Biology subjects

Wu, Q.

Publications and source records attributed to Wu, Q..

304 records · Page 17Linked to original sources

bioRxiv2018

The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features

Current evidence to support extensive use of probiotics in inflammatory bowel disease is limited and factors contribute to the inconsistent effectiveness of clinical probiotic therapy are not completely known. Here, as a proof-of-concept, we utilized Bifidobacterium longum JDM 301, a widely used commercial probiotic strain in China, to study potential factors that may influence the beneficial effect of probiotics in experimental colitis. We found that the probiotic therapeutic effect was varied across individual mouse even with the same genetic background and consuming the same type of food. The different probiotic efficacy was highly correlated with different microbiome features in each mouse. Consumption of a diet rich in fat can change the host sensitivity to mucosal injury-induced colitis but did not change the host responsiveness to probiotic therapy. Finally, the host genetic factor TLR2 was required for a therapeutic effect of B. longum JDM 301. Together, our results suggest that personalized microbiome and genetic features may modify the probiotic therapeutic effect.

microbiology↗

bioRxiv2018

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

Many DNA methylome profiling methods cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Since 5mC typically acts as a repressive mark whereas 5hmC is an intermediate form during active demethylation, the inability to separate their signals could lead to incorrect interpretation of the data. Meanwhile, many analysis pipelines quantify methylation level by the count or ratio of methylated reads, but the proportion of discordant reads (PDR) has recently been proposed to be a better indicator of gene expression level. Is the amount of extra information contained in 5hmC signals and PDR worth the additional experimental and computational costs? Here we combine whole-genome bisulfite sequencing (WGBS) and oxidative WGBS (oxWGBS) data in normal human lung and liver tissues and their paired tumors to investigate the quantitative relationships between gene expression and signals of the two forms of DNA methylation at promoters, transcript bodies, and immediate downstream regions. We find that 5mC and 5hmC signals correlate with gene expression in the same direction in most samples, but considering both types of signals increases the accuracy of expression levels inferred from methylation data by a median of 18.2% as compared to having only standard WGBS data, showing that the two forms of methylation provide complementary information about gene expression. In addition, differential analysis between matched tumor and normal pairs is particularly affected by the superposition of 5mC and 5hmC signals in WGBS data, with at least 25-40% of the differentially methylated regions (DMRs) identified from 5mC signals not detected from WGBS data. We do not find PDR to be more informative about expression levels than ratio of methylated reads, and integrating the two types of methylation features only improves the accuracy of inferred expression levels by at most 9.8%. Our results also confirm previous finding that methylation signals at transcript bodies are more indicative of gene expression levels than promoter methylation signals, and further show that in addition to the first exon, methylation signals at the last exon and internal introns also contain non-redundant information about gene expression. Overall, our study provides concrete data for evaluating the cost effectiveness of some experimental and analysis options in the study of DNA methylation in normal and cancer samples.

genomics↗

bioRxiv2018

Eradication of ENO1-deleted Glioblastoma through Collateral Lethality

Inhibiting glycolysis remains an aspirational approach for the treatment of cancer. We recently demonstrated that SF2312, a natural product phosphonate antibiotic, is a potent inhibitor of the glycolytic enzyme Enolase with potential utility for the collateral lethality-based treatment of Enolase-deficient glioblastoma (GBM). However, phosphonates are anionic at physiological pH, limiting cell and tissue permeability. Here, we show that addition of pivaloyloxymethyl (POM) groups to SF2312 (POMSF) dramatically increases potency, leading to inhibition of glycolysis and killing of ENO1-deleted glioma cells in the low nM range. But the utility of POMSF in vivo is dose-limited by severe hemolytic anemia. A derivative, POMHEX, shows equipotency to POMSF without inducing hemolytic anemia. POMHEX can eradicate intracranial orthotopic ENO1-deleted tumors, despite sub-optimal pharmacokinetic properties. Taken together, our data provide in vivo proof-of-principal for collateral lethality in precision oncology and showcase POMHEX as a useful molecule for the study of glycolysis in cancer metabolism.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/331538_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@1b78ebcorg.highwire.dtl.DTLVardef@1fc0ccforg.highwire.dtl.DTLVardef@ad268corg.highwire.dtl.DTLVardef@1bdee32_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2018

High throughput single cell sequencing of both T-cell-receptor-beta alleles

Allelic exclusion is a vital mechanism for the generation of monospecificity to foreign antigens in B- and T-lymphocytes. Here we developed a high-throughput barcoded method to simultaneously analyze the VDJ recombination status of both mouse T cell receptor beta alleles in hundreds of single cells using Next Generation Sequencing.

immunology↗

bioRxiv2018

Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs

Postzygotic single-nucleotide mosaicisms (pSNMs) have been extensively studied in tumors and are known to play critical roles in tumorigenesis. However, the patterns and origin of pSNMs in normal organs of healthy humans remain largely unknown. Using whole-genome sequencing and ultra-deep amplicon re-sequencing, we identified and validated 164 pSNMs from 27 postmortem organ samples obtained from five healthy donors. The mutant allele fractions ranged from 1.0% to 29.7%. Inter- and intra-organ comparison revealed two distinctive types of pSNMs, with about half originating during early embryogenesis (embryonic pSNMs) and the remaining more likely to result from clonal expansion events that had occurred more recently (clonal expansion pSNMs). Compared to clonal expansion pSNMs, embryonic pSNMs had higher proportion of C>T mutations with elevated mutation rate at CpG sites. We observed differences in replication timing between these two types of pSNMs, with embryonic and clonal expansion pSNMs enriched in early- and late-replicating regions, respectively. An increased number of embryonic pSNMs were located in open chromatin states and topologically associating domains that transcribed embryonically. Our findings provide new insights into the origin and spatial distribution of postzygotic mosaicism during normal human development.\n\nAuthor SummaryGenomic mosaicism led by postzygotic mutation is the major cause of cancers and many non-cancer developmental disorders. Theoretically, postzygotic mutations should be accumulated during the developmental process of healthy individuals, but the genome-wide characterization of postzygotic mosaicisms across many organ types of the same individual remained limited. In this study, we identified and validated two types of postzygotic mosaicism from the whole-genomes of 27 organs obtained from five healthy donors. We further found that the postzygotic mosaicisms arising during early embryogenesis and later clonal expansion events show distinct genomic patterns in mutation spectrum, replication timing, and chromatin status.

genomics↗

bioRxiv2018

In silico mouse study identifies tumor growth kinetics as biomarkers for the outcome of anti-angiogenic treatment

Angiogenesis is a crucial step in tumor progression, as this process allows tumors to recruit new blood vessels and obtain oxygen and nutrients to sustain growth. Therefore, inhibiting angiogenesis remains a viable strategy for cancer therapy. However, anti-angiogenic therapy has not proved to be effective in reducing tumor growth across a wide range of tumors, and no reliable predictive biomarkers have been found to determine the efficacy of anti-angiogenic treatment. Using our previously established computational model of tumor-bearing mice, we sought to determine whether tumor growth kinetic parameters could be used to predict the outcome of anti-angiogenic treatment. A model trained with datasets from six in vivo mice studies was used to generate a randomized in silico tumor-bearing mouse population. We analyzed tumor growth in untreated mice (control) and mice treated with an anti-angiogenic agent and determined the Kaplan-Meier survival estimates based on simulated tumor volume data. We found that the ratio between two kinetic parameters, k0 and k1, which characterize the tumors exponential and linear growth rates, as well as k1 alone, can be used as prognostic biomarkers of population survival outcome. Our work demonstrates a robust, quantitative approach for identifying tumor growth kinetic parameters as prognostic biomarkers and serves as a template that can be used to identify other biomarkers for anti-angiogenic treatment.

systems biology↗

bioRxiv2018

Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos

Single-cell RNA-seq experiments cannot record cell division history and therefore cannot directly connect intercellular differences at a later developmental stage to their progenitor cells. We developed Rainbow-seq to combine cell division lineage tracing with single-cell RNA-seq. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA-seq experiment to simultaneously read single-cell transcriptomes and decode the lineage marker genes. We traced the lineages deriving from each blastomere in two-cell mouse embryos and observed inequivalent contributions to the embryonic and abembryonic poles in 72% of the blastocysts evaluated. Rainbow-seq on four- and eight-cell embryos with lineage tracing triggered at two-cell stage exhibited remarkable transcriptome-wide differences between the two cell lineages at both stages, including genes involved in negative regulation of transcription and signaling. These data provide critical insights on cell fate choices in cleavage embryos. Rainbow-seq bridged a critical gap between cellular division history and single-cell RNA-seq assays.

developmental biology↗

bioRxiv2018

Comparative Transcriptomic and Metabolomic Analyses in Response to Cold in Tartary Buckwheat (Fagopyrum tataricum)

Plants recognize multiple environmental signals that lead to substantial changes in the regulation of primary and secondary metabolism in order to adapt to environmental stresses. In this study, we investigate the effects of cold on the metabolome and transcriptome of tartary buckwheat, focusing on the phenylpropanoid biosynthetic pathway. Using RNA-sequencing analysis of the cold-regulated transcriptome of buckwheat, we identified several phenylpropanoid biosynthetic transcripts that accumulated in response to cold. To confirm the transcriptome data, we analyzed the expression of the phenylpropanoid biosynthetic transcripts in cold-treated buckwheat and showed that all the phenylpropanoid biosynthetic transcripts were upregulated in coldtreated buckwheat seedlings with the exception of FtDFR. From the metabolic profiling based on the GC-TOF-MS analysis, we show that most of the sugars and their derivatives significantly increase in response to cold, while some of amino acids and their derivatives decrease in cold-treated plants. Some organic acids derived from the tricarboxylic acid (TCA) cycle increased in the cold-treated plants compared with in the plants grown at 25{degrees}C. In particular, the contents of anthocyanins and proanthocyanidins were significantly increased by cold treatment. In summary, these results indicate that the metabolome and transcriptome of tartary buckwheat are extensively affected by cold stresses.\n\nHighlightUsing the RNA-sequencing data and the metabolic profiling analysis, we identified the changes that occur in the transcriptome and metabolome of tartary buckwheat in response to cold, focusing on the flavonoid biosynthetic pathway.\n\nAbbreviations

systems biology↗

bioRxiv2018

GITAR: An open source tool for analysis and visualization of Hi-C data

Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present GITAR (Genome Interaction Tools and Resources), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, visualization and topologically associated domains (TADs) analysis. GITAR is composed of two main modules: 1) HiCtool, a Python library to process and visualize Hi-C data, including TADs analysis and 2) Processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline which goes from the raw Hi-C data to the computation, visualization and optimized storage of intra-chromosomal contact matrices and topological domain coordinates. A large collection of standardized processed data allows to compare different datasets in a consistent way and it saves time of work to obtain data for visualization or additional analyses. GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data and it is freely available for the public at http://genomegitar.org as an open source software.

bioinformatics↗

bioRxiv2017

Pyk2 suppresses contextual fear memory in a kinase-independent manner

Post-traumatic stress disorder (PTSD) is a psychological illness characterized by recalling a feeling of distress when re-experiencing the original trauma-related cues. This associative fear response plays an important role in some psychiatric disorders and elucidation of the underlying mechanisms is of great importance. Here, we constructed Pyk2 null mice and found that these mutant mice showed enhancement in contextual-fear memory, but no changes in auditory-cued and spatial-referenced learning and memory. Moreover, using kinase mutant mice, we observed that Pyk2 suppressed contextual fear memory in a kinase-independent pathway. Using high-throughput RNA sequencing, we found that immediate early genes (IEGs), such as Npas4, cFos, Zif268/Egr1, Arc, and Nr4a1, were enhanced in Pyk2 null mice. We further demonstrated that Pyk2 disruption affected pyramidal neuronal complexity and spine dynamics. Thus, we demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2 null mice provides a model for understanding fear-related disorders.

genetics↗

bioRxiv2017

The CLAVATA receptor FASCIATED EAR2 responds to different CLE peptides by signaling through different downstream effectors.

Meristems contain groups of indeterminate stem cells that are critical for organ initiation throughout plant development. The shoot apical meristem (SAM) maintains itself and initiates all shoot organs, such as leaves, floral organs and axillary branch meristems. Development and balanced proliferation of the SAM is regulated by a feedback loop between CLAVATA (CLV) and WUSCHEL (WUS) signaling. CLV signaling is initiated by secretion of the CLV3 peptide ligand, which is perceived directly or indirectly by a number of Leucine-Rich-Repeat (LRR) receptor-like kinases, including CLV1 and BARELY ANY MERISTEM (BAM) 1-3, and RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2), as well as the receptor-like protein CLV2 in a complex with the CORYNE (CRN) pseudokinase. However, CLV2, and its maize ortholog FASCIATED EAR2 (FEA2) appear to function in signaling by several related CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide ligands, including CLV3. Nevertheless, it remains unknown how CLV2 or FEA2 transmit specific signals from distinct CLE peptides. Here we show that FEA2 is involved in signaling from at least 2 distinct CLE peptides, ZmCLE7, a maize CLV3 ortholog, and ZmFON2-LIKE CLE PROTEIN1 (ZmFCP1), a newly identified CLE peptide functioning in SAM regulation. Signaling from these 2 different CLE peptides appears to be transmitted through 2 different candidate downstream effectors, COMPACT PLANT2 (CT2), the alpha subunit of the maize heterotrimeric G protein, and maize CRN. Our data provide a novel framework to understand how diverse signaling peptides can activate different downstream pathways through common receptor proteins.

plant biology↗

bioRxiv2017

In vivo relevance of intercellular calcium signaling in Drosophila wing development

Recently, organ-scale intercellular Ca2+ transients (ICTs) were reported in the Drosophila wing disc. However, the functional in vivo significance of ICTs remains largely unknown. Here we demonstrate the in vivo relevance of intercellular Ca2+ signaling and its impact on wing development. We report that Ca2+ signaling in vivo decreases as wing discs mature. Ca2+ signaling ex vivo responds to fly extract in a dose-dependent manner. This suggests ICTs occur in vivo due to chemical stimulus that varies in concentration during development. RNAi mediated inhibition of genes required for ICTs results in defects in the size, shape, and vein patterning of adult wings. It also leads to reduction or elimination of in vivo Ca2+ transients. Further, perturbations to the extracellular matrix along the basal side of the wing disc stimulates intercellular Ca2+ waves. This is the first identified chemically defined, non-wounding stimulus of ICTs. Together, these results point toward specific in vivo functions of intercellular Ca2+ signaling to mediate mechanical stress dissipation and ensure robust patterning during development.

developmental biology↗

bioRxiv2017

Predictive model identifies strategies to enhance TSP1-mediated apoptosis signaling

This study explores strategies to enhance thrombospondin-1 (TSP1) induced apoptosis in endothelial cells, an important function that contributes to TSP1s anti-angiogenic effect. We established a mathematical model of TSP1-mediated intracellular signaling via the CD36 receptor. This model was used to investigate the effects of several approaches to perturb the TSP1-CD36 signaling network. Model simulations predict the population-based response to strategies to enhance TSP1-mediated apoptosis, such as downregulating the apoptosis inhibitor XIAP and inhibiting phosphatase activity. The model also postulates a new mechanism of low dosage doxorubicin treatment in combination with TSP1 stimulation. Using computational analysis, we predict which cells will undergo apoptosis, based on the initial intracellular concentrations of particular signaling species. Overall, the modeling framework predicts molecular strategies that increase TSP1-mediated apoptosis, which is useful in many disease settings.

systems biology↗

bioRxiv2017

Precise And Predictable DNA Fragment Editing Reveals Principles Of Cas9-Mediated Nucleotide Insertion

DNA fragment editing (DFE) or chromosomal engineering including inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate structural genome variations and developmental gene regulation, but little is known about the underlying mechanisms. Here we report that debilitating CtIP, which is thought to function in NHEJ, enhances precise DNA fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA fragment inversions, deletions, and duplications, we find that Cas9 cleaves the noncomplementary strand with a flexible profile upstream of the PAM site and rationally-designed Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions of DFE are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DFEs could be achieved by perturbing DNA repair genes and using appropriate PAM configurations. These findings have important applications regarding 3D chromatin folding and enhancer insulation during gene regulation.

genetics↗

bioRxiv2017

Molecular Mapping Of YrTZ2, A Stripe Rust Resistance Gene In Wild Emmer Accession TZ-2 And Its Comparative Analyses With Aegilops tauschii

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that can cause severe yield losses. Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease. Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailing Pst races in China. A set of 200 F6:7 recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation. Genetic analysis indicated that the stripe rust resistance of TZ-2 to Pst race CYR34 was controlled by a single dominant gene, temporarily designated YrTZ2. Through bulked segregant analysis (BSA) and SSR mapping, YrTZ2 was located on chromosome arm 1BS and flanked by SSR markers Xwmc230 and Xgwm413 with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively. By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consist of 250 SNP markers) closely linked with YrTZ2 were identified. YrTZ2 was further delimited into a 0.8 cM genetic interval between SNP marker IWB19368 and SSR marker Xgwm413, and co-segregated with SNP marker IWB28744 (attached with 28 SNP markers). Comparative genomics analyses revealed high level of collinearity between the YrTZ2 genomic region and the orthologous region of Aegilops tauschii 1DS. The genomic region between loci IWB19368 and IWB31649 harboring YrTZ2 is orthologous to a 24.5 Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS. The genetic and comparative maps of YrTZ2 provide framework for map-based cloning and marker-assisted selection (MAS) of YrTZ2.

plant biology↗

bioRxiv2017

Morphogen signalling patterns calcium waves in the Drosophila wing disc

Organ development is driven by a set of patterned inductive signals. However, how these signals are integrated to coordinate tissue patterning is still poorly understood. Calcium ions (Ca2+) are critical signaling components involved in signal integration and are regulated by a core Ca2+ signaling toolkit. Ca2+ signaling encodes a significant fraction of information in cells through both amplitude and frequency-dependent regulation of transcription factors and key regulatory enzymes. A range of intercellular Ca2+ transients, including coordinated oscillations, recently have been reported in Drosophila wing discs. In an accompanying paper, we show that impaired Ca2+ signaling impacts the final size and shape of the wing. Here, we discover specific spatiotemporal signatures of Ca2+ transients during wing disc development. To do so, we developed a new neural-network-based approach for registration of oscillatory signals in organs that frequently move during imaging, and a pipeline for spatiotemporal analysis of intercellular Ca2+ oscillations. As a specific test case, we further demonstrated that the morphogen pathway, Hedgehog, controls frequencies of Ca2+ oscillations uniformly in the tissue and is required for spatial patterning of oscillation amplitudes. Thus, the time-averaged dynamics of spontaneous intercellular Ca2+ transients reflect the morphogenetic signaling state of the tissue during development. This suggests a general mechanism of physiological signaling that provides a memory of morphogenetic patterns. Additionally, our study provides a powerful approach for registering and quantifying oscillatory dynamics in developing organs.

developmental biology↗