Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 577 records · Page 32Linked to original sources

bioRxiv2022

Regulation of protein translation by TRIM21

AbstractRegulation of translation initiation is essential for maintenance of protein homeostasis and typically involves the phosphorylation of translation initiation factor eIF2 in eukaryotes. In response to stressors, cells employ eIF2-dependent signaling to control translation initiation, which regulates multiple biological and physiological processes. However, the precise regulatory mechanism remains unclear. In this study, we focus on the role of TRIM21 in the regulation of protein translation mediated by protein kinase R (PKR), one of the classic kinases that phosphorylates eIF2. TRIM21 deficiency enhances the activation of PKR under different types of stress. TRIM21 interacts with PKR, and the E3 ligase activity of TRIM21 is crucial for stress-triggered PKR inactivation. TRIM21 interacts with the PKR phosphatase PP1 and promotes K6-linked polyubiquitination of PP1 under stresses. Ubiquitination of PP1 augments its interaction with PKR, causing PKR inactivation and subsequent dephosphorylation of eIF2, initiating protein synthesis. Moreover, TRIM21 constitutively restricts viral infection by reversing PKR-mediated inhibition of the protein synthesis of intrinsic antiviral genes. The TRIM21-PP1 axis acts as a newly discovered program that regulates PKR-associated protein synthesis and broadens our knowledge of antiviral genes. Moreover, TRIM21-mediated regulation of PKR activation provides evidence that TRIM21 may anticipate the interferon-dependent immunotherapy. Our study highlights the essential role of TRIM21 in regulating protein translation and may provide a novel target for the treatment of translation-associated diseases.

immunology↗

bioRxiv2022

Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectral Alignment For Discovery of Structurally Related Molecules

Spectrum alignment of tandem mass spectrometry (MS/MS) data using the modified cosine similarity and subsequent visualization as molecular networks have been demonstrated to be a useful strategy to discover analogs of molecules from untargeted MS/MS-based metabolomics experiments. Recently, a neutral loss matching approach has been introduced as an alternative to MS/MS-based molecular networking, with an implied performance advantage in finding analogs that cannot be discovered using existing MS/MS spectrum alignment strategies. To comprehensively evaluate the scoring properties of neutral loss matching, the cosine similarity, and the modified cosine similarity, similarity measures of 955,228 peptide MS/MS spectrum pairs and 10 million small molecule MS/MS spectrum pairs were compared. This comparative analysis revealed that the modified cosine similarity outperformed neutral loss matching and the cosine similarity in all cases. The data further indicated that the performance of MS/MS spectrum alignment depends on the location and type of the modification, as well as the chemical compound class of fragmented molecules.

bioinformatics↗

bioRxiv2022

The immunogenomic landscape of cattle

Here, we report the de novo assembly of a cattle genome using ultra-long-read nanopore sequencing in conjunction with other advanced technologies. The assembled genome contains only 145 contigs (N50 [~] 74.0 Mb). Compare to the current reference cattle genome ARS-UCD1.2, 154 gaps are closed, and 467 scaffolds are further placed in our assembly. Importantly, except two remained gaps in the T-cell receptor /{delta} (TRA/TRD) region, the gene loci of other TRs and immunoglobulins (IGs) are seamlessly assembled and exquisitely annotated. With the characterization of 258 IG genes and 626 TR genes that distributed in seven genomic loci, we illustrate the highest immune gene diversity in mammals to our knowledge. Moreover, the gene structures of major histocompatibility complex (MHC) are integrally depicted with properly phased haplotypes. Thus, our work not only reports a cattle genome with the most continuity and completeness, but also provide a comprehensive view of the complex immune- genome.

genomics↗

bioRxiv2022

A universal system for streamlined genome integrations with CRISPR-associated transposases

Genome engineering tools in bacteria are limited by their targeting abilities, cargo size capacities, and integration efficiencies. Programmable Cas-directed transposons have been shown to bypass these constraints; however, genome integrations with these Cas-directed transposons require a cargo plasmid carrying the desired DNA payload flanked by directed repeat transposon arms. This cloning pre-requisite significantly hinders the modularity and streamlining capabilities of Cas-directed transposon systems, diminishing their utility for genome engineering. Here, we present a system that can robustly integrate a linear DNA payload into the genome of E. coli by employing a Type I-F CRISPR-associated transposon from Vibrio cholerae. This system bypasses the traditional limiting factors of Cas-directed transposons by leveraging oligonucleotide design and nested polymerase chain reactions to reconstitute the transposon arms onto a designated cargo. Our findings demonstrate that this programmable linear integration method has high efficiencies in integrating large DNA payloads across multiple genomic loci.

synthetic biology↗

bioRxiv2022

Single-cell perspectives on the function and development of deep-sea mussel bacteriocytes

The authors have withdrawn their manuscript because the authors need to re-organize the data and writing, meanwhile more experimental evidence from more RNA-seq replications, immunofluorescence assay and in vivo knock-down assays will be added to support the viewpoints. In this preprint, only one individual of decolonized mussel was employed for transcriptome sequencing while combined data from single cell transcriptomics with in situ hybridization is not enough convincing to draw some of the conclusion. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2022

SARS-CoV-2 Omicron BA.2.12.1, BA.4, and BA.5 subvariants evolved to extend antibody evasion

SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 have surged dramatically to become dominant in the United States and South Africa, respectively1,2. These novel subvariants carrying additional mutations in their spike proteins raise concerns that they may further evade neutralizing antibodies, thereby further compromising the efficacy of COVID-19 vaccines and therapeutic monoclonals. We now report findings from a systematic antigenic analysis of these surging Omicron subvariants. BA.2.12.1 is only modestly (1.8-fold) more resistant to sera from vaccinated and boosted individuals than BA.2. However, BA.4/5 is substantially (4.2-fold) more resistant and thus more likely to lead to vaccine breakthrough infections. Mutation at spike residue L452 found in both BA.2.12.1 and BA.4/5 facilitates escape from some antibodies directed to the so-called class 2 and 3 regions of the receptor-binding domain3. The F486V mutation found in BA.4/5 facilitates escape from certain class 1 and 2 antibodies but compromises the spike affinity for the viral receptor. The R493Q reversion mutation, however, restores receptor affinity and consequently the fitness of BA.4/5. Among therapeutic antibodies authorized for clinical use, only bebtelovimab retains full potency against both BA.2.12.1 and BA.4/5. The Omicron lineage of SARS-CoV-2 continues to evolve, successively yielding subvariants that are not only more transmissible but also more evasive to antibodies.

microbiology↗

bioRxiv2022

A Remarkable Adaptive Paradigm Of Heart Performance And Protection Emerges In Response To The Constitutive Challenge Of Marked Cardiac-Specific Overexpression Of Adenylyl Cyclase Type 8

Adult mice with cardiac-specific overexpression of adenylyl cyclase (AC) type VIII (TGAC8) adapt to an incessantly increased cAMP-induced cardiac workload ([~]30% increases in heart rate, ejection fraction and cardiac output) for up to a year without signs of heart failure or excessive mortality. Here we show that despite markedly increased cardiac work, classical cardiac hypertrophy markers were absent in TGAC8, total left ventricular (LV) mass was not increased: a reduced LV cavity volume in TGAC8 was encased by thicker LV walls harboring an increased number of small cardiac myocytes and a network of small interstitial non-cardiac myocytes, manifesting increased proliferation markers and compared to WT. Protein synthesis, proteosome activity, autophagy, and Nrf-2, Hsp90, ACC2 protein levels were increased in TGAC8, but LV ATP and phosphocreatine levels in vivo did not differ by genotype. 2,323 transcripts and 2,184 proteins identified in unbiased omics analyses, spanning a wide array of biological processes and molecular functions in numerous cellular compartments differed in TGAC8 vs WT; and over 250 canonical signaling pathways characteristic of adaptive survival circuitry of cancers, including PI3K and growth factor signaling, cytokine and T cell receptor signaling, immune responses, ROS scavenging, proliferation, protection from apoptosis, and nutrient sensing, were activated in TGAC8; and compared to WT there was a shift from fatty acid oxidation to increased aerobic glycolysis in the context of increased utilization of the pentose phosphate shunt and nucleotide synthesis. Thus, the adaptive paradigm, that becomes activated in the LV of TGAC8 in response to severe chronic, intense AC/PKA/Ca2+ signaling embodies many hallmarks of cancer.

physiology↗

bioRxiv2022

Massive Horizontal Gene Transfer in Amphioxus Illuminates the Early Evolution of Deuterostomes

Amphioxus is considered the best-known living proxy to the chordate ancestor and an irreplaceable model organism for evolutionary studies of chordates and deuterostomes. In this study, a high-quality genome of the Beihai amphioxus, Branchiostoma belcheri beihai, was de novo assembled and annotated. Within four amphioxus genomes, twenty-eight groups of gene novelties were identified, revealing new genes that lack homologs in non-deuterostome metazoa, but share unexpectedly high similarities with those from non-metazoan species. These gene innovation events have played roles in amphioxus adaptations, including innate immunity responses, glycolysis, and regulation of calcium balance. The gene novelties related to innate immunity, such as a group of lipoxygenases and a DEAD-box helicase, boosted amphioxus immune responses. The novel genes for alcohol dehydrogenase and ferredoxin could aid in the glycolysis of amphioxus. A proximally arrayed cluster of EF-hand calcium-binding protein genes were identified to resemble those of bacteria. The copy number of this gene cluster was negatively correlated to the sea salinity of the collection region, suggesting that it may enhance their survival at different calcium concentrations. This comprehensive study collectively reveals insights into adaptive evolution of cephalochordates and provides valuable resources for research on early evolution of deuterostomes.

evolutionary biology↗

bioRxiv2022

Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimers brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

bioinformatics↗

bioRxiv2022

Monozygotic twins discordant for schizophrenia differ in maturation and synaptic transmission

Schizophrenia affects approximately 1% of the world population. Genetics, epigenetics, and environmental factors are known to play a role in this psychiatric disorder. While there is a high concordance in monozygotic twins, about half of twin pairs are discordant for schizophrenia. We characterized human-induced pluripotent stem cell (iPSC)-derived hippocampal neurons from two pairs of monozygotic twins that are discordant for a schizophrenia diagnosis. We compared the affected and the non-affected siblings and compared all of them to twin sets where none of the siblings suffered from schizophrenia. We found that the neurons derived from the schizophrenia patients were less arborized, were hypoexcitable with immature spike features, and exhibited a significant reduction in synaptic activity with dysregulation in synapse-related genes. Interestingly, the neurons derived from the co-twin siblings who did not have schizophrenia formed another distinct group that was different from the neurons in the group of the affected twin siblings but also different from the neurons in the group of the control twins. The neurons in the unaffected co-twin group were also less arborized than the neurons from controls but more arborized than those from affected siblings. Some of their spike features were immature (but less immature than neurons derived from the affected siblings). Importantly, their synaptic activity was not affected. Since schizophrenia is a genetically complex disorder, our twin study allows the measurement of neuronal phenotypes with a similar genetic background. The differences between the siblings may arise due to changes that occurred after the split of the egg into twins. Therefore, our study confirms that dysregulation of synaptic pathways, as well as changes in the rate of synaptic events, distinguishes between individuals affected with schizophrenia and unaffected individuals, even in those having a very similar genetic background.

neuroscience↗

bioRxiv2022

Fermented foods restructure gut microbiota and promote immune regulation via microbial metabolites

Fermented foods are ancient and ubiquitous, thought to be consumed in nearly every culture over the last 10,000 years and as part of the hominin diet for millions of years. A growing body of evidence supports their potential health benefits, but the mechanistic basis of their effects on the gut microbiome and host immunity remain to be elucidated. Fermented foods are diverse, each representing a complex mixture of food, microbes, and metabolites creating a significant challenge to disentangle the effects of individual components. Herein, we further define the chemical signature of individual fermented foods to categorize them based on the primary metabolic end-products of fermentation. Using mouse models, we find that fermented foods have both microbiome directed as well as differential host directed effects that correspond to their metabolite composition. Fermented food brine drink shows site-specific restructuring of the gut microbiome and promotion of tolerogenic barrier immunity; fractionation of the brine to examine the effects of the microbe-free, metabolite rich supernatant shows similar activity. Lactate, the main metabolite of lactic acid fermentation and the major metabolite within the brine drink, when administered in water, fuels a trans-kingdom metabolic network to selectively promote the growth of Akkermansia muciniphila. in the small intestine, while promoting immune tolerance via an increase in microbiota-dependent Regulatory T-cells. These findings suggest that the beneficial effects of fermented food consumption can be mediated by microbial metabolites within fermented foods, independent of microbial content, and highlight the importance of further defining the diverse chemical landscape of fermented foods to inform their potential health benefits and therapeutic use.

microbiology↗

bioRxiv2022

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Deep sea cold seep sediments host abundant and diverse bacterial and archaeal populations that significantly influence biogeochemical cycles. While numerous studies have revealed the community structure and functional capabilities of cold seep microbiomes, little is known about their genetic heterogeneity within species. Here, we examined intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 4.3 mbsf across six cold seep sites from around the world. These species were predicted to participate in methane oxidation and sulfate reduction, and based on their metabolic capabilities, grouped as aerobic methane-oxidizing bacteria (MOB), anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). These physiologically and phylogenetically diverse MOB, ANME and SRB display different degrees of intrapopulation sequence divergence and different evolutionary trajectories. Populations were in general characterized by low rates of homologous recombination and strong purifying selection with most of the nucleotide variation being synonymous. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms were found to be under strong purifying selection in the vast majority of species investigated, although examples of active positive selection were also observed. These genes differed in evolutionary trajectories across phylogenetic clades but are functionally conserved across cold seep sites. Intrapopulation diversification of MOB, ANME and SRB species as well as their mcrA and dsrA genes was observed to be depth-dependent and undergo divergent selection pressures throughout the sediment column. These results highlight the role of the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep sediments and shed light on how microbial populations adapt in the subseafloor biosphere.

microbiology↗

bioRxiv2022

Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants

The global emergence of SARS-CoV-2 variants has led to increasing breakthrough infections in vaccinated populations, calling for an urgent need to develop more effective and broad-spectrum vaccines to combat COVID-19. Here we report the preclinical development of RQ3013, an mRNA vaccine candidate intended to bring broad protection against SARS-CoV-2 variants of concern (VOCs). RQ3013, which contains pseudouridine-modified mRNAs formulated in lipid nanoparticles, encodes the spike(S) protein harboring a combination of mutations responsible for immune evasion of VOCs. Here we characterized the expressed S immunogen and evaluated the immunogenicity, efficacy, and safety of RQ3013 in various animal models. RQ3013 elicited robust immune responses in mice, hamsters, and nonhuman primates (NHP). It can induce high titers of antibodies with broad cross-neutralizing ability against the Wild-type, B.1.1.7, B.1.351, B.1.617.2, and the omicron B.1.1.529 variants. In mice and NHP, two doses of RQ3013 protected the upper and lower respiratory tract against infection by SARS-CoV-2 and its variants. We also proved the safety of RQ3013 in NHP models. Our results provided key support for the evaluation of RQ3013 in clinical trials.

immunology↗

bioRxiv2022

Highly efficient healing of critical sized articular cartilage defect in situ using a chemically nucleoside-modified mRNA-enhanced cell therapy

Critical sized cartilage defects heal poorly and MSC-based therapies holds promise functional cartilage regeneration either used alone or in combination with growth factors. However, Recombinant protein growth factors were proven to have minimal benefits while to have adverse side effects and high cost. Nonviral mRNA delivery provides a promising, alternative approach to delivering therapeutic proteins within defect lesion for an extended period of time. Despite successful therapeutic outcome in bone and other vascularized tissues, the therapeutic application of mRNA in poorly vascularized tissues such as cartilage is still facing many challenges and rarely studied. We report here using chemically modified messenger RNA encoding TGF-{beta}3(TGF-{beta}3 cmRNA) to enhance the therapeutic efficacy of BMSCs to efficient repair of cartilage defect. Local administration of TGF-{beta}3 cmRNA enhanced BMSCs therapy restored critical-sized cartilage defects in situ in a rat model within 6 weeks with structural and molecular markers similar to its nature counterparts. In addition, the development of osteoarthritis caused by cartilage damage was prevented by this mRNA-enhanced BMSCs therapy evidenced by minimal late-stage OA pharmacological presentations. This novel mRNA enhanced-MSC technology extend the development of new therapeutic approaches for treating functional cartilage repair.

synthetic biology↗

bioRxiv2022

Identification of key molecules and biological processes in TCF21 treated tumor pericytes

Colorectal cancer has become a major public health problem in the US. Transcription factor 21 (TCF21) is reported to be silenced in colorectal cancer tissues. However, the mechanism of TCF21 in tumor pericytes is still unclear. In our study, we aim to identify the key biological processes and signaling pathways by analyzing the RNA-seq data. The GSE200064 was produced by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses showed that MAPK signaling pathway and complement/coagulation cascades are the major changed signaling pathways in the progression of tumor pericytes with overexpression of TCF21. Moreover, we identified several interactive molecules including VEGFA, MMP2, CCL2, COL3A1, COL1A2, CXCL12, ELN, PDGFRB, VWF, and APOE. These findings may benefit the study of colorectal cancer treatment.

bioinformatics↗

bioRxiv2022

Nrf1 is an indispensable redox-determining factor for mitochondrial homeostasis by integrating multi-hierarchical regulatory networks

To defend a vast variety of challenges in the oxygenated environments, all life forms have been evolutionally established a set of antioxidant, detoxification and cytoprotective systems during natural selection and adaptive survival, in order to maintain cell redox homeostasis and organ integrity in the healthy development and growth. Such antioxidant defense systems are predominantly regulated by two key transcription factors Nrf1 and Nrf2, but the underlying mechanism(s) for their coordinated redox control remains elusive. Here, we found that loss of full-length Nrf1 led to a dramatic increase in reactive oxygen species (ROS) and oxidative damages in Nrf1-/- cells, and this increase was not eliminated by drastic elevation of Nrf2, even though the antioxidant systems were also substantially enhanced by hyperactive Nrf2. Further studies revealed that the increased ROS production in Nrf1-/- resulted from a striking impairment in the mitochondrial oxidative respiratory chain and its gene expression regulated by nuclear respiratory factors, called PalNRF1 and GABPNRF2. In addition to antioxidant capacity of cells, glycolysis was greatly augmented by aberrantly-elevated Nrf2, so to partially relieve the cellular energy demands, but aggravate its mitochondrial stress. The generation of ROS was also differentially regulated by Nrf1 and Nrf2 through miR-195 and/or mIR-497-mediated UCP2 pathway. Consequently, the epithelial-mesenchymal transformation (EMT) of Nrf1-/- cells was activated by putative ROS-stimulated signaling via MAPK, HIF1, NF-kB, PI3K and AKT, all players involved in cancer development and progression. Taken together, it is inferable that Nrf1 acts as a potent integrator of redox regulation by multi-hierarchical networks.

molecular biology↗

bioRxiv2022

Mapping the T cell repertoire to a complex gut bacterial community

Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response1-5. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with a complex defined community (97 or 112 bacterial strains) and profile T cell responses to each strain individually. Unexpectedly, the pattern of T cell responses suggests that many T cells in the gut repertoire recognize multiple bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all of the bacteria-specific TCRs exhibit a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that are polyspecific for 18 Firmicutes in the community. By screening three pooled bacterial genomic libraries against 13 pooled hybridomas, we discover that they share a single target: a conserved substrate-binding protein (SBP) from an ABC transport system. Treg and Th17 cells specific for an epitope from this protein are abundant in community-colonized and specific-pathogen-free mice. Our work reveals that T cell recognition of Firmicutes is focused on a widely conserved cell-surface antigen, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.

immunology↗

bioRxiv2022

Genomic analyses identify significant biological processes in DDX21-mediated colorectal cancer cells

Colorectal cancer is the third most common cancer in the US. There has been an incline in the number of young patients with colorectal cancer due to unclear reasons at this point in time. Currently, DEAD-box RNA helicase protein DDX21 is identified as a prognosis marker for early-stage colorectal cancer. However, the mechanism of DDX21 mediated-colorectal cancer is still unknown. Here, our objective is to determine the key molecules and signaling by analyzing the RNA-seq data. The GSE184726 was created by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses indicated Neuroactive ligand-receptor interaction and Ras signaling pathway were the key signaling pathways during the knockdown of DDX21 in colorectal cancer. Moreover, we identified several interactive genes including PTPRC, FN1, ITGAM, RAD51, TRAF6, CCNB1, FOXP3, CCNA2, HIST2H2AC, and HSPA5. Our study may provide new insights into the treatment of colorectal cancer.

bioinformatics↗