Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 541 records · Page 30Linked to original sources

bioRxiv2022

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

BackgroundThe Microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, MORC proteins also have RdDM-independent functions; although, their underlying mechanisms are unknown. ResultsIn this study, we examined regions of MORC binding where RdDM does not occur in order to shed light on the RdDM-independent functions of MORC proteins. We found that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors (TFs), thereby repressing gene expression. We also found that MORC-mediated repression of gene expression was particularly important under conditions of stress. We showed that MORC proteins regulate TFs through either direct or indirect interactions, and these TFs can in some cases regulate their own transcription, resulting in feedforward loops. ConclusionsOur findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

plant biology↗

bioRxiv2022

Genetic ablation of dentate hilar somatostatin-positive GABAergic interneurons is sufficient to induce cognitive impairment

Aging is often associated with a decline in cognitive function. A reduction in the number of somatostatin-positive (SOM+) interneurons in the dentate gyrus (DG) has been described in cognitively impaired but not in unimpaired aged rodents. However, it remains unclear whether the reduction in SOM+ interneurons in the DG hilus is causal for age-related cognitive dysfunction. We hypothesized that hilar SOM+ interneurons play an essential role in maintaining cognitive function and that a reduction in the number of hilar SOM+ interneurons might be sufficient to induce cognitive dysfunction. Hilar SOM+ interneurons were ablated by expressing a diphtheria toxin transgene specifically in these interneurons, which resulted in a reduction in the number of SOM+/GAD-67+ neurons and dendritic spine density in the DG. C-fos and Iba-1 immunostainings were increased in DG and CA3 but not in CA1. Behavioral testing revealed a reduced recognition index in the novel object recognition test, a reduction in the percentage of correct alternations in the Y maze tests, and increased latencies and path lengths in the learning and the reversal learning phase of the Morris water maze. Our results show that partial genetic ablation of SOM+ hilar interneurons is sufficient to increase activity in DG and CA3, as has been described to occur with aging and to induce an impairment of learning and memory functions. Thus, partial ablation of hilar SOM+ interneurons may be a significant contributing factor to age-related cognitive dysfunction. These mice may also be useful as a cellularly defined model of hippocampal aging.

neuroscience↗

bioRxiv2022

LSR Targets YAP to Modulate Intestinal Paneth Cell Differentiation

Lipolysis-stimulated lipoprotein receptor (LSR) is a multi-functional protein that is best known for its roles in assembly of epithelial tricellular tight junctions and hepatic clearance of lipoproteins. Here, we investigated whether LSR contributes to intestinal epithelium homeostasis and pathogenesis of intestinal disease. By using multiple conditional deletion mouse models and ex vivo cultured organoids, we find that LSR elimination in intestinal stem cells results in disappearance of Paneth cell without affecting the differentiation of other cell lineages. Mechanistic studies reveal that LSR deficiency increases abundance and nuclear localization of YAP by modulating its phosphorylation and proteasomal degradation. Using gain- and loss-of-function studies we show that LSR protects against necrotizing enterocolitis through enhancement of Paneth cell differentiation in small intestinal epithelium. Thus, this study identifies LSR as an upstream negative regulator of YAP activity, an essential factor for Paneth cell differentiation, and a potential novel therapeutic target for inflammatory bowel disease.

cell biology↗

bioRxiv2022

Vascular endothelial growth factor A contributes to the increasing of mammalian respiratory epithelial permeability induced by Pasteurella multocida infection

Infections with Pasteurella multocida can cause significant zoonotic respiratory problems in both humans and animals. In vivo tests in mouse infection models were used to investigate the mechanisms of respiratory epithelial barrier dysfunction during respiratory bacterial infection with these pathogens. Results revealed that P. multocida infection significantly increased epithelial permeability and increased expression of vascular endothelial growth factor A (VEGFA) and endothelial nitric oxide synthase (eNOS) in murine tracheae and lungs. In murine lung epithelial cell (MLE-12) models, P. multocida infection decreased the expression of tight junctions (ZO-1) and adherens junctions ({beta}-catenin, E-cadherin), but induced the activation of the hypoxia-inducible factor-1 (HIF-1) and VEGFA signaling. When expression of HIF-1 is suppressed, the induction of VEGFA and ZO-1expression by P. multocida infection is decreased. We also found that intervention of HIF-1 and VEGFA signaling affected infection outcomes caused by respiratory bacteria in mouse models. Most importantly, we demonstrated that P. multocida infection increased permeability of human respiratory epithelial cells and this process was associated with the activation of the HIF-1 and VEGFA signaling and likely contributes to the pathogenesis of P. multocida in humans. ImportanceMammalian respiratory epithelium forms the first line of defense against infections with Pasteurella multocida, an important zoonotic respiratory pathogen. In this study, we found P. multocida infection increased respiratory epithelial permeability and promoted the induction of the hypoxia-HIF-1-VEGFA axis in both mouse and murine cell models. Similar findings were also demonstrated in human respiratory epithelial cells. The results from this study gain important knowledge about the pathogenesis of P. multocida causing infections in both animals and humans.

microbiology↗

bioRxiv2022

Chronic intermittent propofol attenuates surgery-induced neuroinflammation, apoptosis, and cognitive impairment in aged mice

Surgery may lead to long-lasting cognitive deficits that are referred to as perioperative neurocognitive disorder (NCD), particularly in elderly patients. Currently, no interventions are routinely employed in clinical practice to prevent perioperative NCD. Here we show that perioperative chronic intermittent administration of propofol to aged mice undergoing laparotomy under isoflurane anesthesia effectively blocks the surgery-induced increase in nitrosative stress, increased expression of proapoptotic proteins, microglial activation, and cognitive deficits. By contrast, in the absence of surgery and anesthesia, propofol had little effect on biochemical parameters and led to cognitive improvement only in a subset of behavioral paradigms. The actions of propofol were largely absent in mice lacking the GABAA receptor 5-subunit, indicating that they are mediated by 5-containing GABAA receptors. These results demonstrate that propofol - via 5-containing GABAA receptors that are redistributed to the cell surface membranes in a sustained manner - can attenuate surgery-induced neuroinflammation and postsurgical cognitive deficits.

neuroscience↗

bioRxiv2022

Antibody avidity and multi-specificity combined to confer protection against SARS-CoV-2 and resilience against viral escape

SARS-CoV-2, the causative agent of COVID-19, has been responsible for a global pandemic. Monoclonal antibodies have been used as antiviral therapeutics, but have been limited in efficacy by viral sequence variability in emerging variants of concern (VOCs), and in deployment by the need for high doses. In this study, we leverage the MULTI-specific, multi-Affinity antiBODY (Multabody, MB) platform, derived from the human apoferritin protomer, to drive the multimerization of antibody fragments and generate exceptionally potent and broad SARS-CoV-2 neutralizers. CryoEM revealed a high degree of homogeneity for the core of these engineered antibody-like molecules at 2.1 [A] resolution. We demonstrate that neutralization potency improvements of the MB over corresponding IgGs translates into superior in vivo protection: in the SARS-CoV-2 mouse challenge model, comparable in vivo protection was achieved for the MB delivered at 30x lower dose compared to the corresponding IgGs. Furthermore, we show how MBs potently neutralize SARS-CoV-2 VOCs by leveraging augmented avidity, even when corresponding IgGs lose their ability to neutralize potently. Multiple mAb specificities could also be combined into a single MB molecule to expand the neutralization breadth beyond SARS-CoV-2 to other sarbecoviruses. Our work demonstrates how avidity and multi-specificity combined can be leveraged to confer protection and resilience against viral diversity that exceeds that of traditional monoclonal antibody therapies.

immunology↗

bioRxiv2022

Metformin attenuates hyperglycaemia-stimulated pro-fibrotic gene expression in vascular adventitial fibroblasts via inhibition of Discoidin Domain Receptor 2

Molecular mechanisms underlying the diverse therapeutic effects of anti-diabetic metformin, beyond its anti-hyperglycaemic effects, remain largely unclear. Metformin is reported to reduce the long-term complications of diabetes, including cardiovascular fibrosis and remodelling. Our recent investigations show that Discoidin Domain Receptor 2 (DDR2), a collagen receptor tyrosine kinase, has an obligate regulatory role in collagen type I gene expression in cardiac and vascular adventitial fibroblasts, and that it may be a molecular link between arterial fibrosis and metabolic syndrome in rhesus monkeys. Using gene knockdown and over-expression approaches, the present study examined whether DDR2 is a target of metformin, and whether, by targeting DDR2, it inhibits fibronectin and collagen expression in vascular adventitial fibroblasts exposed to hyperglycaemic conditions. Metformin was found to attenuate hyperglycaemia-induced increase in DDR2 mRNA and protein expression by inhibiting TGF-{beta}1/ Smad2/3 signalling that mediates the stimulatory effect of hyperglycaemia on DDR2 expression. Metformin also inhibited DDR2-dependent expression of fibronectin and collagen, indicating that it regulates these matrix proteins via DDR2 inhibition. The findings identify DDR2, a major mediator of cardiovascular remodelling, as a molecular target of metformin, thereby uncovering the molecular basis of its protective role in vascular fibrosis, and possibly, cardiac fibrosis associated with diabetic cardiomyopathy.

molecular biology↗

bioRxiv2022

R-loop editing by DNA cytosine deaminase APOBEC3B determines the activity of estrogen receptor enhancers

Estrogen receptor (ER) activation results in the formation of DNA double strand breaks (DSB), which promote genomic instability and tumour heterogeneity in ER-positive breast cancers. The single-stranded DNA (ssDNA) cytosine deaminase APOBEC3B (A3B) regulates ER activity by inducing DSB at ER enhancers. To delineate how A3B recognises its substrates and unveil the underlying mechanism leading to the formation of ER-induced DSB, we sampled A3B-mediated deamination sites using whole genome sequencing in a human breast cancer cell model lacking base excision repair function. Our genome-wide analysis revealed that C>U conversions carried out by A3B in R-loop structures are processed into DSB in the vicinity of ER promoters or enhancers. A mechanism which required both the processing of A3B-editing sites and R-loops by distinct DNA damage repair mechanisms. In addition, using BioID-enabled mass-spectroscopy proteomics, we identified TDRD3 as a key A3B-binding partner directing the activity of A3B to ER-induced R-loops. This study suggests a function for A3B in sustaining tumour evolution as an adaptive response at the transcriptional and epigenetic level and supports A3B as a promising target to control ER activity in cancer.

cancer biology↗

bioRxiv2022

Multi-Omic Analysis of Tyrophagus putrescentiae Reveals Insights into the Allergen Complexity of Storage Mites

BackgroundThe storage mite Tyrophagus putrescentiae is one of the major mites causing allergies in Chinese and Korean populations, but its allergen profile in incomplete when compared with that of house dust mites. Multiple genome-based methods have been introduced into the allergen study of mites and have enabled a better understanding of these medically important organisms. ObjectiveWe sought to reveal a comprehensive allergen profile of Tyrophagus putrescentiae and advance the allergen study of storage mites. MethodsBased on a high-quality assembled and annotated genome, an in silico analysis was performed by searching reference sequences to identify allergens. Immunoassay ELISA assessed the allergenicities of recombinant proteins. MALDI-TOF mass spectrometry identified the IgE-binding proteins. Comparative genomics analysis was employed for the important allergen gene families. ResultsA complete allergen profile of Tyrophagus putrescentiae was revealed, including thirty-seven allergen groups (up to Tyr p 42). Among them, five novel allergens were verified using the sera of allergy patients. Massive allergen homologs were identified as the result of gene duplications in genome evolution. Proteomic identification again revealed a wide range of allergen homologs. In the NPC2 family and GSTs, comparative analysis shed light on the expansion and diversification of the allergen groups. ConclusionUsing multi-omic approaches, the comprehensive allergen profile including massive homologs was disclosed in Tyrophagus putrescentiae, which revealed the allergen complexity of the storage mite and could ultimately facilitate the component-resolved diagnosis.

immunology↗

bioRxiv2022

Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat

The success of common wheat as the global staple crop is derived from genome diversity and redundancy as a result of allopolyploidization [1-3], giving rise to the major question how the divergent and convergent transcription among different subgenomes are achieved and harmonized in a single cell. The regulatory information is largely encoded in DNA regulatory elements (REs) interpreted by sequence specific transcription factors (TFs). Here, we created a catalog of genome-wide TF-binding sites (TFBS) to assemble an extensive wheat regulatory network comprising connections among 189 TFs and 3,714,431 REs, which enhances the understanding of wheat regulatory mechanisms on an unprecedented scale. A significant fraction of subgenome-divergent TFBS are derived from recent subgenome-asymmetric expansion of particular transposable element (TE) families. In contrary, TFBS derived from ancient TE expansion largely underwent parallel purifying selection during independent evolution of each subgenome, despite extensive unbalanced turnover of flanking TEs. Altogether, the subgenome-convergent and -divergent regulation in common wheat is orchestrated via differential evolutionary selection on paleo- and neo-TEs.

bioinformatics↗

bioRxiv2022

Herb-paths, a network and statistical model to explore health-beneficial effects of herbs and herbal constituents

Predictions on bioactivities of herbs and herbal compounds could greatly aid drug development, but require integration of available information on herb and compound effects from various databases. We present Herb-paths, an integrated network connecting information on health-beneficial effects of herbs and herbal constituents. The statistical models included in Herb-paths allow for the calculation of the association strength of herbal (constituents) with health-beneficial effects, for both known and novel effects, and give insight into the major bioactive compounds and molecular mechanisms driving the effects. Herb-paths predictions were tested and validated using a case-study of Panax notoginseng and its derived medicinal extract of Panaxatriol saponins (PTS), used in traditional Chinese medicine to treat stroke and other cardiovascular and cerebrovascular thromboembolic (CCT) disorders. Results showed that Herb-paths predicted known and novel associations between PTS/Notoginseng and CCT phenotypes and diseases, including stroke. Predicted novel associations, such as MoyaMoya disease, are promising putative leads for treatment with PTS/Notoginseng, to be tested in further studies.

bioinformatics↗

bioRxiv2022

Unified and standardized mass spectrometry data processing in Python using spectrum_utils

spectrum_utils is a Python package for mass spectrometry data processing and visualization. Since its introduction, spectrum_utils has grown into a fundamental software solution that powers various applications in proteomics and metabolomics, ranging from spectrum preprocessing prior to spectrum identification and machine learning applications, to spectrum plotting from online data repositories, and assisting data analysis tasks for dozens of other projects. Here we present updates to spectrum_utils, which include new functionality to integrate mass spectrometry community data standards, enhanced mass spectral data processing, and unified mass spectral data visualization in Python. spectrum_utils is freely available as open source at https://github.com/bittremieux/spectrum_utils.

bioinformatics↗

bioRxiv2022

Dissecting the cellular basis of age-related cognitive dysfunction: Chronic chemogenetic inhibition of somatostatin-positive interneurons in the dentate gyrus hilus induces memory impairments

The cellular basis of age-related impairments of hippocampal function is not fully understood. In order to evaluate the role of somatostatin-positive (Sst+) interneurons in the dentate gyrus hilus in this process, we chemogenetically inhibited Sst+ interneurons in the dentate gyrus (DG) hilus. Chronic chemogenetic inhibition (CCI) of these neurons resulted in increased c-Fos staining in the DG hilus, a decrease in the percentage of Gad67- and of Sst-expressing interneurons in the DG, and increased microglial activation in DG, CA3, and CA1. Total dendritic length and spine density were reduced in DG and CA1, suggesting reduced dendritic complexity. Behaviorally, the recognition index in an object recognition task and the percentage of spontaneous alternations in the Y maze were decreased, while in both initial and reversal learning in the Morris water maze the latencies to find the hidden platform were increased, suggesting cognitive dysfunction. Our findings establish a causal role for a reduced function of Sst+ interneurons in the DG hilus for cognitive decline and suggest that this reduced function may contribute to age-related impairments of learning and memory. Furthermore, our CCI mice may represent a cellularly defined model of hippocampal aging. SIGNIFICANCE STATEMENTNeuronal circuits and cellular processes underlying age-related cognitive dysfunction are not well understood. We observed that chronic chemogenetic inhibition of a defined cell type, somatostatin-positive interneurons in the dentate gyrus hilus, which have previously been found to be associated with cognitive dysfunction in aged rodents, is necessary and sufficient to elicit changes in expression of interneuronal markers, an increase in the activity of dentate gyrus granule cells, increased microglial activation across the entire hippocampus and an impairment of learning and memory-related tasks. Thus, inhibition of somatostatin-positive interneurons in the dentate gyrus hilus replicates changes that are also seen with normal aging, representing a novel cellularly defined animal model of hippocampal aging.

neuroscience↗

bioRxiv2022

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

plant biology↗

bioRxiv2022

Crossing-over decision landscape in maize

In most crops, including maize, meiotic double-strand breaks (DSBs) occur in all chromosome regions but crossovers (COs) are predominantly near chromosome ends. To understand how the uniform DSB distribution changes into the U-shaped CO distribution, we generated high-resolution maps of CO intermediates. We found that DSBs with medium resection spans more often result in COs than those with shorter or longer resections. We also discovered that sites of CO intermediates associated with MLH3 in zygotene are uniformly distributed along chromosomes, resembling DSB distribution. However, in late prophase, they show the U-shaped distribution characteristic of COs. While zygotene MLH3 sites exhibit methylation levels similar to the genome average, late prophase sites have reduced DNA methylation. In contrast to DNA methylation, inter-parental DNA sequence polymorphism has limited effect on CO distribution. These data indicate that the final CO landscape shape in maize is established late during recombination and controlled by chromatin state.

plant biology↗

bioRxiv2022

Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2

SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems. One-sentence summaryRational treatment strategies for SARS-CoV-2 derived from human PSC models

microbiology↗

bioRxiv2022

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.

plant biology↗

bioRxiv2022

Modulation effect of non-invasive transcranial ultrasound stimulation in an ADHD rat model

Previous studies have demonstrated that transcranial ultrasound stimulation (TUS) with noninvasive high penetration and high spatial resolution has an effective neuromodulatory effect on neurological diseases. Attention deficit hyperactivity disorder (ADHD) is a persistent neurodevelopmental disorder that severely affects child health. However, the neuromodulatory effects of TUS on ADHD have not been reported to date. To reveal the neuromodulatory effects, TUS was performed in ADHD model rats for 2 consecutive weeks, and the behavioral improvement of ADHD, neural activity of ADHD from neurons and neural oscillation levels, and the plasma membrane dopamine transporter (DAT) and brain-derived neurotrophic factor (BDNF) in the brains of ADHD rats were evaluated. The results showed that TUS can improve cognitive behavior in ADHD rats, and that TUS altered neuronal firing patterns and modulated the relative power and sample entropy of local field potentials in an ADHD rat model. In addition, TUS can also enhance BDNF expression in the brain tissue of the ADHD rat model. In conclusion, TUS has an effective neuromodulatory effect on ADHD and thus has the potential to clinically improve cognitive dysfunction in ADHD.

neuroscience↗