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Tong, J.

Publications and source records attributed to Tong, J..

54 records · Page 3Linked to original sources

Parallel lipid-carried epitope pillars enhance stimulation of chimeric antigen receptor T cells

Chimeric antigen receptor T cells are genetically engineered to express a specific T cell receptor of interest, such as to target a cancer-specific antigen. Signaling events in chimeric antigen receptor T cells are essential for their proliferation, survival, and function. To achieve optimal antitumor efficacy, signaling motifs as well as the structure of the transmembrane domain of the chimeric antigen receptor have to be carefully designed. However, it remains unclear whether the arrangement, and therefore the movement and elasticity, of tumor antigens influence their stimulation of chimeric antigen receptor T cells. Here we show that MUC1 molecules tethered to a glycosylphosphatidylinositol anchor drastically increased its stimulation of chimeric antigen receptor T cells. In particular, MUC1 molecules containing one tandem repeat sequence showed significantly greater stimulatory activity than five tandem repeat sequences. Thus glycosylphosphatidylinositol-anchored, tumor antigen epitope pillars in parallel are attractive targets for the design of chimeric antigen receptor T cells. These novel findings, which we propose as the parallel lipid-carried epitope model, emphasize the importance of epitope arrangement in selecting highly effective chimeric antigen receptor T cells, potentially revolutionizing the applicability of this therapy. Furthermore, our data have implications for the necessity of methodologies to measure the elasticity, movement, and density of antigen pillars in parallel, as key tools to guide future chimeric antigen receptor T cell therapy.

immunology↗

Local activation of focal adhesion kinase orchestrates the positioning of presynaptic scaffold proteins and Ca2+ channel function to control glucose dependent insulin secretion.

A developing understanding suggests that spatial compartmentalisation of components the glucose stimulus-secretion pathway in pancreatic {beta} cells are critical in controlling insulin secretion. To investigate the mechanisms, we have developed live-cell sub-cellular imaging methods using the organotypic pancreatic slice. We demonstrate that the organotypic pancreatic slice, when compared with isolated islets, preserves intact {beta} cell structure, and enhances glucose dependent Ca2+ responses and insulin secretion. Using the slice technique, we have discovered the essential role of local activation of integrins and the downstream component, focal adhesion kinase, in regulating {beta} cells. Integrins and focal adhesion kinase are exclusively activated at the {beta} cell capillary interface and using in situ and in vitro models we show their activation both positions presynaptic scaffold proteins, like ELKS and liprin, and regulates glucose dependent Ca2+ responses and insulin secretion. We conclude that focal adhesion kinase orchestrates the final steps of glucose dependent insulin secretion within the restricted domain where {beta} cells contact the islet capillaries.

cell biology↗

m6A modifications regulate intestinal immunity and rotavirus infection

N6-methyladenosine (m6A) is an abundant mRNA modification and affects many biological processes. However, how m6A levels are regulated during physiological or pathological processes such as virus infections, and the in vivo function of m6A in the intestinal immune defense against virus infections are largely unknown. Here, we uncover a novel antiviral function of m6A modification during rotavirus (RV) infection in small bowel intestinal epithelial cells (IECs). We found that rotavirus infection induced global m6A modifications on mRNA transcripts by down-regulating the m6a eraser ALKBH5. Mice lacking the m6A writer enzymes METTL3 in IECs (Mettl3{Delta}IEC) were resistant to RV infection and showed increased expression of interferons (IFNs) and IFN-stimulated genes (ISGs). Using RNA-sequencing and m6A RNA immuno-precipitation (RIP)-sequencing, we identified IRF7, a master regulator of IFN responses, as one of the primary m6A targets during virus infection. In the absence of METTL3, IECs showed increased Irf7 mRNA stability and enhanced type I and III IFN expression. Deficiency in IRF7 attenuated the elevated expression of IFNs and ISGs and restored susceptibility to RV infection in Mettl3{Delta}IEC mice. Moreover, the global m6A modification on mRNA transcripts declined with age in mice, with a significant drop from 2 weeks to 3 weeks post birth, which likely has broad implications for the development of intestinal immune system against enteric viruses early in life. Collectively, we demonstrated a novel host m6A-IRF7-IFN antiviral signaling cascade that restricts rotavirus infection in vivo.

immunology↗

A metabolically stable PET tracer for imaging synaptic vesicle protein 2A: Synthesis and preclinical characterization of SDM-16

PurposeTo investigate the synaptic vesicle glycoprotein 2A (SV2A) expression in the whole central nervous system and peripheral tissues, a metabolically stable SV2A radiotracer is desirable to minimize a potential confounding effect of radiometabolites. The aim of this study was to develop and evaluate a metabolically stable SV2A radiotracer, [18F]SDM-16, in nonhuman primate brains. MethodsThe racemic SDM-16 (4-(3,5-difluorophenyl)-1-((2-methyl-1H-imidazol-1-yl)methyl)pyrrolidin-2-one) was synthesized and assayed for in vitro SV2A binding affinity. We synthesized the enantiopure [18F]SDM-16 using the corresponding arylstannane precursor. Nonhuman primate brain PET was performed on a FOCUS 220 system. Arterial blood was drawn for metabolite analysis and construction of plasma input function. Regional time-activity curves (TACs) were evaluated with the one-tissue compartment (1TC) model to obtain the volume of distribution (VT). Binding potential (BPND) was calculated using either the nondisplaceable volume of distribution (VND) or the centrum semiovale (CS) as the reference region. ResultsRacemic SDM-16 was synthesized in 3 steps with 44% overall yield and has high affinity (Ki = 3.7 nM) to human SV2A. [18F]SDM-16 was prepared in greater than 99% radiochemical and enantiomeric purity. This radiotracer displayed high specific binding in brain and was metabolically more stable than other SV2A PET tracers. The plasma free fraction (fP) of [18F]SDM-16 was 69%, which was higher than those of [11C]UCB-J (46%), [18F]SynVesT-1 (43%), [18F]SynVesT-2 (41%), and [18F]UCB-H (43%). The TACs were well described with the 1TC. The averaged test-retest variability (TRV) was -9{+/-}8%, and averaged absolute TRV (aTRV) was 10{+/-}7% for all analyzed brain regions. ConclusionWe have successfully synthesized a metabolically stable and high affinity SV2A PET tracer, [18F]SDM-16, which showed high specific and reversible binding in the NHP brain. [18F]SDM-16 may have potential application in the visualization and quantification of SV2A beyond the brain.

neuroscience↗

The cardiac STAT3 intercalated disc specific expression in tail suspension rat

BackgroundThe cardiovascular system is significantly agitated by loss of gravity. In microgravity, the body fluids shift toward the thoracic cavity, induced the heart becomes more spherical. This further increased the cardiac preload with an increasing of transmural central venous pressure, affects the right heart ventricles to tolerating the enhanced preload on the right ventricular wall. MethodIn this study we investigated the rat right ventricle remodeling in simulating persistent microgravity by using tail-suspension model, examined the remolding of the heart and the specific STAT3 expression in right heart myocardium. ResultThe results indicated that microgravity induced heart remodeling included a significant increasing of the ventricular weight in the left. However, the right ventricle was not increased significantly in the microgravity simulation rats. The histological study demonstrated that the outstanding development on right ventricular wall which included the gap junction remodeling and STAT3 signaling protein specific accumulation in the right ventricles. ConclusionThe results existed that the right cardiac ventricle has a distinctive remodeling process during microgravity simulation which was not the muscular hypertrophy and relative weight increasing, but manifested the STAT3 accumulation and the electrical gap junction remodeling. The effect of microgravity induced right ventricle remodeling and the STAT3 specific accumulation can be used for multi-purpose research.

physiology↗

Potent neutralization antibodies induced by a recombinant trimeric Spike protein vaccine candidate containing PIKA adjuvant for COVID-19

Neutralizing antibodies are critical to prevent corona virus infection. The structures of immunogens to elicit most potent neutralization antibodies are still under investigation. Here we tested the immunogenicity of the trimeric, full length Spike protein with 2 proline mutations to preserve its prefusion conformation. Recombinant trimeric Spike protein expressed by CHO cells was used with polyI:C (PIKA) adjuvant to immunize mice by 0-7-14 day schedule. The results showed that Spike-specific antibody was induced at day 21 with titer of more than 50,000 in average as measured by direct binding to Spike protein. The titer of neutralization reached more than 1000 in average when tested by a pseudo-virus system, using monoclonal antibodies (40592-MM57 and 40591-MM43) with neutralizing IC50 at 1 g/ml as standards. Protein/peptide array showed that the antibodies induced by trimeric S protein vaccine bind similarly to natural infection with the receptor binding domain (RBD) as major immunodominant region. No linear epitopes were found in RBD, although several linear epitopes were found in C-terminal domain right after RBD, and heptad repeat regions. Our study supports the efficacy of recombinant trimeric Spike protein vaccine candidate for COVID-19, with excellent safety and readiness for storage and distribution in developing countries.

immunology↗

Retinal glial cells under hypoxia possibly function in mammalian myopia by responding to mechanical stimuli, affecting hormone metabolism and peptide secretion

PurposeChanges in the retina and the choroid blood vessels are regularly observed in myopia. The aim of this study is to test if the retinal glial cells, which directly contact blood vessels, play a role in mammalian myopia. MethodWe adapted the common form-deprivation myopia mouse model and used the retina slice and whole-mount immunofluorescence technique to evaluate changes in the morphology, and distribution of retinal glial cells. We then searched the Gene Expression Omnibus database for series on myopia and retinal glial cells (astrocytes and Muller cells). Using review articles and the National Center for Biotechnology Information gene database, we obtained clusters of myopia-related gene lists. By searching SwissTargetPrediction, we collected information on atropine target proteins. We then used online tools to find the Gene Ontology analysis enriched clusters, pathways, and proteins that provide correlative evidence. ResultGlial fibrillary acidic protein fluorescence was observed in mice eyes that were covered and deprived of light for five days compared to uncovered eyes, and the cell morphology became more star-like. From in silico experiments, we identified several pathways and proteins that were common to both myopia and retinal glial cells in hypoxic conditions. The common pathways in human astrocytes represented response to mechanical stimuli, peptide secretion, skeletal system development, and monosaccharide binding. In mouse Muller cells, the pathways represented membrane raft and extracellular structure organisation. The proteins common to myopia and hypoxic glial cells were highly relevant to atropine target proteins. ConclusionRetinal astrocytes and Muller cells under hypoxic conditions contribute to the development of myopia, and may be a valid target for atropine.

bioinformatics↗

VirusDIP: Virus Data Integration Platform

MotivationThe Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created. ResultsTo facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide. Availabilityhttps://db.cngb.org/virus/ Contactweixiaofeng@cngb.org

bioinformatics↗

CNSA: a data repository for archiving omics data

With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-dimensional biological data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its analytical data and related metadata which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly, and Variation at present. Moreover, CNSA has created the correlation model of living samples, sample information, and analytical data on some projects, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for the storage, management and sharing of omics data, improving the data standards, and providing free access to open data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL: https://db.cngb.org/cnsa/

genomics↗

Learning from local to global - an efficient distributed algorithm for modeling time-to-event data

ObjectivesWe developed and evaluated a privacy-preserving One-shot Distributed Algorithm to fit a multi-center Cox proportional hazard model (ODAC) without sharing patient-level information across sites. MethodsUsing patient-level data from a single site combined with only aggregated information from other sites, we constructed a surrogate likelihood function, approximating the Cox partial likelihood function obtained using patient-level data from all sites. By maximizing the surrogate likelihood function, each site obtained a local estimate of the model parameter, and the ODAC estimator was constructed as a weighted average of all the local estimates. We evaluated the performance of ODAC with (1) a simulation study, and (2) a real-world use case study using four datasets from the Observational Health Data Sciences and Informatics (OHDSI) network. ResultsOur simulation study showed that ODAC provided estimates nearly the same as the estimator obtained by analyzing, in a single dataset, the combined patient-level data from all sites (i.e., the pooled estimator). The relative bias was less than 0.1% across all scenarios. The accuracy of ODAC remained high across different sample sizes and event rates. On the other hand, the metaanalysis estimator, which was obtained by the inverse variance weighted average of the sitespecific estimates, had substantial bias when the event rate is less than 5%, with the relative bias reaching 20% when the event rate is 1%. In the OHDSI network application, the ODAC estimates have a relative bias less than 5% for 15 out of 16 log hazard ratios; while the meta-analysis estimates had substantially higher bias than ODAC. ConclusionsODAC is a privacy-preserving and non-iterative method for implementing time-to-event analyses across multiple sites. It provides estimates on par with the pooled estimator and substantially outperforms the meta-analysis estimator when the event is uncommon, making it extremely suitable for studying rare events and diseases in a distributed manner.

bioinformatics↗

The roles of wrinkle structures in the veins of Asian Ladybird and bioinspiration

The deployable hind wings of the Asian ladybird beetle (Harmonia axyridis) play important roles in their flight. Wrinkle structures of veins are found on the bending zones of the hind wings of H. axyridis. This paper investigates the effect of the wrinkle structures of the veins of the hind wing on its deformation. Based on the nanomechanical properties of the veins, morphology of the hind wing, surface structures of veins and microstructures of the cross sections, including the veins and wing membranes, we establish four three-dimensional coupling models for hind wings with/without wrinkles with different and uniform reduced modulus. Relative to the bending and twisting model shapes, Model I, which includes the wrinkle structure and different reduced-modulus veins, has much more flexibility of passive deformation to control wing deformations. The results show that both the wrinkle structures in the bending zone and varying reduced modulus of the veins contribute to the flight performance of bending and twisting deformations of the hind wings, which have important implications for the bionic design of the biomimetic deployable wing of micro air vehicles (MAVs).

biophysics↗

An antibody drug conjugate targeting a GSTA glycosite-signature epitope of mucin1 expressed by non-small cell lung cancer

BackgroundAntibodies targeting abnormally glycosylated proteins have been ineffective in treating cancer. Antibody-drug conjugates are emerging as an efficient option, which allow specific delivery of drugs into tumors. We and others have dissected the abnormally glycosylated tandem repeat region of MUC1 glycoprotein as three site-specific glycosylated neoantigen peptide motifs (PDTR, GSTA, GVTS) for monoclonal antibody binding. MethodsInternalization of monoclonal antibodies was studied by immunofluorescence staining and colocalization with lysosomal markers in live cells. Antibody positivity in tumor and peritumoral tissue samples were studied by immunohistochemistry. The efficacy of anti-MUC1 ADCs were evaluated with various cancer cell lines and mouse tumor xenograft model. ResultsWe describe an anti-MUC1 ADC by conjugating GSTA neoantigen-specific 16A with monomethyl auristatin E (MMAE). 16A-MMAE showed potent antitumoral efficacy with IC50 ranging from 0.2 to 49.4 nM toward multiple types of cancer cells. In vivo, 16A-MMAE showed dose-dependent inhibition of tumor growth in mouse xenograft of NCI-H838 NSCLC cell line, with minimum effective dose at 1 mg/kg. At the dose of 3 mg/kg, 16A-MMAE did not cause significant toxicity in a transgenic mouse expressing human MUC1. ConclusionsThe high antitumoral efficacy of 16A-MMAE suggest that aberrant glycosylated MUC1 neoantigen is a target with high positivity in multiple cancer types for ADC development. Personalized therapy may be achieved by development of glycosite-specific antibody-drug conjugates.

pharmacology and toxicology↗

Evaluation of phenotyping errors on polygenic risk score predictions

Accurate disease risk prediction is essential in healthcare to provide personalized disease prevention and treatment strategies not only to the patients, but also to the general population. In addition to demographic and environmental factors, advancements in genomic research have revealed that genetics play an important role in determining the susceptibility of diseases. However, for most complex diseases, individual genetic variants are only weakly to moderately associated with the diseases. Thus, they are not clinically informative in determining disease risks. Nevertheless, recent findings suggest that the combined effects from multiple disease-associated variants, or polygenic risk score (PRS), can stratify disease risk similar to that of rare monogenic mutations. The development of polygenic risk score provides a promising tool to evaluate the genetic contribution of disease risk; however, the quality of the risk prediction depends on many contributing factors including the precision of the target phenotypes. In this study, we evaluated the impact of phenotyping errors on the accuracies of PRS risk prediction. We utilized electronic Medical Records and Genomics Network (eMERGE) data to simulate various types of disease phenotypes. For each phenotype, we quantified the impact of phenotyping errors generated from the differential and non-differential mechanism by comparing the prediction accuracies of PRS on the independent testing data. In addition, our results showed that the rate of accuracy degradation depended on both the phenotype and the mechanism of phenotyping error.

genomics↗

Normal development and fertility of Fut1, Fut2, and Sec1 triple knockout mice

The fucose alpha(1,2) galactose structure (H antigen) is synthesized by 1,2 fucosyltransferases Fut1, Fut2 and Sec1. H antigen has been reported to be involved in cancer progression, neurite migration, synaptic plasticity, host-microbe interaction, blastocyst implantation, and the maintenance of gut microbiome. Genetic depletion of Fut1 or Fut2 only cause defects of alpha1,2 fucosylation in limited tissues because of enzyme redundancy. In this study, we generated mice with deficiencies in Fut1, Fut2, and Sec1 genes to deplete H antigen through BAC Engineering for the generation of ES Cell-Targeting construct. The homogenous triple knockout mice showed no significant decrease of viability or development. Mass spectrometry and Western blot analysis confirmed the absence of H blood group antigen in multiple organs. These results indicate normal development and fertility of mice devoid of blood group H. The fine pathophysiological alterations in these mice remain to be carefully studied, and they may serve as valuable tools to study gut microbiome and host-microbe interactions.

biochemistry↗

Evosep One Enables Robust Quantitative Deep Proteome Coverage using Tandem Mass Tags while Significantly Reducing Instrument Time

The balance between comprehensively analyzing the proteome and using valuable mass spectrometry time is a genuine challenge in the field of proteomics. Multidimensional fractionation strategies have significantly increased proteome coverage, but often at the cost of increased mass analysis time, despite advances in mass spectrometer acquisition rates. Recently, the Evosep One liquid chromatography system was shown to analyze peptide samples in a high throughput manner without sacrificing in depth proteomics coverage. We demonstrate incorporation of Evosep One technology into our multiplexing workflow for quantitative analysis of tandem mass tag (TMT)-labeled non-small cell lung carcinoma (NSCLC) patient-derived xenografts (PDXs). Using a 30 samples per day Evosep workflow, >12,000 proteins were identified in 48 hours of mass spectrometry time, which is comparable to the number of proteins identified by our conventional concatenated EASY-nLC workflow in 67.5 hours. Shorter Evosep gradient lengths reduced the number of protein identifications by 10%, while decreasing mass analysis time by 50%. Thus, our Evosep workflow enables quantitative analysis of multiplexed samples in less time without conceding depth of proteome coverage.

systems biology↗

Generation of four iPSC lines from peripheral blood mononuclear cells (PBMCs) of an Attention Deficit Hyperactivity Disorder (ADHD) individual and a healthy sibling in an Australia-Caucasian family

Peripheral blood mononuclear cells were donated by a male teenager with clinically diagnosed Attention Deficit Hyperactivity Disorder under the Diagnostic and Statistical Manual of Mental Disorders IV criteria and his unaffected male sibling. Induced pluripotent stem cells were developed using integration-free Sendai Reprogramming factors containing OCT, SOX2, KLF4, and c-MYC. All four iPSC lines displayed pluripotent cell morphology, pluripotency-associated factors at protein level, alkaline phosphatase enzymatic activity, male karyotype of 46, XY, and in vitro differentiation capacity into all the three germ layers and negative for Mycoplasma.

neuroscience↗

Non-driver somatic alteration burden confers good prognosis in non-small cell lung cancer

BackgroundGenomic profiling of patient tumors has linked somatic driver mutations to survival outcomes of non-small cell lung cancer (NSCLC) patients, especially for those receiving targeted therapies. However, it remains unclear whether specific non-driver mutations have any prognostic utility.\n\nMethodsWhole exomes and transcriptomes were measured from NSCLC xenograft models of patients with diverse clinical outcomes. Penalised regression analysis was performed to identify a set of 865 genes associated with patient survival. The number of somatic copy number aberrations, point mutations and associated expression changes within the 865 genes were used to stratify independent NSCLC patient populations, filtered for chemotherapy naive and early-stage. In-depth genomic analysis and functional testing was conducted on the genomic alterations to understand their effect on improving survival.\n\nResultsHigh burden of somatic alterations are associated with longer disease-free survival (HR=0.153, P=1.48x10-4) in NSCLC patients. When somatic alterations burden was integrated with gene expression, we were able to predict prognosis in three independent patient datasets. Patients with high alteration burden could be further stratified based on the presence of immunogenic mutations, revealing another subgroup of patients with even better prognosis (85% with >5 years survival), and associated with cytotoxic T-cell expression. In addition, 95% of these 865 genes lack documented activity relevant to cancer, but are in pathways regulating cell proliferation, motility and immune response were implicated.\n\nConclusionOur results demonstrate that non-driver somatic alterations may influence the outcome of cancer patients by increasing beneficial immune response and inhibiting processes associated to tumorigenesis.

cancer biology↗

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows fed the same diets were investigated. Sixteen lactating dairy cows with similar parity were divided into two groups based on their milk yield: high-yield (HY) and low-yield (LY) groups. On day 21, rumen content samples were collected, and the microbiota composition was determined using Illumina MiSeq sequencing of the 16S rRNA gene. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat (P=0.08), protein (P=0.01) and total solid (P=0.04) contents than that of the HY group, though the HY group had higher ruminal acetate (P=0.05), propionate (P=0.02) and volatile fatty acid (VFA) (P=0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community composition and structure between the HY group and LY group. Overall, Bacteroidetes (HY group: 52.91{+/-}3.06%; LY group: 61.88{+/-}3.03%) was the predominant phylum, followed by Firmicutes (HY group: 41.10{+/-}2.74%; LY group: 32.11{+/-}2.97%). The abundances of Ruminococcus 2, Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, 3 genera--Anaerostipes, Bacteroidales and Anaeroplasma--were identified as biomarker species with the greatest impacts on the ruminal community structure in the LY group. These findings facilitate the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.

microbiology↗