Biology subjects

Chen, M.

Publications and source records attributed to Chen, M..

At least 361 records · Page 20Linked to original sources

bioRxiv2022

A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing

As part of the Human Cell Atlas initiative, we generated transcriptomic (scRNA-seq; 86,708 cells) and regulatory (scATAC-seq; 59,118 cells) profiles of the normal postmenopausal ovary and fallopian tube (FT) at single-cell resolution. In the FT, 22 cell clusters integrated into 11 cell types, including ciliated and secretory epithelial cells, while the ovary had 17 distinct cell clusters defining 6 major cell types. The dominant cell type in both the postmenopausal ovary and FT was stromal cells, which expressed several genes associated with aging. The fimbrial end of the FT had a significant number and variety of immune cells and active communication with the ovary; the ovary contained mostly stromal cells but few immune cells. The epithelial cells of the normal FT expressed multiple ovarian cancer risk-associated genes (CCDC170, RND3, TACC2, STK33, and ADGB). By integrating paired single-cell transcriptomics and chromatin accessibility data we found that the regulatory landscape of the fimbriae was markedly different from the isthmus and ampulla. Intriguingly, several cell types in the FT had comparable gene expression but different transcriptional regulations. Our single-cell transcriptional and regulatory maps allowed us to disentangle the complex cellular makeup of the postmenopausal FT and ovary and will contribute to a better understanding of gynecologic diseases in menopause.

genomics↗

bioRxiv2022

A multispecific antibody confers pan-reactive SARS-CoV-2 neutralization and prevents immune escape

Summary ParagraphDespite effective countermeasures, SARS-CoV-2 persists worldwide due to its ability to diversify and evade human immunity1. This evasion stems from amino-acid substitutions, particularly in the receptor-binding domain of the spike, that confer resistance to vaccines and antibodies 2-16. To constrain viral escape through resistance mutations, we combined antibody variable regions that recognize different receptor binding domain (RBD) sites17,18 into multispecific antibodies. Here, we describe multispecific antibodies, including a trispecific that prevented virus escape >3000-fold more potently than the most effective clinical antibody or mixtures of the parental antibodies. Despite being generated before the evolution of Omicron, this trispecific antibody potently neutralized all previous variants of concern and major Omicron variants, including the most recent BA.4/BA.5 strains at nanomolar concentrations. Negative stain electron microscopy revealed that synergistic neutralization was achieved by engaging different epitopes in specific orientations that facilitated inter-spike binding. An optimized trispecific antibody also protected Syrian hamsters against Omicron variants BA.1, BA.2 and BA.5, each of which uses different amino acid substitutions to mediate escape from therapeutic antibodies. Such multispecific antibodies decrease the likelihood of SARS-CoV-2 escape, simplify treatment, and maximize coverage, providing a strategy for universal antibody therapies that could help eliminate pandemic spread for this and other pathogens.

immunology↗

bioRxiv2022

Comparative analyses of the N-glycoproteomes in HCT116 cancer cells and their non-tumorigenic DNMT1/3b double knockout (DKO1) cells and insight into the Mannose-6-phosphate pathway

N-glycoproteomic analyses provide valuable resources for investigation of cancer mechanisms, biomarkers, and therapeutic targets. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 display hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells.

biochemistry↗

bioRxiv2022

Growth mindset promotes children's working memory performance through cortico-striatal interaction and fronto-parietal activation

Growth mindset--the belief that abilities are malleable through effort--drives motivation, action and achievement. Yet, the underlying mechanisms remain elusive, necessitating a unified framework that integrates cognitive, neural, and developmental processes. Leveraging longitudinal neuroimaging and computational modeling to reveal moment-to-moment decision responses and brain state dynamics during working memory (WM), we show that growth mindset enhances WM development from middle childhood to adolescence via nuanced cortico-striatal network dynamics that balance between brain state flexibility and stability. Behaviorally, children with higher growth mindset exhibited better WM performance both cross-sectionally and longitudinally, attributed to faster evidence accumulation during moment-to-moment information updating, especially under high task demands. Neurally, a higher growth mindset was associated with greater activation of the dorsal striatum, cingulo-opercular (action-mode), and fronto-parietal networks during WM, which further accounted for longitudinal WM improvement and latent evidence accumulation. Such cortico-striatal activation covaried with neurochemical mediators critical for motivation and executive functioning. Analyzing non-stationary network dynamics revealed that growth mindset optimized dynamical organization of cortico-striatal networks, with an activated state highly flexible to support moment-to-moment information updating and a deactivated state remaining stable across blocks to suppress irrelevant information. This suggests a balanced allocation of resources for accumulating evidence while suppressing noise during WM. Together, our findings support a neurocognitive framework in which growth mindset enhances WM development via nuanced orchestration of cortico-striatal networks to enable efficient dynamic computations and foster far-reaching cognitive development.

neuroscience↗

bioRxiv2022

Using polygenic risk score about complex traits to predict production performance in crossbreeding of yeast

The cultivation of hybrids with favorable complex traits is one of the important goals for animal, plant, and microbial breeding practices. A method that can well predict the production performance of hybrids will be of great significance to the whole research and practice. In our study, polygenic risk scores (PRS) were introduced to estimate the production performance of Saccharomyces Cerevisiae. The genetic variation of 971 published isolates and their growth ratios under 35 medium conditions were analyzed by genome-wide association analysis, and the precise p-value threshold for each phenotype was calculated. Risk markers for the above 35 phenotypes were obtained. By estimating genotype of F1 hybrids according to that of the parents, the PRS of 613 F1 hybrids was predicted. There was a significant linear correlation between YPD40 and PRS in F1 and their parents (R2=0.2582, R2=0.2414, respectively), which indicates that PRS can be used to estimate the production performance of individuals and their hybrids. Our method can provide a reference for strains selection and F1 prediction in yeasts cross-breeding, reduce the workload and improve the work efficiency.

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

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

Plants often generate secondary metabolites as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier of antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocalgates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a translation initiation factor (eIF). De novo transcriptome assembly revealed that the fungus belongs to Ophiocordyceps genus and its eIF4A, a molecular target of rocaglates, contains a amino acid substitution critical for rocaglate binding. Ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered Colletotrichum orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.

molecular biology↗

bioRxiv2022

PhysiCell training apps: Cloud hosted open-source apps to learn cell-based simulation software

Cell-based tissue simulations require not only the ability to write new code in a simulation framework, but also an understanding of underlying mathematical models, background biology, and parameters for each behavior of an agent. This can entail a steep learning curve for interdisciplinary researchers joining computational biology research. We have created a suite of cloud-hosted open-source tools to separately explore and learn key components of an agent-based cellular simulation framework. This creates an self-contained environment to learn and test functions of cells and the micro-environment in a modular fashion before creating more detailed, research-focused simulation models.

systems biology↗

bioRxiv2022

High-Coverage Four-Dimensional Data-Independent Acquisition Proteomics and Phosphoproteomics Enabled by Deep Learning-Driven Multi-Dimensional Prediction

Four-dimensional (4D) data-independent acquisition (DIA)-based proteomics is an emerging technology that has been proven to have high precursor ion sampling efficiency and higher precursor identification specificity. However, the current 4D DIA proteomics is still dependent on the building of project-specific experimental library which is time-consuming and limits the coverage for identification/quantification. Herein, a workflow of 4D DIA proteomics by using the predicted multi-dimensional in silico library was established. A deep learning model Deep4D that could high-accurately predict the CCS and RT of both the unmodified and phosphorylated peptides was developed. By using an integrated 4D in silico library containing millions of peptides, we have identified 25% more protein than using experimental libraries in the DIA proteomics analysis of HeLa cells. We further demonstrate that the introduction of in silico prediction library can greatly complement the experimental library of directly obtained phosphorylated peptides, resulting in a greater increase in the identification of phosphorylated peptides and phosphorylated proteins.

bioinformatics↗

bioRxiv2022

Transcriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation

The thermotolerant yeast Kluyveromyces marxianus has great potential for high-temperature ethanol fermentation, but it produces excess acetic acid during high-temperature fermentation, which inhibits ethanol production. The mechanisms of K. marxianuss responses to acetic acid have not been fully understood. In this study, the transcriptomic changes of K. marxianus DMKU3-1042 resulted from acetic acid stress during high-temperature ethanol fermentation were investigated based on high-throughput RNA sequencing. We identified 611 differentially expressed genes (DEGs) under acetic acid stress (fold change > 2 or < 0.5, P-adjust <0.05), with 166 up-regulated and 445 down-regulated. GO terms and pathways enriched in these DEGs were identified. Protein-protein interaction (PPI) networks were constructed based on the interactions between proteins coded by the DEGs, and hub genes and key modules in the PPI networks were identified. The results in this study indicated that during high-temperature fermentation, acetic acid stress promoted protein catabolism but repressed protein synthesis, which affected the growth and metabolism of K. marxianus and led to the decrease of ethanol production. The findings in this study provide a better understanding of the response mechanism of K. marxianus to acetic acid stress, and provide a basis for subsequent increase of ethanol production by K. marxianus.

microbiology↗

bioRxiv2022

Nature's design of the osteochondral unit: microstructural differences between terrestrial and aquatic mammals

During evolution, animals have returned from land to water, adapting with morphological modifications to life in an aquatic environment. We compared the osteochondral units of the humeral head of marine and terrestrial mammals across species spanning a wide range of body weights, focusing on microstructural organization and biomechanical performance. Aquatic mammals feature cartilage with essentially random collagen fiber configuration, lacking the depth-dependent, arcade-like organization characteristic of terrestrial mammalian species. They have a less stiff articular cartilage at equilibrium with a significantly lower peak modulus, and at the osteochondral interface do not have a calcified cartilage layer, displaying only a thin, highly porous subchondral bone plate. This totally different constitution of the osteochondral unit in aquatic mammals reflects that accommodation of loading is the primordial function of the osteochondral unit. Recognizing the crucial importance of the microarchitecture-function relationship is pivotal for understanding articular biology and, hence, for the development of durable functional regenerative approaches for treatment of joint damage, which are thus far lacking.

evolutionary biology↗

bioRxiv2022

Structural dynamics underlying gating and regulation in IP3R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP in IP3R1, revealing conformational changes that couple ligand-binding to channel opening. Using a GMM based deep learning approach and 3D variability analysis, we extracted dynamic properties of the key protein domains. From this, we find that IP3 binding relies upon intrinsic flexibility of the cytoplasmic ARM2 domain. Our results highlight a key role of dynamic side chains surrounding the ion conduction path in regulating gating behavior of IP3R channels. Altogether, this work defines a structural platform for mechanistic understanding of the molecular dynamics underlying ligand-binding, activation and regulation of the IP3R activity.

biophysics↗

bioRxiv2022

Ratiometric NAD+ sensors reveal subcellular NAD+ modulators

Mapping NAD+ dynamics in live cells and human are essential for translating NAD+ interventions into effective therapies. Yet genetically encoded NAD+ sensors with better specificity and pH-resistance are still needed for cost-effective monitoring of subcellular and clinical NAD+. We introduce multicolor, resonance energy transfer-based NAD+ sensors that cover nano- to milli-molar concentration ranges for clinical NAD+ measurement and subcellular NAD+ visualization. The sensors captured the blood NAD+ increase induced by NMN supplementation and revealed the distinct subcellular effects of NAD+ supplements and modulators. Then, the sensors enabled high-throughput screenings for mitochondrial and nucleic NAD+ modulators and identified -GPC, a cognition-related metabolite, induces NAD+ redistribution from mitochondria to nucleus relative to the total adenine nucleotides, which was confirmed by NAD+ FRET microscopy.

bioengineering↗

bioRxiv2022

Metformin decreases Cyp26a1 to prevent hepatocarcinogenesis through down- regulating CD8+ T cells

Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer, which limits the selectivity of prevention and treatment. Preclinical and clinical studies suggested that in patients with diabetes, prolonged use of metformin, the AMPK activator, was associated with a reduction of HCC incidence. This association promotes us to investigate the possible functions and mechanisms of metformin in HCC without diabetes backgrounds. Here, we found that several unique pathways that changed during chronic liver injury of Fah-/- mice, including glucose metabolic process and retinol metabolism. Further, metformin suppressed the tumor formation in chronic liver injury of Fah-/- mice. RNA sequencing, in vivo and in vitro experiments showed that metformin suppressed Cyp26a1 gene expression of hepatocyte. Moreover, the down-regulation of Cyp26a1 leads to the increased level of all-trans-retinoic acid (atRA), which could suppress the tumor formation in our model. On the other hand, flow multicolor analysis showed that the cell number and proportion of cancer promoting (pro-tumor) CD8+ T cells increased significantly during chronic liver injury in Fah-/- mice, and both metformin and atRA treatment could reduce the number and proportion of pro-tumor CD8+ T cells. We also found metformin decreased the Cyp26a1 expression through the AMPK/JNK/c-Jun pathway. In short, the association between the metformin and atRA may explain the commonness of their anti-tumor activities. Our findings highlight the importance of targeting the precancerous microenvironment for the prognosis, prevention and treatment of HCC.

cancer biology↗

bioRxiv2022

Broadly neutralizing antibodies target the coronavirus fusion peptide

The potential for future coronavirus outbreaks highlights the need to develop strategies and tools to broadly target this group of pathogens. Here, using an epitope-agnostic approach, we identified six monoclonal antibodies that bound to spike proteins from all seven human-infecting coronaviruses. Epitope mapping revealed that all six antibodies target the conserved fusion peptide region adjacent to the S2 cleavage site. Two antibodies, COV44-62 and COV44-79, broadly neutralize a range of alpha and beta coronaviruses, including SARS-CoV-2 Omicron subvariants BA.1 and BA.2, albeit with lower potency than RBD-specific antibodies. In crystal structures of Fabs COV44-62 and COV44-79 with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine at the S2 cleavage site. Importantly, COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings identify the fusion peptide as the target of the broadest neutralizing antibodies in an epitope-agnostic screen, highlighting this site as a candidate for next-generation coronavirus vaccine development. One-Sentence SummaryRare monoclonal antibodies from COVID-19 convalescent individuals broadly neutralize coronaviruses by targeting the fusion peptide.

immunology↗

bioRxiv2022

Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants

SARS-CoV-2 infection of the upper airway and the subsequent immune response are early, critical factors in COVID-19 pathogenesis. By studying infection of human biopsies in vitro and in a hamster model in vivo, we demonstrated a transition in tropism from olfactory to respiratory epithelium as the virus evolved. Analyzing each variants revealed that SARS-CoV-2 WA1 or Delta infects a proportion of olfactory neurons in addition to the primary target sustentacular cells. The Delta variant possesses broader cellular invasion capacity into the submucosa, while Omicron displays longer retention in the sinonasal epithelium. The olfactory neuronal infection by WA1 and the subsequent olfactory bulb transport via axon is more pronounced in younger hosts. In addition, the observed viral clearance delay and phagocytic dysfunction in aged olfactory mucosa is accompanied by a decline of phagocytosis related genes. Furthermore, robust basal stem cell activation contributes to neuroepithelial regeneration and restores ACE2 expression post-infection. Together, our study characterized the nasal tropism of SARS-CoV-2 strains, immune clearance, and regeneration post infection. The shifting characteristics of viral infection at the airway portal provides insight into the variability of COVID-19 clinical features and may suggest differing strategies for early local intervention.

pathology↗

bioRxiv2022

Molecular Architecture of the Chikungunya Virus Replication Complex

All positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) for viral RNA synthesis in virus-infected cells. However, how these multi-component RCs assemble and function in synthesizing, processing, and transporting viral RNAs to the cytosol remains poorly defined. Here, we determined both the structure of the core RNA replicase of chikungunya virus (family Togaviridae) at a near-atomic level and the native RC architecture in its cellular context at the subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase (nsP1+2+4), the viral RNA-dependent RNA polymerase nsP4, in complex with nsP2 helicase-protease, was found to co-fold with the membrane-anchored nsP1 RNA-capping dodecameric ring and is located asymmetrically within nsP1 central pore. This complex forms the minimal core RNA replicase, while the addition of a large cytoplasmic ring next to the C-terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses. At last, our study will direct the needed development of antiviral therapies targeting RCs of pathogenic viruses. SummaryCryoEM structure of the chikungunya virus replication complex reveals a multicomponent RNA synthesis nanomachine embedded in the plasma membrane of the host cell.

microbiology↗

bioRxiv2022

Genomic legacies of ancient adaptation illuminate the GC-content evolution in bacterial genomes

In conventional views, the bacterial adaptation is characterized by strong purifying selection as well as rapid evolution in changing environments. However, the genomic GC content varies greatly but has some degree of phylogenetic stability. Using 11,083 representative genomes, we report a phylogenetically constrained bimodal distribution of the genomic GC. Results suggest that such divergence of the genomic GC can be well explained by the DNA replication and repair (DRR) system, in which multiple pathways are observed correlated to the genomic GC. The biased conservations of various stress-related genes especially the DRR-related ones imply distinct adaptive evolution of the ancestral lineages of high or low GC clades which may be induced by major environmental changes in early evolution. Furthermore, our findings support that the mutational biases resulted from these legacies of adaptation have changed the course of adaptive evolution in bacteria thus causing great variation in the genomic GC. This study demonstrates the importance of indirect effects from natural selection which may be easily misinterpreted as neutral processes.

evolutionary biology↗