Biology subjects

Chen, Q.

Publications and source records attributed to Chen, Q..

At least 325 records · Page 18Linked to original sources

bioRxiv2022

Cytosolic peptide accumulation activates the NLRP1 and CARD8 inflammasomes

NLRP1 and CARD8 are related sensors that form inflammasomes, but the danger signals that they detect are not fully established. These proteins undergo autoproteolysis, generating repressive N-terminal (NT) and inflammatory C-terminal (CT) fragments. The proteasome- mediated degradation of the NT releases the CT from autoinhibition, but the CT is then sequestered in a complex with the full-length sensor and DPP9. Here, we show that cytosolic peptide accumulation activates these inflammasomes. We found that a diverse array of peptides accelerates NT degradation, and those with N-terminal XP sequences also destabilize the ternary complexes. Peptides interfere with many biological processes, including protein folding. We show that unrelated agents that disrupt protein folding also induce NT degradation, but do not cause inflammasome activation because DPP9 sequesters the CT fragments in the absence of XP peptides. Overall, these results indicate that NLRP1 and CARD8 detect protein misfolding that is associated with peptide accumulation.

immunology↗

bioRxiv2022

Effects of Sanhuang plaster on expression of MyD88, TRAF6, MIP-1β and IL-23 in rats infected by MRSA

Objective: To investigate the effects of Sanhuang plaster on expression of myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-related factor 6 (TRAF6), macrophage inflammatory protein-l{beta} (MIP-1{beta}) and its mediated cytokine interleukin-23 (IL-23) in soft tissues of rats infected by methicillin-resistant Staphylococcus aureus (MRSA). Methods: Ninety-six healthy rats were randomly divided into normal control group, model control group, Mupirocin group, high, medium and low dose groups of Sanhuang plaster, with 16 rats in each group. MRSA bacterial liquid was used to make skin and soft tissue infection models. The rats in the normal control group and the model control group were not given any treatment measures. The high, medium, and low dose groups of Sanhuang plaster were given to the affected area with Sanhuang plaster, and the Mupirocin group was given to the affected area for treatment for 10 days. The wound pathological changes were observed. The levels of MIP-1{beta} and IL-23 in serum and infected tissues of rats in each group were measured by ELISA. The mRNA expressions of MyD88, TRAF6, MIP-l{beta} and IL-23 were measured by Quantitative Real-time PCR, and Western blot was used to measure MyD88 and TRAF6 protein expression. Results: Compared with the model control group, the general condition of the Sanhuang plaster groups was significantly improved, and the pathological damage was reduced. The MIP-1{beta} and IL-23 levels in the serum and infected tissues of the high dose group of Sanhuang plaster, the mRNA expressions of MyD88, TRAF6, MIP-1{beta} and IL-23and in large and medium dose groups of Sanhuang plaster, and the protein expressions of Myd88 and TRAF6 in high dose of Sanhuang plaster were significantly decreased (p<0.05 or p<0.01). Conclusion: Sanhuang plaster may play a role in promoting healing of infected wounds by down-regulating the expression levels of MyD88, TRAF6, and MIP-1{beta}, and inhibiting the abnormal secretion of cytokine IL-23.

molecular biology↗

bioRxiv2022

TFIIB-related factor 1 is a nucleolar protein that promotes RNA polymerase I-directed transcription and tumour cell growth

RNA polymerase I (Pol I) products play pivotal roles in ribosomal assembly, protein synthesis and cell growth. Dysregulation of Pol I product synthesis closely correlates with tumourigenesis. However, the factors and pathways governing Pol I-dependent transcription remain to be identified. Here, we report that TFIIB-related factor 1 (BRF1), a subunit of TFIIIB required for Pol III-mediated transcription, is a nucleolar protein and modulates the rRNA synthesis directed by Pol I. We show that BRF1 can be co-localized with nucleolar protein markers in several human cell types. BRF1 expression positively correlates with Pol I product levels and tumour cell growth in vitro and in vivo. Mechanistically, BRF1 binds to the Pol I transcription machinery factors and is recruited to the rDNA promoter with them. Alteration of BRF1 expression affected the recruitment of Pol I transcription machinery at the rDNA promoter, the rDNA promoter activity and expression of TBP and TAF1A, indicating that BRF1 modulates Pol I-direct transcription by controlling the expression of selective factor 1 subunits. Collectively, we demonstrate that BRF1 acts as a positive factor to regulate Pol I-directed transcription, suggesting that BRF1 can concurrently modulate Pol I and Pol III transcription and acts as a key coordinator between them.

molecular biology↗

bioRxiv2022

Generating Functional Cells Through Enhanced Interspecies Chimerism with Human Pluripotent Stem Cells

Obtaining functional human cells through interspecies chimerism with human pluripotent stem cells (hPSCs) remains unsuccessful due to its extreamly low efficiency. Here, we show that hPSCs failed to differentiate and contribute teratoma in presence of mouse PSCs (mPSCs). While, MYCN, a pro-growth factor dramatically promotes hPSC contribution in teratoma co-formation by hPSCs/mPSCs. MYCN combined with BCL2 (M/B) greatly enhanced conventional hPSCs to integrate into preimplantation embryos of different species, such as mice, rabbits and pigs and substrantially contributed to mouse post-implantation chimera in embryonic and extra-embyonic tissues. Strikingly, M/B-hPSCs injected into preimplantation Flk-1+/- mouse embryos show further enhanced chimerism that allows obtaining live human CD34+ blood progenitor cells from chimeras through cell sorting. The chimera derived human CD34+ cells further gave rise to various subtype blood cells in typical colony forming unit(CFU) assay. Thus, we proof the concept to obtain functional human cells through enchanced interspecies chimerism with hPSCs.

cell biology↗

bioRxiv2022

Pre-B cell receptor acts as a selectivity switch for Galectin-1 at the pre-B cell surface

Galectins are glycan binding proteins translating the sugar-encoded information of cellular glycoconjugates into many physiological activities including immunity, cell migration, and signaling. During early B lymphocytes (BL) development at the pre-B cell stage, BL express the pre-B cell receptor (pre-BCR) and are supported by mesenchymal stromal cells secreting Galectin-1 (Gal-1). Gal-1 interacts with glycosylated receptors from stromal and pre-B cell surfaces but also with the pre-BCR through a direct carbohydrate-independent contact. How this interaction might interplay with the glycan-decoding function of Gal-1 is unknown. Here, we investigated Gal-1 binding to cell surface ligands using NMR spectroscopy on native membranes. We showed that pre-BCR regulates Gal-1 binding to specifically target 2,3-sialylated receptors on pre-B cells. Upon pre-BCR interaction, dynamic changes resulted in additional contacts with 2,3-sialylated glycans converting Gal-1 from an exo- to an endo-type lectin. Remarkably, this selectivity switch is able to promote pre-B cell survival. Altogether, we shed light on a new mechanism allowing fine-tuning of Galectin specificity at the cell surfaces.

biochemistry↗

bioRxiv2022

Mutations of SARS-CoV-2 variants of concern escaping Spike-specific T cells

The amino acid (AA) mutations that characterise the different variants of concern (VOCs), which replaced the ancestral SARS-CoV-2 Wuhan-Hu-1 isolate worldwide, provide biological advantages such as increased infectivity and partial escape from humoral immunity. Here we analysed the impact of these mutations on vaccination- and infection-induced Spike-specific T cells. We confirmed that, in the majority of infected or vaccinated individuals, different mutations present in a single VOC (Delta) or a combined mosaic of more than 30 AA substitutions and deletions found in Alpha, Beta, Gamma, Delta and Omicron VOCs cause modest alteration in the global Spike-specific T cell response. However, distinct numerically dominant Spike-specific CD4 and CD8 T cells preferentially targeted regions affected by AA mutations and do not recognise the mutated peptides. Importantly, some of these mutations, such as N501Y (present in Alpha, Beta, Gamma, and Omicron) and L452R (present in Delta), known to provide biological advantage to SARS-CoV-2 in terms of infectivity also abolished CD8 T cell recognition. Taken together, our data show that while global mRNA vaccine- and infection-induced Spike-specific T cells largely tolerate the diverse mutations present in VOCs, single Spike-specific T cells might contribute to the natural selection of SARS-CoV-2 variants.

immunology↗

bioRxiv2022

The sowing date changed the temperature and light conditions in the field modified the cadmium content of brown rice (Oryza sativa L.) by regulating the expression of Cd-related genes

Cadmium (Cd) contamination in rice is a potential health hazard when ingested through the food chain worldwide. Reducing the Cd content in rice through agronomic measures is an effective way to reduce the risk of Cd contamination to human health. In order to clarify the correlation between temperature and light conditions and Cd accumulation (Cd-A) and Cd content of brown rice (CdBR) during the field growth period (FGP) of rice, consequently provide a theoretical basis for the selection of sowing date (SD) for "Low-Cd-Rice" production, field experiment with different SDs was carried out by using two rice varieties with different Cd accumulation characteristics (Luliangyou 996, V1, a high Cd accumulation variety; Zhuliangyou 819, V2, a low Cd accumulation variety). The results showed that the temperature and light factors such as mean soil temperature (ST), mean air temperature (AT), soil accumulation temperature (SAT), air accumulation temperature (AAT), ultraviolet radiation accumulation (UR), photosynthetic radiation accumulation (PR), light intensity accumulation (I) and sunshine hours accumulation (SH) varied to different degrees under different SDs; The difference in CdBR in two varieties could be up to 2.82 and 8.48 times respectively among SDs, with the CdBR of S4 and S5 of V2 being lower than the national standard of 0.2 mg/kg. The relative expression of OsIRT1 in the root system was significantly positively correlated with ST, SAT, AT, AAT, and SH, while OsNramp5, OsNramp1, and OsHMA3 showed significant negative correlations with ST, SAT, AT, AAT, and SH in relative expression in the root system; OsIRT1 expressed in the roots of V1 was significantly negatively correlated with CdBR, while OsHMA3 expression was significantly positively correlated with CdBR; OsLCD, OsNramp1, and OsHMA3 expression in the roots of V2 were significantly positively correlated with Cd-A and CdBR, while OsIRT1 in the roots of V2 and OsLCT1 in the leaves were significantly negatively correlated with Cd-A; The expression of OsNramp5 in roots was significantly negatively correlated with Cd-A and CdBR in both V1 and V2. Bias correlation analysis showed that ST, SAT, AT, and AAT were significantly negatively correlated with both Cd-A and CdBR; SH was significantly negatively correlated with CdBR in V1. Summarily, the temperature and light conditions during the FGP of rice and their regulation of the expression levels of related genes could be changed by sowing selection, so as to achieve safe production of rice under Cd-contaminated fields.

physiology↗

bioRxiv2022

SELINA: Single-cell Assignment using Multiple-Adversarial Domain Adaptation Network with Large-scale References

The rapid accumulation of single-cell RNA-seq data has provided rich resources to characterize various human cell types. Cell type annotation is the critical step in analyzing single-cell RNA-seq data. However, accurate cell type annotation based on public references is challenging due to the inconsistent annotations, batch effects, and poor characterization of rare cell types. Here, we introduce SELINA (single cELl identity NAvigator), an integrative annotation transferring framework for automatic cell type annotation. SELINA optimizes the annotation for minority cell types by synthetic minority over-sampling, removes batch effects among reference datasets using a multiple-adversarial domain adaptation network (MADA), and fits the query data with reference data using an autoencoder. Finally, SELINA affords a comprehensive and uniform reference atlas with 1.7 million cells covering 230 major human cell types. We demonstrated the robustness and superiority of SELINA in most human tissues compared to existing methods. SELINA provided a one-stop solution for human single-cell RNA-seq data annotation with the potential to extend for other species.

bioinformatics↗

bioRxiv2022

Crystal Structure of Caskin1/CASK complex reveals the molecular basis of the binding specificity of CASK_CAMK domain and its binding partners

CASK is a unique scaffold protein in the synapse system. It links numerous proteins to the pre- or post-synaptic region and is critical to the homeostasis of synaptic vesicles. The N-terminus of CASK is a calcium/calmodulin-dependent protein kinase (CAMK) domain, which has diverse functions and interacts with downstream proteins to form a scaffold platform. Caskin1 is one of the brain-specific adaptor proteins of CASK. Previous studies showed that CASK_CAMK domain interacts with Caskin1 CID domain with relatively low affinity. In this study, we re-visit this interaction by remapping the interaction boundary and solving their complex structure. Based on the structure, we systematically compared the interactions between CASK_CAMK and other binding partners. Our results showed that CAMK domain occupies the CID peptide by using its C-lobe groove (between the 1 and 2) and there is a highly conserved signature motif ({zeta}-x-{psi}-W-{psi}-x-R) in the CID domain, where {zeta} is acidic side chain containing residues, x is any amino acid residue, {psi} is hydrophobic residues, W is for tryptophan, and R is arginine. These findings allowed us to identify several new potential cytoplasmic binding partners for CASK_CAMK.

biochemistry↗

bioRxiv2022

Hypoxia Dynamically Regulates DBC1 Ubiquitination and Stability by SIAH2 and OTUD5 in Breast Cancer Progression

DBC1 has been characterized as a key regulator of physiological and pathophysiological activities, such as DNA damage, senescence and tumorigenesis. However, the mechanism by which the functional stability of DBC1 is regulated has yet to be elucidated. Here, we report that the ubiquitination-mediated degradation of DBC1 is dynamically regulated by the E3 ubiquitin ligase SIAH2 and deubiquitinase OTUD5 under hypoxic stress. Mechanistically, hypoxia promoted the competitive binding of SIAH2 with OTUD5 to DBC1, resulting in the ubiquitination and subsequent degradation of DBC1 through the ubiquitin-proteasome pathway. Siah2 knockout inhibited tumor cell proliferation and migration, which could be rescued by double knockout of Siah2/DBC1. Human tissue microarray analysis further revealed that the SIAH2/DBC1 axis was responsible for tumor progression under hypoxic stress. These findings define a key role of the hypoxia-mediated SIAH2-DBC1 pathway in the progression of human breast cancer and provide novel insights into the metastatic mechanism of breast cancer.

cell biology↗

bioRxiv2021

Endothelial-immune crosstalk contributes to vasculopathy in non-alcoholic fatty liver disease

The top cause of mortality in patients with non-alcoholic fatty liver disease (NAFLD) is cardiovascular complications. However, the mechanisms of NAFLD-associated vasculopathy remain understudied. We developed blood outgrowth endothelial cell (BOEC) models from NAFLD and healthy subjects. NAFLD BOECs exhibited global transcriptional upregulation of chemokine hallmarks and human leukocyte antigens. In mouse models of diet-induced NAFLD, we further confirmed enhanced endothelial expressions of CXCL12 in the aortas and liver vasculatures. To elucidate endothelial-immune crosstalk, we performed immunoprofiling by single-cell analysis, uncovering T cell intensification and potentially T-helper type 1 inflammation in NAFLD patients. Functionally, interference of the CXCL12-CXCR4 axis by small molecule AMD3100 selectively modulated the chemotaxis of patient-derived CD4+ T cells and natural killer cells towards NAFLD BOECs, restoring endothelial barrier integrity. Clinically, we detected three folds more circulating damaged endothelial cells in NAFLD patients than healthy controls. Our work provides insights for modulation of interactions with effector immune subsets to mitigate endothelial injury in NAFLD.

cell biology↗

bioRxiv2021

Two decades of suspect evidence for adaptive molecular evolution - Negative selection confounding positive selection signals

There is a large literature in the last two decades affirming adaptive DNA sequences evolution between species. The main lines of evidence are from i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and ii) the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on the genomic data of Drosophila and Arabidopsis. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectation. Because the non-concordance could be due to low powers leading to high false-negatives, we merge every 20 - 30 genes into a "supergene". At the supergene level, the power of detection is large but the calls still do not overlap. We rule out methodological reasons for the non-concordance. In particular, extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML, but not both. Since molecular evolution is governed by positive and negative selection concurrently, a fundamental assumption for estimating one (say, positive selection) is that the other is constant. However, in a broad survey of primates, birds, Drosophila and Arabidopsis, we found that negative selection rarely stays constant for long in evolution. As a consequence, the variation in negative selection is often mis-construed as signals of positive selection. In conclusion, MK, PAML or any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection. In a companion study, we propose a possible path forward in two stages - first, by mapping out the changes in negative selection and then using this map to estimate positive selection. For now, the large literature on positive selection between species has to await the re-assessment.

evolutionary biology↗

bioRxiv2021

Patient induced pluripotent stem cell-derived hepatostellate organoids establish a basis for liver pathologies in telomeropathies

Patients with dyskeratosis congenita (DC) and related telomeropathies resulting from premature telomere dysfunction suffer from multi-organ failure. In the liver, DC patients present with nodular hyperplasia, steatosis, inflammation, and cirrhosis. We model DC liver pathologies using isogenic human induced pluripotent stem (iPS) cells harboring a causal DC mutation in DKC1, or a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-corrected control allele. Differentiation of these iPS cells into hepatocytes or hepatic stellate cells followed by generation of genotype-admixed hepatostellate organoids revealed a dominant phenotype in the parenchyma, with DC hepatocytes eliciting a pathogenic hyperplastic response in stellate cells independent of stellate cell genotype. Pathogenic phenotypes could be rescued via suppression of AKT activity, a central regulator of MYC-driven hyperplasia downstream of DKC1 mutation. Thus, isogenic iPS-derived admixed hepatostellate organoids offer insight into the liver pathologies in telomeropathies and provide a framework for evaluating emerging therapies.

cell biology↗

bioRxiv2021

KIBRA-PKCγ signaling pathway modulates memory performance in mice and humans

Human memory is a polygenic cognitive trait that is fundamental to individual competence. Genome-wide association studies (GWAS) have identified KIBRA as a novel gene associated with human memory performance. KIBRA interacts with AMPA receptors (AMPARs) and proteins essential for synaptic plasticity. The deletion of Kibra in mice impairs synaptic plasticity and learning and memory. However, the molecular basis through which KIBRA regulates dynamic AMPAR trafficking underlying synaptic plasticity is still unknown. Here we report that KIBRA interacts with the neuronal specific kinase PKC{gamma} to modulate AMPAR trafficking upon learning, and KIBRA-PKC{gamma} signaling pathway also associates with human memory performance. We find PKC{gamma} is an essential kinase that phosphorylates AMPARs upon learning, and the loss of KIBRA in mouse brain impedes PKC{gamma}-AMPAR interaction. Activation of PKC{gamma} enables KIBRA to recruit phosphorylated AMPARs to the synapse to promote LTP and learning. We further performed transcriptomic and genetic analyses in human postmortem brain samples, and behavioral and fMRI evaluations in living human subjects, to demonstrate the genetic interactions between KIBRA and PRKCG on memory performance and memory associated physiological engagement of the hippocampal memory system. Overall, our results support that the KIBRA-PKC{gamma} signaling pathway is crucial for modulating memory performance in mice and humans.

neuroscience↗

bioRxiv2021

S100A8 and S100A9, biomarkers of SARS-Cov-2-infected patients, suppress HIV replication in primary macrophages

S100A8 and S100A9 are members of the Alarmin family; these proteins are abundantly expressed in neutrophils and form a heterodimer complex. Recently, both proteins were identified as novel biomarkers of SARS-CoV-2 infection and were shown to play key roles in inducing an aggressive inflammatory response by mediating the release of large amounts of pro-inflammatory cytokines, called the "cytokine storm." Although co-infection with SARS-CoV-2 in people living with HIV-1 may result in an immunocompromised status, the role of the S100A8/A9 complex in HIV-1 replication in primary T cells and macrophages is still unclear. Here, we evaluated the roles of the proteins in HIV replication to elucidate their functions. We found that the complex had no impact on virus replication in both cell types; however, the subunits of S100A8 and S100A9 inhibits HIV in macrophages. These findings provide important insights into the regulation of HIV viral loads in SARS-CoV2 co-infection.

microbiology↗

bioRxiv2021

Performance Comparison of Computational Prediction Methods for the Function and Pathogenicity of Non-coding Variants

Non-coding variants in the human genome greatly influence some traits and complex diseases by their own regulation and modification effects. Hence, an increasing number of computational methods are developed to predict the effects of variants in the human non-coding sequences. However, it is difficult for users with insufficient knowledge about the performances of computational methods to select appropriate computational methods from dozens of methods. In order to solve this problem, we assessed 12 performance measures of 24 methods on four independent non-coding variant benchmark datasets: (I) rare germline variant from ClinVar, (II) rare somatic variant from COSMIC, (III) common regulatory variant dataset, and (IV) disease associated common variant dataset. All 24 tested methods performed differently under various conditions, indicating that these methods have varying strengths and weaknesses under different scenarios. Importantly, the performance of existing methods was acceptable in the rare germline variant from ClinVar with area under curves (AUCs) of 0.4481 - 0.8033 and poor in the rare somatic variant from COSMIC (AUCs: 0.4984 - 0.7131), common regulatory variant dataset (AUCs: 0.4837 - 0.6472), and disease associated common variant dataset (AUCs: 0.4766 -0.5188). We also compared the prediction performance among 24 methods for non-coding de novo mutations in autism spectrum disorder and found that the CADD and CDTS methods showed better performance. Summarily, we assessed the performances of 24 computational methods under diverse scenarios, providing preliminary advice for proper tool selection and new method development in interpreting non-coding variants.

bioinformatics↗

bioRxiv2021

Non-conserved metabolic regulation by LKB1 distinguishes human and mouse lung adenocarcinoma

KRAS is the most frequently mutated oncogene in human lung adenocarcinomas (hLUAD) and activating mutations in KRAS frequently co-occur with loss-of-function mutations in the tumor suppressor genes, TP53 or STK11/LKB1. However, mutation of all three genes is rarely observed in hLUAD, even though engineered mutations of all three genes produces a highly aggressive lung adenocarcinoma in mice (mLUAD). Here we provide an explanation of this difference between hLUAD and mLUAD by uncovering an evolutionary divergence in regulation of the glycolytic enzyme triosephosphate isomerase (TPI1). Using KRAS/TP53 mutant hLUAD cell lines, we show that TPI1 enzymatic activity can be altered via phosphorylation at Ser21 by the Salt Inducible Kinases (SIKs) in an LKB1-dependent manner; this allows modulation of glycolytic flux between completion of glycolysis and production of glycerol lipids. This metabolic flexibility appears to be critical in rapidly growing cells with KRAS and TP53 mutations, explaining why loss of LKB1 creates a metabolic liability in these tumors. In mice, the amino acid at position 21 of TPI1 is a Cys residue which can be oxidized to alter TPI1 activity, allowing regulation of glycolytic flux balance without a need for SIK kinases or LKB1. Our findings reveal an unexpected role for TPI1 in metabolic reprogramming and suggest that LKB1 and SIK family kinases are potential targets for treating KRAS/TP53 mutant hLUAD. Our data also provide a cautionary example of the limits of genetically engineered murine models as tools to study human diseases such as cancers.

cancer biology↗

bioRxiv2021

An Attempt to Develop an Aptamer Lateral-Flow Assay (ALFA) for Easy, Rapid, and Sensitive Detection of Lethal Mushroom Toxin α-amanitin

Amatoxins contribute to the majority of mushroom poisoning, most prominently, -amanitin. Since mushroom is a common foodstuff worldwide, an easy, rapid, sensitive test for -amanitin is needed. Several detection methods for -amanitin have been developed, including HPLC, LC-MS, and ELISA, and LFIA. Aptamers have several advantages compared to antibodies: easy development via SELEX, longer shelf life, and higher temperature- and pH-tolerance. Aptamer Lateral Flow Assay (ALFA) is a similar technology compared to LFIA but incorporates aptamers as target-recognizing agents. This study attempted to develop an ALFA test strip for -amanitin using a previously-developed aptamer, however failure of generating a colorimetric readout at the test line is persisted throughout all experiments, even though the concept is fully-proved and the control line functions normally. The failure is attributed to the small size of the molecule, leading to immobilization difficulties on the nitrocellulose membrane to form the test line, and the hindering of effective "surround" mechanism of aptamer-target binding (instead of "adhere", when the target molecule is large, e.g. a protein). It is concluded that ALFAs for small-molecules whose aptamer-target interaction has not yet been studied and modelled in detail remains a challenge, despite ALFAs large potential.

molecular biology↗