Peters anomaly

Peters anomaly, the most common cause of congenital corneal opacity, stems from corneal-lenticular adhesion. Despite numerous identified mutations, a cohesive molecular framework of the diseases etiology remains elusive. Here, we identified Abl kinases as pivotal regulators of FGF signaling, as genetic ablation of Abl kinases restores lens induction even in the absence of FGF signaling. Intriguingly, both Abl kinase deficiency and increased FGF-Ras activity result in Peters anomaly independent of ERK signaling, which can be rescued by allelic deletion of Abl substrate, Crk. However, contrary to the prevailing belief that Abl kinases regulate Crk proteins by direct phosphorylation, mutations at Abl kinase phosphorylation sites on Crk and CrkL did not yield any observable effects. Instead, our findings reveal that Abl kinases phosphorylate Ptpn12, which in turn inhibits p130Cas phosphorylation and Crk recruitment, crucial for Rho GTPases activation and cytoskeletal dynamics. Consequently, Abl kinase deficiency reduces actomyosin contractility within the lens vesicle and genetically interacts with RhoA inhibition. Conversely, Rac1 deletion mitigates Peters anomaly in models with aberrant FGF, Abl kinase and RhoA signaling. Our results demonstrate that Abl kinases regulate FGF signaling to balance RhoA and Rac1 activity via the Ptpn12-p130Cas pathway, suggesting that targeting tension-mediated lens vesicle separation could be a therapeutic strategy for Peters anomaly.

developmental biology↗

bioRxiv2024

NINJ1 is activated by calcium-driven plasma membrane lipid scrambling during lytic cell death

NINJ1 is the terminal executioner of cellular rupture in multiple lytic cell death pathways through its clustering in the plasma membrane. Its activation trigger, however, remains unknown. We found that NINJ1-mediated plasma membrane rupture depends on calcium influx into the cell, which suffices to induce NINJ1-mediated rupture. Using genetic and pharmacologic approaches in macrophages, we show calcium drives membrane rupture through phospholipid scrambling by the calcium-activated scramblase TMEM16F. We next tested whether this calcium-activated NINJ1 mechanism is the elusive pathway by which extracellular ATP stimulates cellular rupture. We show that ATP-stimulation of P2X7R induces NINJ1-mediated cell lysis via calcium influx and TMEM16F lipid scrambling, independently of inflammasomes, pannexins and gasdermin D. Our work reveals the mechanism of NINJ1 activation and solves the long-standing mystery of ATP-induced cytolysis. SummaryElevated cytosolic calcium drives NINJ1-mediated cellular rupture during lytic cell death through plasma membrane lipid scrambling.

cell biology↗

bioRxiv2024

Change in brain molecular landscapes following electrical stimulation of the nucleus accumbens

Deep brain stimulation (DBS) targeting the nucleus accumbens (NAc) is a promising therapeutic intervention for treatment-resistant neuropsychiatric disorders such as depression, anxiety, and addiction. However, the molecular mechanisms underlying the clinical efficacy of NAc DBS remain largely unknown. One approach to address this question is by performing spatial gene expression analysis on cells located in different regions of the same circuit following NAc DBS. In this study, we utilized high-resolution spatial transcriptomics (Stereo-seq) to investigate gene expression changes induced by NAc DBS in the mouse brain. Mice were randomly allocated to received continuous electrical stimulation (0.1 mA, 130 Hz) or sham treatment (electrode implanted, no electrical stimulation given) for one week, and subsequent Stereo-seq analysis identified differentially expressed genes (DEGs) across various brain regions. Our findings reveal widespread alterations in synaptic function and neuronal connectivity, particularly in glutamate receptor-expressing neurons in the NAc, which play a key role in the reward circuitry. Functional enrichment analysis highlighted changes in transporter activity and glutamate receptor binding in brain regions such as the anterior cingulate cortex and lateral septal nucleus. Single-cell resolution mapping further identified key molecular players, including Nlgn1, Snca, PDE10a, and Syt1, which are critical for synaptic plasticity and neurotransmitter release, and have been implicated in various psychiatric disorders. These findings shed light on the molecular underpinnings of NAc DBS and provide insights into its therapeutic potential in modulating neural circuits associated with neuropsychiatric disorders.

molecular biology↗

bioRxiv2024

Somatic mtDNA Mutation Burden Shapes Metabolic Plasticity in Leukemogenesis

The role of somatic mitochondrial DNA (mtDNA) mutations in leukemogenesis remains poorly characterized. To determine the impact of somatic mtDNA mutations on the process, we assessed the leukemogenic potential of hematopoietic progenitor cells (HPCs) from mtDNA mutator mice (Polg D257A) with or without NMyc overexpression. We observed a higher incidence of spontaneous leukemogenesis in recipients transplanted with heterozygous Polg HPCs and a lower incidence of NMyc-driven leukemia in those with homozygous Polg HPCs compared to controls. Although mtDNA mutations in heterozygous and homozygous HPCs caused similar baseline impairments in mitochondrial function, only heterozygous HPCs responded to and supported altered metabolic demands associated with NMyc overexpression. Homozygous HPCs showed altered glucose utilization with pyruvate dehydrogenase inhibition due to increased phosphorylation, exacerbated by NMyc overexpression. The impaired growth of NMyc-expressing homozygous HPCs was partially rescued by inhibiting pyruvate dehydrogenase kinase, highlighting a relationship between mtDNA mutation burden and metabolic plasticity in leukemogenesis. TEASERSomatic mtDNA mutations as drivers of metabolic change in the development of leukemia.

cancer biology↗