Biology subjects

Zhang, Q.

Publications and source records attributed to Zhang, Q..

At least 343 records · Page 19Linked to original sources

bioRxiv2024

Systems genetics approach uncovers associations between host amylase locus, gut microbiome and metabolic traits in hyperlipidemic mice

The molecular basis for how host genetic variation impacts gut microbial community and bacterial metabolic niches remain largely unknown. We leveraged 90 inbred hyperlipidemic mouse strains from the Hybrid Mouse Diversity Panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these we detected a genetic locus surrounding multiple amylase genes that was associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar metabolism functions. We also found that lower amylase gene number in the mouse genome was associated with higher gut Muribaculaceae levels. Previous work suggests that modulation of host amylase activity impacts the availability of carbohydrates to the host and potentially to gut bacteria. The genetic variants described above were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes. This work reveals novel relationships between host genetic variation, gut microbial enterotypes and host physiology/disease phenotypes in mice.

genetics↗

bioRxiv2024

Decoupling the molecular versatility of aminoglycosides via drug or target modification enables community-wide antiphage defense

The ongoing arms race between bacteria and phages has forced bacteria to evolve a sophisticated set of antiphage defense mechanisms that constitute the bacterial immune system. In our previous study, we highlighted the antiphage properties of aminoglycoside antibiotics, which are naturally secreted by Streptomyces. Successful inhibition of phage infection was achieved by addition of pure compounds and supernatants from a natural producer strain highlighting the potential for community-wide antiphage defense. However, given the dual functionality of these compounds, neighboring bacterial cells require resistance to the antibacterial activity of aminoglycosides to benefit from the protection they confer against phages. In this study, we demonstrated the successful uncoupling of antiphage and antibacterial properties via different aminoglycoside-resistance mechanisms encompassing drug and target site modifications. Furthermore, we confirmed the antiphage impact of aminoglycosides in a community context by co-culturing phage-susceptible, apramycin-resistant S. venezuelae with the apramycin-producing strain Streptoalloteichus tenebrarius. Given the prevalence of aminoglycoside resistance among natural bacterial isolates that allow functional uncoupling of these compounds, this study highlights the ecological relevance of chemical defense via aminoglycosides at the community level.

microbiology↗

bioRxiv2024

Ovarian disrupting effects and mechanisms of long- and short-chain per- and polyfluoroalkyl substances in mice

BackgroundThe extensive use of per- and polyfluoroalkyl substances (PFAS) has led to environmental contamination and bioaccumulation. Previous research linked PFAS exposure to female reproductive disorders, but the mechanism remains elusive. Further, most studies focused on legacy long-chain PFOA and PFOS, yet the reproductive impacts of other long-chain PFAS and short-chain alternatives are rarely explored. ObjectivesWe investigated the effects and mechanisms of long- and short-chain PFAS on the ovary and associated ovarian functions. MethodsA 3D in vitro ovarian follicle culture system and an in vivo mouse model, together with approaches of reverse transcription-quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, RNA-sequencing, pharmacological treatment, in situ zymography, histology, in situ hybridization, analytical chemistry, and benchmark dose modeling (BMD), were used to test environmentally relevant exposure levels of six long- and short-chain PFAS on follicle maturation, hormone secretion, and ovulation. ResultsIn vitro exposure revealed that long-but not short-chain PFAS interfered with gonadotropin-dependent follicle maturation, ovulation, and hormone secretion. Mechanistically, long-chain perfluorononanoic acid (PFNA) acted as a peroxisome proliferator-activated receptor gamma (PPAR{gamma}) agonist in granulosa cells to disrupt follicle-stimulating hormone (FSH)-dependent follicle maturation, luteinizing hormone (LH)-stimulated ovulation, and associated gene regulatory pathways. In vivo mouse exposure confirmed the ovarian accumulation of PFNA and the mechanism of PPAR{gamma}-mediated ovarian toxicities of PFNA observed in vitro. The BMD analysis of in vitro and in vivo results suggested human relevant exposure levels of long-chain PFAS in our study pose an extra risk of ovarian defects, with follicular rupture as the most sensitive endpoint. DiscussionUsing in vitro follicle culture and in vivo mouse models, we discovered that long-chain PFAS interfere with gonadotropin-dependent follicle maturation, hormone secretion, and ovulation, posing a non-negligible risk to womens reproductive health including anovulation, irregular menstrual cycles, and sub- or infertility.

pharmacology and toxicology↗

bioRxiv2024

Normative and individual, non-normative intrinsic networks and the transition to impaired cognition

Despite their temporal lobe pathology, a significant subgroup of temporal lobe epilepsy (TLE) patients are able to maintain normative cognitive functioning. Here, we identify TLE patients with intact versus impaired cognitive profiles, and interrogate for the presence of both normative and highly individual intrinsic connectivity networks(ICN) - all towards understanding the transition from impaired to intact neurocognitive status. We retrospectively investigated data from 88 TLE patients and matched 91 healthy controls with resting-state functional MRI. Functional MRI data were decomposed using independent component analysis to obtain individualized ICNs. Here, we calculated the degree of match between individualized ICNs and canonical ICNs (e.g., Yeo et.al 17 resting-state network) and divided each participants ICNs into normative or non-normative status based on the degree of match. We found that the individualized networks matched the canonical networks less well in the cognitively impaired compared to the cognitively intact TLE patients. The cognitively impaired patients showed significant abnormalities in the profiles of both normative and non-normative networks, whereas the intact patients showed abnormalities only in non-normative networks. At the same time, we found normative networks held a strong, positive association with the neuropsychological measures, with this association negative in non-normative networks. We were able to provide the initial data demonstrating that significant cognitive deficits are associated with the status of highly-individual ICNs, making clear that the transition from intact to impaired cognitive status is not simply the result of disruption to normative brain networks.

neuroscience↗

bioRxiv2024

Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TG Mice

COVID-19, caused by SARS-CoV-2, is associated with arterial and venous thrombosis, thereby increasing mortality. SARS-CoV-2 spike protein (SP), a viral envelope structural protein, is implicated in COVID-19-associated thrombosis. However, the underlying mechanisms remain unknown. Thymidine phosphorylase (TYMP), a newly identified prothrombotic protein, is upregulated in the plasma, platelets, and lungs of patients with COVID-19 but its role in COVID-19-associated thrombosis is not defined. In this study, we found that wild-type SARS-CoV-2 SP significantly promoted arterial thrombosis in K18-hACE2TG mice. SP-accelerated thrombosis was attenuated by inhibition or genetic ablation of TYMP. SP increased the expression of TYMP, resulting in the activation of signal transducer and activator of transcription 3 (STAT3) in BEAS-2B cells, a human bronchial epithelial cell line. A siRNA-mediated knockdown of TYMP inhibited SP-enhanced activation of STAT3. Platelets derived from SP-treated K18-hACE2TG mice also showed increased STAT3 activation, which was reduced by TYMP deficiency. Activated STAT3 is known to potentiate glycoprotein VI signaling in platelets. While SP did not influence ADP- or collagen-induced platelet aggregation, it significantly shortened activated partial thromboplastin time and this change was reversed by TYMP knockout. Additionally, platelet factor 4 (PF4) interacts with SP, which also complexes with TYMP. TYMP enhanced the formation of the SP/PF4 complex, which may potentially augment the prothrombotic and procoagulant effects of PF4. We conclude that SP upregulates TYMP expression, and TYMP inhibition or knockout mitigates SP-enhanced thrombosis. These findings indicate that inhibition of TYMP may be a novel therapeutic strategy for COVID-19-associated thrombosis. Key PointsO_LISARS-CoV-2 spike protein, thymidine phosphorylase, and platelet factor 4 form a complex that may promote clot formation. C_LIO_LIInhibiting thymidine phosphorylase attenuates SARS-CoV-2 spike protein-enhanced thrombosis, platelet activation, and coagulation. C_LI

cell biology↗

bioRxiv2024

Dose-response functional and transcriptomic effects of follicle-stimulating hormone on ex vivo mouse folliculogenesis

The gonadotropin-dependent phase of ovarian folliculogenesis primarily requires follicle-stimulating hormone (FSH) to support one or multiple antral follicles, dependent on the species, to mature fully, enabling ovarian steroidogenesis, oogenesis, and ovulation to sustain female reproductive cycles and fertility. FSH binds to its membrane receptor in granulosa cells to activate various signal transduction pathways and gene regulatory networks. Poor female reproductive outcomes can result from both FSH insufficiency owing to genetic or non-genetic factors and FSH excess as encountered with ovarian stimulation in assisted reproductive technology (ART), but the underlying molecular mechanisms remain elusive. Herein, we conducted single-follicle and single-oocyte RNA sequencing analysis along with other approaches in an ex vivo mouse folliculogenesis and oogenesis system to investigate the effects of different concentrations of FSH on key follicular events. Our study revealed that a minimum FSH threshold is required for follicle maturation into the high estradiol-secreting preovulatory stage, and the threshold is moderately variable among individual follicles. FSH at subthreshold, threshold, and suprathreshold levels induced distinct expression patterns of follicle maturation-related genes and the follicular transcriptomics. The RNA-seq analysis identified novel genes and signaling pathways that may critically regulate follicle maturation. Suprathreshold FSH resulted in multiple ovarian disorders including premature luteinization, high production of androgen and proinflammatory factors, and reduced expression of energy metabolism-related genes in oocytes. Together, this study improves our understanding of gonadotropin-dependent folliculogenesis and provides crucial insights into how high doses of FSH used in ART may impact follicular health, oocyte quality, pregnancy outcome, and systemic health.

molecular biology↗

bioRxiv2024

Non-Invasive dsRNA Delivery via Feeding for Effective Gene Silencing in Teleost Fish: A Novel Approach in the Study of Gene Function Analysis

RNA interference is a powerful technique for gene silencing, involving post-transcriptional regulation of gene expression. Successful application of RNAi has been demonstrated in various organisms like nematodes, insects, and oysters by ingesting dsRNA-expressing bacteria. In this study, we attempted a non-invasive feeding method in the marine economy teleost fish, Sebastes schlegelii. To validate the feasibility of this approach in S. schlegelii, we utilized rotifers (Brachionus plicatilis), Artemia nauplii, and commercial pellet feed as vectors to deliver Escherichia coli strain HT115 engineered to express double-stranded RNA (dsRNA), targeting dead end (dnd) gene, known to be important for primordial germ cells (PGCs) migration and proliferation in fish. Our experimental results consistently showed that knockdown of the dnd gene effectively inhibited the development of PGCs in S. schlegelii, resulting in gonadal dysplasia and even sex reversal. This study marks a significant advancement in understanding gene function in teleost fish, laying the groundwork for future large-scale research in this field.

genetics↗

bioRxiv2024

A multiscale model of the mammalian liver circadian clock supports synchronization of autonomous oscillations by intercellular communication.

Expression of core circadian clock genes in hepatocytes across the liver lobule is temporally synchronized despite cell-autonomous oscillations in gene expression. This spatial synchronization has been attributed to an unknown intercellular coupling mechanism. Here we have developed multicellular computational models of the murine liver lobule with and without intercellular coupling to investigate the role of synchronization in circadian gene expression. Our models demonstrated that intercellular coupling was needed to generate sustained circadian oscillations with a near 24-hour period. Without coupling the simulated period was variable within the 21-28-hour range. Further model analysis revealed that a robust near-24-hour oscillation period can be generated with a wide range of circadian protein degradation rates. In contrast, only a small window of circadian gene transcription rates was able to generate realistic oscillatory periods. The coupled model accurately captured the temporal dynamics of circadian genes derived from single-nuclei transcriptomic data. Overall, this study provides novel insights into the mammalian hepatic circadian clock through modeling of spatial and temporal gene expression patterns and data-driven analysis.

systems biology↗

bioRxiv2024

A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry

Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of COVID-19 patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 over-expression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we investigate the functional effects of PLSCR1 variants present in humans and discuss an association between PLSCR1 and severe COVID-19 reported recently.

immunology↗

bioRxiv2024

The first discovery of SFTSV in the Centre of Metropolitan Beijing, China

Severe fever with thrombocytopenia virus (SFTSV), an emerging tick-borne bandavirus, poses a significant public health threat in rural China. Since 2021, an increase in local cases has been noted in the rural-urban fringe surrounding Beijing. This study aimed to assess the formation of natural foci in urban areas by conducting a field survey of ticks and hedgehogs from Beijings second to fifth ring roads. Our survey revealed a diverse tick population in city parks, including the major SFTSV vector, H. longicornis. Parthenogenetic H. longicornis, known for its role in rapid SFTSV spread, was identified in key locations like Beihai Park and Taoranting Park, near the Forbidden City. Notably, high SFTSV seroprevalence and RNA prevalence were found in hedgehogs and parasitic ticks in the center of Beijing. These findings highlight the circulation of SFTSV in central Beijing, underscoring the need for urgent attention and enhanced surveillance measures.

microbiology↗

bioRxiv2024

Cross-species prediction of transcription factor binding by adversarial training of a novel nucleotide-level deep neural network

Cross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In this study, we first propose a novel Nucleotide-Level Deep Neural Network (NLDNN) to predict TF binding within or across species. NLDNN regards the task of TF binding prediction as a nucleotide-level regression task. Beyond predictive performance, we also assess model performance by locating potential TF binding regions, discriminating TF-specific single-nucleotide polymorphisms (SNPs), and identifying causal disease-associated SNPs. Then, we design a dual-path framework for adversarial training of NLDNN to further improve the cross-species prediction performance by pulling the domain space of human and mouse species closer.

bioinformatics↗

bioRxiv2024

Cholinergic modulation of interhemispheric inhibition in the mouse motor cortex

Interhemispheric inhibition (IHI) of the homotopic motor cortex is believed to be effective for accurate unilateral motor function. However, the cellular mechanisms underlying IHI during unilateral motor behavior remain unclear. Furthermore, the impact of the neuromodulator acetylcholine (ACh) on IHI and the associated cellular mechanisms are not well understood. To address this knowledge gap, we conducted recordings of neuronal activity from the bilateral motor cortex of mice during the paw-reaching task. Subsequently, we analyzed interhemispheric spike correlation at the cell-pair level, classifying putative cell types to explore the underlying cellular circuitry mechanisms of IHI. We found a cell-type pair-specific enhancement of the interhemispheric spike correlation when the mice were engaged in the reaching task. We also found that the interhemispheric spike correlation was modulated by pharmacological ACh manipulation. The local field responses to contralateral excitation differed along the cortical depths, and muscarinic receptor antagonism enhanced the inhibitory component of the field response in deep layers. The muscarinic subtype M2 receptor is predominantly expressed in deep cortical neurons, including GABAergic interneurons. These results suggest that GABAergic interneurons expressing muscarinic receptors in deep layers mediate the neuromodulation of IHI in the homotopic motor cortex.

neuroscience↗

bioRxiv2024

BioXNet: a biologically inspired neural network for deciphering anti-cancer drug response in precision medicine

Accurate prediction of anti-cancer drug responses in preclinical and clinical studies is crucial for drug discovery and personalized medicine. While machine learning models have demonstrated promising prediction accuracy in this task, their translational value in cancer therapy is constrained by the lack of model interpretability and insufficient patients data with genomic profiles to calibrate models. The rich cell line data has the potential to supplement patients data, but the difference between the drug response mechanisms in cell lines and human body needs to be characterized quantitatively. To address these challenges, we proposed the BioXNet, which captures drug response mechanisms by seamlessly integrating drug target information with genomic profiles (genetic and epigenetic modifications) into a single biologically inspired neural network. BioXNet exhibited superior performance in drug response prediction tasks in both preclinical and clinical settings. An analysis of BioXNets interpretability revealed its ability to identify significant differences in drug response mechanisms between cell lines and the human body. Notably, the key factor of drug response is the drug targeting genes in cell lines but methylation modifications in the human body. Furthermore, we developed an online human-readable interface of BioXNet for drug response exploration by medical professionals and laymen. BioXNet represents a step further towards unifying drug, cell line and patients data under a holistic interpretable machine learning framework for precision medicine in cancer therapy.

cancer biology↗

bioRxiv2024

Postharvest partial dehydration of blueberries enhanced blueberry wine aroma via upregulating phenylalanine metabolism and terpene biosynthesis

Postharvest partial dehydration of blueberries can enhance blueberry wine aroma, while the underlying mechanisms remain unclear. In this study, the key odor-active volatiles in blueberry wines fermented from dehydrated blueberries (30% weight loss) were identified via aroma extract dilution analysis. Results showed that increased levels of phenylalanine-derived compounds such as phenylethanol, and terpenes such as linalool and geraniol, primarily led to the enhancement of sweet, floral and fruity aromas of blueberry wines. Postharvest partial dehydration increased the contents of these compounds, which could be linked to the upregulation of VcGOT2 and VcPAR involved in phenylalanine metabolism, and the upregulation of VcDXS, VcHDR and VcTPS involved in terpene biosynthesis. Notably, the upregulated VcTPS encoded a monoterpene synthase responsible for producing linalool. These findings provided insight into the impact of postharvest dehydration on phenylalanine and terpene metabolism in blueberries, offering a reference for improving blueberry wine aroma through postharvest partial dehydration techniques.

biochemistry↗

bioRxiv2024

A Multiscale Spatial Modeling Framework for the Germinal Center Response

The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymph organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-{kappa}B, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanic and applied research questions in future.

immunology↗

bioRxiv2024

Deciphering the Molecular Mechanism of Post-Acute Sequelae of COVID-19 through Comorbidity Network Analysis

IntroductionThe post-acute sequelae of COVID-19 presents a significant health challenge in the post-pandemic world. Our study aims to analyze longitudinal electronic health records to determine the impact of COVID-19 on disease progression, provide molecular insights into these mechanisms, and identify associated biomarkers. MethodWe included 58,710 patients with COVID-19 records from 01/01/2020 to 31/08/2022 and at least one hospital admission before and after the acute phase of COVID-19 (28 days) as the treatment group. A healthy control group of 174,071 individuals was established for comparison using propensity score matching based on pre-existing diseases (before COVID-19). We built a comorbidity network using Pearson correlation coefficient differences between pairs of pre-existing disease and post-infection disease in both groups. Disease-protein mapping and protein-protein interaction network analysis revealed the impact of COVID-19 on disease trajectories through protein interactions in the human body. ResultsThe disparity in the weight of prevalent disease comorbidity patterns between the treatment and control groups highlights the impact of COVID-19. Certain specific comorbidity patterns show a more pronounced influence by COVID-19. For each comorbidity pattern, overlapping proteins directly associated with pre-existing diseases, post-infection diseases, and COVID-19 help to elucidate the biological mechanism of COVID-19s impact on each comorbidity pattern. Proteins essential for explaining the biological mechanism can be identified based on their weights. ConclusionDisease comorbidity associations influenced by COVID-19, as identified through longitudinal electronic health records and disease-protein mapping, can help elucidate the biological mechanisms of COVID-19, discover intervention methods, and decode the molecular basis of comorbidity associations. This analysis can also yield potential biomarkers and corresponding treatments for specific disease patterns. Ethical approvalEthical approval for this study was granted by the Institutional Review Board of the University of Hong Kong/HA HK West Cluster (UW20-556, UW21-149 and UW21-138). RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for research articles up to Nov 30, 2022, with no language restrictions, using the terms "Post-Acute Sequelae of COVID-19" OR "PASC" OR "Long COVID" AND "comorbidity" OR "multimorbidity" OR "co-morbidity" OR "multi-morbidity". We found most related papers focus on the comorbidity or multimorbidity patterns among PASC. Some papers focus on the associations between specific diseases and PASC. However, no study investigated the biological mechanism of PASC from the perspective of comorbidity network. Added value of this studyThis study investigated the biological mechanism of PASC based on the comorbidity network including the impact of pre-existing diseases (diseases diagnosed within 730 days before COVID-19) on the development of PASC. We classified pairs of pre-existing disease and post-infection disease (new diseases diagnosed in 28 days to 180 days after COVID-19) as comorbidity associations. Through a comparison of the frequency of comorbidity associations in health people group and patients with COVID-19 infection group, we identified comorbidity patterns that are significantly influenced by COVID-19 infection and constructed a comorbidity network comprising of 117 nodes (representing diseases) and 271 edges (representing comorbidity patterns). These comorbidity patterns suggest COVID-19 patients with these pre-existing diseases have higher risk for post-infection diseases. Through the analysis of the Protein-Protein interaction (PPI) network and associations between diseases and proteins, we identified key proteins in the topological distance of each comorbidity pattern and important biological pathways by GO enrichment analysis. These proteins and biological pathways provide insights into the underlying biological mechanism of PASC. Implications of all the available evidenceThe identification of elevated-risk comorbidity patterns associated with COVID-19 infection is crucial for the effective allocation of medical resources, ensuring prompt care for those in greatest need. Furthermore, it facilitates the recovery process of patients from COVID-19, offering a roadmap for their path back to health. The key proteins identified in our study have the potential to serve as biomarkers and targets for therapeutic intervention, thereby establishing a foundation for the development of new drugs and the repurposing of existing ones. Further research should focus on drug discovery and the development of drug recommendations for patients with COVID-19 infections.

pathology↗

bioRxiv2024

Identification of a distinct cluster of GDF15high macrophages exhibiting anti-inflammatory activities

Macrophage-mediated inflammatory response may have crucial roles in the pathogenesis of a variety of human diseases. Growth differentiation factor 15 (GDF15) is a cytokine of the transforming growth factor-{beta} superfamily, with potential anti-inflammatory activities. Previous studies observed in human lungs some macrophages which expressed a high level of GDF15. In the present study, we employed multiple techniques, including immunofluorescence, flow cytometry, and single-cell RNA sequencing, in order to further clarify the identity of such GDF15high macrophages. We demonstrated that macrophages derived from human peripheral blood mononuclear cells and rat bone marrow mononuclear cells by in vitro differentiation with granulocyte-macrophage colony stimulating factor contained a minor population ([~]1%) of GDF15high cells. GDF15high macrophages did not exhibit a typical M1 or M2 phenotype, but had a unique molecular signature as revealed by single-cell RNA sequencing. Functionally, GDF15high macrophages were associated with reduced responsiveness to pro-inflammatory activation; furthermore, GDF15high macrophages could inhibit the pro-inflammatory functions of other macrophages via a paracrine mechanism. We further confirmed that GDF15 per se was a key mediator of the anti-inflammatory effects of GDF15high macrophage. Also, we provided direct evidence showing that GDF15high macrophages were also present in other macrophage-residing human tissues in addition to the lungs. Our results suggest that the GDF15high macrophage may represent a distinct cluster of macrophage cells with intrinsic anti-inflammatory functions. The (patho)physiological importance of these cells in vivo warrants further investigation.

immunology↗

bioRxiv2024

D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability

The large majority of oxidative DNA lesions occurring in the G1 phase of the cell cycle are repaired by base excision repair (BER) rather than mismatch repair (MMR) to avoid long resections that can lead to genomic instability and cell death. However, the molecular mechanisms dictating pathway choice between MMR and BER have remained unknown. Here, we show that, during G1, D-type cyclins are recruited to sites of oxidative DNA damage in a PCNA- and p21-dependent manner. D-type cyclins shield p21 from its two ubiquitin ligases CRL1SKP2 and CRL4CDT2 in a CDK4/6-independent manner. In turn, p21 competes through its PCNA-interacting protein degron with MMR components for their binding to PCNA. This inhibits MMR while not affecting BER. At the G1/S transition, the CRL4AMBRA1-dependent degradation of D-type cyclins renders p21 susceptible to proteolysis. These timely degradation events allow the proper binding of MMR proteins to PCNA, enabling the repair of DNA replication errors. Persistent expression of cyclin D1 during S-phase increases the mutational burden and promotes microsatellite instability. Thus, the expression of D-type cyclins inhibits MMR in G1, whereas their degradation is necessary for proper MMR function in S. One-Sentence SummaryTo maintain genome stability, D-type cyclins limit mismatch repair (MMR) in G1, whereas their degradation is necessary for proper MMR function in S phase.

cell biology↗