Biology subjects

Sun, L.

Publications and source records attributed to Sun, L..

At least 271 records · Page 15Linked to original sources

bioRxiv2022

CARD8 negatively regulates NLRP1 inflammasome activation level by interaction with NLRP1

NLRP1 inflammasome functions as canonical cytosolic sensor in response to intracellular infections and is implicated in auto-inflammatory diseases. But the regulation and signal transduction mechanisms of NLRP1 are incompletely understood. Here, we show that the T60 variant of CARD8, but not the canonical T48 isoform, negatively regulates NLRP1 inflammasome activation by directly interacting with the receptor molecule NLRP1 and inhibiting inflammasome assembly. Furthermore, our results suggest that the different ASC preference in three types of inflammasomes, namely ASC-indispensable NLRP1 inflammasome, ASC-dispensable mNLRP1b inflammasome and ASC-independent CARD8 inflammasome, is mainly caused by the CARD domain, not the UPA subdomain. Based on the systematic site-directed mutagenesis and structural analysis, we find that the signal transduction of NLRP1 inflammasome relies on multiple interaction surfaces on its death domain superfamily member CARD domain. Finally, our results partly explain the mechanism of the NLRP1 mutation-derived auto-inflammatory diseases caused by the overactivation of the NLRP1 inflammasome. In conclusion, our study not only reveals how CARD8 downregulates NLRP1 inflammasome activation, but also provides insights into the mechanisms of CARD-containing inflammasome assembly.

immunology↗

bioRxiv2022

The mechanosensitive ion channel Piezo1 modulates the migration and immune response of microglia

Microglia are the brains resident immune cells, performing surveillance to promote homeostasis and healthy functioning. While chemical signaling in microglia is well-studied, the mechanical cues regulating their function are less well-understood. Here, we investigate the role of the mechanosensitive ion channel Piezo1 in microglia migration, pro-inflammatory cytokine production and stiffness sensing. We demonstrated the functional expression of Piezo1 in microglia and identified genes whose expression was affected by conditional Piezo1 knockout in transgenic mice. Functional assays revealed that Piezo1-deficiency in microglia enhanced migration towards amyloid {beta}-protein, and decreased levels of pro-inflammatory cytokines produced upon stimulation by lipopolysaccharide, both in vitro and in vivo. The phenomenon could be mimicked or reversed using a Piezo1-specific agonist or antagonist. Finally, we also showed that Piezo1 mediated the effect of substrate stiffness-induced migration and cytokine expression. Altogether, we show that Piezo1 is an important molecular mediator for microglia, its activation modulating their migration and immune responses.

neuroscience↗

bioRxiv2022

Dominant constraints on the evolution of rhythmic gene expression

Although the individual transcriptional regulators of the core circadian clock are distinct amongst different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, whether analogous design principles govern the gene expression output of circadian clocks is unknown. Herein, we performed a comparative analysis of rhythmic gene expression in eight diverse species and captured four common distribution patterns of cycling gene expression across these species. We hypothesized that maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the late- and early-phase peaks of rhythmic expression have been subjected to this type of selective pressure. Therefore, energetic costs have constricted the cycling transcriptome throughout evolutionary history.

cell biology↗

bioRxiv2022

An empirical study of sex-stratified vs. sex-combined analysis in the presence of genetic effect heterogeneity

The effect of a genetic variant on a complex trait may differ between female and male, and in the presence of such genetic effect heterogeneity, sex-stratified analysis is often used. For example, genetic effects are sex-specific for testosterone levels, and sex-stratified analysis of testosterone in literature provided easy-to-interpret, sex-specific effect size estimates. However, from the perspective of association testing power, sex-stratified analysis may not be the best approach. As sex-specific genetic effect implies SNPxSex interaction effect, jointly testing SNP main and SNPxSex interaction effects may be more powerful than sex-stratified analysis or the standard main-effect testing approach. Moreover, since individual data may be unavailable, it is then of interest to study if the interaction analysis can be derived from sex-stratified summary statistics. We considered several different sex-combined methods and evaluated them through extensive simulation studies. We observed that a) the joint SNP main and SNPxSex interaction analysis is most robust to a wide range of genetic models, and b) this joint interaction testing result can be obtained by quadratically combining sex-stratified summary statistics (i.e. squared sum of the sex-stratified summary statistics). We then reanalysed the testosterone levels of the UK Biobank data using sex-combined interaction analysis, which identified 27 new loci that were missed by the sex-stratified approach and the standard sex-combined analysis. Finally, we provide supporting association evidence for nine new loci, uniquely identified by the sex-combined interaction analysis, from earlier association studies of either testosterone level or steroid biosynthesis pathway where testosterone is synthesized. We thus recommend sex-combined interaction analysis, particularly for traits with known sex differences, for most powerful association testing, then followed by sex-stratified analysis for effect size estimation and interpretation.

genetics↗

bioRxiv2022

Long non coding RNA L13Rik promotes high glucose-induced mesangial cell injury by regulating miR-2861/CDKN1B axis

Diabetic nephropathy (DN) is a frequent and severe microvascular complication of diabetes. Glomerular mesangial cell (MC) injury occurs at the initial phase of DN and acts as a critical role in the pathogenesis of DN. Given the importance of long non-coding RNA (lncRNA) in regulating MC hyperplasia and extracellular matrix (ECM) accumulation, it is essential to identify functional lncRNAs during MC injury. Here a novel lncRNA, C920021L13Rik (L13Rik for short), was identified to up-regulated in DN progression. The expression of L13Rik in DN patients and diabetic rats was assessed using quantitative real-time PCR (qRT-PCR), and the function of L13Rik on regulating HG-induced MC injury was assessed using cell counting kit-8 (CCK-8) and western blot assay to analyze MC viability and ECM accumulation. We found that L13Rik level was significantly increased while miR-2861 level was significantly decreased in peripheral blood of DN patients, renal tissues of diabetic rats, and HG-treated MCs. Functionally, both L13Rik depletion and miR-2861 overexpression effectively reduced HG-induced MC survival, ECM accumulation, and cell hypertrophy. Mechanistically, L13Rik functioned as a competing endogenous RNA (ceRNA) to sponge miR-2861, resulting in the de-repression of its target cyclin-dependent kinase inhibitor 1B (CDKN1B), a gene known to accelerate MC injury. Collectively, the current results demonstrate that up-regulated L13Rik is correlated with DN, and may be a hopeful therapeutic target for DN.

cancer biology↗

bioRxiv2022

Secretin modulates appetite via brown adipose tissue - brain axis

Secretin activates brown adipose tissue (BAT) and induces satiation in both mice and humans. However, the exact brain mechanism of this satiety inducing, secretin-mediated gut-BAT-brain axis is unknown. In this placebo-controlled, single-blinded neuroimaging study, firstly using [18F]FDG-PET measures (n = 15), we established that secretin modulated brain glucose consumption through the BAT-brain axis. Predominantly, we found that BAT and caudate glucose uptake levels were negatively correlated (r = -0.54, p = 0.037) during secretin but not placebo condition. Then, using functional magnetic resonance imaging (fMRI; n = 14), we found that secretin down-regulated the brain response to appetizing food images and improved inhibitory control. Finally, in a PET-fMRI fusion analysis (n = 10), we disclosed the patterned correspondence between caudate glucose uptake and neuroactivity to reward and inhibition, showing that the secretin-induced neurometabolic coupling pattern promoted satiation. These findings suggest that secretin modulates the BAT-brain metabolic crosstalk and subsequent neurometabolic coupling to induce satiation, bearing potential clinical benefits for treating eating disorders. Significance of the studySecretin activates brown adipose tissue and induces satiation, but the underlying brain mechanisms are still unclear. This placebo-controlled PET-fMRI study uses brain metabolic and BOLD measures to dissect the modulatory effects of secretin on brain functions associative to satiation. Findings show that secretin i) modulates caudate glucose metabolism via the BAT-brain axis, ii) enhances BOLD response in inhibitory control, and iii) reduces reward-related BOLD response. Further evidence shows that these measured effects are tightly linked via the secretin-mediated brain neurometabolic coupling. This study significantly advances our knowledge on how secretin leads to satiation and highlights the potential role of secretin in treating eating disorders and obesity.

neuroscience↗

bioRxiv2022

Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages

SARS-CoV-2 variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding working mechanisms and developing therapeutic agents. In this study, we characterized previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-EM structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.

biochemistry↗

bioRxiv2022

SpatialDEG: Identification of differentially expressed genes by leveraging spatial information in spatially resolved transcriptomic studies

MotivationSpatially resolved transcriptomics (SRT) technologies have been developed to simultaneously profile gene expression while retaining physical information. To explore differentially expressed genes using SRT in the context of various conditions, statistical methods are needed to perform spatial differential expression analysis. ResultsWe propose that a new probabilistic framework, spatialDEG, can perform differential expression analysis by leveraging spatial information on gene expression with spatial information. SpatialDEG utilizes the average information algorithm and can be scalable to tens of thousands of genes. Comprehensive simulations demonstrated that spatialDEG can identify genes differentially expressed in tissues across different conditions with a controlled type-I error rate. We further applied spatialDEG to analyze datasets for human dorsolateral prefrontal cortex and mouse whole liver. AvailabilityThe R package spatialDEG can be downloaded from https://github.com/Shufeyangyi2015310117/spatialDEG.

genetics↗

bioRxiv2022

PILS proteins provide a homeostatic feedback on auxin signaling output

Auxin is a crucial regulator of plant growth and development. Multiple internal and external signals converge at the regulation of auxin metabolism, intercellular transport, and signaling (Pernisova and Vernoux, 2021; Anfang and Shani, 2021). Considering this complexity, it remains largely unknown how plant cells monitor and ensure the homeostasis of auxin responses. PIN-LIKES (PILS) intracellular auxin transport facilitators at the endoplasmic reticulum (ER) are suitable candidates to buffer cellular auxin responses, because they limit nuclear abundance and signaling of auxin (Barbez et al., 2012; Beziat et al., 2017; Feraru et al., 2019; Sun et al., 2020). We used forward genetics to identify mechanisms that define the PILS6 protein abundance and thereby auxin signaling outputs. We screened for gloomy and shiny pils (gasp) mutants that define the levels of PILS6-GFP under a constitutive promoter. In this study, we show that GASP1 encodes for an uncharacterized RING/U-box superfamily protein and impacts on auxin signaling output. We conclude that the low auxin signaling in gasp1 mutants correlates with reduced abundance of PILS proteins, such as PILS5 and PILS6, which consequently balances auxin-related phenotypes. In agreement, we show that high and low auxin conditions increase and reduce PILS6 protein levels, respectively. Accordingly, non-optimum auxin concentrations are buffered by alterations in PILS6 abundance, consequently leading to homeostatic auxin output regulation. We envision that this feedback mechanism provides robustness to auxin-dependent plant development.

plant biology↗

bioRxiv2022

Biophysical, Molecular and Proteomic profiling of Human Retinal Organoids derived Exosomes

Extracellular vesicles (EVs) are phospholipid bilayer-bound particles released by cells that play a role in cell-cell communication, signal transduction, and extracellular matrix remodeling. There is a growing interest in EVs for ocular applications as therapeutics, biomarkers, and drug delivery vehicles. EVs secreted from mesenchymal stem cells (MSCs) have shown to provide therapeutic benefits in ocular conditions. However, very little is known about the properties of bioreactors cultured-3D human retinal organoids secreted EVs. This study provides a comprehensive morphological, nanomechanical, molecular, and proteomic characterization of retinal organoid EVs and compares it with human umbilical cord (hUC) MSCs. Nanoparticle tracking analysis indicated the average size of EV as 100-250 nm. Atomic force microscopy showed that retinal organoid EVs are softer and rougher than the hUCMSC EVs. Gene expression analysis by qPCR showed a high expression of exosome biogenesis genes in late retinal organoids derived EVs (>120 days). Immunoblot analysis showed highly expressed exosomal markers Alix, CD63, Flotillin-2, HRS and Hsp70 in late retinal organoids compared to early retinal organoids EVs (<120 days). Protein profiling of retinal organoid EVs displayed a higher differential expression of retinal function-related proteins and EV biogenesis/marker proteins than hUCMSC EVs, implicating that the use of retinal organoid EVs may have a superior therapeutic effect on retinal disorders. This study adds supplementary knowledge on the properties of EVs secreted by retinal organoids and suggests their potential use in the diagnostic and therapeutic treatments for ocular diseases.

bioengineering↗

bioRxiv2022

Ribo-macs derived from nucleoli:big ribosome clusters in the cytoplasm of naive stem cells

Primed stem cells and naive stem cells are important for understanding early development, but their ribosomes have not been focused on. In this study, we find that big ribosome clusters named Ribo-macs exist in the cytoplasm of naive stem cells. Then, we prove that Ribo-macs are dynamic and physiological in the cytoplasm, and can synthesize proteins associated with biogenesis of endoplasmic reticulum and mitochondria. We also discover and demonstrate that Ribo-macs are the nucleoli, which of significance is promoting us to rethink our understanding of nucleoli. Besides, we reveal that Ribo-macs have a compatible relation with P-bodies and stress granules. In a word, all the results about Ribo-macs provide us with a new insight to understand how cells adapt quickly to environment.

developmental biology↗

bioRxiv2022

Rational design by structural biology of industrializable, long-acting antihyperglycemic GLP-1 receptor agonists

Glucagon-like peptide-1 (GLP-1) is easily degraded by dipeptidyl peptidase-4 (DPP-4) in the human body, limiting its therapeutic effect on type II diabetes. Therefore, improving GLP-1 receptor agonist (GLP-1RA) stability is a major obstacle for drug development. We analyzed human GLP-1, DPP-4, and GLP-1 receptor structures and designed three GLP-1RAs, which were introduced into fusion protein fragments and changed in the overall conformation. This modification effectively prevented GLP-1RAs from entering DPP-4 active center without affecting GLP-1Ras ability to bind to GLP-1R, the new GLP-1RA hypoglycemic effect lasting for >24 h. Through molecular modeling, molecular dynamics calculation, and simulation, possible tertiary structure models of GLP-1RAs were obtained; molecular docking with DPP-4 and GLP-1R showed access to the fusion protein. The overall conformational change of GLP-1RAs prevented DPP-4 binding, without affecting GLP-1Ras affinity to GLP-1R. This study provides important drug design ideas for GLP-1RA development and a new example for application of structural biology-based protein design in drug development.

bioengineering↗

bioRxiv2022

Photoperiod modulates mu-opioid receptor availability in brown adipose tissue

Photoperiod drives metabolic activity of brown adipose tissue (BAT), and affects food intake and weight gain in mammals. Sympathetic innervation in BAT controls thermogenesis and facilitates physiological adaption to seasons, but the exact mechanism remains elusive. Previous studies show that the central opioid signaling tunes BAT heating and the brain muopioid receptor (MOR) levels have seasonal patterns. It is hence intriguing to know whether the peripheral MOR signaling shows seasonal variation. Here, we examined the effect of photoperiod on BAT MOR availability using [11C]carfentanil positron emission topography (PET). Adult rats (n = 9) were repeatedly imaged under changing photoperiods which simulates the local seasons. Long photoperiod downregulated MOR availability in BAT, while MOR availability in the muscles was unaffected. We confirmed the expression of MOR in BAT and muscle using immunofluorescence imaging. We conclude that photoperiod causally affects MOR availability in BAT, and sympathetic innervation of BAT may influence thermogenesis via the peripheral MOR system. Significance of the studyPhotoperiod impacts the metabolic activity of brown adipose tissue (BAT) with the exact mechanism still unclear. The current study shows that photoperiod causally affects the mu-opioid receptor (MOR) levels in BAT, with longer photoperiod leading to lower MOR availability. This possibly indicates down-regulated innervation during bright seasons. Immunofluorescence staining data reveal expression of MOR in both brain and peripheral tissues, drawing attention to the under-investigated peripheral MOR system. Also, the study highlights the feasibility of [11C]carfentanil PET in studying the peripheral MOR signaling.

molecular biology↗

bioRxiv2022

Bumblebees retrieve only the ordinal ranking of foraging options when comparing memories obtained in distinct settings

Are animals preferences determined by absolute memories for options (e.g., reward sizes) or by their remembered ranking (better/worse)? The only studies examining this question suggest humans and starlings utilize memories for both absolute and relative information. We show that bumblebees make decisions using only memories of ordinal comparisons. After learning to discriminate pairs of different flowers by sucrose concentration, bumblebees preferred flowers (in novel pairings) with 1) higher ranking over equal absolute reward, 2) higher ranking over higher absolute reward, and 3) identical qualitative ranking but different quantitative ranking equally. Despite these suboptimal choices, bumblebees found the optimal option in an ecologically relevant foraging task. Our results illuminate a divergent mechanism of learned preferences that may have arisen from adaptations to bumblebees natural environment.

animal behavior and cognition↗

bioRxiv2022

A dual mechanism of APC/C inhibition by MAP kinases

Mitotic anaphase onset is a key cellular process that is tightly regulated by multiple kinases. The involvement of mitogen-activated protein kinases (MAPKs) in this process has been established long ago in Xenopus egg extracts. However, despite its importance, it is still unclear which MAPK(s) is actually involved, this impedes the further understanding of the regulatory cascade. In this study, we first demonstrated that the involvement of MAPKs in mitotic anaphase onset regulation is evolutionarily conserved in the fission yeast (Schizosaccharomyces pombe). Then, we found that two of the three fission yeast MAPK signaling pathways act in concert to restrain anaphase-promoting complex/cyclosome (APC/C) activity upon activation of the spindle assembly checkpoint (SAC). The first pathway involves the phosphorylation of Mad2, a component of the core mitotic check complex (MCC), by MAPK Sty1, which enhances the tight binding of MCC to APC/C. The second pathway involves MAPK Pmk1 phosphorylation of Slp1Cdc20, the fission yeast homologue of Cdc20 and the co-activator of APC/C, which promotes the degradation of Slp1Cdc20. Both phosphorylation events are required to sustain mitotic arrest in response to spindle defects. These results clarified a detailed regulation cascade of the ubiquitous MAPK signaling in spindle checkpoint activation, APC/C inhibition and anaphase entry, which is vital for accurate chromosome segregation and cell viability.

cell biology↗

bioRxiv2022

Unifying genetic association tests via regression: Prospective and retrospective, parametric and non-parametric, and genotype- and allele-based tests

Genetic association analysis, evaluating the relationship between genetic markers and complex and heritable traits, is the basis of genome-wide association studies. In response, many association tests have been developed, and they are generally classified as prospective vs. retrospective, parametric vs. non-parametric, and genotype- vs. allele-based association tests. While method classification is useful, it is confusing and challenging for practitioners to decide on the optimal test to use for their data. Although there are known differences between some of the popular association tests, we provide new results that show the analytical connections between the different tests for both population- and family-based study designs. ResumeInserer votre resume ici. We will supply a French abstract for those authors who cant prepare it themselves.

genomics↗

bioRxiv2022

CIS calibrates GM-CSF signalling strength to regulate macrophage polarization via a STAT5-IRF8 axis

The cytokine granulocyte-macrophage-colony stimulating factor (GM-CSF) possesses the ability to differentiate macrophages (MOs) with opposing functions, namely proinflammatory M1-like and immunosuppressive M2-like. Despite the importance and opposing functional outcomes of these processes, the intrinsic mechanism that regulates the functional polarization of MOs under GM-CSF signaling remains elusive. Here we show that GM-CSF induced MOs polarisation resulted in the expression of the Cytokine-inducible SH2-containing protein (CIS), and that CIS deficiency diverted differentiation of monocytes into immunosuppressive M2-like MOs expression. CIS deficiency resulted in the hyperactivation of the JAK-STAT5 signaling pathway, consequently promoting the downregulation of the transcription factor Interferon Regulatory Factor 8 (IRF8). Loss and gain of function approaches highlighted IRF8 as a critical instructor of the M1-like polarisation program. In vivo, CIS deficiency led to skewing to M2-like macrophages, which induced strong Th2 immune responses characterised by the development of severe experimental asthma. Collectively, we reveal a CIS-censored mechanism interpreting the opposing actions of GM-CSF in MO differentiation and uncovering its role in controlling allergic inflammation.

immunology↗

bioRxiv2022

High Quality Phasing Using Linked-Read Whole Genome Sequencing of Patient Cohorts Informs Genetic Understanding of Complex Traits

Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. For population studies, phase is often inferred from external data but read-based phasing approaches that span long genomic distances would be more accurate because they enable both genotype and phase to be obtained from a single dataset. To demonstrate how read-based phasing can provide functional insights, we sequenced 477 individuals with Cystic Fibrosis (CF) using linked-read sequencing. We benchmark read-based phasing with different short- and long-read sequencing technologies, prioritize linked-read technology as the most informative and produce a benchmark phase call set from reference sample HG002 for the community. The 477 samples display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, which facilitates understanding of complex CF alleles. Fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus demonstrates a 20 kb deletion and a PRSS2 missense variant p.Thr8Ile (rs62473563) independently contribute to meconium ileus risk (p=0.0028, p=0.011, respectively) and are PRSS2 pancreas eQTLs (p=9.5e-7 and p=1.4e-4, respectively), explaining the mechanism by which these polymorphisms contribute to CF. Phase enables access to haplotypes that can be used for genome graph or reference panel construction, identification of cis-effects, and for understanding disease associated loci. The phase information from linked-reads provides a causal explanation for variation at a CF-relevant locus which also has implications for the genetic basis of non-CF pancreatitis to which this locus has been reported to contribute.

genetics↗