Biology subjects

Wu, A.

Publications and source records attributed to Wu, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Degenerated CRISPRs widely regulate Cas expression to balance immunity and cost

CRISPR RNAs (crRNAs) and Cas proteins together provide prokaryotes with adaptive immunity against genetic invaders. How Cas expression is fine-tuned to avoid energy burden while satisfying the dynamic need of crRNAs remains poorly understood. Here we experimentally demonstrated widespread degenerated mini-CRISPRs encode CreR (Cas-regulating) RNAs to mediate autorepression of type I-B, I-E and V-A Cas proteins, based on their partial complementarity to cas promoters. This autorepression decreases energy burden and autoimmune risks, thus mitigating the fitness cost on host cell, and remarkably, senses and responds to alterations in the volume of canonical crRNAs, which compete with CreR for Cas proteins. Moreover, CreR-guided Cas autorepression can be subverted by diverse anti-CRISPR (Acr) proteins that destruct Cas proteins, which in turn replenishes the weapon depot. Our data unveil a general degenerated crRNA-guided autorepression paradigm for diverse Cas effectors, which highlights the intricate (self-)regulation of CRISPR-Cas and its transcriptional counterstrategy against Acr attack.

microbiology↗

bioRxiv2023

A MSTNDel273C mutation with FGF5 knockout sheep by CRISPR/Cas9 promotes skeletal muscle myofiber hyperplasia via MEK-ERK-FOSL1 axis

Mutations in the well-known Myostatin (MSTN) produce a "double-muscle" phenotype, which makes it commercially invaluable for improving livestock meat production and providing high-quality protein for humans. However, mutations at different loci of the MSTN often produce a variety of different phenotypes. In the current study, we increased the delivery ratio of Cas9 mRNA to sgRNA from the traditional 1:2 to 1:10, which improves the efficiency of the homozygous mutation of biallelic gene. Here, a MSTNDel273C mutation with FGF5 knockout sheep, in which the MSTN and FGF5 dual-gene biallelic homozygous mutations were produced via the deletion of 3-base pairs of AGC in the third exon of MSTN, resulting in cysteine-depleted at amino acid position 273, and the FGF5 double allele mutation led to inactivation of FGF5 gene. The MSTNDel273C mutation with FGF5 knockout sheep highlights a dominant "double-muscle" phenotype, which can be stably inherited. Both F0 and F1 generation mutants highlight the excellent trait of high-yield meat with a smaller cross-sectional area and higher number of muscle fibers per unit area. Mechanistically, the MSTNDel273C mutation with FGF5 knockout mediated the activation of FOSL1 via the MEK-ERK-FOSL1 axis. The activated FOSL1 promotes skeletal muscle satellite cell proliferation and inhibits myogenic differentiation by inhibiting the expression of MyoD1, and resulting in smaller myotubes. In addition, activated ERK1/2 may inhibit the secondary fusion of myotubes by Ca2+-dependent CaMKII activation pathway, leading to myoblasts fusion to form smaller myotubes.

cell biology↗

bioRxiv2023

Pioneer factor Foxa2 mediates chromatin conformation changes in ligand-dependent activation of nuclear receptor FXR

ABSTACTActivation of nuclear receptors, a family of ligand-dependent transcription factors, is used extensively in development of drug targets. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXR during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation. We performed Foxa2 HiChIP to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of FXR agonist. Hence, we determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.

pharmacology and toxicology↗

bioRxiv2023

Multi-omics and Pharmacological Characterization of Patient-derived Glioma Cell Lines

Glioblastoma (GBM) is the most common brain tumor and is currently incurable. Primary GBM cultures are widely used tools for screening potentially therapeutic drugs; however, there is a lack of genomic and pharmacological characterization of these primary GBM cultures. Here, we collected 52 patient-derived glioma cell (PDGC) lines and characterized them through whole- genome sequencing (WGS), RNA-seq, and drug response screening. We identified three molecular subtypes among PDGCs: mesenchymal (MES), proneural (PN), and oxidative phosphorylation (OXPHOS). Upon profiling the responses of PDGCs to 214 drugs, we found that the PN subtype PDGCs were sensitive to tyrosine kinase inhibitors, whereas the OXPHOS subtype PDGCs were sensitive to histone deacetylase inhibitors, oxidative phosphorylation inhibitors, and HMG-CoA reductase inhibitors. PN and OXPHOS subtype PDGCs stably formed tumors in vivo upon intracranial transplantation into immunodeficient mice, while most MES subtype PDGCs were incapable of tumorigenesis in vivo. In addition, profiling and follow-up investigations showed that the serum-free culture system used for PDGCs enriched and propagated rare MYC/MYCN- amplified glioma cells. Our study provides a resource for understanding primary glioma cell cultures and aiding clinical translation. SignificanceOur study provides a resource for patient-derived glioma cell lines (PDGCs) on transcriptome, genome, drug response, and tumorigenic abilities. PDGCs are categorized into PN, MES, and OXPHOS subtypes, with MES-subtype PDGCs incapable of tumorigenesis in vivo. Notably, the serum-free culture system for PDGCs enriches glioma cells with MYC/MYCN amplification.

cancer biology↗

bioRxiv2023

Grapevine scion gene expression is driven by rootstock and environment interaction

BACKGROUNDGrafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings. RESULTSIn the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment. CONCLUSIONSOur results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.

plant biology↗

bioRxiv2022

Exploring the genome and protein space of viruses

Recent metagenomic studies have identified a vast number of viruses. However, the systematic assessment of the true genetic diversity of the whole virus community on our planet remains to be investigated. Here, we explored the genome and protein space of viruses by simulating the process of virus discovery in viral metagenomic studies. Among multiple functions, the power function was found to best fit the increasing trends of virus diversity and was therefore used to predict the genetic space of viruses. The estimate suggests that there are at least 8.23e+08 viral Operational Taxonomic Units (vOTUs) and 1.62e+09 viral protein clusters on Earth when assuming the saturation of the virus genetic space, taking into account the balance of costs and the identification of novel viruses. Its noteworthy that less than 3% of the viral genetic diversity has been uncovered thus far, emphasizing the vastness of the unexplored viral landscape. To saturate the genetic space, a total of 3.08e+08 samples would be required. Analysis of viral genetic diversity by ecosystem yielded estimates consistent with those mentioned above. Furthermore, the estimate of the virus genetic space remained robust when accounting for the redundancy of sampling, sampling time, sequencing platform, and parameters used for protein clustering. This study provides a guide for future sequencing efforts in virus discovery and contributes to a better understanding of viral diversity in nature.

microbiology↗

bioRxiv2022

"Double-Effect" strategy against Triple-Negative Breast Cancer via a synergistic therapy of Magneto-mechanical Force enhancing NIR-II Hypothermal Ablation

Triple-negative breast cancer (TNBC) is a form of breast cancer that is more aggressive and harder to treat than others, with a higher probability of relapse. Its highly efficient capabilities for migrating and invading other parts of the body together with the current lack of clinically established effective therapies account for a low survival rate. Thus, we propose the in-tandem use of two complementary therapeutic routes to effectively combat TNBC. Herein, a versatile magnetic-photothermal converter (MPC) is elaborately designed via integrating zinc-doped ferrite nanoparticles and polyethene glycol, synergistically enhanced through magneto-mechanical force (MMF) and near-infrared-II (NIR-II) hypothermal ablation, thereby displaying excellent therapeutic efficiency. Their combined use, which is less aggressive to the human body compared to conventional chemotherapeutic approaches, results in the splendid suppression of TNBC migration and invasion. Remotely controlling the MPCs by an external magnetic stimulus, results in cellular MMF effects that cause direct mechanical destruction to the cancer cell membrane, leading to its necrosis. Furthermore, the MMF disrupts intracellular lysosomes, thereby triggering the release of large amounts of protein hydrolases, which induce intracellular oxidative stress, and accelerate the induction of apoptosis. Complementing the therapeutic approach based on MMF, the excellent photothermal performance of the MPC in the NIR-II region (1064nm) is exploited to enable effective hypothermal ablation of the tumours, which can be achieved in deep tissue layers. The proposed multifunctional nanocomposites, together with the demonstrated "double effect" therapeutic approach, hold significant potential to pave the way for future cutting-edge weapons against the dreadful TNBC.

cancer biology↗

bioRxiv2022

Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution

Mouse lemurs (Microcebus spp.) are an emerging primate model organism. However, little is known about their genetics or cellular and molecular biology. In the accompanying paper, we used large-scale single cell RNA-sequencing of 27 organs and tissues to identify over 750 molecular cell types, characterize their full transcriptomic profiles, and study evolution of primate cell types. Here we use the atlas to characterize mouse lemur genes, mutations, physiology, and disease. We uncover thousands of previously unidentified lemur genes and hundreds of thousands of new splice junctions that globally define lemur gene structures and reveal over 85,000 primate splice junctions missing in mice. We systematically explore the lemur immune system, comparing the global expression profiles of key immune genes in health and disease, and molecular mapping of immune cell development, trafficking, and their local and global activation to infection. We characterize primate/lemur-specific physiology and disease including molecular features of the immune program, of lemur adipocytes that exhibit dramatic seasonal rhythms, and of metastatic endometrial cancer that resembles the human malignancy. We identify and describe the expression patterns of over 400 primate genes missing in mice, many with similar expression patterns in human and lemur and some implicated in human disease. Finally, we provide an experimental framework for reverse genetic analysis by identifying naturally-occurring nonsense (null) mutations in three primate genes missing in mice and analyzing their transcriptional phenotypes. This work establishes mouse lemur as a tractable primate model organism for genetic and molecular analysis, and it prioritizes primate genes, splice junctions, physiology, and disease for future study.

genetics↗

bioRxiv2022

A cross-scale analysis to understand and quantify effects of photosynthetic enhancement on crop growth and yield

Photosynthetic manipulation provides new opportunities for enhancing crop yield. However, understanding and quantifying effectively how the seasonal growth and yield dynamics of target crops might be affected over a wide range of environments is limited. Using a state-of-the-art cross-scale model we predicted crop-level impacts of a broad list of promising photosynthesis manipulation strategies for C3 wheat and C4 sorghum. The manipulation targets have varying effects on the enzyme-limited (Ac) and electron transport-limited (Aj) rates of photosynthesis. In the top decile of seasonal outcomes, yield gains with the list of manipulations were predicted to be modest, ranging between 0 and 8%, depending on the crop type and manipulation. To achieve the higher yield gains, large increases in both Ac and Aj are needed. This could likely be achieved by stacking Rubisco function and electron transport chain enhancements or installing a full CO2 concentrating system. However, photosynthetic enhancement influences the timing and severity of water and nitrogen stress on the crop, confounding yield outcomes. Strategies enhancing Ac alone offers more consistent but smaller yield gains across environments, Aj enhancement alone offers higher gains but is undesirable in less favourable environments. Understanding and quantifying complex cross-scale interactions between photosynthesis and crop yield will challenge and stimulate photosynthesis and crop research. Summary StatementLeaf-canopy-crop prediction using a state-of-the-art cross-scale model improves understanding of how photosynthetic manipulation alters wheat and sorghum growth and yield dynamics. This generates novel insights for quantifying impacts of photosynthetic enhancement on crop yield across environments.

plant biology↗

bioRxiv2022

Distinct airway progenitor cells drive epithelial heterogeneity in the developing human lung

Recent advances using single cell genomic approaches have identified new epithelial cell types and uncovered cellular heterogeneity in the murine and human lung (1). Here, using scRNA-seq and microscopy we identify and describe a secretory-like cell that is enriched in the small airways of the developing human lung and identified by the unique co-expression of SCGB3A2/SFTPB/CFTR. To place these cells in the hierarchy of airway development, we apply a single cell barcode-based lineage tracing method track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro (2). Lineage tracing revealed that these cells have distinct developmental potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells (PNECs) and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. We conclude that SCGB3A2/SFTPB/CFTR cells act as a progenitor cell contributing to the cellular diversity and heterogeneity in the developing human airway. SIGNIFICANCE STATEMENTThe current study identifies a novel secretory cell type that is present predominantly in the small airway of the developing human lung. These secretory cells are defined by co-expression of SCGB3A2/SFTPB/CFTR, and functional studies show that this cell gives rise to pulmonary neuroendocrine cells and a sub-population of multiciliated cells, thereby leading to cellular heterogeneity.

developmental biology↗

bioRxiv2022

A Development-Inspired Niche for Homeostatic Human Mini-Intestines

Epithelial organoids derived from intestinal tissue, also referred to as mini-intestines or mini-guts, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Murine intestinal organoids represent a homeostatic system that balances stem cell maintenance within a crypt-like compartment and differentiation within a villus-like compartment1-3. However, this homeostatic balance and spatial organization has not been achieved with human intestinal organoids4. Here, we leverage single cell RNA-seq data (scRNA-seq) and high-resolution imaging to interrogate the developing human intestinal stem cell niche. We identified an EGF-family member, EPIREGULIN (EREG), as uniquely expressed in the developing crypt, and found that EREG can take the place of EGF as an in vitro niche factor. Unlike EGF, which leads to growth of thin-walled cystic organoids, EREG-organoids are spatially resolved into budded and proliferative crypt domains and a differentiated villus-like central lumen. Transcriptomics and epigenomics showed that EREG-organoids are globally similar to the native intestine while EGF-organoids have an altered chromatin landscape, downregulate the master intestinal transcription factor CDX25,6, and ectopically express stomach genes.

developmental biology↗

bioRxiv2022

vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data

Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is public available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely-used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. The study would greatly facilitate effective identification of vsRNAs.

bioinformatics↗

bioRxiv2022

GhCO and GhCRY1 accelerate floral meristem initiation in response to blue light to shorten cotton breeding

The shoot apical meristem (SAM) is a special category of tissue with pluripotency that forms new organs and individuals, especially floral individuals. However, little is known about the fate of cotton SAMs as a tunica corpus structure. Here, we demonstrate that cotton SAM fate decisions depend on light signals and circadian rhythms, and the genes GhFKF1, GhGI, GhCRY1 and GhCO were responsible for SAM fate decisions and highlighted via RNA sequencing (RNA-seq) analysis of different cotton cultivars, as confirmed by genetic analysis via the CRISPR-Cas9 system. In situ hybridization (ISH) analysis showed that the GhCO gene, induced by a relatively high blue light proportion, was highly upregulated during the initiation of floral meristems (FMs). Further blue light treatment analysis showed that the transition from vegetative to reproductive growth of SAM was promoted by a high proportion of blue light, coupled with high expression of the blue light-responsive genes GhCO and GhCRY1. Taken together, our study suggests that blue light signalling plays a key role in the fate decision of cotton SAM. These results provide a strategy to regulate the SAM differentiation of cotton by using the CRISPR-Cas9 system to change the ratio of red and blue light absorption to breed early-maturity cotton. One-sentence summaryThe SAM differentiation especially the initiation of floral meristem of upland cotton were mediated by genes GhCO and GhCRY1 which in response to blue light.

developmental biology↗

bioRxiv2021

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

Mouse lemurs are the smallest, fastest reproducing, and among the most abundant primates, and an emerging model organism for primate biology, behavior, health and conservation. Although much has been learned about their physiology and their Madagascar ecology and phylogeny, little is known about their cellular and molecular biology. Here we used droplet- and plate-based single cell RNA-sequencing to profile 226,000 cells from 27 mouse lemur organs and tissues opportunistically procured from four donors clinically and histologically characterized. Using computational cell clustering, integration, and expert cell annotation, we defined and biologically organized over 750 mouse lemur molecular cell types and their full gene expression profiles. These include cognates of most classical human cell types, including stem and progenitor cells, and the developmental programs for spermatogenesis, hematopoiesis, and other adult tissues. We also described dozens of previously unidentified or sparsely characterized cell types and subtypes. We globally compared cell type expression profiles to define the molecular relationships of cell types across the body, and explored primate cell and gene expression evolution by comparing mouse lemur cell transcriptomes to those of human, mouse, and macaque. This revealed cell type specific patterns of primate specialization, as well as many cell types and genes for which lemur provides a better human model than mouse. The atlas provides a cellular and molecular foundation for studying this primate model organism, and establishes a general approach for other emerging model organisms.

genetics↗

bioRxiv2021

The influence of unmeasured confounding on the MR Steiger approach

The Mendelian Randomization (MR) Steiger approach is used to determine the direction of a possible causal effect between two phenotypes [1]. For two phenotypes, denoted phenotype 1 and 2, the MR Steiger approach is composed of two parts: (1) MR is performed for a set of single nucleotide polymorphisms (SNPs) that serve as instrumental variables for phenotype 1 and (2) the difference of two correlations, the correlation between the SNPs and phenotype 1 and the correlation between the SNPs and phenotype 2, is calculated. These two parts are then used to determine the direction of a possible causal effect between the two phenotypes. The original MR Steiger paper [1] shows that unmeasured confounding of the two phenotypes affects the validity of the MR Steiger approach, but does not elucidate as to how this occurs. In particular, it was argued that if the magnitude of the observational variance explained between the two phenotypes is above 0.2, the MR Steiger method may return the incorrect causal direction due to unmeasured confounding. This may initially seem surprising since unmeasured confounding does not induce spurious associations between the SNP and phenotype 2, as we demonstrate using directed acyclic graphs. In this note, we show that this is because unmeasured confounding may rescale the magnitude of a non-zero association, and thereby distort the comparison of the correlation between the SNP and phenotype 2 and the correlation between the SNP and phenotype 1. We will end with a number of cautionary remarks on the MR Steiger method, which are partly motivated by this and mentioned in the original MR Steiger paper [1].

genetics↗

bioRxiv2021

An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses

Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. This study curated an atlas of human viruses from public databases and literatures, and built the Human Virus Database (HVD) available at http://computationalbiology.cn/humanVirusBase/#/. The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue range of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue range of DNA viruses was predicted using a random-forest algorithm with a medium performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses.

microbiology↗

bioRxiv2021

Genomic evidence for divergent co-infections of SARS-CoV-2 lineages

Recently, patients co-infected by two SARS-CoV-2 lineages have been sporadically reported. Concerns are raised because previous studies have demonstrated co-infection may contribute to the recombination of RNA viruses and cause severe clinic symptoms. In this study, we have estimated the compositional lineage(s), tendentiousness, and frequency of co-infection events in population from a large-scale genomic analysis for SARS-CoV-2 patients. SARS-CoV-2 lineage(s) infected in each sample have been recognized from the assignment of within-host site variations into lineage-defined feature variations by introducing a hypergeometric distribution method. Of all the 29,993 samples, 53 (~0.18%) co-infection events have been identified. Apart from 52 co-infections with two SARS-CoV-2 lineages, one sample with co-infections of three SARS-CoV-2 lineages was firstly identified. As expected, the co-infection events mainly happened in the regions where have co-existed more than two dominant SARS-CoV-2 lineages. However, co-infection of two sub-lineages in Delta lineage were detected as well. Our results provide a useful reference framework for the high throughput detecting of SARS-CoV-2 co-infection events in the Next Generation Sequencing (NGS) data. Although low in average rate, the co-infection events showed an increasing tendency with the increased diversity of SARS-CoV-2. And considering the large base of SARS-CoV-2 infections globally, co-infected patients would be a nonnegligible population. Thus, more clinical research is urgently needed on these patients.

microbiology↗

bioRxiv2021

RSC-mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription

The directionality of gene promoters - the ratio of protein-coding over divergent noncoding transcription - is highly variable and regulated. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus a decrease in promoter directionality. We find that RSC facilitates nucleosome positioning upstream in promoters at the sites of divergent transcription. These highly directional promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription. We propose that any DNA binding factor, when stably associated with cryptic transcription start sites, form barriers for repressing divergent transcription. Our study provides an explanation as to why certain promoters are more directional than others.

molecular biology↗