Biology subjects

Qiao, L.

Publications and source records attributed to Qiao, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Integrating multi-modal transcriptomics identifies cellular subtypes with distinct roles in PDAC progression

BackgroundPancreatic ductal adenocarcinoma (PDAC) features a complex tumor microenvironment (TME) that significantly influences patient outcomes. Understanding the TMEs cellular composition and interactions is crucial for identifying therapeutic targets to improve treatment. MethodsWe performed an integrative analysis combining 88 single-cell RNA sequencing (scRNA-seq) samples with 187,520 cells, 20 Visium spatial transcriptomics (ST-seq) samples with 67,933 spots, and 1383 bulk RNA-seq samples and 2 Xenium high-resolution ST-seq samples with 307,679 cells, to delineate and characterize distinct subpopulations of fibroblasts, macrophages, T/NK cells, and B/plasma cells within the PDAC microenvironment. Correlations among major cell types across 12 PDAC datasets were assessed through gene set variation analysis (GSVA). Kaplan-Meier survival analysis was used to evaluate the prognostic significance of cell subtypes. Furthermore, multiplex immunohistochemistry (mIHC) and the Xenium platform was utilized to validate cellular interactions in human PDAC tissues at both protein and RNA levels. ResultsSix fibroblast subtypes and eight macrophage/monocyte subtypes were identified. POSTN high fibroblasts and SPP1 high macrophages highly infiltrated tumor tissues and were associated with poor prognosis. Most immune cell subtypes mediate adverse prognoses, except for CCL4 high CD8+ T EFF cells and IGHG1 high plasma cells, which are linked to favorable outcomes. ST-seq revealed spatial colocalization of POSTN high Fibro and SPP1 high Macro cells, as well as CCL4 high CD8+ T EFF and IGHG1 high plasma cells. These findings were corroborated by mIHC and validated using Xenium spatial transcriptomics with single-cell resolution, which confirmed the expression and spatial proximity of these markers at both the gene and protein levels. ConclusionThis integrative analysis of the PDAC TME underscores the prognostic importance of POSTN high fibroblasts and SPP1 high macrophages, while also highlighting the protective roles of CCL4 high CD8+ T EFF cells and IGHG1 high plasma cells. These insights could improve PDAC treatment strategies.

cancer biology↗

bioRxiv2024

Increased versatility and convenience: advances and strategy optimization of ReMOT-mediated genetic modification in insects

Genetic modification via gene editing has become a widely adopted and demonstrably effective method in functional gene research within entomology. However, the optimal efficiency and simplicity of delivering exogenous guide RNA-clustered regularly interspaced short palindromic repeats-associated protein 9 (gRNA-Cas9) complexes into target tissues are crucial for successful gene editing. The Receptor-Mediated Ovary Transduction of Cargo (ReMOT) strategy, which simplifies the delivery process, target site selection, technical requirements, and delivery cost compared with embryonic microinjection, enabling efficient editing at the germline level, is gaining increasing attention. Although the feasibility and advantages of this technique have been demonstrated in various insect species, further optimization of operational details and the overcoming of further bottlenecks are still required. This review focuses on advances in developing ReMOT as a valuable technology, exploring its applicability, rationale for selecting the ovary as a delivery target site, factors influencing its efficiency, and recommendations for improvement. The versatility and effectiveness of ReMOT make it a promising method for researchers looking to make precise genetic modifications with greater ease and efficiency.

genetics↗

bioRxiv2024

Chromosome engineering to restore euploidy in cells harboring a complex rearrangement of chromosome 8

Chromosomal rearrangements on the short arm of Chromosome 8 cause 8p syndrome, a rare developmental disorder characterized by neurodevelopmental delays, epilepsy, and cardiac abnormalities. While significant progress has been made in managing the symptoms of 8p syndrome and other conditions caused by large-scale chromosomal aneuploidies, no therapeutic approach has yet been demonstrated to target the underlying disease-causing chromosome. Here, we establish a two-step approach to eliminate the abnormal copy of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute to 8p syndrome pathology. Furthermore, we demonstrate that the proband exhibits a significant defect in neural differentiation that could be partially rescued by treatment with small-molecule inhibitors of cell death. Our work demonstrates the feasibility of using chromosome engineering to correct complex aneuploidies in vitro and establishes a platform to further dissect the pathophysiology of 8p syndrome and other conditions caused by chromosomal rearrangements.

developmental biology↗

bioRxiv2024

Chromosome-scale assembly and annotation of the wildwheat relative Aegilops comosa

Wild relatives of wheat are valuable sources for enhancing the genetic diversity of common wheat. Aegilops comosa, an annual diploid species with an MM genome constitution, possesses numerous agronomically valuable traits that can be exploited for wheat improvement. In this study, we report a chromosome-level genome assembly of Ae. comosa accession PI 551049, generated using PacBio high-fidelity (HiFi) reads and high-throughput chromosome conformation capture (Hi-C) data. The assembly spans 4.47 Gb, featuring a contig N50 of 23.59 Mb and a scaffold N50 of 619.05 Mb. A total of 39,063 gene models were annotated through a combination of homoeologous proteins, Iso-Seq, and RNA-Seq data. Comparative genome analysis revealed a terminal intrachromosomal translocation in chromosome 2M of Ae. comosa (and Ae. umbellulata) compared to its homoeologous chromosomes in other diploid wheat species. Phylogenetic analysis showed a close relationship between Ae. comosa and Ae. umbellulata. This newly constructed reference genome of Ae. comosa will serve as an important genomic resource for comparative genomic studies and the cloning of agriculturally important genes.

genomics↗

bioRxiv2024

A sensitive red/far-red photoswitch for controllable gene therapy in mouse models of metabolic diseases

Red light optogenetic systems are in high demand for the precise control of gene expression for gene- and cell-based therapies. Here, we report a red/far-red light-inducible photoswitch (REDLIP) system based on the chimeric photosensory protein FnBphP (Fn-REDLIP) or PnBphP (Pn-REDLIP) and their interaction partner LDB3, which enables efficient dynamic regulation of gene expression with a timescale of seconds without exogenous administration of a chromophore in mammals. We used the REDLIP system to establish the REDLIP-mediated CRISPR-dCas9 (REDLIPcas) system, enabling optogenetic activation of endogenous target genes in mammalian cells and mice. The REDLIP system is small enough to support packaging into adeno-associated viruses (AAVs), facilitating its therapeutic application. Demonstrating its capacity to treat metabolic diseases, we show that an AAV-delivered Fn-REDLIP system achieved optogenetic control of insulin expression to effectively lower blood glucose levels in type 1 diabetes model mice and control an anti-obesity therapeutic protein (thymic stromal lymphopoietin, TSLP) to reduce body weight in obesity model mice. REDLIP is a compact and sensitive optogenetic tool for reversible and non-invasive control that can facilitate basic biological and biomedical research.

synthetic biology↗

bioRxiv2024

Quantitative site-specific glycoproteomics by ZenoTOF reveals glyco-signatures for breast cancer diagnosis

Intact glycopeptide characterization by mass spectrometry has proven a versatile tool for site-specific glycoproteomics analysis and biomarker screening. Here, we present a method using the ZenoTOF instrument with optimized fragmentation for intact glycopeptide identification and demonstrate its ability to analyze large-cohort glycoproteomes. From 124 clinical serum samples of breast cancer, non-cancerous diseases, and non-disease controls, a total of 6901 unique site-specific glycans on 807 gly-cosites of proteins were detected. Much more differences of glycoproteome were observed in breast diseases than the proteome. By employing machine learning, 15 site-specific glycans were determined as potential glyco-signatures in detecting breast cancer. The results demonstrate that our method provides a powerful tool in glycoproteomic analyses for biomarker discovery studies.

cancer biology↗

bioRxiv2024

Genomics-FM: Universal Foundation Model for Versatile andData-Efficient Functional Genomic Analysis

Artificial intelligence (AI) plays a crucial role in functional genomic analysis, offering great potential for comprehending biological phenomena such as heredity, development, diseases, and evolution. However, the development of AI models needs substantial labeled data, and these models are typically task-specific with limited generalizability to various applications. Here, we develop Genomics-FM, a genomic vocabulary driven foundation model that enables versatile and label-efficient functional genomic analysis. Specifically, Genomics-FM is first pretrained with ensemble genomic vocabulary on vast unlabelled data to learn comprehensive and generalizable representations and then finetuned with specific genomic vocabulary on limited labeled data to selectively activate and adapt the pretraining knowledge for specific tasks. We show that Genomics-FM significantly reduces the dependence on labeled data, and demonstrates the capability to outperform existing models across a comprehensive suite of tasks including genome annotation, epigenomic and expression profile prediction, and variant effect assessment. Remarkably, Genomics-FM even shows impressive zero-shot predictive capabilities across diverse species and tissues and exhibits noticeable adaptability to RNA-related tasks. With feasibility in data scarcity and even cross-domain biological scenarios, Genomics-FM will promote the broad application of AI and empower researchers to tackle previously insurmountable challenges, paving the way for groundbreaking research and discoveries.

bioinformatics↗

bioRxiv2024

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

bioinformatics↗

bioRxiv2024

Targeting PRMT3 Impairs Methylation and Oligomerization of HSP60 to Boost Anti-Tumor Immunity by Activating cGAS/STING Signaling

Hepatocellular carcinoma (HCC) is a highly lethal cancer for which current available treatment options have limited efficacy. Immunotherapy has emerged as a promising therapeutic option for HCC, yet resistance to immunotherapy is a major challenge. Here, we uncover protein arginine methyltransferase 3 (PRMT3) as a novel driver of immunotherapy resistance in HCC. We show that PRMT3 expression is induced by activated T cells in response to immune checkpoint blockade (ICB) via an interferon-gamma (IFN{gamma})-STAT1 signaling pathway, and that high PRMT3 expression inversely correlates with tumor-infiltrating CD8+ T cells and predicts poor response to ICB in HCC patients. We demonstrate that genetic depletion and pharmacological inhibition of PRMT3 induce a profound influx of T cells into tumors and activate anti-tumor immunity to suppress HCC progression. Mechanistically, we demonstrate that PRMT3 methylates HSP60, a mitochondrial chaperone protein, at R446, and that this novel post-translational modification is required for HSP60 oligomerization and maintaining mitochondrial homeostasis. We reveal that targeting PRMT3-dependent HSP60-R446 methylation boosts anti-tumor immunity by disrupting mitochondrial function, increasing mitochondrial DNA (mtDNA) leakage, and activating the cGAS/STING pathway, a key innate immune sensor of cytosolic DNA. Importantly, we provide genetic and pharmacologic evidence that targeting PRMT3 enhances anti-PD1 efficacy and anti-tumor immunity in HCC mouse models. Our study identifies PRMT3 as a potential biomarker and therapeutic target to overcome immunotherapy resistance in HCC.

cancer biology↗

bioRxiv2024

Deep Learning Prediction of Glycopeptide Tandem Mass Spectra Powers Glycoproteomics

Protein glycosylation plays a significant role in numerous physiological and pathological cellular functions. Glycoproteomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) studies the protein glycosylation on a proteome-wide scale to get combinational information on glycosylation site, glycosylation level and glycan structure. However, the current sequence searching-based methods for glycoproteomics often fall short in glycan structure determination due to the limited occurrence of structure-determining ions. While spectral searching methods can utilize fragment intensity information to facilitate the identification of glycopeptides, its application is hindered by the difficulties in spectral library construction. In this work, we present DeepGP, a hybrid deep learning framework based on Transformer and graph neural network (GNN), for the prediction of MS/MS spectra and retention time of glycopeptides. Two GNN modules are utilized to capture the branched glycan structure and predict glycan ions intensity, respectively. Additionally, a pre-training strategy is implemented to alleviate the insufficiency of glycoproteomics data. Testing on multiple biological datasets, we demonstrate that DeepGP can predict MS/MS spectra and retention time of glycopeptides closely aligning with the experimental results. Comprehensive benchmarking of DeepGP on synthetic and biological datasets validates its effectiveness in distinguishing similar glycoforms. Remarkably, DeepGP can differentiate isomeric glycopeptides using MS/MS spectra without diagnostic ions. Based on various decoy methods, we demonstrated that DeepGP in combination with database searching can significantly increase the detection sensitivity of glycopeptides. We outlook that DeepGP can inspire extensive future work in glycoproteomics.

bioinformatics↗

bioRxiv2024

Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop

The nanoscale organization of enzymes associated with the dynamics of second messengers is critical for ensuring compartmentation and localization of signaling molecules in cells. Specifically, the spatiotemporal orchestration of cAMP and Ca2+ oscillations is critical for many cellular functions. Previous experimental studies have shown that the formation of nanodomains of A-kinase anchoring protein 79/150 (AKAP150) and adenylyl cyclase 8 (AC8) on the surface of pancreatic MIN6 {beta} cells modulates the phase of Ca2+-cAMP oscillations from out-of-phase to in-phase. In this work, we develop computational models of the Ca2+/cAMP pathway and AKAP/AC nanodomain formation that give rise to the two important predictions: instead of an arbitrary phase difference, the out-of-phase Ca2+/cAMP oscillation reaches Ca2+ trough and cAMP peak simultaneously, which is defined as inversely out-of-phase; the in-phase and inversely out-of-phase oscillations associated with Ca2+-cAMP dynamics on and away from the nanodomains can be explained by an incoherent feedforward loop. Factors such as cellular surface-to-volume ratio, compartment size, and distance between nan-odomains do not affect the existence of in-phase or inversely out-of-phase Ca2+/cAMP oscillation, but cellular surface-to-volume ratio and compartment size can affect the time delay for the inversely out-of-phase Ca2+/cAMP oscillation while the distance between two nanodomains does not. Finally, we predict that both the Turing pattern-generated nanodomains and experimentally measured nan-odomains demonstrate the existence of in-phase and inversely out-of-phase Ca2+/cAMP oscillation when the AC8 is at a low level, consistent with the behavior of an incoherent feedforward loop. These findings unveil the key circuit motif that governs cAMP and Ca2+ oscillations and advance our understanding of how nanodomains can lead to spatial compartmentation of second messengers.

systems biology↗

bioRxiv2023

Three-dimensional dipole orientation mapping with high temporal-spatial resolution using polarization modulation

Fluorescence polarization microscopy is widely used in biology for molecular orientation properties. However, due to the limited temporal resolution of single-molecule orientation localization microscopy and the limited orientation dimension of polarization modulation techniques, achieving simultaneous high temporal-spatial resolution mapping of the three-dimensional (3D) orientation of fluorescent dipoles remains an outstanding problem. Here, we present a super-resolution 3D orientation mapping (3DOM) microscope that resolves 3D orientation by extracting phase information of the six polarization modulation components in reciprocal space. 3DOM achieves an azimuthal precision of 2{degrees} and a polar precision of 3{degrees} with spatial resolution of 128 nm in the experiments. We validate that 3DOM not only reveals the heterogeneity of the milk fat globule membrane, but also elucidates the 3D structure of biological filaments, including the 3D spatial conformation of {lambda}-DNA and the structural disorder of actin filaments. Furthermore, 3DOM images the dipole dynamics of microtubules labeled with green fluorescent protein in live U2OS cells, reporting dynamic 3D orientation variations. Given its easy integration into existing wide-field microscopes, we expect the 3DOM microscope to provide a multi-view versatile strategy for investigating molecular structure and dynamics in biological macromolecules across multiple spatial and temporal scales.

molecular biology↗

bioRxiv2023

Continuity of Mitochondrial Budding: Insights from BS-C-1 Cells by in-situ Cryo-Electron Tomography

Mitochondrial division is a fundamental biological process that is crucial to cellular functionality and vitality. The prevailing hypothesis of Drp1 regulation with the involvement of ER and cytoskeleton does not account for all the observations. Following up our previous study in HeLa cells which led to the new hypothesis of mitochondrial division by budding, we employed in-situ Cryo-Electron Tomography (Cryo-ET) to visualize mitochondrial budding in intact healthy monkey kidney cells (BS-C-1 cells). Our findings reaffirm single and multiple mitochondrial budding, supporting the new hypothesis. Notably, the budding regions vary significantly in diameter and length, which may represent different stages of budding. More interestingly, no rings, or ring-like structures, or ER wrapping is presented in the budding regions suggesting mitochondrial budding is independent from Drp1 and ER. Meanwhile, we uncovered direct interactions between mitochondria and large vesicles, distinct from small mitochondrial-derived vesicles and extracellular mitovesicles. We propose these interacting vesicles may have mitochondrial origins.

biophysics↗

bioRxiv2023

High-efficiency gene editing in Anopheles sinensis using ReMOT control

CRISPR/Cas9-mediated gene editing provides an effective method for deciphering the molecular mechanisms underlying mosquito development and mosquito-borne disease transmission, as well as for exploring genetic control strategies. However, delivering the Cas9 ribonucleoprotein complex by embryo injection to produce genetic modifications is challenging, is mostly confined to model mosquitoes and specialized laboratories, and has low editing efficiency. Here, we established an effective Receptor-Mediated Ovary Transduction of Cargo (ReMOT) control method, enabling the introduction of heritable mutations into Anopheles sinensis, the major malaria vector in China and Southeast Asia, via the injection of female adult mosquitoes. Injection of a mixture of P2C-DsRed and saponin resulted in red fluorescence in the ovaries, with a 100% success rate. Using this system, we knocked-out the pigment synthesis genes, Aswhite and Asyellow, using injected wild-type (WT) females mated with WT males, resulting in the highest efficiency of gene editing among mosquitoes under the same mating conditions. Furthermore, the gene-editing efficiency was increased by at least 2.1-fold using injected WT females mated with mutant males. This improved ReMOT control method exhibits high editing efficiency, with important benefits in terms of functional genomics research and genetic control strategies in An. sinensis. Moreover, this represents a convenient method for gene manipulation in laboratories that are unable to perform embryo injection or that lack embryo-injection equipment.

genetics↗

bioRxiv2023

Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics

Microbiota are closely associated to human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. One of the main challenges is constructing a protein sequence database that best fits the microbiota sample. Herein, we proposed an accurate taxonomic annotation pipeline from metagenomic data for deep metaproteomic coverage, namely contigs directed gene annotation (ConDiGA). We mixed 12 known bacterial species to derive a synthetic microbial community to benchmark metagenomic and metaproteomic pipelines. With the optimized taxonomic annotation strategy by ConDiGA, we built a protein sequence database from the metagenomic data for metaproteomic analysis and identified about 12,000 protein groups, which was very close to the result obtained with the reference proteome protein sequence database of the 12 species. We also demonstrated the practicability of the method in real fecal samples, achieved deep proteome coverage of human gut microbiome, and compared the function and taxonomy of gut microbiota at metagenomic level and metaproteomic level. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database for metaproteomics. The unique dataset of metagenomic and the metaproteomic data of the 12 bacterial species is publicly available as a standard benchmarking sample for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of real microbiota samples.

bioinformatics↗

bioRxiv2023

Single-cell time-resolved multi-omics reveal apoptotic and ferroptotic heterogeneity during foam cell formation

Macrophage-derived foam cell plays a pivotal role in the plaque formation and rupture during the progression of atherosclerosis. Foam cells are destined to divergent cell fate and functions in response to external stimuli based on their internal states, which however is hidden in the traditional studies based on population of cells. Herein, we used time-resolved and single-cell multi-omics to investigate the macrophage heterogeneity along foam cell formation. Dynamic metabolome and lipidome outlined the dual regulating axis of inflammation and ferroptosis. Single cell metabolomics and lipidomics further demonstrated a macrophage continuum featuring a differed susceptibility to apoptosis and ferroptosis. Using single-cell transcriptomic profiling, we verified the divergent cell fate toward apoptosis or ferroptosis. Therefore, the molecular choreography underlying the divergent cell fate during foam cell formation was revealed, which is of high significance for the understanding of the pathogenesis of atherosclerosis and development of new drug targets.

systems biology↗

bioRxiv2023

Neutrophilic Inflammation in Models of Bronchopulmonary Dysplasia and Chronic Obstructive Pulmonary Disease is Rescued by a Lactobacilli Based Live Biotherapeutic

Bronchopulmonary dysplasia (BPD) is a chronic lung disease of prematurity. Exposure to noxious stimuli such as hyperoxia, volutrauma, and infection in infancy can have long-reaching impacts on lung health and predispose towards the development of conditions such as chronic obstructive pulmonary disease (COPD) in adulthood. BPD and COPD are both marked by lung tissue degradation, neutrophil influx, and decreased lung function. Both diseases also express a change in microbial signature dominated by Proteobacteria abundance and Lactobacillus scarcity. However, the relationship between pulmonary microbial dysbiosis and the mechanisms of downstream disease development has yet to be elucidated. We hypothesized that a double-hit hyperoxia and LPS murine model of BPD would show heightened Ac-PGP pathway and neutrophil activity. Through gain- and loss-of-function studies in the same model we showed that Ac-PGP plays a critical role in driving BPD development. We tested a novel inhaled live biotherapeutic using active Lactobacillus strains to counteract lung dysbiosis in in vitro and in vivo models of BPD and COPD. The Lactobacillus LBP is effective in improving lung structure and function, reducing neutrophil influx, and reducing a broad swath of pro-inflammatory markers in these models of chronic pulmonary disease. Live inhaled microbiome-based therapeutics show promise in addressing common pathways of disease progression that in the future can be targeted in a variety of chronic lung diseases.

microbiology↗

bioRxiv2023

Artificial nanovesicles for dsRNA delivery in spray induced gene silencing for crop protection

Spray-Induced Gene Silencing (SIGS) is an innovative and eco-friendly technology where topical application of pathogen gene-targeting RNAs to plant material can enable disease control. SIGS applications remain limited because of the instability of dsRNA, which can be rapidly degraded when exposed to various environmental conditions. Inspired by the natural mechanism of crosskingdom RNAi through extracellular vesicle trafficking, we describe herein the use of artificial nanovesicles (AVs) for dsRNA encapsulation and control against the fungal pathogen, Botrytis cinerea. AVs were synthesized using three different cationic lipid formulations, DOTAP + PEG, DOTAP, and DODMA, and examined for their ability to protect and deliver dsRNA. All three formulations enabled dsRNA delivery and uptake by B. cinerea. Further, encapsulating dsRNA in AVs provided strong protection from nuclease degradation and from removal by leaf washing. This improved stability led to prolonged RNAi-mediated protection against B. cinerea both on pre- and post-harvest plant material using AVs. Specifically, the AVs extended the protection duration conferred by dsRNA to 10 days on tomato and grape fruits and to 21 days on grape leaves. The results of this work demonstrate how AVs can be used as a new nanocarrier to overcome dsRNA instability in SIGS for crop protection.

plant biology↗