Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 1,081 records · Page 60Linked to original sources

bioRxiv2019

A Novel LysR-Type Global Regulator RpvA Controls Persister Formation and Virulence in Staphylococcus aureus

Staphylococcus aureus is the leading cause of wound and nosocomial infections. Persister formation and virulence factors play crucial roles during S. aureus infection. However, the mechanisms of persister formation and its relationship to virulence in S. aureus are poorly understood. In this study, we screened a transposon mutant library and identified a LysR-type global transcriptional regulator NWMN_0037, which we called RpvA, for regulator of persistence and virulence, whose mutation leads to higher susceptibility to antibiotics ampicillin and norfloxacin and various stresses including oxidative stress, heat, and starvation in late exponential and early stationary phase. Interestingly, the rpvA mutant was highly attenuated for virulence compared with the parent S. aureus Newman strain as shown by a much higher lethal dose, reduced ability to survive in macrophages and to form abscess in the mouse model. Transcriptional profiling and metabolomic analysis revealed that RpvA could repress multiple genes including gapR, gapA, tpi, pgm, eno, glpD, and acs expression and enhance production of numerous intermediate metabolites including dihydroxyacetone phosphate, 2-phosphoglycerate, acetyl-CoA, glycerol 3-phosphate, L-glutamate in the cells. The differentially expressed genes and altered production of metabolites are distributed in global metabolism including carbohydrate metabolism, amino acid metabolism, energy metabolism and metabolism of cofactors and vitamins. These metabolic adjustments could cause the cell to go into dormancy, thus promoting S. aureus to convert to persisters. In addition, RpvA could upregulate the expression of virulence genes including hla, hlgA, hlgB, hlgC, lukF, lukS, lukD, sea and coa, and carotenoid biosynthesis genes (crtI, crtM, crtN). Gel shift assay confirmed that RpvA could bind to the promoters of candidate target genes hla, hlgB and crtM, thus promoting S. aureus virulence. Because of the important functions of the RpvA, it may serve as an attractive target for developing new drugs and vaccines to more effectively control S. aureus infections.

microbiology↗

bioRxiv2019

A resource of targeted mutant mouse lines for 5,061 genes

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This nearly triples the number of genes with reporter alleles and almost doubles the number of conditional alleles available to the scientific community. When combined with more than 30 years of community effort, the total mutant allele mouse resource covers more than half of the genome. The extensively validated collection is archived and distributed through public repositories, facilitating availability to the worldwide biomedical research community, and expanding our understanding of gene function and human disease.

genetics↗

bioRxiv2019

In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. Here, we performed in vivo selective 2-hydroxyl acylation analysed by primer extension (SHAPE) chemical profiling on Arabidopsis nuclear RNAs and generated the in vivo nuclear RNA structure landscape. We found that nuclear mRNAs fold differently from cytosolic mRNAs. Notably, we discovered a two-nucleotide single-stranded RNA structure feature upstream of 5 splice sites that is strongly associated with splicing and the selection of alternative 5 splice sites. Moreover, we found the single-strandedness of branch point is also associated with 3 splice site recognition. We also identified an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. Our work demonstrates an RNA structure regulatory mechanism for mRNA processing.

plant biology↗

bioRxiv2019

Variation in the life history strategy of cells underlies tumor’s functional diversity

Classical r- vs. K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology1-5. While its impact has waned in the recent past, cancer evolution may rekindle it6-10. Indeed, solid tumors are an ideal theater for r- and K-selection and, hence, a good testing ground for ideas on life-history strategy evolution11,12. In this study, we impose r- or K-selection on HeLa cells to obtain strongly proliferative r cells and highly competitive K cells. RNA-seq analysis indicates that phenotypic trade-offs in r and K cells are associated with distinct patterns of expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively and rapidly in naive cell lines. It is conceivable that the contrasting selective pressure may operate in a realistic ecological setting of actual tumors. When the r and K cells are mixed in vitro, they exhibit strikingly different spatial and temporal distributions in the resultant cultures. Thanks to this niche separation, the fitness of the entire tumor increases. Our analyses of life-history trade-offs are pertinent to evolutionary ecology as well as cancer biology.

evolutionary biology↗

bioRxiv2019

Deep convolutional neural network and attention mechanism based pan-specific model for interpretable MHC-I peptide binding prediction

Accurate prediction of peptide binding affinity to the major histocompatibility complex (MHC) proteins has the potential to design better therapeutic vaccines. Previous work has shown that pan-specific prediction algorithms can achieve better prediction performance than other approaches. However, most of the top algorithms are neural networks based black box models. Here, we propose DeepAttentionPan, an improved pan-specific model, based on convolutional neural networks and attention mechanisms for more flexible, stable and interpretable MHC-I binding prediction. With the attention mechanism, our ensemble model consisting of 20 trained networks achieves high and more stabilized prediction performance. Extensive tests on IEDBs weekly benchmark dataset show that our method achieves state-of-the-art prediction performance on 21 test allele datasets. Analysis of the peptide positional attention weights learned by our model demonstrates its capability to capture critical binding positions of the peptides, which leads to mechanistic understanding of MHC-peptide binding with high alignment with experimentally verified results. Furthermore, we show that with transfer learning, our pan model can be fine-tuned for alleles with few samples to achieve additional performance improvement. DeepAttentionPan is freely available as an open source software at https://github.com/jjin49/DeepAttentionPan.\n\nAuthor summaryHuman leukocyte antigen (HLA) proteins are classes of proteins that are responsible for immune system regulation in humans. The peptides are short chains of amino acids. HLA class I group present peptides from inside the cell to the cell surface for scrutiny by T cell receptors. For instance, if the cell is infected by a virus, the HLA system will bind to the peptides derived from viral proteins and bring them to the surface of the cell so that the cell can be destroyed by the immune system. Since the HLA genes exhibit extensive polymorphism, there are many HLA alleles binding to different peptides. And this diversity represents challenges in predicting binders for different HLA alleles, which are important in vaccine designs and characterization of immune responses. Before computational algorithms are used to predict the binding relationships of HLA-peptide pairs, scientists need to conduct costly biological experiments to do preliminary screening among a number of peptides and need to use mutant experiments to identify key peptide positions that contribute to the binding. While previous computational methods have been proposed to predict the binding affinity, identifying the binding anchors is not well addressed. Here we developed a deep neural network models with the attention mechanism to learn the binding relationships automatically in an end-to-end way. Our models are able to identify the important binding positions of the peptide sequence by learning the positional importance distribution, which used to be studied a lot only through costly experimental methods. Our model thus not only improves the performance of binding affinity prediction but also allows us to gain biological insight of binding motifs of different alleles via interpreting the learned deep neural network models.

bioinformatics↗

bioRxiv2019

DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction

Human leukocyte antigen (HLA) complex molecules play an essential role in immune interactions by presenting peptides on the cell surface to T cells. With significant progress in deep learning, a series of neural network based models have been proposed and demonstrated with their good performances for peptide-HLA class I binding prediction. However, there still lack effective binding prediction models for HLA class II protein binding with peptides due to its inherent challenges. In this work, we present a novel sequence-based pan-specific neural network structure, DeepSeaPanII, for peptide-HLA class II binding prediction. Compared with existing pan-specific models, our model is an end-to-end neural network model without the need for pre- or post-processing on input samples. Besides state-of-the-art peformance in binding affinity prediction, DeepSeqPanII can also extract biological insight on the binding mechanism over the peptide and HLA sequences by its attention mechanism based binding core prediction capability. The leave-one-allele-out cross validation and benchmark evaluation results show that our proposed network model achieved state-of-the-art performance in HLA-II peptide binding. The source code and trained models are freely available at https://github.com/pcpLiu/DeepSeqPanII.

bioinformatics↗

bioRxiv2019

Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome

Methylated cytosine is an effector of epigenetic gene regulation. In the mammalian brain, the DNA methyltransferase, Dnmt3a, is the sole \"writer\" of atypical non-CpG methylation (mCH), and methyl CpG binding protein 2 (MeCP2) is the only known \"reader\" for mCH. We set out to determine if MeCP2 is the sole reader for Dnmt3a dependent methylation by comparing mice lacking either Dnmt3a or MeCP2 in GABAergic inhibitory neurons. Loss of either the writer or the reader causes overlapping and distinct features from the behavioral to the molecular level. Loss of Dnmt3a results in global loss of mCH and a small subset of mCG sites resulting in more widespread transcriptional alterations and severe neurological dysfunction than seen upon MeCP2 loss. These data indicate that MeCP2 is responsible for reading part of the Dnmt3a dependent methylation in the brain. Importantly, the impact of MeCP2 on genes differentially expressed in both cKO models shows a strong dependence on mCH, but not Dnmt3a dependent mCG, consistent with mCH playing a central role in the pathogenesis of Rett Syndrome.

neuroscience↗

bioRxiv2019

Rapidly cycling stem cells regenerate the intestine independent of Lgr5high cells

The +4 cells in intestinal crypts are DNA damage-resistant and contribute to regeneration. However, their exact identity and the mechanism underlying +4 cell-mediated regeneration remain unclear. Using lineage tracing, we show that cells marked by an Msi1 reporter (Msi1+) are enriched at the +4 position in intestinal crypts and exhibit DNA damage resistance. Single-cell RNA sequencing reveals that the Msi1+ cells are heterogeneous with the majority being intestinal stem cells (ISCs). The DNA damage-resistant subpopulation of Msi1+ cells is characterized by low-to-negative Lgr5 expression and is more rapidly cycling than Lgr5high radio-sensitive crypt base columnar stem cells (CBCs); they enable fast repopulation of the intestinal epithelium independent of CBCs that are largely depleted after irradiation. Furthermore, relative to CBCs, Msi1+ cells preferentially produce Paneth cells during homeostasis and upon radiation repair. Together, we demonstrate that the DNA damage-resistant Msi1+ cells are rapidly cycling ISCs that maintain and regenerate the intestinal epithelium.

cell biology↗

bioRxiv2019

Evaluation of Commercially Available Exosomal Isolation Kits from Human Plasma

Exosomes are cell-derived lipid bilayer particles which are abundant in biological fluids. Exosome is an emerging source of biomarkers to diagnose various human diseases. Sequencing based exosomal studies could provide a comprehensive view of exosomal RNA and protein. To extracted these inclusions, exosomes should be isolated from the plasma first. Several exosome isolation methods were introduced since the discover of exosome. To promote the clinical application of exosomal inclusions, different isolation methods should be compared. We isolated exosomes from human plasma by using user-friendly and commercially available kits, SBI ExoQuick and QIAGEN exoRNeasy. Subsequently, small RNA sequencing was performed with two groups of isolated exosome samples and one group of plasma samples. No fundamental differences of exRNA yield between SC and EQ were found. In RNA profile analysis, the small RNA aligned reads, miRNA pattern, sample clustering varied as a result of methodological differences. Small RNA isolated by ExoQuick presented better data quality and RNA profile than exoRNeasy. This study compared sRNA sequencing data generated from two exosome isolation kits, it provides a reference for future small RNA studies and biomarker prediction in human plasma exosome.

bioinformatics↗

bioRxiv2019

MeCP2 deletion impaired layer 2/3-dominant dynamic reorganization of cortical circuit during motor skill learning

Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.

neuroscience↗

bioRxiv2019

Coordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance

Acquired therapy resistance is a major problem for anticancer treatment, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model for endocrine resistance, we show that hormone resistance is associated with enhanced phenotypic plasticity, indicated by a general downregulation of luminal/epithelial differentiation markers and upregulation of basal/mesenchymal invasive markers. Our extensive omics studies, including GRO-seq on enhancer landscapes, demonstrate that the global enhancer gain/loss reprogramming driven by the differential interactions between ER and other oncogenic transcription factors (TFs), predominantly GATA3 and AP1, profoundly alters breast cancer transcriptional programs. Our functional studies in multiple biological systems including culture and xenograft models of MCF7 and T47D lines support a coordinate role of GATA3 and AP1 in enhancer reprogramming that promotes phenotypic plasticity and endocrine resistance. Collectively, our study implicates that changes in TF-TF and TF-enhancer interactions can lead to genome-wide enhancer reprogramming, resulting in transcriptional dysregulations that promote plasticity and cancer therapy-resistance progression.

cancer biology↗

bioRxiv2019

Single-cell profiling and SCOPE-seq reveal the lineage dynamics of adult neurogenesis and NOTUM as a key V-SVZ regulator

Neural stem cells (NSCs) and their progeny reside in specialized niches in the adult mammalian brain where they generate new neurons and glia throughout life. Adult NSCs of the ventricular-subventricular zone (V-SVZ) are prone to rapid exhaustion; thus timely, context-dependent neurogenesis demands adaptive signaling among the vast number of neighboring progenitors nestled between the ventricular surface and nearby blood vessels. To dissect adult neuronal lineage progression and regulation, we profiled >56,000 V-SVZ and olfactory bulb (OB) cells by single-cell RNA-sequencing (scRNA-seq). Our analyses revealed the diversity of V-SVZ-derived OB neurons, the temporal dynamics of lineage progression, and a key intermediate NSC population enriched for expression of Notum, which encodes a secreted WNT antagonist. Single Cell Optical Phenotyping and Expression (SCOPE-seq), a technology linking live cell imaging with scRNA-seq, uncovered dynamic control of cell size concomitant with NSC differentiation with Notum+ NSCs at a critical size poised for cell division, and a preference of NOTUM surface binding to neuronal precursors with active WNT signaling. Finally, in vivo pharmacological inhibition of NOTUM significantly expanded neuronal precursor pools in the V-SVZ. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, a secreted enzyme that ensures efficient neurogenesis by preventing WNT signaling activation in NSC progeny.

neuroscience↗

bioRxiv2019

Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance, but is usually with low-grade virulence. Although a mouse model revealed different virulence grades of clinical carbapenem-resistant A. baumannii (CRAB) strains, the genetic basis remains unknown. We collected 61 CRAB isolates from intensive care unit of Shenzhen Peoples Hospital (Shenzhen, China), and analyzed them used whole genome sequencing (WGS), multilocus sequence typing (MLST) and core genome MLST (cgMLST), transmission chain reconstruction and Comparative genomic tools. A mouse pneumonia model was used to confirm the hypervirulent phenotype. Eleven complex types (CT) were identified based on core genome multilocus sequence typing scheme. CT512 showed higher transmissibility and bloodstream infection rates than other CTs. A genomic region Lyb-2-4 was shared by CT512 and CT2092 but not CT2085. The mortality rates of patient infected with CRAB harboring Lyb-2-4 was significantly higher than those infected with CRAB isolates without Lyb-2-4 (77.8% vs 24.5%, p < 0.01). In the mouse model, the survival rates of strains containing the Lyb-2-4 region (LAC-4, 5122 and 2092) were significantly lower than for strains without Lyb-2-4 (7152, 71517, 20859 and ATCC17978). One open reading frame (ORF) was a marker for the presence of Lyb-2-4, and PCR of a segment of this ORF, designated as hvcT, served as a tag for hypervirulent CRAB. Our study should be very useful in advising the clinician to implement medical intervention earlier, and also making the worldwide surveillance of these hypervirulent CRAB strains easier.\n\nIMPORTANCEHypervirulent CRAB strains are expected to pose a threat to human health because infection of these strains is associated with high mortality and multidrug resistance. The rapid hypervirulent CRAB identification assay will facilitate prompt medical intervention. Our findings should provoke surveillance for hypervirulent CRAB strains harboring Lyb-2-4 in other countries. Further research should focus on the mechanism of hypervirulence, the acquisition of this genomic region and the development of control measures to prevent further dissemination.

microbiology↗

bioRxiv2019

Systematic Pan-Cancer Analysis Reveals the Functional Roles of Ferroptosis Across Cancers

Ferroptosis is a type of cell death that related to cancer, however, the characteristics of ferroptosis in cancers are still uncertain. Based on the data in The Cancer Genome Atlas, we found that most ferroptosis regulator genes (FRGs) were differentially expressed in tumors, copy number alterations (CNA) and DNA methylation contributed to their aberrant expression. We established the ferroptosis potential index (FPI) to reveal the functional roles of ferroptosis and noticed that the FPI was higher in tumors than in normal tissues in most cancers, and was associated with subtypes and clinical features. The FPI was negatively correlated with several metabolism pathways but positively associated with several important metastasis-related pathways and immune-related pathways. Higher FPI predicted worse prognosis in several tumors, while FPI and FRGs impacted drug sensitivity. Our study presents a systematical analysis of ferroptosis and its regulatory genes, and highlights the potential of ferroptosis-based cancer therapy.

cancer biology↗

bioRxiv2019

Genome sequencing and neurotoxin diversity of a wandering spider Pardosa pseudoannulata (pond wolf spider)

Spiders constitute an extensive and diverse branch of the phylum Arthropoda. Whereas the genomes of four web-weaver spider species and a single cave-living spider have been determined, similar studies have not been reported previously for a wandering spider. The pond wolf spider, Pardosa pseudoannulata, is a wandering hunter that immobilizes prey using venom rather than a web. It is also an important predator against a range of agriculturally important insect pests. The increasing interest in its wandering lifestyle and in the potential of spider venom as a tool for pest control have prompted a detailed study on this wandering spider species. We have generated a high-quality genome sequence of P. pseudoannulata and analysed genes associated with the production of silk and venom toxins. Sequencing reveals that P. pseudoannulata has a large genome of 4.26 Gb. The presence of only 16 spidroin genes and four types of silk glands is consistent with the moderate use of silk and the lack of a prey-catching web. A large number of genes encode neurotoxins and there is evidence that the majority are highly selective for invertebrates. Comparison between spider species reveals a correlation between spider neurotoxin selectivity for target organisms and spider prosoma size, suggesting a possible coevolution of these two features. The genome data provides valuable insights into the biology of P. pseudoannulata and its potential role as a natural enemy in pest control.

genomics↗

bioRxiv2019

Prognostic value of Red Blood Cell Distribution Width in Acute Kidney Injury Patients:A Systematic Review and Meta-analysis

BackgroundThe conflicting result with regard to Red Cell Distribution Width (RDW) with Acute Kidney Injury (AKI) has been reported. This systematic review and meta-analysis were aimed to investigate RDW and prognostic value in AKI patients.\n\nMethods/Main ResultsThis meta-analysis included 1251 cases and 1663 controls with a total of 7 enrolled published papers. The results of RDW levels were significantly associated with patients of AKI (WMD=1.127, 95% CI=0.426-1.827; P=0.002), with statistically significant heterogeneity (I2 =95.80%, Pheterogeneity =0.000, random-effects model).\n\nConclusionsIn conclusion, the results of this present meta-analysis suggest that the RDW value is a positive prognostic indicator in patients with AKI. However, these results were obtained on the basis of RCS or small sample sizes studies. Further functional studies with additional data would be needed to validate our findings.

cell biology↗

bioRxiv2019

Familial relationships in electronic health records (EHR) v2

Heritability is an important statistic for evaluating genetic contribution to phenotypes. Estimating heritability, however, requires a laborious recruitment of a large number of relatives. Electronic health records (EHR) contain massive relative information in emergency contact forms. Recently, we presented RIFTEHR, an algorithm for extracting relationships from EHR. Here, we present an updated version and reconstructed 4.2 million familial relationships from the latest New York-Presbyterian/Columbia University Irving Medical Center (CUIMC) EHR system. The number of updated relationships is 30 percent more than the last version. We present a new implementation of RIFTEHR, which runs in linear time, thus largely improves the speed of the algorithm. We also present a data encryption method, to protect patient privacy in running the algorithm. These resources can be used for generalized use of familial relationships from EHR in genetic studies.

genetics↗

bioRxiv2019

Stromal ISLR promotes intestinal regeneration and cancer by suppressing epithelial Hippo signaling

The YAP signaling activation in epithelial cells is essential for intestinal regeneration and tumorigenesis. However, the molecular mechanism linking stromal signals to YAP-mediated intestinal regeneration and tumorigenesis is poorly defined. Here we report a stroma-epithelia YAP signaling axis essential for stromal cells to modulate epithelial cell growth during intestinal regeneration and tumorigenesis. Specifically, upon inflammation and in cancer, an oncogenic transcription factor ETS1 in stromal cells induces expression of a secreted protein ISLR that can directly binds to a transmembrane protocadherin FAT1 on the surface of epithelial cells. This binding suppressed the Hippo signaling by disrupting MST1-FAT1 association, resulting in YAP signaling activation. Deletion of Islr in stromal cells in mice markedly impaired intestinal regeneration, and suppressed tumorigenesis in the colon. Moreover, the expression of stromal cell-specific ISLR and ETS1 significantly increased in inflamed mucosa of human IBD patients and in human colorectal adenocarcinoma, accounting for the epithelial YAP hyperactivation. Collectively, our findings uncovered a molecular mechanism governing signals for communication between stroma and epithelium during tissue regeneration and tumorigenesis.

cancer biology↗