Biology subjects

Mao, S.

Publications and source records attributed to Mao, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Ripening and synchronization of biomolecular condensates in a heterogeneous elastic medium

Biomolecular condensates play a crucial role in regulating gene expression, but their behavior in chromatin remains poorly understood. Classical theories of phase separation are limited to thermal equilibrium, and traditional methods can only simulate a limited number of condensates. In this paper, we introduce a novel mean-field-like method that allows us to simulate millions of condensates in a heterogeneous elastic medium to model the dynamics of transcriptional condensates in chromatin. Using this method, we unveil an elastic ripening process in which the average condensate radius exhibits a unique temporal scaling, [<]R[>] [~] t1/5, different from the classical Ostwald ripening, and we theoretically derive the exponent based on energy conservation and scale invariance. We also introduce active dissolution to model the degradation of transcriptional condensates upon RNA accumulation. Surprisingly, three different kinetics of condensate growth emerge, corresponding to constitutively expressed, transcriptional-bursting, and silenced genes. Notably, multiple distributions of transcriptional-bursting kinetics from simulations, e.g., the burst frequency, agree with transcriptome-wide experimental data. Furthermore, the timing of growth initiation can be synchronized among bursting condensates, with power-law scaling between the synchronization period and dissolution rate. Our results shed light on the complex interplay between biomolecular condensates and the elastic medium, with important implications for gene expression regulation.

biophysics↗

bioRxiv2022

Promoting Axon Regeneration By Inhibiting RNA N6-methyladenosine Demethylase ALKBH5

A key limiting factor of successful axon regeneration is the intrinsic regenerative ability in both the peripheral (PNS) and central nervous system (CNS). Previous studies have identified axon regeneration regulators that act on gene expression in injured neurons. However, it is less known if RNA modifications play a role in this process. Here, we systematically screened the functions of all common m6A modification-related enzymes in axon regeneration and report ALKBH5, an evolutionarily conserved RNA m6A demethylase, as a regulator of axonal regeneration. In PNS, knockdown of ALKBH5 enhanced sensory axonal regeneration, whereas overexpressing ALKBH5 impaired axonal regeneration in an m6A-dependent manner. Mechanistically, ALKBH5 increased the stability of Lpin2 mRNA and thus limited regenerative growth associated lipid metabolism in DRG neurons. Moreover, in CNS, knockdown of ALKBH5 enhanced the survival and axonal regeneration of retinal ganglion cells after optic nerve injury. Together, our results suggest a novel mechanism regulating axon regeneration and point ALKBH5 as a potential target for promoting axon regeneration in both PNS and CNS.

neuroscience↗

bioRxiv2022

The Prophylactic and Therapeutic Efficacy of the Broadly Active Antiviral Ribonucleoside N4-Hydroxycytidine (EIDD-1931) in a Mouse Model of Lethal Ebola Virus Infection

The unprecedented magnitude of the 2013-2016 Ebola virus (EBOV) epidemic in West Africa resulted in over 11,000 deaths and spurred an international public health emergency. A second outbreak in 2018-2020 in DRC resulted in an additional >3400 cases and nearly 2300 deaths (WHO Disease Outbreak News: Update 26 June, 2020). These large outbreaks across geographically diverse regions highlight the need for the development of effective oral therapeutic agents that can be easily distributed for self-administration to populations with active disease or at risk of infection. Herein, we report the in vivo efficacy of N4-hydroxycytidine (EIDD-1931), a broadly active ribonucleoside analog and the active metabolite of the prodrug EIDD-2801 (molnupiravir), in murine models of lethal EBOV infection. Twice daily oral dosing with EIDD-1931 at 200 mg/kg for 7 days, initiated either with a prophylactic dose 2 hours before infection, or as therapeutic treatment starting 6 hours post-infection, resulted in 92-100% survival of mice challenged with lethal doses of EBOV, reduced clinical signs of Ebola virus disease (EVD), reduced serum virus titers, and facilitated weight loss recovery. These results support further investigation of molnupiravir as a potential therapeutic or prophylactic treatment for EVD.

microbiology↗

bioRxiv2022

Mitochondrial ROS production by neutrophils is required for host antimicrobial function against Streptococcus pneumoniae and is controlled by A2B adenosine receptor signaling

Polymorphonuclear cells (PMNs) control Streptococcus pneumoniae (pneumococcus) infection through various antimicrobial activities. We previously found that reactive oxygen species (ROS) were required for optimal antibacterial function, however, the NADPH oxidase is known to be dispensable for the ability of PMNs to kill pneumococci. In this study, we explored the role of ROS produced by the mitochondria in PMN antimicrobial defense against pneumococci. We found that the mitochondria are an important source of overall intracellular ROS produced by murine PMNs in response to infection. We investigated the host and bacterial factors involved and found that mitochondrial ROS (MitROS) are produced independent of bacterial capsule or pneumolysin but presence of live bacteria that are in direct contact with PMNs enhanced the response. We further found that MyD88-/- PMNs failed to produce MitROS in response to pneumococcal infection suggesting that released bacterial products acting as TLR ligands are sufficient for inducing MitROS production in PMNs. To test the role of MitROS in PMN function, we used an opsonophagocytic killing assay and found that MitROS were required for the ability of PMNs to kill pneumococci. We then investigated the role of MitROS in host resistance and found that MitROS are produced by PMNs in response to pneumococcal infection. Importantly, treatment of mice with a MitROS scavenger prior to systemic challenge resulted in reduced survival of infected hosts. In exploring host pathways that control MitROS, we focused on extracellular adenosine, which is known to control PMN anti-pneumococcal activity, and found that signaling through the A2B adenosine receptor inhibits MitROS production by PMNs. A2BR-/- mice produced more MitROS and were significantly more resistant to infection. Finally, we verified the clinical relevance of our findings using human PMNs. In summary, we identified a novel pathway that controls MitROS production by PMNs, shaping host resistance against S. pneumoniae. Author summaryDespite the presence of antibiotics and vaccines, Streptococcus pneumoniae infections remain a serious cause of mortality and morbidity globally. Understanding protective host responses is key for designing improved therapies against infection. Neutrophils are innate immune cells that are crucial for control of S. pneumoniae infection. In this study we explored the mechanisms by which neutrophils kill S. pneumoniae. We found that the mitochondria, whose primary role is energy production, also produce reactive oxygen species (ROS) that are critical for the ability of neutrophils to kill S. pneumoniae. We explored the bacterial and host factors involved in mitochondrial ROS (MitROS) production by neutrophils. We found that recognition of bacterial products by neutrophils triggers this response and that the host A2B adenosine receptor regulates it. Importantly, MitROS were required for host resistance against S. pneumoniae. This study describes a novel pathway that controls anti-microbial responses and can be a future therapeutic target.

immunology↗

bioRxiv2021

Genetic loci of the R. anatipestifer serotype discovered by Pan-GWAS and its application for the development of a multiplex PCR serotyping method

The disease caused by Riemerella anatipestifer (R. anatipestifer) causes large economic losses to the global duck industry every year. Serotype-related genomic variation (such as in O-antigen and capsular polysaccharide gene clusters) has been widely used for the serotyping in many gram-negative bacteria. To date, there have been few studies focused on genetic basis of serotypes in R. anatipestifer. Here, we used pan-genome-wide association studies (Pan-GWAS) to identify the serotype-specific genetic loci of 38 R. anatipestifers strain. Analyses of the loci of 11 serotypes showed that the loci could be well mapped with the serotypes of the corresponding strains. We constructed the knockout strain for the wzy gene at the locus, and the results showed that the mutant lost the agglutination characteristics to positive antisera. Based on the of Pan-GWAS results, we developed a multiple PCR method to identify serotypes 1, 2, and 11 of R. anatipestifer. Our study provides a precedent for systematically analysing the genetic basis of the R anatipestifer serotypes and establishing a complete serotyping system in the future. HighlightsO_LIR. anatipestifer serotype-specific locus was identified by Pan-GWAS for the first time. C_LIO_LIMolecular serotyping multiplex PCR was developed based on O-antigen biosynthesis gene clusters C_LI

genomics↗

bioRxiv2021

ARID1A loss derepresses human endogenous retrovirus-H to modulate BRD4-dependent transcription

The transposable elements (TEs) through evolutionary exaptation have become an integral part of human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis are recognized, their role in malignancy has only started to emerge. Here we show that many TEs, especially the pluripotency-related endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. The transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors including ARID1A. Knockout of ARID1A in CRC cells leads to increased accessibility at HERVH loci and enhanced transcription, which is dependent on ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulate their dynamics, and co-regulate many target genes. Altogether, we uncover a critical role for ARID1A in restraining HERVH, which can promote tumorigenesis by stimulating BRD4-dependent transcription when ARID1A is mutated.

cancer biology↗

bioRxiv2021

Spatial transcriptome sequencing revealed spatial trajectory in the Non-Small Cell Lung Carcinoma

Deepening understanding in the heterogeneity of tumors is critical for clinical treatment. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal lung cancer using the spatial transcriptomics (ST) technology. We identified gene expression gradients in stroma adjacent to tumor regions that allow for re-understanding of the tumor micro-environment. The establishment of these profiles was the first step towards an unbiased view of lung cancer and can serve as a dictionary for future studies. Tumor subclones were detected by ST technology in our research, while we contrast the EMT ability among in subclones which inferred the possible trajectory of tumor metastasis and invasion, which was confirmed by constructing the pseudo-time model of spatial transition within subclones. Together, these results uncovered lung cancer spatial heterogeneity, highlight potential tumor micro-environment differences and spatial evolution trajectory, and served as a resource for further investigation of tumor microenvironment.

cancer biology↗

bioRxiv2020

Base Pairing and Functional Insights into N3-methylcytidine (m3C) in RNA

N3-methylcytidine (m3C) is present in both eukaryotic tRNA and mRNA and plays critical roles in many biological processes. We report the synthesis of the m3C phosphoramidite building block and its containing RNA oligonucleotides. The base-pairing stability and specificity studies show that the m3C modification significantly disrupts the stability of the Watson-Crick C:G pair. Further m3C decreases the base pairing discrimination between C:G and the other mismatched C:A, C:U, and C:C pairs. Our molecular dynamic simulation study further reveals the detailed structural insights into the m3C:G base pairing pattern in an RNA duplex. More importantly, the biochemical investigation of m3C using reverse transcription shows that N3-methylation specifies the C:A pair and induces a G to A mutation using HIV-1-RT, MMLV-RT and MutiScribe-RT enzymes, all with relatively low replication fidelity. For other reverse transcriptases with higher fidelity like AMV-RT, the methylation could completely shut down DNA synthesis.

biochemistry↗

bioRxiv2020

Single species RNA purification with DNA nanoswitches

We report a novel method to purify individual RNA species using programmable DNA nanoswitches to facilitate RNA capture, release, and isolation. We validate sequence-based purification of microRNA, rRNA, and an mRNA fragment from total RNA, demonstrate multiplexing with two different RNA species, and show an application with downstream LC/MS analysis to identify RNA modifications. The simplicity, low cost, and low sample requirements of our method make it suitable for easy adoption.Competing Interest StatementLZ, ARC, and KH have intellectual property related to DNA nanoswitches. All other authors declare no competing interests.View Full Text

molecular biology↗

bioRxiv2020

CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature

Single-cell RNA sequencing (scRNA-seq) is widely used for analyzing gene expression in multi-cellular systems and provides unprecedented access to cellular heterogeneity. scRNA-seq experiments aim to identify and quantify all cell types present in a sample. Measured single-cell transcriptomes are grouped by similarity and the resulting clusters are mapped to cell types based on cluster-specific gene expression patterns. While the process of generating clusters has become largely automated, annotation remains a laborious ad-hoc effort that requires expert biological knowledge. Here, we introduce CellMeSH - a new automated approach to identifying cell types based on prior literature. CellMeSH combines a database of gene-cell type associations with a probabilistic method for database querying. The database is constructed by automatically linking gene and cell type information from millions of publications using existing indexed literature resources. Compared to manually constructed databases, CellMeSH is more comprehensive and scales automatically. The probabilistic query method enables reliable information retrieval even though the gene-cell type associations extracted from the literature are necessarily noisy. CellMeSH achieves up to 60% top-1 accuracy and 90% top-3 accuracy in annotating the cell types on a human dataset, and up to 58.8% top-1 accuracy and 88.2% top-3 accuracy on three mouse datasets, which is consistently better than existing approaches. AvailabilityWeb server: https://uncurl.cs.washington.edu/db_query and API: https://github.com/shunfumao/cellmesh

bioinformatics↗

bioRxiv2020

Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population

During the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10-212 and p = 2.98 x 10-261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.

microbiology↗

bioRxiv2020

UNCURL-App: Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data

MotivationAnalysis of single cell RNA sequencing (scRNA-seq) datasets is a complex and time-consuming process, requiring both biological knowledge and technical skill. With the rapid growth in scRNA-seq datasets, there is a need to simplify and systematize this process. ResultsWe introduce UNCURL-App, an online GUI-based interactive tool which integrates the scRNA-seq analysis pipeline with prior knowledge. UNCURL-App introduces two key innovations: First, cell type databases are integrated directly with the rest of the analysis process, allowing the user to identify potential cell types or pathways directly from the data. Second, tools for interactive re-analysis allow the user to create, merge, or delete clusters. In addition, UNCURL-App integrates multiple stages of the data analysis pipeline into a single interface, including dimensionality reduction, clustering, differential expression, and cell type identification. AvailabilityThe web tool is available at https://uncurl.cs.washington.edu/. Source code is available at https://github.com/yjzhang/uncurl_app Contactgseelig@uw.edu

bioinformatics↗

bioRxiv2020

Novel mosaic mice with diverse applications

Gene-deficient mouse models are indispensable for interrogating mammalian gene functions, but the conventional models allow the study of only one or few genes per mouse line, which has been a bottleneck in functional genomics. To confront the challenge, we have combined the CRISPR-Cas and Cre-Lox systems to develop a novel type of mosaic mice termed MARC (Mosaic Animal based on gRNA and Cre) for targeting many genes per mouse but only one gene per cell. This technology employs a transgene comprising a modified U6 promoter upstream of a series of floxed gRNA genes linked together in tandem, with one gRNA expressed per cell following Cre-mediated recombination. At least 61 gRNA genes can be stably maintained in the transgene, and importantly, enables robust proof-of-principle in vivo screens, demonstrating the potential for quickly evaluating the functions of many genes in diverse tissues in a single MARC line. In theory, MARC can also be analyzed by single-cell sequencing, and should enable cost-effective derivation of conventional single-gene-KO lines via simple breeding. Our study establishes MARC as an important addition to the mouse genetics toolbox.

genetics↗

bioRxiv2020

Tracing the origin of a new organ by inferring the genetic basis of rumen evolution

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We used 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen origin and evolution. Comparative analyses reveal that the rumen and the first-chamber stomachs of camels and cetaceans shared a common tissue origin from the esophagus. The rumen recruited genes from other tissues/organs and up-regulated many esophagus genes to aquire functional innovations involving epithelium absorption, improvement of the ketone body metabolism and regulation of microbial community. These innovations involve such genetic changes as ruminant-specific conserved elements, newly evolved genes and positively selected genes. Our in vitro experiements validate the functions of one enhancer, one positively selected gene and two newly evolved antibacterial genes. Our study provides novel insights into the origin and evolution of a complex organ.

evolutionary biology↗

bioRxiv2019

Extensive Mammalian Germline Genome Engineering

Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO{middle dot}3KO{middle dot}9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO{middle dot}3KO{middle dot}9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence SummaryExtensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation

synthetic biology↗

bioRxiv2019

QAlign: Aligning nanopore reads accurately using current-level modeling

MotivationEfficient and accurate alignment of DNA / RNA sequence reads to each other or to a reference genome / transcriptome is an important problem in genomic analysis. Nanopore sequencing has emerged as a major sequencing technology and many long-read aligners have been designed for aligning nanopore reads. However, the high error rate makes accurate and efficient alignment difficult. Utilizing the noise and error characteristics inherent in the sequencing process properly can play a vital role in constructing a robust aligner. In this paper, we design QAlign, a pre-processor that can be used with any long-read aligner for aligning long reads to a genome / transcriptome or to other long reads. The key idea in QAlign is to convert the nucleotide reads into discretized current levels that capture the error modes of the nanopore sequencer before running it through a sequence aligner. ResultsWe show that QAlign is able to improve alignment rates from around 80% up to 90% with nanopore reads when aligning to the genome. We also show that QAlign improves the average overlap quality by 9.2%, 2.5% and 10.8% in three real datasets for read-to-read alignment. Read-to-transcriptome alignment rates are improved from 51.6% to 75.4% and 82.6% to 90% in two real datasets. Availabilityhttps://github.com/joshidhaivat/QAlign.git

bioinformatics↗

bioRxiv2019

Correction of Niemann-Pick type C1 disease with the histone deacetylase inhibitor valproic acid

Niemann-Pick type C (NPC) disease is primarily caused by mutations in the NPC1 gene and is characterized by the accumulation of unesterified cholesterol and lipids in the late endosomal (LE) and lysosomal (Ly) compartments. The most prevalent disease-linked mutation is the I1061T variant of NPC1, which exhibits defective folding and trafficking from the endoplasmic reticulum to the LE/Ly compartments. We now show that the FDA-approved histone deacetylase inhibitor (HDACi) valproic acid (VPA) corrects the folding and trafficking defect associated with I1061T-NPC1 leading to restoration of cholesterol homeostasis, an effect that is largely driven by a reduction in HDAC7 expression. The VPA-mediated trafficking correction is in part associated with an increase in the acetylation of lysine residues in the cysteine-rich domain of NPC1. The HDACi-mediated correction is synergistically improved by combining it with the FDA-approved anti-malarial, chloroquine, a known lysosomotropic compound, which improved the stability of the LE/Ly-localized fraction of the I1061T variant. We posit that combining the activity of VPA, to modulate epigentically the cellular acetylome, with chloroquine, to alter the lysosomal environment to favor stability of the trafficked I1061T variant protein, can have a significant therapeutic benefit in patients carrying at least one copy of the I1061T variant of NPC1, the most common disease-associated mutation leading to NPC disease. Given its ability to cross the blood brain barrier, we posit VPA provides a potential mechanism to improve the response to 2-hydroxypropyl-{beta}-cyclodextrin, by restoring functional NPC1 to cholesterol managing compartment as an adjunct therapy.

cell biology↗

bioRxiv2019

CELF1 is an EIF4E binding protein that promotes translation of epithelial-mesenchymal transition effector mRNAs

Mounting evidence is revealing a granularity within gene regulation that occurs at the level of mRNA translation. Within mammalian cells, canonical cap-dependent mRNA translation is dependent upon the interaction between the m7G cap-binding protein eukaryotic initiation factor 4E (eIF4E) and the scaffolding protein eukaryotic initiation factor 4G (eIF4G), the latter of which facilitates pre-translation initiation complex assembly, mRNA circularization, and ultimately ribosomal scanning. In breast epithelial cells, we previously demonstrated that the CELF1 RNA-binding protein promotes the translation of epithelial to mesenchymal transition (EMT) effector mRNAs containing GU-rich elements (GREs) within their 3 untranslated regions (UTRs). Here we show that within this context, CELF1 directly binds to both the eIF4E cap-binding protein and Poly(A) binding protein (PABP), promoting translation of GRE-containing mRNAs in mesenchymal cells. Disruption of this CELF1/eIF4E interaction inhibits both EMT induction and experimental metastasis. Our findings illustrate a novel way in which non-canonical mechanisms of translation initiation underlie transitional cellular states within the context of development or human disease.

cancer biology↗