Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 775 records · Page 43Linked to original sources

bioRxiv2024

StereoMM: A Graph Fusion Model for Integrating Spatial Transcriptomic Data and Pathological Images

Spatially resolved omics technologies generating multimodal and high-throughput data lead to the urgent need for advanced analysis to allow the biological discoveries by comprehensively utilizing information from multi-omics data. The H&E image and spatial transcriptomic data indicate abundant features which are different and complementary to each other. AI algorithms can perform nonlinear analysis on these aligned or unaligned complex datasets to decode tumoral heterogeneity for detecting functional domain. However,the interpretability of AI-generated outcomes for human experts is a problem hindering application of multi-modal analysis in clinic. We presented a machine learning based toolchain called StereoMM, which is a graph fusion model that can integrate gene expression, histological images, and spatial location. StereoMM firstly performs information interaction on transcriptomic and imaging features through the attention module, guaranteeing explanations for its decision-making processes. The interactive features are input into the graph autoencoder together with the graph of spatial position, so that multimodal features are fused in a self-supervised manner. Here, StereoMM was subjected to mouse brain tissue, demonstrating its capability to discern fine tissue architecture, while highlighting its advantage in computational speed. Utilizing data from Stereo-seq of human lung adenosquamous carcinoma and 10X Visium of human breast cancer, we showed its superior performance in spatial domain recognition over competing software and its ability to reveal tumor heterogeneity. The fusion approach for imaging and gene expression data within StereoMM aids in the more accurate identification of domains, unveils critical molecular features, and elucidates the connections between different domains, thereby laying the groundwork for downstream analysis.

bioinformatics↗

bioRxiv2024

MoLst8 regulates autophagy and lipid homeostasis in Magnaporthe oryzae

TOR, a widely conserved eukaryotic protein kinase, forms TORC1 and TORC2 to regulate diverse cell signaling. TORC1 controls protein synthesis, cell cycle, and autophagy, whereas TORC2 manages cell polarity, cytoskeleton, and membrane structure. Our previous research found that MoVast2, along with MoVast1, regulates TOR in rice blast fungus Magnaporthe oryzae, maintaining lipid and autophagy balance. Lst8, a key TOR complex component in yeast and mammalian cells. However, the precise role of MoLst8 in M. oryzae is still unclear. In this study, we obtained the {Delta}Molst8 mutant through high-through gene knockout strategies. The results showed that loss of MoLST8 leading to a series of defects, such as growth and sporulation reduction, abnormal conidia, and loss of virulence. In addition, this mutant is highly sensitive to rapamycin, leading to growth arrest and autophagy impairment, indicated that MoLst8 positively regulates TORC1 for cellular growth, metabolism, and autophagy. Lipidomics analysis in the mutant revealed lipid metabolism dysregulation, sphingolipid reduction, disrupting membrane tension and homeostasis, suggested that TORC2 mediated lipid regulation is disordered in {Delta}Molst8 mutant. Additionally, the study explored TOR-MAPK crosstalk, finding that the mutant shows heightened cell wall stress sensitivity but fails to restore integrity despite MAPK activation. These findings offer insights into MoLst8s role in fungal pathogenesis, contributing to an understanding of fungal biology and disease control strategies.

microbiology↗

bioRxiv2024

Optimized AAV capsids for diseases of the basal ganglia show robust potency and distribution in adult nonhuman primates

Huntingtons disease and other disorders of the basal ganglia create challenges for biomolecule-based medicines given the poor accessibility of these deep brain structures following intracerebral or intravascular delivery. Additionally, for adeno-associated viruses (AAVs) intravascular delivery exposes peripheral tissues to the vast majority of the therapy, increasing the risk of immune responses and the quantity and associated cost of goods required for therapeutically relevant brain penetration levels. Here, we found that low dose, low volume delivery of unbiased AAV libraries into a focused brain region allowed recovery of novel capsids capable of broad access to key deep brain and cortical structures relevant for human therapies at doses orders of magnitude lower than used in current clinical trials. One such capsid, AAV-DB-3, provided transduction of up to 45% of medium spiny neurons in the adult NHP striatum, along with substantial transduction of relevant deep layer neurons in the cortex. Notably, AAV-DB-3 behaved similarly in mice as in NHPs and also potently transduced human neurons derived from induced pluripotent stem cells. Thus, AAV-DB-3 provides a unique AAV for network level brain gene therapies that translates up and down the evolutionary scale for preclinical studies and eventual clinical use.

neuroscience↗

bioRxiv2024

Decoding scalp health and microbiome dysbiosis in dandruff

A balanced scalp microbiome is crucial for scalp health, yet the mechanisms governing this balance and the etiology of dysbiosis in scalp disorders remain elusive. We conducted a detailed investigation of the scalp and hair follicles, in healthy individuals and those with dandruff/seborrheic dermatitis (D/SD). It was demonstrated that the microbiome inhabiting hair follicles serves as a reservoir for the scalp microbiome, thereby integrating the scalp, follicle, and the hair into one functional unit. Using in vitro models, we further elucidated mechanisms governing the assembly and interactions of the follicular microbiome under healthy and D/SD conditions. We show that propionic acid, produced by C. acnes, plays a pivotal role in maintaining microbiome balance, with implications for scalp health, which was validated through a clinical study.

microbiology↗

bioRxiv2024

Nuclear Translocation of SIRT4 Mediates Deacetylation of U2AF2 to Modulate Renal Fibrosis Through Alternative Splicing-mediated Upregulation of CCN2

TGF-{beta} stimulates CCN2 expression which in turn amplifies TGF-{beta} signaling. This process promotes extracellular matrix production and accelerates the pathological progression of fibrotic diseases. Alternative splicing plays an important role in multiple disease development, while U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an essential factor in the early steps of pre-mRNA splicing. However, the molecular mechanism underlying abnormal CCN2 expression upon TGF-{beta} stimulation remains unclear. This study elucidates that SIRT4 acts as a master regulator for CCN2 expression in response to TGF-{beta} by modulating U2AF2-mediated alternative splicing. Analyses of renal biopsy specimens from patients with CKD and mouse fibrotic kidney tissues revealed marked nuclear accumulation of SIRT4. The tubulointerstitial fibrosis was alleviated by global deletion or tubular epithelial cell (TEC)-specific knockout of Sirt4, and aggravated by adeno-associated virus-mediated SIRT4 overexpression in TECs. Furthermore, SIRT4 was found to translocate from the mitochondria to the cytoplasm through the BAX/BAK pore under TGF-{beta} stimulation. In the cytoplasm, TGF-{beta} activated the ERK pathway and induced the phosphorylation of SIRT4 at Ser36, which further promoted its interaction with importin 1 and subsequent nuclear translocation. In the nucleus, SIRT4 was found to deacetylate U2AF2 at K413, facilitating the splicing of CCN2 pre-mRNA to promote CCN2 protein expression. Importantly, exosomes containing anti-SIRT4 antibodies were found to effectively mitigate the UUO-induced kidney fibrosis in mice. Collectively, these findings indicated that SIRT4 plays a role in kidney fibrosis by regulating CCN2 expression via the pre-mRNA splicing.

molecular biology↗

bioRxiv2024

Cell rearrangement progression along the apical-basal axis is linked with 3D epithelial tissue structure

Epithelial tissues undergo extensive structural remodeling during embryonic development. Tissue remodeling is often enabled by oriented cell rearrangements that are linked with patterns of mechanical stress in the tissue and with tissue mechanical properties. Cell rearrangements and their links to tissue structure have largely been studied at the apical side of tissues at the level of adherens junctions. Less is known about the involvement of basolateral domains in cell rearrangements. Here we use live confocal imaging to quantify cell rearrangements, cell packing structure, and cell morphology in 3D in the converging and extending Drosophila germband epithelium. We report gradients in cell shapes and tissue structure along the apical-basal axis of the germband, suggesting that the apical and basolateral domains display distinct behaviors. Cell rearrangements initiate at apical as well as basolateral positions, with initiation frequencies also displaying a gradient along the apical-basal axis. Following initiation, rearrangements propagate across the apical-basal axis and lateral cell contacts remodel; these events involve scutoids and other complex 3D cell shapes as intermediate states. These findings uncover novel aspects of the cell rearrangements that drive dynamic remodeling of epithelia and reveal links between rearrangements and gradients in tissue structure along the apical-basal axis.

developmental biology↗

bioRxiv2024

Mechanisms Of Meristem Maintenance By Maize Transcriptional Corepressors

The formation of the plant body proceeds in a sequential post-embryonic manner through the action of meristems. Tightly coordinated meristem regulation is required for development and reproductive success, eventually determining yield in crop species. In maize, the REL2 family of transcriptional corepressors includes four members, REL2, RELK1 (REL2-LIKE1), RELK2, and RELK3. In a screen for rel2 enhancers, we identified shorter double mutants with enlarged female inflorescence meristems (IMs) carrying mutations in RELK1. Expression and genetic analysis indicate that REL2 and RELK1 cooperatively regulate female IM development by controlling genes involved in redox balance, hormone homeostasis, and differentiation, ultimately tipping the meristem toward an environment favorable to expanded expression of the ZmWUSCHEL1 gene, a key stem-cell promoting transcription factor. We further demonstrate that RELK genes have partially redundant yet diverse functions in the maintenance of various meristem types during development. By exploiting subtle increases in ear IM size in rel2 heterozygous plants, we also show that extra rows of kernels are formed across a diverse set of F1 hybrids. Our findings reveal that the REL2 family maintains development from embryonic initiation to reproductive growth and can potentially be harnessed for increasing seed yield in a major crop species. One sentence summaryREL2-RELKs fine tune hormone and chemical cues to prevent expanded expression of ZmWUSCHEL1 in maize inflorescence meristems, and can potentially be harnessed for increasing seed yield in hybrids.

plant biology↗

bioRxiv2024

xSiGra: Explainable model for single-cell spatial data elucidation

Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multi-channel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multi-modal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of Grad-CAM component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within the complex cellular communications.

bioinformatics↗

bioRxiv2024

Evaluation of Inducible Gene Expression Systems for Beet Cyst Nematode Infection Assays in Arabidopsis thaliana

Cyst nematodes co-opt plant developmental programs for the establishment of a permanent feeding site called a syncytium in plant roots. In recent years, the role of plant developmental genes in syncytium formation has gained much attention. One main obstacle in studying the function of development-related genes in syncytium formation is that mutation or ectopic expression of such genes can cause pleiotropic phenotypes making it difficult to interpret nematode-related phenotypes, or in some cases, impossible to carry out infection assays due to aberrant root development. Here, we tested three commonly used inducible gene expression systems for their application in beet cyst nematode infection assays of the model plant Arabidopsis thaliana. We found that even a low amount of ethanol diminished nematode development, deeming the ethanol-based system unsuitable for use in cyst nematode infection assays; whereas treatment with estradiol or dexamethasone did not negatively affect cyst nematode viability. Dose and time course responses showed that in both systems, a relatively low dose of inducer (1 M) is sufficient to induce high transgene expression within 24 hours of treatment. Transgene expression peaked at 3-5 days post induction and began to decline thereafter, providing a perfect window for inducible transgenes to interfere with syncytium establishment while minimizing any adverse effects on root development. These results indicate that both estradiol- and dexamethasone-based inducible gene expression systems are suitable for cyst nematode infection assays. The employment of such systems provides a powerful tool to investigate the function of development essential plant genes in syncytium formation.

plant biology↗

bioRxiv2024

Engineering PEG10 assembled endogenous virus-like particles with genetically encoded neoantigen peptides for cancer vaccination

Tumor neoantigen peptide vaccines hold potential for boosting cancer immunotherapy, yet efficiently co-delivering peptides and adjuvants to antigen-presenting cells in vivo remains challenging. Virus-like particle (VLP), which is a kind of multiprotein structure organized as virus, can deliver therapeutic substances into cells and stimulate immune response. However, the weak targeted delivery of VLP in vivo and its susceptibility to neutralization by antibodies hinder their clinical applications. Here, we firstly designed a novel protein carrier using the mammalian-derived capsid protein PEG10, which can self-assemble into endogenous VLP (eVLP) with high protein loading and transfection efficiency. Then, an engineered tumor vaccine, named ePAC, was developed by packaging genetically encoded neoantigen into eVLP with further modification of CpG-ODN on its surface to serve as an adjuvant and targeting unit to dendritic cells (DCs). Significantly, ePAC can efficiently target and transport neoantigens to DCs, and promote DCs maturation to induce neoantigen-specific T cells. Moreover, in mouse orthotopic liver cancer and humanized mouse tumor models, ePAC combined with anti-TIM-3 exhibited remarkable antitumor efficacy. Overall, these results support that ePAC could be safely utilized as cancer vaccines for antitumor therapy, showing significant potential for clinical translation.

cancer biology↗

bioRxiv2024

Comprehensive analysis across mammalian tissues and cells decipher the underlying mechanism of m6A specificity

N6-methyladenine (m6A) stands out as the most prevalent internal chemical modification on mammalian mRNA, playing a vital role in diverse biological processes. Despite considerable advancements in individual cell line studies, the characteristics of m6A sites across distinct cell lines or tissues remain elusive. In this study, we have successfully identified approximately 1.5 million high-confidence m6A sites in human and mouse cell lines or tissues using published m6A-seq data. By categorizing m6A sites into different consistency levels, we observe that those of high consistency are notably enriched near the stop codon. Furthermore, they exhibit a higher likelihood of interaction with known m6A binding proteins such as YTHDF1-3, RBM15, YTHDC1, and IGF2BP1, thereby influencing gene expression homeostasis. Additionally, these sites display a higher CpG density in the promoter region of the genes they mark, with METTL3 demonstrating a preference for binding to the promoter region of its marked genes. m6A sites of low consistency levels, including unique m6A sites, show a significant enrichment near the start codon. These sites are more prone to binding by newly discovered m6A-binding proteins such as DDX3X, PRPF8, and EIF3G. The identification of these distinct features of m6A sites lays a foundational understanding for unraveling the functional roles of m6A.

bioinformatics↗

bioRxiv2024

Time-resolved function of cell polarity kinases PRKCZ and PRKCI in CNS myelination

The atypical Protein Kinase C (aPKC) is a critical component of the PAR polarity complex, as well as of cell polarity in general. There are two paralogs of aPKC in the mammalian genome. Their expression pattern and functional role in oligodendrocyte lineage differentiation and development remains heretofore uncharacterized. Here we show that both paralogs of aPKC - PRKCI, the primary transcript of Prkci and PKMz, an alternate transcript of Prkcz - are expressed during oligodendrocyte differentiation, yet are functionally non-redundant. Asymmetric cell division and early specification of the oligodendrocyte fate stage required both paralogs. By contrast, the stage of oligodendrocyte maturation involving membrane polarization and myelination of axons continued to require PKMz, but no longer needed PRKCI. Taken together, our results indicate to a two-stage role of aPKCs and cell polarity in oligodendrocyte differentiation and development.

developmental biology↗

bioRxiv2024

The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modifications in vivo

Cre-loxP technology, a cornerstone in fate mapping and in vivo gene function studies, faces challenges in achieving precise and efficient conditional mutagenesis through inducible systems. This study introduces two innovative genetic tools designed to overcome these limitations. The first, roxCre, enables DreER-mediated Cre release, paving the way for intersectional genetic manipulation that permits increased precision and efficiency. The second, loxCre, facilitates conditional gene targeting by allowing CreER lines to induce Cre expression with significantly enhanced efficiency. These tools incorporate a fluorescent reporter for genetic lineage tracing, simultaneously revealing efficient gene knockout in cells marked by the reporter. These strategies hold great potential for precise and efficient exploration of lineage-specific gene functions, marking a significant advancement in genetic research methodologies.

genetics↗

bioRxiv2024

Matrix Vesicles from Osteoblasts Promote Atherosclerotic Calcification

BackgroundsVascular calcification often occurs with osteoporosis, a contradictory association known as "the calcification paradox". Osteoblast-derived matrix vesicles (Ost-MVs) have been implicated in bone mineralization, and also have a potential role in ectopic vascular calcification. Herein, we aim to investigate the contributions that Ost-MVs make to the bone-vascular calcification paradox and the underlying mechanisms. Methods and ResultsHyperlipidemia-induced atherosclerotic calcification in mice was accompanied with bone mineral loss, as evidenced by reduced deposition of Ost-MVs in the bone matrix and increased release of Ost-MVs into the circulation. Intravenous injection of fluorescent DiI-labeled Ost-MVs revealed a marked fluorescence accumulation in the aorta of atherogenic mice, whereas no fluorescence signals were observed in normal controls. Using proteomics to analyze proteins in non-matrix bound Ost-MVs and mineralized SMC-derived MVs (SMC-MVs), we found Lamp1 was specifically expressed in SMC-MVs, and Nid2 was exclusively expressed in Ost-MVs. We further demonstrated that both Lamp1 and Nid2 were co-localized with Collagen I within calcific plaques, indicating the involvement of both Ost-MVs and SMC-MVs in atherosclerotic calcification. Mechanistically, LPS-induced vascular injury facilitated the transendothelial transport of Ost-MVs. The recruitment of circulating Ost-MVs was regulated by remodeled Collagen I during calcification progression. Furthermore, the phenotypic transition of SMCs determined the endocytosis of Ost-MVs. Finally, we demonstrated that either recruited Ost-MVs or resident SMC-MVs accelerated atherosclerotic calcification, depending on the Ras-Raf-ERK signaling. ConclusionAtherosclerotic calcification-induced Ost-MVs are released into circulation, facilitating the transport from bone to plaque lesions and exacerbating artery calcification progression. The mechanisms of Ost-MVs recruitment include vascular injury allowing transendothelial transport of Ost-MVs, collagen I remodeling promoting Ost-MVs aggregation, and SMC phenotypic switch to facilitate Ost-MVs uptake. Our results further revealed that both recruited Ost-MVs and calcifying SMC-MVs aggravate calcification through the Ras-Raf-ERK pathway.

cell biology↗

bioRxiv2024

Cure or Curse? Simulation Indicates that Microbes Proliferate under Disinfection Measures in the Space Station

The long-term stay on the space station requirement poses a knotty issue about the stable hardware and reliable guarantee of astronauts health. Despite regular cleaning with wipes, microbes still proliferate in the space station. This study distilled three key factors--low-dose ionizing radiation, dilution and quaternary ammonium compound from the scenario. Species abundance and differential metabolites were applied to test their sole/combined influences on the three-simple-species microbial community succession. Mechanisms were built in mathematical models to generate the structural and behavior similarity. Results showed that LDIR, dilution and QAC, solely or jointly, could contribute to microbial proliferation. The synergy of disturbances might convert them from harmful factors to rewarding ones (e.g. the transformation of QAC into nutrients under LDIR), leading to this "Ecological Surprise". These results shed light on mechanisms driving microbial community succession in the space station and highlight the need for tailored biocontrol strategies in the specific environment.

ecology↗

bioRxiv2024

Calneuron 1 reveals the pivotal roles in schizophrenia via perturbing human forebrain development and causing hallucination-like behavior in mice

Schizophrenia is a highly heritable neurodevelopmental disorder with unknown genetic pathogenic mechanisms. Here, we selected 11 schizophrenia risk genes and generated single-gene-knockout-precise-dorsal/ventral-forebrain-organoids (SKOPOS) via CRISPR-Cas9 system. 90 bulk and 249,430 single-cell RNA-sequencing of SKOPOS revealed that knockout of 11 risk genes lead to different levels of deficits in dorsal/ventral forebrain organoids. Among them, calneuron 1 (CALN1) acts as a pivotal pathogenic gene of schizophrenia via severe disruption of gene expression network, interaction with about 32% (34/106) known schizophrenia risk genes, delayed maturation and impaired spontaneous neural circuit in human developing forebrain. Furtherly, including the spontaneous abrupt burst spiking in cortical neurons and the defects of spatial memory, cognition and social ability, Caln1 KO mice surprisingly displayed spontaneous startle behavior and head-twitch response correlated with hallucination-like behavior, which could be inhibited by antipsychotic drug SEP-363856. In summary, CALN1 is identified as a pivotal pathogenic gene of schizophrenia in forebrain development.

neuroscience↗

bioRxiv2024

TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics

Top-down mass spectrometry is widely used for proteoform identification, characterization, and quantification owing to its ability to analyze intact proteoforms. In the last decade, top-down proteomics has been dominated by top-down data-dependent acquisition mass spectrometry (TD-DDA-MS), and top-down data-independent acquisition mass spectrometry (TD-DIA-MS) has not been well studied. While TD-DIA-MS produces complex multiplexed tandem mass spectrometry (MS/MS) spectra, which are challenging to confidently identify, it selects more precursor ions for MS/MS analysis and has the potential to increase proteoform identifications compared with TD-DDA-MS. Here we present TopDIA, the first software tool for proteoform identification by TD-DIA-MS. It generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data and then searches the pseudo MS/MS spectra against a protein sequence database for proteoform identification. We compared the performance of TD-DDA-MS and TD-DIA-MS using Escherichia coli K-12 MG1655 cells and demonstrated that TD-DIA-MS with TopDIA increased proteoform and protein identifications compared with TD-DDA-MS.

bioinformatics↗

bioRxiv2024

The fascinating role of neuropeptide Bursicon and its receptor in shaping insect seasonal polyphenism

Seasonal polyphenism enables organisms to adapt to environmental challenges by increasing phenotypic diversity. Cacopsylla chinensis exhibits remarkable seasonal polyphenism, specifically in the form of summer-form and winter-form, which have distinct morphological phenotypes. Previous research has shown that low temperature and the temperature receptor CcTRPM regulate the transition from summer-form to winter-form in C. chinensis by impacting cuticle content and thickness. However, the underling neuroendocrine regulatory mechanism remains largely unknown. Bursicon, also known as the tanning hormone, is responsible for the hardening and darkening of the insect cuticle. In this study, we report for the first time on the novel function of Bursicon and its receptor in the transition from summer-form to winter-form in C. chinensis. Firstly, we identified CcBurs- and CcBurs-{beta} as two typical subunits of Bursicon in C. chinensis, which were regulated by low temperature (10{degrees}C) and CcTRPM. Subsequently, CcBurs- and CcBurs-{beta} formed a heterodimer that mediated the transition from summer-form to winter-form by influencing the cuticle chitin contents and cuticle thickness. Furthermore, we demonstrated that CcBurs-R acts as the Bursicon receptor and plays a critical role in the up-stream signaling of the chitin biosyntheis pathway, regulating the transition from summer-form to winter-form. Finally, we discovered that miR-6012 directly targets CcBurs-R, contributing to the regulation of Bursicon signaling in the seasonal polyphenism of C. chinensis. In summary, these findings reveal the novel function of neuroendocrine regulatory mechanism underlying seasonal polyphenism and provide critical insights into insect Bursicon and its receptor.

ecology↗