Biology subjects

Qi, W.

Publications and source records attributed to Qi, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Sexual Failure Decreases Sweet Taste Perception in Male Drosophila via Dopaminergic Signaling

Sweet taste perception, a critical aspect of the initiation of feeding behavior, is primarily regulated by an animals internal metabolic state. However, non-metabolic factors, such as motivational and emotional states, can also influence peripheral sensory processing and hence feeding behavior. While mating experience is known to induce motivational and emotional changes, its broader impact on other innate behaviors, such as feeding, remains largely uncharacterized. In this study, we demonstrated that mating failure of male fruit flies suppressed sweet taste perception via dopamine signaling in specific neural circuitry. Upon repetitive failure in courtship, male flies exhibited a sustained yet reversible decline of sweet taste perception, as measured by the proboscis extension reflex (PER) towards sweet tastants as well as the neuronal activity of sweet-sensing Gr5a+ neurons in the proboscis. Mechanistically, we identified a small group of dopaminergic neurons projecting to the subesophageal zone (SEZ) and innervating with Gr5a+ neurons as the key modulator. Repetitive sexual failure decreased the activity of these dopaminergic neurons and in turn suppressed Gr5a+ neurons via Dop1R1 and Dop2R receptors. Our findings revealed a critical role for dopaminergic signaling in integrating reproductive experience with appetitive sensory processing, providing new insights into the complex interactions between different innate behaviors and the role of brains reward systems in regulating internal motivational and emotional states.

neuroscience↗

bioRxiv2024

A FRET-Based FLIM Method to Probe Membrane-Induced Alpha-Synuclein Aggregation in Neurons

1Parkinsons disease (PD) involves the aggregation of the protein alpha-synuclein, a process promoted by interactions with intracellular membranes. To study this phenomenon in neurons for the first time, we developed a fluorescence lifetime imaging (FLIM) method using Forster resonance energy transfer and self-quenching reporters, analyzed with a custom-built FLIM microscope. This method offers insights into aggregate formation in PD and can be broadly applied to probe protein-membrane interactions in neurons.

neuroscience↗

bioRxiv2024

Mechanisms of Alpha-Synuclein Seeded Aggregation in Neurons Revealed by Fluorescence Lifetime Imaging

1The brains of Parkinsons disease (PD) patients are characterized by the presence of Lewy body inclusions enriched with fibrillar forms of the presynaptic protein alpha-synuclein (aSyn). Despite related evidence that Lewy pathology spreads across different brain regions as the disease progresses, the underlying mechanism hence the fundamental cause of PD progression is unknown. The propagation of aSyn pathology is thought to potentially occur through the release of aSyn aggregates from diseased neurons, their uptake by neighboring healthy neurons via endocytosis, and subsequent seeding of native aSyn aggregation in the cytosol. A critical aspect of this process is believed to involve the escape of internalized ag-gregates from the endolysosomal compartment, though direct evidence of this mechanism in cultured neuron models remains lacking. In this study, we utilize a custom-built, time-gated fluorescence lifetime imaging microscope (FLIM) to investigate the progression of seeded ag-gregation over time in live cortical neurons. By establishing fluorescence lifetime sensitivity to aSyn aggregation level, we are able to monitor the proteins aggregation state. Through a FLIM analysis of neurons expressing aSyn-mVenus and exposed to aSyn preformed fibrils labeled with the acid-responsive dye pHrodo, we reveal the proteins aggregation state in both the cytosol and the endolysosomal compartment. The results indicate that aSyn seeds undergo partial disassembly prior to escaping the endocytic pathway, and that this escape is closely linked to the aggregation of cytosolic aSyn. In certain neurons, monomeric aSyn is found to translocate from the cytosol into the endolysosomal compartment, where it appar-ently forms aggregates in proximity to retained seeds. Additional analyses reveals zones of neuritic aSyn aggregates that overlaps with regions of microtubule disruption. Collectively, these findings enhance our understanding of aSyn pathology propagation in PD and other synucleinopathies, motivate additional experiments along these lines, and offer a path to guide the development of disease-modifying therapies.

neuroscience↗

bioRxiv2024

Distinct duration and diet dependent lipid profiles and renal complicationsin GCK-MODY

Heterozygous inactivating mutations in the glucokinase (GCK) gene cause one of the most common types of maturity-onset diabetes of the young type 2 (MODY2), also named GCK-MODY. Studies suggest that, unlike other types of diabetes, patients with GCK-MODY do not have increased risk of diabetic complications and therefore do not typically require antihyperglycemic therapy. However, long-term outcomes of GCK-MODY on lipid profiles and chronic complications under different dietary scenarios remain unclear. Herein, using a knock-in mouse model expressing a novel MODY causing mutation GCK-Q26L (GCKMut), we examined age- and diet-related lipid profiles and diabetic complications. We found that, although GCKMut mice exhibited mild elevated blood glucose, the lipid profiles, body fat composition, and diabetic kidney disease (DKD) were initially improved in high-fat-diet (HFD) fed mice at the age of 28 weeks, supporting potential beneficial effects of GCKMut on lipid metabolism and kidney health. Unexpectedly however, those protective effects diminished by 40 weeks, and became more severe dyslipidemia and kidney injury associated with renal fibrosis and inflammation at 60-week-old mice fed with normal diet (ND) or HFD. Those findings revealed distinct duration- and diet-dependent effects of inactivating GCK mutation on lipid profiles and DKD, highlighting previously unrealized long-term chronic complications in GCK-MODY.

physiology↗

bioRxiv2024

Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE

A key advantage of single-cell multimodal joint profiling is the modality interplay, which is essential for deciphering the cell fate. However, while current analytical methods can leverage the additive benefits, they fall short to explore the synergistic insights of joint profiling, thereby diminishing the advantage of joint profiling. Here, we introduce CellMATE, a Multi-head Adversarial Training-based Early-integration approach specifically developed for multimodal joint profiling. CellMATE can capture both additive and synergistic benefits inherent in joint profiling through auto-learning of multimodal distributions and simultaneously represents all features into a unified latent space. Through extensive evaluation across diverse joint profiling scenarios, CellMATE demonstrated its superiority in ensuring utility of cross-modal properties, uncovering cellular heterogeneity and plasticity, and delineating differentiation trajectories. CellMATE uniquely unlocks the full potential of joint profiling to elucidate the dynamic nature of cells during critical processes as differentiation, development and diseases. Graphical abstracts O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/610031v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@8a3f46org.highwire.dtl.DTLVardef@401d5aorg.highwire.dtl.DTLVardef@1472aecorg.highwire.dtl.DTLVardef@1530b62_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Neural representational precision of distance predicts arithmetic performance

Focusing on the distance between magnitudes as the start point to investigate the mechanism of relationship detecting and its contribution to mathematical thinking, this study explores the precision of neural representations of numerical distance and their impact on arithmetic performance. By employing neural decoding techniques and representational similarity analysis, the present study investigates how accurately the brain represents numerical distances and how this precision relates to arithmetic skills. Thirty-two children participated, completing a dot number comparison task during fMRI scanning and an arithmetic fluency test. Results indicated that neural activation patterns in the intra-parietal sulcus decoded the distance between the presented pair of dots, and higher precision in neural distance representation correlates with better arithmetic performance. These findings suggest that the accuracy of neural decoding can serve as an index of the neural representation precision and that the ability to precisely encode numerical distances in the brain is a key factor in mathematical abilities. This provides new insights into the neural basis of mathematical cognition and learning. HighlightsO_LIUtilizing representational similarity analysis and neural decoding techniques, the research proposes that the accuracy of neural decoding serve as an index of neural representation precision. C_LIO_LIThe precision of neural representation of numerical distances in the brain predicts task performance and math arithmetic proficiency in children. C_LIO_LIThese findings imply the potential significance of relational information in general cognition and learning beyond mathematical learning. C_LI

neuroscience↗

bioRxiv2024

Targeting the paralog protein for degradation accounts for the opposite roles of NRBP1 and NRBP2 in regulating LINE1 retrotransposition

Gene duplication generates paralogs undergoing diverse fates during evolution and serves as a potent catalyst of biological complexity. Paralogs frequently share redundant functions and may also exhibit antagonistic activities by competing for common interaction partners. Here we show that the gene paralogs NRBP1 and NRBP2 oppositely regulate LINE1 retrotransposition, via influencing integrity of the LINE1 ribonucleoprotein complex. We demonstrate that the opposite roles of NRBP1 and NRBP2 are not results of a competitive mechanism, but rather due to targeting NRBP1 for proteasome-mediated decay by NRBP2, probably through heterodimer formation. Moreover, our phylogenetic analysis shows that the regulatory function of NRBP2 may be acquired later during evolution, suggesting that evolutionary pressure has favored this functional fine-tuning of NRBP1. In summary, our discovery not only identifies NRBP1/2 as novel LINE1 regulators and implicates their involvement in human pathogenesis, but also provides a novel insight into the regulatory details arising from gene duplication.

cell biology↗

bioRxiv2024

The novel role of Kallistatin in linking metabolic syndromes and cognitive memory deterioration by inducing amyloid-β plaques accumulation and tau protein hyperphosphorylation

Accumulation of amyloid {beta} (A{beta}) peptides and hyperphosphorylated tau proteins in the hippocampus triggers cognitive memory decline in Alzheimers disease (AD). The incidence and mortality of sporadic AD were tightly associated with diabetes and hyperlipidemia, while the exact linked molecular is uncertain. Here, we reported that serum Kallistatin concentrations were meaningfully higher in AD patients, with a higher concentration of fasting blood glucose and triglyceride. In addition, the constructed Kallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype and lower LTP in hippocampal CA1 neurons accompanied by increased A{beta} deposition and tau phosphorylation. Mechanistically, Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling, resulting in A{beta} cleavage and production. Besides, Kallistatin could promote the phosphorylation of tau by activating GSK-3{beta}. Fenofibrate, a hypolipidemic drug, could alleviate cognitive memory impairment by down-regulating A{beta} and tau phosphorylation of KAL-TG mice. Collectively, our data clarified a novel mechanism for A{beta} accumulation and tau protein hyperphosphorylation regulation by Kallistatin, which might play a crucial role in linking metabolic syndromes and cognitive memory deterioration, and suggested that fenofibrate might have the potential for treating metabolism-related AD. HighlightsO_LIKallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype accompanied by increased A{beta} deposition and tau phosphorylation. C_LIO_LIKallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling. C_LIO_LIFenofibrate could alleviate cognitive memory impairment and down-regulate the serum Kallistatin level. C_LI

neuroscience↗

bioRxiv2024

Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids

Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternative splice isoforms. This complex phenomenon can be revealed by an in-depth understanding of cellular heterogeneity at the single-cell level. Recent advances in single-cell long- read sequencing technologies enable comprehensive transcriptome sequencing at the single-cell level. In this study, we have generated single-cell long-read sequencing of Patient-Derived Organoid (PDO) cells of clear-cell Renal Cell Carcinoma (ccRCC), an aggressive and lethal form of cancer that arises in kidney tubules. We have used the Multiplexed Arrays Sequencing (MAS-ISO-Seq) protocol of PacBio to sequence full-length transcripts exceptionally deep across 2,599 single cells to obtain the most comprehensive view of the alternative landscape of ccRCC to date. On average, we uncovered 86,182 transcripts across PDOs, of which 31,531 (36.6%) were previously uncharacterized. In contrast to known transcripts, many of these novel isoforms appear to exhibit cell-specific expression. Nonetheless, >50% of these novel transcripts were predicted to possess a complete protein-coding open reading frame. This finding suggests a biological role for these transcripts within kidney cells. Moreover, an analysis of the most dominant transcript switching events between ccRCC and non-ccRCC cells revealed that many switching events were cell and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC. Overall, our research elucidates the intricate transcriptomic architecture of ccRCC, potentially exposing the mechanisms underlying its aggressive phenotype and resistance to conventional cancer therapies.

cancer biology↗

bioRxiv2024

Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach

Single-cell RNA sequencing is used in profiling gene expression differences between cells. Short-read sequencing platforms provide high throughput and high-quality information at the gene-level, but the technique is hindered by limited read length, failing in providing an understanding of the cell heterogeneity at the isoform level. This gap has recently been addressed by the long-read sequencing platforms that provide the opportunity to preserve full-length transcript information during sequencing. To objectively evaluate the information obtained from both methods, we sequenced four samples of patient-derived organoid cells of clear cell renal cell carcinoma and one healthy sample of kidney organoid cells on Illumina Novaseq 6000 and PacBio Sequel IIe. For both methods, for each sample, the cDNA was derived from the same 10x Genomics 3 single-cell gene expression cDNA library. Here we present the technical characteristics of both datasets and compare cell metrics and gene-level information. We show that the two methods largely overlap in the results but we also identify sources of variability which present a set of advantages and disadvantages to both methods.

genomics↗

bioRxiv2024

Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

Phosphorus is essential in all cells structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence. Author SummaryFungi must be able to access enough phosphate in order to invade the human body. Virulence of Candida albicans, the most common invasive human fungal pathogen, is known to decrease when one of the proteins that brings phosphate into the fungal cell, called Pho84, is disabled. We identified three more proteins in C. albicans that transport phosphate into the cell. We found that Pho84 plays the largest role among them across the broadest range of environmental conditions. After eliminating all 4 of these transporters, we let two resulting mutants evolve for two months in limited phosphate and analyzed the growth and stress resistance of the resulting populations. We analyzed genomes of representative populations and found that early adaptations to phosphate scarcity occurred together with major changes to chromosome configurations. In later stages of the adaptation process, these large-scale changes disappeared as populations presumably gained small-scale mutations that increased cells ability to grow in limited phosphate. Some but not all of these favorable mutations improved resistance of evolving populations to stressors like membrane- and cell wall stress. Pinpointing distinct mutation combinations that affect stress resistance differently in populations adapting to scarce phosphate, may identify useful antifungal drug targets.

microbiology↗

bioRxiv2024

Discovery of orally active SARS-CoV-2 papain-like protease (PLpro) inhibitors

Vaccines and first-generation antiviral therapeutics have provided important protection against coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there remains a need for additional therapeutic options that provide enhanced efficacy and protection against potential viral resistance. The SARS-CoV-2 papain-like protease (PLpro) is one of two essential cysteine proteases involved in viral replication. While inhibitors of the SARS-CoV-2 main protease (Mpro) have demonstrated clinical efficacy, known PLpro inhibitors have to date lacked the inhibitory potency and requisite pharmacokinetics to demonstrate that targeting PLpro translates to in vivo efficacy in a preclinical setting. Herein, we report the machine learning-driven discovery of potent, selective, and orally available SARS-CoV-2 PLpro inhibitors, with lead compound PF-07957472 (4) providing robust efficacy in a mouse-adapted model of COVID-19 infection.

microbiology↗

bioRxiv2023

Reactive oxygen species accelerate de novo acquisition of antibiotic resistance in E. coli

Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. However, the role of ROS in the development of de novo resistance as a result of sublethal levels of bactericidal antibiotics has barely been investigated. Here, we report that single-gene knockout strains with reduced ROS scavenging exhibited enhanced ROS accumulation and more rapid acquisition of resistance when exposed to sublethal levels of bactericidal antibiotics. Consistent with this observation, the ROS scavenger thiourea in the medium decelerated resistance development. Thiourea downregulated the transcriptional level of error-prone DNA polymerase and DNA glycosylase MutM, which counters the incorporation and accumulation of 8-hydroxy-2-deoxyguanosine (8-HOdG) in the genome. The level of 8-HOdG significantly increased following incubation with bactericidal antibiotics but decreased after treatment with the ROS scavenger thiourea. These observations suggest that in E. coli sublethal levels of ROS stimulate de novo development of resistance, providing a mechanistic basis for hormetic responses induced by antibiotics. ImportanceExposure to sublethal concentrations of antimicrobials is known to result in de novo resistance development against the specific compound. Particularly, the use of antibiotics as feed additives to enhance productivity may result in the development of drug resistance in environmental and veterinary microorganisms, which could subsequently transfer to human populations. Nevertheless, the mechanisms underlying de novo resistance development have not been extensively explored. In this study, we indicate the role of ROS in promoting the formation of resistance to bactericidal antibiotics and show the potential of ROS scavengers to reduce mutation rates and slow down resistance formation under long-term selection. Thus, the supplementary use of antioxidants during prolonged antibiotic administration potentially contributes to mitigating the emergence of antimicrobial resistance.

microbiology↗

bioRxiv2023

WNT2B Deficiency Causes Increased Susceptibility to Colitis in Mice and Impairs Intestinal Epithelial Development in Humans

Background and aimsWNT2B is a canonical Wnt ligand previously thought to be fully redundant with other Wnts in the intestinal epithelium. However, humans with WNT2B deficiency have severe intestinal disease, highlighting a critical role for WNT2B. We sought to understand how WNT2B contributes to intestinal homeostasis. MethodsWe investigated the intestinal health of Wnt2b knock out (KO) mice. We assessed the impact of inflammatory challenge to the small intestine, using anti-CD3{chi} antibody, and to the colon, using dextran sodium sulfate (DSS). In addition, we generated human intestinal organoids (HIOs) from WNT2B-deficient human iPSCs for transcriptional and histological analyses. ResultsMice with WNT2B deficiency had significantly decreased Lgr5 expression in the small intestine and profoundly decreased expression in the colon, but normal baseline histology. The small intestinal response to anti-CD3{chi} antibody was similar in Wnt2b KO and wild type (WT) mice. In contrast, the colonic response to DSS in Wnt2b KO mice showed an accelerated rate of injury, featuring earlier immune cell infiltration and loss of differentiated epithelium compared to WT. WNT2B-deficient HIOs showed abnormal epithelial organization and an increased mesenchymal gene signature. ConclusionWNT2B contributes to maintenance of the intestinal stem cell pool in mice and humans. WNT2B deficient mice, which do not have a developmental phenotype, show increased susceptibility to colonic injury but not small intestinal injury, potentially due to a higher reliance on WNT2B in the colon compared to the small intestine. WNT2B deficiency causes a developmental phenotype in human intestine with HIOs showing a decrease in their mesenchymal component and WNT2B-deficient patients showing epithelial disorganization. Data Transparency StatementAll RNA-Seq data will be available through online repository as indicated in Transcript profiling. Any other data will be made available upon request by emailing the study authors.

molecular biology↗

bioRxiv2023

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the models ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances, namely local, medium, or distant associations.This paper addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference- and alignment-free, providing additional methodologies for testing, including a highly-flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar.The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.

bioinformatics↗

bioRxiv2022

The critical role of BTRC in hepatic steatosis as an ATGL E3 ligase

ObjectiveNon-alcoholic fatty liver disease (NAFLD), characterized by hepatic steatosis, is one of the most common causes of liver dysfunction. ATGL is closely related to hepatic steatosis as the speed-limited triacylglycerol lipase. Nevertheless, the expression and regulation of ATGL in NAFLD remain unclear. MethodsUsing immunohistochemistry and qRT-PCR to detect the expression of ATGL and BTRC in different models with hepatic steatosis. Co-IP evaluated the binding of ATGL and BTRC. Knockdown of BTRC employed by adenoviruses and then analyzed the ATGL expression, triglyceride levels, and lipid droplets accumulation. ResultsOur results revealed that ATGL protein level was decreased in animal and cellular models of hepatic steatosis and the liver tissues of cholangioma/hepatic carcinoma patients with hepatic steatosis, while the ATGL mRNA level had hardly changed; which means the decreased ATGL mainly degraded through the proteasome pathway. BTRC was identified as the E3 ligase for ATGL, up-regulated, and negatively correlated with ATGL level. Moreover, adenovirus-mediated knockdown of BTRC ameliorated hepatic steatosis via up-regulating ATGL level. ConclusionsOur study demonstrates a crucial role of elevated BTRC in hepatic steatosis through promoting ATGL proteasomal degradation as a new ATGL E3 ligase and suggests BTRC may serve as a potential therapeutic target for NAFLD. FundingThis study was supported by The National Natural Science Foundation of China (Grants 82070888, 82070882, 82100917, 81872165, 82273116, 82203661, 81901557 and 81902693); Key Project of Nature Science Foundation of Guangdong Province, China (Grant 2019B1515120077); National Key R&D Program of China (Grant 2018YFA0800403); Guangdong Special Support Program for Young Top Scientist (Grant 201629046); Guangdong Natural Science Fund (Grant 2019A1515011810, 2021A1515010434, 2022A1515012423 and 2022A1515012513); Key Sci-Tech Research Project of Guangzhou Municipality (Grants 202201010820) Fundamental Research Funds for the Central Universities (Grant 50000-31620106); China Postdoctoral Science Foundation (Grant 2021M703679, 2020M683110).

cell biology↗

bioRxiv2022

Down-regulated GAS6 impairs synovial macrophage efferocytosis and promotes obesity-associated osteoarthritis

Obesity has always been considered a significant risk factor in OA progression, but the underlying mechanism of obesity-related inflammation in OA synovitis remains unclear. The present study found that synovial macrophages infiltrated and polarized in the obesity microenvironment and identified the essential role of M1 macrophages in impaired macrophage efferocytosis using pathology analysis of obesity-associated OA. The present study revealed that obese OA patients and ApoE-/- mice showed a more pronounced synovitis and enhanced macrophage infiltration in synovial tissue, accompanied by dominant M1 macrophage polarization. Obese OA mice had a more severe cartilage destruction and increased levels of synovial apoptotic cells than OA mice in the control group. Enhanced M1-polarized macrophages in obese synovium decreased growth arrest-specific 6 (GAS6) secretion, resulting in impaired macrophage efferocytosis in synovial apoptotic cells. Intracellular contents released by accumulated apoptotic cells further triggered an immune response and lead to a release of inflammatory factors, such as TNF-, IL-1{beta}, and IL-6, which induce chondrocyte homeostasis dysfunction in obese OA patients. Intra-articular injection of GAS6 restored the phagocytic capacity of macrophages, reduced the accumulation of local apoptotic cells, and decreased the levels of TUNEL- and caspase-3-positive cells, preserving cartilage thickness and preventing the progression of obesity-associated OA. Therefore, blocking M1 macrophage polarization or intra-articular injection of GAS6 is a potential therapeutic strategy for obesity-associated OA.

immunology↗

bioRxiv2022

Guild-level microbiome signature associated with COVID-19 severity and prognosis

COVID-19 severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples collected from 300 in-hospital COVID-19 patients at time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), Redundancy Analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Random Forest model based on these 33 HQMAGs classified patients from different severity groups (average AUC = 0.79). Co-abundance network analysis found that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Random Forest regression showed that these 33 HQMAGs at admission had the capacity to predict 8 clinical parameters, which are predictors for COVID-19 prognosis, at Day 7 in hospital. Moreover, the dominance of Guild 1 over Guild 2 at admission predicted the death/discharge outcome of the critical patients (AUC = 0.92). Random Forest models based on these 33 HQMAGs classified patients with different COVID-19 symptom severity, and differentiated COVID-19 patients from healthy subjects, non-COVID-19, and pneumonia controls in three independent datasets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission.

microbiology↗