Biology subjects

Qian, Y.

Publications and source records attributed to Qian, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

RNA-programmable cell type monitoring and manipulation in the human cortex with CellREADR

Reliable and systematic access to diverse cell types is necessary for understanding the organization, function, and pathophysiology of human neural circuits. Methods for targeting human neural populations are scarce and currently center on identifying transcriptional enhancers and engineering viral capsids. Here we demonstrate the utility of CellREADR, a programmable RNA sensor-effector technology that couples cellular RNA sensing to effector protein translation, for accessing, monitoring, and manipulating specific neuron types in human cortex, ex vivo. We designed CellREADRs to target two subpopulations, CALB2 GABAergic interneurons and FOXP2 glutamatergic projection neurons, then validated targeting specificity using histological, electrophysiological, and transcriptomic methods. CellREADR expression of channelrhodopsin and GCamp enabled the manipulation and monitoring of these populations in live cortical microcircuits. By demonstrating specific, reliable, and programmable experimental access to human neuronal subpopulations, our results highlight CellREADRs potential for studying neural circuits and treating brain disorders.

neuroscience↗

bioRxiv2024

RNA programmable cell targeting and manipulation with CellREADR

Methods that provide specific, easy, and scalable experimental access to animal cell types and cell states will have broad applications in biology and medicine. CellREADR - Cell access through RNA sensing by Endogenous ADAR (adenosine deaminase acting on RNA), is a programmable RNA sensor-actuator technology that couples the detection of a cell-defining RNA to the translation of an effector protein to monitor and manipulate the cell. The CellREADR RNA device consists of a 5 sensor region complementary to a cellular RNA and a 3 payload coding region; payload translation is gated by the removal of a STOP codon in the sensor region upon base pairing with the cognate cellular RNA through an ADAR-mediated A- to-I editing mechanism ubiquitous to metazoan cells. CellREADR thus highlights the potential for RNA-based monitoring and manipulation of animal cells in ways that are simple, versatile, and generalizable across tissues and species. Here, we describe a detailed protocol for implementing CellREADR experiments in cell cultures and in animals. The procedure includes sensor and payload design, cloning, validation and characterization in mammalian cell cultures. The in vivo animal protocol focuses on AAV-based delivery of CellREADR using brain tissue as examples. We describe current best practices, various experimental controls and trouble-shooting steps. Beginning from sensor design, the validation of RNA sensor-actuators in cell cultures can be completed in 2-3 weeks. The construction of AAV vectors and their in vivo validation and characterization will take additional 6-8 weeks.

molecular biology↗

bioRxiv2024

Loss of PI3Kδ activity drives autoimmune colitis by impairing extrathymic Treg differentiation

Peripherally-derived regulatory T cells (pTregs) have a prominent role in maintaining intestinal immune homeostasis. In cases of phosphoinositide-3-kinase {delta} (PI3K{delta}) inactivation, such as in patients receiving PI3K{delta} inhibitor idelalisib as a cancer treatment, breakdown of intestinal immune tolerance occurs frequently in the form of diarrhoea and colon inflammation. In a mouse model of systemic PI3K{delta} inactivation, both enhancement of anti-tumor immunity and colitis have been described, as a result of Treg impairment. However, in view of the critical role for Tregs in the prevention of systemic autoimmunity, the basis for such tissue-restricted breach of immune tolerance upon loss of PI3K{delta} function is not yet understood. We report here that mice lacking PI3K{delta} activity do not suffer a general defect in Treg immunosuppression, but specifically fail to develop Helios- pTregs in the colon. We demonstrate reduced extrathymic Treg induction, in vitro and in vivo, from naive CD4+ T cells with inactive PI3K{delta}, along with dysregulation of a tissue-resident phenotype. These results suggest a non-redundant role for PI3K{delta}-dependent pTreg differentiation in maintaining tolerance to commensal microbial antigens in the gut.

immunology↗

bioRxiv2024

LP-Micro Offers Interpretable Disease Outcome Prediction by Leveraging Microbial Biomarkers and Their Time-Varying Effects

Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.

bioinformatics↗

bioRxiv2024

GlycoRNA-L and glycoRNA-S mediate human monocyte adhesion via binding to Siglec-5

It was recently reported that RNAs can be glycosylated, and a majority of such glycosylated RNAs (referred to as glycoRNAs) are located on the outer cell surface. We here reported that there are two forms of glycoRNAs, named as glycoRNA-L and glycoRNA-S, robustly expressed in human monocytes. Both of glycoRNA-L and glycoRNA-S contributed to the interaction of human monocytes and endothelial cells via directly binding to Siglec-5. GlycoRNA-L predominantly expressed in most of tissues and cell lines. GlycoRNA-S only expressed in some cell lines and tissues. Siglec-5 preferentially binds to glycoRNA-L than glycoRNA-S. The composition of glycan chains in glycoRNA-L and glycoRNA-S is different. GlycoRNA-L contains more sialic acid, whereas glycoRNA-S contains more GlcNAc. Together, these results demonstrate that two forms of glycoRNAs exist, which may play significant role in controlling the interaction of human monocytes and endothelial cells and contribute to the pathogenesis of inflammatory diseases.

cell biology↗

bioRxiv2024

Orally surface engineered probiotic system for ulcerative colitis therapy via modulating gut microbiota and immune homeostasis

Oral probiotics have emerged as a promising therapeutical strategy for effectively managing ulcerative colitis (UC) in the world. The existing researches successfully preserve probiotic viability in the upper gastrointestinal tract, but they fall short in achieving precise release profile and effective colonization of probiotics at the site of colitis in colon as well as the understanding of therapeutic mechanism with suboptimal efficacy. This constraint poses a significant barrier to rational design and effective development of oral probiotic system. Here, we fabricate an orally layered-by-layered probiotic (Escherichia coli Nissle 1917, EcN) system (so-called CML@EcN) based on carboxymethyl modified lignin (CML) which can significantly protect EcN in gastric and small intestinal microenvironment and efficiently control release EcN in colon. Interestingly, the release and proliferation process of EcN in the colon are detected and can be modeled as a plug-flow mode. We derive a mathematical expression that highly matches the experimental results, providing a theoretical basis for quantitatively calculation of the release process. Furthermore, CML@EcN significantly alleviates symptoms in dextran sulfate sodium (DSS)-induced UC mice by modulating the multiple organ immune disorder and gut microbiota (GM)/metabolites profile as well as reconstructing the colon barrier. Importantly, we explore the mechanism of immune homeostasis regulation via metabolism from GM. Moreover, the CML armour is excreted and would not influence the process. This work not only reports a novel oral therapeutic for UC treatment with high efficacy as well as the exploration of mechanism between GM and immune homeostasis, but also provides a general approach to engineer probiotics for oral administration.

microbiology↗

bioRxiv2024

Exploring potential targets for quercetin treatment of colorectal cancer through network pharmacology and molecular docking technology

ObjectiveTo explore the potential targets of quercetin in the treatment of colorectal cancer through network pharmacology and molecular docking technology. MethodDownload the 3D structure of quercetin from Pubchem database, use PharmaMapper database for reverse docking, and screen protein targets based on zscore; GEO database screening for colorectal cancer datasets and screening for differentially expressed genes; Screening common genes for protein targets and differentially expressed genes using Wayne diagrams; Use DAVID database for GO and KEGG analysis. Use ChemDraw, 20.0 AutoDock, and Pymol for molecular docking. ResultThe results showed that 24 common genes and 13 signaling pathways were identified from the reverse docking data of quercetin and the GSE33113 gene chip data of colorectal cancer; Molecular docking results showed that quercetin showed good binding energy with 1ykc, 1k3y, 1kbq, 2bkz, 1xo2, 1og5, 2bsm. ConclusionQuercetin may exert its therapeutic effect on colorectal cancer through a multi target and multi channel mechanism.

pharmacology and toxicology↗

bioRxiv2024

Exploring the Mechanism of Gentiana in Treating Pancreatic Cancer Based on Network Pharmacology and Molecular Docking Techniques

ObjectiveThis study aims to investigate the mechanism of Gentiana in treating pancreatic cancer using network pharmacology and molecular docking techniques. MethodsActive compounds of Gentiana were screened from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The 3D structures of the active compounds were downloaded from the PubChem database. Reverse docking was performed using the PharmMapper database to identify potential target proteins. Differential gene expression data related to colorectal cancer were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes were selected. Venn diagram analysis was employed to identify common genes between the protein targets and differentially expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) tool. Molecular docking was performed using ChemDraw 20.0, AutoDock, and PyMOL. ResultsA total of 72 common genes and 15 signaling pathways were identified from the reverse docking data of Gentiana and the pancreatic cancer dataset (GSE196009). Molecular docking results demonstrated favorable binding energies between the active compounds of Gentiana and proteins 1og5, 1pq2, 2bxr, 2bk3, 1u3w, 1wma, 1wuu, 1tdi, 1mlw, 1egc, 1s1p, 1f12, 1m51, 1kqu, 1ls6, 1ry0, 1nhx, and 1db4. ConclusionGentiana may exert its therapeutic effects on pancreatic cancer through a multi-component, multi-target, and multi-pathway mechanism.

pharmacology and toxicology↗

bioRxiv2024

Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile

Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile, offering key insights for developing anti-C. difficile strategies.

systems biology↗

bioRxiv2024

A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome

The T6SS of Pseudomonas aeruginosa plays an essential role in the establishment of chronic infections. Inflammatory cytokines mediated by inflammasomes are crucial for the body to resist bacterial infections. Here we found that during the infection of P. aeruginosa, non-canonical inflammasome was activated in macrophages, but the activation of downstream NLRP3 inflammasome was inhibited. The VgrG2b of P. aeruginosa is recognized and cleaved by caspase-11, generating a free C-terminal fragment. The VgrG2b C-terminus can bind to NLRP3, inhibiting the activation of the NLRP3 inflammasome by rejecting NEK7 binding to NLRP3. Administrating a specific peptide that inhibits the cleavage of VgrG2b by caspase-11 to mice can significantly improve their survival rate during infection. Our discovery elucidates a mechanism by which P. aeruginosa inhibits host immune response, providing a new approach for the future clinical treatment of P. aeruginosa infections.

immunology↗

bioRxiv2024

Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy

BackgroundTransmission electron microscopy (TEM) images can visualize kidney glomerular filtration barrier ultrastructure, including the glomerular basement membrane (GBM) and podocyte foot processes (PFP). Podocytopathy is associated with glomerular filtration barrier morphological changes observed experimentally and clinically by measuring GBM or PFP width. However, these measurements are currently performed manually. This limits research on podocytopathy disease mechanisms and therapeutics due to labor intensiveness and inter-operator variability. MethodsWe developed a deep learning-based digital pathology computational method to measure GBM and PFP width in TEM images from the kidneys of Integrin-Linked Kinase (ILK) podocyte-specific conditional knockout (cKO) mouse, an animal model of podocytopathy, compared to wild-type (WT) control mouse. We obtained TEM images from WT and ILK cKO littermate mice at 4 weeks old. Our automated method was composed of two stages: a U-Net model for GBM segmentation, followed by an image processing algorithm for GBM and PFP width measurement. We evaluated its performance with a 4-fold cross-validation study on WT and ILK cKO mouse kidney pairs. ResultsMean (95% confidence interval) GBM segmentation accuracy, calculated as Jaccard index, was 0.73 (0.70-0.76) for WT and 0.85 (0.83-0.87) for ILK cKO TEM images. Automated and manual GBM width measurements were similar for both WT (p=0.49) and ILK cKO (p=0.06) specimens. While automated and manual PFP width measurements were similar for WT (p=0.89), they differed for ILK cKO (p<0.05) specimens. WT and ILK cKO specimens were morphologically distinguishable by manual GBM (p<0.05) and PFP (p<0.05) width measurements. This phenotypic difference was reflected in the automated GBM (p<0.05) more than PFP (p=0.06) widths. ConclusionsThese results suggest that certain automated measurements enabled via deep learning-based digital pathology tools could distinguish healthy kidneys from those with podocytopathy. Our proposed method provides high-throughput, objective morphological analysis and could facilitate podocytopathy research and translate into clinical diagnosis. Key pointsO_LIWe leveraged U-Net architecture in an algorithm to measure the widths of glomerular basement membrane and podocyte foot processes. C_LIO_LIDeep learning-based automated measurement of glomerular filtration barrier morphology has promise in podocytopathy research and diagnosis. C_LI

pathology↗

bioRxiv2024

Therapeutic expression of RAS Degrader RRSP in Pancreatic Cancer via Nanocarrier-mediated mRNA delivery

Therapeutic gene expression can address many of the challenges associated with the controlled delivery of intracellularly active biologics, such as enzymes that degrade RAS for treatment of RAS-driven cancers. Here, we demonstrate that an optimized synthetic nonviral gene delivery platform composed of poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-PPS) can block copolymers conjugated to a dendritic cationic peptide (PPDP2) for nontoxic delivery and therapeutic expression of mRNA within human pancreatic cancer cells and tumors. The naturally occurring bacterial enzyme RAS/RAP1-specific endopeptidase (RRSP) is a potent RAS degrader that specifically targets all RAS isoforms. Using PPDP2, rrsp-mRNA is delivered to human pancreatic cells resulting in RRSP protein expression, degradation of RAS, and loss of cell proliferation. Further, pancreatic tumors are reduced with residual tumors lacking detectable RAS and phosphorylated ERK. Using structural modeling, we further demonstrate that a noncatalytic RAS-binding domain of RRSP provides high specificity for RAS. These data support that the synthetic nanocarrier PPDP2 can deliver rrsp-mRNA to pancreatic tumor cells to interrupt the RAS signaling system.

cancer biology↗

bioRxiv2024

Molecular mechanism of the flotillin complex in membrane microdomain organization

Flotillin-1 and flotillin-2 form hetero-oligomers to create flotillin membrane microdomains essential for endocytosis and protein sorting. However, the mechanisms of flotillin oligomerization and microdomain organization remain incompletely understood. Here, we present the cryo-EM structure of human flotillin complex, showing that flotillin-1 and -2 form a 44-mer, membrane attached, and dome-shaped structure that defines a 30-nm circular membrane domain. The cryo-ET data demonstrates that while attached to the cytoplasmic leaflet in situ, flotillin complexes possess intrinsic structural plasticity on the native membrane. Each flotillin complex may represent a fundamental unit of membrane microdomains, with their clustering enabling the formation of larger and more elaborate domains. We further reveal that phosphorylation at residues Y160 (flotillin-1) and Y163 (flotillin-2) may act as a molecular switch to modulate complex assembly, potentially regulating its function in endocytosis. These findings demonstrate the molecular mechanism of flotillin-mediated membrane segregation and microdomain formation, and suggest a previously unrecognized role of flotillin in sequestrating membrane proteins.

biochemistry↗

bioRxiv2024

DeepGene: An Efficient Foundation Model for Genomics based on Pan-genome Graph Transformer

Decoding the language of DNA sequences is a fundamental problem in genome research. Mainstream pre-trained models like DNABERT-2 and Nucleotide Transformer have demonstrated remarkable achievements across a spectrum of DNA analysis tasks. Yet, these models still face the pivotal challenge of (1) genetic language diversity, or the capability to capture genetic variations across individuals or populations in the foundation models; (2) model efficiency, specifically how to enhance performance at scalable costs for large-scale genetic foundational models; (3) length extrapolation, or the ability to accurately interpret sequences ranging from short to long within a unified model framework. In response, we introduce DeepGene, a model leveraging Pan-genome and Minigraph representations to encompass the broad diversity of genetic language. DeepGene employs the rotary position embedding to improve the length extrapolation in various genetic analysis tasks. On the 28 tasks in Genome Understanding Evaluation, DeepGene reaches the top position in 9 tasks, second in 5, and achieves the overall best score. DeepGene outperforms other cutting-edge models for its compact model size and superior efficiency in processing sequences of varying lengths. The datasets and source code of DeepGene are available at GitHub (https://github.com/wds-seu/DeepGene).

bioinformatics↗

bioRxiv2024

Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

5-Methylcytosine (m5C) is one of the post-transcriptional modifications in mRNA and is involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we develop a detection method named DRAM (deaminase and reader protein assisted RNA methylation analysis), in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available BS-seq datasets and allows for a more stable and comprehensive identification of the m5C loci. In addition, DRAM system even supports ultra-low input RNA (10ng). We anticipate that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.

biochemistry↗

bioRxiv2024

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

The human gut pathogen Clostridioides difficile displays extreme genetic variability and confronts a changeable nutrient landscape in the gut. We mapped gut microbiota inter-species interactions impacting the growth and toxin production of diverse C. difficile strains in different nutrient environments. Although negative interactions impacting C. difficile are prevalent in environments promoting resource competition, they are sparse in an environment containing C. difficile-preferred carbohydrates. C. difficile strains display differences in interactions with Clostridium scindens and the ability to compete for proline. C. difficile toxin production displays substantial community-context dependent variation and does not trend with growth-mediated inter-species interactions. C. difficile shows substantial differences in transcriptional profiles in the presence of the closely related species C. hiranonis or C. scindens. In co-culture with C. hiranonis, C. difficile exhibits massive alterations in metabolism and other cellular processes, consistent with their high metabolic overlap. Further, Clostridium hiranonis inhibits the growth and toxin production of diverse C. difficile strains across different nutrient environments and ameliorates the disease severity of a C. difficile challenge in a murine model. In sum, strain-level variability and nutrient environments are major variables shaping gut microbiota interactions with C. difficile.

systems biology↗

bioRxiv2024

The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector

The regulatory mechanisms governing cell fate determination, particularly lineage diversification during mammalian embryonic development, remain poorly understood with in-depth regulatory paradigms yet to be fully elucidated. Here, leveraging the epigenetic landscape of mouse gastrula, we identified p-Enh, a pre-marked enhancer in primitive streak region, as pivotal regulator for posterior tissue development in mouse embryos. Morphological and single-cell transcriptomic analyses confirmed embryonic lethality phenotype with disrupted posterior tissue development trajectories in p-Enh-KO embryos. Molecularly, apart from regulating the neighboring coding-gene Cdx2 in cis, our findings suggest that p-Enh also modulate the global transcriptome and epigenomic landscape, which might through the transient production of eRNA in trans. Further investigation revealed p-Enh participate in the regulatory cascades of TGF-{beta} signaling. Chemical modulation of TGF-{beta} signaling can largely rescue the posterior development deficiency in in vitro gastruloids through a Cdx2-independent mechanism. Thus, we propose a potential model in which the broadly distributed p-Enh transcripts within the nucleus could serve as essential cross-modular coordinators, priming the posterior development of mouse embryo.

developmental biology↗

bioRxiv2024

UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank

Summary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while minimizing the risk of compromising individual-level data privacy. However, these summary statistics, such as those from the UK Biobank (UKB) provided by Neales lab, are often adjusted by a fixed set of covariates to all traits (12 covariates including 10 PCs, sex and age), preventing the exploration of trait-specific summary statistics. In this study, we present a novel computational device UK BioCoin (UKC), which is designed to provide an efficient framework for trait-specific adjustment for covariates. Without requiring access to individual-level data from UKB, UKC leverages summary statistics regression technique and resources from UKB (289 GB of 199 phenotypes and 10 million SNPs), to enable the generation of GWAS summary statistics adjusted by user-specified covariates. Through a comprehensive analysis of height under trait-specific adjustments, we demonstrate that the GWAS summary statistics generated by UKC closely mirror those generated from individual-level UKB GWAS ({rho} [≥] 0.99 for effect sizes and{rho} [≥] 0.99 for p-values). Furthermore, we demonstrate the results for GWAS, SNP-heritability estimation, polygenic score, and Mendelian randomization, after various trait-specific covariate adjustments as allowed by UKC, indicating UKC a platform that harnesses in-depth exploration for researchers lacking access to UKB. The whole framework of UKC is portable for other biobank, as demonstrated in Westlake Biobank, which can equivalently be converted to a UKC-like" platform and promote data sharing. UKC has its computational engine fully optimized, and the computational efficiency of UKC is about 70 times faster than that of UKB. We package UKC as a Docker image of 20 GB (https://github.com/Ttttt47/UKBioCoin), which can be easily deployed on an average computer (e.g. laptop). One sentence summaryWe develop UK BioCoin (UKC), which allows fine-tuning of covariates for each UK Biobank trait but does not relay on UK Biobank individual-level data. It will change the current landscape of GWAS and reshape its downstream analyses.

genetics↗