Biology subjects

Yu, J.

Publications and source records attributed to Yu, J..

At least 307 records · Page 17Linked to original sources

bioRxiv2023

Continuous, long-term crawling behavior characterized by a robotic transport system

Detailed descriptions of behavior provide critical insight into the structure and function of nervous systems. In Drosophila larvae and many other systems, short behavioral experiments have been successful in characterizing rapid responses to a range of stimuli at the population level. However, the lack of long-term continuous observation makes it difficult to dissect comprehensive behavioral dynamics of individual animals and how behavior (and therefore the nervous system) develops over time. To allow for long-term continuous observations in individual fly larvae, we have engineered a robotic instrument that automatically tracks and transports larvae throughout an arena. The flexibility and reliability of its design enables controlled stimulus delivery and continuous measurement over developmental time scales, yielding an unprecedented level of detailed locomotion data. We utilize the new systems capabilities to perform continuous observation of exploratory behavior over a duration of six hours with and without a thermal gradient present, and in a single larva for over 30 hours. Long-term free-roaming behavior and analogous short-term experiments show similar dynamics that take place at the beginning of each experiment. Finally, characterization of larval thermotaxis in individuals reveals a bimodal distribution in navigation efficiency, identifying distinct phenotypes that are obfuscated when only analyzing population averages.

animal behavior and cognition↗

bioRxiv2023

Drought Recovery Induced Immunity Confers Pathogen Resistance

All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organism, yet stress recovery is understudied. To begin unraveling the stress recovery process we studies recovery from drought stress in Arabidopsis thaliana. We performed a fine-scale time series of bulk RNA sequencing starting 15 minutes after rehydration following moderate drought. We reveal that drought recovery is a rapid process involving the activation of thousands of recovery-specific genes. To capture these rapid recovery responses in different leaf cell types, we performed single-nucleus transcriptome analysis at the onset of post-drought recovery, identifying a cell type-specific transcriptional state developing within 15 minutes of rehydration independently across cell types. Furthermore, we reveal a recovery-induced activation of the immune system that occurs independent of infection, which enhances pathogen resistance in vivo in A. thaliana, wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Since rehydration promotes microbial proliferation and thereby increases the risk of infection1-2, drought recovery-induced immunity may be crucial for plant survival in natural environments. These findings indicate that drought recovery coincides with a preventive defense response, unraveling the complex regulatory mechanisms that facilitate stress recovery in different plant cell types.

plant biology↗

bioRxiv2023

NeoTCR: an immunoinformatic database of experimentally-supported functional neoantigen-specific TCR sequences

Neoantigen-based immunotherapy has demonstrated of long-lasting antitumor activity. Recognition of neoantigens by T cell receptors (TCRs) is considered a trigger for antitumor responses. Due to the overwhelming number of TCR repertoires in the human genome, it is challenging to computationally pinpoint neoantigen-specific TCRs. Recent studies have identified a number of functional neoantigen-specific TCRs, but the corresponding information is scattered across published literature and is difficult to retrieve. To improve access to these data, we developed the NeoTCR, an immunoinformatic database containing a unified description of publicly available neoantigen-specific TCR sequences, as well as relevant information on targeted neoantigens, from experimentally supported studies across 18 cancer subtypes. A user-friendly web interface allows interactive browsing and running of complex database queries based on numerous criteria. To facilitate rapid identification of neoantigen-specific TCRs from raw sequencing data, NeoTCR offers a one-stop analysis for annotation and visualization of TCR clonotypes, discovery of existing neoantigen-specific TCRs, and exclusion of bystander viral-associated TCRs. NeoTCR will serve as a valuable platform to study the biological functions of neoantigen-associated T-cells in anti-tumor immunity to better apply neoantigen-specific TCRs in clinics. NeoTCR is available at http://www.neotcrdb.com/.

bioinformatics↗

bioRxiv2023

Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes

Identification and visualization of large insertion and deletion (indel) polymorphisms, which contribute significantly to natural phenotypic variation, are challenge from a pan-genome. Here, through streamlining two unsupervised machine learning algorithms, we developed a BRIDGEcereal webapp for surveying and graphing indel-based haplotypes for genes of interest from publicly accessible pangenomes. Over hundreds of assemblies from five major cereals were compiled. We demonstrated the potential of BRIDGEcereal in exploring natural variation with wheat candidate genes within QTLs and GWAS intervals. BRIDGEcereal is available from https://bridgecereal.scinet.usda.gov.

bioinformatics↗

bioRxiv2023

SUMOylation of PTEN promotes DNA end resection through directly dephosphorylating 53BP1 in homologous recombination repair

Homologous recombination (HR) repair for DNA double-strand breaks (DSBs) is critical for maintaining genome stability and cell survival. Nuclear PTEN plays a key role in HR repair, but the underlying mechanism remains largely elusive. We find that SUMOylated PTEN promotes HR repair but represses non-homologous end joining (NHEJ) repair by directly dephosphorylating 53BP1. During DNA damage responses (DDR), p14ARF was phosphorylated and then interacted efficiently with PTEN, thus promoting PTEN SUMOylation as an atypical SUMO E3 ligase. Interestingly, SUMOylated PTEN was subsequently recruited to the chromatin at DNA-break sites. This was because that SUMO1 conjugated to PTEN was recognized and bound by the SUMO-interacting motif (SIM) of BRCA1, which has been located to the core of 53BP1 foci on the chromatin during S/G2 stage. Further, these chromatin-loaded PTEN directly and specifically dephosphorylated pT543 of 53BP1, resulting in the dissociation of 53BP1-complex, which facilitated DNA end resection and ongoing HR repair. The SUMOylation-deficient PTENK254R mice also showed decreased DNA damage repair in vivo. Blocking PTEN SUMOylation pathway with either an SUMOylation inhibitor or a p14ARF(2-13) peptide sensitized tumor cells to chemotherapy. Our study therefore provides the new mechanistic understanding of PTEN in HR repair and clinical intervention of chemo-resistant tumors.

cell biology↗

bioRxiv2023

scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data

The sparse nature of single-cell omics data makes it challenging to dissect the wiring and rewiring of the transcriptional and signaling drivers that regulate cellular states. Many of the drivers, referred to as "hidden drivers", are difficult to identify via conventional expression analysis due to low expression and inconsistency between RNA and protein activity caused by post-translational and other modifications. To address this issue, we developed scMINER, a mutual information (MI)-based computational framework for unsupervised clustering analysis and cell-type specific inference of intracellular networks, hidden drivers and network rewiring from single-cell RNA-seq data. We designed scMINER to capture nonlinear cell-cell and gene-gene relationships and infer driver activities. Systematic benchmarking showed that scMINER outperforms popular single-cell clustering algorithms, especially in distinguishing similar cell types. With respect to network inference, scMINER does not rely on the binding motifs which are available for a limited set of transcription factors, therefore scMINER can provide quantitative activity assessment for more than 6,000 transcription and signaling drivers from a scRNA-seq experiment. As demonstrations, we used scMINER to expose hidden transcription and signaling drivers and dissect their regulon rewiring in immune cell heterogeneity, lineage differentiation, and tissue specification. Overall, activity-based scMINER is a widely applicable, highly accurate, reproducible and scalable method for inferring cellular transcriptional and signaling networks in each cell state from scRNA-seq data. The scMINER software is publicly accessible via: https://github.com/jyyulab/scMINER.

systems biology↗

bioRxiv2023

Plasma membrane association and resistosome formation of plant helper immune receptors

Intracellular plant immune receptors, termed NLRs, respond to pathogen effectors delivered into plant cells. Activation of NLRs typically confers immunity. Sensor NLRs, involved in effector recognition, are either TIR-NLRs (TNLs) or CC-NLRs (CNLs). Helper NLRs, required for sensor NLR signaling, include CCR-NLRs (RNLs) and a special class of CNLs known as NRCs. Activated TNLs produce small molecules that induce an association between the EDS1/SAG101 heterodimer and the NRG1s helper RNLs. Auto active NRG1s oligomerize and form calcium signaling channels largely localized at the plasma membrane (PM). The molecular mechanisms of helper NLR PM association and effector induced NRG1 oligomerization are not well characterized. We find that both RNLs and NRCs require positively charged residues in the second and fourth helices of their CCR or CC domain for phospholipid binding and PM association before and after activation, despite conformational changes that accompany activation. We demonstrate that effector activation of TNLs induces NRG1 oligomerization at the PM and that the cytoplasmic pool of EDS1/SAG101 is critical for cell death function. EDS1/SAG101 cannot be detected in the oligomerized NRG1 resistosome, suggesting that additional unknown triggers might be required to induce the dissociation of EDS1/SAG101 from the previously described NRG1/EDS1/SAG101 heterotrimer before subsequent NRG1 oligomerization, or that the conformational changes resulting from NRG1 oligomerization abrogate the interface for EDS1/SAG101 association. Our data provide new observations regarding dynamic PM association during helper NLR activation and underpin an updated model for effector induced NRG1 resistosome formation.

plant biology↗

bioRxiv2023

Spatiotemporal Dynamics of Vcam1 Regulates Cholangiocarcinoma Mass Expansion and Tumor Dissemination under Growth-suppressive Peritumoral Myofibroblasts

Intrahepatic cholangiocarcinoma (iCCA) is characterized by its highly desmoplastic stroma. Myofibroblasts (MFs) are present both within the tumor mass (intratumoral MFs, iMFs) and at the tumor border (peritumoral MFs, pMFs). Using a spheroid-based coculture system, we show that the initial iCCA-pMF contact is growth suppressive to the tumor cells. However, prolonged iCCA-pMF interaction elicits significant tumor cell invasion and dissemination. We find that vascular cell adhesion molecule-1 (Vcam1) level is elevated in tumor cells in contact with pMFs but low in disseminated tumor cells both in vitro and in vivo. A gene regulatory network analysis of mouse and patient iCCA tumors and Vcam1 knockout (Vcam1KO) demonstrate a heavy involvement of Vcam1 in epithelial-to-mesenchymal transition. While Vcam1KO has only a limited impact on tumor cell growth in their monoculture, Vcam1KO spheroids exhibit instant dissemination and a severe growth defect when cocultured with pMFs. When transplanted into the liver, Vcam1KO iCCA cells show a similar increase in dissemination but a significant defect in establishing primary and metastatic tumors. Incomplete blocking of Vcam1 in vivo reduces the size but increase the number of metastatic lesions. Overall, our study shows a spatiotemporal regulation of iCCA growth and dissemination by pMFs in a Vcam1-dependent manner.

cancer biology↗

bioRxiv2023

Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse

Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 (RRM2) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B. Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.

cancer biology↗

bioRxiv2023

SARS-CoV-2 Envelope protein triggers depression and dysosmia via TLR2 mediated neuroinflammation

BackgroundDepression and dysosmia have been regarded as the main neurological symptoms in COVID-19 patients, the mechanism of which remains unclear. Current studies have demonstrated that SARS-CoV-2 envelope protein served as a pro-inflammatory factor as sensed by Toll like receptor 2 (TLR2), suggesting the viral infection independent pathological feature of E protein. In this study, we aim to determine the role of E protein in depression, dysosmia and associated neuroinflammation in central nervous system (CNS). MethodsDepression and olfactory function were observed in both female and male mice as receiving intracisternal injection of envelope protein. Immunohistochemistry was applied in conjunction with RT-PCR to assess the glial activation, blood-brain barrier status and mediators synthesis in cortex, hippocampus and olfactory bulb. TLR2 was pharmacologically blocked to determine its role in E protein related depression and dysosmia. ResultsIntracisternal injection of envelope protein evoked depression and dysosmia in both female and male mice. Immunohistochemistry suggested that envelope protein upregulated IBA1 and GFAP in cortex, hippocampus and olfactory bulb, while ZO-1 was downregulated. Moreover, IL-1{beta}, TNF-, IL-6, CCL2, MMP2 and CSF1 were upregulated in both cortex and hippocampus, whereas IL-1{beta}, IL-6 and CCL2 were upregulated in olfactory bulb. Furtherly, inhibiting microglia, but not astrocyte, alleviated depression and dysosmia induced by envelope protein. Finally, RT-PCR and immunohistochemistry suggested that TLR2 was upregulated in cortex, hippocampus and olfactory bulb, the blocking of which mitigated depression and dysosmia induced by envelope protein. ConclusionsOur study demonstrates that envelope protein could directly induce depression and dysosmia together with obvious neuroinflammation in CNS. TLR2 mediated depression and dysosmia induced by envelope protein, which could serve as a promising therapeutic target for neurological manifestation in COVID-19 patients.

neuroscience↗

bioRxiv2023

VHL Mutation Drives Human Clear Cell Renal Cell Carcinoma Progression Through PI3K/AKT-Dependent Cholesteryl Ester Accumulation

BackgroundCholesteryl ester (CE) accumulation in intracellular lipid droplets (LDs) is an essential signature of clear cell renal cell carcinoma (ccRCC), but its molecular mechanism and pathological significance remain elusive. MethodsEnabled by the label-free Raman spectromicroscopy, which integrated stimulated Raman scattering microscopy with confocal Raman spectroscopy on the same platform, we quantitatively analyzed LD distribution and composition at the single cell level in intact ccRCC cell and tissue specimens in situ without any processing or exogenous labeling. Since we found that commonly used ccRCC cell lines actually did not show the CE-rich signature, primary cancer cells were isolated from human tissues to retain the lipid signature of ccRCC with CE level as high as the original tissue, which offers a preferable cell model for the study of cholesterol metabolism in ccRCC. Moreover, we established a patient-derived xenograft (PDX) mouse model that retained the CE-rich phenotype of human ccRCC. FindingsSurprisingly, our results revealed that CE accumulation was induced by tumor suppressor VHL mutation, the most common mutation of ccRCC. Moreover, VHL mutation was found to promote CE accumulation by upregulating HIF and subsequent PI3K/AKT/mTOR/SREBPs pathway. Inspiringly, inhibition of cholesterol esterification remarkably suppressed ccRCC aggressiveness in vitro and in vivo with negligible toxicity, through the reduced membrane cholesterol-mediated downregulations of integrin and MAPK signaling pathways. InterpretationCollectively, our study improves current understanding of the role of CE accumulation in ccRCC and opens up new opportunities for treatment. FundingThis work was supported by National Natural Science Foundation of China (No. U23B2046 and No. 62027824), National Key R&D Program of China (No. 2023YFC2415500), Fundamental Research Funds for the Central Universities (No. YWF-22-L-547), PKU-Baidu Fund (No. 2020BD033), Peking University First Hospital Scientific and Technological Achievement Transformation Incubation Guidance Fund (No.2022CX02), and Beijing Municipal Health Commission (No. 2020-2Z-40713).

cancer biology↗

bioRxiv2023

Ythdf2 ablation protects aged retina from RGC dendrite shrinking and visual decline

Aging-related retinal degeneration and vision loss have been severely affecting the elder worldwide. Previously we showed that the m6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells (RGC) in mice (Niu et al. 2022). Here, we show that conditional ablation of Ythdf2 protects retina from RGC dendrite shrinking and vision loss in the aged mice. Further, we identify Hspa12a and Islr2 as the YTHDF2 target mRNAs mediating these effects. Together our results indicate that m6A modification regulates retinal degeneration caused by aging, which might provide therapeutical potentials for developing new treatment approaches against aging-related vision loss.

neuroscience↗

bioRxiv2022

FOXC2 marks and maintains the primitive spermatogonial stem cells subpopulation in the adult testis

In adult mammals, spermatogenesis embodies the complex developmental process from spermatogonial stem cells (SSCs) to spermatozoa. At the top of this developmental hierarchy lie a series of SSC subpopulations. Their individual identities as well as the relationships with each other, however, remain largely elusive. Using single-cell analysis and lineage tracing, we discovered both in mice and humans the quiescent adult SSC subpopulation marked specifically by forkhead box protein C2 (FOXC2). All spermatogenic progenies can be derived from FOXC2+ SSCs and the ablation of FOXC2+ SSCs led to the depletion of the undifferentiated spermatogonia pool. During germline regeneration, FOXC2+ SSCs were activated and able to completely restore the process. Germ cell specific Foxc2 knockout resulted in an accelerated exhaustion of SSCs and eventually led to male infertility. Furthermore, FOXC2 prompts the expressions of negative regulators of cell cycle thereby ensures the SSCs reside in quiescence. Thus, this work proposes that the quiescent FOXC2+ SSCs are essential for maintaining the homeostasis and regeneration of spermatogenesis in adult mammals.

developmental biology↗

bioRxiv2022

Non-specific vs specific DNA binding free energetics of a transcription factor domain protein for target search and recognition

Transcription factor (TF) proteins regulate gene expression by binding to specific sites on the genome. In the facilitated diffusion model, an optimized search process is achieved by the TF protein alternating between 3D diffusion in the bulk and 1D diffusion along DNA. While undergoing 1D diffusion, the protein can switch from a search mode for fast diffusion along non-specific DNA to a recognition mode for stable binding to specific DNA. It was recently noticed that for a small TF domain protein, re-orientations on DNA other than conformational changes happen between the non-specific and specific DNA binding. We here conducted all-atom molecular dynamics simulations with steering forces to reveal the protein-DNA binding free energetics, with a difference between the non-specific and specific binding about 10 kBT, confirming that the search and recognition modes are distinguished only by protein orientations on the DNA. As the binding free energy difference differs from that being estimated from experimental measurements about 4-5 kBT on 15-bp DNA constructs, we hypothesize that the discrepancy comes from DNA sequences flanking the 6-bp central binding sites impacting on the dissociation kinetics measurements. The hypothesis is supported by a simplified spherical protein-DNA model along with stochastic simulations and kinetic modeling.

biophysics↗

bioRxiv2022

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

Lycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimers disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated the Lycopodium clavatum L. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in the L. clavatum genome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.

genomics↗

bioRxiv2022

Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants

The SARS-CoV-2 Omicron variant continues to evolve, with new BQ and XBB subvariants now rapidly expanding in Europe/US and Asia, respectively. As these new subvariants have additional spike mutations, they may possess altered antibody evasion properties. Here, we report that neutralization of BQ.1, BQ.1.1, XBB, and XBB.1 by sera from vaccinees and infected persons was markedly impaired, including sera from individuals who were boosted with a WA1/BA.5 bivalent mRNA vaccine. Compared to the ancestral strain D614G, serum neutralizing titers against BQ and XBB subvariants were lower by 13-81-fold and 66-155-fold, respectively, far beyond what had been observed to date. A panel of monoclonal antibodies capable of neutralizing the original Omicron variant, including those with Emergency Use Authorization, were largely inactive against these new subvariants. The spike mutations that conferred antibody resistance were individually studied and structurally explained. Finally, the ACE2-binding affinities of the spike proteins of these novel subvariants were found to be similar to those of their predecessors. Taken together, our findings indicate that BQ and XBB subvariants present serious threats to the efficacy of current COVID-19 vaccines, render inactive all authorized monoclonal antibodies, and may have gained dominance in the population because of their advantage in evading antibodies.

microbiology↗

bioRxiv2022

Single-Cell ATAC-seq analysis via Network Refinement with peaks location information

Single-cell ATAC-seq (scATAC-seq) data provided new insights into the elaboration of cellular heterogeneity and transcriptional regulation. However, scATAC-seq data posed challenges for data analysis because of its near binarization, high sparsity, and ultra-high dimensionality properties. Here we proposed a novel network diffusion-based method to comprehensively analyze scATAC-seq data, named Single-Cell ATAC-seq Analysis via Network Refinement with Peaks Location Information (SCARP). By modeling the prior probability of co-accessibility between adjacent peaks as a decreasing function of genomic distance, SCARP is the first scATAC-seq analysis method that utilizes the genomic information of peaks, which contributed to characterizing co-accessibility of peaks. SCARP used network to model the accessible relationships between cells and peaks, aggregated information with the diffusion method, and then performed dimensionality reduction to obtain low-dimensional cell embeddings as well as peak embeddings. We have demonstrated through sufficient experiments that SCARP facilitated superior analysis of scATAC-seq data. Specifically, SCARP exhibited outstanding cell clustering performance to better elucidate cell heterogeneity, and can be used to reveal new biologically significant cell subpopulations. SCARP was also instrumental in portraying co-accessibility relationships of accessible regions and providing new insight into transcriptional regulation, and those SCARP-derived genes were involved in some key KEGG pathways related to diseases. To sum up, our studies suggested that SCARP is a promising tool to comprehensively analyze the scATAC-seq data from a new perspective.

bioinformatics↗

bioRxiv2022

PathExpSurv: Pathway Expansion for Explainable Survival Analysis and Disease Gene Discovery

MotivationIn the field of biology and medicine, the interpretability and accuracy are both important when designing predictive models. The interpretability of many machine learning models such as neural networks is still a challenge. Recently, many researchers utilized prior information such as biological pathways to develop bioinformatics methods based on neural networks, so that the prior information can provide some insights and interpretability for the models. However, the prior biological knowledge may be incomplete and there still exists some unknown information to be explored. ResultsWe proposed a novel method, named PathExpSurv, to gain an insight into the black-box model of neural network for cancer survival analysis. We demonstrated that PathExpSurv could not only incorporate the known prior information into the model, but also explore the unknown possible expansion to the existing pathways. We performed downstream analyses based on the expanded pathways and successfully identified some key genes associated with the diseases and original pathways. AvailabilityPython source code of PathExpSurv is freely available at https://github.com/Wu-Lab/PathExpSurv. Contactlywu@amss.ac.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗