Biology subjects

Huang, Q.

Publications and source records attributed to Huang, Q..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Neuron-glia Integrity: Functional Assessment, Molecular Underpinnings, and Implication for Higher Brain Functions

We developed a theory of neuron-glia integrity to underline the fact that neurons and glia cells work together in the central nervous system. Here we substantiated this theory and exemplified the implication of intact neuron-glia integrity for higher brain functions. An animal model of maternal separation with early weaning (MSEW) was applied to neonatal rats to mimic early life neglect and abuse in humans. Behavioral performance of rats was evaluated at adulthood, followed by functional assessments of neuron-glia integrity in living rats, and the demonstration of molecular underpinnings of impaired neuron-glia integrity in MSEW rats. MSEW rats showed higher levels of anxiety and explorative activity, higher glutamate level, but lower GABA level in PFC and hippocampus. MSEW procedure down-regulated protein levels of GLT-1 and ATP-, but up-regulated GAD65 and GS, while had no effects on GLAST and PAG. Moreover, it reduced the fractional anisotropy values in various brain regions, in addition to increasing NAA levels. Concurrently, MSEW led to hypomyelination in PFC as evidenced by relevant cellular and molecular changes.

neuroscience↗

bioRxiv2020

LZTR1 inactivation promotes MAPK/ ERK pathway activation in glioblastoma by stabilizing oncoprotein RIT1

Large-scale sequencing studies on glioblastoma have identified numerous genetic alterations. Leucine-zipper-like transcription regulator 1 (LZTR1) is inactivated by non-synonymous mutations and copy number losses, suggesting that it is a tumor suppressor in glioblastoma. However, how LZTR1 mutations contribute to glioblastoma pathogenesis remains poorly understood. Here, we revealed that LZTR1, as an adaptor of the CUL3 E3 ubiquitin ligase complex, recognizes and triggers ubiquitin-dependent degradation of oncoprotein RIT1, a RAS-like GTPase. Wild-type LZTR1 suppresses glioblastoma cell proliferation and migration by inactivating the MAPK/ERK signaling pathway in a RIT1-dependent manner. However, the effects were abrogated by the glioblastoma-associated LZTR1 mutations. Our findings revealed the underlying molecular mechanism of LZTR1 mutations-driven glioblastoma, and provide novel therapeutic target for LZTR1 mutations-driven glioblastoma.

cancer biology↗

bioRxiv2020

Schistosoma Japonicum infection in Treg-specific USP21 knock-out mice

USP21, an E3 de-ubiquitin enzyme playing vital roles in physiological activities, is important for Treg cells to maintain immune homeostasis and control immune tolerance. To understand its diverse functions and potential mechanism is essential for disease development. We, using the USP21 gene-conditional knock-out mice model of Schistosoma Japonicum infection, found more cercariae developed into adults, and more eggs deposited in the liver in KO mice. However, immunohistochemistry showed the degree and the area of egg granuloma and liver fibrosis were both reduced. This suggested knock-out USP21 did affect the immunoregulation between schistosomes and the host. In KO mice the content of IFN-gamma and IL-4, and the expression of anti-SEA IgG and anti-SWAP IgG both increased in the liver, spleen and blood by flow cytometry, while the content of IL-10, lL-17A, IL-23, IL-9 and the expression of USP21 and anti-SEA IgM decreased. This indicated USP21-knockout-Tregs promoted both Th1-type and Th2-type immunity and inhibited other immunities during schistosomes infection, which disordered the host immunity. This study revealed the immunomodulatory of USP21 and preliminarily suggests it might be essential to regulate the complex immune network between the host and schistosomes. USP21 provides a new possible target for schistosomiasis treatment in the future. Author summarySchistosomiasis is a common neglected tropical disease that affects more than 230 million people worldwide. Therefore, the study on the mechanism of immune interaction between schistosomas and the host is not only helpful for the understanding of immune homeostasis, but also helpful for the further development of the treatment of schistosomiasis. Ubiquitin Specific Protease 21(USP21) has been shown to be involved in the regulation of many biological processes, such as maintaining immune homeostasis and regulating cell growth. Here, we observed that the specific deletion of USP21 led to the decrease of mices ability to resist schistosomes infection and promoted the survival of schistosomes. It was also proved that unstable regulatory T cells would produce polarization phenomenon and promote differentiation to helper T cells, which would lead to disorder of immune response in mice. However, this process reduced the serious immune pathological damage caused by egg granuloma. Our findings reveal that USP21 may be an important molecule regulating immune interaction between Schistosoma japonicum and the host.

immunology↗

bioRxiv2020

Children Developing Celiac Disease Have a Distinct and Proinflammatory Gut Microbiota in the First 5 Years of Life

Celiac disease (CD) is an autoimmune disorder triggered by gluten consumption. To identify the role of gut microbes in CD onset, we performed a longitudinal study focusing on two important phases of gut microbiota development at ages 2.5 and 5 (n=16). We obtained samples from children who developed CD during or after the study (CD progressors) and age, sex, and HLA-matched healthy controls. CD progressors had a distinct gut microbiota composition and IgA-sequencing identified unique IgA targets in the gut. Three cytokines, one chemokine, and 19 plasma metabolites were significantly altered in CD progressors at age 5. Feeding C57BL/6J mice with taurodeoxycholic acid (TDCA), a 2-fold increased microbiota-derived metabolite in CD progressors, caused villous atrophy, increased intraepithelial lymphocytes (IELs), CD4+ T-cells, Natural Killer cells, and Qa-1 expression on T-cells while decreasing T-regulatory cells in IELs. Thus, TDCA drives inflammation in the small intestines that potentially contribute to the CD onset. HighlightsO_LICD progressors have a distinct gut microbiome composition compared to healthy controls in two important phases of gut microbiota development (age 2.5 and 5 years) C_LIO_LICD progressors have more IgA-coated bacteria in their gut at age 5 compared to healthy controls. Further, IgA-sequencing identified unique bacterial targets in CD progressors. C_LIO_LIThree plasma proinflammatory cytokines and a chemokine were increased in CD progressors years before diagnosis, indicating an early inflammatory response. C_LIO_LIWe identified 19 metabolites that are significantly altered in CD progress at age 5 and microbiota-derived TDCA increased two-fold. C_LIO_LITDCA treatment in B6 mice increased CD4+ cells and NK cells while decreasing CD8+ T-regulatory (Treg) cells. It also increased Qa-1 expression on immune cells. C_LI

microbiology↗

bioRxiv2020

Quantitative LCMS for ceramides/dihydroceramides: pregnancy baseline biomarkers and potential metabolic messengers

Ceramides and dihydroceramides are sphingolipids that present in abundance at the cellular membrane of eukaryotes. Although their metabolic dysregulation has been implicated in many diseases, our knowledge about circulating ceramide changes during the pregnancy remains limited. In this study, we present the development and validation of a high-throughput liquid chromatography-tandem mass spectrometric (LC/MS/MS) method for simultaneous quantification of 16 ceramides and 10 dihydroceramides in human serum within 5 mins by using stable isotope-labeled ceramides as internal standards (ISs). This method employs a protein precipitation method for high throughput sample preparation, reverse phase isocratic elusion for chromatographic separation, and Multiple Reaction Monitoring (MRM) for mass spectrometric detection. To qualify for clinical applications, our assay was validated against the FDA guidelines: the Lower Limit of Quantitation (LLOQ as low as 1 nM), linearity (R2>0.99), precision (Coefficient of Variation<15%), accuracy (Percent Error<15%), extraction recovery (>90%), stability (>85%), and carryover (<0.1%). With enhanced sensitivity and specificity from this method, we have, for the first time, determined the serological levels of ceramides and dihydroceramides to reveal unique temporal gestational patterns. Our approach could have value in providing insights into disorders of pregnancy.

biochemistry↗

bioRxiv2020

Human-induced changes in habitat preference by capybaras (Hydrochoerus hydrochaeris) and their potential effect on zoonotic disease transmission

Human activities are changing landscape structure and function globally, affecting wildlife space use, and ultimately increasing human-wildlife conflicts and zoonotic disease spread. Capybara (Hydrochoerus hydrochaeris) is a conflict species that has been implicated in the spread and amplification of the most lethal tick-borne disease in the world, the Brazilian spotted fever (BSF). Even though essential to understand the link between capybaras, ticks and the BSF, many knowledge gaps still exist regarding the effects of human disturbance in capybara space use. Here, we analyzed diurnal and nocturnal habitat selection strategies of capybaras across natural and human-modified landscapes using resource selection functions (RSF). Selection for forested habitats was high across human- modified landscapes, mainly during day- periods. Across natural landscapes, capybaras avoided forests during both day- and night periods. Water was consistently selected across both landscapes, during day- and nighttime. This variable was also the most important in predicting capybara habitat selection across natural landscapes. Capybaras showed slightly higher preferences for areas near grasses/shrubs across natural landscapes, and this variable was the most important in predicting capybara habitat selection across human-modified landscapes. Our results demonstrate human-driven variation in habitat selection strategies by capybaras. This behavioral adjustment across human-modified landscapes may be related to BSF epidemiology.

ecology↗

bioRxiv2020

Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)

The outbreaks of 2002/2003 SARS, 2012/2015 MERS and 2019/2020 Wuhan respiratory syndrome clearly indicate that genome evolution of an animal coronavirus (CoV) may enable it to acquire human transmission ability, and thereby to cause serious threats to global public health. It is widely accepted that CoV human transmission is driven by the interactions of its spike protein (S-protein) with human receptor on host cell surface; so, quantitative evaluation of these interactions may be used to assess the human transmission capability of CoVs. However, quantitative methods directly using viral genome data are still lacking. Here, we perform large-scale protein-protein docking to quantify the interactions of 2019-nCoV S-protein receptor-binding domain (S-RBD) with human receptor ACE2, based on experimental SARS-CoV S-RBD-ACE2 complex structure. By sampling a large number of thermodynamically probable binding conformations with Monte Carlo algorithm, this approach successfully identified the experimental complex structure as the lowest-energy receptor-binding conformations, and hence established an experiment-based strength reference for evaluating the receptor-binding affinity of 2019-nCoV via comparison with SARS-CoV. Our results show that this binding affinity is about 73% of that of SARS-CoV, supporting that 2019-nCoV may cause human transmission similar to that of SARS-CoV. Thus, this study presents a method for rapidly assessing the human transmission capability of a newly emerged CoV and its mutant strains, and demonstrates that post-genome analysis of protein-protein interactions may provide early scientific guidance for viral prevention and control.

genomics↗

bioRxiv2020

Transmission dynamics of 2019 novel coronavirus (2019-nCoV)

RationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear. ObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS. MethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS. Measurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic. ConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS. What This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.

systems biology↗

bioRxiv2020

Bcl6 Preserves the Suppressive Function of Regulatory T Cells during Tumorigenesis

During tumorigenesis, tumor infiltrating regulatory T (Treg) cells restrict the function of effector T cells in tumor microenvironment and thereby promoting tumor growth. The anti-tumor activity of effector T cells can be therapeutically unleashed, and is now being exploited for the treatment of various types of human cancers. However, the immune suppressive function of Treg cells remains a major hurdle to broader effectiveness of tumor immunotherapy. In this article, we reported that the deletion of Bcl6 specifically in Treg cells led to stunted tumor growth, which was caused by impaired Treg cell responses. Notably, Bcl6 is essential in maintaining the lineage stability of Treg cells in tumor microenvironment. Meanwhile, we found that the absence of follicular regulatory T (Tfr) cells, which is a result of Bcl6 deletion in Foxp3+ cells, was dispensable for tumor control. Importantly, the increased Bcl6 expression in Treg cells is associated with poor prognosis of human colorectal cancer and lymph node metastasis of skin melanoma. Furthermore, Bcl6 deletion in Treg cells exhibits synergistic effects with immune checkpoint blockade therapy. Collectively, these results indicate that Bcl6 actively participates in regulating Treg cell immune responses during tumorigenesis and can be exploited as a therapeutic target of anti-tumor immunity.

immunology↗

bioRxiv2020

Investigating the impact of combination phage and antibiotic therapy: a modeling study

Antimicrobial resistance (AMR) is a serious threat to global health today. The spread of AMR, along with the lack of new drug classes in the antibiotic pipeline, has resulted in a renewed interest in phage therapy, which is the use of bacteriophages to treat pathogenic bacterial infections. This therapy, which was successfully used to treat a variety of infections in the early twentieth century, had been largely dismissed due to the discovery of easy to use antibiotics. However, the continuing emergence of antibiotic resistance has motivated new interest in the use of phage therapy to treat bacterial infections. Though various models have been developed to address the AMR-related issues, there are very few studies that consider the effect of phage-antibiotic combination therapy. Moreover, some of biological details such as the effect of the immune system on phage have been neglected. To address these limitations, we utilized a mathematical model to examine the role of the immune response in concert with phage-antibiotic combination therapy compounded with the effects of the immune system on the phages being used for treatment. We explore the effect of phage-antibiotic combination therapy by adjusting the phage and antibiotics dose or altering the timing. The model results show that it is important to consider the host immune system in the model and that frequency and dose of treatment are important considerations for the effectiveness of treatment. Our study can lead to development of optimal antibiotic use and further reduce the health risks of the human-animal-plant-ecosystem interface caused by AMR.

microbiology↗

bioRxiv2019

Cep57 and Cep57l1 cooperate to recruit the Cep63-Cep152 complex for centriole biogenesis

Cep152 and Cep63 act as the cradle and recruit Plk4 to initiate the centriole biogenesis in a mother centriole dependent manner. However, how the Cep152-Cep63 complex is targeted to the proximal end of mother centrioles is unclear. In this study, we show that Cep57 and its paralog, Cep57l1, colocalize with Cep63 and Cep152 at the proximal end of mother centrioles in both cycling cells and differentiated multiciliated cells. Both Cep57 and Cep57l1 associate with the Cep152-Cep63 complex by directly binding to the centrosomal targeting region of Cep63. Co-depletion of Cep57 and Cep57l1 blocks the loading of Cep63-Cep152 to the centriole and subsequently prevents centriole duplication. We propose that Cep57 and Cep57l1 act together to ensure the recruitment of the Cep63-Cep152 complex to the mother centrioles for procentriole formation. Summary statementCep57 and its paralog, Cep57l1, cooperatively act as a molecular scaffold to recruit the Cep63-Cep152 cradle to the proximal end of centrioles in the early stages of centriole duplication.

cell biology↗

bioRxiv2019

Evaluation of Cell Type Deconvolution R Packages on Single Cell RNA-seq Data

Annotating cell types is a critical step in single cell RNA-Seq (scRNA-Seq) data analysis. Some supervised/semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking to provide practical guidelines. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics data are adaptable to scRNA-Seq analysis. In this study, we evaluated ten cell-type annotation methods publicly available as R packages. Eight of them are popular methods developed specifically for single cell research (Seurat, scmap, SingleR, CHETAH, SingleCellNet, scID, Garnett, SCINA). The other two methods are repurposed from deconvoluting DNA methylation data: Linear Constrained Projection (CP) and Robust Partial Correlations (RPC). We conducted systematic comparisons on a wide variety of public scRNA-seq datasets as well as simulation data. We assessed the accuracy through intra-dataset and inter-dataset predictions, the robustness over practical challenges such as gene filtering, high similarity among cell types, and increased classification labels, as well as the capabilities on rare and unknown cell-type detection. Overall, methods such as Seurat, SingleR, CP, RPC and SingleCellNet performed well, with Seurat being the best at annotating major cell types. Also, Seurat, SingleR, CP and RPC are more robust against down-sampling. However, Seurat does have a major drawback at predicting rare cell populations, and it is suboptimal at differentiating cell types that are highly similar to each other, while SingleR and RPC are much better in these aspects. All the codes and data are available at: https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark.

bioinformatics↗

bioRxiv2019

Functional effects of chimeric antigen receptor co-receptor signaling domains in human Tregs

Antigen-specific regulatory T cells (Tregs) engineered with chimeric antigen receptor (CARs) are a potent immunosuppressive cellular therapy in multiple disease models. To date the majority of CAR Treg studies employed second generation CARs, encoding a CD28 or 4-1BB co-receptor signaling domain and CD3{zeta}, but it was not known if this CAR design was optimal for Tregs. Using an HLA-A2-specific CAR platform and human Tregs, we compared ten CARs with different co-receptor signaling domains and systematically tested their function. Tregs expressing a CAR encoding wild-type CD28 were markedly superior to all other CARs tested in an in vivo model of graft-versus-host disease. In vitro assays revealed stable expression of Helios and ability to suppress CD80 expression on DCs as key in vitro predictors of in vivo function. This comprehensive study of CAR signaling-domain variants in Tregs can be leveraged to optimize CAR design for use in antigen-specific Treg therapy.

immunology↗

bioRxiv2019

A 3D High Resolution Generative Deep-learning Network for Fluorescence Microscopy Image

Deep learning technology enables us acquire high resolution image from low resolution image in biological imaging free from sophisticated optical hardware. However, current methods require a huge number of the precisely registered low-resolution (LR) and high-resolution (HR) volume image pairs. This requirement is challengeable for biological volume imaging. Here, we proposed 3D deep learning network based on dual generative adversarial network (dual-GAN) framework for recovering HR volume images from LR volume images. Our network avoids learning the direct mappings from the LR and HR volume image pairs, which need precisely image registration process. And the cycle consistent network makes the predicted HR volume image faithful to its corresponding LR volume image. The proposed method achieves the recovery of 20x/1.0 NA volume images from 5x/0.16 NA volume images collected by light-sheet microscopy. In essence our method is suitable for the other imaging modalities.

neuroscience↗

bioRxiv2019

Identifying gene function and module connections by the integration of multi-species expression compendia

The functions of many eukaryotic genes are still poorly understood. We developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multi-species expression compendia--1,700 datasets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast--collected in this study. Unlike most existing bioinformatics tools, GeneBridge exploits both positive and negative gene/module-module associations. We constructed association networks, such as those bridging mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available at systems-genetics.org, to facilitate the identification of connections linking genes, modules, phenotypes, and diseases.

systems biology↗

bioRxiv2019

Deep-learning enables proteome-scale identification of phase-separated protein candidates from immunofluorescence images

Intrinsically disordered region (IDR) analysis has been widely used in the screening of phase-separated proteins. However, the precise sequences determining phase separation remain unclear. Furthermore, a large number of phase-separated proteins that exhibit relatively low IDR content remain uncharacterized. Phase-separated proteins appear as spherical droplet structures in immunofluorescence (IF) images, which renders them distinguishable from non-phase-separated proteins. Here, we transformed the problem of phase-separated protein recognition into a binary classification problem of image recognition. In addition, we established a method named IDeepPhase to identify IF images with spherical droplet structures based on convolutional neural networks. Using IDeepPhase on proteome-scale IF images from the Human Protein Atlas database, we generated a comprehensive list of phase-separated candidates which displayed spherical droplet structures in IF images, allowing nomination of proteins, antibodies and cell lines for subsequent phase separation study.

bioinformatics↗

bioRxiv2019

Manipulating serial replay during memory retention rapidly alters human sequence memory

Temporarily storing a list of items in working memory (WM), a fundamental ability in cognition, has been posited to rely on the temporal dynamics of multi-item neural representations during retention. Here, we develop a "dynamic perturbation" approach to manipulate the relative memory strength of a list of WM items, by interfering with their neural dynamics during the delay period in a temporally correlated way. Six experiments on human subjects confirm the effectiveness of this WM manipulation method. A computational model combining continuous attractor neural network (CANN) and short-term synaptic plasticity (STP) principles further reproduces all the empirical findings. The model shows that the "dynamic perturbation" modifies the synaptic efficacies of WM items through STP principles, eventually leading to changes in their relative memory strengths. Our results support the causal role of temporal dynamics of neural network in mediating multi-item WM and offer a promising, non-invasive approach to manipulate WM.

neuroscience↗

bioRxiv2019

Enhancer-promoter association determines Sox2 transcription regulation in mouse pluripotent cells

Distal enhancer-promoter associations are essential for transcription control and emerging as a common epigenetic way to determine gene expression in eukaryotes. However, it remains as an uncultivated land on how their diversity influences gene transcription during development. In this study, we select three defined Sox2 associated enhancers (E1, E2 and E3), representing different distal interaction categories, to further explore their biological effects. We construct three enhancer-knockout cells via CRISPR/Cas9 system in mouse embryonic stem cells. Results show that these associations carry out various biological features. Embryonic stem cell specific association (E1) speeds up cell cycle and involves in cardiac development, which has been validated in vivo. In contrast, the indirect one (E2) restrains nerve differentiation and has potential effect on lipid metabolism. The common one (E3) promotes nerve differentiation and inhibits oxidation-reduction process. Together, these different associations determine Sox2 transcription and function specificity in mouse embryonic stem cells. Our study will enable a way for exploring miscellaneous spatiotemporal gene transcription control and advancing quantitative knowledge by utilizing three-dimensional genomic information.\n\nSummary statementSox2 transcription is complicated in mouse embryonic stem cells. It involves in heavily enhancer-promoter associations, which might make it a suitable model for phase-separation study. To decompose this cooperative regulation, diverse interactions are investigated. The biological effects have been explored in multiple perspectives. This may represent a quantitative way to explore and a potential new strategy to transcription control study.

molecular biology↗