Biology subjects

Chen, Z.

Publications and source records attributed to Chen, Z..

At least 577 records · Page 32Linked to original sources

bioRxiv2022

EMC holdase:CaV1.2/CaVβ3 complex and CaV1.2 channel structures reveal CaV assembly and drug binding mechanisms

Voltage-gated ion channels (VGICs) comprise multiple structural units whose assembly is required for function1,2. There is scant structural understanding of how VGIC subunits assemble and whether chaperone proteins are required. High-voltage activated calcium channels (CaVs)3,4 are paradigmatic multi-subunit VGICs from electrically excitable tissues whose function and trafficking is powerfully shaped by interactions between pore-forming CaV1 or CaV2 CaV13 and auxiliary CaV{beta}5, and CaV2{delta} subunits6,7. Here, we present cryo-EM structures of human brain and cardiac CaV1.2 bound with CaV{beta}3 to a chaperone, the endoplasmic reticulum membrane protein complex (EMC)8,9, and of the isolated CaV1.2/CaV{beta}3/CaV2{delta}-1 channel. These provide an unprecedented view of an EMC holdase:client complex and define EMC sites, the TM and Cyto docks, whose interaction with the client channel cause partial extraction of a pore subunit and splay open the CaV2{delta} interaction site. The structures further identify the CaV2{delta} binding site for gabapentinoid anti-pain and anti-anxiety drugs6, show that EMC and CaV2{delta} channel interactions are mutually exclusive, and indicate that EMC to CaV2{delta} handoff involves a Ca2+-dependent step and ordering of multiple CaV1.2 elements. Together, the structures unveil a CaV assembly intermediate and previously unknown EMC client binding sites that have broad implications for biogenesis of VGICs and other membrane proteins.

biophysics↗

bioRxiv2022

Multiomics reveal that silk fibroin and sericin differentially potentiate the paracrine functions of mesenchymal stem cells and enhance tissue regeneration

Silk fibroin (SF) and sericin (SS), the two major proteins of silk, are attractive biomaterials that show great potential in regenerative medicine. However, their biochemical interactions with stem cells were not fully understood. Here, we employed multiomics to obtain a global view of the triggered cellular processes and pathways of MSCs by SF and SS. Integrated RNA-seq and proteomics revealed that SF and SS strongly enhanced the paracrine activity of MSCs through differentially activating integrin and glycolytic pathways, rather than directly regulating stem cell fate to initiate multiple but distinct biological processes in MSCs. Those specific paracrine signals of MSCs stimulated by SF and SS effectively promoted skin wound healing by influencing the behaviors of multiple resident cells in skin wound microenvironments. This study provides comprehensive and reliable insights into the cellular interactions with SF and SS, enabling future development of silk-based therapeutics for tissue engineering and stem cell therapy.

bioengineering↗

bioRxiv2022

De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography

Understanding molecular mechanisms of cellular pathways requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by in vitro structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our in situ cryo-electron tomography and subtomogram averaging provided 6.0 [A] resolution reconstructions of axonemal microtubules and their associated proteins. The well-resolved secondary and tertiary structures allowed us to computationally match, in an unbiased manner, novel densities in our 3D reconstruction maps with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105 and SPACA9 as novel microtubule inner proteins that form an extensive network crosslinking the lumen of microtubule and existing proteins. Additional biochemical and mass spectrometry analyses helped validate potential candidates. The novel axonemal sperm structures identified by this approach form an extensive interaction network within the lumen of microtubules, suggesting they have a role in the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella.

biophysics↗

bioRxiv2022

Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against Omicron

The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this work, we carried out a systematic and comprehensive analysis of the reported spike protein antibodies, counting the antibodies epitopes and genotypes. We further comprehensively analyzed the impact of Omicron mutations on antibody epitopes and classified these antibodies according to their binding patterns. We found that the epitopes of one class of antibodies were significantly less affected by Omicron mutations than other classes. Binding and virus neutralization experiments show that such antibodies can effectively inhibit the immune escape of Omicron. Cryo-EM results show that this class of antibodies utilizes a conserved mechanism to neutralize SARS-CoV-2. Our results greatly help us deeply understand the impact of Omicron mutations. At the same time, it also provides guidance and insights for developing Omicron antibodies and vaccines.

microbiology↗

bioRxiv2022

Molecular Mechanisms of Holliday Junction Branch Migration Catalyzed by an Asymmetric RuvB Hexamer

The Holliday junction (HJ) is a universal DNA intermediate of homologous recombination that is involved in many fundamental physiological processes. In bacteria, RuvB, a motor protein of the AAA+ ATPase superfamily, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here, we report two cryo-EM structures of RuvB in complex with DNA and nucleotides, providing a comprehecomplex, which was further purified nsive understanding of HJ branch migration. Six RuvB protomers assemble into a spiral staircase, in the shape of a ring, with DNA in the central pore. Four protomers of RuvB hexamer interact with the backbone of the DNA substrate, suggesting a pulling-and-revolving mechanism of DNA translocation with a basic step size of 2 nucleotides. Moreover, the variation of nucleotide-binding states in our RuvB hexamer supports a sequential model for ATP hydrolysis, ADP release, and ATP reloading, which occur at specific positions on the RuvB hexamer. Furthermore, the asymmetric assembly of RuvB also explains the 6:4 stoichiometry between RuvB and RuvA, which assembles into a complex to coordinate HJ migration in cells. Taken together, we provide a comprehensive framework for the mechanistic understanding of HJ branch migration facilitated by RuvB motor protein, which may be universally shared in both prokaryotic and eukaryotic organisms.

biochemistry↗

bioRxiv2022

DEED: A Dataset for Dream-related Emotion Research

Emotion is closely related to human cognition and behaviour. In recent years, scholars have conducted extensive research on emotion in waking state based on electroencephalography (EEG) and achieved certain results. However, Emotional activity continues after sleep, with a concentrated response of sleep emotions in dreams. Sleep emotions are concentrated in dreams, which can better reflect a series of real physical and psychological states of the human body. Currently, there is no publicly available dataset for the assessment of dream mood. Therefore, we present a physiological dataset Dream Emotion Evaluation Dataset (DEED) for the assessment of dream mood, which recorded EEG signals from 38 participants over 89 whole sleep nights and 533 dream segments(after exclusion of unqualified nights, those dream segments are extracted from 82 whole sleep nights). We studied the correlations between the subjective ratings and the EEG signals and brain network patterns for dream emotions. In addition, the relationship between the asymmetry of left and right brain bands and positive and negative dream emotions was studied. The machine learning algorithm was also used to classify different emotional EEG, which confirmed the validity of the dataset. In the meantime, we encourage other researchers to explore the underlying neural mechanisms involved in sleep.

neuroscience↗

bioRxiv2022

Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

Single-cell level characterization of embryonic development is a major benchmark of human developmental biology. Spatiotemporal analysis of stem-cell-derived embryos offers conceptual and technical advances in the field. Here, we defined the single-cell spatiotemporal gene expression landscape of human embryonic development with stem-cell-derived organoids. We established the human embryonic organoid (HEMO) from expanded potential stem cells and achieved both embryonic and extraembryonic tissues in the same organoid. Time-series single-cell RNA sequencing paired with single-cell resolution spatial revealed human embryonic development signatures such as extraembryonic placenta, yolk sac hematopoiesis neural crest, blood vessels, and cardiac mesoderm. Hematopoietic tissues eventually predominated HEMO with erythropoiesis, mekagaryopiesis, and myelopoiesis. Cell-cell communication network analysis demonstrated that trophoblast-like tissues supplied WNT signaling in neural crest cells to facilitate maturation and migration. Single-cell resolution spatial transcriptomics defined the yolk sac erythro-megakaryopoietic niche. Vitronectin-integrin signaling, a major contributor to megakaryocyte maturation, was predominant in the yolk sac niche in HEMO and to human fetal samples. Overall, our study advances the spatiotemporal analysis of human embryonic development in stem-cell-derived organoids. HighlightsO_LIModeling human embryonic development from stem cells C_LIO_LIUsed of both 10X Chromium and 10X Visium to define the gene expression landscape of embryonic development and hematopoiesis C_LIO_LIWNT signaling as a regulator of neural crest maturation and EMT C_LIO_LIVTN-ITGA2B as the main contributor to Mk maturation within the yolk sac erythro-megakaryopoietic niche C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/505700v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1710d00org.highwire.dtl.DTLVardef@10ca8e0org.highwire.dtl.DTLVardef@2310d1org.highwire.dtl.DTLVardef@252728_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

The combination of morphogenic regulators BABY BOOM and GRF-GIF improves maize transformation efficiency

Transformation is an indispensable tool for plant genetics and functional genomic studies. Although stable transformation no longer represents a major technology bottleneck in maize, there is still need for easily accessible and efficient transformation methods in most academic labs. Here we present the GGB transformation system, a rapid and highly efficient transformation system optimized for the immature embryo transformation of two maize genetic backgrounds, including the inbred line B104. The combination of distinct morphogenetic factors, the maize BABY BOOM transcriptional regulator (ZmBBM/EREB53) and the wheat GRF4-GIF1 (GROWTH REGULATING FACTOR4 - GRF-INTERACTING FACTOR1) chimera, together with a modified QuickCorn protocol, regenerated transformed maize seedlings in approximately two months with an efficiency of 26 to 37%; notably, the efficiency was 7-fold higher than with using either component in isolation. Additionally, ectopic expression of both morphogenetic factors did not show obvious effects on B104 development, and in particular fertility was not affected, obviating the need to remove the morphogenetic regulators post Agrobacterium infections. The GGB transformation system is designed for CRISPR-Cas9 editing but can be adapted for other purposes and should be easy to implement in most academic labs with little transformation experience.

plant biology↗

bioRxiv2022

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization

Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in a zebrafish model of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.

cell biology↗

bioRxiv2022

HepaCAM Suppresses Glioblastoma Stem Cell Invasion in the Brain

Glioblastoma (GBM) is a malignant brain cancer that contains sub-populations of highly invasive tumor cells that drive progression and recurrence after surgery and radiochemotherapy. The exact mechanisms that enable GBM cells to disperse from the main tumor mass and navigate throughout the brain microenvironment remain largely unknown. As a result, there is a lack of effective strategies to block cancer cell invasive growth in primary and recurrent GBM. Here we report that hepatocyte cell adhesion molecule (hepaCAM), which is normally expressed in perivascular astrocytes, plays central roles in controlling the invasive growth features of GBM cells. Genetically targeting HEPACAM induces a transition from GBM cell proliferation/self-renewal to invasion. Increased invasion is due, in part, to an activation of focal adhesion signaling pathways and enhanced GBM cell adhesion to the extracellular matrix (ECM) in the brain microenvironment. Transcriptional profiling of GBM cells reveals various HEPACAM-regulated genes with links to polarity and invasion. Collectively, these data show that hepaCAM balances ECM adhesion and signaling pathways to control cancer cell proliferation versus invasion in the brain parenchyma. Targeting select components of the hepaCAM pathway may be an effective way to block tumor progression and recurrence in patients with GBM.

cancer biology↗

bioRxiv2022

A small-molecule lycorine derivative reveals Na+/K+-ATPase α3 as an anti-obesity target

Obesity remains a severe global public health challenge, with contemporary therapeutic approaches primarily focusing on appetite suppression. Here, we discovered HLY72, a lycorine-derived small molecule that potently counteracts obesity in mice at doses without affecting food intake, by promoting sympathetic activation-mediated lipolysis and thermogenesis in adipose tissues. Mass spectrometry identified Na+/K+-ATPase (NKA) 3, the brain-specific isoform, as HLY72s target. Only blood-brain barrier-permeable NKA inhibitors reproduce HLY72s anti-obesity effects, and resistance to HLY72 treatment occurs specifically in NKA 3 (not 1) knockin mice harboring a HLY72-binding mutation. Similar to the chemical inhibition by HLY72, genetic inhibition of NKA 3 also effectively protects mice from diet-induced obesity. These findings point NKA 3 as a potent anti-obesity drug target and highlight HLY72s potential in treating and preventing obesity independent of appetite control.

physiology↗

bioRxiv2022

The Chromosome-based Genome of Paspalum vaginatum Provides New Insights into Salt-stress Adaptation

Salinization is increasingly a major factor limiting production worldwide. Revealing the mechanism of salt tolerance could help to create salt-tolerant crops and improve their yields. We reported a chromosome-scale genome sequence of the halophyte turfgrass Paspalum vaginatum, and provided structural evidence that it shared a common ancestor with Z. mays and S. bicolor. A total of 107 P. vaginatum germplasms were divided into two groups (China and foreign group) based on the re-sequenced data, and the grouping findings were consistent with the geographical origin. Genome-wide association study (GWAS) of visually scored wilting degree and withering rates identified highly significant QTL on chromosome 6. Combination with RNA-seq, we identified a significantly up-regulated gene under salt stress, which encodes High-affinity K+ Transporter 7 (PvHKT7), as strong candidates underlying the QTL. Overexpression of this gene in Arabidopsis thaliana significantly enhanced salt tolerance by increasing K+ absorption. This study adds new insights into salt-stress adaptation of P. vaginatum and serve as a resource for salt-tolerant improvement of grain crops.

genomics↗

bioRxiv2022

Inhibition inputs from hippocampal CA1 to retrosplenial agranular cortex gate social behavior

Retrosplenial cortex has been implicated in processing sensory information and spatial learning, with abnormal neural activity observed in association with psychedelics and in mouse and non-human primate models of autism spectrum disorders (ASD). The direct role of the retrosplenial cortex in regulating social behaviors remains unclear. This work reveals that the neural activity of retrosplenial agranular cortex (RSA), a subregion of retrosplenial cortex, is initially activated, then quickly suppressed upon social contact. The up-down phase of RSA neurons is crucial for normal social behaviors. PV-positive GABAergic neurons in the hippocampal CA1 region were found to send inhibitory projections to RSA. Blocking these CA1-RSA inhibitory inputs significantly impaired social behavior. Notably, enhancing the CA1-RSA inhibitory input could rescue social behavior defects in an ASD mouse model. This work suggests a neural mechanism for salience processing of social behavior and identifies a potential target for ASD intervention using neural modulation approaches.

neuroscience↗

bioRxiv2022

Soluble amyloid-β precursor peptide does not regulate GABAB receptor activity

Amyloid-{beta} precursor protein (APP) regulates neuronal activity through the release of secreted APP (sAPP) acting at cell-surface receptors. APP and sAPP were reported to bind to the extracellular sushi domain 1 (SD1) of GABAB receptors (GBRs). A 17 amino-acid peptide (APP17) derived from APP was sufficient for SD1 binding and shown to mimic the inhibitory effect of sAPP on neurotransmitter release and neuronal activity. The functional effects of APP17 and sAPP were similar to those of the GBR agonist baclofen and blocked by a GBR antagonist. These experiments led to the proposal that sAPP activates GBRs to exert its neuronal effects. However, whether APP17 and sAPP indeed influence classical GBR signaling pathways in heterologous cells was not analyzed. Here, we confirm that APP17 binds to GBRs with nanomolar affinity. However, biochemical and electrophysiological assays indicate that APP17 does not influence GBR activity in heterologous cells. Moreover, we found no evidence for APP17 regulating K+ currents in cultured neurons, neurotransmitter release in brain slices, or neuronal activity in vivo. Our results show that APP17 is not a functional GBR ligand and indicate that sAPP exerts neuronal effects through receptors other than GBRs.

neuroscience↗

bioRxiv2022

Dynamic changes in the niche and transcription trigger early murine and human pluripotent stem cell-derived liver organogenesis

The shift from collective migration to differentiation is a crucial process in epithelial biology but recreating this intricate transition has thus far proved elusive. We provide experimental, mechanistic, in vivo, and bioinformatic data supporting an undoubtable link between human pluripotent stem cell (hPSC)- derived collectively migrating hepatoblasts (MHB), and transcriptionally mature, functional hPSC- hepatocytes (HEPs), which incorporates two unrecognized steps. The protocol induces FOXA-dependent induction of HBs, leading to TBX3-positive, YAP-TEAD active MHBs which provide a transcriptional match with murine liver E9.5 MHBs. Simple cultivation changes trigger MHBs to rapidly form functional day 18 HEPs, predicted by a deep-learning designed gene circuit, resulting in a [~]236% fold- increase in maturation (PACNet), on par with the highest score, but with enhanced global transcriptional shaping. Overall, incorporating the MHB to HEP transition establishes a new, unrecognized, and highly efficient mechanism for differentiation that can be cumulatively integrated with existing methods to overcome barriers to maturation.

bioengineering↗

bioRxiv2022

Bioinformatics analysis of immune-related prognostic genes and immunotherapy in renal clear cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is an immunogenic tumor and investigating the immunorelated genes is of great significance. To investigate the immunoprognostic genes of ccRCC, we analyzed the data assimilated from a public database (The Cancer Genome Atlas (TCGA) database and the gene expression omnibus (GEO) database) using bioinformatics. Then, a immunoprognosis model was constructed to identify 4 hub genes with moderate predictive values for the prognosis of ccRCC patients. Interestingly, these 4 genes were associated with the prognosis of ccRCC patients based on Oncomine and Gena Expression Profiling Interactive Analysis (GEPIA) databases. The correlation analysis between the immune infiltrate, immune checkpoints, and immunotherapy and this immunoprognosis model showed that immune infiltrate and could predict the immunotherapy effects. We also conducted a quantitative real-time polymerase chain reaction analysis and found that the expressions of 3 hub genes were associated with tumor progression (P<0.1). In conclusion, 4 genes that may serve as potential biomarkers in ccRCC were identified with respect to prognosis.

cancer biology↗

bioRxiv2022

The novel compensatory reciprocal interplay between neutrophils and monocytes drives cancer progression

Myeloid cells comprise the majority of immune cells in tumors, contributing to tumor growth and therapeutic resistance. Incomplete understanding of myeloid cells response to tumor driver mutation and therapeutic intervention impedes effective therapeutic design. Here, by leveraging CRISPR/Cas9-based genomic editing, we generated a mouse model that is deficient of all monocyte chemoattractant proteins (MCP). Using this strain, we effectively abolished monocyte infiltration in glioblastoma (GBM) and hepatocellular carcinoma (HCC) murine models, which were enriched for monocytes or neutrophils, respectively. Remarkably, eliminating monocyte chemoattraction invokes a significant compensatory neutrophil influx in GBM, but not in HCC. Single-cell RNA sequencing revealed that intratumoral neutrophils promoted proneural-to-mesenchymal transition in GBM, and supported tumor aggression by facilitating hypoxia response via TNF production. Importantly, genetic or pharmacological inhibiting neutrophil in HCC or qMCP-KO GBM extended the survival of tumor-bearing mice. Our findings emphasize the importance of targeting both monocytes and neutrophils simultaneously for cancer immunotherapy. In BriefEliminating monocyte chemoattraction invokes compensatory neutrophil influx in tumor, and vice versa, rendering current myeloid-targeted therapies ineffective. Using genetic and pharmacological approaches combined with novel mouse models of GBM and HCC, we provide credence advocating for combinational therapies aiming at inhibiting both monocytes and neutrophils simultaneously. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/500690v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@bbbae5org.highwire.dtl.DTLVardef@eb3eecorg.highwire.dtl.DTLVardef@702696org.highwire.dtl.DTLVardef@f54734_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights* Blocking monocyte chemoattraction results in increased neutrophil infiltration. * Increased neutrophil recruitment induces GBM PN to MES transition. * Inhibiting neutrophil infiltration in monocyte-deficient tumors improves mouse GBM survival. * Blocking neutrophil, but not monocyte, infiltration in HCC prolongs mouse survival.

immunology↗

bioRxiv2022

A unified model for the surveillance of translation in diverse noncoding sequences

Translation is pervasive outside of canonical coding regions, occurring in lncRNAs, UTRs, and introns. While the resulting polypeptides are often non-functional, translation in noncoding regions is nonetheless necessary for the birth of new coding regions. The mechanisms underlying the surveillance of translation in diverse noncoding regions and how escaped polypeptides evolve new functions remain unclear. Intriguingly, noncoding sequence-derived functional peptides often localize to membranes. Here, we show that the intrinsic nucleotide bias in the noncoding genome and in the genetic code frequently results in polypeptides with a hydrophobic C-terminal tail, which is captured by the ribosome-associated BAG6 membrane protein triage complex for either proteasomal degradation or membrane targeting. In contrast, canonical proteins have evolved to deplete C-terminal hydrophobic residues. Our results uncovered a fail-safe mechanism for the surveillance of unwanted translation from diverse noncoding regions and suggest a possible biochemical route for the preferential membrane localization of newly evolved proteins. HighlightsO_LITranslation in diverse noncoding regions is mitigated by proteasomal degradation C_LIO_LIC-terminal hydrophobicity is a hallmark of noncoding sequence derived polypeptides C_LIO_LIA genome-wide CRISPR screen identified the BAG6 membrane protein triage pathway C_LIO_LIRibosome-associated BAG6 complex targets C-terminal hydrophobicity for degradation C_LI

molecular biology↗