Biology subjects

Luo, P.

Publications and source records attributed to Luo, P..

34 records · Page 2Linked to original sources

bioRxiv2022

BEST: a web application for comprehensive biomarker exploration on large-scale data in solid tumors

SummaryData mining from RNA-seq or microarray data has become an essential part of cancer biomarker exploration. Certain existing web servers are valuable and broadly utilized, but the meta-analysis of multiple datasets is absent. Most web servers only contain tumor samples from the TCGA database with only one cohort for each cancer type, which also means that the analysis results mainly derived from a single cohort are thin and unstable. Indeed, consistent performance across multiple independent cohorts is the foundation for an excellent biomarker. Moreover, many analytical functions researchers require remain adequately unmet by these tools. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. BEST includes more than 50,000 samples of 27 cancer types. To ensure the comparability of genes between different sequencing technologies and the legibility of clinical traits, we re-annotated transcriptome data based on the GRCh38 patch 13 sequences and unified the nomenclature of clinical traits. BEST delivers fast and customizable functions, including clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration. Together, our web server provides multiple cleaned-up independent datasets and diverse analysis functionalities, helping unleash the value of current data resources. It is freely available at https://rookieutopia.com/. The bigger pictureBioinformatics web servers enable researchers without computational programming skills to conduct various bioinformatics analyses. However, most web servers only contain tumor samples from the TCGA database with only one cohort for each cancer type, which also means that the analysis results mainly derived from a single cohort are thin and unstable. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. BEST includes more than 50,000 samples of 27 cancer types that have been uniformly re-annotated based on the GRCh38 patch 13 sequences, which ensures the comparability of genes between different sequencing technologies. BEST also offers prevalent functions including clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration. Together, BEST provides a curated database and innovative analytical pipelines to explore cancer biomarkers at high resolution.

genomics↗

bioRxiv2022

MOAHIT: A Web Tool for visualizing tumormulti-omics data with human anatomy heatmaps

Multi-omics data plays an important role in cancer research, helping clinicians to better explore drug targets and biomarkers. At present, there exist several databases including TCGA (the Cancer Genome Atlas) and GDSC (Genomics of Drug Sensitivity in Cancer), which contain multi omics data on multiple cancer species, as well as various web tools for analyzing the multi-omics data, which are widely used in oncology research. Tumor heterogeneity is a widespread phenomenon, reflected by differences in multi-omics data of cancers originating from different tissues and organs. However, there is a lack of convenient analysis and visualization tools to explore tumor heterogeneity. As a result, we developed a web tool called Multi-Omics Anatomy Heatmap in Tumors (MOAHIT) based on shiny programming. This tool enables users to analyze and visualize the heterogeneity of human tissues. In addition, MOAHIT enables users to produce a beautiful human anatomy heatmap to visualize the heterogeneity between distinct cancers in the multi-omics data.

bioinformatics↗

bioRxiv2022

Estrogen signaling in the dorsal raphe regulates binge-like drinking in mice

The ovarian hormone estrogens promote binge alcohol drinking and contribute to sex differences in alcohol use disorder. However, the mechanisms for estrogen-induced binge drinking are largely unknown. This study aims to test if estrogens act on 5-hydroxytryptamine neurons in the dorsal raphe nucleus (5-HTDRN) to promote binge drinking. We used the drinking in the dark (DID) behavioral test in mice to mimic binge drinking in humans. We found that female mice drank more alcohol than male mice in chronic DID tests. This sex difference was associated with distinct alterations in mRNA expression of estrogen receptor (ER) and 5-HT-related genes in the DRN, suggesting a potential role of estrogen/ERs/5-HT signaling in binge alcohol drinking. In supporting this view, 5-HTDRN neurons from naive male mice had lower baseline neuronal firing activity but higher sensitivity to alcohol-induced excitation compared to 5-HTDRN neurons from naive female mice. Notably, this higher sensitivity was blunted by 17{beta}-estradiol treatment in males, indicating an estrogen-dependent mechanism. We further showed that both ER and ER{beta} are expressed in 5-HTDRN neurons, whereas ER agonist propyl pyrazole triol (PPT) depolarizes 5-HTDRN neurons and ER{beta} agonist diarylpropionitrile (DPN) hyperpolarizes 5-HTDRN neurons. Notably, both PPT and DPN treatments blocked the stimulatory effects of alcohol on 5-HTDRN neurons in males, despite the fact that they have antagonistic effects on the activity dynamics of 5-HTDRN neurons. These results suggest that ERs inhibitory effects on ethanol-induced burst firing of 5-HTDRN neurons may contribute to higher levels of binge drinking in females. Consistently, chemogenetic activation of ER- or ER{beta}-expressing neurons in the DRN reduced binge alcohol drinking. These results support a model in which estrogens act on ER/{beta} to prevent alcohol-induced activation of 5-HTDRN neurons, which in return leads to higher binge alcohol drinking.

neuroscience↗

bioRxiv2022

Respiratory mucosal vaccination of peptide-poloxamine-DNA nanoparticles provides complete protection against lethal SARS-CoV-2 challenge

The ongoing SARS-CoV-2 pandemic represents a brutal reminder of the continual threat of mucosal infectious diseases. Mucosal immunity may provide robust protection at the predominant sites of SARS-CoV-2 infection. However, it remains unclear whether respiratory mucosal administration of DNA vaccines could confer protective immune responses against SARS-CoV-2 challenge due to the insurmountable barriers posed by the airway. Here, we applied self-assembled peptide-poloxamine nanoparticles with mucus-penetrating properties for pulmonary inoculation of a COVID-19 DNA vaccine (pSpike/PP-sNp). Not only displays the pSpike/PP-sNp superior gene-transfection and favorable biocompatibility in the mouse airway, but pSpike/PP-sNp promotes a tripartite immunity consisting of systemic, cellular and mucosal immune responses that are characterized by mucosal IgA secretion, high levels of neutralizing antibodies, and resident memory phenotype T-cell responses in the lungs of mice. Most importantly, pSpike/PP-sNp completely eliminates SARS-CoV-2 infection in both upper and lower respiratory tracts and enables 100% survival rate of mice following lethal SARS-CoV-2 challenge. Our findings indicate PP-sNp might be a promising platform in mediating DNA vaccines to elicit all-around mucosal immunity against SARS-CoV-2.

immunology↗

bioRxiv2022

Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co- stimulation in a mice acute-on-chronic liver failure model

Boosting stem cell resilience against an extrinsically harsh recipient environment is critical to therapeutic efficiency of stem cell-based transplantation innovations in liver disease contexts. We aimed to establish the efficacy of a transient plasmid-based preconditioning strategy to boost mesenchymal stromal cells (MSCs) capacity for anti-inflammation/antioxidant defense and paracrine actions on recipient hepatocytes. In MSCs, the master antioxidant regulator Nrf2 was found to bind directly to the antioxidant response element in the DKK1 promoter region. Activation of Nrf2 and DKK1 enhanced the anti-stress capacities of MSCs in vitro. In an acute-on-chronic liver failure (ACLF) murine model, transient co-overexpression of Nrf2 and DKK1 via plasmid transfection markedly improved MSC resilience against inflammatory and oxidative assaults, boosted MSC transplantation efficacy and promoted recipient liver regeneration because of a shift from the activation of the anti-regenerative IFN-{gamma}/STAT1 pathway to the pro-regenerative IL-6/STAT3 pathway in the liver. Moreover, specific ablation of DKK1 receptor CKAP4 but not LRP6 in recipient hepatocytes nullified therapeutic benefits from MSC transplantation. In long-term observations, tumorigenicity was undetected in mice following transplantation of such transiently preconditioned MCSs. In conclusion, co-stimulation of Nrf2/DKK1 signaling decisively and safely improves the efficacy of human MSC-based therapies in mouse ACLF models through apparently CKAP4-dependent paracrine mechanisms.

molecular biology↗

bioRxiv2022

Impact of Pericytes on the Stabilisation of Microvascular Networks in Microfluidic Systems in Response to Nanotoxicity

Recapitulating the normal physiology of the microvasculature is pivotal in the development of more complex in vitro models and organ-on-chip design. Pericytes are an important component of the vasculature, promoting vessel stability, inhibiting vascular permeability and maintaining the vascular hierarchical architecture. This report presents a microfluidic model exploring interactions between endothelial cells and pericytes. We identify basal conditions required to form stable and reproducible endothelial networks. We then investigate interactions between endothelial cells and pericytes via direct co-culture. In our system, pericytes inhibited vessel hyperplasia and maintained vessel length in prolonged culture (>10 days). In addition, these vessels displayed barrier function and expression of junction markers associated with vessel maturation, including VE-cadherin, {beta}-catenin and ZO-1. Furthermore, pericytes maintained vessel integrity following stress (nutrient starvation) and inhibited vessel regression, in contrast to the striking dissociation of networks in endothelial monocultures. This response was also observed when endothelial/pericyte co-cultures were exposed to high concentrations of moderately toxic cationic nanoparticles used for gene delivery. This study highlights the importance of pericytes in protecting vascular networks from stress and external agents and their importance to the design of advanced in vitro models, including for the testing of nanotoxicity, to better recapitulate physiological response and avoid false positives.

bioengineering↗

bioRxiv2022

Onlinemeta: A Web Serve For Meta-Analysis Based On R-shiny

Meta-analysis is a common statistical method used to summarize multiple studies that cover the same topic. It can provide less biased results and explain heterogeneity between studies. Although there exists a variety of meta-analysis softwares, they are rarely both convenient to use and capable of comprehensive analytical functions. As a result, we are motivated to establish a meta-analysis web tool called Meta-Analysis Online (Onlinemeta). Onlinemeta includes three major modules: risk bias analysis, meta-analysis and network meta-analysis. The risk bias analysis module can produce heatmaps and histograms, whereas the meta-analysis module accepts many types of data as input, including dichotomous variables, single-armed dichotomous variables, continuous variables, single-armed continuous variables, survival data, deft method and diagnostic experiments, and outputs well-tuned forest plots, sensitivity analysis forest plots, funnel plots, comparison table of effects, SROC curve, and crosshair plots. For network meta-analysis module, the tool can process dichotomous variables or continuous variables, and generate network plots, forest plots, SUCRA (Surface Under the Cumulative Ranking) plots, rank plots and heatmaps. Onlinemeta is available at https://smuonco.Shinyapps.io/Onlinemeta/.

bioinformatics↗

bioRxiv2021

Broad neutralization against SARS-CoV-2 variants induced by a modified B.1.351 protein-based COVID-19 vaccine candidate

Beginning in late 2020, the emergence and spread of multiple variant SARS-CoV-2 strains harboring mutations which may enable immune escape necessitates the rapid evaluation of second generation COVID-19 vaccines, with the goal of inducing optimized immune responses that are broadly protective. Here we demonstrate in a mouse immunogenicity study that two doses of a modified B.1.351 spike (S)-Trimer vaccine (B.1.351 S-Trimer) candidate can induce strong humoral immune responses that can broadly neutralize both the original SARS-CoV-2 strain (Wuhan-Hu-1) and Variants of Concern (VOCs), including the UK variant (B.1.1.7), South African variant (B.1.351) and Brazil variant (P.1). Furthermore, while immunization with two doses (prime-boost) of Prototype S-Trimer vaccine (based on the original SARS-CoV-2 strain) induced lower levels of cross-reactive neutralization against the B.1.351 variant, a third dose (booster) administered with either Prototype S-Trimer or B.1.351 S-Trimer was able to increase neutralizing antibody titers against B.1.351 to levels comparable to neutralizing antibody titers against the original strain elicited by two doses of Prototype S-Trimer.

immunology↗

bioRxiv2021

AAV-mediated gene therapy produces fertile offspring in the Lhcgr-deficient mouse model of Leydig cell failure

Leydig cell failure (LCF) caused by gene mutation results in testosterone deficiency and infertility. Serum testosterone levels can be recovered via testosterone replacement; however, established therapies have shown limited success in restoring fertility. Here, we used a luteinizing hormone/choriogonadotrophin receptor (Lhcgr)-deficient mouse model of genetic LCF to investigate the feasibility of gene therapy for restoring testosterone production and fertility. We screened several adeno-associated virus (AAV) serotypes and identified AAV8 as an efficient vector to drive exogenous Lhcgr expression in progenitor Leydig cells through interstitial injection. We observed considerable testosterone recovery and Leydig cell maturation after AAV8-Lhcgr treatment in pubertal Lhcgr-/- mice. This gene therapy substantially recovered sexual development, partially restored spermatogenesis and effectively produced fertile offspring. Furthermore, these favorable effects could be reproduced in adult Lhcgr-/- mice. Our proof-of-concept experiments in this mouse model demonstrate that AAV-mediated gene therapy may represent a promising therapeutic approach for patients with genetic LCF.

developmental biology↗

bioRxiv2020

Whole-brain connectivity atlas of glutamatergic and GABAergic neurons in mouse dorsal and median raphe nucleus

The dorsal raphe nucleus (DR) and median raphe nucleus (MR) contain populations of glutamatergic and GABAergic neurons regulating diverse behavioral functions. Their whole-brain input-output circuits remain incompletely understood. We used viral tracing combined with fluorescence micro-optical sectioning tomography to generate a comprehensive whole-brain atlas of inputs and outputs of glutamatergic and GABAergic neurons in the DR and MR. We discovered that these neurons receive inputs from similar upstream brain regions. The glutamatergic and GABAergic neurons in the same raphe nucleus have divergent projection patterns with differences in critical brain regions. Specifically, MR glutamatergic neurons project to the lateral habenula via multiple pathways. Correlation and cluster analysis indicated that glutamatergic and GABAergic neurons in the same raphe nucleus receive inputs from heterogeneous neurons in upstream brain regions and send different collateral projections. This connectivity atlas provides insights into the cell heterogeneity, anatomical connectivity and behavioral functions of the raphe nucleus.

neuroscience↗

bioRxiv2020

Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation

Scientific fraud by image duplications and manipulations within western blot images is a rising problem. Currently, problematic western blot images are mainly detected by checking repeated bands or through visual observation. However, the completeness of the above methods in detecting problematic images has not been demonstrated. Here we show that Generative Adversarial Nets (GANs) can generate realistic western blot images that indistinguishable from real western blots. The overall accuracy of researchers for identifying synthetic western blot images is 0.52, which almost equal to blind guess (0.5). We found that GANs can generate western blot images with bands of the expected lengths, widths, and angles in desired positions that can fool researchers. For the case study, we find that the accuracy of detecting the synthetic western blot images is related to years of researchers performed studies relevant to western blots, but there was no apparent difference in accuracy among researchers with different academic degrees. Our results demonstrate that GANs can generate fake western blot images to fool existing problematic image detection methods. Therefore, more information is needed to ensure that the western blots appearing in scientific articles are real. We argue to require every western blot image to be uploaded along with a unique identifier generated by the laboratory machine and to peer review these images along with the corresponding submitted articles, which may reduce the incidence of scientific fraud.

scientific communication and education↗

bioRxiv2020

S-Trimer, a COVID-19 subunit vaccine candidate, induces protective immunity in nonhuman primates

SARS-CoV-2 is the underlying cause for the COVID-19 pandemic. Like most enveloped RNA viruses, SARS-CoV-2 uses a homotrimeric surface antigen to gain entry into host cells. Here we describe S-Trimer, a native-like trimeric subunit vaccine candidate for COVID-19 based on Trimer-Tag technology. Immunization of S-Trimer with either AS03 (oil-in-water emulsion) or CpG 1018 (TLR9 agonist) plus alum adjuvants induced high-levels of neutralizing antibodies and Th1-biased cellular immune responses in animal models. Moreover, rhesus macaques immunized with adjuvanted S-Trimer were protected from SARS-CoV-2 challenge compared to vehicle controls, based on clinical observations and reduction of viral loads in lungs. Trimer-Tag may be an important new platform technology for scalable production and rapid development of safe and effective subunit vaccines against current and future emerging RNA viruses.

immunology↗

bioRxiv2020

CReSCENT: CanceR Single Cell ExpressioN Toolkit

CReSCENTCanceR Single Cell ExpressioN Toolkit (https://crescent.cloud), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data for tumour specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology. CReSCENT uses public data sets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.

bioinformatics↗

bioRxiv2019

LncRNA MIR4435-2HG mediates cisplatin resistance in HCT116 cells by regulating Nrf2 and HO-1

PURPOSECisplatin resistance is still a serious problem in clinic. However, the underlying mechanism remains unclear. In this study investigated the drug resistance of cisplatin by the cisplatin resistance cell line HCT116R.\n\nRESULTSIn this study, we found that LncRNA MIR4435-2HG level dramatically increased in the cisplatin resistance cell line HCT116R. Knockdown of MIR4435-2HG in HCR116R significantly restored the sensitivity to cisplatin, inhibited cell proliferation and promoted cell apoptosis. Furthermore, Nrf2 and HO-1 mRNA level, as the critical molecular of the oxidative stress pathway, was inhibited by the siRNA targeting to MIR4435-2HG, displaying MIR4435-2HG-mediated cisplatin resistance through the Nrf2/HO-1 pathway.\n\nCONCLUSIONOur findings demonstrated that LncRNA MIR4435-2HG as a main factor could drive the cisplatin resistance of HCT116.

cancer biology↗

bioRxiv2018

Experimental infection characteristics of Bordetella pertussis via aerosol challenge on rhesus macaques

The effect of aerosol challenge of rhesus macaques with Bordetella pertussis and the feasibility of using rhesus monkeys as an animal model for pertussis infection were evaluated in this study. Four 1-year old rhesus macaques were aerosol challenged with B. pertussis at the concentration of 105 CFU/mL for 30 min (group 1) or 60 min (group 2). Rectal temperature was found slightly increased at days 3 and 5 and returned to baseline levels at day 21 after challenge. White blood cell counts peaked at day 7, with a 4.7~6.1-fold increase and returned to baseline levels at day 45. Bacteria colonization of nasopharyngeal swabs was observed, and the number of colonies was gradually increased and peaked at day 14, reaching 5.4-8.1 x 106/mL. The seroconversion rate of anti-pertussis toxin (PT), pertactin (PRN), and filamentous hemagglutinin(FHA) antibodies was 100%, with an increase in geometric mean titers after challenge. Analysis of cytokines revealed that the levels of cytokines including IL-2, IL-6, IL-8, IL-10, IL-17A, IL-13, IL-12, and IL-18 were significantly increased at days 5 to 14 in group 2. These results demonstrate that the characteristic of pertussis infection in infant rhesus macaque was similar as in human beings, which provide a clue to using infant rhesus macaque as a candidate model for pertussis infection in the future studies

microbiology↗

bioRxiv2018

Preliminary study on the application of PspA as carrier

The aim of the study is to research the feasibility of pneumococcal surface protein A (PspA) using as carrier protein. Three recombinant pneumococcal surface proteins A (come from family1 and family 2) were expressed by prokaryotic expression system and were conjugated to group A meningococcal polysaccharide (GAMP) to make three polysaccharide-protein conjugates. The conjugates, un-conjugated proteins, GAMP and GAMP-TT vaccine bulk (used as positive control) were immunized to mice and their immune effects were evaluated by the method of ELISA, FCM and SBA. The results showed that the polysaccharide-protein conjugates can produce higher levels of anti-GAMP IgG titers (P < 0.05), higher ratios of Th1/Th2 (P < 0.05) and higher levels of serum bactericidal activity (P < 0.05) compared with the un-conjugated GAMP. The conjugation of PspAs to GAMP also enhanced the anti-PspA responses compared with un-conjugated PspAs except PspA3. In conclusion, all the results indicated that three PspAs were suitable carrier protein as demonstrated by the characteristics of a T-cell dependent response to the GAMP, and would protect against group A of epidemic cerebrospinal meningitis and also have the potential to provide broad protection from Streptococcus pneumonia.

immunology↗