Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 811 records · Page 45Linked to original sources

bioRxiv2020

Novel inhibitors of E. coli lipoprotein diacylglyceryl transferase are insensitive to resistance caused by lpp deletion

Lipoprotein diacylglyceryl transferase (Lgt) catalyzes the first step in the biogenesis of Gram-negative bacterial lipoproteins which play crucial roles in bacterial growth and pathogenesis. We demonstrate that Lgt depletion in a clinical uropathogenic Escherichia coli strain leads to permeabilization of the outer membrane and increased sensitivity to serum killing and antibiotics. Importantly, we identify the first ever described Lgt inhibitors that potently inhibit Lgt biochemical activity in vitro and are bactericidal against wild-type Acinetobacter baumannii and E. coli strains. Unlike inhibition of other steps in lipoprotein biosynthesis, deletion of the major outer membrane lipoprotein, lpp, is not sufficient to rescue growth after Lgt depletion or provide resistance to Lgt inhibitors. Our data validate Lgt as a novel druggable antibacterial target and suggest that inhibition of Lgt may not be sensitive to one of the most common resistance mechanisms that invalidate inhibitors of downstream steps of bacterial lipoprotein biosynthesis and transport.

microbiology↗

bioRxiv2020

Brazilin Removes Toxic alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium

Alpha-synuclein (-syn) fibrils, a major constituent of the neurotoxic Lewy Bodies in Parkinsons disease, form via nucleation dependent polymerization and can replicate by a seeding mechanism. Brazilin, a small molecule derived from red cedarwood trees in Brazil, has been shown to inhibit the fibrillogenesis of amyloid-beta (A{beta}) and -syn, prompting our inquiry in its mechanism of action. Here we test the effects of Brazilin on both seeded and unseeded -syn fibril formation and show that the natural polyphenol inhibits fibrillogenesis of -syn by a unique mechanism that is distinct from other polyphenols and is also distinct from its effect on A{beta}. Brazilin preserves the natively unfolded state of -syn by stabilizing the compact conformation of the -syn monomer over the aggregation-competent extended conformation. Molecular docking of Brazilin shows the molecule to interact both with unfolded -syn monomers and with the cross-{beta} sheet structure of -syn fibrils. Brazilin eliminates seeding competence of -syn assemblies from Parkinsons disease patient brain tissue, and treatment of pre-formed fibril assemblies with Brazilin significantly reduces their toxicity in primary neurons. Our findings suggest that Brazilin has substantial potential as a neuroprotective and therapeutic agent for Parkinsons Disease. Highlights- The natural polyphenol Brazilin binds to monomeric, oligomeric and fibrillar -syn - Brazilin shifts the equilibrium away from aggregation-competent monomer conformations - Brazilin inactivates seeding-competent -syn isolated from Parkinson patients brains - Brazilin detoxifies -syn aggregation intermediates and stabilizes mature amyloid fibrils Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=117 HEIGHT=200 SRC="FIGDIR/small/318220v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@447629org.highwire.dtl.DTLVardef@a9871dorg.highwire.dtl.DTLVardef@1e5a83dorg.highwire.dtl.DTLVardef@8843eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Mitochondria fragment and reassemble to initiate the formation and development of the nucleus

The function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).

cell biology↗

bioRxiv2020

Tissue-specific accumulation profiles of phorbol esters in Jatropha curcas and gene induction in response to abiotic and biotic stresses

Jatropha curcas L. (J. curcas), a shrub plant of the Euphorbiaceae family, has received enormous attention as a promising biofuel plant for the production of biodiesel and medical potential in ethnopharmacology. However, the tumor-promoter toxin phorbol esters present in J. curcas raises concerns for health and environmental risk as its large-scale cultivation limits the use of meal obtained after oil extraction for animal feed. Here, we determined the variation of phorbol ester profiles and contents in eight J. curcas tissues by high performance liquid chromatography (HPLC) and found phorbol esters present in all parts of the plant except the seed shell. We showed tissue-specific patterns of accumulation of phorbol esters and associated terpenoids at the transcriptomic level with high transcript levels in reproductive and young tissues. Genes involved in the same module of terpenoids biosynthesis were positively correlated. We further present diverse abiotic and biotic stresses that had different effects on the accumulation of transcripts in terpenoids shared and branched terpenoid pathways in plant seedlings. The fine-tuning of terpenoids biosynthesis may link with ecological functions in plants under extreme environments and defense against pathogens.

plant biology↗

bioRxiv2020

IF1 connects obesity and insulin resistance through mitochondrial reprogramming in association with ANT2

IF1 (ATPIF1) is a nuclear DNA-encoded protein with an activity in the inhibition of catalytic activity of F1Fo-ATP synthase (ATPase), an enzyme for ATP synthesis in mitochondria. A role of IF1 remains unknown in the metabolic disorder in obesity. In this study, IF1 was examined in the diet-induced obese (DIO) mice and a decrease in IF1 protein was observed in several tissues including the skeletal muscle, liver and intestine in the absence of mRNA alteration. Significance of the reduction was investigated in the IF1-KO mice, in which insulin sensitivity was improved in the absence of body weight alteration on Chow diet. On a high fat diet (HFD), the IF1-KO mice gain more body weight as a result of enhanced fat tissue growth. The energy expenditure and locomotion activity were decreased in the KO mice without an alteration in food intake. The increase in insulin sensitivity remained in the obese KO mice. The colon tissue exhibited a resistance to the HFD-induced atrophy with less cell apoptosis and more secretion of GLP-1. Mitochondria exhibited an enhanced ATP production and maximal oxygen consumption without an alteration in the respiratory chain proteins. However, the ATP level was reduced in the fasting condition in the muscle as well as the liver. Mitophagy was enhanced with elevated accumulation of PINK1 and Parkin proteins in the mitochondria. The protein abundance of ADP/ATP translocase 2 (ANT2) was decreased in the inner membrane of mitochondria to account for the reduced apoptosis and enhanced mitophagy. The data suggest that the IF1 reduction in obesity leads to reprogramming of mitochondrial metabolism in a compensatory response to maintain the insulin sensitivity through down-regulation of ANT2 protein.

physiology↗

bioRxiv2020

CVB3 VP1 interacts with MAT1 to inhibit cell proliferation by interfering with Cdk-activating kinase complex activity in CVB3-induced acute pancreatitis

Coxsackievirus B3 (CVB3) belongs to the genus Enterovirus of the family Picornaviridae and can cause acute acinar pancreatitis in adults. However, the molecular mechanisms of pathogenesis underlying CVB3-induced acute pancreatitis have remained unclear. In this study, we discovered that CVB3 capsid protein VP1 inhibited pancreatic cell proliferation and exerted strong cytopathic effects on HPAC cells. Through yeast two-hybrid, co-immunoprecipitation, and confocal microscopy, we show that Menage a trois 1 (MAT1), a subunit of the Cdk-Activating Kinase (CAK) complex involved in cell proliferation and transcription, is a novel interaction protein with CVB3 VP1. Moreover, CVB3 VP1 inhibited MAT1 accumulation and localization, thus interfering with its interaction with CDK7. Furthermore, CVB3 VP1 could suppress CAK complex enzymic phosphorylation activity towards RNA Pol II and CDK4/6, direct substrates of CAK. VP1 also suppresses phosphorylation of retinoblastoma protein (pRb), an indirect CAK substrate, especially at phospho-pRb Ser780 and phospho-pRb Ser807/811 residues, which are associated with cell proliferation. Finally, we present evidence using deletion mutants that the C-terminal domain (VP1-D8, 768-859aa) is the minimal VP1 region required for its interaction with MAT1, and furthermore, VP1-D8 alone was sufficient to arrest cells in G1/S phase as observed during CVB3 infection. Taken together, we demonstrate that CVB3 VP1 can inhibit CAK complex assembly and activity through direct interaction with MAT1, to block MAT1-mediated CAK-CDK4/6-Rb signaling, and ultimately suppress cell proliferation in pancreatic cells. These findings substantially extend our basic understanding of CVB3-mediated pancreatitis, providing strong candidates for strategic therapeutic targeting.

microbiology↗

bioRxiv2020

YY1 cistrome analysis uncovers an essential requirement of the YY1:BRD4-PFKP regulatory axis for promoting tumorigenesis of castration-resistant prostate cancer

Castration-resistant prostate cancer (CRPC) is a terminal disease, demanding a better understanding of its pathogenesis. Targeted therapy needs to be developed for CRPC due to its heterogeneity and resistance to current treatments. Here, through cistrome study of YY1, a transcription factor significantly overexpressed during prostate cancer progression, we identify a YY1-PFKP axis to be essential for CRPC tumorigenesis. Depletion of YY1 in independent CRPC models dramatically reduced tumor cell growth in vitro and delayed oncogenic progression in vivo. Importantly, YY1 functions as a master regulator of prostate tumor metabolism including the Warburg effect and mitochondria respiration. Loss-of-function and rescue studies further reveals a mechanistic underpinning in which YY1 directly binds and trans-activates PFKP, a gene encoding the rate-limiting enzyme for glycolysis, significantly contributing to the YY1-enforced oncogenic phenotypes such as enhanced tumor cell glycolysis and malignant growth. Additionally, a vast majority of gene-regulatory element in advanced prostate cancer cells are bound by YY1, lending a support for its role as a master regulator of prostate cancer progression. YY1 interactome studies point to bromodomain-containing coactivators in prostate cancer, which act as functional partners of YY1 to potentiate YY1-related target gene activation. Altogether, this study unveils an unexplored YY1:BRD4-PFKP oncogenic axis operating in advanced prostate cancer with implications for therapy.

cancer biology↗

bioRxiv2020

Antimicrobial emulsifier - glycerol monolaurate impacts gut micobiome inducing distinct effects on metabolic syndrome in low-fat diet fed mice

Previous study demonstrated 150 mg{middle dot}kg-1 glycerol monolaurate (GML) consumption induced gut microbiota dysbiosis and metabolic syndrome (MetS) in low-fat diet fed mice. However, little is known about the dose-effect of dietary GML modulating the gut microbiome alterations and its impacts on the induction of MetS in low-fat diet. Dietary GML-induced effects on MetS and gut microbiota alterations were investigated, combined with antibiotics-treated germ-free experiment and specific gut microbiota transplantation. Our results demonstrated that high-dose (500 mg{middle dot}kg-1) GML alleviated MetS by significantly decreasing the body weight, weight gain, food intake, fat droplet size and percentage of abdominal fat, serum triglycerides (TG), LDL, LPS, TNF- and atherogenic index, compared to the medium-dose (150 mg{middle dot}kg-1) GML. Importantly, high-dose GML significantly increased Lactobacillus reuteri compared to the medium-dose GML. Co-occurrence network analysis revealed Lactobacillus reuteri was positively associated with the metabolic improvement of high-dose GML. Notably, antibiotics-treated germ-free experiment and Lactobacillus reuteri transplantation demonstrated that altered gut microbiota was necessary and sufficient for GML-induced distinct effects on metabolic syndrome. Our results indicate that GML impacts gut microbiome inducing distinct effects on metabolic syndrome, thereby calling for reassessing the safe dosage of GML and other non-specific antibacterial food additives. IMPORTANCEGrowing evidence indicate that the broad use of food emulsifying agents may lead to increase the societal incidence of obesity/ MetS and other chronic inflammatory diseases. GML is widely and regularly consumed as a generally safe food emulsifier and as a potent antimicrobial agent in commonly foods such as meat products, cereals and soft beverage by the general public. Our results indicate that GML impacts gut microbiome inducing distinct effects on metabolic syndrome. Our study provides important and timely evidence supporting the emerging concept that non-specific antibacterial food additives have two-sided effect on gut microbiota contributing to the uncertainties for the incidence of obesity/metabolic syndrome and other chronic inflammatory diseases.

microbiology↗

bioRxiv2020

Representation of Color, Form, and their Conjunctionacross the Human Ventral Visual Pathway

Despite decades of neuroscience research, our understanding of the relationship between color and form processing in the primate ventral visual pathway remains incomplete. Using fMRI multivoxel pattern analysis, this study examined the coding of color with both a simple form feature (orientation) and a mid-level form feature (curvature) in human early visual areas V1 to V4, posterior and central color regions, and shape areas in ventral and lateral occipito-temporal cortex. With the exception of the central color region (which showed color but not form decoding), successful color and form decoding was found in all other regions examined, even for color and shape regions showing univariate sensitivity to one feature. That said, all regions exhibited significant feature decoding biases, with decoding from color and shape regions largely consistent with their univariate preferences. Color and form are thus represented in neither a completely distributed nor a completely modular manner, but a biased distributed manner. Interestingly, coding of one feature in a brain region was always tolerant to changes in the other feature, indicating relative independence of color and form coding throughout the ventral visual cortex. Although evidence for interactive coding of color and form also existed, the effect was weak and only existed for color and orientation conjunctions in early visual cortex. No evidence for interactive coding of color and curvature was found. The predominant relationship between color and form coding in the human brain appears to be one of anatomical coexistence (in a biased distributed manner), but representational independence.

neuroscience↗

bioRxiv2020

A Transferable Deep Learning Approach to Fast Screen Potent Antiviral Drugs against SARS-CoV-2

The COVID-19 pandemic calls for rapid development of effective treatments. Although various drug repurpose approaches have been used to screen the FDA-approved drugs and drug candidates in clinical phases against SARS-CoV-2, the coronavirus that causes this disease, no magic bullets have been found until now. We used directed message passing neural network to first build a broad-spectrum anti-beta-coronavirus compound prediction model, which gave satisfactory predictions on newly reported active compounds against SARS-CoV-2. Then we applied transfer learning to fine-tune the model with the recently reported anti-SARS-CoV-2 compounds. The fine-tuned model was applied to screen a large compound library with 4.9 million drug-like molecules from ZINC15 database and recommended a list of potential anti-SARS-CoV-2 compounds for further experimental testing. As a proof-of-concept, we experimentally tested 7 high-scored compounds that also demonstrated good binding strength in docking study against the 3C-like protease of SARS-CoV-2 and found one novel compound that inhibited the enzyme with an IC50 of 37.0 M. Our model is highly efficient and can be used to screen large compound databases with billions or more compounds to accelerate the drug discovery process for the treatment of COVID-19.

bioinformatics↗

bioRxiv2020

Predicting identity-preserving object transformations across the human ventral visual stream

In everyday life, we have no trouble recognizing and categorizing objects as they change in position, size, and orientation in our visual fields. This phenomenon is known as object invariance. Previous fMRI research suggests that higher-level object processing regions in the human lateral occipital cortex may link object responses from different affine states (i.e. size and viewpoint) through a general linear mapping function with the learned mapping capable of predicting responses of novel objects. In this study, we extended this approach to examine the mapping for both Euclidean (e.g. position and size) and non-Euclidean (e.g. image statistics and spatial frequency) transformations across the human ventral visual processing hierarchy, including areas V1, V2, V3, V4, ventral occipitotemporal cortex (VOT), and lateral occipitotemporal cortex (LOT). The predicted pattern generated from a linear mapping could capture a significant amount, but not all, of the variance of the true pattern across the ventral visual pathway. The derived linear mapping functions were not entirely category independent as performance was better for the categories included in the training. Moreover, prediction performance was not consistently better in higher than lower visual regions, nor were there notable differences between Euclidean and non-Euclidean transformations. Together, these findings demonstrate a near-orthogonal representation of object identity and non-identity features throughout the human ventral visual processing pathway, with the non-identity features largely untangled from the identity features early in the visual processing. Significance StatementPresently we still do not fully understand how object identity and non-identity (e.g. position, size) information are simultaneously represented in the primate ventral visual system to form invariant representations. Previous work suggests that the human lateral occipital cortex may be linking different affine states of object representations through general linear mapping functions. Here we show that across the entire human ventral processing pathway, we could link object responses in different states of non-identity transformations through linear mapping functions for both Euclidean and non-Euclidean transformations. These mapping functions are not identity-independent, suggesting that object identity and non-identity features are represented in a near, rather than a completely, orthogonal manner.

neuroscience↗

bioRxiv2020

Joint Representation of Color and Shape in Convolutional Neural Networks: A Stimulus-rich Network Perspective

To interact with real-world objects, any effective visual system must jointly code the unique features defining each object. Despite decades of neuroscience research, we still lack a firm grasp on how the primate brain binds visual features. Here we apply a novel network-based stimulus-rich representational similarity approach to study color and shape binding in five convolutional neural networks (CNNs) with varying architecture, depth, and presence/absence of recurrent processing. All CNNs showed near-orthogonal color and shape processing in early layers, but increasingly interactive feature coding in higher layers, with this effect being much stronger for networks trained for object classification than untrained networks. These results characterize for the first time how multiple visual features are coded together in CNNs. The approach developed here can be easily implemented to characterize whether a similar coding scheme may serve as a viable solution to the binding problem in the primate brain.

neuroscience↗

bioRxiv2020

The development of transformation tolerant visual representations differs between the human brain and convolutional neural networks

Forming transformation-tolerant object representations is critical to high-level primate vision. Despite its significance, many details of tolerance in the human brain remain unknown. Likewise, despite the ability of convolutional neural networks (CNNs) to exhibit human-like object categorization performance, whether CNNs form tolerance similar to that of the human brain is unknown. Here we provide the first comprehensive documentation and comparison of three tolerance measures in the human brain and CNNs. We measured fMRI responses from human ventral visual areas to real-world objects across both Euclidean and non-Euclidean feature changes. In single fMRI voxels in higher visual areas, we observed robust object response rank-order preservation across feature changes. This is indicative of functional smoothness in tolerance at the fMRI meso-scale level that has never been reported before. At the voxel population level, we found highly consistent object representational structure across feature changes towards the end of ventral processing. Rank-order preservation, consistency, and a third tolerance measure, cross-decoding success (i.e., a linear classifiers ability to generalize performance across feature changes) showed an overall tight coupling. These tolerance measures were lower for Euclidean than non-Euclidean feature changes in lower visual areas, but increased over the course of ventral processing in most cases. These characteristics of tolerance, however, were absent in eight CNNs pretrained with ImageNet images with varying network architecture, depth, the presence/absence of recurrent processing, or whether a network was pretrained with the original or stylized ImageNet images that encouraged shape processing. Most notably, CNNs do not show increased representational consistency across feature changes at the higher layers. CNNs thus do not appear to develop the same kind of tolerance as the human brain over the course of visual processing. Significant StatementPerceiving object identity among changes in non-identity features and forming transformation-tolerant object representations is essential to high-level primate vision. Here we provide a comprehensive documentation and comparison of three tolerance measures between the human brain and CNNs pretrained for object classification. While all three measures show increased tolerance in the human brain across four types of feature changes towards the end of ventral visual processing, CNNs fail to develop the same kind of tolerance with visual processing.

neuroscience↗

bioRxiv2020

The relative coding strength of object identity and nonidentity features in human occipito-temporal cortex and convolutional neural networks

Any given visual object input is characterized by multiple visual features, such as identity, position and size. Despite the usefulness of identity and nonidentity features in vision and their joint coding throughout the primate ventral visual processing pathway, they have so far been studied relatively independently. Here we document the relative coding strength of object identity and nonidentity features in a brain region and how this may change across the human ventral visual pathway. We examined a total of four nonidentity features, including two Euclidean features (position and size) and two non-Euclidean features (image statistics and spatial frequency content of an image). Overall, identity representation increased and nonidentity feature representation decreased along the ventral visual pathway, with identity outweighed the non-Euclidean features, but not the Euclidean ones, in higher levels of visual processing. A similar analysis was performed in 14 convolutional neural networks (CNNs) pretrained to perform object categorization with varying architecture, depth, and with/without recurrent processing. While the relative coding strength of object identity and nonidentity features in lower CNN layers matched well with that in early human visual areas, the match between higher CNN layers and higher human visual regions were limited. Similar results were obtained regardless of whether a CNN was trained with real-world or stylized object images that emphasized shape representation. Together, by measuring the relative coding strength of object identity and nonidentity features, our approach provided a new tool to characterize feature coding in the human brain and the correspondence between the brain and CNNs. SIGNIFICANCE STATEMENTThis study documented the relative coding strength of object identity compared to four types of nonidentity features along the human ventral visual processing pathway and compared brain responses with those of 14 CNNs pretrained to perform object categorization. Overall, identity representation increased and nonidentity feature representation decreased along the ventral visual pathway, with the coding strength of the different nonidentity features differed at higher levels of visual processing. While feature coding in lower CNN layers matched well with that of early human visual areas, the match between higher CNN layers and higher human visual regions were limited. Our approach provided a new tool to characterize feature coding in the human brain and the correspondence between the brain and CNNs.

neuroscience↗

bioRxiv2020

Membrane Nanoparticles Derived from ACE2-rich Cells Block SARS-CoV-2 Infection

The ongoing COVID-19 epidemic worldwide necessitates the development of novel effective agents against SARS-CoV-2. ACE2 is the main receptor of SARS-CoV-2 S1 protein and mediates viral entry into host cells. Herein, the membrane nanoparticles prepared from ACE2-rich cells are discovered with potent capacity to block SARS-CoV-2 infection. The membrane of human embryonic kidney-239T cell highly expressing ACE2 is screened to prepare nanoparticles. The nanomaterial termed HEK-293T-hACE2 NPs contains 265.1 ng mg-1 of ACE2 on the surface and acts as a bait to trap SARS-CoV-2 S1 in a dose-dependent manner, resulting in reduced recruitment of the viral ligand to host cells. Interestingly, SARS-CoV-2 S1 can translocate to the cytoplasm and affect the cell metabolism, which is also inhibited by HEK-293T-hACE2 NPs. Further studies reveal that HEK-293T-hACE2 NPs can efficiently suppress SARS-CoV-2 S pseudovirions entry into human proximal tubular cells and block viral infection with a low half maximal inhibitory concentration. Additionally, this biocompatible membrane nanomaterial is sufficient to block the adherence of SARS-CoV-2 D614G-S1 mutant to sensitive cells. Our study demonstrates a easy-to-acheive memrbane nano-antagonist for curbing SARS-CoV-2, which enriches the existing antiviral arsenal and provides new possibilities to treat COVID-19. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/247338v1_ufig1.gif" ALT="Figure 1"> View larger version (81K): org.highwire.dtl.DTLVardef@4086baorg.highwire.dtl.DTLVardef@4d239eorg.highwire.dtl.DTLVardef@5d8b76org.highwire.dtl.DTLVardef@16f2581_HPS_FORMAT_FIGEXP M_FIG Graphical Table of Contents C_FIG

microbiology↗

bioRxiv2020

Diversity and biogeography of Woesearchaeota: A comprehensive analysis of multi-environment data

Woesearchaeota is a newly proposed archaeal phylum frequently detected in various environments. Due to the limited systematical study, little is known about their distribution, taxonomy, and metabolism. Here, we conducted a comprehensive study for Woesearchaeota with 16S ribosomal RNA (rRNA) gene sequencing data of 27,709 samples and metagenomic whole genome sequencing (WGS) data of 1,266 samples. We find that apart from free-living environments, Woesearchaeota also widely distribute in host-associated environments. And host-associated environmental parameters greatly affect their distribution. 81 Woesearchaeota genomes, including 33 genomes firstly reconstructed in this project, were assigned to 59 Woesearchaeota species, suggesting their high taxonomic diversity. Comparative analysis indicated that Woesearchaeota have an open pan-genome with small core genome. Metabolic reconstruction showed that particular metabolic pathway absence in specific environments, demonstrated the metabolic diversity of Woesearchaeota varies in differences environments. These results have placed host-associated environments into the global biogeography of Woesearchaeota and have demonstrated their genomic diversity for future investigation of adaptive evolution.

ecology↗

bioRxiv2020

Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

BackgroundIn response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. MethodsEighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. ResultsBy examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. ConclusionsThe hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

genomics↗

bioRxiv2020

Genome-Wide Mapping of Cisplatin Damaged Gene Loci

Cisplatin is a DNA targeting anticancer drug, yet its damaged gene loci have remained unclear. In the present work, combining affinity isolation and high throughput sequencing, we genome-widely mapped 17729 gene loci containing platination lesions, which mainly function as enzymes, transcription regulators, transporters and kinases, and of which 445 genes account for 71% of potential gene targets for cancer therapy reported in the literature. The most related core signaling pathway, disease and tissue toxicity of 7578 genes with an enrichment fold (EFG) of >12, where EFG refers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with association P values of < 1x10-22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage. SPAG9 is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. Given SPAG9 abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers.

pharmacology and toxicology↗