Biology subjects

Xia, J.

Publications and source records attributed to Xia, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Structural insights into ligand recognition and selectivity of the human hydroxycarboxylic acid receptor HCAR2

Hydroxycarboxylic acid receptor 2 (HCAR2) belongs to the family of class A G-protein-coupled receptors with key roles in regulating lipolysis and free fatty acid formation in humans. It is deeply involved in many pathophysiological processes and serves as an attractive target for the treatment of neoplastic, autoimmune, neurodegenerative, inflammatory, and metabolic diseases. Here, we report four cryo-EM structures of human HCAR2-Gi1 complexes with or without agonists, including the drugs niacin and acipimox, and the highly subtype-specific agonist MK-6892. Combined with molecular docking and functional analysis, we have revealed the recognition mechanism of HCAR2 for different agonists and summarized the general pharmacophore features of HCAR2 agonists, which are based on three key residues R1113.36, S17945.52, and Y2847.43. Notably, the MK-6892-HCAR2 structure shows an extended binding pocket relative to other agonist-bound HCAR2 complexes. In addition, the key residues that determine the ligand selectivity between the HCAR2 and HCAR3 are also illuminated. Our findings provide structural insights into the ligand recognition, selectivity, activation, and G protein coupling mechanism of HCAR2, which sheds light on the design of new HCAR2-targeting drugs for greater efficacy, higher selectivity, and fewer or no side effects.

cell biology↗

bioRxiv2023

Dynamics of Innate Immune Response Due to Bacteria-Induced Pulpitis

IntroductionPulpitis is associated with dental carries and can lead to irreversible pulp damage. As bacteria penetrate deeper into dentin and pulp tissue, a pulpal innate immune response is initiated. However, an understanding of the types of immune cells in the pulp, how this relates to bacterial infiltration, and the dynamics of the immune response during pulpitis is limited. As conserving the vitality of the pulp tissue through conservative therapies becomes an important part of dental practice, there is a greater need to understand the kinetics and composition of the immune response during pulpitis. MethodsDental pulp exposure in molars of mice was used as an animal model of pulpitis. To investigate the kinetics of immune response, pulp tissue was collected from permanent molars at different time points after injury (baseline, day 1, and day 7). Flow cytometry analysis of CD45+ leukoctyes including macrophages, T cells, neutrophils and monocytes was performed. 16S in situ hybridization captured bacterial invasion of the pulp, and immunohistochemistry for F4/80 investigated spatial and morphological changes of macrophages during pulpitis. Data were analyzed using two-way ANOVA with Tukeys multiple comparisons. ResultsBacteria mostly remained close to the injury site, with some expansion towards non-injured pulp horns. We found that F4/80+ macrophages were the main immune cell population in healthy pulp. Upon injury, CD11b+Ly6Ghigh neutrophils and CD11b+Ly6GintLy6Cint monocytes constituted 70-90% of all immune populations up to 7 days after injury. Even though there was a slight increase in T cells at day 7, myeloid cells remained the main drivers of the immune response. ConclusionsAs bacteria proliferate within the pulp chamber, innate immune cells including macrophages, neutrophils and monocytes predominate as the major immune populations, with minimal signs of transitioning to an adaptive immune response.

immunology↗

bioRxiv2022

Neuronal-immune Axis Alters Pain and Sensory Afferent Damage During Dental Pulp Injury

Dental pulp tissue is densely innervated by afferent fibers of the trigeminal ganglion. When bacteria cause dental decay near the pulpal tissue, a strong neuronal and immune response occur, creating pulpitis, which is associated with severe pain and pulp tissue damage. Neuro-immune interactions have the potential to modulate both the pain and pathological outcome of pulpitis. We first investigated the role of the neuropeptide calcitonin-gene related peptide (CGRP), released from peptidergic sensory afferents, in dental pain and immune responses by using calca knock out (calca-/-) and wild type (calca+/+) mice, in a model of pulpitis by creating a mechanical exposure of the dental pulp horn. While CGRP did not contribute to facial mechanical hypersensitivity, at an early time point, it did contribute to spontaneous pain-like behavior. We also found that CGRP contributed to recruitment of neutrophils and monocytes, while not clearly affecting the progression of pulpal pathology histologically. When we depleted neutrophils and monocytes, we found that there was more sensory afferent loss, tissue damage and deeper spread of bacteria into the pulp tissue, while there was a reduction in facial mechanical hypersensitivity compared to control animals at a later time point. Overall, we showed that there is a crosstalk between peptidergic neurons and neutrophils in the pulp, modulating the pain and inflammatory outcomes of the disease.

neuroscience↗

bioRxiv2022

Transposable elements as tissue-specific enhancers in cancers of endodermal lineage

Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

genomics↗

bioRxiv2022

Sex-specific deubiquitylation drives immune-related neurodegeneration in Drosophila

Risk of neurodegenerative disease such as late onset Alzheimers is linked to aberrant ubiquitinylation and accumulation of non-degraded proteins in brain cells. A glial network of innate immune genes modulates inflammatory responses to such protein deposition. However, vulnerability differs between the sexes. Here, we show that the Drosophila homologue of the deubiquitylase Trabid can align the sex-specific aspects of neurodegenerative phenotypes with changes in ubiquitylation and inflammatory activity. An enzymatically null Trabid in flies, caused sex-specific changes in locomotion, sleep patterns, brain histology and ultimately, lifespan. These changes were underscored by altered ubiquitin and proteome enrichment profiles and the same enzymatic activity as its human counterpart. When the sex-determination gene transformer was silenced in astrocytes or immunocompetent tissues, sex differences were significantly reduced. Our results indicate that Trabid underscores sex-specificity in disease neurology, by controlling the balance between ubiquitylation and inflammation.

immunology↗

bioRxiv2022

Medicago truncatula ABCG40 is a cytokinin importer negatively regulating lateral root density and nodule number

Numerous studies suggest that cytokinin (CK) distribution plays a relevant role in shaping plant morphology in changing environments. Nonetheless, our knowledge about the involvement of short-distance CK translocation in root mineral nutrition remains scarce, and the specific role of CK transporters in root morphology has yet to be established. Therefore, the molecular identity of CK transporters should be determined to increase knowledge on root plasticity during soil fertility, as well as more frequently encountered plant nutrient deficiencies. In this work, we identified and characterized the Medicago truncatula full-size ATP-binding cassette (ABC) transporter of the G subfamily MtABCG40 as a plasma membrane CK importer. Its expression is root-specific and is induced by nitrogen deprivation and CKs. Our analyses indicate that MtABCG40 exerts a negative impact on lateral root density by decreasing lateral root initiation and enhancing primary root elongation. Moreover, we also observed that this transporter negatively influenced the nodule number. Our results suggest that MtABCG40 action affects CK signalling, which impacts the cellular response to auxin. In summary, we identified a novel ABCG-type CK transporter that regulates lateral root density and nodule number.

plant biology↗

bioRxiv2022

Chemical inhibition of PIN auxin transporters by the anti-inflammatory drug Naproxen

The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we uncover that Naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN transporters in plants. Physiological experiments indicate that exogenous Naproxen treatment affects pleiotropic auxin-regulated developmental processes. Further cellular and biochemical evidence supports that Naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analysis confirms that Naproxen binds directly to PIN1 protein, via the same binding cavity as the IAA substrate. Thus, by combining cellular, biochemical, and structural approaches, this study well establishes that Naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of the compound may advance our understanding on the molecular mechanisms of PIN-mediated auxin transport, and expand our toolkit in auxin biology and agriculture.

plant biology↗

bioRxiv2022

The RNA m6A reader YTHDF1 promotes hematopoietic malignancy by maintaining oncogenic translation

N6-methyladenosine (m6A), the most abundant modification in mRNAs, has been defined as a crucial modulator in the progression of acute myeloid leukemia (AML), while the detailed mechanism remains elusive. Here we report that YTHDF1, an m6A reader protein, is overexpressed in human AML samples with enrichment in leukemia stem cells (LSCs). Whereas YTHDF1 is dispensable for normal hematopoiesis in mice, depletion of YTHDF1 attenuates self-renewal and proliferation of patient-derived LSCs, and impedes leukemia establishment in immunodeficient mice. Mechanistically, YTHDF1 promotes the translation of diverse m6A-modified oncogene mRNAs particularly cyclin E2. We applied a structure-based virtual screening of FDA-approved drugs and identified tegaserod as a potential YTHDF1 inhibitor. Tegaserod blocks the direct binding of YTHDF1 with m6A-modified mRNAs and inhibits YTHDF1-regulated mRNA translation. Moreover, tegaserod inhibits leukemogenesis in vitro and in mice, phenocopying the loss of YTHDF1. Together, our study defines YTHDF1 as an integral regulator of AML progression at the translational level and identifies tegaserod as a potential therapeutic agent for AML by targeting YTHDF1. Statement of SignificanceO_LIThe RNA m6A reader YTHDF1 is an oncoprotein in AML. C_LIO_LIYTHDF1 promotes the translation of m6A-modified oncogene mRNAs. C_LIO_LITegaserod, an FDA-approved drug for irritable bowel syndrome, inhibits YTHDF1-regulated mRNA translation and leukemogenesis. C_LI Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cancer biology↗

bioRxiv2022

Synapsing with oligodendrocyte precursor cells stop sensory axons regenerating into the spinal cord

Primary sensory axons stop regenerating as they re-enter the spinal cord, resulting in incurable sensory loss. What arrests them has remained unclear. We previously showed that axons stop by forming synaptic contacts with unknown non-neuronal cells. Here, we identified these cells in adult mice as oligodendrocyte precursor cells (OPCs). We also found that only a few axons stop regenerating by forming dystrophic endings, exclusively at the CNS:PNS borderline where OPCs are absent. Most axons stop in contacts with a dense network of OPC processes. Live imaging, immuno-EM and OPC-DRG co-culture additionally suggest that axons are rapidly immobilized by forming synapses with OPCs. Genetic OPC ablation enables many axons to continue regenerating deep into the spinal cord. We propose that sensory axons stop regenerating by encountering OPCs that induce presynaptic differentiation. Our findings identify OPCs as a major regenerative barrier that prevents intraspinal restoration of sensory circuits following spinal root injury.

neuroscience↗

bioRxiv2022

Identification of Biomarker Genes Based on Multi-Omics Analysis in Non-Small Cell Lung Cancer

BackgroundNon-small cell lung cancer (NSCLC) is a complex disease with a high mortality rate and a poor prognosis, but its molecular mechanisms and effective biomarkers are still unclear. Comprehensive analysis of multiple histological data can effectively exclude random events and is helpful in improving the reliability of the findings. In this study, we used three types of omics data, RNA-seq, microRNA-seq, and DNA methylation data, from public databases to explore the potential biomarker genes of two major subtypes of NSCLC. ResultsThrough the combined differential analysis of multi-omics, we found 873 and 1378 potential high-risk genes in LUAD and LUSC, respectively. Then, we used WGCNA and PPI analyses to identify hub-genes and LASSO regression to construct prognostic models, and we obtained 15 prognostic genes. We also used survival analysis, univariate COX analysis, and GEO datasets to validate prognostic genes. Finally, we found ten genes associated with NSCLC, and eight of them have been reported in previous research. ConclusionsIn this study, two novel biomarker genes were identified: NES and ESAM. The two genes were both gene expression down-regulation and DNA methylation up-regulation, and regulated by miR-122 and miR-154. Moreover, the NES gene can contribute to the clinical diagnosis and prognosis of NSCLC.

molecular biology↗

bioRxiv2022

Recovery of structural integrity of epithelial monolayer in response to massive apoptosis-induced defects

Apoptosis exists ubiquitously in organisms and plays an essential role in maintaining the homeostasis of functional tissues. While the signaling pathway of cell apoptosis has been widely studied, the mechanism of how apoptotic cells regulate the structural homeostasis of a living tissue still remains largely elusive. Using a functional epithelial monolayer as a model system, we find that the integrity of the epithelium is interrupted by apoptosis-induced defects, with an increasing permeability to small molecules across the epithelium. The defects promote a structural reorganization through enhanced cell spreading and migratory dynamics, resulting in a quick recovery of epithelium integrity. Moreover, we show the epithelial monolayer remodeling is driven by local enhanced traction force after apoptosis, which triggers the process of fluidization and mesenchymal-like migration. Our results show the quick recovery of epithelial homeostasis when being interrupted by cell apoptosis, and indicate the importance of apoptosis-induced mechanical force in mediating cell behaviors to maintain the structural integrity of epithelium.

biophysics↗

bioRxiv2022

Multimodal electrocorticogram active electrode array based on zinc oxide-thin film transistors

Active electrocorticogram (ECoG) electrodes can amplify the weak electrophysiological signals and improve the anti-interference ability, but the traditional active electrodes are so opaque that cannot realize photoelectric collaborative observation. Here an active and fully-transparent ECoG array based on zinc oxide-thin film transistors (ZnO-TFTs) was developed as the local neural signal amplifier for electrophysiological monitoring. The transparency of the proposed ECoG array was up to 85% which is superior to previous reported active electrode array. Various electrical characterizations demonstrated its ability of electrophysiological signal recording, with a higher signal-to-noise ratio of 19.9 dB compared to the Au grid one (13.2 dB). The high transparency of ZnO-TFT electrode array allowed the collecting electrophysiological signals under direct light stimulation on optogenetic mice brain concurrently. The ECoG array could also work under 7-Tesla magnetic resonance imaging to record local brain signal without affecting brain tissue imaging. As the most transparent active ECoG array to date, it provides a powerful multimodal tool for brain observation, including recording brain activity under synchronized optical modulation and 7-Tesla magnetic resonance imaging.

bioengineering↗

bioRxiv2022

Multi-Domain Characterization and Rapid Detection Technology for Cocaine and Methamphetamine Acute Abuse based on EEG

Multi-domain characterization and a new fast detection method for acute illegal psychostimulants abuse detection based on waking-state EEG of mice is proposed in this paper. To get corftical electroencephalogram (EEG), three groups of mice were injected with cocaine (Coca), methamphetamine (Meth), and saline (Sali) respectively following the experimental paradigm of drug abuse. The EEG features were extracted out by multi-domain views, including time, frequency, complexity, dynamics, and independent domains to obtain acute drug abuse effects on the brain. New strategy combing time domain with frequency domain is developed as multi-domain input and by means of dimension transformation approach preserving temporal information, the performance of drug abuse detection is greatly improved with deep learning models of ResNet50. Results show that comparing to support vector machine (SVM), k nearest neighbor (kNN), random forest (RF), and long short-term memory fully convolutional networks (LSTM-FCN), ResNet50 based on our proposed multi-domain features has best F1-score of 95.10%. This promising method provides a low-cost, fast, and widely assisted technology for psychostimulants abuse identification.

bioinformatics↗

bioRxiv2022

Structure-Preserving and Batch-Correcting Visualization Using Deep Manifold Transformation for Single-cell RNA-Seq Profiles

Dimensionality reduction and visualization play an important role in biological data analysis, such as data interpretation of single-cell RNA sequence (scRNA-seq). It is desired to have a visualization method that can not only be applicable to various application scenarios, including cell clustering and trajectory inference, but also satisfy a variety of technical requirements, especially the ability to preserve inherent structure of data and handle with batch effects. However, no existing methods can accommodate these requirements in a unified framework. In this paper, we propose a general visualization method, deep visualization (DV), that possesses the ability to preserve inherent structure of data and handle batch effects and is applicable to a variety of datasets from different application domains and dataset scales. The method embeds a given dataset into a 2- or 3-dimensional visualization space, with either a Euclidean or hyperbolic metric depending on a specified task type with type static (at a time point) or dynamic (at a sequence of time points) scRNA-seq data, respectively. Specifically, DV learns a structure graph to describe the relationships between data samples, transforms the data into visualization space while preserving the geometric structure of the data and correcting batch effects in an end-to-end manner. The experimental results on nine datasets in complex tissue from human patients or animal development demonstrate the competitiveness of DV in discovering complex cellular relations, uncovering temporal trajectories, and addressing complex batch factors. We also provide a preliminary attempt to pre-train a DV model for visualization of new incoming data.

bioinformatics↗

bioRxiv2022

Endothelial TET2 Regulates Cardiac Remodeling by Modifying Endothelial-to-Mesenchymal Transition

DNA methylation modification has been proved to play an important role in heart diseases. In this study, the role of Ten-Eleven Translocation-2 (TET2), which is a key demethylation enzyme, is investigated in cardiac remodeling. TET2 is abundant in endothelial cells but decreased in hypertrophic hearts. TET2 knockdown in endothelial cells triggers endothelial-to-mesenchymal transition (EndMT), while overexpression of TET2 inhibits the EndMT. In vivo, Cdh5-CreERT2/TET2flox/flox; Rosa26-mTmG+/- mice are developed and undergo transverse aortic constriction (TAC) subsequently to induce pathological cardiac hypertrophy model. Hearts of Cdh5-CreERT2/TET2flox/flox mice show more severe hypertrophy and fibrosis than controls in the TAC model. Furthermore, EGLN3 is identified to participate in EndMT as the downstream target of TET2 by using RNA sequencing and whole-genome bisulfite sequencing (WGBS). Finally, vitamin C, which can mimic TET2 restoration, is found to partially improve cardiac function and inhibit myocardial fibrosis. These insights into how TET2 alleviates cardiac fibrosis may open new avenues for treating cardiac remodeling in the future.

genetics↗

bioRxiv2022

A phospho-switch provided by LRR receptor-like kinase, ALK1/QSK1/KIN7, prioritizes ABCG36/PEN3/PDR8 transport toward defense

Based on its proposed substrate preferences, the ABC transporter, ABCG36/PDR8/PEN3, from the model plant Arabidopsis stands at the cross-road between growth and defence. Recently, ABCG36 was shown to export a few indolic compounds, including the auxin precursor, indole-3-butyric acid (IBA), and to be implicated in the export of the major phytoalexin of Arabidopsis, camalexin, although clear-cut proof of camalexin transport activity is still lacking. Here we provide strong evidence that ABCG36 catalyses the direct, ATP-dependent export of camalexin over the plasma membrane, however, most likely in functional interplay with non-camalexin transporting ABCG isoforms. We identify the leucin-rich repeat receptor-like kinase, Auxin-induced LRR Kinase1 (ALK1/KIN7/QSK1), as a functional kinase to physically interact with and phosphorylate ABCG36. ABCG36 phosphorylation by ALK1 represses unilaterally IBA but not camalexin export leading to a prioritization of ABCG transport toward defense. As a consequence, phospho-dead mutants of ABCG36, like alk1 and abcg36 alleles, are hypersensitive toward infection with the root pathogen, F. oxysporum, caused by elevated fungal progression. Our findings indicate a novel, direct regulatory circuit between a receptor kinase and an ABC transporter determining transporter substrate specificity. It appears that growth and defense balance decisions in plants are performed on the transporter level by means of a reversible phospho-switch.

plant biology↗

bioRxiv2022

Resource requirements for ecotoxicity testing: A comparison of traditional and new approach methods

Toxicity testing is under transformation as it aims to harness the potential of New Approach Methods (NAMs) as alternative test methods that may be less resource intensive (i.e., fewer animals, cheaper costs, quicker assays) than traditional approaches while also providing more data and information. While many stakeholders are of the opinion that this unfolding transformation holds significant promise as a more efficient and ethical way forward, few studies have compared the resources required for NAMs versus those needed for traditional animal-based toxicity tests, particularly in the field of ecotoxicology. The objective was to compare resources needed for traditional animal-based ecotoxicity tests versus alternative tests using emergent NAMs. From a bibliometric review, we estimate that traditional tests for a single chemical cost $118,000 USD, require 135 animals, and take 8 weeks. In comparison, alternative tests cost $2,600, require 20 animals (or none), and take up to 4 weeks to test 16 (to potentially hundreds of) chemicals. Based on our analysis we conclude that NAMs in ecotoxicology can be more advantageous than traditional methods in terms of resources required (i.e., monetary costs, number of animals needed, and testing times). We note, however, that the evidence underpinning these conclusions is relatively sparse. Moving forward, groups developing and applying NAMs should provide more detailed accounts of the resources required. In addition, there is also a need for carefully designed case studies that demonstrate the domain of applicability of NAMs (and make comparisons to traditional tests) to ultimately build confidence among the user community.

pharmacology and toxicology↗

bioRxiv2021

Influence of sequencing depth on the fidelity and sensitivity of 1%-5% low-frequency mutation detection and recommendation for standardization of sequencing depth

Sequencing depth has always played an important role in the accurate detection of low-frequency mutations. The increase of sequencing depth and the reasonable setting of threshold can maximize the probability of true positive mutation, or sensitivity. Here, we found that when the threshold was set as a fixed number of positive mutated reads, the probability of both true and false-positive mutations increased with depth. However, When the number of positive mutated reads increased in an equal proportion with depth (the threshold was transformed from a fixed number to a fixed percentage of mutated reads), the true positive probability still increased while false positive probability decreased. Through binomial distribution simulation and experimental test, it is found that the "fidelity" of detected-VAFs is the cause of this phenomenon. Firstly, we used the binomial distribution to construct a model that can easily calculate the relationship between sequencing depth and probability of true positive (or false positive), which can standardize the minimum sequencing depth for different low-frequency mutation detection. Then, the effect of sequencing depth on the fidelity of NA12878 with 3% mutation frequency and circulating tumor DNA (ctDNA of 1%, 3% and 5%) showed that the increase of sequencing depth reduced the fluctuation range of detected-VAFs around the expected VAFs, that is, the fidelity was improved. Finally, based on our experiment result, the consistency of single-nucleotide variants (SNVs) between paired FF and FFPE samples of mice increased with increasing depth, suggesting that increasing depth can improve the precision and sensitivity of low-frequency mutations. HighlightsThe normalized relationship between sequencing depth and the probability of true positive mutation (sensitivity) is established based on binomial distribution. The probability of true positive increases and the probability of false positive decreases when the number of positive mutated reads increases (threshold) in an equal proportion with depth. Detected-VAFs fluctuates regularly around expected-VAFs. The amplitude of detected-VAFs fluctuation decreases with sequencing depth and the "fidelity" increases. The increase of "fidelity" leads to a higher degree of differentiation between true and false positive mutations, which ultimately increases the true positive probability and decreases the false positive probability.

genomics↗