Biology subjects

Wen, X.

Publications and source records attributed to Wen, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

A Toolbox for Generating Multidimensional 3-D Objects with Fine-Controlled Feature Space: Quaddle 2.0

Multidimensional 3D-rendered objects are an important component of vision research and video- gaming applications, but it has remained challenging to parametrically control and efficiently generate those objects. Here, we describe a toolbox for controlling and efficiently generating 3D rendered objects composed of ten separate visual feature dimensions that can be fine-adjusted using python scripts. The toolbox defines objects as multi-dimensional feature vectors with primary dimensions (object body related features), secondary dimensions (head related features) and accessory dimensions (including arms, ears, or beaks). The toolkit interfaces with the freely available Blender software to create objects. The toolbox allows to gradually morph features of multiple feature dimensions, determine the desired feature similarity among objects, and automatize the generation of multiple objects in 3D object and 2D image formats. We document the use of multidimensional objects in a sequence learning task that embeds objects in a 3D- rendered augmented reality environment controlled by the gaming engine unity. Taken together, the toolbox enables the efficient generation of multidimensional objects with fine control of low- level features and higher-level object similarity useful for visual cognitive research and immersive visual environments.

animal behavior and cognition↗

bioRxiv2024

Flexible Learning and Re-ordering of Context-dependent Object Sequences in Nonhuman Primates

Intelligent behavior involves mentally arranging learned information in novel ways and is particularly well developed in humans. While nonhuman primates (NHP) will learn to arrange new items in complex serial order and re-arrange neighboring items within that order, it has remained contentious whether they are capable to re-assign items more flexibly to non-adjacent positions. Such mental re-indexing is facilitated by inferring the latent temporal structure of experiences as opposed to learning serial chains of item-item associations. Here, we tested the ability for flexible mental re-indexing in rhesus macaques. Subjects learned to serially order five objects. A change of the background context indicated when the object order changed, probing the subjects to mentally re-arrange objects to non-adjacent positions of the learned serial structure. Subjects successfully used the context cue to pro-actively re-index items to new, non-adjacent positions. Mental re-indexing was more likely when the initial order had been learned at a higher level, improved with more experience of the re-indexing rule and correlated with working memory performance in a delayed match-to-sample task. These findings suggest that NHPs inferred the latent serial structure of experiences beyond a chaining of item-item associations and mentally re-arrange items within that structure. The pattern of results indicates that NHPs form non-spatial cognitive maps of their experiences, which is a hallmark for flexible mental operations in many serially ordered behaviors including communication, counting or foraging.

animal behavior and cognition↗

bioRxiv2024

Probabilistic Fine-mapping of Putative Causal Genes

Integrative genetic analysis of molecular and complex trait data, including colocalization analysis and transcriptome-wide association studies (TWAS), has shown promise in linking GWAS findings to putative causal genes (PCGs) underlying complex diseases. However, existing methods have notable limitations: TWAS tend to produce an excess of false-positive PCGs, while colocalization analysis often lacks sufficient statistical power, resulting in many false negatives. This paper introduces a probabilistic fine-mapping method, INTERFACE, which is designed to identify putative causal genes while accounting for direct variant-to-trait effects within genomic regions harboring multiple gene candidates. INTERFACE lever-ages interpretable, data-informed priors that incorporate both colocalization and TWAS evidence, enhancing the sensitivity and specificity of PCG inference and setting it apart from existing methods. Additionally, INTERFACE implements analytical measures to improve the accuracy of gene-to-trait effect estimation. We apply INTERFACE to METSIM plasma metabolite GWASs and UK Biobank pQTL data to identify causal genes regulating blood metabolite levels and demonstrate the unique biological insights INTERFACE provides.

genetics↗

bioRxiv2024

Afterload-induced Decreases in Fatty Acid Oxidation Develop Independently of Increased Glucose Utilization

BackgroundMetabolic substrate utilization in HFpEF (heart failure with preserved ejection fraction), the leading cause of heart failure worldwide, is pivotal to syndrome pathogenesis and yet remains ill defined. Under resting conditions, oxidation of free fatty acids (FFA) is the predominant energy source of the heart, supporting its unremitting contractile activity. In the context of disease-related stress, however, a shift toward greater reliance on glucose occurs. In the setting of obesity or diabetes, major contributors to HFpEF pathophysiology, the shift in metabolic substrate use toward glucose is impaired, sometimes attributed to the lower oxygen requirement of glucose oxidation versus fat metabolism. This notion, however, has never been tested conclusively. Furthermore, whereas oxygen demand increases in the setting of increased afterload, myocardial oxygen availability remains adequate for fatty acid oxidation (FAO). Therefore, a "preference" for glucose has been proposed. Methods and ResultsPyruvate dehydrogenase complex (PDC) is the rate-limiting enzyme linking glycolysis to the TCA cycle. As PDK4 (PDC kinase 4) is up-regulated in HFpEF, we over-expressed PDK4 in cardiomyocytes, ensuring that PDC is phosphorylated and thereby inhibited. This leads to diminished use of pyruvate as energy substrate, mimicking the decline in glucose oxidation in HFpEF. Importantly, distinct from HFpEF-associated obesity, this model positioned us to abrogate the load-induced shift to glucose utilization in the absence of systemic high fat conditions. As expected, PDK4 transgenic mice manifested normal cardiac performance at baseline. However, they manifested a rapid and severe decline in contractile performance when challenged with modest increases in afterload triggered either by L-NAME or surgical transverse aortic constriction (TAC). This decline in function was not accompanied by an exacerbation of the myocardial hypertrophic growth response. Surprisingly, metabolic flux analysis revealed that, after TAC, fractional FAO decreased, even when glucose/pyruvate utilization was clamped at very low levels. Additionally, proteins involved in the transport and oxidation of FFA were paradoxically downregulated after TAC regardless of genotype. ConclusionsThese data demonstrate that cardiomyocytes in a setting in which glucose utilization is robustly diminished and prevented from increasing do not compensate for the deficit in glucose utilization by up-regulating FFA use.

cell biology↗

bioRxiv2024

Genome-wide identification of stable RNA-chromatin interactions

RNA-chromatin interactions play crucial roles in gene regulation and genome organization, but the interaction landscape remains poorly understood. In this study, we conducted an in-depth analysis of a previously published dataset on RNase-treated in situ mapping of the RNA-genome interactome in human embryonic stem cells. This dataset globally profiles RNase-insensitive RNA-chromatin interactions. Our analysis revealed that RNase treatment selectively preserved long-range RNA-chromatin interactions while removing promiscuous interactions resulting from the local diffusion of nascent transcripts. RNase-insensitive chromatin-associated RNAs (RI-caRNAs) exhibited high sequence conservation and preferentially localized to functional genomic regions, including promoters, transcription factor binding sites, and regions with specific histone modifications. Interestingly, coding and non-coding RNA transcripts showed distinct sensitivities to RNase, with lncRNAs and disease-associated transcripts being enriched among RI-caRNAs. Furthermore, we identified specific caRNA classes associated with individual transcription factors and histone modifications. Altogether, our findings reveal a RNase-inaccessible regulatory RNA-chromatin interactome and provide a resource for understanding RNA-mediated chromatin regulation.

genomics↗

bioRxiv2024

Genome-Wide Mapping of RNA-Protein Associations via Sequencing

RNA-protein interactions are crucial for regulating gene expression and cellular functions, with their dysregulation potentially impacting disease progression. Systematically mapping these interactions is resource-intensive due to the vast number of potential RNA and protein interactions. Here, we introduce PRIM-seq (Protein-RNA Interaction Mapping by sequencing), a method for the concurrent de novo identification of RNA-binding proteins (RBPs) and the elucidation of their associated RNAs. PRIM-seq works by converting each RNA-protein pair into a unique chimeric DNA sequence, which is then decoded through DNA sequencing. Applied to two human cell types, PRIM-seq generated a comprehensive human RNA-protein association network (HuRPA), consisting of more than 350,000 RNA-proteins pairs involving approximately 7,000 RNAs and 11,000 proteins. The data revealed an enrichment of previously reported RBPs and RNA-protein interactions within HuRPA. We also identified LINC00339 as a protein-associating non-coding RNA and PHGDH as an RNA-associating protein. Notably, PHGDH interacts with BECN1 and ATF4 mRNAs, suppressing their protein expression and consequently inhibiting autophagy, apoptosis, and neurite outgrowth while promoting cell proliferation. PRIM-seq offers a powerful tool for discovering RBPs and RNA-protein associations, contributing to more comprehensive functional genome annotations.

molecular biology↗

bioRxiv2024

Integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits.

We present multi-integration of transcriptome-wide association studies and colocalization (Multi-INTACT), an algorithm that models multiple gene products (e.g. encoded RNA transcript and protein levels) to implicate causal genes and relevant gene products. In simulations, Multi-INTACT achieves higher power than existing methods, maintains calibrated false discovery rates, and detects the true causal gene product(s). We apply Multi-INTACT to GWAS on 1,408 metabolites, integrating the GTEx expression and UK Biobank protein QTL datasets. Multi-INTACT infers 52% to 109% more metabolite causal genes than protein-alone or expression-alone analyses and indicates both gene products are relevant for most gene nominations.

bioinformatics↗

bioRxiv2023

Functional characterization of eQTLs and asthma risk loci with scATAC-seq across immune cell types and contexts

Cis-regulatory elements (CREs) control gene transcription dynamics across cell types and in response to the environment. In asthma, multiple immune cell types play an important role in the inflammatory process. Genetic variants in CREs can also affect gene expression response dynamics and contribute to asthma risk. However, the regulatory mechanisms underlying control of transcriptional dynamics across different environmental contexts and cell-types at single cell resolution remains to be elucidated. To resolve this question, we performed scATAC-seq in activated peripheral blood mononuclear cells (PBMC) from 16 children with asthma with phytohemagglutinin (PHA) or lipopolysaccharide (LPS), and treated with dexamethasone (DEX), an antiinflammatory glucocorticoid. We analyzed changes in chromatin accessibility, measured transcription factor motif activity, and identified treatment and cell-type specific transcription factors that drive changes in both gene expression mean and variability. We observed strong positive linear dependence between motif response and their target gene expression changes, but negative in variability changes. This result suggests that an increase of transcription factor binding tightens the variability of gene expression around the mean. We then annotated genetic variants in chromatin accessibility peaks and response motifs followed by computational fine-mapping of eQTL signals from a pediatric asthma cohort. We found that eQTLs were 5-fold enriched in peaks with response motifs and refined the credible set for 410 asthma risk genes, with 191 having the causal variant in response motifs. In conclusion, scATAC-seq enhances the understanding of molecular mechanisms for asthma risk variants mediated by gene expression.

genomics↗

bioRxiv2023

Regulation of transcription patterns, poly-ADP-ribose, and RNA-DNA hybrids by the ATM protein kinase

The ATM protein kinase is a master regulator of the DNA damage response and also an important sensor of oxidative stress. Analysis of gene expression in Ataxia-telangiectasia patient brain tissue shows that large-scale transcriptional changes occur in patient cerebellum that correlate with expression level and GC content of transcribed genes. In human neuron-like cells in culture we map locations of poly-ADP-ribose and RNA-DNA hybrid accumulation genome-wide with ATM inhibition and find that these marks also coincide with high transcription levels, active transcription histone marks, and high GC content. Antioxidant treatment reverses the accumulation of R-loops in transcribed regions, consistent with the central role of ROS in promoting these lesions. Based on these results we postulate that transcription-associated lesions accumulate in ATM-deficient cells and that the single-strand breaks and PARylation at these sites ultimately generate changes in transcription that compromise cerebellum function and lead to neurodegeneration over time in A-T patients.

molecular biology↗

bioRxiv2023

Use of TSAR, Thermal Shift Analysis in R, to identify Folic Acid as a Molecule that Interacts with HIV-1 Capsid

The thermal shift assay (TSA) is a versatile biophysical technique for studying protein-ligand interactions in vitro. Here, we report a free, open-source software tool, TSAR ("Thermal Shift Analysis in R"), to expedite the analysis of TSA data. The TSAR package incorporates multiple workflows that facilitate TSA analyses, returns publication-ready graphics, and includes an optional graphic user interface. The package is available at https://bioconductor.org/packages/TSAR/. Applying TSAR, we screened two chemical libraries and found multiple molecules that potentially interact in vitro with the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1). First, a library of vitamins exemplifies the different graphic outputs of TSAR, and we report a change in the 50% melting temperature ({Delta}Tm) for folic acid-treated CA hexamers (CAHEX). Since HIV-1 CAHEX interacts with host-derived acids like inositol hexaphosphate (IP6) or dNTPs, a second library was screened containing 96 organic, acidic metabolites; multiple anionic ligands caused a {Delta}Tm for CAHEX. Subsequent investigation of these interactions includes biolayer interferometry, antiviral activity against pseudotyped HIV-1, and endogenous reverse transcriptase assays that were used to validate and investigate the biological impact of these native ligands that thermally-stabilize CAHEX. One compound hit, gallic acid, exhibited anti-HIV-1 activity as previously reported, and we show interacts with CAHEX as a potentially novel mechanism. Overall, the TSAR package facilitated quick analysis of TSA data from multiple libraries to help identify a biologically relevant hit, gallic acid, as a molecule that can inhibit HIV-1 replication and targets CAHEX. ImportanceThe TSAR package is freely available (AGPL-3) and is designed for both experienced or new R users, having command-line code for handling large and challenging datasets while also including an optional GUI that enables easy use by non-programmers. This is the first TSA analysis program written in R, a free and open-source language; TSAR simplifies TSA analysis while maintaining diverse visualization options for small-to-large libraries and multidimensional analysis. Additionally, we report multiple endogenous metabolites that potentially interact with the HIV-1 capsid protein hexamers (CAHEX) in vitro, including folic acid, gallic acid, and multiple others, primarily from the tricarboxylic acid (TCA) cycle. Various methods validate gallic acid interactions with CAHEX, leading to a novel suggested mechanism of action, and in-line with previous reports, this metabolite has potential for natural-based treatments of HIV-1. Further, we advance the understanding of the potential mechanism(s) for HIV-1 inhibition by gallic acid treatment.

biochemistry↗

bioRxiv2023

A Multi-task Platform for Profiling Cognitive and Motivational Constructs in Humans and Nonhuman Primates

BackgroundUnderstanding the neurobiological substrates of psychiatric disorders requires comprehensive evaluations of cognitive and motivational functions in preclinical research settings. The translational validity of such evaluations will be supported by (1) tasks with high construct validity that are engaging and easy to teach to human and nonhuman participants, (2) software that enables efficient switching between multiple tasks in single sessions, (3) software that supports tasks across a broad range of physical experimental setups, and (4) by platform architectures that are easily extendable and customizable to encourage future optimization and development. New MethodWe describe the Multi-task Universal Suite for Experiments (M-USE), a software platform designed to meet these requirements. It leverages the Unity video game engine and C# programming language to (1) support immersive and engaging tasks for humans and nonhuman primates, (2) allow experimenters or participants to switch between multiple tasks within-session, (3) generate builds that function across computers, tablets, and websites, and (4) is freely available online with documentation and tutorials for users and developers. M-USE includes a task library with seven pre-existing tasks assessing cognitive and motivational constructs of perception, attention, working memory, cognitive flexibility, motivational and affective self-control, relational long-term memory, and visuo-spatial problem solving. ResultsM-USE was used to test NHPs on up to six tasks per session, all available as part of the Task Library, and to extract performance metrics for all major cognitive and motivational constructs spanning the Research Domain Criteria (RDoC) of the National Institutes of Mental Health. Comparison with Existing MethodsOther experiment design and control systems exist, but do not provide the full range of features available in M-USE, including a pre-existing task library for cross-species assessments; the ability to switch seamlessly between tasks in individual sessions; cross-platform build capabilities; license-free availability; and its leveraging of video-engine capabilities used to gamify tasks. ConclusionsThe new multi-task platform facilitates cross-species translational research for understanding the neurobiological substrates of higher cognitive and motivational functions.

animal behavior and cognition↗

bioRxiv2023

Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain

SUMMARY PARAGRAPHThe dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA (caRNA) 1-3. Chromatin complex compositions change during cellular differentiation and aging, and are expected to be highly heterogeneous among terminally differentiated single cells 4-7. Here we introduce the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within individual nuclei. Applied to 14 human frontal cortex samples from elderly donors, MUSIC delineates diverse cortical cell types and states. We observed the nuclei exhibiting fewer short-range chromatin interactions are correlated with an "older" transcriptomic signature and with Alzheimers pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci (cis eQTLs) and a promoter tends to be the cell type where these cis eQTLs specifically affect their target genes expression. Additionally, the female cortical cells exhibit highly heterogeneous interactions between the XIST non-coding RNA and Chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploring chromatin architecture and transcription at cellular resolution in complex tissues.

genomics↗

bioRxiv2023

HIV-1 resistance to islatravir/tenofovir combination therapy in wild-type or NRTI resistant strains of diverse HIV-1 subtypes

Tenofovir disoproxil fumarate (TDF) and islatravir (ISL, 4-ethynyl-2-fluoro-2-deoxyadensine, or MK-8591) are highly potent nucleoside reverse transcriptase inhibitors. Resistance to TDF and ISL is conferred by K65R and M184V, respectively. Furthermore, K65R and M184V increase sensitivity to ISL and TDF, respectively. Therefore, these two nucleoside analogs have opposing resistance profiles and could present a high genetic barrier to resistance. To explore resistance to TDF and ISL in combination, we performed passaging experiments with HIV-1 WT, K65R, or M184V in the presence of ISL and TDF. We identified K65R, M184V, and S68G/N mutations. The mutant most resistant to ISL was S68N/M184V, yet it remained susceptible to TDF. To further confirm our cellular findings, we implemented an endogenous reverse transcriptase assay to verify in vitro potency. To better understand the impact of these resistance mutations in the context of global infection, we determined potency of ISL and TDF against HIV subtypes A, B, C, D, and circulating recombinant forms (CRF) 01_AE and 02_AG with and without resistance mutations. In all isolates studied, we found K65R imparted hypersensitivity to ISL whereas M184V conferred resistance. We demonstrated that the S68G polymorphism can enhance fitness of drug-resistant mutants in some genetic backgrounds. Collectively, the data suggest that the opposing resistance profiles of ISL and TDF suggest that a combination of the two drugs could be a promising drug regimen for the treatment of patients infected with any HIV-1 subtype, including those who have failed 3TC/FTC-based therapies.

microbiology↗

bioRxiv2023

Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods

Causal gene discovery methods are often evaluated using gold-standard (GS) sets of causal genes. However, GS gene sets are always incomplete, leading to mis-estimation of sensitivity, specificity, AUC. Labeling biases in GS gene sets can also lead to inaccurate ordering of discovery methods. We argue that evaluation of these methods should rely on statistical techniques like those used for variant discovery, rather than on comparison with GS gene sets.

genetics↗

bioRxiv2023

A rapid and bidirectional reporter of neural activity reveals neural correlates of social behaviors in Drosophila

Neural activity is modulated over different timescales encompassing sub-seconds to days reflecting changes in external environment, internal state, and behavior. Using Drosophila as a model, we have developed a rapid and bidirectional reporter that provides a robust cellular readout of recent neural activity. This reporter utilizes nuclear vs cytoplasmic distribution of CREB-regulated transcriptional coactivator, CRTC. Subcellular distribution of GFP-tagged CRTC (CRTC::GFP) bidirectionally changes on the order of minutes and reflects both increases and decreases in neural activity. We establish an automated machine-learning-based routine for efficient quantification of reporter signal. Using this reporter, we demonstrate acute mating- evoked activation of peptidergic neurons. We further investigate the functional role of the master courtship regulator gene, fruitless, and show that fruitless is necessary to ensure activation of male arousal neurons by female cues. Together, our results establish CRTC::GFP as a bidirectional reporter of recent neural activity suitable for examining neural correlates in behavioral contexts.

neuroscience↗

bioRxiv2023

The Role of Terminal Uridyl Transferases in the Circadian Rhythm

The 3 terminal oligo-uridylation, a post-transcriptional mRNA modification, is conserved among eukaryotes and drives mRNA degradation, thereby affecting several key biological processes such as animal development and viral infection. Our TAIL-seq experiment of mouse liver mRNA collected from six zeitgeber times reveals transcripts with rhythmic poly(A) tail lengths and demonstrates that overall 3 terminal uridylation frequencies at mRNA poly(A) tail very-ends undergo rhythmic change. Consistently, major terminal uridylyl transferases, TUT4 and TUT7, have cycling protein expression in mouse liver corresponding to 3 terminal uridylation rhythms, indicating that the cycling expression of TUTases correlates with the rhythmic pattern of uridylation. Furthermore, the double knockdown of TUT4 and TUT7 in U2OS cells lengthens the circadian period and decreases the rhythmic amplitude of clock gene expression. Our work thoroughly profiles the dynamic changes in poly(A) tail lengths and terminal modifications and uncovers uridylation as a post-transcriptional modulator in the mammalian circadian clock.

molecular biology↗

bioRxiv2023

Multi-species polyploidization, chromosome shuffling, and genome extraction in Zea/Tripsacum hybrids

By hybridization and special sexual reproduction, we sequentially aggregated Zea mays, Zea perennis, and Tripsacum dactyloides in an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize and Z. perennis by natural genome extraction, extended their first six selfed generations, and finally constructed amphitetraploid maize using nascent allotetraploids as a genetic bridge. Transgenerational chromosome inheritance, subgenomes stability, chromosome pairings and rearrangements, and their impacts on an organisms fitness were investigated by fertility phenotyping and molecular cytogenetics techniques GISH and FISH. Results showed that diversified sexual reproductive methods produced highly differentiated progenies (2n=35-84) with varying proportions of subgenomic chromosomes, of which one individual (2n=54, MMMPT) overcame self-incompatibility barriers and produced self-fertile nascent near-allotetraploid by preferentially eliminating Tripsacum chromosomes. Nascent near-allotetraploid progenies showed persistent chromosome changes, intergenomic translocations, and rDNA variations for at least up to the first six selfed generations; however, ploidy tended to stabilize at near-tetraploid level (2n=40) with full integrity of 45SrDNA pairs, and a trend of decreasing variations by advancing generations with an average of 25.53, 14.14, and 0.37 maize, Z. perennis, and T. dactyloides chromosomes, respectively. The mechanisms for three genome stabilities and karyotype evolution for formatting new polyploid species were discussed.

genetics↗

bioRxiv2022

Characterization of caffeine response regulatory variants in vascular endothelial cells

Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 29 variants that regulate the gene expression response to caffeine (GxE, FDR<10%). When overlapping our GxE results with eQTLs colocalized with CAD and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.

genomics↗