Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 541 records · Page 30Linked to original sources

bioRxiv2019

Tumor-draining lymph nodes resection and chemotherapy have diverse impacts on cancer immunotherapies

Immunotherapies are used as adjuvant therapies for cancers. However, knowledge of how traditional cancer treatments affect immunotherapies is limited. Using mouse models, we demonstrate that tumor-draining lymph nodes (TdLNs) are critical for tumor antigen-specific T-cell response. However, removing TdLNs concurrently with established primary tumors did not affect the immune checkpoint blockade (ICB) response on localized secondary tumor due to immunotolerance in TdLNs and distribution of antigen-specific T cells in peripheral lymphatic organs. Notably, treatment response improved with sequential administration of 5-fluorouracil (5-FU) and ICB compared to concurrent administration of ICB with 5-FU. Immune profiling revealed that using 5-FU as induction treatment increased tumor visibility to immune cells, decreased immunosuppressive cells in the tumor microenvironment, and limited chemotherapy-induced T-cell depletion. We show that the effect of traditional cytotoxic treatment, not TdLNs, influences immunotherapy response in localized secondary tumors. We postulate essential considerations for successful immunotherapy strategies in clinical conditions. Graphic abstractThe effects of tumor-draining lymph nodes (TdLNs) resection and a combination of cytotoxic chemotherapy on immune checkpoint blockade therapies are evaluated in this study. TdLNs resection was adverse in eliciting an antitumor immune response in early-stage tumors, but not in late-stage tumors. Further, sequential treatments with cytotoxic chemotherapy and immunotherapy showed better tumor control compared to concurrent combinatorial treatments.

cancer biology↗

bioRxiv2019

Entecavir resistance mutations rtL180M/T184L/M204V combined with rtA200V lead to tenofovir resistance

Background & AimsTenofovir disoproxil fumarate (TDF) imposes a high genetic barrier to drug resistance and potently inhibits replication of multidrug-resistant hepatitis B virus (MDR HBV) and few clinical cases with confirmed TDF-resistance have been reported to date. We reported a quadruple mutant which showed moderate resistant to TDF.\n\nMethods and resultsViral rebound was reported in a patient with chronic hepatitis B who underwent TDF monotherapy and harbored a quadruple mutant consisting of classic ETV-resistance mutations (rtL180M/T184L/M204V) together with an rtA200V mutation in the reverse transcriptase gene. Sequencing analysis revealed that this quadruple mutant emerged as a major viral population. In vitro phenotyping demonstrated that the rtL180M/T184L/A200V/M204V mutant had moderate resistance to TDF treatment, with a 4.52-fold higher half maximal effective concentration than that of wild-type virus. Importantly, this patient with TDF resistance achieved virological suppression after TDF/ETV combination rescue therapy.\n\nConclusionAn rtL180M/T184L/A200V/M204V mutant with moderate resistance to TDF monotherapy was selected during sequential NA treatment in a stepwise manner. ETV/TDF combination therapy effectively suppressed replication of this TDF resistant mutant. Our studies provide novel insights into the treatment of NA-naive patients as well as patients with TDF resistance.

microbiology↗

bioRxiv2019

Environment rapidly upregulates serotonin 2A receptor expression via the immediate early gene Egr3

Serotonin 2A receptors (5-HT2ARs) mediate the effects of hallucinogenic drugs and antipsychotic medications, and are reduced in schizophrenia patients brains. However, the mechanisms that regulate 5-HT2AR expression remain poorly understood. We show that an environmental stimulus, sleep deprivation, upregulates 5-HT2ARs in the mouse frontal cortex (FC) in just 6-8 hours. This induction requires the immediate early gene transcription factor early growth response 3 (Egr3). Further, EGR3 binds to the Htr2a promoter in the FC in vivo, and drives reporter construct expression in vitro via two Htr2a promoter binding sites. These findings suggest that EGR3 directly regulates FC Htr2a expression in response to physiologic stimuli, providing a mechanism by which environment rapidly alters levels of a brain receptor that mediates symptoms, and treatment, of mental illness. One Sentence SummaryJust 6-8 hours of sleep deprivation upregulates brain levels of the receptor that mediates the response to hallucinogens.

neuroscience↗

bioRxiv2019

Synaptic mechanisms of context-dependent sensory responses in the hippocampus

As animals navigate, they must identify features in context. The hippocampus-a structure critical for navigation-exhibits a different code for each environment, uniquely representing locations and objects within each environment in the firing rates of its neurons. It is unknown how or where these context-specific codes emerge. For example, it is unknown whether pyramidal neurons in the CA1 subregion produce these codes (by combining separate inputs from local sensory cues and the environmental context) or inherit conjunctive codes from upstream brain areas. We performed electrical recordings in the hippocampus as mice navigated in two distinct virtual environments. In CA1, subthreshold synaptic responses to a visual cue in one environment were absent when the same cue occurred in the second environment. In CA3, cue-driven spiking also strongly depended on environmental context. These results indicate that context-dependent sensory coding in CA1 is inherited from its CA3 input.

neuroscience↗

bioRxiv2019

A novel deep learning scheme for morphology-based classification of mycobacterial infection in unstained macrophages

ObjectiveMycobacterium tuberculosis (Mtb) is an airborne, contagious bacterial pathogen that causes widespread infections in humans. Using Mycobacterium marinum (Mm), a surrogate model organism for Mtb research, the present study develops a deep learning-based scheme that can classify the Mm-infected and uninfected macrophages in tissue culture solely based on morphological changes.\n\nMethodsA novel weak-and semi-supervised learning method is developed to detect and extract the cells, firstly. Then, transfer learning and fine-tuning from the CNN is built to classify the infected and uninfected cells.\n\nResultsThe performance is evaluated by accuracy (ACC), sensitivity (SENS) and specificity (SPEC) with 10-fold cross-validation. It demonstrates that the scheme can classify the infected cells accurately and efficiently at the early infection stage. At 2 hour post infection (hpi), we achieve the ACC of 0.923 {+/-} 0.005, SENS of 0.938 {+/-} 0.020, and SPEC of 0.905 {+/-} 0.019, indicating that the scheme has detected significant morphological differences between the infected and uninfected macrophages, although these differences are hardly visible to naked eyes. Interestingly, the ACC at 12 and 24 hpi are 0.749 {+/-} 0.010 and 0.824 {+/-} 0.009, respectively, suggesting that the infection-induced morphological changes are dynamic throughout the infection. Finally, deconvolution with guided propagation maps the key morphological features contributing to the classification.\n\nSignificanceThis proof-of-concept study provides a novel venue to investigate bacterial pathogenesis in a macroscopic level and has a great promise in diagnosis of bacterial infections.

bioengineering↗

bioRxiv2019

Risk variant in miR-544a binding site in CCDC170 is associated with osteoporosis

MicroRNAs (miRNAs) play essential roles in regulating bone formation and homeostasis. Genomic variations within miRNA target sites may therefore be important sources of genetic differences in osteoporosis risk. To investigate this possibility, we searched for miRNA recognition sites within genes using the TargetScan, miRNASNP and miRbase databases. In this study, we showed that miR-544a differentially regulated the allele variants of rs6932603 in the CCDC170 3 ' untranslated (3'-UTR). We also showed that miR-544a suppressed osteogenesis and promoted osteoclastogenesis by regulating the expressions of Runx2, Osterix, Alp, Col1a1, Osteopontin (OPN) ,Osteocalcin (OCN) and Osteoprotegerin (OPG). Our results suggest that allele-specific regulation of CCDC170 by miR-544a explains the observed disease risk, and provides a potential therapeutic target for osteoporosis therapy.

genetics↗

bioRxiv2019

Dynamics of soil nematode communities revealed significant variation in greenhouse with different continuous cropping years

Continuous cropping usually resulted in a series of soil problems, especially root knot nematode disaster in greenhouse because of imbalance in soil nematode community. However, the dynamic change in soil nematode community in greenhouse with various continuous cropping years during plant growing season is unclear. Here, soil nematode communities in greenhouse after 2 and 10 years of continuous cropping were comparatively analyzed using 18S rDNA high-throughput sequencing to reveal the changing processes in soil nematode communities. Compared to the 2-year greenhouse, soil in the 10-year greenhouse showed soil acidification, nutrients accumulation, salinization. In term of -diversity, Bacterial-feeding nematodes (BF) were dominant in the 2-year greenhouse over the whole growing season, but plant-parasitic nematodes (PP) became the dominant group in the 10-year greenhouse in the late growing season. Meloidogyne gradually became the dominant group (Relative abundance 70.9%) in the 10-year greenhouse, while Rhabditidae (Relative abundance from 99.8% to 26.8%) was the predominant members in the 2-year greenhouse. For {beta}-diversity, hierarchical clustering analysis, unWeighted UniFrac principal component analysis (PCA) and principal co-ordinates analysis (PCoA) all revealed that soil nematode communities in the two types of greenhouses exhibited significant differences. Redundancy analysis (RDA) showed that soil nematode communities in the 10-year greenhouse were related to high soil organic material, total nitrogen, electrical conductivity and disease index of root knot nematode. Fisher exact test and Pearson correlation coefficients revealed that Meloidogyne caused main differences in soil nematode communities between the two types of greenhouses. Meanwhile, population dynamics of Meloidogyne were divided into dormant phase, low-level increasing phase and exponential phase during the whole season. In total, the significant variation led different dynamics of soil nematode communities in the 2-year and 10-year greenhouse.

ecology↗

bioRxiv2019

Integration of pathway, cellular and genetic context reveals principles of synthetic lethality that affect reproducibility

Synthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies. Using KRAS as a model, we identified that published synthetic lethal screens significantly overlap at the pathway rather than gene level. Analysis of pathways encoded as protein networks identified synthetic lethal candidates that were more reproducible than those previously reported. Lack of overlap likely stems from biological rather than technical limitations as most synthetic lethal phenotypes were strongly modulated by changes in cellular conditions or genetic context, the latter determined using a pairwise genetic interaction map that identified numerous interactions that suppress synthetic lethal effects. Accounting for pathway, cellular and genetic context nominates a DNA repair dependency in KRAS-mutant cells, mediated by a network containing BRCA1. We provide evidence for why most reported synthetic lethals are not reproducible which is addressable using a multi-faceted testing framework.\n\nSTATEMENT OF SIGNIFICANCESynthetic lethal screens have the power to identify new targets in cancer, although have thus far come up short of expectation. We use computational and experimental approaches to delineate principles for identifying robust synthetic lethal targets that could aid in the development of effective new therapeutic strategies for genetically defined cancers.

cancer biology↗

bioRxiv2019

Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex

Variation in gene expression underlies neurotypical development, while genomic variants contribute to neuropsychiatric disorders. BrainVar is a unique resource of paired whole-genome sequencing and bulk-tissue RNA-sequencing from the human dorsolateral prefrontal cortex of 176 neurotypical individuals across prenatal and postnatal development, providing the opportunity to assay genomic and transcriptomic variation in tandem. Leveraging this resource, we identified rare premature stop codons with commensurate reduced and allele-specific expression of corresponding genes, and common variants that alter gene expression (expression quantitative trait loci, eQTLs). Categorizing eQTLs by prenatal and postnatal effect, genes affected by temporally-specific eQTLs, compared to constitutive eQTLs, are enriched for haploinsufficiency, protein-protein interactions, and neuropsychiatric disorder risk loci. Expression levels of over 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell type specific genes and neuropsychiatric disorder loci, underscoring the importance of cataloguing developmental trajectories in understanding cortical physiology and pathology.\n\nHighlightsO_LIWhole-genome and RNA-sequencing across human prefrontal cortex development in BrainVar\nC_LIO_LIGene-specific developmental trajectories characterize the late-fetal transition\nC_LIO_LIIdentification of constitutive, prenatal-specific, postnatal-specific, and rare eQTLs\nC_LIO_LIIntegrated analysis reveals genetic and developmental influences on CNS traits and disorders\nC_LI

neuroscience↗

bioRxiv2019

An open resource of structural variation for medical and population genetics

Structural variants (SVs) rearrange large segments of the genome and can have profound consequences for evolution and human diseases. As national biobanks, disease association studies, and clinical genetic testing grow increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integral for interpreting genetic variation. To date, no large-scale reference maps of SVs exist from high-coverage sequencing comparable to those available for point mutations in protein-coding genes. Here, we constructed a reference atlas of SVs across 14,891 genomes from diverse global populations (54% non-European) as a component of gnomAD. We discovered a rich landscape of 433,371 distinct SVs, including 5,295 multi-breakpoint complex SVs across 11 mutational subclasses, and examples of localized chromosome shattering, as in chromothripsis. The average individual harbored 7,439 SVs, which accounted for 25-29% of all rare protein-truncating events per genome. We found strong correlations between constraint against damaging point mutations and rare SVs that both disrupt and duplicate protein-coding sequence, suggesting intolerance to reciprocal dosage alterations for a subset of tightly regulated genes. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than any effect on noncoding SVs. Finally, we benchmarked carrier rates for medically relevant SVs, finding very large ([≥]1Mb) rare SVs in 3.8% of genomes (~1:26 individuals) and clinically reportable incidental SVs in 0.18% of genomes (~1:556 individuals). These data have been integrated directly into the gnomAD browser (https://gnomad.broadinstitute.org) and will have broad utility for population genetics, disease association, and diagnostic screening.

genomics↗

bioRxiv2019

Endothelial PKA targets ATG16L1 to regulate angiogenesis by limiting autophagy

The cAMP-dependent protein kinase A (PKA) regulates a plethora of cellular functions in health and disease. During angiogenesis, PKA activity in endothelial cells controls the transition from sprouting to vessel maturation and limits tip cell formation independently of Notch signaling. The molecular PKA targets mediating these effects remain unknown. We report a chemical genetics screen identifying endothelial-specific substrates of PKA in human umbilical vein endothelial cells (HUVEC). We identified ATG16L1, a regulator of autophagy, as novel target of PKA. Biochemical validation, mass spectrometry and peptide spot arrays revealed that PKA phosphorylates ATG16L1 at Ser268 and ATG16L1{beta} at Ser269. The phosphorylations drive degradation of ATG16L1 protein. Knocking down PKA or inhibiting its activity increased ATG16L1 protein levels and endothelial autophagy. In vivo genetics and pharmacological experiments demonstrated that autophagy inhibition partially rescues vascular hypersprouting caused by PKA deficiency. We propose that endothelial PKA activity restricts active sprouting by reducing endothelial autophagy through phosphorylation of ATG16L1.

biochemistry↗

bioRxiv2019

Molecular subtyping and prognostic assessment based on tumor mutation burden in patients with lung adenocarcinomas

Tumor mutation burden (TMB) is a potential biomarker for response to immunotherapy. The subset of patients with TMB has not been well characterized in lung adenocarcinomas. Here we performed molecular subtyping based on TMB and compared the features of different subtypes including clinical features, somatic driver genes and mutational signatures. We found that patients with lower tumor mutation burden had a longer disease-free survival, while higher tumor mutation burden is associated with smoking and aging. Analysis of somatic driver genes and mutational signatures demonstrates a significant association between somatic RYR2 mutations and the subtype with higher mutation burden. Overall, our study identified two molecular subtypes based on TMB and described the corresponding difference in their clinical and genomic levels.

genomics↗

bioRxiv2019

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

Antibodies are essential for elucidating the roles of genes decoded by genome sequencing. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed the Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 mAbs against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic feature of an antibody. Distinctive combinations of 10,000-20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-target pairs were discovered for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for human membrane proteins and ChIP-seq mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues discovered internalizing tumor antigens for antibody-drug conjugates. By discovering high affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.

systems biology↗

bioRxiv2019

In situ structures of periplasmic flagella in Borrelia reveals conformational changes essential for flagellar rotation

The bacterial flagellar motor is a molecular machine that rotates the flagellar filament at high speed. Torque is generated by the stator-rotor interaction coupled to an ion flux through the torque-generating stator. Here, we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirochete Borrelia burgdorferi. By analysis of the motor structures of wild-type and stator mutants, we localize the torque-generating units precisely and determine three-dimensional structure of the stator and its interactions with the rotor. Our study shows that the cytoplasmic domains of the stator are packed regularly around the circumference of the flagellar C-ring. The stator-rotor interaction induces a profound conformational change in the C-ring. Analysis of the motors of a less motile motB-D24E mutant and a non-motile motB-D24N mutant, in which the proton translocation is reduced and blocked, respectively, provides evidence that the conformational change of the C-ring is essential for flagellar rotation.

microbiology↗

bioRxiv2019

The chromatin structuring protein HMGA2 influences human subtelomere stability and cancer chemosensitivity

The transient build-up of DNA supercoiling during the translocation of replication forks threatens genome stability and is controlled by DNA topoisomerases (TOPs). This crucial process has been exploited with TOP poisons for cancer chemotherapy. However, pinpointing cellular determinants of the best clinical response to TOP poisons still remains enigmatic. Here, we present an integrated approach and demonstrate that endogenous and exogenous expression of the oncofetal high-mobility group AT-hook 2 (HMGA2) protein exhibited broad protection against the formation of hydroxyurea-induced DNA breaks in various cancer cells, thus corroborating our previously proposed model in which HMGA2 functions as a replication fork chaperone that forms a protective DNA scaffold at or close to stalled replication forks. We now further demonstrate that high levels of HMGA2 also protected cancer cells against DNA breaks triggered by the clinically important TOP1 poison irinotecan. This protection is most likely due to the recently identified DNA supercoil constraining function of HMGA2 in combination with exclusion of TOP1 from binding to supercoiled substrate DNA. In contrast, low to moderate HMGA2 protein levels surprisingly potentiated the formation of irinotecan-induced genotoxic covalent TOP1-DNA cleavage complexes. Our data from cell-based and several in vitro assays indicate that, mechanistically, this potentiating role involves enhanced drug-target interactions mediated by HMGA2 in ternary complexes with supercoiled DNA. Subtelomeric regions were found to be extraordinarily vulnerable to these genotoxic challenges induced by TOP1 poisoning, pointing at strong DNA topological barriers located at human telomeres. These findings were corroborated by an increased irinotecan sensitivity of patient-derived xenografts of colorectal cancers exhibiting low to moderate HMGA2 levels. Collectively, we uncovered a therapeutically important control mechanism of transient changes in chromosomal DNA topology that ultimately leads to enhanced human subtelomere stability. Author SummaryDNA replication fork stability in rapidly dividing cancer cells is of utmost importance for the maintenance of genome stability and cancer cell viability. Cancer cells efficiently prevent fork collapse into lethal double strand breaks as a first line of defense during replication stress, but the corresponding protective mechanisms often remain elusive. Uncontrolled high levels of DNA supercoiling that are generally regulated by topoisomerases can cause replication stress and are major threats to fork stability. Using a multidisciplinary approach, we identified a possible regulatory mechanism of replication stress, which appears to involve mitigating the consequences of DNA topological changes by the oncofetal replication fork chaperone HMGA2. Our work provides mechanistic insights into the control of DNA damage triggered by clinically important anti-cancer drugs, which is mediated by the replication fork chaperone HMGA2. We thereby also identify HMGA2 expression as a predictive therapeutic marker, which could allow clinicians to take informed decisions to prevent tumor recurrence and improve survival.

cancer biology↗

bioRxiv2019

A plant protein NbP3IP induces autophagy and mediates the autophagic degradation of RSV p3 to inhibit viral infection

In plants, autophagy is involved in responses to viral infection. However, understanding of new host factors mediating autophagic clearance of plant viruses is very limited. We here identified a new host factor NbP3IP participating in autophagy-mediated plant defense against viral infection. NbP3IP interacted with p3, a RNA silencing suppressor encoded by Rice stripe virus (RSV), a negative-strand RNA virus, and mediated its autophagic degradation. NbP3IP could also interact with NbATG8f, which was required for NbP3IP-miediated p3 degradation. Overexpression of NbP3IP induced autophagy and down-regulation of NbP3IP reduced autophagy. Both overexpression of NbP3IP and silencing of GAPC, which also induces autophagy, inhibited RSV infection. In contrast, silencing of ATG7 promoted RSV infection. Thus, through identification of a new potential selective autophagy receptor P3IP, we revealed a new mechanism of autophagy-mediated plant defense against plant viruses and provided the first evidence that plant autophagy can also play an antiviral role against negative-strand RNA viruses.

plant biology↗

bioRxiv2019

A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

genomics↗

bioRxiv2019

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning

A plethora of biological functions are performed through various types of protein-peptide binding. Prime examples include the protein kinase phosphorylation on peptide substrates and the binding of major histocompatibility complex to neoantigens in the immune system. Understanding the specificity of protein-peptide interactions is critical for unraveling the architectures of functional pathways and the mechanisms of cellular processes in human cells. Despite mass-spectrometric techniques were developed for the identification of protein-peptide interactions, our understanding of the preferences of proteins on their binding peptides is still rudimentary. As a complementary direction, a line of computational prediction methods has been recently proposed to predict protein-peptide bindings which efficiently provide rich functional annotations on a large scale. To achieve a high prediction accuracy, these computational methods require a sufficient amount of data to build the prediction model. However, the number of experimentally verified protein-peptide bindings is often limited in real cases. For example, a majority of protein kinases have very few experimentally verified phosphorylation sites (e.g., less than 30 sites) in existing databases. These methods are thus limited to building accurate prediction models for only well-characterized proteins with a large volume of known binding peptides and cannot be extended to predict new binding peptides for less-studied proteins. In this paper, we introduce a generic framework to address this issue of data scarcity in protein binding prediction. We demonstrate the applicability of our framework in predicting kinase-specific phosphorylation sites. Our method uses an effective training strategy to build a prediction model with robust transferability. The model is able to predict the phosphorylation sites of a less-studied kinase, even if there is only a small number of phosphorylation sites known for this kinase. To achieve this, we train the model via a meta-learning phase followed by a few-shot learning phase. We demonstrate our framework has better transferability than state-of-the-art methods and is effective in utilizing limited data to accurately predict phosphorylation sites for less-characterized kinases. The implementation of our framework is available at https://github.com/luoyunan/MetaKinase.

bioinformatics↗