Biology subjects

Mu, W.

Publications and source records attributed to Mu, W..

At least 19 recordsLinked to original sources

bioRxiv2026

CollapsedChrom: resolving the assembly of collapsed chromosomal segments in polyploid genomes of the model grass genus Brachypodium

Polyploidization plays a fundamental role in plant evolution and crop domestication. However, due to the high similarity of genomic sequences between some homologous or homeologous chromosomes, the assembly of some polyploid genomes is extremely difficult, frequently resulting in erroneous assemblies, such as sequence chimeras and sequence collapse. The genus Brachypodium is an important model system for the study of polyploidy in grasses. However, high-quality reference genomes are still lacking for its complex polyploid perennial species. In this study, we developed a bioinformatic pipeline for the accurate assembly of high-quality reference genomes at the chromosomal level for two representative perennial Brachypodium species with conflicting collapsed segments, the allotetraploid B. phoenicoides (2n = 4x = 28) and the autohexaploid B. boissieri (2n = 6x = 48). We developed an innovative methodology (CollapsedChrom) that uses depth-of-read profiling and relies on prior karyotypic information to systematically detect and rescue collapsed regions. This depth-sensitive curation strategy successfully recovered 328.9 Mb and 195.8 Mb of previously collapsed sequences in the genomes of B. phoenicoides and B. boissieri, respectively. Comprehensive quality assessments demonstrated the high quality of our final assemblies. Our chromosomal-level assemblies fully capture the genomic architectures of these species. These robust genomic resources overcome long-standing challenges in polyploid assembly and provide an essential foundation for future research on the evolutionary dynamics, subgenomic interactions, and functional biology of complex polyploid plant genomes.

genomics↗

bioRxiv2026

Functional Annotation of the Major Histocompatibility Complex Locus

The human major histocompatibility complex (MHC) locus has the greatest density of disease-associations in the human genome, including links to over 100 polygenic disorders. Its complex haplotype structure, rich gene density, and high degree of linkage disequilibrium combine to make deciphering the gene regulatory logic of the MHC locus extremely challenging. Employing complementary high-throughput CRISPR interference (CRISPRi) and activation (CRISPRa) epigenetic screens coupled with single-cell transcriptome profiling across three distinct human cell types, we identified hundreds of new connections between cis-regulatory elements (CREs) and their target genes in this locus. These CRE-gene links are largely cell type-specific and act as enhancers. Additionally, some CREs have complex features, including harboring both active and repressive histone marks, lacking chromatin accessibility, targeting multiple genes, or acting as silencers. Computational methods fail to predict a majority of these CRE-gene connections. These findings emphasize the potential for functional perturbation experiments to dissect complex loci and reveal shared and cell type-specific regulatory mechanisms relevant to genomics of complex diseases. Collectively, this study provides a unique resource for understanding the complex regulatory landscape within the MHC locus and supports the need for creating new models that encompass CRE-gene interactions, cell type-specific gene expression, and disease genetics in the noncoding genome.

genomics↗

bioRxiv2026

Leveraging HIV-Specific CAR T Cells and Rapamycin Treatment in Kick-and-Kill HIV Cure Approaches

HIV is not cured with currently available combination antiretroviral therapy (ART) alone in large part because the virus establishes virologic latency in long lived CD4+ cells. To eliminate this latent reservoir, as required for HIV eradication, latency reversing agents (LRAs) are being developed to force HIV out of latency and induce infected cells to express viral proteins leading to their clearance, in a so-called "Kick-and-Kill" approach. This strategy relies on the immune system to clear the productively-infected cells and is thus limited by HIV immune evasion and the immunological exhaustion that occurs during HIV infection. To counter these limitations and augment an LRA-mediated HIV cure approach, we report herein the utility of HIV-specific truncated CD4-based D1D2 CAR T cells combined with LRA treatment and the mTORC1 inhibitor rapamycin to reduce immune exhaustion and specifically target and kill LRA-stimulated HIV infected cells. We demonstrate that rapamycin does not prevent HIV latency reversal via multiple classes of LRAs in several in vitro models, suggesting that it is compatible with cure approaches utilizing these LRAs. Additionally, rapamycin does not inhibit the early T cell activation (CD69 upregulation) in primary T cells that occurs during protein kinase C (PKC) modulator-mediated HIV latency reversal. Furthermore, in vitro chronically exhausted CAR T cells were found to have a higher frequency of terminally exhausted PD-1+Tim-3+ and CD69+PD-1+ cells when compared to CAR T cells that were cultured under the same conditions in the presence of rapamycin, validating the use of the mTORC1 inhibitor rapamycin to prevent immune exhaustion of CAR T cells. Finally, we found that latently-infected cells that were stimulated to express HIV proteins using a designed, synthetic PKC modulator LRA (SUW133) were efficiently recognized and killed by CAR T cells. Overall, these data demonstrate the compatibility of immune rejuvenation using rapamycin with HIV reservoir depletion using LRAs and CAR T cells. This combination therapy strategy represents a promising approach to more effectively target the latent reservoir in HIV cure approaches.

immunology↗

bioRxiv2025

Gut Microbiome Signatures Reflect Within-Host Subtype Diversity of Blastocystis in Non-Human Primates

Blastocystis is a prevalent gut eukaryote intricately associated with the gut microbiota. This genetically diverse protozoan exhibits significant intra-host subtype heterogeneity, yet the implications of this diversity for the host gut microbiome remain poorly understood. Here, we investigated the interactions between Blastocystis and gut microbiota in non-human primates at the level of subtypes, using a comprehensive investigation of gut microbiota for Blastocystis carriers of captive Macaca fascicularis (discovery cohort, n = 100) and Macaca mulatta (validation cohort, n = 26). We identified highly prevalent intra-host co-occurrence patterns of Blastocystis SSU rRNA-based subtypes, primarily dominated by Subtype 1(ST1) or ST3. These patterns were associated with compositional and structural variations in the gut microbiome but were not significantly influenced by host covariates such as sex, age, or BMI. Specifically, Ruminococcaceae-enterotype was enriched in the patterns dominated by ST1, whereas Limosilactobacillus-enterotype was predominantly identified in the patterns dominated by ST3. We discovered that the absolute abundance of Blastocystis was a critical determinant in elucidating this association across concurrent patterns. In vivo experiments in a new cohort (n = 11) demonstrated that lactic acid bacteria, enriched in the Limosilactobacillus-enterotype, were sufficient to reduce Blastocystis load. We validated the strong association between gut microbiome composition and Blastocystis load in M. mulatta, confirming that specific microbial features could quantitatively predict Blastocystis status in both species. Our findings establish a direct link between gut microbial variations, intra-host genetic heterogeneity, and absolute abundance in Blastocystis for non-human primates.

microbiology↗

bioRxiv2024

Rapamycin Enhances CAR-T Control of HIV Replication and Reservoir Elimination in vivo.

Chimeric Antigen Receptor (CAR) T cell therapy has emerged as a powerful immune therapy for various diseases. Our studies in humanized mice and non-human primates (NHPs) demonstrate that hematopoietic stem cell (HSCs) modified with anti-HIV CAR leads to lifelong engraftment and supply of functional anti-viral CAR-T cells, leading to significantly reduced viral rebound after ART withdrawal. However, T cell exhaustion, driven by chronic immune activation, remains a major challenge for the continuous efficacy of CAR-T therapy, necessitating additional measures to achieve functional cure. We recently showed that in vivo treatment with low dose rapamycin reduced chronic inflammation and improved anti-HIV T cell function in HIV-infected humanized mice. Here, we report that rapamycin significantly improved CAR-T cell function both in vitro and in vivo. In vitro treatment with rapamycin improved CAR-T cell mitochondria respiration and cytotoxicity. In vivo treatment with low-dose rapamycin in HIV-infected, CAR-HSC treated mice reduced chronic inflammation, prevented exhaustion of CAR-T cells and improved CAR-T control of viral replication compared to CAR-HSCs treatment alone. RNAseq analysis of sorted CAR-T cells from humanized mice showed that rapamycin significantly modified the CAR-T cell transcriptome, including the downregulation of multiple check point inhibitors and the upregulation of key genes related to cell survival. We also observed significantly delayed viral rebound after ART withdrawal and diminished HIV reservoir in mice that were treated with rapamycin and CAR-HSCs as compared to CAR-HSCs treatment alone. Taken together, our data indicate that HSCs-based anti-HIV CAR-T combined with rapamycin treatment is a promising approach for treating persistent inflammation and improving immune control of HIV replication.

immunology↗

bioRxiv2024

Machine learning methods for predicting guide RNA effects in CRISPR epigenome editing experiments

CRISPR epigenomic editing technologies enable functional interrogation of non-coding elements. However, current computational methods for guide RNA (gRNA) design do not effectively predict the power potential, molecular and cellular impact to optimize for efficient gRNAs, which are crucial for successful applications of these technologies. We present "launch-dCas9" (machine LeArning based UNified CompreHensive framework for CRISPR-dCas9) to predict gRNA impact from multiple perspectives, including cell fitness, wild-type abundance (gauging power potential), and gene expression in single cells. Our launch-dCas9, built and evaluated using experiments involving >1 million gRNAs targeted across the human genome, demonstrates relatively high prediction accuracy (AUC up to 0.81) and generalizes across cell lines. Method-prioritized top gRNA(s) are 4.6-fold more likely to exert effects, compared to other gRNAs in the same cis-regulatory region. Furthermore, launch-dCas9 identifies the most critical sequence-related features and functional annotations from >40 features considered. Our results establish launch-dCas9 as a promising approach to design gRNAs for CRISPR epigenomic experiments.

bioinformatics↗

bioRxiv2023

The tidyomics ecosystem: Enhancing omic data analyses

The growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor1 provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming2 offers a revolutionary standard for data organisation and manipulation. Here, we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning, and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analysing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas3, spanning six data frameworks and ten analysis tools.

bioinformatics↗

bioRxiv2023

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains one of the most interesting issues in evolutionary biology. However, the patterns of the underlying genetic divergences across the genome vary between different groups. Here we report that Brachypodium stacei, an inbreeding grass species, has been involved in sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses suggest that diploid B. stacei diverged sympatrically in two slopes with contrasting biomes at Evolution Canyon I (ECI), Mount Carmel, Israel, where gene flow has continued freely but reduced with the time. This ecological divergence involved the scattered divergence of many unlinked loci across the total genome that include both coding and non-coding regions. We also identified significantly differential expressions of ABA signaling pathway genes, and contrasting metabolome composition between the arid-vs forest-adapted B. stacei ECI populations. These results suggest that many small loci involved in environmental responses act additively to account for the ecological usages of this species in contrasted environments with gene flow. SignificanceEcological divergence provides evidence for the origin of species through natural selection that has governed evolutionists attention since Darwin. In this study, we present multiple-omics analyses of two plant populations growing sympatrically in contrasted environments and revealed their distinct differentiation across all examined data. These two populations share the most recent ancestor compared with other populations and their divergence started in the early Holocene. We revealed that gene flow had continued but with a progressive reduction over time. The genetic divergences are scattered across the total genome involving many unlinked coding and non-coding regions. These findings highlight the significance of natural selection in the ecological divergence that may finally lead to species formation without geographic isolation.

evolutionary biology↗

bioRxiv2022

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

SummaryExclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g., centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R/Bioconductor data package, also accessible via the BEDbase.org API. The package provides unified access to 82 GenomicRanges objects covering six organisms, multiple genome assemblies and types of exclusion regions. For human hg38 genome assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as the most well-curated and annotated, and sets generated by the Blacklist tool for other organisms. Availability and implementationhttps://bioconductor.org/packages/excluderanges/ ContactMikhail G. Dozmorov (mdozmorov@vcu.edu) Supplementary informationPackage website: https://dozmorovlab.github.io/excluderanges/

bioinformatics↗

bioRxiv2022

bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing

bootRanges provides fast functions for generation of bootstrapped genomic ranges representing the null sets in enrichment analysis. We show that shuffling or permutation schemes may result in overly narrow test statistics null distributions, while creating new ranges sets with a block bootstrap preserves local genomic correlation structure and generates more reliable null distributions. It can also be used in more complex analyses, such as accessing correlations between cis-regulatory elements (CREs) and genes across cell types or providing optimized thresholds, e.g. log fold change (logFC) from differential analysis. The bootRanges functions are available in the R/Bioconductor package nullranges at https://bioconductor.org/packages/nullranges.

bioinformatics↗

bioRxiv2022

matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling

Deriving biological insights from genomic data commonly requires comparing attributes of selected genomic loci to a null set of loci. The selection of this null set is non trivial, as it requires careful consideration of potential covariates, a problem that is exacerbated by the non-uniform distribution of genomic features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow selection of null sets from a pool of possible items while controlling for multiple covariates; however, existing packages do not operate on genomic data classes and can be slow for large data sets making them difficult to integrate into genomic workflows. To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework.

bioinformatics↗

bioRxiv2021

Reversable deformation of artificial cell colony for muscle behavior mimicry triggered by actin polymerization

The mimicry of living tissues from artificial cells is beneficial to understanding the interaction mechanism among cells, as well as holding great potentials in the tissue engineering field. Self-powered artificial cells capable of reversible deformation are developed by encapsulating living mitochondria, actin proteins, and methylcellulose. Upon the addition of pyruvate molecules, the mitochondria produce ATP molecules as energy sources to trigger the polymerization of actin. ATP molecules were produced by mitochondria (2.76x1010/ml) with the concentrations of 35.8{+/-}3.2 {micro}M, 158.2{+/-}19.3 {micro}M and 200.7{+/-}20.1 M by adding pyruvate molecules with the concentration of 3 M, 12 M and 21 M, respectively. The reversible deformation of artificial cells is experienced with spindle shape resulting from the polymerization of actins to form filaments adjacent to the lipid bilayer, subsequently back to spherical shape resulting from the depolymerization of actin filaments upon laser irradiations. The linear colonies composed of these artificial cells exhibit collective contraction and relaxation behavior to mimic muscle tissues. At the stage of maximum contraction, the long axis of each GUV is in parallel to each other. All colonies are synchronized in the contraction phase. The deformation of each GUV in the colonies is influenced by its adjacent GUVs. The muscle-like artificial cell colonies paved the path to develop sustainably self-powered artificial tissues in the field of tissue engineering.

bioengineering↗

bioRxiv2021

Impact of Grain for Green Project on Water Resources and Ecological Water Stress in Yanhe River Basin

Grain for Green project (GGP) initialed by China government since 1999 has achieved substantial achievements accompanied with surface runoff decrease in the Loess Plateau but impacts of large-scale afforestation on regional water resources are uncertain. Hence, the objective of this study is to explore the impact of land use change on generalized water resources and ecological water stress using blue and green water concept taking Yanhe River Basin as a case study. Soil and Water Assessment Tool (SWAT) is applied to quantify summary of green and blue water which is defined as generalized water resources, ecological water requirement of vegetation (forest and grass), agricultural water footprint and virtual water flow are considered as regional water requirements. Land use types of 1980 (scenario I), 2017 (scenario II) are input in SWAT model while keeps other parameters constant in order to isolate the influence of land use changes. Results show that average annual difference of blue, green and generalized water resources is -72.08 million m3, 24.34 million m3, -47.74 million m3 respectively when simulation results of scenario II subtracts scenario I and it presents that land use change caused by GGP leads to decrease in blue and generalized water resources whereas increase in green water resources. SURQ in scenario I is more than that in scenario IIin all the study period from 1980-2017, green water storage in scenario I is more than that in scenario II in all the study period except in 1998; whereas LATQ in scenario I is less than that in scenario II except in 2000 and 2015, GWQ in 1992, 2000 and 2015, green water flow in 1998. Blue water, green water storage and green water flow in scenario II is less than that in scenario I in the whole basin, 12.89 percent of the basin and 99.21 percent of the basin respectively. Total WF increases from 1995 to 2010 because forest WF increases significantly in this period though agricultural WF and grass WF decreases. Ecological water stress index has no obvious temporal change trend in both land use scenarios but ecological water stress index in scenario II is more than that in scenario I which illustrates that GGP leads to increase of ecological water stress from perspective of generalized water resources

ecology↗

bioRxiv2021

Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

MotivationAllelic expression analysis aids in detection of cis-regulatory mechanisms of genetic variation which produce allelic imbalance (AI) in heterozygotes. Measuring AI in bulk data lacking time or spatial resolution has the limitation that cell-type-specific (CTS), spatial-, or time-dependent AI signals may be dampened or not detected. ResultsWe introduce a statistical method airpart for identifying differential CTS AI from single-cell RNA-sequencing (scRNA-seq) data, or other spatially- or time-resolved datasets. airpart outputs discrete partitions of data, pointing to groups of genes and cells under common mechanisms of cis-genetic regulation. In order to account for low counts in single-cell data, our method uses a Generalized Fused Lasso with Binomial likelihood for partitioning groups of cells by AI signal, and a hierarchical Bayesian model for AI statistical inference. In simulation, airpart accurately detected partitions of cell types by their AI and had lower RMSE of allelic ratio estimates than existing methods. In real data, airpart identified differential AI patterns across cell states and could be used to define trends of AI signal over spatial or time axes. AvailabilityThe airpart package is available as an R/Bioconductor package at https://bioconductor.org/packages/airpart.

bioinformatics↗

bioRxiv2021

RBBP4 modulates gene activity through acetylation and methylation of histone H3 lysine 27

RBBP4 is a core subunit of polycomb repressive complex 2 (PRC2) and HDAC1/2-containing complexes, which are responsible for histone H3 lysine 27 (H3K27) methylation and deacetylation respectively. However, the mechanisms by which RBBP4 modulates the functions of these complexes remain largely unknown. We generated viable mouse embryonic stem cell lines with RBBP4 mutations that disturbed methylation and acetylation of H3K27 on target chromatin and found that RBBP4 is required for PRC2 assembly and H3K27me3 establishment on target chromatin. Moreover, in the absence of EED and SUZ12, RBBP4 maintained chromatin binding on PRC2 loci, suggesting that the pre-existence of RBBP4 on nucleosomes serves to recruit PRC2 to restore H3K27me3 on newly synthesized histones. As such, disruption of RBBP4 function led to dramatic changes in transcriptional profiles. In spite of the PRC2 association, we found that transcriptional changes were more closely tied to the deregulation of H3K27ac rather than H3K27me3 where increased levels of H3K27ac were found on numerous cis-regulatory elements, especially putative enhancers. These data suggest that RBBP4 controls acetylation levels by adjusting the activity of HDAC complexes. As histone methylation and acetylation have been implicated in cancer and neural disease, RBBP4 could serve as a potential target for disease treatment.

genomics↗

bioRxiv2021

High-throughput production of functional prototissues capable of producing NO for vasodilation

Bottom-up synthesis of prototissues helps us to understand the internal cellular communications in the natural tissues and their functions, as well as to improve or repair the damaged tissues. The existed prototissues are rarely used to improve the function of living tissues. We demonstrated a methodology to produce spatially programmable prototissues based on the magneto-Archimedes effect in a high-throughput manner. More than 2000 prototissues are produced once within 2 hours. Two-component and three-component spatial coded prototissues are fabricated by varying the addition giant unilamellar vesicles (GUVs) order/number, and the magnetic field distributions. Two-step and three-step signal communications in the prototissues are realized using cascade enzyme reactions. More importantly, the two-component prototissues capable of producing nitric oxide (NO) cause vasodilation of rat blood vessels in the presence of glucose and hydroxyurea. The tension force decreases 2.59 g, meanwhile the blood vessel relaxation is of 31.2%. Our works pave the path to fabricate complicated programmable prototissues, and hold great potential in tissue transplantation in the biomedical field.

bioengineering↗

bioRxiv2021

An artificial cell containing cyanobacteria for endosymbiosis mimicking

The bottom-up constructed artificial cells help to understand the cell working mechanism and provide the evolution clues for organisms. Cyanobacteria are believed to be the ancestors of chloroplasts according to endosymbiosis theory. Herein we demonstrate an artificial cell containing cyanobacteria to mimic endosymbiosis phenomenon. The cyanobacteria sustainably produce glucose molecules by converting light energy into chemical energy. Two downstream "metabolic" pathways starting from glucose molecules are investigated. One involves enzyme cascade reaction to produce H2O2 (assisted by glucose oxidase) first, followed by converting Amplex red to resorufin (assisted by horseradish peroxidase). The more biological one involves nicotinamide adenine dinucleotide (NADH) production in the presence of NAD+ and glucose dehydrogenase. Further, NADH molecules are oxidized into NAD+ by pyruvate catalyzed by lactate dehydrogenase, meanwhile, lactate is obtained. Therefore, the sustainable cascade cycling of NADH/NAD+ is built. The artificial cells built here simulate the endosymbiosis phenomenon, meanwhile pave the way for investigating more complicated sustainable energy supplied metabolism inside artificial cells.

synthetic biology↗

bioRxiv2020

Targeting hypoxic habitats with hypoxia pro-drug evofosfamide in preclinical models of sarcoma

Hypoxic regions (habitats) within tumors are heterogeneously distributed and can be widely variant. Hypoxic habitats are generally pan-therapy resistant. For this reason, hypoxia-activated prodrugs (HAPs) have been developed to target these resistant volumes. The HAP evofosfamide (TH-302) has shown promise in preclinical and early clinical trials of sarcoma. However, in a phase III clinical trial, TH-302 did not improve survival in combination with doxorubicin (dox), most likely due to a lack of patient stratification based on hypoxic status. Herein, our goal was to develop deep-learning (DL) models to identify hypoxic habitats, using multiparametric (mp) MRI and co-registered histology, and to non-invasively monitor response to TH-302 in a patient-derived xenograft (PDX) of rhabdomyosarcoma and a syngeneic model of fibrosarcoma (RIF-1). A DL convolutional neural network showed strong correlations (>0.81) between the true hypoxic portion in histology and the predicted hypoxic portion in multiparametric MRI. TH-302 monotherapy or in combination with Dox delayed tumor growth and increased survival in the hypoxic PDX model (p<0.05), but not in the RIF-1 model, which had lower volume of hypoxic habitats. Control studies showed that RIF-1 resistance was due to hypoxia and not to other causes. Notably, PDX tumors developed resistance to TH-302 under prolonged treatment. In conclusion, response to TH-302 can be attributed to differences in hypoxia status prior therapy. Development of non-invasive MR imaging to assess hypoxia is crucial in determining the effectiveness of TH-302 therapy and to follow response. In further studies, our approach can be used to better plan therapeutic schedules to avoid resistance. One Sentence SummaryDevelopment of non-invasive MR imaging to assess hypoxia is crucial in determining the effectiveness of TH-302 therapy and to follow response.

cancer biology↗