Biology subjects

Yuan, W.

Publications and source records attributed to Yuan, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A Novel COE-D8-Fosfomycin Conjugate Effectively Against First-line Antibiotic Resistant Uropathogenic Escherichia coli

Recurrent urinary tract infections (UTIs) are increasingly associated with antibiotic resistance, posing significant clinical challenges. This study evaluates the antimicrobial efficacy of the membrane-intercalating conjugated oligoelectrolyte COE-D8 against uropathogenic Escherichia coli (UPEC). Among 93 clinical UPEC isolates, over 50% demonstrated resistance to first-line antibiotics, with compound sulfamethoxazole showing the highest resistance (75% at a minimum inhibitory concentration (MIC) >512 g/mL). COE-D8 significantly reduced resistance rates, achieving less than 50% at 32 g/mL and below 5% at 512 g/mL, while demonstrating at least fourfold faster bacterial elimination than standard antibiotics. Mechanistic studies revealed that COE-D8 disrupts bacterial membranes, inducing rapid lysis. However, its cytotoxicity in mammalian cells at 2 g/mL limits clinical application. To address this, a combination therapy with fosfomycin was explored, significantly reducing COE-D8 toxicity by at least fourfold in vitro. In mouse models, fosfomycin co-administration mitigated COE-D8-induced toxicity and prevented mortality at higher doses without compromising antimicrobial efficacy. These findings highlight the potential of COE-D8, particularly in combination with fosfomycin, as a promising strategy to combat antibiotic-resistant UPEC while addressing toxicity challenges.

microbiology↗

bioRxiv2024

H3.1K27M-induced misregulation of the TSK/TONSL-H3.1 pathway causes genomic instability

The oncomutation lysine 27-to-methionine in histone H3 (H3K27M) is frequently identified in tumors of patients with diffuse midline glioma-H3K27 altered (DMG-H3K27a). H3K27M inhibits the deposition of the histone mark H3K27me3, which affects the maintenance of transcriptional programs and cell identity. Cells expressing H3K27M are also characterized by defects in genome integrity, but the mechanisms linking expression of the oncohistone to DNA damage remain mostly unknown. In this study, we demonstrate that expression of H3.1K27M in the model plant Arabidopsis thaliana interferes with post-replicative chromatin maturation mediated by the H3.1K27 methyltransferases ATXR5 and ATXR6. As a result, H3.1 variants on nascent chromatin remain unmethylated at K27 (H3.1K27me0), leading to ectopic activity of TONSOKU (TSK), which induces DNA damage and genomic alterations. Elimination of TSK activity suppresses the genome stability defects associated with H3.1K27M expression, while inactivation of specific DNA repair pathways prevents survival of H3.1K27M-expressing plants. Overall, our results suggest that H3.1K27M disrupts the chromatin-based mechanisms regulating TSK/TONSL activity, which causes genomic instability and may contribute to the etiology of DMG-H3K27a.

genetics↗

bioRxiv2024

A Mouse-adapted SARS-CoV-2 Model for Investigating Post-acute Sequelae of COVID infection

The coronavirus disease of 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), remains a major health issue after nearly 7 millions of death toll in the last four years. As the world is recovering with improving vaccines and antiviral treatments, the alarming rate of long-COVID, or Post-acute Sequelae of COVID-19 (PASC), calls for further investigations. Among a list of symptoms associated with multi-organ dysfunctions, the neurological complications are particularly intriguing, yet the underlying mechanisms remain elusive. With the recently developed mouse adapted SARS-CoV-2 stain, we are now able to model the mild COVID infection in C57BL/6 mice and study the chronic immune responses and subsequent damages in different organs long after the viruses are clearly naturally in the body. More specifically, we found adult C57BL/6J mice developed neurological impairments, including behavior changes related to sensorimotor coordination, depression- and anxiety-like behaviors, and inflammation in multiple organs including lung, liver and brain, which persisted over at least 4 weeks in mice even with mild infection. Therefore, this model can be used to further explopred the mechanisms of PASC, as well as potential intervention or therapeutic approaches.

neuroscience↗

bioRxiv2024

Revealing Acute Consequences of Rapid Protein Elimination at Individual Synapses using Auxin-Inducible Degron 2 Technology

A powerful approach to assess a protein of interest (POI) function is its specific elimination. Common knock-out and knock-down strategies, however, are protracted and often irreversible, challenging the assessment of acute or temporary consequences in the same cells and tissues. Here we describe the use of Auxin-Inducible Degron 2 (AID2) technology to study the real-time consequences of acute POI elimination in nerve cell synapses. We demonstrate its capacity in cultured neurons and in vivo to rapidly eliminate postsynaptic scaffold proteins fused at N-terminal, C-terminal, or nested sites to GFP derivatives or HaloTag. We show that acute PSD-95 or gephyrin elimination leads to the concomitant loss of AMPA or GABAA receptors at the same synapses, and that, surprisingly, acute GKAP, but not PSD-95 elimination reduces postsynaptic scaffold size. Our findings highlight the utility of AID2 technology for rapidly eliminating synaptic POIs and studying real-time consequences in the same neurons and synapses.

neuroscience↗

bioRxiv2024

Peristaltic pump-triggered amyloid formation suggests shear stresses are in vivo risk factors of amyloid nucleation

Amyloid fibrils, crystal-like fibrillar aggregates of denatured proteins, are formed linked with the breakdown of supersaturation, causing a series of amyloidosis including Alzheimers and Parkinsons diseases. Although varying in vitro factors are known, in vivo factors breaking supersaturation are unclear. We found that flowing by a peristaltic pump effectively triggers amyloid formation of hen egg white lysozyme, a model amyloidogenic protein, and, moreover, amyloidosis-associated proteins (i.e. -synuclein, amyloid {beta} 1-40, and {beta}2-microglobulin). The peristaltic pump-dependent amyloid formation was visualized by a fluorescence microscope with looped flow system, revealing dynamic motions under flow. Among them, amyloid fibrils of amyloid {beta} 1-40 were stickier than others, self-associating, absorbing to loop surfaces, and surging upon flicking the loop, implying early stages of cerebral amyloid angiopathy. On the other hand, {beta}2-microglobulin at a neutral pH showed unique two-step amyloid formation with an oligomeric trapped intermediate, which might mimic amyloid formation in patients. Peristalsis-caused strong shear stresses were considered to mechanically break supersaturation. Shearing stresses occur in vivo at varying levels, suggesting that they break otherwise persistent supersaturation, thus triggering amyloid formation and ultimately leading to amyloidosis. (182 words <200 words)

biophysics↗

bioRxiv2024

Platelet PI3Kβ regulates breast cancer metastasis

Platelets promote tumor metastasis by several mechanisms. Platelet-tumor cell interactions induce the release of platelet cytokines, chemokines, and other factors that promote tumor cell epithelial-mesenchymal transition and invasion, granulocyte recruitment to circulating tumor cells (CTCs), and adhesion of CTCs to the endothelium, assisting in their extravasation at metastatic sites. Previous studies have shown that platelet activation in the context of thrombus formation requires the Class IA PI 3-kinase PI3K{beta}. We now define a role for platelet PI3K{beta} in breast cancer metastasis. Platelet PI3K{beta} is essential for platelet-stimulated tumor cell invasion through Matrigel. Consistent with this finding, in vitro platelet-tumor cell binding and tumor cell-stimulated platelet activation are reduced in platelets isolated from PI3K{beta} mutant mice. RNAseq and proteomic analysis of human breast epithelial cells co-cultured with platelets revealed that platelet PI3K{beta} regulates the expression of EMT and metastasis-associated genes in these cells. The EMT and metastasis-associated proteins PAI-1 and IL-8 were specifically downregulated in co-cultures with PI3K{beta} mutant platelets. PI3K{beta} mutant platelets are impaired in their ability to stimulate YAP and Smad2 signaling in tumor cells, two pathways regulating PAI-1 expression. Finally, we show that mice expressing mutant PI3K{beta} show reduced spontaneous metastasis, and platelets isolated from these mice are less able to stimulate experimental metastasis in WT mice. Taken together, these data support a role for platelet PI3K{beta} in promoting breast cancer metastasis and highlight platelet PI3K{beta} as a potential therapeutic target. SignificanceWe demonstrate that platelet PI3K{beta} regulates metastasis, broadening the potential use of PI3K{beta}-selective inhibitors as novel agents to treat metastasis.

cancer biology↗

bioRxiv2024

Improving the value utilization of tuna peptide powder for the cosmetics field through ozone oxidation

To improve the utilization efficiency of small molecule peptides in marine proteins and promote their application in cosmetics, this study adopts ozone oxidation to conduct deodorization research on tuna small molecule peptides. To devise a method for the ozone oxidation and deodorization of tuna peptide powder suitable for the cosmetics field, orthogonal tests were carried out. The time, ozone concentration, and temperature were adjusted to determine the optimal conditions for ozonation and deodorization of tuna peptide powder. The results showed that at 50{degrees}C and an ozone concentration of 99.10 x 103 mg/m3, wet ozone oxidation for 40 min can also significantly reduce the fishy smell. Under these conditions, the color of tuna peptide powder treated with wet ozone was lighter. In addition, the main volatile compounds were detected by gas chromatography-mass spectrometry (GC-MS). The content of the main fishy volatile substance, hexanal, decreased by 66.4%, and two octyl aldehydes were observed. The results also showed that the protein activity of tuna peptide powder after ozonation remained unchanged. Thus, this study presents an approach to the ozone oxidation of tuna peptide powder that is suitable for cosmetics.

bioengineering↗

bioRxiv2024

Field conditions greatly modify a major growth-defense tradeoff in Arabidopsis thaliana

When plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plant Arabidopsis thaliana is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in the ACD6 gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by their ACD6 genotype, suggesting that additional abiotic and/or microbial signals present outdoors - but not in the greenhouse - greatly modulate ACD6 activity.

plant biology↗

bioRxiv2024

Microglia-specific transduction via AAV11 armed with IBA1 promoter and miRNA-9 targeting sequences

Microglia, as resident immune cells in the central nervous system (CNS), are closely related to human health and the pathogenesis of various CNS diseases, making them compelling targets for therapeutic interventions. However, functional and therapeutic studies of microglia remain significant challenges largely due to the lack of tools capable of efficiently and specifically transducing microglia. Herein, we evaluated the specificity and efficiency of various adeno-associated virus (AAV) vectors armed with the mIBA1 promoter and miRNA-9 targeting sequences in transducing microglia within the caudate putamen (CPu) brain region, and found that AAV11 mediates more specific and efficient transduction of microglia. Subsequently, we further demonstrated that AAV11 also exhibits high transduction specificity for microglia across various brain areas and within the spinal cord. Finally, by reducing the injection dosage, we employed AAV11 for sparse labeling of microglia. This work provides a promising tool for advancing both the functional investigation and therapeutic targeting of microglia.

neuroscience↗

bioRxiv2024

Cryptic Variation in Adaptive Phenotypes Revealed by Panspecific flc Mutants

The study of mutants is one of the best tools for understanding the genetic basis of phenotypes that contribute to adaptation. Oddly, mutant analyses are almost always restricted to single genetic backgrounds and findings therefore can not be easily generalized. A case in point is the key regulator of flowering, FLOWERING LOCUS C (FLC), which has been inferred to explain much of the flowering time variation in Arabidopsis thaliana, yet mutants have been examined in very few backgrounds. We have previously established a set of panspecific flc mutants in 62 accessions of A. thaliana (Ruffley et al. 2024). Here, we investigate how genetic background modulates mutant effects on flowering and vegetative traits, as well as on physiology and transcriptomes. Time to onset of flowering in the genome-edited flc lines was reduced by up to 83%, but considerable variation remained. Genetic mapping showed that extremely early flowering in the absence of FLC was mostly explained by natural variation at the known FLC target FT, with additional contribution from loci colocalizing with FLC. Prognostic sequence analyses of accessions did not suggest that extremely-early combinations of engineered flc and natural FT alleles would be deleterious, yet extremely early flowering accessions are not represented in the commonly used collections of A. thaliana accessions. To test whether this discrepancy could be due to sampling bias, we undertook a focused collection effort of wild populations in Southern Italy, which confirmed that extremely early flowering accessions exist in natural populations. Apart from its specific role in flowering time regulation, FLC has pleiotropic effects on other ecophysiological traits such as growth, and these were also dependent on the genetic background, which was further supported by transcriptomic comparisons. Together we conclude that the various roles of FLC have greatly diversified in different genetic backgrounds. Our study provides a proof-of-concept on how analysis of panspecific mutants can reveal the true extent of genetic networks in which a focal gene participates in.

plant biology↗

bioRxiv2024

AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer

Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.

cancer biology↗

bioRxiv2024

CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data

Single-cell DNA sequencing (scDNA-seq) has significantly advanced cancer research by enabling precise detection of chromosomal aberrations, such as copy number variations (CNVs), at a single-cell level. These variations are crucial for understanding tumor progression and heterogeneity among tumor subclones. However, accurate CNV inference in scDNA-seq has been constrained by several factors, including low coverage, sequencing errors, and data variability. To address these challenges, we introduce CNVeil, a robust quantitative algorithm designed to accurately reveal CNV profiles while overcoming the inherent noise and bias in scDNA-seq data. CNVeil incorporates a unique bias correction method using normal cell profiles identified by a PCA-based Gini coefficient, effectively mitigating sequencing bias. Subsequently, a multi-level hierarchical clustering, based on selected highly variable bins, is employed to initially identify coarse subclones for robust ploidy estimation and further identify fine subclones for segmentation. To infer the CNV segmentation landscape, a novel change rate-based across-cell breakpoint identification approach is specifically designed to diminish the effects of low coverage and data variability on a per-cell basis. Finally, a consensus segmentation is utilized to further standardize read depth for the inference of the final CNV profile. In comprehensive benchmarking experiments, where we compared CNVeil with seven state-of-the-art CNV detection tools, CNVeil exhibited exceptional performance across a diverse set of simulated and real scDNA-seq data in cancer genomics. CNVeil excelled in subclone identification, segmentation, and CNV profiling. In light of these results, we anticipate that CNVeil will significantly contribute to single-cell CNV analysis, offering enhanced insights into chromosomal aberrations and genomic complexity.

bioinformatics↗

bioRxiv2024

Neuronal-class specific molecular cues drive differential myelination in the neocortex

In the neocortex, oligodendrocytes produce distinct amounts of myelin in each cortical layer and along the axons of individual neuron types. Here we present a comprehensive single-cell molecular map of mouse cortical oligodendrocytes across different cortical layers and stages of myelination, spanning the initiation of cortical myelination into adulthood. We apply this dataset to show that neuron-class specific signals drive oligodendrocyte maturation and differential myelination across cortical layers. We find that each layer contains a similar compendium of oligodendrocyte classes, indicating that oligodendrocyte heterogeneity cannot explain layer-specific myelination. To evaluate whether neuronal diversity drives differential myelination across cortical layers, we generated a predicted ligand-receptor interactome between projection neuron types and oligodendrocyte states, across cortical layers and time. In vivo functional testing identified Fgf18, Ncam1, and Rspo3 as novel, neuron-derived pro-myelinating signals. Our results highlight neuron-class-dependent control of myelin distribution in the neocortex.

neuroscience↗

bioRxiv2024

SARS-COV-2 induces blood-brain barrier and choroid plexus barrier impairments and vascular inflammation in mice

The coronavirus disease of 2019 (COVID-19) pandemic that has led to more than 700 million confirmed cases and near 7 million deaths. Although Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus mainly infects the respiratory system, neurological complications are widely reported in both acute infection and long-COVID cases. Despite the success of vaccines and antiviral treatments, neuroinvasiveness of SARS-CoV-2 remains as an important question, which is also centered on the mystery whether the virus is capable of breaching the barriers into the central nervous system. By studying the K18-hACE2 infection model, we observed clear evidence of microvascular damage and breakdown of the blood-brain barrier (BBB). Mechanistically, SARS-CoV-2 infection caused pericyte damage, tight junction loss, endothelial activation and vascular inflammation, which together drive microvascular injury and BBB impairment. In addition, the blood-cerebrospinal fluid barrier at the choroid plexus was also impaired after infection. Therefore, cerebrovascular and choroid plexus dysfunctions are important aspects of COVID-19 and may contribute to the neurological complications both acutely and in long COVID.

neuroscience↗

bioRxiv2023

Aberrant methylation and expression of TNXB promotes chondrocyte apoptosis and extracullar matrix degradation in hemophilic arthropathy via AKT signaling

Recurrent joint bleeding in hemophilia patients frequently causes hemophilic arthropathy (HA). Drastic degradation of cartilage is a major characteristic of HA, but its pathological mechanisms has not yet been clarified. In HA cartilages, we found server matrix degradation and increased expression of DNA methyltransferase proteins. We thus performed genome-wide DNA methylation analysis on human HA (N = 5) and osteoarthritis (N = 5) articular cartilages, and identified 1228 differentially methylated regions (DMRs) associated with HA. Functional enrichment analyses revealed the association between DMR genes (DMGs) and extracellular matrix (ECM) organization. Among these DMGs, Tenascin XB (TNXB) expression was down-regulated in human and mouse HA cartilages. The loss of Tnxb in F8-/- mouse cartilage provided a disease-promoting role in HA by augmenting cartilage degeneration and subchondral bone loss. Tnxb knockdown also promoted chondrocyte apoptosis and inhibited phosphorylation of AKT. Importantly, AKT agonist showed chondroprotective effects following Tnxb knockdown. Together, our findings indicate that exposure of cartilage to blood leads to alterations in DNA methylation, which is functionally related to ECM homeostasis, and further demonstrate a critical role of TNXB in HA cartilage degeneration by activating AKT signaling. These mechanistic insights allow development of potentially new strategies for HA cartilage protection.

molecular biology↗

bioRxiv2023

Beta-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation leading to the development of glucocorticoid-induced osteonecrosis of femoral head

Glucocorticoid-induced osteonecrosis of the femoral head (GONFH) is a common refractory joint disease characterized by bone damage and the collapse of femoral head structure. However, the exact pathological mechanisms of GONFH remain unknown. Here, we observed abnormal osteogenesis and adipogenesis associated with decreased {beta}-catenin in the necrotic femoral head of GONFH patients. In vivo and in vitro studies further revealed that glucocorticoid exposure disrupted osteogenic/adipogenic differentiation of bone marrow mesenchymal cells (BMSCs) by inhibiting {beta}-catenin signaling in glucocorticoid-induced GONFH rats. Col2+ lineage largely contributes to BMSCs, and was found an osteogenic commitment in the femoral head through 9 months of lineage trace. Specific deletion of {beta}-catenin in Col2+ cells shifted their commitment from osteoblasts to adipocytes, leading to a full spectrum of disease phenotype of GONFH in adult mice. Overall, we uncover that {beta}-catenin inhibition disrupting the homeostasis of osteogenic/adipogenic differentiation contributes to the development of GONFH, and identify an ideal genetic modified mouse model of GONFH.

pathology↗

bioRxiv2023

The origin, divergence and inter-subspecies hybridization of house mice (Mus musculus)

House mice (Mus musculus) are the ancestors of laboratory mouse strains and an excellent model for evolutionary biology. The origin, divergence and inter-subspecies hybridization of the three main subspecies (Mus musculus domesticus, M. m. musculus, M. m. castaneus) were not well-resolved. Population genomic analyses with 349 samples from Eurasia confirmed the Himalayas-India-Pakistan junctional region as the origin centre. The divergence of M. m. domesticus, M. m. musculus and M. m. castaneus occurred [~]333.6, 308.3 and 134.4 thousand years ago, respectively, which located in different interglacial stages in Pleistocene. Hybridization among M. m. domesticus, M. m. musculus, and M. m. castaneus after secondary contact during spread and gene flow between the ancestral population and different subspecies produced distinct genomic mixtures in populations from different regions of Eurasia. Long-distance introgression from M. m. musculus into M. m. castaneus and from M. m. castaneus into M. m. musculus happened in southern China and northern China, respectively. And extensive genomic introgression occurred on both autosomes and the X chromosomes. Genomic introgression in hybrids from East Asia and Europe revealed that the level of genomic differentiation, recombination rate and benefits for the survival and reproduction of hybrids determined the introgression capability of distinct genomic regions in inter-subspecies hybridization of house mice. Unidirectional introgression of the Y chromosome made all wild mice in East Asia hold the musculus-type Y chromosome. Our study provided comprehensive insights into the origin, divergence and inter-subspecies genomic introgression of house mice.

evolutionary biology↗

bioRxiv2023

Induction of T-DNA amplification by retrotransposon-derived sequences

Transformation via Agrobacterium tumefaciens (Agrobacterium) is the predominant method used to introduce exogenous DNA into plants. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in concatenated forms in plant genomes, but the mechanisms affecting final T-DNA structure remain unknown. In this study, we demonstrate that the inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase transgene copy number by more than 50-fold in Arabidopsis thaliana (Arabidopsis). RT-mediated amplification of T-DNA results in large concatemers in the Arabidopsis genome, which are primarily induced by the long terminal repeats (LTRs) of RTs. T-DNA amplification is dependent on the activity of DNA repair proteins associated with theta-mediated end joining (TMEJ). Finally, we show that T-DNA amplification can increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA amplification for plant gene editing.

plant biology↗