Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 883 records · Page 49Linked to original sources

bioRxiv2022

Neuronal nuclear calcium signaling suppression of microglial reactivity is mediated by osteoprotegerin after traumatic brain injury

BackgroundTraumatic Brain Injury (TBI) is characterized by massive changes in neuronal excitation, from acute excitotoxicity to chronic hyper- or hypoexcitability. Nuclear calcium signaling pathways are involved in translating changes in synaptic inputs and neuronal activity into discrete transcriptional programs which not only affect neuronal survival and synaptic integrity, but also the crosstalk between neurons and glial cells. Here we report the effects of blunting neuronal nuclear calcium signals in the context of TBI. MethodsWe used AAV vectors to express the genetically-encoded and nuclear-targeted calcium buffer parvalbumin (PV.NLS.mCherry) or the calcium/calmodulin buffer CaMBP4.mCherry in neurons only. Upon TBI, the extent of neuroinflammation, neuronal death and synaptic loss were assessed by immunohistochemistry and targeted transcriptome analysis. Modulation of the overall level of neuronal activity was achieved by PSAM/PSEM chemogenetics targeted to parvalbumin interneurons. The functional impact of neuronal nuclear Calcium buffering in TBI was assessed by quantification of spontaneous whisking. ResultsBuffering neuronal nuclear calcium unexpectedly resulted in a massive and long-lasting increase in the recruitment of reactive microglia to the injury site, which was characterised by a disease-associated and phagocytic phenotypes. This effect was accompanied by a substantial surge in synaptic loss and significantly reduced whisking activity. Transcriptome analysis revealed a complex effect of TBI in the context of neuronal nuclear calcium buffering, with upregulation of complement factors, chemokines and interferon-response genes, as well as the downregulation of synaptic genes and epigenetic regulators compared to control conditions. Notably, nuclear calcium buffering led to a substantial loss in neuronal osteoprotegerin (OPG). Whereas stimulation of neuronal firing induced OPG expression. Viral re-expression of OPG resulted in decreased microglial recruitment and synaptic loss. OPG upregulation was also observed in the CSF of human TBI patients, underscoring its translational value. ConclusionNeuronal nuclear calcium signals regulate the degree of microglial recruitment and reactivity upon TBI via, among others, osteoprotegerin signals. Our findings support a model whereby neuronal activity altered after TBI exerts a powerful impact on the neuroinflammatory cascade, which in turn contributes to the overall loss of synapses and functional impairment.

neuroscience↗

bioRxiv2022

Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes

Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the ecological success of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1 day, 4 days and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved 26 nearly complete genomes of bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Apparently, oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. Rapid (1-day) dynamics yielded more stochasticity, both in community dynamics and gene expression, indicating that bet-hedging might be an effective coping strategy for relatively rapid environmental change. Codon-usage bias, previously associated with copiotrophic and oligotrophic lifestyles, was found to be a powerful predictor of ecological success at different frequencies, with copiotrophs and oligotrophs more successful at a rapid and a slow pace of change, respectively, independent of growth rate.

microbiology↗

bioRxiv2022

Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks

Addressing global biodiversity loss requires an expanded focus on multiple dimensions of biodiversity. While most studies have focused on the consequences of plant interspecific diversity, our mechanistic understanding of how the diversity within a given plant species (genetic diversity) affects plant productivity remains limited. Here, we use a tree species x genetic diversity experiment to disentangle the effects of species diversity and genetic diversity, and how they are related to tree functional diversity and trophic feedbacks. Tree species as well as genetic diversity increased tree productivity via increased tree functional diversity, reduced soil fungal diversity and marginally reduced herbivory. The effect of tree genetic diversity on productivity was partly different between tree species monocultures and mixtures: the functional diversity effect resulting from tree genetic diversity was only found in tree species monocultures, but the trophic feedbacks via herbivory were similar in species monocultures and mixtures. Given the complexity of interactions between tree species and genetic diversity, tree functional diversity and trophic feedbacks on productivity, we suggest that both tree species and genetic diversity should be considered in reforestation.

ecology↗

bioRxiv2022

Phase-separated TRB-PRC2 aggregates contribute to Polycomb silencing in plants

Local accumulation of Polycomb Repressive Complex 2 (PRC2) is essential to gene silencing. Liquid-liquid phase separation (LLPS) mechanism is emerging as a paradigm to concentrate transcriptional machinery for effective gene regulation. Here, we elucidate that a rice single Myb transcription factor TRBF2 forms phase-separated droplets, which aggregate with PRC2 through direct protein interaction. Furthermore, TRB1, the closest homolog of TRBF2 in Arabidopsis, also forms phase-separated aggregates with PRC2. Mutants of TRBF2 and PRC2 component CLF display similar developmental defects, share common differentially expressed genes, and reduced H3K27me3 chromatin regions. Chromatin immunoprecipitation analysis supports that TRBF2 concentrates PRC2 at target loci to promote H3K27me3 deposition. Therefore, we propose that the aggregation of the plant-specific TRBs with PRC2 by the LLPS mechanism contributes to Polycomb silencing. One-Sentence SummaryThe phase-separated plant-specific single Myb transcription factor aggregates with PRC2 to facilitate Polycomb silencing.

plant biology↗

bioRxiv2022

SPACA6 structure reveals a conserved superfamily of gamete fusion-associated proteins

SPACA6 is a sperm-expressed surface protein that is critical for gamete fusion during mammalian sexual reproduction. Despite this fundamental role, little is known about how SPACA6 specifically functions. We elucidated the crystal structure of SPACA6 at 2.2-[A] resolution, revealing a two-domain protein containing a four-helix bundle and Ig-like {beta}-sandwich connected via a quasi-flexible linker. Based on the structural analysis, we propose SPACA6 is a founding member of a superfamily of gamete fusion-associated proteins, herein dubbed the IST superfamily. The IST superfamily is defined structurally by its distorted four-helix bundle and a pair of disulfide-bonded CXXC motifs. A structure-based search of the AlphaFold human proteome identified more protein members to this superfamily; remarkably, many of these proteins are linked to gamete fusion. The SPACA6 structure and its connection to other IST-superfamily members provide a missing link in our knowledge of mammalian gamete fusion. Significance StatementSPACA6 is a human sperm protein vital for the fusion of gametes, though its exact function remains a mystery. We present the first solved structure of SPACA6: a two-domain fold comprised of an Ig-like domain and a distorted four-helix bundle. Dali searches of the PDB and AlphaFold reveal a family of structurally related proteins, several of which are also known to play a role in gamete fusion; as such, SPACA6 is a founding member of a conserved protein superfamily, dubbed the IST superfamily. Evolutionary analysis to ascertain functionally relevant structural elements in SPACA6 show a conservation of flexibility between the two domains and several conserved surfaces that could function as protein-protein interfaces.

developmental biology↗

bioRxiv2022

Global Spatial Transcriptome of Macaque Brain at Single-Cell Resolution

Global profile of gene expression at single-cell resolution remains to be determined for primates. Using a recently developed technology ("Stereo-seq"), we have obtained a comprehensive single-cell spatial transcriptome map at the whole-brain level for cynomolgus monkeys, with [~]600 genes per cell for 10 m-thick coronal sections (up to 15 cm2 in size). Large-scale single-nucleus RNA-seq analysis for [~]1 million cells helped to identify cell types corresponding to Stereo-seq gene expression profiles, providing a 3-D cell type atlas of the monkey brain. Quantitative analysis of Stereo-seq data revealed molecular fingerprints that mark distinct neocortical layers and subregions, as well as domains within subcortical structures including hippocampus, thalamus, striatum, cerebellum, hypothalamus and claustrum. Striking whole-brain topography and coordinated patterns were found in the expression of genes encoding receptors and transporters for neurotransmitters and neuromodulators. These results pave the way for cellular and molecular understanding of organizing principles of the primate brain.

cell biology↗

bioRxiv2022

Accelerating PERx Reaction Enables Covalent Nanobodies for Potent Neutralization of SARS-Cov-2 and Variants

The long-lasting COVID-19 pandemic and increasing SARS-CoV-2 variants demand effective drugs for prophylactics and treatment. Protein-based biologics offer high specificity yet their noncovalent interactions often lead to drug dissociation and incomplete inhibition. Here we developed covalent nanobodies capable of binding with SARS-CoV-2 spike protein irreversibly via proximity-enabled reactive therapeutic (PERx) mechanism. A novel latent bioreactive amino acid FFY was designed and genetically encoded into nanobodies to accelerate PERx reaction rate. After covalent engineering, nanobodies binding with the Spike in the down state, but not in the up state, were discovered to possess striking enhancement in inhibiting viral infection. In comparison with the noncovalent wildtype nanobody, the FFY-incorporated covalent nanobody neutralized both authentic SARS-CoV-2 and its Alpha and Delta variants with potency drastically increased over tens of folds. This PERx-enabled covalent nanobody strategy and uncovered insights on potency increase can be valuable to developing effective therapeutics for various viral infections.

synthetic biology↗

bioRxiv2022

High-throughput Production of Diverse Xenobiotic Metabolites with P450-transduced Huh7 Hepatoma Cell Lines

Precision medicine requires methods to assess drug metabolism and distribution, including the identification of known and undocumented drug and chemical exposures as well as their metabolites. Recent work demonstrated high-throughput generation of xenobiotic metabolites with human liver S-9 fractions and detection in human plasma and urine. Here, we developed a panel of lentivirally transduced human hepatoma cell lines (Huh7) that stably express individual cytochrome P450 (P450) enzymes and generate P450-specific xenobiotic metabolites. We verified protein expression by immunoblotting and demonstrated that the cell lines generate P450-specific metabolites from probe substrates. To increase analytical throughput, we used a pooling strategy where 36 chemicals were grouped into 12 unique mixtures, each mixture containing 6 randomly selected compounds, and each compound being present in two separate mixtures. Each mixture of compounds was incubated with 8 different P450 cell lines with cell extracts analyzed at 0 and 2 h. Extracts were analyzed using liquid chromatography-high resolution mass spectrometry. Cell lines selectively metabolized test substrates, with pazopanib metabolized by CYP3A4 and CYP2C8 cells, bupropion by CYP2B6, and {beta}-naphthoflavone by CYP1A2 for example, showing substrate-enzyme specificity. Predicted metabolites from the remaining 33 compounds as well as many unidentified m/z features were detected. We also show that a specific metabolite generated by CYP2B6 cells, but not detected in the S9 system, was identified in human samples. Our data show that incubating these cell lines with chemical mixtures accelerated characterization of xenobiotic chemical space, while simultaneously allowing for the contributions of specific P450 enzymes to be identified. Significance statementHigh resolution mass spectrometry enables the identification of exposures to drugs and other xenobiotics in human samples. This paper demonstrates a workflow for high throughput production of xenobiotic metabolites using a panel of engineered cytochrome P450-expressing hepatoma cells. Active substrate-enzyme pairs can be identified using this workflow and generated metabolites can be used as surrogate standards to validate xenobiotic detection in humans.

pharmacology and toxicology↗

bioRxiv2022

Oligomer-to-Monomer Transition Underlies the Chaperone Function of AAGAB in AP1/AP2 Assembly

Assembly of protein complexes is facilitated by assembly chaperones. Alpha and gamma adaptin binding protein (AAGAB) is a chaperone governing the assembly of the heterotetrameric adaptor complexes 1 and 2 (AP1 and AP2) involved in clathrin-mediated membrane trafficking. Here, we found that before AP1/2 binding, AAGAB exists as a homotetramer. AAGAB tetramerization is mediated by its C-terminal domain, which is critical for AAGAB stability and is missing in mutant proteins found in patients with the skin disease punctate palmoplantar keratoderma type 1 (PPKP1). We solved the crystal structure of the tetramerization domain (TD), revealing a dimer of dimer assembly. Interestingly, AAGAB uses the same TD to recognize and stabilize the {gamma} subunit in the AP1 complex and the subunit in the AP2 complex, forming binary complexes containing only one copy of AAGAB. These findings demonstrate a dual role of TD in stabilizing resting AAGAB and binding to substrates, providing a molecular explanation for disease-causing AAGAB mutations. The oligomerization state transition mechanism may also underlie the functions of other assembly chaperones.

biochemistry↗

bioRxiv2022

Cryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase

The enteropeptidase (EP) initiates the intestinal digestion by proteolytic processing of trypsinogen, generating catalytic active trypsin. The dysfunction of EP will cause a series of pancreatic diseases, the most severe of which is acute necrotizing pancreatitis. However, the molecular mechanism of EP activation and substrate recognition remain elusive due to the lack of structural information, hampering the structure-based research of EP and even further EP-targeted drug design. Here we report cryo-EM structures of human EP in multiple states, covering the functional cycle spanning from inactive to active state and eventually to the substrate binding state, with the inactive core region reached an atomic 2.7-[A]-resolution. The heavy chain of EP exhibits a clamping configuration with the CUB2 domain serving for substrate recognition. The N-terminus of light chain induces the surface loop remodeling from inactive to active conformation, resulting in a highly dynamic and active EP. Then the heavy chain performs like a hinge to ensure the flexibility of light chain for substrate recruitment and subsequent cleavage. Our study provides structural insights of EP remodeling and heavy chain dynamics while performing enzymatic function, facilitating our understanding of the pathogenies of EP-related pancreatitis and the EP-targeted treatment of pancreatitis.

cell biology↗

bioRxiv2022

Transcriptional circuitry of NKX2-1 and SOX1 defines an unrecognized lineage subtype of small cell lung cancer

RationaleThe current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. ObjectivesTo refine the current SCLC classification with epigenomic profiles and to identify features of the re-defined SCLC subtypes. MethodsWe performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. The specific cistromic profiles by ChIP-seq and its functional transcriptional partners using co-immunoprecipitation followed by mass spectrometry were determined. Rb1fl/flTrp53fl/fl and Rb1fl/flNkx2-1fl/fl mouse models were engineered to explore the function of Nkx2-1 in tumor initiation and differentiation. H3K27ac profiles were analyzed to reveal 6 human SCLC specimen and 20 mice tumors epigenomic landscapes. Measurements and Main ResultsWe identified an epigenomic subclusters of the major SCLC-A subtype, named SCLC-A and SCLC-A{sigma}. SCLC-A was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-A. We further found maintenance of this neural identity in SCLC-A is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1. ConclusionsWe comprehensively describe an additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-A subtype by the core regulatory circuitry representing NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.

molecular biology↗

bioRxiv2022

Highly Connected and Highly Variable: A Core Brain Network during Resting State Supports Propofol-induced Unconsciousness

Leading theories of consciousness make diverging predictions for where and how neural activity gives rise to subjective experience. The Global Neuronal Workspace theory (GNW) states that consciousness is instantiated through global broadcasting of information across the prefrontal-parietal regions, whereas the integrated information theory (IIT) postulates that consciousness requires the posterior cortex to produce maximally irreducible integrated information. As both theories seem to partially agree on that the neural correlates of consciousness (NCC) require globally integrated brain activity across a network of functionally specialized modules, it is not known yet whether brain regions with such functional configurations would align with the NCC distribution predicted by the GNW or the IIT. We scanned resting-state fMRI data from 21 subjects during wakefulness, propofol-induced sedation and anesthesia. Graph-theoretical analysis were conducted on awake fMRI data to search for the NCC candidates as brain regions that exhibit both high rich-clubness and high modular variability. Another independent dataset of 10 highly-sampled subjects were used to validate the NCC distribution at individual-level. Brain module-based dynamic analysis was conducted to estimate temporal stability of the NCC candidates. Alterations in functional connectivity and modular variability from awake to propofol-induced anesthesia were assessed to test the involvement of the NCC candidates in conscious processing. NCC candidates that are characterized by both high functional interconnectivity and high modular variability were identified to locate in prefrontal and temporoparietal cortices, which covered brain structures predicted by the GNW as well as the IIT. The identified NCC was found to mainly attributed to higher-order cognitive functions, and associated with genes enriched in synaptic transmission. Dynamic analysis revealed two discrete reoccurring brain states, which were characterized by their difference in temporal stability -- the state dominated by the NCC candidates appearred to be temporally more stable than the other state predominately composed of primary sensory/motor regions, suggesting that the identified NCC members could sustain conscious contents as metastable network representations. Finally, we showed that the prefrontal GNW regions and posterior IIT regions within the identified NCC was differentially modulated in terms of functional connectedness and modular variability in response to loss of consciousness induced by propofol anesthesia. This work offers a framework to search for neural correlates of consciousness by charting the brain network topology, and provides new insights in understanding the distinct roles of the frontoparietal and posterior network in underpinning human consciousness. HighlightsStudies suggest that there are neural correlates of consciousness (NCC) we experience subjectively everyday. By overlapping regions with both high functional interconnectivity (rich-clubness) and high modular variability, we identified the putative NCC distributed in prefrontal and temporoparietal cortices, attributed to higher-order cognitive functions, and associated with genes enriched in synaptic transmission. We further revealed that the NCC members appeared to sustain conscious contents as metastable network representations in a reoccurring NCC dominant state. The identified NCC architecture was significantly modulated in terms of functional connectedness and modular varibility during propofol anesthesia, demonstrating its critical role in supporting consciousness. These findings testify to the NCCs abilities in information integration and differentiation, and provide novel insights in reconciling the ongoing discussion of the contribution of anterior versus posterior regions in supporting human consciousness.

neuroscience↗

bioRxiv2022

Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error

In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.

genetics↗

bioRxiv2022

The Development of 2-stage Microfermentation Protocols for High Throughput Cell Factory Evaluations

Cell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of optimal protocols used for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, the development approach described is adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.

synthetic biology↗

bioRxiv2022

Convergence of monosynaptic inputs from neurons in the brainstem and forebrain on parabrachial neurons that project to the paraventricular nucleus of the thalamus

The paraventricular nucleus of the thalamus (PVT) projects to areas of the forebrain involved in behavior. Homeostatic challenges and salient cues activate the PVT and evidence shows that the PVT regulates appetitive and aversive responses. The brainstem is a source of afferents to the PVT and the present study was done to determine if the lateral parabrachial nucleus (LPB) is a relay for inputs to the PVT. Retrograde tracing experiments with cholera toxin B (CTB) demonstrate that the LPB contains more PVT projecting neurons than other regions of the brainstem including the catecholamine cell groups. The hypothesis that the LPB is a relay for brainstem signals to the PVT was assessed using an intersectional monosynaptic rabies tracing approach. Sources of inputs included the reticular formation, periaqueductal gray (PAG), nucleus cuneiformis, superior and inferior colliculi, and the LPB. Distinctive clusters of input cells to LPB-PVT projecting neurons were also found in the dorsolateral bed nucleus of the stria terminalis (BSTDL) and the lateral central nucleus of the amygdala (CeL). Anterograde viral tracing demonstrates that LPB-PVT neurons densely innervate all of the PVT in addition to providing collateral innervation to the preoptic area, lateral hypothalamus, zona incerta and PAG but not the BSTDL and CeL. The paper discusses the anatomical evidence that suggests that the PVT is part of a network of interconnected neurons involved in arousal, homeostasis, and the regulation of behavioral states with forebrain regions potentially providing descending modulation or gating of signals relayed from the LPB to the PVT.

animal behavior and cognition↗

bioRxiv2022

Omicron booster in ancestral strain vaccinated mouse augments protective immunities against both the Delta and Omicron variants

A booster vaccination is called for constraining the evolving epidemic of SARS-CoV-2. However, the necessity of a new COVID-19 vaccine is currently unclear. To compare the effect of an Omicron-matched S DNA vaccine and an ancestral S DNA vaccine in boosting cross-reactive immunities, we firstly immunized mice with two-dose of a DNA vaccine encoding the spike protein of the ancestral Wuhan strain. Then the mice were boosted with DNA vaccines encoding spike proteins of either the Wuhan strain or the Omicron variant. Specific antibody and T cell responses were measured at 4 weeks post boost. Our data showed that the Omicron-matched vaccine efficiently boosted RBD binding antibody and neutralizing antibody responses against both the Delta and the Omicron variants. Of note, antibody responses against the Omicron variant elicited by the Omicron-matched vaccine were much stronger than those induced by the ancestral S DNA vaccine. Meanwhile, CD8+ T cell responses against both the ancestral Wuhan strain and the Omicron strain also tended to be higher in mice boosted by the Omicron-matched vaccine than those in mice boosted with the ancestral S DNA vaccine, albeit no significant difference was observed. Our findings suggest that an Omicron-matched vaccine is preferred for boosting cross-reactive immunities.

immunology↗

bioRxiv2022

Microbial dysbiosis and metabolic disorders promote rheumatoid arthritis progression across successive stages

BackgroundRheumatoid arthritis (RA) is a chronic inflammatory disease that typically progresses through four stages, from mild stiffness to severe disability. The critical involvement of gut microbial dysbiosis in promoting RA has been intriguing. The aim of this study was to investigate stage-specific roles of microbial dysbiosis and metabolic disorders in pathogenesis across successive stages of RA. MethodsIn this multi-omics cohort study, fecal metagenomic, plasma metabolomic data were collected from 76 patients grouped into four RA stages, 19 patients with osteoarthritis, and 27 healthy individuals in China. A non-redundant gene catalogue was constructed, functionally annotated, and clustered into metagenomic species (MGS). Leave-one-out analysis was performed to determine the MGS that most drove the microbial dysfunctions with RA across stages. Random forest algorithm was performed to investigate diagnostic potential of microbial or metabolic features for each stage. Additionally, to verify the bacterial invasion of the joint synovial fluid, we conducted 16S rRNA gene sequencing, bacterial isolation, and scanning electron microscopy on joint synovial fluid from another cohort of 271 RA patients grouped into four RA stages. FindingsWe found that microbial dysbiosis and metabolic disorders had stage-specific effects on RA progression. For instance, arginine succinyltransferase pathway was elevated mainly in the second and third stages of RA (p=1{middle dot}4x10-3), which was driven by Escherichia coli, and it was correlated with the increase of the rheumatoid factor (p=1{middle dot}35x10-3). Considerable elevation of methoxyacetic acid (p=1{middle dot}28x10-8) and cysteine-S-sulfate (p=4{middle dot}66x10-12) might inhibit osteoblasts in the second stage and enhance osteoclasts in the third stage, respectively. Moreover, fecal microbes Eggerthella lenta and Bifidobacterium longum that were exclusively elevated in the fourth stage, were also detected in the joint synovial fluid. InterpretationOur findings elucidate for the first time the stage-specific roles of microbial dysbiosis and metabolic disorders across successive stages of RA, which open up new avenues for RA prognosis and therapy. We demonstrate the buildup of these effects might induce microbial invasion of the joint synovial fluid in the fourth stage of RA.

microbiology↗

bioRxiv2022

The Transcription Factor Bach2 Negatively Regulates Natural Killer Cell Maturation and Function

BTB domain And CNC Homolog 2 (Bach2) is a transcription repressor that actively participates in T and B lymphocyte development, but it is unknown if Bach2 is also involved in the development of innate immune cells, such as natural killer (NK) cells. Here, we followed the expression of Bach2 during NK cell development, finding that it peaked in CD27+CD11b+ cells and decreased upon further maturation. Bach2 expression positively correlated with that of the transcription factor TCF1 and negatively correlated with genes encoding NK effector molecules as well as genes involved in the cell cycle. Bach2-deficient mice showed increased numbers of terminally differentiated NK cells with increased production of granzymes and cytokines. NK cell-mediated control of tumor metastasis was also augmented in the absence of Bach2. Therefore, Bach2 is a key checkpoint protein regulating NK terminal maturation.

immunology↗