Biology subjects

Wen, X.

Publications and source records attributed to Wen, X..

At least 109 records · Page 6Linked to original sources

bioRxiv2019

Direct synthesis of self-organized blastocyst-like cysts derived from human pluripotent stem cells

We introduce a simple, robust and scalable method to generate self-organized blastocyst-like cysts (soBLCs) from human pluripotent stem cells (hPSCs). We use a copolymer hydrogel of poly(N-isopropylacrylamide) and poly(ethylene glycol) (PNIPAAm-PEG). hPSC aggregates with a diameter of approximately 117.2 {+/-} 5.1 {micro}m are cultured in a medium supplemented with a hydrogel and a serum for three days. Molecular signatures in the medium revealed the generation of trophoblasts and inner cell mass at specific positions in the soBLCs.

bioengineering↗

bioRxiv2019

Development of Dynamic Functional Architecture during Early Infancy

Understanding the moment-to-moment dynamics of functional connectivity (FC) in the human brain during early development is crucial for uncovering neuro-mechanisms of the emerging complex cognitive functions and behaviors. Instead of calculating FC in a static perspective, we leveraged a longitudinal resting-state functional magnetic resonances imaging dataset from fifty-one typically developing infants and, for the first time, thoroughly investigated how the temporal variability of the FC architecture develops at the global (entire brain), meso- (functional system) and local (brain region) levels in the first two years of age. Our results revealed that, in such a pivotal stage, 1) the whole-brain FC dynamics is linearly increased; 2) the high-order functional systems display increased FC dynamics for both within- and between-network connections, while the primary systems show the opposite trajectories; 3) many frontal regions have increasing FC dynamics despite large heterogeneity in developmental trajectories and velocities. All these findings indicate that the brain is gradually reconfigured towards a more flexible, dynamic, and adaptive system with globally increasing but locally heterogeneous trajectories in the first two postnatal years, explaining why infants have emerging and rapidly developing high-order cognitive functions and complex behaviors.

neuroscience↗

bioRxiv2019

Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits

The resources generated by the GTEx consortium offer unprecedented opportunities to advance our understanding of the biology of human diseases. Here, we present an in-depth examination of the phenotypic consequences of transcriptome regulation and a blueprint for the functional interpretation of genome-wide association study-discovered loci. Across a broad set of complex traits and diseases, we demonstrate widespread dose-dependent effects of RNA expression and splicing. We develop a data-driven framework to benchmark methods that prioritize causal genes and find no single approach outperforms the combination of multiple approaches. Using colocalization and association approaches that take into account the observed allelic heterogeneity of gene expression, we propose potential target genes for 47% (2,519 out of 5,385) of the GWAS loci examined. Our results demonstrate the translational relevance of the GTEx resources and highlight the need to increase their resolution and breadth to further our understanding of the genotype-phenotype link.

genetics↗

bioRxiv2019

Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

Transcriptome-wide association studies (TWAS), an integrative framework using expression quantitative trait loci (eQTLs) to construct proxies for gene expression, have emerged as a promising method to investigate the biological mechanisms underlying associations between genotypes and complex traits. However, challenges remain in interpreting TWAS results, especially regarding their causality implications. In this paper, we describe a new computational framework, probabilistic TWAS (PTWAS), to detect associations and investigate causal relationships between gene expression and complex traits. We use established concepts and principles from instrumental variables (IV) analysis to delineate and address the unique challenges that arise in TWAS. PTWAS utilizes probabilistic eQTL annotations derived from multi-variant Bayesian fine-mapping analysis conferring higher power to detect TWAS associations than existing methods. Additionally, PTWAS provides novel functionalities to evaluate the causal assumptions and estimate tissue- or cell-type specific causal effects of gene expression on complex traits. These features make PTWAS uniquely suited for in-depth investigations of the biological mechanisms that contribute to complex trait variation. Using eQTL data across 49 tissues from GTEx v8, we apply PTWAS to analyze 114 complex traits using GWAS summary statistics from several large-scale projects, including the UK Biobank. Our analysis reveals an abundance of genes with strong evidence of eQTL-mediated causal effects on complex traits and highlights the heterogeneity and tissue-relevance of these effects across complex traits. We distribute software and eQTL annotations to enable users performing rigorous TWAS analysis by leveraging the full potentials of the latest GTEx multi-tissue eQTL data.

genetics↗

bioRxiv2019

Cell type specific genetic regulation of gene expression across human tissues

The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci (cis-QTLs) for the majority of genes across a wide range of human tissues. However, the interpretation of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. Here, we map interactions between computational estimates of cell type abundance and genotype to identify cell type interaction QTLs for seven cell types and show that cell type interaction eQTLs provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations to 87 complex traits show a contribution from cell type interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.\n\nOne Sentence SummaryEstimated cell type abundances from bulk RNA-seq across tissues reveal the cellular specificity of quantitative trait loci.

genomics↗

bioRxiv2019

Long non-coding RNA gene regulation and trait associations across human tissues

Long non-coding RNA (lncRNA) genes are known to have diverse impacts on gene regulation. However, it is still a major challenge to distinguish functional lncRNAs from those that are byproducts of surrounding transcriptional activity. To systematically identify hallmarks of biological function, we used the GTEx v8 data to profile the expression, regulation, network relationships and trait associations of lncRNA genes across 49 tissues encompassing 87 distinct traits. In addition to revealing widespread differences in regulatory patterns between lncRNA and protein-coding genes, we identified novel disease-associated lncRNAs, such as C6orf3 for psoriasis and LINC01475/RP11-129J12.1 for ulcerative colitis. This work provides a comprehensive resource to interrogate lncRNA genes of interest and annotate cell type and human trait relevance.\n\nOne Sentence SummarylncRNA genes have distinctive regulatory patterns and unique trait associations compared to protein-coding genes.

genetics↗

bioRxiv2019

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

genetics↗

bioRxiv2019

CO2 per se activates carbon dioxide receptors

Carbon dioxide has been used in traps for more than six decades to monitor mosquito populations and help make informed vector management decisions. CO2 is sensed by gustatory receptors (GRs) housed in neurons in the maxillary palps. CO2-sensitive GRs have been identified from the vinegar fly and mosquitoes, but it remains to be resolved whether these receptors respond to CO2 or bicarbonate. As opposed to the vinegar fly, mosquitoes have three GR subunits, but it is assumed that subunits GR1 and GR3 form functional receptors. In our attempt to identify the chemical species that bind these receptors, we discovered that GR2 and GR3 are essential for receptor function and that GR1 appears to function as a modulator. While Xenopus oocytes coexpressing Culex quinquefasciatus subunits CquiGR1/3 and CquiGR1/2 were not activated, CquiGR2/3 gave robust responses to sodium bicarbonate. Interestingly, CquiGR1/2/3- coexpressing oocytes gave significantly lower responses. That the tertiary combination is markedly less sensitive than the GR2/GR3 combination was also observed with orthologs from the yellow fever and the malaria mosquito. By comparing responses of CquiGR2/CquiGR3- coexpressing oocytes to sodium bicarbonate samples (with or without acidification) and measuring the concentration of aqueous CO2, we showed that there is a direct correlation between dissolved CO2 and receptor response. We then concluded that subunits GR2 and GR3 are essential for these carbon dioxide-sensitive receptors and that they are activated by CO2 per se, not bicarbonate.

neuroscience↗

bioRxiv2019

Growth-regulated Hsp70 phosphorylation regulates stress responses and prion maintenance

Maintenance of protein homeostasis in eukaryotes during normal growth and stress conditions requires the functions of Hsp70 chaperones and associated co-chaperones. Here we investigate an evolutionarily-conserved serine phosphorylation that occurs at the site of communication between the nucleotide-binding and substrate-binding domains of Hsp70. Ser151 phosphorylation in yeast Hsp70 (Ssa1) is promoted by cyclin-dependent kinase (Cdk1) during normal growth and dramatically affects heat shock responses, a function conserved with Hsc70 S153 phosphorylation in human cells. Phospho-mimic forms of Ssa1 (S151D) also fail to relocalize in response to starvation conditions, do not associate in vivo with Hsp40 co-chaperones, Ydj1 and Sis1, and do not catalyze refolding of denatured proteins in vitro in cooperation with Ydj1 and Hsp104. S151 phosphorylation strongly promotes survival of heavy metal exposure and reduces Sup35-dependent [PSI+] prion activity, however, consistent with proposed roles for Ssa1 and Hsp104 in generating self-nucleating seeds of misfolded proteins. Taken together, these results suggest that Cdk1 downregulates Hsp70 function during periods of active growth, reducing propagation of aggregated proteins despite potential costs to overall chaperone efficiency.

molecular biology↗

bioRxiv2019

Integrating Comprehensive Functional Annotations to Boost Power and Accuracy in Gene-Based Association Analysis

Gene-based association tests aggregate genotypes across multiple variants for each gene, providing an interpretable gene-level analysis framework for genome-wide association studies (GWAS). Early gene-based test applications often focused on rare coding variants; a more recent wave of gene-based methods, e.g. TWAS, use eQTLs to interrogate regulatory associations. Regulatory variants are expected to be particularly valuable for gene-based analysis, since most GWAS associations to date are non-coding. However, identifying causal genes from regulatory associations remains challenging and contentious. Here, we present a statistical framework and computational tool to integrate heterogeneous annotations with GWAS summary statistics for gene-based analysis, applied with comprehensive coding and tissue-specific regulatory annotations. We compare power and accuracy identifying causal genes across single-annotation, omnibus, and annotation-agnostic gene-based tests in simulation studies and an analysis of 128 traits from the UK Biobank, and find that incorporating heterogeneous annotations in gene-based association analysis increases power and performance identifying causal genes.

genetics↗

bioRxiv2019

Tau Accumulation via Reduced BAG3-mediated Autophagy Is Required for GGGGCC Repeat Expansion-Induced Neurodegeneration

Expansions of trinucleotide or hexanucleotide repeats lead to several neurodegenerative disorders including Huntington disease (HD, caused by the expanded CAG repeats (CAGr) in the HTT gene) and amyotrophic lateral sclerosis (ALS, could be caused by the expanded GGGGCC repeats (G4C2r) in the C9ORF72 gene), of which the molecular mechanisms remain unclear. Here we demonstrate that loss of the Drosophila orthologue of tau protein (dtau) significantly rescued in vivo neurodegeneration, motor performance impairments, and shortened life-span in Drosophila models expressing mutant HTT protein with expanded CAGr or the expanded G4C2r. Importantly, expression of human tau (htau4R) restored the disease-relevant phenotypes that were mitigated by the loss of dtau, suggesting a conserved role of tau in neurodegeneration. We further discovered that G4C2r expression increased dtau accumulation, possibly due to reduced activity of BAG3-mediated autophagy. Our study reveals a conserved role of tau in G4C2r-induced neurotoxicity in Drosophila models, providing mechanistic insights and potential therapeutic targets.

neuroscience↗

bioRxiv2019

Epigenetic signatures of chronic social stress in stress-susceptible animals

Exposure of mice to chronic social defeat stress (CSDS) produces depressive- and anxiety-like behaviors and widespread transcriptomic changes in several brain regions in susceptible animals. Here we present the first study of genome-wide cytosine methylation patterns of mice susceptible to CSDS using whole-genome bisulfite sequencing on DNA from the nucleus accumbens, a critical region for CSDS effects on behavior. We found extensive evidence for differential methylation following exposure to CSDS in susceptible animals, with a greater proportion of CG hypermethylation than hypomethylation in CSDS-susceptible mice compared to non-stressed controls; non-CG methylation shows the opposite trend. Several genes previously implicated in the effects of CSDS are among those with the greatest number of differentially methylated sites, including estrogen receptor alpha (Esr1), the deleted in colorectal cancer (Dcc) gene and Cacna1c, which has been associated with a range of psychiatric conditions. Informatic analysis of DM sites revealed a gene network with {beta}-catenin as the hub gene of a network that included the {beta}-catenin-related WNT/frizzled signaling pathway as well as both Esr1 and Dcc. Finally, we found considerable overlap between DM genes associated with CSDS in susceptible animals and those associated with human neuroticism in a genome-wide association study. Analysis of these overlapping genes revealed WNT signaling as the top pathway, which features {beta}-catenin as the primary hub gene. These findings reveal a striking convergence between the molecular pathways identified through either transcriptional or epigenomic analyses of the mouse model of susceptibility to chronic stress and the genomic architecture of increased stress susceptibility reflected in neuroticism in humans.

neuroscience↗

bioRxiv2019

Development of equations for converting random-zero to automated oscillometric blood pressure values

ObjectiveThis study aimed to collect data to compare blood pressure values between random-zero sphygmomanometers and automated oscillometric devices and generate equations to convert blood pressure values from one device to the other.\n\nMethodsOmron HEM-907, a widely used automated oscillometric device in many epidemiologic surveys and cohort studies, was compared here with random-zero sphygmomanometers. Two hundred and one participants aged 40-79 years (37% men) were enrolled and randomly assigned to one of two groups with blood pressure measurement first taken by automated oscillometric devices or by random-zero sphygmomanometers. The study design enabled comparisons of blood pressure values between random-zero sphygmomanometers and two modes of this automated oscillometric device - automated and manual, and assessment of effects of measurement order on blood pressure values.\n\nResultsAmong all participants, mean blood pressure levels were lowest when measured with random-zero sphygmomanometers compared with both modes of automated oscillometric devices. Several variables, including age and gender, were found to contribute to the blood pressure differences between random-zero sphygmomanometers and automated oscillometric devices. Equations were developed using multiple linear regression after taking those variables into account to convert blood pressure values by random-zero sphygmomanometers to automated oscillometric devices.\n\nConclusionEquations developed in this study could be used to compare blood pressure values between epidemiologic and clinical studies or identify shift of blood pressure distribution over time using different devices for blood pressure measurements.

epidemiology↗

bioRxiv2019

Trivalent cocktail of de novo designed immunogens enables the robust induction and focusing of functional antibodies in vivo

De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a novel protein design algorithm, termed TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. Both in mice and non-human primates, cocktails of three de novo designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused pre-existing antibody responses towards defined neutralization epitopes. Overall, our de novo design approach opens the possibility of targeting specific epitopes for vaccine and therapeutic antibody development, and more generally will be applicable to design de novo proteins displaying complex functional motifs.

bioengineering↗

bioRxiv2019

BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis

Gene set enrichment analysis has been shown to be effective in identifying relevant biological pathways underlying complex diseases. Existing approaches lack the ability to quantify the enrichment levels accurately, hence preventing the enrichment information to be further utilized in both upstream and downstream analyses. A modernized and rigorous approach for gene set enrichment analysis that emphasizes both hypothesis testing and enrichment estimation is much needed. We propose a novel computational method, Bayesian Analysis of Gene Set Enrichment (BAGSE), for gene set enrichment analysis. BAGSE is built on a Bayesian hierarchical model and fully accounts for the uncertainty embedded in the association evidence of individual genes. We adopt an empirical Bayes inference framework to fit the proposed hierarchical model by implementing an efficient EM algorithm. Through simulation studies, we illustrate that BAGSE yields accurate enrichment quantification while achieving similar power as the state-of-the-art methods. Further simulation studies show that BAGSE can effectively utilize the enrichment information to improve the power in gene discovery. Finally, we demonstrate the application of BAGSE in analyzing real data from a differential expression experiment and a Transcriptome-wide Association Study (TWAS). Our results indicate that the proposed statistical framework is effective in aiding the discovery of potentially causal pathways and gene networks. BAGSE is implemented using the C++ programming language and is freely available from https://github.com/xqwen/bagse/. Simulated and real data used in this paper are also available at the Github repository for reproducibility purposes.

bioinformatics↗

bioRxiv2019

Specialized NADPH diaphorase membrane-related localizations in the brainstem of the pigeons (Columba livia)

NADPH diaphorase (N-d) is used to a histochemical identification of subgroup of neuronal cells. Beside regular intracellular N-d positivity, membrane-related positivity revealed as a specialized staining pattern in the pigeon brain stem. In the investigation of the nervous system of homing pigeons (Columba livia) with N-d staining, we found a specialized structure, which temporally was termed as N-d tubular glomerular body/structure or as T-J body related to the last name of authors. This N-d positive specialization constituted by tubular components bilaterally located in the medial to the lemniscus spinalis in the medulla oblongata. The tubular components were moderate staining. T-J body was a longitudinal oriented structure of 2400 m with N-d staining. N-d positive tubular components were twisted and intermingled together. Beside the young adult pigeons, T-J body s were also consistently detected in the aged pigeons. Membrane-related staining were also detected in the other rostral nuclei in the brain stem. With discussion and review of related scientific literatures, T-J body was considered as a new anatomical structure or a new feature of the existent nucleus. In summary, beside N-d intracellular distribution, there were other three N-d membrane-related localizations: mini-aggregation, patch-aggregation, and arrangement along tubular unit.

neuroscience↗

bioRxiv2019

Efficient Long-Distance Transport in Upper Fluid of Bacterial Swarms

Flagellated bacteria move collectively in a swirling pattern on agar surfaces immersed in a thin layer of viscous \"swarm fluid\", but the role of this fluid in mediating the cooperation of the bacterial population is not well understood. Herein, we use gold nanorods (AuNRs) as single particle tracers to explore the spatiotemporal structure of the swarm fluid. We observed that individual AuNRs are transported in a plane of ~2 m above the motile cells. They can travel for long distances (>700 m) in a 2D plane at high speed (often >50 m2/s) without interferences from bacterial movements. The particles are apparently lifted up and transported by collective mixing of the small vortices around bacteria during localized clustering and de-clustering of the motile cells, exhibiting superdiffusive and non-Gaussian characteristics with alternating large-step jumps and confined lingering. Their motions are consistent with the Levy walk (LW) model, revealing efficient transport flows above swarms. These flows provide obstacle-free highways for long-range material transportations, shed light on how swarming bacteria perform population-level communications, and reveal the essential role of the fluid phase on the emergence of large-scale synergy. This approach is promising for probing complex fluid dynamics and transports in other collective systems.

microbiology↗

bioRxiv2019

A comparative assessment of aging-related NADPH diaphorase positivity in the spinal cord and medullary oblongata between pigeon and murine

NADPH diaphorase (N-d) positive neurons has been examined in many animals. N-d neurodegenerative neurites were detected in some animal models. However, detailed information of N-d positivity and aging related changes was still lack in the spinal cord and medulla oblongata of pigeons. In this study, we evaluated the N-d positivity and aging alterations in the spinal cord and medullary oblongata of the pigeon compared with rat and mouse. In pigeons, N-d neurons were more numerous in the dorsal horn, around the central canal and in the column of Terni in the thoracic and lumbar segments and scattered neurons occurred in the ventral horn of spinal segments. N-d neurons also occurred in the white matter of spinal cord. Morphometrical analysis demonstrated in the lumbosacral, cervical and thoracic regions. Compared with young pigeons, the size of N-d soma was significantly altered in aged pigeons. Meanwhile, the dramatic morphological changes occurred in the lumbar to sacral segments. The most important findings of this study were aging-related N-d positive bodies (ANB) in aged pigeons, mainly in the nucleus cuneatus externus (CuE), occasionally in the nuclei gracilis et cuneatus. ANBs were identified in the gracile nuclei in spinal cord in the aged rats and mice. ANBs were also detected in the CuE spinal nucleus in the aged rats. Immunohistochemistry also showed that the aging changes occurred in the cell types and neuropeptides in aged animals. The results suggested the weak inflammation and neuronal dysfunction in the spinal cord in aged pigeons. Our results suggested that the ANB could be considered as aging marker in the central nervous system.

neuroscience↗