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Han, M.

Publications and source records attributed to Han, M..

At least 55 records · Page 3Linked to original sources

Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles

The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.

microbiology↗

A muscle hypertrophy-derived myokine reprograms the stromal vascular fractions differentiation towards thermogenic adipocytes in subcutaneous adipose tissue

Skeletal muscle plays a significant role in both local and systemic energy metabolism; however, the cross-talk between skeletal muscle and adipose tissue remains largely unexplored. In this study, we identify the HIF2-Bambi-Thbs4 axis as a critical driver of muscle hypertrophy and metabolic improvement. Deletion of Bambi induces muscle hypertrophy and oxidative switching, thereby enhancing local and systemic metabolism under conditions of rodent chow and high-fat diets (HFD). Other than the metabolic regulation of skeletal muscle hypertrophy, we hypothesize that a portion of this improvement may be attributed to the metabolic reprogramming of the stromal vascular fraction (SVFs) of iWAT, promoting the development of beige adipocytes. Leveraging multi-omics approaches, we establish Thbs4 as a newly identified, muscle hypertrophy-derived myokine that serves as an essential regulator of this metabolic reprogramming. Thbs4 is upregulated in skeletal muscle during hypertrophy and aerobic exercise, localizes to the iWAT membrane, and facilitates the transformation of white adipocytes into beige adipocytes under conditions such as cold exposure, muscle hypertrophy, or aerobic exercise. Moreover, overexpression of Thbs4 elevates its plasma levels and leads to the transformation of white to beige adipocytes, therefore offering long-term protection against HFD-induced metabolic disorders. Conversely, Thbs4 knockout (Thbs4-KO) disrupts the metabolic reprogramming of SVFs and exacerbates metabolic syndromes induced by an HFD, mirroring the observed decline in Thbs4 levels in aged mice. Therefore, our findings underscore Thbs4s potential as both a long-term metabolic protective factor and a therapeutic target for the treatment of metabolic disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/558627v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1178e6org.highwire.dtl.DTLVardef@1184d4eorg.highwire.dtl.DTLVardef@7b592aorg.highwire.dtl.DTLVardef@1b0b03_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBambi, a direct target gene of HIF2 in skeletal muscle, when deleted, triggers muscle hypertrophy and the transformation of white into beige adipocytes, improving systemic energy metabolism. C_LIO_LIThe metabolic reprogramming of stromal vascular fractions (SVFs) contributes to the observed improvements in energy metabolism and adipocyte hyperplasia. C_LIO_LIThbs4, a novel myokine produced in skeletal muscle during hypertrophy and aerobic exercise, plays a key role in the transformation of white into beige adipocytes. C_LIO_LIOverexpression of Thbs4 provides enduring protection against high-fat diet (HFD)-induced metabolic disorders, demonstrating its potential as a therapeutic target. C_LIO_LIThbs4 deletion abrogates the beneficial metabolic reprogramming of SVFs and exacerbates HFD-induced metabolic syndromes, further underlining its crucial role in metabolic regulation. C_LI

physiology↗

TGF-β1 inhibits cholesterol metabolism in hepatocytes to facilitate cell death, EMT and signals for HSC activation.

Background and Aims: Transforming growth factor-{beta}1 (TGF-{beta}1) plays important roles in chronic liver diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD involves various biological processes including dysfunctional cholesterol metabolism and contributes to progression to metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). However, the reciprocal regulation of TGF-{beta}1 signaling and cholesterol metabolism in MASLD is yet unknown. Methods: Changes in transcription of genes associated with cholesterol metabolism were assessed by RNA-Seq of murine hepatocyte cell line (AML12) and mouse primary hepatocytes (MPH) treated with TGF-{beta}1. Functional assays were performed on AML12 cells (untreated, TGF-{beta}1 treated, or subjected to cholesterol enrichment (CE) or depletion (CD)), and on mice injected with adeno-associated virus 8 (AAV8)-Control/TGF-{beta}1. Results: TGF-{beta}1 inhibited mRNA expression of several cholesterol metabolism regulatory genes, including rate-limiting enzymes of cholesterol biosynthesis in AML12 cells, MPHs, and AAV8-TGF-{beta}1-treated mice. Total cholesterol levels and lipid droplet accumulation in AML12 cells and liver tissue were also reduced upon TGF-{beta}1 treatment. Smad2/3 phosphorylation following 2 h TGF-{beta}1 treatment persisted after CE or CD and was mildly increased following CD, while TGF-{beta}1-mediated AKT phosphorylation (30 min) was inhibited by CE. Furthermore, CE protected AML12 cells from several effects mediated by 72 h incubation with TGF-{beta}1, including EMT, actin polymerization, and apoptosis. CD mimicked the outcome of long term TGF- {beta}1 administration, an effect that was blocked by an inhibitor of the type I TGF-{beta} receptor. Additionally, the supernatant of CE- or CD-treated AML12 cells inhibited or promoted, respectively, the activation of LX-2 hepatic stellate cells. Conclusions: TGF-{beta}1 inhibits cholesterol metabolism while cholesterol attenuates TGF-{beta}1 downstream effects in hepatocytes.

cell biology↗

Nonstructural protein 1 of swine arterivirus PRRSV downregulates promyelocytic leukemia nuclear bodies and promotes viral replication

Porcine reproductive and respiratory syndrome virus (PRRSV) inhibits the type I interferon (IFN) production and signaling pathways during infection, and the nonstructural protein 1 (nsp1) has been identified as a potent IFN antagonist. Promyelocytic leukemia (PML) protein is a major scaffold protein organizing the PML nuclear bodies (NBs) of the cell and plays a diverse role in maintaining the cellular homeostasis including antiviral response among many other processes. The present study reveals a significant reduction of PML NBs in cells during infection of PRRSV, implicating the negative regulation of PML gene expression by PRRSV. Subsequently, the nsp1{beta} protein was identified as the viral regulator for PML expression. The overexpression of PML isoforms restricted viral replication, while the gene silencing of endogenous PML promoted viral replication. The downregulation of PML expression by PRRSV was post-translational via the ubiquitination-proteasome pathway. Of six isoforms, PML-II and PML-IV exhibited the most potent suppressive activity against viral replication. PRRSV nsp1{beta} bound to PML directly, and this interaction was mediated through the small ubiquitin-like modifier (SUMO)-interacting motifs (SIMs) on nsp1{beta}. Further studies revealed that double mutations in SIM1 and SIM4 abolished the binding of nsp1{beta} to PML and prevented the PML degradation. The PML downregulation by nsp1 was common in other arteriviruses including equine arteritis virus, murine lactate dehydrogenase elevating virus, and simian hemorrhagic fever virus. Our study unveils the evolutionary conservation of the viral immune evasion strategy employed by arteriviruses, which promotes their replication by targeting PML for downregulation. IMPORTANCE OF THE STUDYPorcine reproductive and respiratory syndrome (PRRS) is an economically significant disease in the swine industry worldwide. One of the immunological hallmarks in virus-infected animals is the suppression of type I interferon response during an early-stage infection, leading to the consequence of adaptive immunity and viral persistence. In the present study, we report that the nsp1-beta protein of PRRS virus degrades the promyelocytic leukemia (PML) protein and downregulates PML nuclear body (NB) formation. The PML downregulation by PRRS virus results in enhanced viral replication. The PML downregulation by nsp1 is common in other arteriviruses, unveiling the basic understanding of cell-virus interactions and immune evasion strategies for arteriviruses.

microbiology↗

Cryo-EM structures of lipidic fibrils of amyloid-β (1-40)

Alzheimers disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-{beta} (A{beta}) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew A{beta}40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.

molecular biology↗

Electrically Conductive DNA-Inspired Coating for Intracortical Neural Microelectrodes

Different from conventional electrodes, intracortical neural microelectrodes are the size of one or several neural cells. Due to the limited space for cell-electrode connections, the bio-integration between each neural cell and the electrode surface is critical. To improve bio-integration and electrode functions, various coating materials (such as conductive polymers (CPs), carbon nanotubes (CNTs), and natural hydrogels) have been developed aiming to provide an enhanced interface for neuron recruitment, bio-anchorage, and electrical function. However, synthetic materials usually have limited biocompatibility and/or relatively high cytotoxicity, while biological materials present poor electrical functions. Therefore, current coatings possess biological, functional or electrochemical limitations that are not optimal for intracortical neural microelectrodes. To overcome this obstacle, we developed an electrically conductive coating based on biological molecules, named Janus base nano-coating (JBNc). JBNc is formed by Janus base nanotubes (JBNts) which are a family of nanotubes assembled from engineered DNA base pair units. Based on the long-distance translocation ability of the {pi} electrons of JBNts, we developed them into an electrically conductive coating on the electrode surface. For the first time, we reported the DNA-inspired JBNc had an electrochemical performance that met and exceeded standard metal electrode surface in cyclic voltammetry, impedance spectroscopy, charge injection capacity tests, and neural recording. Moreover, we demonstrated enhanced bio-anchorage and microelectrode interface integration using SEM and AFM. Importantly, we demonstrated enhanced functional response to JBNc microelectrodes with immunohistochemical staining and RNA sequencing (RNAseq) analysis. Using cell viability assays, we also showed the benefits of DNA-mimicking chemistry of Janus base nanomaterials compared to conventional microelectrode coatings. We anticipate that these results will serve as a foundation for the continued development and study of JBNc to enhance interface dynamics and ultimately the performance and reliability of brain microelectrodes.

bioengineering↗

Neuropathy target esterase activity predicts retinopathy among PNPLA6 disorders

Biallelic pathogenic variants in the PNPLA6 gene cause a broad spectrum of disorders leading to gait disturbance, visual impairment, anterior hypopituitarism, and hair anomalies. PNPLA6 encodes Neuropathy target esterase (NTE), yet the role of NTE dysfunction on affected tissues in the large spectrum of associated disease remains unclear. We present a clinical meta-analysis of a novel cohort of 23 new patients along with 95 reported individuals with PNPLA6 variants that implicate missense variants as a driver of disease pathogenesis. Measuring esterase activity of 46 disease-associated and 20 common variants observed across PNPLA6-associated clinical diagnoses unambiguously reclassified 10 variants as likely pathogenic and 36 variants as pathogenic, establishing a robust functional assay for classifying PNPLA6 variants of unknown significance. Estimating the overall NTE activity of affected individuals revealed a striking inverse relationship between NTE activity and the presence of retinopathy and endocrinopathy. This phenomenon was recaptured in vivo in an allelic mouse series, where a similar NTE threshold for retinopathy exists. Thus, PNPLA6 disorders, previously considered allelic, are a continuous spectrum of pleiotropic phenotypes defined by an NTE genotype:activity:phenotype relationship. This relationship and the generation of a preclinical animal model pave the way for therapeutic trials, using NTE as a biomarker.

neuroscience↗

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adjust, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. The Shannon index was significantly higher in sandy samples than in muddy samples. The co-occurrence network was tighter and more species were involved in community building in sandy samples. The principal coordinates analysis identified a significant separation between different sediment types and between stations (LiCun estuary, LC and ZhanQiao Pier, ZQ). Proteobacteria, which had a relative abundance of approximately 50% at all phylum levels, was significantly more abundant at ZQ, while Campilobacterota and Firmicutes were significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. The RDA results, where each months samples were concentrated individually, showed reduced variation between months when the amplicon sequence variant was replaced by KEGG orthologs, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria. HighlightsO_LISandy sediments have more bacterial species involved in community building. C_LIO_LIDifferent substrates from different stations have their own phylum biomarkers. C_LIO_LISubstrates have a greater influence on shaping bacterial function. C_LIO_LITemporal changes have a greater shaping power on bacteria than on gene families. C_LI Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/542048v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1834e64org.highwire.dtl.DTLVardef@18fc695org.highwire.dtl.DTLVardef@369657org.highwire.dtl.DTLVardef@1c85a13_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

DCBLD1 modulates angiogenesis by regulating of the VEGFR-2 endocytosis in endothelial cells

ObjectiveUnwanted angiogenesis is involved in the progression of various malignant tumors and cardiovascular diseases, and the factors that regulate angiogenesis are potential therapeutic targets. We tested the hypothesis that DCBLD1 (Discoidin, CUB, and LCCL domain-containing protein 1) is a co-receptor of VEGFR-2 and modulates angiogenesis in endothelial cells(ECs). Approach and ResultsA carotid artery ligation model and retinal angiogenesis assay were used to study angiogenesis using globe knockout or EC-specific conditional DCBLD1 knockout mice in vivo. Immunoblotting, immunofluorescence staining, plasma-membrane subfraction isolation, Co-immunoprecipitation and mass-spectrum assay were performed to clarify the molecular mechanisms.Loss of DCBLD1 impaired VEGF response and inhibited VEGF-induced EC proliferation and migration. DCBLD1 deletion interfered with adult and developmental angiogenesis. Mechanistically, DCBLD1 bound to VEGFR-2 and regulated the formation of VEGFR-2 complex with negative regulators: protein tyrosine phosphatases, E3 ubiquitin ligases(Nedd4 and c-Cbl), and also DCBLD1 knockdown promoted lysosome-mediated VEGFR-2 degradation in ECs. ConclusionsThese findings demonstrated the essential role of endothelial DCBLD1 in regulating VEGF signaling and provided evidence that DCBLD1 promotes VEGF-induced angiogenesis by limiting the dephosphorylation, ubiquitination, and lysosome degradation after VEGFR-2 endocytosis. We proposed that endothelial DCBLD1 is a potential therapeutic target for ischemic cardiovascular diseases by the modulation of angiogenesis through regulating of the VEGFR-2 endocytosis.

molecular biology↗

MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis

Summarycell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising non-invasive technology to detect cancers and monitor treatments. Several bioinformatics tools are available for cfMeDIP-seq data analysis. However, an easy to implement and flexible pipeline, particularly, for large-scale cfMeDIP-seq profiling, is still lacking. Here we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification and sample aggregation. The major advantages of MEDIPIPE are: 1) it is easy to implement and reproduce with automatically deployed execution environments; 2) it can handle different experimental settings with a single input configuration file; 3) it is computationally efficient for large-scale cfMeDIP-seq profiling data analysis and aggregation. Availability and implementationThis pipeline is an open-source software under the MIT license and it is freely available at https://github.com/yzeng-lol/MEDIPIPE. Contactyzeng@uhnresearch.ca or trevor.pugh@utoronto.ca or hansenhe@uhnresearch.ca Supplementary informationSupplementary data are appended.

bioinformatics↗

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism. HighlightsO_LIFALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effects C_LIO_LIFALCON is applicable to many and diverse cell types C_LIO_LIA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidity C_LIO_LINew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for disease C_LIO_LIC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling C_LI

cell biology↗

Single-cell RNA sequencing reveals aortic cellular heterogeneity in MSC_ITGB3-treated ApoE-/- mice on a high-fat diet

The aorta contains various cell types that are involved in the development of vascular inflammation and atherosclerosis. However, the cellular atlas of heterogeneous aorta cells, cellular responses, and intercellular communication has not been investigated in the background of a high-fat diet (HFD) and treatment with integrin beta 3-modified mesenchymal stem cells (MSC_ITGB3). In this study, 33,782 individual cells from mouse aortas under HFD with or without MSC_ITGB3 treatment were subjected to single-cell RNA sequencing as an unbiased analysis strategy. We generated a compendium of 30 different clusters, mainly smooth muscle cells (SMCs), endothelial cells, and immune cells. The proportion of the different cell types was considerably influenced by HFD and MSC_ITGB3. In the HFD group, genes associated with proliferation, migration, and collagen were highly expressed in the major SMC subpopulations. However, the expression of contraction-related genes in SMC subpopulations was significantly higher in the MSC_ITGB3 group than in the HFD group. After HFD consumption, subpopulations of ECs with active PI3K-Akt signaling pathway, ECM-receptor interaction, and contraction-related genes were significantly enriched. In the MSC_ITGB3 group, the number of dendritic cells (DCs), which are positively correlated with atherosclerotic lesion progression and contribute to lipid accumulation, and levels of inflammatory factors notably decreased. Our findings provide data on the composition, signaling pathways, and cellular communication of the aorta cells following stem cell treatment as well as on the evolution and progression of atherosclerotic disease. The findings may help in improving the treatment of atherosclerosis.

bioinformatics↗

Bacterial muropeptides promote OXPHOS and suppress mitochondrial stress in normal and human mitochondrial disease models

Mitochondrial dysfunction critically contributes to many major human diseases but effective therapeutic methods to combat mitochondrial dysfunction are lacking1,2. Mitochondria of animal cells are sites of interaction between gut microbial metabolites and host factors, and many such interactions may be beneficial to mitochondrial health and host physiology3, albeit that specific beneficial interactions and the underlying mechanisms remain to be uncovered. Here we report the role of muropeptides derived from bacterial cell wall peptidoglycan (PG) in promoting mitochondrial functions in mammalian models. We found that muropeptides directly bind to ATP synthase, which stabilizes the complex and promotes its activity. The benefit is seen in increased oxidative respiration and mitochondrial membrane potential, as well as decreased oxidative stress in human intestinal epithelial cells (IECs). Strikingly, we also found that muropeptide treatment can recover mitochondrial structure and functions, as well as inhibit several pathological phenotypes of mutant fibroblast cells derived from mitochondrial disease patients. In mice, we show muropeptides accumulate in mitochondria of IECs and promote small intestinal homeostasis and nutrient absorption by modulating energy metabolism. This study identifies ATP synthase as a muropeptide receptor and the corresponding physiological function in mammals, and points to a potential treatment for human mitochondrial dysfunction diseases. HighlightsO_LIBacterial muropeptides bind and stabilize ATP synthase complex and enhance its activity C_LIO_LIMuropeptides enhance mitochondrial OXPHOS in human IECs C_LIO_LIMuropeptides recover mitochondrial structure and functions in mitochondrial disease cells C_LIO_LIMuropeptides promote small intestinal epithelial homeostasis and nutrient uptake in mice C_LI

cell biology↗

Expanded Multiplexing on Sensor-Constrained Microfluidic Partitioning Systems

Microfluidics can split samples into thousands or millions of partitions such as droplets or nanowells. Partitions capture analytes according to a Poisson distribution, and in diagnostics, the analyte concentration is commonly calculated with a closed-form solution via maximum likelihood estimation (MLE). Here, we present a generalization of MLE with microfluidics, an extension of our previously developed Sparse Poisson Recovery (SPoRe) algorithm, and an in vitro demonstration with droplet digital PCR (ddPCR) of the new capabilities that SPoRe enables. Many applications such as infection diagnostics require sensitive detection and broad-range multiplexing. Digital PCR coupled with conventional target-specific sensors yields the former but is constrained in multiplexing by the number of available measurement channels (e.g., fluorescence). In our demonstration, we circumvent these limitations by broadly amplifying bacteria with 16S ddPCR and assigning barcodes to nine pathogen genera using only five nonspecific probes. Moreover, we measure only two probes at a time in multiple groups of droplets given our two-channel ddPCR system. Although individual droplets are ambiguous in their bacterial content, our results show that the concentrations of bacteria in the sample can be uniquely recovered given the pooled distribution of partition measurements from all groups. We ultimately achieve stable quantification down to approximately 200 total copies of the 16S gene per sample, enabling a suite of clinical applications given a robust upstream microbial DNA extraction procedure. We develop new theory that generalizes the application of this framework to a broad class of realistic sensors and applications, and we prove scaling rules for system design to achieve further expanded multiplexing. This flexibility means that the core principles and capabilities demonstrated here can generalize to most biosensing applications with microfluidic partitioning.

bioengineering↗

Diversified repertoire of phage defenses in Klebsiella pneumoniae: Bi-directional steering effects impacting antibiotic susceptibility

Bacteriophage (phage) therapy is rising as a promising anti-infective option to combat antimicrobial resistance; however, its clinical utilization is severely hindered by the potential emergence of phage resistance. Fortunately, certain phage resistance mechanisms can restore bacterial antibiotic susceptibility, making the combination of phages with antibiotics a potential strategic approach. Here, we demonstrated that phage resistance can also lead to increased antibiotic resistance and provided mechanistic insights into bacterial phage defense mechanisms. We discovered a repertoire of phage resistance mechanisms in Klebsiella pneumoniae, including the disruption of phage binding site (fhuA::Tn and tonB::Tn), extension of phage latent period (mnmE::Tn and rpoN::Tn) and increased mutation frequency (mutS::Tn and mutL::Tn). Different from the prevailing view that phage resistance re-sensitizes antibiotic-resistant bacteria, we revealed a bidirectional steering effect on the bacterial antibiotic susceptibility. Specifically, it was uncovered that, while rpoN::Tn became more susceptible to colistin, mutS::Tn and mutL::Tn caused increased resistance to rifampicin and colistin. Our findings highlight the diversified strategies utilized by K. pneumoniae to overcome phage infection and the parallel effect on the antibiotic susceptibility. Mechanism-guided phage steering represents a rational strategy that should be incorporated into phage therapy to better inform clinical decisions.

microbiology↗

Genetic Regulators of Sputum Mucin Concentration and Their Associations with COPD Phenotypes

Hyper-secretion and/or hyper-concentration of mucus is a defining feature of multiple obstructive lung diseases, including chronic obstructive pulmonary disease (COPD). Mucus itself is composed of a mixture of water, ions, salt and proteins, of which the gel-forming mucins, MUC5AC and MUC5B, are the most abundant. Recent studies have linked the concentrations of these proteins in sputum to COPD phenotypes, including chronic bronchitis (CB) and acute exacerbations (AE). We sought to determine whether common genetic variants influence sputum mucin concentrations and whether these variants are also associated with COPD phenotypes, specifically CB and AE. We performed a GWAS to identify quantitative trait loci for sputum mucin protein concentration (pQTL) in the Sub-Populations and InteRmediate Outcome Measures in COPD Study (SPIROMICS, n=708 for total mucin, n=215 for MUC5AC, MUC5B). Subsequently, we tested for associations of mucin pQTL with CB and AE using regression modeling (n=822-1300). Replication analysis was conducted using data from COPDGene (n =5740) and by examining results from the UK Biobank. We identified one genome-wide significant pQTL for MUC5AC (rs75401036) and two for MUC5B (rs140324259, rs10001928). The strongest association for MUC5B, with rs140324259 on chromosome 11, explained 14% of variation in sputum MUC5B. Despite being associated with lower MUC5B, the C allele of rs140324259 conferred increased risk of CB (odds ratio (OR) = 1.42; 95% confidence interval (CI): 1.10-1.80) as well as AE ascertained over three years of follow up (OR=1.41; 95% CI: 1.02-1.94). Associations between rs140324259 and CB or AE did not replicate in COPDGene. However, in the UK Biobank, rs140324259 was associated with phenotypes that define CB, namely chronic mucus production and cough, again with the C allele conferring increased risk. We conclude that sputum MUC5AC and MUC5B concentrations are associated with common genetic variants, and the top locus for MUC5B may influence COPD phenotypes, in particular CB. Author SummaryChronic obstructive pulmonary disease (COPD) is characterized by presence of emphysema and/or chronic bronchitis. Excessive mucus production is a defining phenotype of chronic bronchitis, and is associated with several important features of COPD, including exacerbations and loss of lung function. Recent studies have demonstrated that the amount of mucus produced in COPD patients is an important marker of disease state. We investigated whether common genetic variants are associated with the concentration of two key proteins in mucus, MUC5AC and MUC5B, and whether the variants we identified are also associated with COPD outcomes. We identified multiple genetic variants that were associated with MUC5AC or MUC5B concentration. The strongest association we detected, for MUC5B on chromosome 11, was also associated with features of COPD, including chronic bronchitis and acute exacerbations, in one COPD study population but not another. Results from a much larger study, the UK Biobank, indicate that this variant is associated with chronic mucus production and chronic cough, which are key features of chronic bronchitis. Thus, we conclude that the concentration of key proteins in mucus are influenced by genetic variation, and that a variant on chromosome 11 that affects MUC5B may in turn alter COPD outcomes.

genetics↗

Aspartate reduces liver inflammation and fibrosis by suppressing the NLRP3 inflammasome pathway via upregulating NS3TP1 expression

Aspartate (Asp) can act on liver Kupffer cells, inhibit NOD-like receptor-P 3 (NLRP3) inflammatory bodies, and improve liver inflammation in acute hepatitis. However, the effect of Asp on the role of hepatic stellate cells (HSCs) in the pathogenesis of liver fibrosis in chronic liver injury remains unexplored. This study aimed to investigate the effects of Asp on CCl4-induced liver fibrosis in mice and HSCs via the NF-{kappa}B/ NLRP3 signaling pathway. Liver fibrosis was induced in C57BL/6J mice by intraperitoneally (IP) injecting 0.5 mL/kg 2% CCl4 three times weekly for 8 weeks. Asp was administered to mice by gavage once every morning for 4 weeks. Massons trichrome staining, Sirius red staining and hematoxylin and eosin staining were used to detect and analyze the pathological changes in liver tissues. Western blot analysis and immunohistochemistry were applied to determine the protein expression levels of -smooth muscle actin (-SMA), collagen III (COL III), NLRP3, and IL-1{beta}. Also, reverse transcription-quantitative PCR was performed to detect the mRNA expression levels. In the liver fibrosis model, the pathological changes in liver tissues improved following treatment with Asp. A marked decrease was observed in protein and mRNA expression levels of -SMA, COL III, NLRP3, and IL-1{beta}. In addition, HSCs were treated with Asp. The expression levels of -SMA, COL III, NLRP3, and IL-1{beta} reduced in dose- and time-dependent manners. Furthermore, Asp upregulated the expression of NS3TP1 in vivo and in vitro, and NS3TP1 had a significant inhibitory effect on liver fibrosis. Asp attenuated liver fibrosis and reduced collagen production by suppressing the NF-{kappa}B/ NLRP3 signaling pathway via upregulating the expression of NS3TP1.

molecular biology↗

HIV-1 cell-to-cell spread overcomes the virus entry block of non-macrophage-tropic strains in macrophages

Macrophages (M{Phi}) are increasingly recognized as HIV-1 target cells involved in the pathogenesis and persistence of infection. Paradoxically, in vitro infection assays suggest that virus isolates are mostly T-cell-tropic and rarely M{Phi}-tropic. The latter are assumed to emerge under CD4+ T-cell paucity in tissues such as the brain or at late stage when the CD4 T-cell count declines. However, assays to qualify HIV-1 tropism use cell-free viral particles and may not fully reflect the conditions of in vivo M{Phi} infection through cell-to-cell viral transfer. Here, we investigated the capacity of viruses expressing primary envelope glycoproteins (Envs) with CCR5 and/or CXCR4 usage from different stages of infection, including transmitted/founder Envs, to infect M{Phi} by a cell-free mode and through cell-to-cell transfer from infected CD4+ T cells. The results show that most viruses were unable to enter M{Phi} as cell-free particles, in agreement with the current view that non-M-tropic viruses inefficiently use CD4 and/or CCR5 or CXCR4 entry receptors on M{Phi}. In contrast, all viruses could be effectively cell-to-cell transferred to M{Phi} from infected CD4+ T cells. We further showed that viral transfer proceeded through Env-dependent cell-cell fusion of infected T cells with M{Phi} targets, leading to the formation of productively infected multinucleated giant cells. Compared to cell-free infection, infected T-cell/M{Phi} contacts showed enhanced interactions of R5 M- and non-M-tropic Envs with CD4 and CCR5, resulting in a reduced dependence on receptor expression levels on M{Phi} for viral entry. Altogether, our results show that virus cell-to-cell transfer overcomes the entry block of isolates initially defined as non-macrophage-tropic, indicating that HIV-1 has a more prevalent tropism for M{Phi} than initially suggested. This sheds light into the role of this route of virus cell-to-cell transfer to M{Phi} in CD4+ T cell rich tissues for HIV-1 transmission, dissemination and formation of tissue viral reservoirs. Author SummaryUnderstanding how HIV-1 hijacks the functions of immune cells to promote viral spreading remains a challenge in the fight against infection. M{Phi} are ubiquitous tissue-resident cells, involved in tissue homeostasis and immunity. In HIV-1 infection, along with CD4+ T lymphocytes, M{Phi} serve as vectors for virus dissemination and as viral reservoirs, impeding HIV-1 eradication. However, the mechanisms of their infection remain incompletely understood. A paradox is that infected M{Phi} are found in a large range of tissues whereas in vitro cellular tropism assays indicate that only a limited number of HIV-1 isolates can enter M{Phi}. We hypothesized that these assays, which evaluate infection using cell-free viruses, might not fully reflect the modes of M{Phi} infection in patients. We report here that virus cell-to-cell transfer through cell-cell fusion with infected CD4+ T cells is a very effective means of infecting M{Phi}, even with virus isolates characterized as non-macrophage tropic in cell-free infection. This intercellular viral transfer is facilitated by enhanced interactions between the HIV-1 envelope glycoproteins and cellular entry receptors. We propose that M{Phi} infection through viral transfer from infected CD4+ T cells impacts different aspects of the pathophysiology of HIV-1 infection, renewing our understanding of the role of M{Phi} in HIV-1 pathogenesis and persistence.

microbiology↗