Biology subjects

Wen, X.

Publications and source records attributed to Wen, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2020

Interspecies variation in hominid gut microbiota controls host gene regulation

The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology, and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterized the transcriptional response of colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We found most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes, while some genes respond only to microbiomes from specific host species. Genes that exhibit such a divergent response are associated with relevant intestinal diseases in humans, such as inflammatory bowel disease and Crohns disease. Lastly, we found that inflammation-associated microbial species regulate the expression of host genes previously associated with inflammatory bowel disease, suggesting health-related consequences for species-specific host-microbiome interactions across hominids.

genomics↗

bioRxiv2020

Interannual variability of net ecosystem carbon production and its climatic and biotic mechanism during 2005-2018 in a rain-fed maize ecosystem

The interannual variation (IAV) of net ecosystem carbon production (NEP) plays an important role in understanding the mechanisms of the carbon cycle in the agriculture ecosystem. In this study, the IAV of NEP, which were expressed as annual values and anomalies, and its climatic and biotic controls mechanism, were investigated based on an eddy covariance dataset of rain-fed spring maize during 2005-2018 in the northeast of China. The annual NEP was 270{+/-}115 g C m-2yr -1. Annual values and anomalies of NEP were positively correlated with that of precipitation (PPT), gross ecosystem production (GEP) and daily maximum NEP (NEPmax). Annual anomalies of NEP were dominantly and positively controlled by the soil water content (SWC) through GEP and the soil temperature (Ts) through RE. In comparison, annual anomalies of NEP were dominantly and negatively controlled by summer VPD through the NEPmax, positively adjusted by spring precipitation and the effective accumulative temperature through the beginning date (BDOY) of the affecting carbon uptake period (CUP), and by autumn precipitation and leaf area index through the end date (EDOY) of the affecting CUP. Residues restrained the carbon release at the beginning of the year, and accelerated the carbon release at the end of the year. Our results hightlight that NEP might be more sensitive to the change of water condition (such as PPT, SWC and VPD) induced by the climate changes.

ecology↗

bioRxiv2020

Psychosocial experiences modulate asthma-associated genes through gene-environment interactions

Social interactions and the overall psychosocial environment have a demonstrated impact on health, particularly for people living in disadvantaged urban areas. Here we investigated the effect of psychosocial experiences on gene expression in peripheral blood immune cells of children with asthma in Metro Detroit. Using RNA-sequencing and a new machine learning approach, we identified transcriptional signatures of 20 variables including psychosocial factors, blood cell composition and asthma symptoms. Importantly, we found 174 genes associated with asthma that are regulated by psychosocial factors, and 349 significant gene-environment interactions for gene expression levels. These results demonstrate that immune gene expression mediates the link between negative psychosocial experiences and asthma risk.

genomics↗

bioRxiv2020

Probabilistic Colocalization of Genetic Variants from Complex and Molecular Traits: Promise and Limitations

Colocalization analysis has emerged as a powerful tool to uncover the overlapping of causal variants responsible for both molecular and complex disease phenotypes. The findings from colocalization analysis yield insights into the molecular pathways of complex diseases. In this paper, we conduct an in-depth investigation of the promise and limitations of the available colocalization analysis approaches. Focusing on variant-level colocalization approaches, we first establish the connections between various existing methods. We proceed to discuss the impacts of various controllable analytical factors and uncontrollable practical factors on outcomes of colocalization analysis through realistic simulations and real data examples. We identify a single analytical factor, the specification of prior enrichment levels, which can lead to severe inflation of false-positive colocalization findings. Meanwhile, the combination of many other analytical and practical factors all lead to diminished power. Consequently, we recommend the following strategies for the best practice of colocalization analysis: i) estimating prior enrichment level from the observed data; and ii) separating fine-mapping and colocalization analysis. Our analysis of 4,091 complex traits and the multi-tissue eQTL data from the GTEx (version 8) suggests that colocalizations of molecular QTLs and GWAS traits are widespread in many complex traits. However, only a small proportion can be confidently identified from currently available data due to a lack of power. Our findings should serve as an important benchmark for the current and future integrative genetic association analysis applications.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2020

Cyclo olefin polymer-based solvent-free mass-productive microphysiological systems

A microphysiological system (MPS) holds a great promise for drug screening and toxicological testing as an alternative to animal models. However, this platform has several issues in terms of the materials used (e.g., polydimethylsiloxane), such as the absorbance of tested drug candidates and fluorescent dyes by the material, as well as the effect on cultured cellular status, thus misleading the results obtained from cell assays and fabrication processes. Hence, to eliminate the issues mentioned above, we developed a cyclo olefin polymer (COP)-based MPS via photobonding process using vacuum ultraviolet (VUV), named COP-VUV-MPS. COP-VUV-MPS showed better chemical resistance and avoided molecule absorption. COP-VUV-MPS could maintain the stemness of environmentally sensitive human-induced pluripotent stem cells without causing undesired cellular phenotypes and gene expression. These results suggested that COP-VUV-MPS might be broadly used for the advancement of MPS and applications in drug development and in vitro toxicological testing.Competing Interest StatementM.Y. is an employee of Ushio Inc. The part of this project was financially supported by Ushio Inc. Kyoto University (K.K.) and Ushio INC. (M.Y.) filed a Japanese patent application based on the research presented herein. The remaining authors declare no competing interests.View Full Text

bioengineering↗

bioRxiv2020

A pathway of NADPH diaphorase positivity between central canal and pial surface at anterior fissure in spinal cord: Supra fissure area with hypothesis configuring from dog, rat, monkey and pigeon

The spinal cord is a cylinder structure in the vertebra and thought a simplified with the gray matter and white matter. Rexed lamination for the gray matter and regional sub-division for whiter matter are completely termed to date. Anterior commissure locates between the central canal and the anterior median fissure. However, some experimental data may still confront with new confined anatomical interpretation. By using NADPH diaphorase [N-d] enzyme histology, we found a vertical oriented neuronal pathway between the central canal and the anterior median fissure in the sacral spinal cord of young adult and aged dog. We used a term "supra fissure area" [SFA] to illustrate the region which consisted of the gray commissure and anterior white commissure. The N-d pathway was notably observable in aged animals. The vertical neurites revealed the cerebrospinal fluid [CSF] contacting neurites between the anterior median fissure and the central canal. We further examined the monkey, rat and pigeon in the region for better understanding of the structure and potential function. The neurodegeneration of N-d dystrophy was detected in the [SFA] in the thoracic spinal cord of the aged monkey. N-d positive fibers were detected in anterior fissure of the rat spinal cord. N-d fibrous structures were also detected in the pigeon spinal cord. These results suggested a new pathway of CSF contacting neurons and the neuronal communications about the central canal.

neuroscience↗

bioRxiv2020

scSTATseq: Diminishing Technical Dropout Enables Core Transcriptome Recovery and Comprehensive Single-cell Trajectory Mapping

The advent of single-cell RNA sequencing has provided illuminating information on complex systems. However, large numbers of genes tend to be scarcely detected in common scRNAseq approaches due to technical dropout. Although bioinformatics approaches have been developed to approximate true expression profiles, assess the dropout events on single-cell transcriptomes is still consequently challenging. In this report, we present a new plate-based method for scRNAseq that relies on Tn5 transposase to tagment cDNA following second strand synthesis. By utilizing pre-amplification tagmentation step, scSTATseq libraries are insulated against technical dropout, allowing for detailed analysis of gene-gene co-expression relationships and mapping of pathway trajectories. The entire scSTATseq library construction workflow can be completed in 7 hours, and recover transcriptome information on up to 8,000 protein-coding genes. Investigation of osteoclast differentiation using this workflow allowed us to identify novel markers of interest such as Rab15. Overall, scSTATseq is an efficient and economical method for scRNAseq that compares favorably with existing workflows.

genomics↗

bioRxiv2020

Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance

The integration of transcriptomic studies and GWAS (genome-wide association studies) via imputed expression has seen extensive application in recent years, enabling the functional characterization and causal gene prioritization of GWAS loci. However, the techniques for imputing transcriptomic traits from DNA variation remain underdeveloped. Furthermore, associations found when linking eQTL studies to complex traits through methods like PrediXcan can lead to false positives due to linkage disequilibrium between distinct causal variants. Therefore, the best prediction performance models may not necessarily lead to more reliable causal gene discovery. With the goal of improving discoveries without increasing false positives, we develop and compare multiple transcriptomic imputation approaches using the most recent GTEx release of expression and splicing data on 17,382 RNA-sequencing samples from 948 post-mortem donors in 54 tissues. We find that informing prediction models with posterior causal probability from fine-mapping (dap-g) and borrowing information across tissues (mashr) lead to better performance in terms of number and proportion of significant associations that are colocalized and the proportion of silver standard genes identified as indicated by precision-recall and ROC (Receiver Operating Characteristic) curves. All prediction models are made publicly available at predictdb.org. Author summaryIntegrating molecular biology information with genome-wide association studies (GWAS) sheds light on the mechanisms tying genetic variation to complex traits. However, associations found when linking eQTL studies to complex traits through methods like PrediXcan can lead to false positives due to linkage disequilibrium of distinct causal variants. By integrating fine-mapping information into the models, and leveraging the widespread tissue-sharing of eQTLs, we improve the proportion of likely causal genes among significant gene-trait associations, as well as the prediction of "ground truth" genes.

genomics↗

bioRxiv2020

Genome architecture and transcription data reveal allelic bias during the cell cycle

Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.

bioinformatics↗

bioRxiv2020

A bottom-up approach for the de novo design of functional proteins

De novo protein design has enabled the creation of novel protein structures. To design novel functional proteins, state-of-the-art approaches use natural proteins or first design protein scaffolds that subsequently serve as templates for the transplantation of functional motifs. In these approaches, the templates are function-agnostic and motifs have been limited to those with regular secondary structure. Here, we present a bottom-up approach to build de novo proteins tailored to structurally complex functional motifs. We applied a bottom-up strategy to design scaffolds for four different binding motifs, including one bi-functionalized protein with two motifs. The de novo proteins were functional as biosensors to quantify epitope-specific antibody responses and as orthogonal ligands to activate a signaling pathway in engineered mammalian cells. Altogether, we present a versatile strategy for the bottom-up design of functional proteins, applicable to a wide range of functional protein design challenges.

bioengineering↗

bioRxiv2020

Building a robust chromatin immunoprecipitation (ChIP) method with substantially improved efficiency

Chromatin immunoprecipitation (ChIP) is the gold-standard method to detect the interactions between proteins and chromatin, and is a powerful tool to identify epigenetic modifications. Although ChIP protocols for plant species have been developed, many specific features of plants, especially woody plants, still hinder the efficiency of immunoprecipitation, resulting inefficient ChIP enrichment. There is an active demand for a highly efficient ChIP protocol. In the present study, we employed Betula platyphylla (birch) and Arabidopsis thaliana as the research materials, and five factors closely associated with ChIP efficiency were identified, including crosslinking, chromatin concentration using centrifugal filter, using new immunoprecipitation buffer, rescue DNA with proteinase K, and using sucrose to increase immunoprecipitation efficiency. Optimization of any these factors can significantly improve ChIP efficiency. Considering these factors together, a robust ChIP protocol was developed, for which the average fold enrichments were 16.88 and 6.43 fold of that gained using standard ChIP in birch and Arabidopsis, respectively. As this built ChIP method works well in both birch and Arabidopsis, it should be also suitable for other woody and herbaceous species. In addition, this ChIP method make it is possible to detect low-abundance TF-DNA interactions, and may extend the application of ChIP in plant kingdom. One sentence summaryBuilding a ChIP method that increases fold enrichment of birch by 16 folds in average and is adapted for both woody and herbaceous plants.

plant biology↗

bioRxiv2020

The LRRC8A:C Heteromeric Channel Is a cGAMP Transporter and the Dominant cGAMP Importer in Human Vasculature Cells

Extracellular 23-cyclic-GMP-AMP (cGAMP) is an immunotransmitter secreted by cancer cells and taken up by host cells to activate the anti-cancer STING pathway. No cGAMP exporter has been identified, and SLC19A1, a recently identified cGAMP importer, does not account for the import activity in most cell types. Here, we identify the LRRC8A:C heteromeric channel, a volume-regulated anion channel (VRAC), as a cGAMP transporter. This channel mediates cGAMP import or export depending on the cGAMP chemical gradient, and channel activation or inhibition modulates cGAMP transport. Other 23-cyclic dinucleotides are also transported by LRRC8A:C channels, including the investigational cancer therapeutic ADU-S100. Furthermore, we demonstrate that the LRRC8A-containing channel is the dominant cGAMP importer in primary human vasculature cells. Given tumor vasculatures regulation of immune infiltration and its disruption in response to STING agonists, we have uncovered a leading molecular mechanism for extracellular cGAMP signaling in this important anti-cancer target.

biochemistry↗

bioRxiv2020

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

BackgroundThe global dissemination of colistin resistance encoded by mcr-1 has been attributed to extensive use of colistin in livestock, threatening colistin efficacy in medicine. The emergence of mcr-1 in common pathogens, such as Escherichia coli, is of particular concern. Therefore, China banned the use of colistin in animal feed from May 1ST 2017. We investigated subsequent changes in mcr-1 prevalence, and the genomic epidemiology of mcr-1-positive Escherichia coli (MCRPEC). MethodsSampling was conducted pre- (October-December 2016) and post-colistin ban (October-December, 2017 and 2018, respectively). 3675 non-duplicate pig fecal samples were collected from 14 provinces (66 farms) in China to determine intervention-related changes in mcr-1 prevalence. 15193 samples were collected from pigs, healthy human volunteers, colonized and infected hospital inpatients, food and the environment in Guangzhou, to characterize source-specific mcr-1 prevalence and the wider ecological impact of the ban. From these samples, 688 MCRPEC were analyzed with whole genome sequencing (WGS), plasmid conjugation and S1-PFGE/Southern blots to characterize associated genomic changes. FindingsAfter the ban, mcr-1 prevalence decreased significantly in national pig farms, from 45{middle dot}0% (308/684 samples) in 2016, to 19{middle dot}4% (274/1416) in 2018 (p<0{middle dot}0001). This trend was mirrored in samples from most sources in Guangzhou (overall 19{middle dot}2% [959/5003 samples] in 2016; 5{middle dot}3% [238/4489] in 2018; p<0{middle dot}0001). The population structure of MCRPEC was diverse (23 sequence clusters [SCs]); ST10 clonal complex isolates were predominant (247/688 [36%]). MCRPEC causing infection in hospitalized inpatients were genetically more distinct and appeared less affected by the ban. mcr-1 was predominantly found on plasmids (632/688 [92%]). Common mcr-1 plasmid types included IncX4, IncI2 and IncHI2 (502/656 [76.5%]); significant increases in IncI2-associated mcr-1 and a distinct lineage of mcr-1-associated IncHI2 were observed post-ban. Changes in the frequency of mcr-1-associated flanking sequences (ISApl1-negative MCRPEC), 63 core genome SNPs and 30 accessory genes were also significantly different after the ban, consistent with rapid genetic adaptation in response to changing selection pressures. InterpretationA rapid, ecosystem-wide, decline in mcr-1 was observed after banning the use of colistin in animal feed, with associated genetic changes in MCRPEC. Genomic surveillance is key to assessing and monitoring stewardship interventions. FundingNational Natural Science Foundation of China

microbiology↗

bioRxiv2020

Pial surface CSF-contacting texture, subpial and funicular plexus in the thoracic spinal cord in monkey: NADPH diaphorase histological configuration

In spinal cord, white matter is distinguished from grey matter in that it contains ascending and descending axonal tracts. While grey matter gets concentrated with neuronal cell bodies. Notable cell bodies and sensory modality of cerebral spinal fluid (CSF) in white matter are still elusive in certain segment of the spinal cord. Monkey Spinal cord was examined by NADPH diaphorase (NADPH-d) histochemistry. We found that NADPH-d positive neurons clustered and featured flat plane in mediolateral funiculus in caudal thoracic and rostral lumber spinal cord, especially evident in the horizontal sections. Majority of NADPH-d funicular neurons were relatively large size and moderately-or lightly-stained neurons. In horizontal section, the multipolar processes of the neurons were thicker than that of regular other neurons. The processes oriented laterally or obliquely in the lateral funiculus. Some of neuronal cell bodies and proximal processes attached NADPH-d positive buttons or puncta. The neuronal processes interlaced network medially linked to lateral horn (intermediolateral nucleus, IML) and laterally to subpial region, in which formed subpial plexus with subpial NADPH-d neurons. Subpial plexus appeared to contacting externally with CSF. The subpial plexus patterned like round brackets located in lateromarginal pial surface. Compared with sympathetic IML in rostral thoracic segments and sacral parasympathetic IML, the funicular plexus configurated a specialized neuro-texture in caudal thoracic segments. The dendritic arbor of funicular neuron featured variety geometric plane shapes. The funicular plexus oriented exclusive layered flat-plane organization between lateral horn and subpial region in caudal thoracic and rostral lumber spinal cord. The subpial plexus may work as CSF sensor outside of spinal cord. The cluster of funicular neurons may function as locomotion sensor, besides visceral regulation. Different to periventricular CSF contacting or pericentral canal structures, NADPH-d funicular neurons and subpial plexus that located in the pial surface. With advantage of NADPH-d, we found funicular neurons which termed academically as funicular plexus and specialized localization for subpial structure we termed subpial plexus. The funicular texture was regarded as neuronal bridge between the interior CSF in the central canal and external CSF out of the pial surface.

neuroscience↗

bioRxiv2019

NADPH diaphorase neuronal dystrophy in gracile nucleus, cuneatus nucleus and spinal trigeminal nucleus in aged rat

NADPH-diaphorase (N-d) activity is commonly used to identify NOS-ergic neurons. In our previous study, N-d positive neuritic dystrophy and spheroid termed aging-related N-d Body is discovered in the lumbosacral spinal cord in the normal aging rats. Histological studies also reveal that N-d positive neurodegenerative changes occur in the gracile nucleus. We re-examined N-d activity in gracile nucleus in aged rat. We found N-d positive neuritic dystrophy and spheroid also occurred in the cuneatus nucleus and spinal trigeminal nucleus. Besides regular coronal section, longitudinal oriented dystrophic neurites were detected in the sagittal and horizontal section in gracile nucleus and dorsal column. We fziurther examined the medullary oblongata with regular classical histology including Golgi staining, immunocytochemistry of NOS and phosphorylated tau protein, neuronal tracing method with wheat germ agglutinin conjugated alexa-fluor-488 through sciatic nerve, and spinal cord transection at thoracic level. Most of N-d positive neuritic dystrophy and spheroid did not showed colocalization with NOS or phosphorylated tau protein. Neuronal tracing and spinal cord transection revealed that N-d dystrophic neurites in gracile nucleus originated from terminal of sensory projection from spinal cord and peripheral somatic input. The results suggested that aging-related N-d dystrophy in the gracile nucleus was unique morphological feature. In conclusion, it was postulated that the N-d dystrophy as a morphological marker of aging degenerative damage in normal aged organisms.

neuroscience↗

bioRxiv2019

TORC1 regulates vacuole membrane composition through ubiquitin- and ESCRT-dependent microautophagy

Cellular adaptation in response to nutrient limitation requires the induction of autophagy and lysosome biogenesis for the efficient recycling of macromolecules. Here, we discovered that starvation and TORC1 inactivation not only lead to the upregulation of autophagy and vacuole proteins involved in recycling, but also result in the downregulation of many vacuole membrane proteins to supply amino acids as part of a vacuole remodeling process. Downregulation of vacuole membrane proteins is initiated by ubiquitination, which is accomplished by the coordination of multiple E3 ubiquitin ligases, including Rsp5, the Dsc complex, and a newly characterized E3 ligase, Pib1. The Dsc complex is negatively regulated by TORC1 through the Rim15-Ume6 signaling cascade. After ubiquitination, vacuole membrane proteins are sorted into the lumen for degradation by ESCRT-dependent microautophagy. Thus, our study uncovered a complex relationship between TORC1 inactivation and vacuole biogenesis.

cell biology↗

bioRxiv2019

Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

BackgroundPopulation structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious findings. The Genotype-Tissue Expression (GTEx) project largely contains individuals of European ancestry, but the final release (v8) also includes up to 15% of individuals of non-European ancestry. Assessing ancestry-based adjustments in GTEx provides an opportunity to improve portability of this research across populations and to further measure the impact of population structure on GWAS colocalization.\n\nResultsHere, we identify a subset of 117 individuals in GTEx (v8) with a high degree of population admixture and estimate genome-wide local ancestry. We perform genome-wide cis-eQTL mapping using admixed samples in six tissues, adjusted by either global or local ancestry. Consistent with previous work, we observe improved power with local ancestry adjustment. At loci where the two adjustments produce different lead variants, we observe only 0.8% of tests with GWAS colocalization posterior probabilities that change by 10% or more. Notably, both adjustments produce similar numbers of significant colocalizations. Finally, we identify a small subset of GTEx v8 eQTL-associated variants highly correlated with local ancestry (R2 > 0.7), providing a resource to enhance functional follow-up.\n\nConclusionsWe provide a local ancestry map for admixed individuals in the final GTEx release and describe the impact of ancestry and admixture on gene expression, eQTLs, and GWAS colocalization. While the majority of results are concordant between local and global ancestry-based adjustments, we identify distinct advantages and disadvantages to each approach.

genetics↗

bioRxiv2019

PhenomeXcan: Mapping the genome to the phenome through the transcriptome

Large-scale genomic and transcriptomic initiatives offer unprecedented ability to study the biology of complex traits and identify target genes for precision prevention or therapy. Translation to clinical contexts, however, has been slow and challenging due to lack of biological context for identified variant-level associations. Moreover, many translational researchers lack the computational or analytic infrastructures required to fully use these resources. We integrate genome-wide association study (GWAS) summary statistics from multiple publicly available sources and data from Genotype-Tissue Expression (GTEx) v8 using PrediXcan and provide a user-friendly platform for translational researchers based on state-of-the-art algorithms. We develop a novel Bayesian colocalization method, fastENLOC, to prioritize the most likely causal gene-trait associations. Our resource, PhenomeXcan, synthesizes 8.87 million variants from GWAS on 4,091 traits with transcriptome regulation data from 49 tissues in GTEx v8 into an innovative, gene-based resource including 22,255 genes. Across the entire genome/phenome space, we find 65,603 significant associations (Bonferroni-corrected p-value of 5.5 x 10-10), where 19,579 (29.8 percent) were colocalized (locus regional colocalization probability > 0.1). We successfully replicate associations from PheWAS Catalog (AUC=0.61) and OMIM (AUC=0.64). We provide examples of (a) finding novel and underreported genome-to-phenome associations, (b) exploring complex gene-trait clusters within PhenomeXcan, (c) studying phenome-to-phenome relationships between common and rare diseases via further integration of PhenomeXcan with ClinVar, and (d) evaluating potential therapeutic targets. PhenomeXcan (phenomexcan.org) broadens access to complex genomic and transcriptomic data and empowers translational researchers. One-Sentence SummaryPhenomeXcan is a gene-based resource of gene-trait associations with biological context that supports translational research.

genetics↗