[Low disease activity and remission status of systemic lupus erythematosus in a real-world study].

OBJECTIVE: To investigate the rates of low disease activity and clinical remission in patients with systemic lupus erythematosus (SLE) in a real-world setting, and to analyze the related factors of low disease activity and clinical remission. METHODS: One thousand patients with SLE were enrolled from 11 teaching hospitals. Demographic, clinical and laboratory data, as well as treatment regimes were collec-ted by self-completed questionnaire. The rates of low disease activity and remission were calculated based on the lupus low disease activity state (LLDAS) and definitions of remission in SLE (DORIS). Charac-teristics of patients with LLDAS and DORIS were analyzed. Multivariate Logistic regression analysis was used to evaluate the related factors of LLDAS and DORIS remission. RESULTS: 20.7% of patients met the criteria of LLDAS, while 10.4% of patients achieved remission defined by DORIS. Patients who met LLDAS or DORIS remission had significantly higher proportion of patients with high income and longer disease duration, compared with non-remission group. Moreover, the rates of anemia, creatinine elevation, increased erythrocyte sedimentation rate (ESR) and hypoalbuminemia was significantly lower in the LLDAS or DORIS group than in the non-remission group. Patients who received hydroxychloroquine for more than 12 months or immunosuppressant therapy for no less than 6 months earned higher rates of LLDAS and DORIS remission. The results of Logistic regression analysis showed that increased ESR, positive anti-dsDNA antibodies, low level of complement (C3 and C4), proteinuria, low household income were negatively related with LLDAS and DORIS remission. However, hydroxychloroquine usage for longer than 12 months were positively related with LLDAS and DORIS remission. CONCLUSION: LLDAS and DORIS remission of SLE patients remain to be improved. Treatment-to-target strategy and standar-dized application of hydroxychloroquine and immunosuppressants in SLE are recommended.

SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments.

MOTIVATION: On-target gene knockdown, using siRNA, ideally results from binding fully complementary regions in mRNA transcripts to induce direct cleavage. Off-target siRNA gene knockdown can occur through several modes, one being a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated off-target effects occur when the ∼8 nucleotides at the 5' end of the guide strand, called a seed region, bind the 3' untranslated regions of mRNA, causing reduced translation. Experiments using siRNA knockdown paired with RNA-seq can be used to detect siRNA sequences with off-target effects driven by the seed region. However, there are limited computational tools designed specifically for detecting siRNA off-target effects mediated by the seed region in differential gene expression experiments. RESULTS: SeedMatchR is an R package developed to provide users a single, unified resource for detecting and visualizing seed-mediated off-target effects of siRNA using RNA-seq experiments. SeedMatchR is designed to extend current differential expression analysis tools, such as DESeq2, by annotating results with predicted seed matches. Using publicly available data, we demonstrate the ability of SeedMatchR to detect cumulative changes in differential gene expression attributed to siRNA seed region activity. AVAILABILITY: SeedMatchR is available on CRAN. Documentation and example workflows are available through the SeedMatchR GitHub page at https://github.com/tacazares/SeedMatchR.

Dissecting the Imbalance of Synovial Macrophages in Rheumatoid Arthritis.

Objective: This study sought to identify candidate genes of rheumatoid arthritis (RA) synovial macrophages using bioinformatics and to explore their pathways in the pathogenesis of RA. Methods: The microarray datasets GSE10500 and GSE97779 were obtained from the Gene Express Omnibus and analyzed with synovial macrophages of 14 RA patients and 8 healthy donors. The researchers used R software to identify differentially expressed genes and determine functional enrichment pathways. A protein-protein interaction network was then constructed using STRING and Cytoscape. Gene expression was validated with the GSE71370 dataset and RT-qPCR analysis. Results: 102 DEGs were identified in RA synovial macrophages relative to normal samples. Of these, 72 were upregulated; 30 were downregulated. GO and KEGG pathway analyses suggested that DEGs mainly regulated the immune response and signaling pathways associated with inflammatory activation, apoptosis, and cancer. The top five hub genes and top 1 gene module from the PPI network of DEGs were VEGFA, MMP9, FN1, IGF1, CXCL9, ISG20, RSAD2, IFI27, GBP2, and GBP1. The GSE71370 dataset and RT-qPCR analysis showed that CXCL9 and GBP1 were significantly upregulated (P ≤ .05). Conclusions: CXCL9 and GBP1 may contribute to RA pathogenesis and serve as potential biomarkers and therapeutic targets for RA.

Bioengineering of a human physiologically relevant microfluidic blood-cerebrospinal fluid barrier model.

The human blood-cerebrospinal fluid barrier (hBCSFB) plays a crucial role in regulating brain interstitial fluid homeostasis, and disruption of the hBCSFB is associated with various neurological diseases. Generation of a BCSFB model with human physiologically relevant structural and functional features is crucial to reveal the cellular and molecular basis of these diseases and discover novel neurologic therapeutic agents. Unfortunately, thus far, few humanized BCSFB models are available for basic and preclinical research. Here, we demonstrate a bioengineered hBCSFB model on a microfluidic device constructed by co-culturing primary human choroid plexus epithelial cells (hCPECs) and human brain microvascular endothelial cells (hBMECs) on the two sides of a porous membrane. The model reconstitutes tight junctions of the hBCSFB and displays a physiologically relevant molecular permeability. Using this model, we further generate a neuropathological model of the hBCSFB under neuroinflammation. Overall, we expect that this work will offer a high-fidelity hBCSFB model for studying neuroinflammation-related diseases.

Rational Design and Acoustic Assembly of Human Cerebral Cortex-Like Microtissues from hiPSC-Derived Neural Progenitors and Neurons.

Development of biologically relevant and clinically relevant human cerebral cortex models is demanded by mechanistic studies of human cerebral cortex-associated neurological diseases and discovery of preclinical neurological drug candidates. Here, rational design of human-sourced brain-like cortical tissue models is demonstrated by reverse engineering and bionic design. To implement this design, the acoustic assembly technique is employed to assemble hiPSC-derived neural progenitors and neurons separately in a label-free and contact-free manner followed by subsequent neural differentiation and culture. The generated microtissues encapsulate the neuronal microanatomy of human cerebral-cortex tissue that contains six-layered neuronal architecture, a 400-µm interlayer distance, synaptic connections between interlayers, and neuroelectrophysiological transmission. Furthermore, these microtissues are infected with herpes simplex virus type I (HSV-1) virus, and the HSV-induced pathogenesis associated with Alzheimer's disease is determined, including neuron loss and the expression of Aß. Overall, a high-fidelity human-relevant in vitro histotypic model is provided for the cerebral cortex, which will facilitate wide applications in probing the mechanisms of neurodegenerative diseases and screening the candidates for neuroprotective agents.

Inhibition of NEMO alleviates arthritis by blocking the M1 macrophage polarization.

The nuclear factor-kappa B (NF-κB) signaling pathway and macrophages are critically involved in the pathogenesis of rheumatoid arthritis (RA). Recent studies have identified NF-κB essential modulator (NEMO), a regulatory subunit of the inhibitor of NF-κB kinase (IKK), as a potential target to inhibit NF-κB signaling pathway. Here, we investigated the interactions between NEMO and M1 macrophage polarization in RA. NEMO inhibition led to the suppression of proinflammatory cytokines secreted from M1 macrophages in collagen-induced arthritis mice. From lipopolysaccharide (LPS)-stimulated RAW264, knocking down NEMO blocked M1 macrophage polarization accompanied by lesser M1 proinflammatory subtype. Our findings link the novel regulatory component of NF-κB signaling and human arthritis pathologies which will pave the way towards the identification of new therapeutic targets and the development of innovative preventive strategies.

Pregnancy in patients with systemic lupus erythematosus: a systematic review.

Systemic lupus erythematosus (SLE)-a most common disorder in women of reproductive age-has been described to be associated with adverse pregnancy outcomes. Despite the increased health risks for the mother (preeclampsia, lupus flare, arterial hypertension, gestational diabetes mellitus and thrombotic risk when antiphospholipid antibodies are present) and fetus (miscarriage, stillbirth, premature birth, intrauterine growth restriction and neonatal lupus), the majority of patients can deliver healthy neonates. With appropriate management by a multidisciplinary team, composing rheumatologists, obstetricians and neonatologists, women with SLE can achieve better pregnancy outcomes by monitoring associated predictive indicators, raising major concern for severe complications and somewhat early delivery if necessary. In this review, we summarize the latest advances in secondary infertility and pregnancy-related risk perception for lupus patients, with an emphasis on the safety of biological agents (mainly belimumab and rituximab) and traditional therapeutic regimens.

Size- and density-dependent acoustic differential bioassembly of spatially-defined heterocellular architecture.

Emerging acoustic bioassembly represents an attractive strategy to build cellular closely-packed organotypic constructs in a tunable manner for biofabrication. However, simultaneously assemble heterogeneous cell types into heterocellular functional units with spatially-defined cell arrangements, such as complementary and sandwich cytoarchitectures, remains a long-lasting challenge. To overcome this challenge, herein we present an acoustic differential bioassembly technique to assemble different cell types at the distinct positions of the acoustic field based on their inherent physical characteristics including cellular size and buoyant density. Specifically, different cell types can be differentially assembled beneath the nodal or the antinode regions of the Faraday wave to form complementary cytoarchitectures, or be selectively positioned at the center or edge area beneath either the nodal or the antinode regions to form sandwich cytoarchitectures. Using this technique, we assemble human induced pluripotent stem cell-derived liver spheroids and endothelial cells into hexagonal cytoarchitecturesin vitroto mimic the cord and sinusoid structures in the hepatic lobules. This hepatic lobule model reconstitutes liver metabolic and synthetic functions, such as albumin secretion and urea production. Overall, the acoustic differential bioassembly technique facilitates the construction of human relevantin vitroorganotypic models with spatially-defined heterocellular architectures, and can potentially find wide applications in tissue engineering and regenerative medicine.

IL-17A Promotes the Migration, Invasion and the EMT Process of Lung Cancer Accompanied by NLRP3 Activation.

Background: Lung cancer is a deadly cancer worldwide, and its pathogenesis and treatment methods require continuous research and exploration. As a representative factor of adaptive immunity, the role of interleukin-17A (IL-17A) in lung cancer is still unclear. The purpose of the present study was to investigate the effect of IL-17A on the biological behaviour of lung cancer cells and the relative mechanism. Methods: The human lung adenocarcinoma A549 and H1299 cell lines were used for in vitro study. The effects of IL-17A on cell proliferation, migration and invasion were assessed by CCK-8 assay, wound-healing assay, transwell invasion assay and real-time cell analysis (RTCA). The expression levels of marker proteins in the process of epithelial-mesenchymal transition (EMT) were detected by western blot analysis. Caspase-1 activity and the concentration of IL-1ß after NLRP3 inflammasome activation were measured by a Caspase-1 Activity Assay Kit and an IL-1ß ELISA kit, respectively. Results: Compared to the control group, IL-17A treatment did not affect the proliferation of A549 and H1299 cells in vitro, but it promoted cell migration, invasion and the EMT process. IL-17A treatment increased NLRP3 expression, caspase-1 activity and IL-1ß level. Blockade of NLRP3 alleviated the cell migration, invasion and the EMT process induced by IL-17A. Conclusions: In conclusion, these findings indicated that NLRP3 participates in the migration, invasion and the EMT process of IL-17A-stimulated lung cells in vitro.

Iguratimod ameliorates bleomycin-induced pulmonary fibrosis by inhibiting the EMT process and NLRP3 inflammasome activation.

BACKGROUND: Pulmonary fibrosis is the deadliest manifestation of connective tissue disease (CTD). Iguratimod (IGU) is a new drug that is used for controlling CTD. Clinical studies have found that IGU has certain advantages in improving lung function and shows great potential for pulmonary fibrosis therapy. However, the specific mechanism is not clear. This study was designed to observe and investigate the therapeutic effects of IGU on bleomycin-induced pulmonary fibrosis and further investigate its underlying mechanism. METHODS: A mouse model of pulmonary fibrosis was induced by intratracheal injection of bleomycin (BLM). Model mice were randomly assigned to receive different concentrations of IGU. A TGF-ß (T)-induced A549 epithelial-mesenchymal transition (EMT) cell model was utilized to investigate the effects of IGU on EMT in vitro. The NLRP3 inflammasome was activated by the costimulation of LPS+ATP (LA) to evaluate the effects of IGU in vitro. RESULTS: We found that IGU resulted in favourable therapeutic outcomes by affecting inflammatory infiltration and collagen deposition. Additionally, the markers of the BLM-mediated EMT phenotype and NLRP3-activated phenotype in the lung were also attenuated after IGU administration. In vitro experiments, the results confirmed its anti-EMT and anti-NLRP3 inflammasome activation effects.We then found that the anti-lung fibrosis effect of IGU was accompanied by a decrease in reactive oxygen species (ROS) production. CONCLUSION: IGU can inhibit the EMT process and NLRP3 inflammasome activation and reduce ROS production to ameliorate pulmonary fibrosis, which may provide new insights into the further application of IGU in interstitial pulmonary fibrosis.

Development of a high-throughput micropatterned agarose scaffold for consistent and reproducible hPSC-derived liver organoids.

Liver organoids represent emerging human-relevantin vitroliver models that have a wide range of biomedical applications in basic medical studies and preclinical drug discovery. However, the generation of liver organoids currently relies on the conventional Matrigel dome method, which lacks precise microenvironmental control over organoid growth and results in significant heterogeneity of the formed liver organoids. Here, we demonstrate a novel high-throughput culture method to generate uniform liver organoids from human pluripotent stem cell-derived foregut stem cells in micropatterned agarose scaffold. By using this approach, more than 8000 uniformly-sized liver organoids containing liver parenchyma cells, non-parenchymal cells, and a unique stem cell niche could be efficiently and reproducibly generated in a 48-well plate with a size coefficient of variation significance smaller than that in the Matrigel dome. Additionally, the liver organoids highly expressed liver-specific markers, including albumin (ALB), hepatocyte nuclear factor 4 alpha (HNF4α), and alpha-fetoprotein (AFP), and displayed liver functions, such as lipid accumulation, glycogen synthesis, ALB secretion, and urea synthesis. As a proof of concept, we evaluated the acute hepatotoxicity of acetaminophen (APAP) in these organoids and observed APAP-induced liver fibrosis. Overall, we expect that the liver organoids will facilitate wide biomedical applications in hepatotoxicity analysis and liver disease modeling.

IFN-γ, should not be ignored in SLE.

Systemic lupus erythematosus (SLE) is a typical autoimmune disease with a complex pathogenesis and genetic predisposition. With continued understanding of this disease, it was found that SLE is related to the interferon gene signature. Most studies have emphasized the important role of IFN-α in SLE, but our previous study suggested a nonnegligible role of IFN-γ in SLE. Some scholars previously found that IFN-γ is abnormally elevated as early as before the classification of SLE and before the emergence of autoantibodies and IFN-α. Due to the large overlap between IFN-α and IFN-γ, SLE is mostly characterized by expression of the IFN-α gene after onset. Therefore, the role of IFN-γ in SLE may be underestimated. This article mainly reviews the role of IFN-γ in SLE and focuses on the nonnegligible role of IFN-γ in SLE to gain a more comprehensive understanding of the disease.

Polynomial time algorithm for minmax scheduling with common due-window and proportional-linear shortening processing times.

This article deals with common due-window assignment and single-machine scheduling with proportional-linear shortening processing times. Objective cost is a type of minmax, that is, the maximal cost among all processed jobs is minimized. Our goal is to determine an optimal schedule, the optimal starting time, and size of due-window that minimize the worst cost, which consist of four parts: earliness, tardiness, starting time and length of the due-window. Optimal properties of the problem are given, and then an optimal polynomial algorithm is proposed to solve the problem.

Cerebral Organoids for Modeling of HSV-1-Induced-Amyloid ß Associated Neuropathology and Phenotypic Rescue.

Herpes simplex virus type I (HSV-1) infection is a potential risk factor involved in the Amyloid ß (Aß) associated neuropathology. However, further understanding of the neuropathological effects of the HSV-1 infection is hampered by the limitations of existing infection models due to the distinct differences between human brains and other mammalians' brains. Here we generated cerebral organoid models derived from pluripotent stem cells to investigate the HSV-induced Aß associated neuropathology and the role of antiviral drugs in the phenotypic rescue. Our results identified that the HSV-1-infected cerebral organoids recapitulated Aß associated neuropathology including the multicellular Aß deposition, dysregulated endogenous AD mediators, reactive gliosis, neuroinflammation, and neural loss, indicating that cerebral organoids offer an opportunity for modeling the interaction of HSV-1 with the complex phenotypes across the genetic, cellular, and tissue levels of the human Alzheimer's disease (AD). Furthermore, we identified that two antiviral drugs, namely Ribavirin (RBV) and Valacyclovir (VCV), inhibited HSV-1 replication and rescued the neuropathological phenotypes associated with AD in the HSV-1-infected cerebral organoids, implying their therapeutic potential to slow down the progression of AD. Our study provides a high-fidelity human-relevant in-vitro HSV-1 infection model to reconstitute the multiscale neuropathological features associated with AD and discover therapeutic drug candidates relevant to the AD viral hypothesis.

Acoustic Fabrication of Living Cardiomyocyte-based Hybrid Biorobots.

Organized assemblies of cells have demonstrated promise as bioinspired actuators and devices; still, the fabrication of such "biorobots" has predominantly relied on passive assembly methods that reduce design capabilities. To address this, we have developed a strategy for the rapid formation of functional biorobots composed of live cardiomyocytes. We employ tunable acoustic fields to facilitate the efficient aggregation of millions of cells into high-density macroscopic architectures with directed cell orientation and enhanced cell-cell interaction. These biorobots can perform actuation functions both through naturally occurring contraction-relaxation cycles and through external control with chemical and electrical stimuli. We demonstrate that these biorobots can be used to achieve controlled actuation of a soft skeleton and pumping of microparticles. The biocompatible acoustic assembly strategy described here should prove generally useful for cellular manipulation in the context of tissue engineering, soft robotics, and other applications.

Erythropoiesis signature and ubiquitin-mediated proteolysis are enriched in systematic juvenile idiopathic arthritis.

Systemic Juvenile Idiopathic Arthritis (sJIA) is a distinctive subtype of Juvenile Idiopathic Arthritis (JIA). The pathogenesis of sJIA is still unclear with the limited treatment options. Although previous bioinformatics analyses have identified some genetic factors underlying sJIA, these studies were mostly single centre with a small sample size and the results were often inconsistent. Herein, we combined two data sets of GSE20307 and GSE21521 and select the matrix of patients diagnosed as sJIA in it for further analysis. The GSE20307 and GSE21521 matrixes downloaded from the Gene Expression Omnibus (GEO) were analysed using online tools GEO2R, Venny, Metascape, STRING and Cytoscape to identify differentially expressed genes (DEGs), enrichment pathways, protein-protein interaction (PPI), main module and hub genes between sJIA individuals and healthy controls. A total of 289 overlapping genes (consisting of 41 downregulated genes and 248 upregulated genes) were identified. Hub genes were primarily related to erythropoiesis. And the KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of overlapping DEGs were mainly involved in malaria and non-small cell lung cancer. Besides, DEGs in main module were involved in ubiquitin-mediated proteolysis. Our study suggests that the erythropoiesis signature indeed exists in sJIA similar to previous reports. And ubiquitin-mediated proteolysis is important in sJIA.

Prediction and analysis of functional RNA structures within the integrative genomics viewer.

In recent years, interest in RNA secondary structure has exploded due to its implications in almost all biological functions and its newly appreciated capacity as a therapeutic agent/target. This surge of interest has driven the development and adaptation of many computational and biochemical methods to discover novel, functional structures across the genome/transcriptome. To further enhance efforts to study RNA secondary structure, we have integrated the functional secondary structure prediction tool ScanFold, into IGV. This allows users to directly perform structure predictions and visualize results-in conjunction with probing data and other annotations-in one program. We illustrate the utility of this new tool by mapping the secondary structural landscape of the human MYC precursor mRNA. We leverage the power of vast 'omics' resources by comparing individually predicted structures with published data including: biochemical structure probing, RNA binding proteins, microRNA binding sites, RNA modifications, single nucleotide polymorphisms, and others that allow functional inferences to be made and aid in the discovery of potential drug targets. This new tool offers the RNA community an easy to use tool to find, analyze, and characterize RNA secondary structures in the context of all available data, in order to find those worthy of further analyses.

[Recent advances in emerging three-dimensional in vitro models for sport-related traumatic brain injury].

Sports-related traumatic brain injury (srTBI) is a traumatic brain injury (TBI) caused by sports, which can result in cognitive and motor dysfunction. Currently, research on the molecular mechanism of srTBI and related drug development mainly relies on monolayer culture models and animal models. However, many differences exist in cell populations and inflammatory responses between these models and human pathophysiological processes. Most of the researches derived from the models can't effectively conducted translational research. Emerging three-dimensional (3D) in vitro models bridge the limitations of traditional models in simulating the pathophysiological processes of human srTBI and provide new means to understand srTBI. A literature has reported the research progress of emerging 3D in vitro models in neurological diseases, but there is a lack of systematic summary of the mentioned models in srTBI studies. Here, we review the research progress of emerging 3D in vitro models of srTBI, discuss the advantages and limitations of existing models, and further prospect the future trend of srTBI models. This paper aims to provide a new research perspective for researchers in tissue engineering and sports medicine to study the molecular mechanisms of srTBI and develop neuroprotective drugs.

Metabolomic analysis of synovial fluids from rheumatoid arthritis patients using quasi-targeted liquid chromatography-mass spectrometry/mass spectrometry.

OBJECTIVES: Synovial fluid (SF) accumulates extensively in joints of individuals with rheumatoid arthritis (RA), which reflects the pathological state of the synovium and disease activity. This study applied quasi-targeted liquid chromatography-mass spectrometry/mass spectrometry, an advanced metabolomics technique, to find characteristic metabolisms in RA. METHODS: SF samples from the patients (n=20) were collected and examined using the metabolomic technique. SF samples from patients with osteoarthritis (OA) (n=20) were used as controls. RESULTS: Four hundred and seventy-nine variable metabolites were detected, and 250 of these metabolites were identified by searching the Human Metabolome Database (HMDB) and a self-constructed information list of possible metabolites. S-plot and volcano plot analysis detected 22 metabolites with differential levels in RA SF compared with those in OA SF. With these 22 candidate metabolites, pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database detected upregulation of pyrimidine metabolism and purine metabolism, and downregulation of fatty acid biosynthesis and unsaturated fatty acid biosynthesis in RA SF. Receiver operating characteristic (ROC) analysis and logistic regression models detected increased levels of guaiacol, naringenin, phenylpropanolamine and vanillylmandelic acid in RA SF. Furthermore, the naringenin level showed positive correlation with rheumatic factor (RF) and anti-cyclic citrillinated peptides (anti-CCP) levels. CONCLUSIONS: Our study suggests disturbed pyrimidine metabolism, purine metabolism, fatty acid biosynthesis and unsaturated fatty acid biosynthesis, as well as increased naringenin level, are characteristic metabolisms in RA.

IL-6 promotes collagen-induced arthritis by activating the NLRP3 inflammasome through the cathepsin B/S100A9-mediated pathway.

Rheumatoid arthritis (RA) is an inflammatory disease with symmetric polyarthritis. IL-6 and NLRP3 inflammasome in macrophages contribute to the pathogenesis of RA. This study aimed to investigate the relationship between IL-6 and the NLRP3 inflammasome in RA. Here, we found that IL-6 inhibition reduced NLRP3 inflammasome activation in mice with collage-induced arthritis (CIA). In vitro studies showed that IL-6 directly induced NLRP3 inflammasome activation via cathepsin B (CTSB) in the presence of ATP. In addition, S100A9 induced by ATP stimulation promoted the interaction of CTSB and NLRP3 to activate the NLRP3 inflammasome. Our findings show a novel mechanism of NLRP3 inflammasome activation by IL-6 that may lead to a potential therapy for RA by interrupting the interaction between IL-6 and the NLRP3 inflammasome.