Biology subjects

Zhao, B.

Publications and source records attributed to Zhao, B..

At least 163 records · Page 9Linked to original sources

bioRxiv2021

Azacytidine targeting SARS-CoV-2 viral RNA as a potential treatment for COVID-19

The COVID-19 pandemic is a global health disaster. Moreover, emerging mutated virus strains present an even greater challenge for existing vaccines and medications. One possible solution is to design drugs based on the properties of virus epigenome, which are more common among coronaviruses. Here, we reported an FDA-approved drug for myelodysplastic syndrome, azacytidine (5Aza), limited virus infection and protected mice against SARS-CoV-2. We demonstrated that this antiviral effect is related to 5Aza incorporation into viral RNA, which disrupt m5C RNA methylation modification profile. This work suggests that targeting viral epigenomes is a viable therapeutic strategy, potentially opening new pathways for treating COVID-19.

microbiology↗

bioRxiv2021

A natural marmoset model of genetic generalized epilepsy.

As a common neurological disease, epilepsy has been extensively studied. Efforts have been made on rodent and other animal models to reveal the pathogenic mechanisms of epilepsy and develop new drugs as treatment. However, the features of current epilepsy models cannot fully mimic different kinds of epilepsy in human, asking for non-human primates models of epilepsy. The common marmoset (Callithrix jacchus) is a New World monkey that is widely used to study brain function. Here, we show a natural marmoset model of generalized epilepsy. In this unique marmoset family, generalized epilepsy was successfully induced by handling operation in some individuals. We mapped the marmoset family with handling-sensitive epilepsy and found that epileptic marmoset had an autosomal dominant genetic predisposition. Those marmosets were more sensitive to epilepsy inducers pentylenetetrazol (PTZ). By electrocorticogram (ECoG) recording, we detected epileptic discharge in marmoset with history of seizures. However, there was no significant change in the overall structure of epileptic marmoset brain. In summary, we report a family of marmosets with generalized seizures induced by handling operation. This epileptic marmoset family provides insights to better understand the mechanism of generalized epilepsy and helps to develop new therapeutic methods. Short summaryDespite the rodent and other animal models on epilepsy, a common neurological disease, the understanding of the pathogenic mechanisms of epilepsy and treatment are yet to be advanced., Non-human primates are good experimental animals for modelling neurological disease. Here we report a common marmoset family with generalized epilepsy induced by handling stimulation. We mapped the epileptic marmoset family and found that epilepsy had a genetic predisposition. The present report deals in detail with the phenotypes and characteristics of epileptic marmosets. This natural marmoset reflect epilepsy model will help to better understand the mechanism of epilepsy and develop new therapeutic methods.

neuroscience↗

bioRxiv2021

Protection of the prodomain 1-helix correlates with latency in the transforming growth factor- family

The 33 members of the transforming growth factor beta (TGF-{beta}) family are fundamentally important for organismal development and homeostasis. Family members are synthesized and secreted as pro-complexes of prodomains that are non-covalently bound to the growth factor (GF). The pro-complexes of some members are latent and require activation steps to release the GF for signaling. Why some members are latent while others are non-latent is incompletely understood, but crystal structures and hydrogen-deuterium exchange (HDX) of four family members have begun to unravel how latency is regulated. Here, we extend this understanding by comparing pro-complex conformation in negative stain EM (nsEM) and HDX of ActA, BMP7, BMP9, BMP10, GDF8, TGF-{beta}1, and TGF-{beta}2. nsEM revealed that family members varied in either adopting cross-armed, open-armed, or V-armed configurations. Latency was achieved in both cross-armed and V-armed but not open-armed conformations. HDX revealed remarkably varying patterns of exchange between family members, consistent with large prodomain sequence divergence. We observed a strong correlation between latency and protection of the prodomain 1-helix from exchange, which in latent members coincided with greater buried surface area of the 1-helix and more hydrogen and cation-pi bonds from the prodomain fastener and GF to the 1-helix. Strong sequence conservation of the 1-helix and fastener only in latent members suggests that similar interactions are conserved and sufficient to confer latency. Moreover, most members exhibited rapid exchange in the unstructured "association region" at the prodomain N-terminus, highlighting their availability for interacting with factors that may regulate latency and extracellular storage.

biophysics↗

bioRxiv2021

Live-Cell Imaging of (p)ppGpp with RNA-based Fluorescent Sensors

Guanosine tetra- and pentaphosphate, (p)ppGpp, are important alarmone nucleotides that regulate bacterial survival in stressful environment. A direct detection of (p)ppGpp in living cells is critical for our understanding of the mechanism of bacterial stringent response. However, it is still challenging to directly image and measure cellular (p)ppGpp. Here, we report a type of RNA-based fluorescent sensors for live-cell imaging of (p)ppGpp. Our sensor is engineered by conjugating a recently identified (p)ppGpp-specific riboswitch with a fluorogenic RNA aptamer, Broccoli. These sensors can be genetically encoded and enable direct monitoring of cellular (p)ppGpp accumulation. Unprecedented information on cell-to-cell variation and cellular dynamics of (p)ppGpp levels can now be obtained under different nutritional conditions. We predict that these RNA-based sensors will be broadly adapted to study bacterial stringent response.

cell biology↗

bioRxiv2021

Adipsin promotes bone marrow adiposity by priming mesenchymal stem cells

BackgroundBone marrow (BM) adipose tissue (BMAT) has been shown to be vital for regulating metabolism and maintaining skeletal homeostasis in the marrow niche. As a reflection of BM remodeling, BMAT is highly responsive to nutrient fluctuations, hormonal changes and metabolic disturbances such as obesity and diabetes mellitus. Expansion of BMAT has also been strongly associated with bone loss in mice and humans. However, the regulation of BM plasticity remains poorly understood, as does the mechanism that links changes in marrow adiposity with bone remodeling. MethodsUsing C57BL/6 mice as a model, we employed the bone-protected PPAR{gamma} constitutive deacetylation (2KR), Adipsin, and its downstream effector, C3, knockout mice. These mice were challenged to thiazolidinedione treatment, calorie restriction, or aging in order to induce bone loss and MAT expansion. Analysis of bone density and marrow adiposity was performed using a CT scanner and by RNA analysis to assess adipocyte and osteoblast markers. For in vitro studies, primary bone marrow stromal cells (BMSCs) were isolated and subjected to osteoblastogenic or adipogenic differentiation or chemical treatment followed by morphological and molecular analyses. Clinical data was obtained from samples of a previous clinical trial of fasting and high calorie diet in healthy human volunteers. ResultsWe have shown that Adipsin is the most up-regulated adipokine during BMAT expansion in mice and humans, in a PPAR{gamma} acetylation-dependent manner. Ablation of Adipsin in mice specifically inhibited BMAT expansion but not peripheral adipose depots, and improved bone mass during calorie restriction, thiazolidinedione treatment, and aging. These effects were mediated through its downstream effector, complement component C3, to prime common progenitor cells toward adipogenesis rather than osteoblastogenesis through inhibiting Wnt/{beta}- catenin signaling. ConclusionsAdipsin promotes new adipocyte formation and affects skeletal remodeling in the BM niche. Our study reveals a novel mechanism whereby the BM sustains its own plasticity through paracrine and endocrine actions of a unique adipokine. FundingThis work was supported by the National Institutes of Health T32DK007328 (NA), F31DK124926 (NA), R01DK121140 (JCL), R01AR068970 (BZ), R01AR071463 (BZ), R01DK112943 (LQ), and P01HL087123 (LQ).

molecular biology↗

bioRxiv2021

Understanding binary classifier model structure based on Shapley feature interaction patterns

There is increasing emphasis on the interpretability of machine learning models, including in understanding biological systems. The well-known Shapley value framework based on game theory works in principle with any models to attribute feature importance. While feature interactions are critical to understand and can be interpreted within this framework, much attention is paid in practice on global feature importance and general trends of interactions. The inter-relationships between underlying model structure and Shapley value and its decomposition is less clear. Here we use binary classifiers to systematically examine how logical and additive interactions affect marginal contributions. These decomposed main and interaction effects are reflected in resulting Shapley dependence plots. The directionality of inequalities or logical/additive operators influence independently the main and marginal/interaction effects. Lastly, we show that these principles are applicable for models with noise.

systems biology↗

bioRxiv2021

Bacterial retrons enable precise gene editing in human cells

Retrons are bacterial genetic elements involved in anti-phage defense. They have the unique ability to reverse transcribe RNA into multicopy single-stranded DNA (msDNA) that remains covalently linked to their template RNA. Retrons coupled with CRISPR-Cas9 in yeast have been shown to improve editing efficiency of precise genome editing via homology-directed repair (HDR). HDR editing efficiency has been limited by challenges associated with delivering extracellular donor DNA encoding the desired mutation. In this study, we tested the ability of retrons to produce msDNA as donor DNA and facilitate HDR by tethering msDNA to guide RNA in HEK293T and K562 cells. Through heterologous reconstitution of retrons from multiple bacterial species with the CRISPR-Cas9 system, we demonstrated HDR rates of up to 11.3%. Overall, our findings represent the first step in extending retron-based precise gene editing to human cells.

bioengineering↗

bioRxiv2021

scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

While the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies, using bulk sequencing, ignore much of this heterogeneity, reducing discovery and explanatory power. Single-cell approaches combined with F1 genetic designs provide a new opportunity to address this problem, however suitable computational methods to model these complex relationships are lacking. Here, we developed scDALI, an analysis framework that integrates single-cell chromatin accessibility for unbiased cell state identification with allelic quantifications to assay genetic effects. scDALI builds on Gaussian process regression and can differentiate between homogeneous (pervasive) allelic imbalances and cell state-specific regulation. As a proof-of-principle, we applied scDALI to whole Drosophila embryos from F1 crosses, profiling sciATAC-seq at three embryonic stages. Even in these very complex samples, scDALI discovered hundreds of peaks with heterogeneous allelic imbalance, having effects in specific lineages and/or developmental stages. Our study provides a general strategy to identify the cellular context of allelic imbalance, a crucial step in linking genetic traits to cellular phenotypes.

genomics↗

bioRxiv2021

Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

genomics↗

bioRxiv2021

Dopamine modulates visual threat processing in the superior colliculus via D2 receptors

Dopamine (DA) system is intriguing in the aspect that distinct, typically opposing physiological functions are mediated by D1 dopamine receptors (Drd1) and D2 dopamine receptors (Drd2). Both Drd1+ and Drd2+ neurons were identified in superior colliculus (SC), a visuomotor integration center known for its role in defensive behaviors to visual threats. We hypothesized that Drd1+ and Drd2+ neurons in the SC may play a role in promoting instinctive defensive responses. Optogenetic activation of Drd2+ neurons, but not Drd1+ neurons, in the SC triggered strong defensive behaviors. Chemogenetic inhibition of SC Drd2+ neurons decreased looming-induced defensive behavior, suggesting involvement of SC Drd2+ neurons in defensive responses. To further confirm this functional role of Drd2 receptors, pretreatment with the Drd2+ agonist quinpirole in the SC impaired looming-evoked defensive responses, suggesting an essential role of Drd2 receptors in the regulation of innate defensive behavior. Inputs and outputs of SC Drd2+ neurons were investigated using viral tracing: SC Drd2+ neurons mainly receive moderate inputs from the Locus Coeruleus (LC), whilst we did not find any incoming projections from other dopaminergic structures. Our results suggest a sophisticated regulatory role of DA and its receptor system in innate defensive behavior.

neuroscience↗

bioRxiv2021

A Safe and Effective Mucosal RSV Vaccine Consisting of RSV Phosphoprotein and Flagellin Variant

Respiratory syncytial virus (RSV) is a major cause of serious acute lower respiratory tract infection in infants and the elderly. No licensed RSV vaccine available thus far calls for the development of vaccines with new target(s) and vaccination strategies. Here, we constructed a recombinant protein, designated P-KFD1, comprised of RSV phosphoprotein (P) and E. coli K12 strain-derived flagellin variant KFD1. Intranasal (i.n.) immunization with P-KFD1 inhibits RSV replication in both upper and lower respiratory tract, and protects mice against lung disease without vaccine-enhanced disease (VED). The P-specific CD4+ T cells provoked by P-KFD1 i.n. immunization, either reside in or migrate to respiratory tract, mediate protection against RSV infection. Sc-RNA seq and carboxyfluorescein succinimidyl ester (CFSE) labeled cell transfer further characterized the Th1 and Th17 responses induced by P-KFD1. Finally, we found the anti-viral protection depends on either IFN-{gamma} or IL-17A. Collectively, P-KFD1 is promising as a safe and effective mucosal vaccine candidate to prevent RSV infection. HIGHLIGHTSO_LIA new subunit RSV vaccine candidate with new target and vaccination strategy, P-KFD1, is designed and generated C_LIO_LIIntranasal immunization with P-KFD1 protects mice against RSV infection and averts vaccine-enhanced disease C_LIO_LISc-RNA seq and CFSE-labelled cell transfer identified characteristics of the protective CD4+ T cells C_LIO_LILocal and peripheral CD4+ T cells provide protection against RSV infection dependent on either IFN-{gamma} or IL-17A C_LI

immunology↗

bioRxiv2021

Differential Conditioning Produces Merged Long-term Memory in Drosophila

Multiple spaced trials of aversive differential conditioning can produce two independent long-term memories (LTMs) of opposite valence. One is an aversive memory for avoiding the conditioned stimulus (CS+), and the other is a safety memory for approaching the non-conditioned stimulus (CS-). Here, we show that a single trial of aversive differential conditioning yields one merged LTM (mLTM) for avoiding both CS+ and CS-. Such mLTM can be detected after sequential exposures to the shock-paired CS+ and unpaired CS-, and be retrieved by either CS+ or CS-. The formation of mLTM relies on triggering aversive-reinforcing dopaminergic neurons and subsequent new protein synthesis. Expressing mLTM involves {beta} Kenyon cells and corresponding approach-directing mushroom body output neurons (MBONs), in which similar-amplitude long-term depression of responses to CS+ and CS- seems to signal the mLTM. Our results suggest that animals can develop distinct strategies for occasional and repeated threatening experiences.

neuroscience↗

bioRxiv2021

Epstein-Barr Virus Induced Cytidine Metabolism Roles in Transformed B-cell Growth and Survival

Epstein-Barr virus (EBV) is associated with 200,000 cancers annually, including B-cell lymphomas in immunosuppressed hosts. Hypomorphic mutations of the de novo pyrimidine synthesis pathway enzyme cytidine 5 triphosphate synthase 1 (CTPS1) suppress cell mediated immunity, resulting in fulminant EBV infection and EBV+ central nervous system (CNS) lymphomas. Since CTP is a critical precursor for DNA, RNA and phospholipid synthesis, this observation raises the question of whether the isozyme CTPS2 or cytidine salvage pathways help meet CTP demand in EBV-infected B-cells. Here, we found that EBV upregulated CTPS1 and CTPS2 with distinct kinetics in newly infected B-cells. While CRISPR CTPS1 knockout caused DNA damage and proliferation defects in lymphoblastoid cell lines (LCL), which express the EBV latency III program observed in CNS lymphomas, double CTPS1/2 knockout caused stronger phenotypes. EBNA2, MYC and non-canonical NF-{square}B positively regulated CTPS1 expression. CTPS1 depletion impaired EBV lytic DNA synthesis, suggesting that latent EBV may drive pathogenesis with CTPS1 deficiency. Cytidine rescued CTPS1/2 deficiency phenotypes in EBV-transformed LCL and Burkitt B-cells, highlighting CTPS1/2 as a potential therapeutic target for EBV-driven lymphoproliferative disorders. Collectively, our results suggest that CTPS1 and CTPS2 have partially redundant roles in EBV-transformed B-cells and provide insights into EBV pathogenesis with CTPS1 deficiency.

cancer biology↗

bioRxiv2020

A common genetic architecture enables the lossy compression of large CRISPR libraries

There are thousands of ubiquitously expressed mammalian genes, yet a genetic knockout can be lethal to one cell, and harmless to another. This context specificity confounds our understanding of genetics and cell biology. 2 large collections of pooled CRISPR screens offer an exciting opportunity to explore cell specificity. One explanation, synthetic lethality, occurs when a single "private" mutation creates a unique genetic dependency. However, by fitting thousands of machine learning models across millions of omic and CRISPR features, we discovered a "public" genetic architecture that is common across cell lines and explains more context specificity than synthetic lethality. This common architecture is built on CRISPR loss-of-function phenotypes that are surprisingly predictive of other loss-of-function phenotypes. Using these insights and inspired by the in silico lossy compression of images, we use machine learning to identify small "lossy compression" sets of in vitro CRISPR constructs where reduced measurements produce genome-scale loss-of-function predictions.

systems biology↗

bioRxiv2020

Molecular Parallelisms and Divergences Between Human and Canine Mammary Cancer

Canine mammary cancer is poorly characterized at the genomic level. Dog really can be an appropriate experimental model for human cancers from the genomic and evolutionary perspective or not? Here, we perform a cross-species cancer genomics analysis, independent evolution of cancer from normal tissues, which provide us an excellent opportunity to address an evolutionary perspective of cancer. As, evolutionary theories are critical for understanding tumorigenesis at the level of species as well as at the level of cells and tissues, for the development of effective therapies. Analysis of canine mammary cancer reveals a diversity of histological types as compare to human breast cancer. Our systematic analysis of 24 canine mammary tumors with whole-genome sequences, reveals 185 protein-coding cancer genes carried exonic mutations. Cross-species comparative analysis of 1080 human breast cancers identifies higher median mutation frequency in human breast cancer and canine mammary cancer shows lower across exonic regions (2.67 and 0.187 average no. of mutations per tumor per megabase (Mb), respectively). A comparison of somatic mutations in the PIK3CA gene, reveals common recurrence of the conserved mutations, in both species. However, the Ka/Ks ratio in the human PIK3CA gene 2.37 is higher and 1.43 in dogs is lower. To address the mutation accumulation and antagonistic pleiotropy theory, we investigated Ka/Ks value 237 aging-related genes from human and canine, the aging-related genes do not show selection in canine mammary cancer. It demonstrates new aspects of cancer genes that are evolving in different species instantaneously. These findings may suggest, the same organs in different mammals impose different selective pressures on the same set of genes in cancer. In both species, some genes may experience strong selective pressures, but do not converge genetically or the conserved genes do not show the same selection pressure in both species. However, human breast cancer shows transcriptomic similarity with canine mammary carcinoma but the other subtypes are quite different. We found canine mammary tumor can be used as a model for inter and intra-tumor heterogeneity. These findings provided insight into mammary cancer across species and possessed potential clinical significance. Collectively, these studies suggest a convergence of some genetic changes in mammary cancer between species but also distinctly different paths to tumorigenesis.

genomics↗

bioRxiv2020

Ilomastat contributes to the survival of mouse after irradiation via promoting the recovery of hematopoietic system

Ilomastat, a broad-spectrum inhibitor of matrix metalloproteinases (MMPs), has drawn attentions for its function in alleviating radiation damage. However, the detailed mechanisms of Ilomastats protection from animal model remain not fully clear. In this study, the C57BL/6 mice were pre-administrated with Ilomastat or vihicle for 2 h, and then total body of mice were exposed to 6 Gy of {gamma}-rays. The protective effect of Ilomastat on the hematopoietic system in the irradiated mice were investigated. We found that pretreatment with Ilomastat significantly reduced the level of TGF-{beta}1 and TNF-, and elevated the number of bone marrow (BM) mononuclear cells in the irradiated mice. Ilomastat pretreatment also increased the fraction of BM hematopoietic progenitor cells (HPCs) and hematopoietic stem cells (HSCs) at day 30 after irradiation, and protected the spleen of mouse from irradiation. These results suggest that Ilomastat promotes the recovery of hematopoietic injury in the irradiated mice, and thus contributes to the survival of mouse after irradiation.

pharmacology and toxicology↗

bioRxiv2020

Common variants contribute to intrinsic functional architecture of human brain

The human brain remains active in the absence of explicit tasks and forms networks of correlated activity. Resting-state functional magnetic resonance imaging (rsfMRI) measures brain activity at rest, which has been linked with both cognitive and clinical outcomes. The genetic variants influencing human brain function are largely unknown. Here we utilized rsfMRI from 44,190 individuals of multiple ancestries (37,339 in the UK Biobank) to discover and validate the common genetic variants influencing intrinsic brain activity. We identified hundreds of novel genetic loci associated with intrinsic functional signatures (P < 2.8 x 10-11), including associations to the central executive, default mode, and salience networks involved in the triple network model of psychopathology. A number of intrinsic brain activity associated loci colocalized with brain disorder GWAS (e.g., Alzheimers disease, Parkinsons disease, schizophrenia) and cognition, such as 19q13.32, 17q21.31, and 2p16.1. Particularly, we detected a colocalization between one (rs429358) of the two variants in the APOE {varepsilon}4 locus and function of the default mode, central executive, attention, and visual networks. Genetic correlation analysis demonstrated shared genetic influences between brain function and brain structure in the same regions. We also detected significant genetic correlations with 26 other complex traits, such as ADHD, major depressive disorder, schizophrenia, intelligence, education, sleep, subjective well-being, and neuroticism. Common variants associated with intrinsic brain activity were enriched within regulatory element in brain tissues.

genetics↗

bioRxiv2020

A Speedy Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors

The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2MPro) to digest two of its translated polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replication in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1MPro), we have designed and synthesized a series of SC2MPro inhibitors that contain {beta}-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2MPro active site cysteine C145. All inhibitors display high potency with IC50 values at or below 100 nM. The most potent compound MPI3 has as an IC50 value as 8.5 nM. Crystallographic analyses of SC2MPro bound to 7 inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549 cells. Two inhibitors MP5 and MPI8 completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 M and A549 cells at 0.16-0.31 M. Their virus inhibition potency is much higher than some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2MPro inhibitors with extreme potency. Due to the urgent matter of the COVID-19 pandemic, MPI5 and MPI8 may be quickly advanced to preclinical and clinical tests for COVID-19.

biochemistry↗