Biology subjects

Fu, C.

Publications and source records attributed to Fu, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Cortical ductility governs cell-cell adhesion mechanics

This paper challenges our understanding of cell-cell adhesion by emphasising the role of mechanical dissipation at the cellular level. We have developed new microdevices to measure the energy dissipated during the rupture of junctions between cell-cell doublets. Using a synthetic cadherin approach, we decoupled the role of cadherin binding energy, signalling and downstream regulation of cytoskeletal architecture. This yielded a phase diagram in which cell junctions transition from a ductile to a brittle fracture mode based on their ratio of cortical tension and shape relaxation time. We recapitulated our results using a descriptive mechanical simulation approach. Our results shift our understanding of cell-cell adhesion from the current focus on bond energy and tension to the key role played by energy dissipation in the cytoskeleton during junction deformation and its active mechanosensitive regulation.

cell biology↗

bioRxiv2023

Multimodal single cell-resolved spatial proteomics reveals pancreatic tumor heterogeneity

Despite the advances in antibody-guided cell typing and mass spectrometry-based proteomics, their integration is hindered by challenges for processing rare cells in the heterogeneous tissue context. Here, we introduce Spatial and Cell-type Proteomics (SCPro), which combines multiplexed imaging and flow cytometry with ion exchange-based protein aggregation capture technology to characterize spatial proteome heterogeneity with single cell resolution. The SCPro was employed to explore the pancreatic tumor microenvironment and revealed the spatial alternations of over 5,000 proteins by automatically dissecting up to 100 single cells guided by multi-color imaging of centimeter-scale formalin-fixed, paraffin-embedded tissue slide. To enhance cell-type resolution, we characterized the proteome of 14 different cell types by sorting up to 1,000 cells from the same tumor, which allows us to deconvolute the spatial distribution of immune cell subtypes and leads to the discovery of a novel subtype of regulatory T cells. Together, the SCPro provides a multimodal spatial proteomics approach for profiling tissue proteome heterogeneity.

systems biology↗

bioRxiv2023

Kin selection underpins family dynamics in rural China

The number of co-resident members is an important characteristic of human families and thus plays an important role in human evolution. However, an inclusive fitness model of how many members should co-reside has not been explicitly tested. Here we use an evolutionary game model and a decade of family dynamic data from a rural population of southwestern China (1,110 households) to show that the existence of an evolutionary stable family size can be understood by considering the average local relatedness and average inclusive fitness of the family. Empirical data analyses show that average relatedness [Formula] decreased with increasing family size, and [Formula] was associated with helping behavior (especially for the elders) in the family, so the family tended to keep a higher level of average relatedness by adjusting the number of co-resident members. These findings are helpful to understand the variation in family size in different cultures and to demonstrate the importance of kin selection in regulating family dynamics.

evolutionary biology↗

bioRxiv2023

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form "super-silencers" and whether they are linked to cancer progression. Here, through interrogating two putative silencer components of FGF18 gene, we found that two nearby silencers can cooperate via compensatory chromatin interactions to form a "super-silencer". Furthermore, double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes of cell identity. To perturb the "super-silencers", we applied combinational treatment of an EZH2 inhibitor GSK343, and a REST inhibitor, X5050 ("GR"). We found that GR led to severe loss of TADs and loops, while the use of one inhibitor by itself only showed mild changes. Such changes in TADs and loops were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GSK343 and X5050 synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects both in vitro and in vivo. Overall, our data demonstrated the first example of a "super-silencer" and showed that combinational usage of GSK343 and X5050 to disrupt "super-silencers" could potentially lead to cancer ablation.

molecular biology↗

bioRxiv2023

Fully automated and integrated proteomics sample preparation platform for high-throughput drug target identification

With the increased demand of large-cohort proteomic analysis, fast and reproducible sample preparation has become the critical issue that needs to be solved. Herein, we developed a fully automated and integrated proteomics sample preparation workflow (autoSISPROT), enabling the simultaneous processing of 96 samples in less than 2.5 hours. Benefiting from its 96-channel all-in-tip operation, protein digestion, peptide desalting, and TMT labeling could be achieved in a fully automated manner. The autoSISPROT demonstrated good sample preparation performances, including >94% of digestion efficiency, nearly 100% of alkylation efficiency, >98% of TMT labeling efficiency, and >0.9 of intra- and inter-batch Pearson correlation coefficients. Furthermore, by combining with cellular thermal shift assay-coupled to mass spectrometry (CETSA-MS), the autoSISPROT was able to process and TMT-label 40 samples automatically and accurately identify the known target of methotrexate. Importantly, taking advantage of the data independent acquisition and isothermal CETSA-MS, the autoSISPROT was well applied for identifying known targets and potential off-targets of 20 kinase inhibitors by automatedly processing 87 samples, affording over a 10-fold improvement in throughput when compared to classical CETSA-MS. Collectively, we developed a fully automated and integrated workflow for high-throughput proteomics sample preparation and drug target identification.

systems biology↗

bioRxiv2023

A KDELR-mediated ER retrieval system guides the signaling pathways of UPR and AMPK to maintain cellular homeostasis

KDELR (Erd2 in yeasts) mediates the retrieval of ER-resident proteins from the Golgi apparatus, yet how the KDELR-mediated ER retrieval system is involved in regulating cellular homeostasis has been unclear. Here we report that the loss of the Erd2-mediated ER retrieval system induces the unfolded protein response (UPR) and increases mitochondrial respiration and reactive oxygen species (ROS) in an UPR-dependent manner. Moreover, transcriptomic analysis revealed that expression of the genes involved in mitochondrial respiration and the tricarboxylic acid cycle is enhanced in an UPR-dependent manner in cells lacking Erd2. In cells lacking Erd2, the enhancement of mitochondrial respiration and ROS is required for maintaining cell viability. The loss of the Erd2-mediated ER retrieval system also activates AMPK, and consequently derepresses carbon catabolite repression. Hence, our work establishes a role of the KDELR/Erd2-mediated ER retrieval system in guiding the signalling pathways of AMPK and UPR and underscores the crucial role of the KDELR/Erd2-mediated ER retrieval system in the maintenance of cellular homeostasis.

cell biology↗

bioRxiv2023

A modular metagenomics analysis system for integrated multi-step data exploration

MotivationComputational analysis of large-scale metagenomics sequencing datasets have proven to be both incredibly valuable for extracting isolate-level taxonomic, and functional insights from complex microbial communities. However, due to an ever-expanding ecosystem of metagenomics-specific methods and file-formats, designing seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. One-click bioinformatics pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues, and preclude replication. MethodsTo address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed a module-based metagenomics analysis system "Core Analysis Modular Pipeline" (CAMP), written in Snakemake, a popular workflow management system, along with a standardized module and working directory architecture. Each module can be run independently or conjointly with a series of others to produce the target data format (e.g. short-read preprocessing alone, or short-read preprocessing followed by de novo assembly), and outputs aggregated summary statistics reports and semi-guided Jupyter notebook-based visualizations. ResultsWe have applied CAMP to a set of ten metagenomics samples to demonstrate how a modular analysis system with built-in data visualization at intermediate steps facilitates rich and seamless inter-communication between output data from different analytic purposes. AvailabilityThe CAMP ecosystem (module template and analysis modules) can be found https://github.com/Meta-CAMP.

bioinformatics↗

bioRxiv2023

Step-wise mechanical unfolding and dissociation of the GAIN domains of ADGRG1/GPR56, ADGRL1/Latrophilin-1 and ADGRB3/BAI3: insights into the mechanical activation hypothesis of adhesion G protein-coupled receptors

Adhesion G protein-coupled receptors (aGPCRs) are a large family within the superfamily of G protein-coupled receptors involved in various physiological processes. One unique feature of aGPCRs is their long N-terminal extracellular regions (ECRs), which contain adhesive domains and a GPCR autoproteolysis-inducing (GAIN) domain. This GAIN domain promotes autoproteolytic cleavage of aGPCRs into N- and C-terminal fragments (NTF, CTF, respectively) after receptor biosynthesis. aGPCR signaling involves an interplay between the NTF and CTF that can be me-chanically activated or modulated. However, how force affects the conformation/structure of the GAIN domain as a central structural element in aGPCR activation remains largely unknown. In this study, we investigated the mechanical stability of the GAIN domains of three aGPCRs from subfamilies B, G and L at a loading rate of 1 pN/s. Our findings demonstrate that the GAIN domains can be destabilized by forces from a few to 20 piconewtons (pN). Specifically, for the autocleaved aGPCRs, ADGRG1/GPR56 and ADGRL1/Latrophilin-1, forces over this range can cause detachment of the GAIN domain from the membrane-proximal Stachel element, which serves as an endogenous tethered agonist to aGPCRs, typically preceded with GAIN domain unfolding. For the non-cleavable aGPCR ADGRB3/BAI3, the GAIN domain undergoes complex mechanical unfolding over a similar force range. We also demonstrate that detachment of the GAIN domain can take place during cell migration, provided that the linkage between aGPCR and extracellular matrix is sufficiently stable. These results suggest that both structural stability of the GAIN domain and NTF/CTF dissociation are sensitive to physiological ranges of tensile forces, providing insights into the mechanical activation hypothesis of aGPCRs.

biophysics↗

bioRxiv2023

Proliferating cell nuclear antigen involves in temperature stress tolerance of Ulva prolifera

Ulva prolifera is the dominant species of "green tide", and has higher tolerance to environmental stresses such as temperature. However, the molecular mechanisms are still unclear. Here, transcriptome analysis, Western blot and RT-qPCR analysis of U. prolifera suggested that, under temperature stresses (4{degrees}C, 36{degrees}C), the expression of PCNA and CyclinA was promoted, and the MAPK signaling was activated. Besides, the results showed that PCNA interacted with CyclinA. Interestingly, the expression of miR-2916, which was predicted to bind PCNA at -552[~]-772, was negatively correlated with the expression of PCNA under temperature stresses (4{degrees}C, 36{degrees}C). In addition, the results showed that low temperature (4{degrees}C) had no obvious effect on the survival, the formation of cell walls, and the division of protoplasts. However, high temperature (36{degrees}C) had obvious effect on them. PCNA inhibitors increased the sensitivity of the protoplasts under temperature stresses. Together, our results suggested PCNA regulating the proliferation in response to the temperature stress of U. prolifera was associated with miR-2916/PCNA/CyclinA/MAPK pathway. In conclusion, the study preliminarily illuminates the molecular mechanism in response to temperature stress of U. prolifera, and may provide a new insight for prevention of green tide.

cell biology↗

bioRxiv2023

Crystal structure of a mammalian CMTM6 and its interaction model with PD-L1

CKLF-like MARVEL transmembrane domain-containing protein 6 (CMTM6) is a master regulator of PD-L1. By binding PD-L1 at the plasma membrane and recycling endosomes, CMTM6 prevents the lysosomal degradation of PD-L1 and maintains its cell surface expression, thus stabilizing the inhibitory PD-1/PD-L1 axis. However, the mechanism of CMTM6/PD-L1 interaction is unknown. Here we report the first experimentally determined structure of CMTM6 from bovine. Combined with a low-resolution cryo-EM map, computational docking analysis and a protein binding assay an interaction model between CMTM6 and PD-L1 was proposed, providing a structural framework for the CMTM6 regulation on PD-L1.

biophysics↗

bioRxiv2022

Cell dichotomous role of STING in pulmonary hypertension

RationalePatients with constitutive activation of DNA sensing pathway through stimulator of interferon genes (STING), such as those with STING-Associated Vasculopathy with onset in Infancy (SAVI), frequently have complications related to pulmonary hypertension (PH). However, the role of STING-signaling in adult PH patients is heretofore undescribed. ObjectiveTo investigate the role of STING in PH development. Methods and ResultsPH was induced in global STING deficient or cell-specific STING deficient mice using either bleomycin or chronic hypoxia exposure. PH development was evaluated with right ventricular systolic pressure, Fulton index, histological and flow cytometric measurements. STING expression in patient lungs were examined using both immunohistochemistry and flow cytometry. Herein, we describe how STING overactivation in a SAVI mouse model results in a baseline elevation in pulmonary pressures, while global STING deficiency protects mice from PH development. Furthermore, STING-associated PH appears to be independent of type I Interferon (IFN) signaling. We further demonstrate a cellular dichotomous role of STING in PH development with STING expression by smooth muscle cells contributing to PH, and its activation on myeloid cells being pivotal in severe disease prevention. Finally, we demonstrate a STING-PD-L1 axis as necessary for disease progression, suggesting future potential therapeutic applications. ConclusionsOverall, these data provide concrete evidence of STING involvement in PH, establishing biologic plausibility for STING-related therapies in PH treatment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/518422v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7f5b50org.highwire.dtl.DTLVardef@143e485org.highwire.dtl.DTLVardef@4fe1a4org.highwire.dtl.DTLVardef@66fe26_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

Bursts in biosynthetic gene cluster transcription are accompanied by surges of natural compound production in the myxobacterium Sorangium sp.

We have investigated the time course of genome-wide transcription in the myxobacterium Sorangium sp. So ce836 in relation to its production of natural compounds. Time-resolved RNA sequencing revealed that core biosynthesis genes from 48 biosynthetic gene clusters (BGCs; 92% of all BGCs encoded in the genome) were actively transcribed at specific time points in a batch culture. The majority (80%) of polyketide synthase and non-ribosomal peptide synthetase genes displayed distinct peaks of transcription during exponential bacterial growth. Strikingly, these bursts in BGC transcriptional activity were associated with surges in the production of known natural compounds, indicating that their biosynthesis was critially regulated at the transcriptional level. In contrast, BGC read counts from single time points had limited predictive value about biosynthetic activity, since transcription levels varied >100-fold among BGCs with detected natural products. Taken together, our time-course data provide unique insights into the dynamics of natural compound biosynthesis and its regulation in a wild-type myxobacterium, challenging the commonly cited notion of preferential BGC expression under nutrient-limited conditions. The close association observed between BGC transcription and compound production warrants additional efforts to develop genetic engineering tools for myxobacterial producer strains, to boost compound yields by manipulating transcriptional activity.

genomics↗

bioRxiv2022

Insights into the biosynthesis of icumazole unveiling a distinctive family of crotonyl-CoA carboxylase/reductase

Icumazoles are potent antifungal polyketides with intriguing structural features. Here, we present the polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) hybrid biosynthetic gene cluster of icumazoles. Surprisingly, an unusual non-terminal thioesterase domain divides the PKS/NRPS assembly line. The succeeding PKS modules potentially form a rare precursor 4-methyl-2-hexenoyl-ACP thus deviating from the previously proposed polyoxypeptin pathway. The 4-methyl-2-hexenoyl-ACP is further reductive carboxylated to 2-methylbutylmalonyl-ACP essential for icumazole biosynthesis by IcuL, representing a new type of crotonyl-CoA carboxylase/reductase (CCR). We characterize IcuL and its homologs TgaD and Leu10 in vitro, suggesting a stricter substrate specificity of this new family of CCRs than found in canonical ones. Intriguingly, we also find that TgaD unprecedently utilizes both NADPH and NADH as cofactors with similar efficiency, diverging from the NADPH-specific characteristic of canonical CCRs. Furthermore, a sequence similarity network-based bioinformatic survey reveals that the IcuL-like CCRs are evolutionarily separated from canonical CCRs.

biochemistry↗

bioRxiv2022

A ZTF-7/RPS-2 complex mediates the cold-warm response in C. elegans

Temperature greatly affects numerous biological processes in all organisms. How multicellular organisms respond to and are impacted by hypothermic stress remains elusive. Here, we found that cold-warm stimuli induced depletion of the RNA exosome complex in the nucleoli but enriched it in the nucleoplasm. To further understand the function and mechanism of cold-warm stimuli, we conducted forward genetic screening and identified ZTF-7, which is required for RNA exosome depletion from nucleoli upon transient cold-warm exposure in C. elegans. ZTF-7 is a putative ortholog of human ZNF277 that may contribute to language impairments. Immunoprecipitation followed by mass spectrometry (IP-MS) found that ZTF-7 interacted with RPS-2, which is a ribosomal protein of the small subunit and participates in pre-rRNA processing. A partial depletion of RPS-2 and other proteins of the small ribosomal subunit blocked the cold-warm stimuli-induced reduction of exosome subunits from the nucleoli. These results established a novel mechanism by which C. elegans responds to environmental cold-warm exposure.

genetics↗

bioRxiv2022

The role of proton in a eukaryotic zinc transporter

Zinc transporter 8 (ZnT8) is mainly expressed in pancreatic islet {beta} cells and is responsible for H+-coupled uptake (antiport) of Zn2+ into the lumen of insulin secretory granules. Structures of human ZnT8 and its prokaryotic homolog YiiP have provided structural basis for constructing a plausible transport cycle for Zn2+. However, the mechanistic role that protons play in the transport process remains unclear. Here we present a lumen-facing cryo-EM structure of ZnT8 from Xenopus tropicalis (xtZnT8) in the presence of Zn2+ at a luminal pH (5.5). Compared to a Zn2+-bound xtZnT8 structure at a cytosolic pH (7.5), the low-pH structure displays an empty transmembrane Zn2+-binding site with a disrupted coordination geometry. Combined with a Zn2+-binding assay our data suggest that protons may disrupt Zn2+ coordination at the transmembrane Zn2+-binding site in the lumen-facing state, thus facilitating Zn2+ release from ZnT8 into the lumen.

biochemistry↗

bioRxiv2022

Wnt7a Suppresses Adipogenesis of Skeletal Muscle Mesenchymal Stem Cells and Fatty Infiltration Through the Alternative Wnt-Rho-YAP/TAZ Signaling Axis

Intramuscular fatty infiltration in muscle injuries and diseases, caused by aberrant adipogenesis of fibro-adipogenic progenitors, negatively impacts function. Intramuscular delivery of Wnt7a offers a promising strategy to stimulate muscle regeneration but its effects on adipogenic conversion of fibro-adipogenic progenitors remain unknown. Here we show that Wnt7a inhibits adipogenesis of FAPs through the alternative Wnt-Rho-YAP/TAZ signaling that subsequently upregulates the canonical Wnt pathway. Furthermore, intramuscular injection of Wnt7a in vivo effectively suppresses fatty infiltration in mice. Our results collectively suggest Wnt7a as a potential protein-based therapeutic for inhibiting adipogenesis of FAPs and intramuscular fatty infiltration in pathological muscle injuries or diseases.

cell biology↗

bioRxiv2022

DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data

BackgroundThe advancement of high content optical microscopy has enabled the acquisition of very large 3D image datasets. Image analysis tools and three dimensional visualization are critical for analyzing and interpreting 3D image volumes. The analysis of these volumes require more computational resources than a biologist may have access to in typical desktop or laptop computers. This is especially true if machine learning tools are being used for image analysis. With the increased amount of data analysis and computational complexity, there is a need for a more accessible, easy-to-use, and efficient network-based/cloud-based 3D image processing system. ResultsThe Distributed and Networked Analysis of Volumetric Image Data (DINAVID) system was developed to enable remote analysis of 3D microscopy images for biologists. DINAVID is a server/cloud-based system with a simple web interface that allows biologists to upload 3D volumes for analysis and visualization. DINAVID is designed using open source tools and has two main sub-systems, a computational system for 3D microscopy image processing and analysis as well as a 3D visualization system. ConclusionsIn this paper, we will present an overview of the DINAVID system and compare it to other tools currently available for microscopy image analysis.

cell biology↗

bioRxiv2022

Novel ERR pan-agonists ameliorate heart failure through boosting cardiac fatty acid metabolism and mitochondrial function

Cardiac metabolic dysfunction is a hallmark of heart failure. Estrogen related receptors ERR and ERR{gamma} are essential regulators for cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for heart failure. However, no natural or synthetic ERR agonist is available to demonstrate their pharmacological effect in vivo. Using a structure-based design approach, we designed and synthesized two structurally distinct pan-ERR agonists, SLU-PP-332 (332) and SLU-PP-915 (915), which significantly improved ejection fraction and ameliorated fibrosis against pressure overload-induced heart failure without affecting cardiac hypertrophy. Mechanistically, a broad-spectrum of metabolic genes were transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function, which were mainly mediated by ERR{gamma}. Metabolomics analysis showed significant normalization of metabolic profiles in fatty acid/lipid and TCA/OXPHOS metabolites by 915 in the mouse heart with 6-week pressure overload. Autophagy was also induced by ERR agonists in cardiomycoyte. On the other hand, ERR agonism led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocyte. In summary, ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced heart failure in vivo. Our results provided direct pharmacological evidence supporting the further development of ERR agonists as novel heart failure therapeutics in vivo.

pharmacology and toxicology↗