Next generation sequencing facilitates quantitative analysis of bulk hippocampal tissue in lupus mice.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE217939 | GEO | 2023/05/17
REPOSITORIES: GEO
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Project description:Up to 75% of systematic lupus erythematosus (SLE) patients experience neuropsychiatric (NP) symptoms, called neuropsychiatric SLE (NPSLE), yet the underlying mechanisms remain elusive. Microglia control synaptic pruning during early postnatal brain development. The process in NPSLE remains unclear. Here, we show that microglia-coordinated elimination of synaptic terminals participated in NPSLE in MRL/lpr mice, a lupus-prone murine model. We elucidated that lupus mice developed increased depression- and anxiety-like behaviors and persistent phagocytic microglia reactivation before overt peripheral lupus pathology. Microglial engulfment of synapses explained behavioral disorders. To elucidate the mechanism of synaptic pruning by microglia, we sequenced the gene expression in sorted microglia from both lupus (MRL/lpr) mice and the wild-type (MRL/mpj) controls.
2024-03-27 | GSE201282 | GEO
Project description:Objectives. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by multi-organ dysfunction. Neuropsychiatric SLE (NPSLE) occurs in 30~40% of patients with lupus and is the most severe presentation of SLE, frequently resulting in limitation of daily life. Recent studies have shown that microglia, tissue-resident macrophages in the central nervous system, are involved in the pathogenesis of NPSLE. Herein, we explored new therapeutic targets for NPSLE focusing on microglia. Methods. RNA sequencing of microglia in MRL/lpr, lupus-prone mice, as well as that of microglia cultured in vitro with cytokines were performed. A candidate gene, which could be a therapeutic target for NPSLE, was identified and its role on microglial activation and phagocytosis was investigated using specific inhibitors and siRNA. The effect of intracerebroventricular administration of the inhibitor on the behavioural abnormalities of MRL/lpr was also evaluated. Results. Transcriptome analysis revealed the upregulation of Ikbke, which encodes the inhibitor of nuclear factor kappa-B kinase epsilon (IKBKE) in both microglia from MRL/lpr mice and cytokine-stimulated microglia in vitro. Intracerebroventricular administration of an IKBKE inhibitor ameliorated cognitive function and suppressed microglial activation in MRL/lpr mice. Mechanistically, IKBKE inhibition reduced glycolysis, which dampened microglial activation and phagocytosis. Conclusions. These findings suggest that IKBKE plays a vital role in the pathogenesis of NPSLE via microglial activation, and it could serve as a therapeutic target for NPSLE.
2022-09-13 | GSE199662 | GEO
Project description:Up to 75% of systematic lupus erythematosus (SLE) patients experience neuropsychiatric (NP) symptoms, called neuropsychiatric SLE (NPSLE), yet the underlying mechanisms remain elusive. Complement cascades mediate synaptic pruning by microglia during early postnatal brain development. The process in NPSLE remains unclear. Here, we show that complement-coordinated elimination of synaptic terminals participated in NPSLE in MRL/lpr mice, a lupus-prone murine model. We elucidated that lupus mice developed increased anxiety-like behaviors and persistent phagocytic microglia reactivation before overt peripheral lupus pathology. Microglial engulfment of synapses explained behavioral disorders. We further determined that neuronal Nr4a1 signaling was essential for attracting C1q synaptic deposition then apposition of phagocytic microglia, ensuing synaptic loss and neurological disease. Minocycline-deactivated microglia, antibody-blocked C1q, or neuronal Nr4a1 restore protected lupus mice from synapse loss and NP manifestations. Our findings revealed an active role of neurons in coordinating microglia-mediated synaptic loss and highlight neuronal Nr4a1 and C1q as critical components amenable to pharmacological intervention.
2022-02-23 | GSE154288 | GEO
Project description:Purpose: Next-generation sequencing (NGS) technology was used to map expression profiles of effector (spleen) and key target tissues (kidney and brain) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total brain, total kidney and total spleen using Trizol and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Paired-end 37-bp mRNA sequencing was performed on Illumina HiSeq2000 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined kidney-specific molecular signatures of the murine lupus transcriptome that mirrors nephritis-specific transcriptome alterations in human SLE. Conclusions: By the use of the mouse kidney-specific transcriptome and through training of a large whole-blood RNA-sequencing dataset of SLE patients, we developed and validated an algorithm that predicts patients with active LN from SLE patients without LN and suggest vigilance in the monitoring of these patients and potential enrollment in LN prevention studies.
2022-10-01 | GSE186367 | GEO
Project description:Objectives: Molecular medicine raised expectations for strategically targeted biologics in systemic lupus erythematosus (SLE), but clinical trials have been disappointing and difficult to interpret. Most studies add investigational agents to various, often effective, standard of care (SoC) immunosuppressants used at baseline, with unknown treatment interactions. Eliminating polypharmacy in trials of active lupus patients remains controversial. The BOLD study tested immunosuppressant withdrawal as a novel approach to interpretable SLE trials. Methods: In 41 patients with active, non-organ threatening SLE flare (Group A), temporary steroids were given while background immunosuppressants were withdrawn. Time to loss of disease suppression (“flare”) and safety were evaluated; SoC was immediately resumed when symptoms recurred. Immunologic impacts of SoC treatments were studied at baseline by multiplex assay, ELISA, and mRNA array in Group A plus 62 additional patients donating a single sample (Group B). Results: Patients with lower or higher baseline disease had median times-to-flare of 71 or 45 days, respectively; 98% (40/41) flared by six months. All flares were treated and resolved within six weeks. No serious adverse events occurred from flare or infection. Type I interferon, TH17, and BLyS pathways tracked together. Baseline immunosuppressants had distinct impacts on TH17 and BLyS, depending on interferon signature. Conclusion: Trials in active, non-organ-threatening SLE can safely withdraw background treatments if patients who flare are designated non-responders and returned to SoC. Immunologic effects of SoC vary between interferon-defined subsets. These findings provide a strategy for minimizing or optimizing treatment combinations in lupus trials and clinical care.
2017-08-30 | GSE92776 | GEO
Project description:We previously reported the establishment of a rabbit (Oryctolagus cuniculus) model of Systemic Lupus Erythematosus (SLE) in which peptide immunization led to lupus-like autoantibody production including anti-Sm, -RNP, -SS-A, -SS-B and -dsDNA. Some neurological symptoms in form of seizures and nystagmus were observed. The animals used in the previous and in the present study were from a National Institute of Allergy and Infectious Diseases colony of rabbits that were pedigreed, immunoglobulin allotype-defined but not inbred. Their genetic heterogeneity may correspond to that found among patients of a given ethnicity. We extended the information about this rabbit model of SLE by microarray based expression profiling. We first demonstrated that human expression arrays could be used with rabbit RNA to yield information on molecular pathways. We then designed a study evaluating gene expression profiles in 8 groups of control and SLE rabbits (46 rabbits in total). Genes significantly upregulated in SLE rabbits were associated with NK cytotoxicity, antigen presentation, leukocyte migration, cytokine activity, protein kinases, RNA spliceosomal ribonucleoproteins, intracellular signaling cascades, and glutamate receptor activity. These results link increased immune activation with up-regulation of components associated with neurological and anti-RNP responses, demonstrating the utility of the rabbit SLE model to uncover biological pathways related to SLE-induced clinical symptoms, including Neuropsychiatric Lupus. Our finding of distinct gene expression patterns in rabbits that made anti-dsDNA compared to those that only made other anti-nuclear antibodies should be further investigated in subsets of SLE patients with different autoantibody profiles. An important goal of biomedical research is to translate basic findings into clinical applications. Models in inbred mice that spontaneously develop SLE, along with various mutant, transgenic and knockout models have documented a variety of genetic defects leading to SLE, but from the clinical perspective, the degree to which these findings using the inbred or homogeneous artificially mutated strains apply to individuals in heterogeneous outbred human populations is open to question. Given that there is still no cure available for SLE, it is important that we continue to explore possibilities using new animal models of SLE including neuropsychiatric lupus (NPSLE). The gene expression study reported here was conducted to expand our understanding of SLE and in particular NPSLE using our rabbit model. We reported earlier that immunization of rabbits with the SM- or GR-MAP peptides led to development of anti-nuclear autoantibodies, including anti-dsDNA, as well as neurological symptoms in the form of seizures and nystagmus in some rabbits. After establishing that it was possible to use the Affymetrix U95 human microarray for the rabbit gene expression studies, through comparative hybridization of identically prepared cRNA from human and rabbit PWBC, the human microarray was used due to lack of rabbit-specific microarrays. We describe unique gene expression changes associated with lupus like serological patterns in immunized rabbits. Our results also demonstrate that caution must be applied when choosing the structure of the carrier Multiple Antigen Peptide (MAP-peptide) for immunization. We discovered that using MAP-4 rather than MAP-8 significantly altered patterns of immune response and gene expression. Currently, microarrays specific for study of gene expression profiles are not available for rabbits. Therefore, we first conducted studies that compared identically prepared rabbit and human cRNA binding to the Affymetrix U95 microarray available for human gene expression analyses. It was determined that the human microarray could be used with rabbit cRNA to yield information on genetic pathways activated and/or suppressed in autoantibody-producing immunized rabbits. In the current report, gene expression profiles of a total of 46 rabbits, from 4 generations within a pedigreed group of control and immunized rabbits, were obtained and analyzed.
2010-07-23 | E-GEOD-23076 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) technology was exploited to map genome-wide expression profile of hematopoietic stem and progenitor cells (HSPCs) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted as described by manufacturer (NucleoSpin® RNA XS) and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: Transcriptomic analysis of F1-L LSK indicates activation as they respond to type I IFN, displayed increased proliferation and replicative stress, and profoundly prefer to differentiate towards myeloid/granulocytic lineage. Gene expression analysis of F1-L CMPs suggests arrest of differentiation at the level of myeloid progenitors as key regulators including Cebpa, Cebpe, Irf8 are suppressed. Conclusions: Our study suggests deregulation of differentiation at the level of CMPs and “priming” of LSK cells towards granulocytic branch proposing an alternative granulopoiesis route. This comparison indicates an arrest at the progenitor stage both in murine lupus hematopoiesis as important regulators for terminal differentiation are downregulated.
2020-03-17 | GSE128692 | GEO
Project description:[Objectives]: Neuropsychiatric systemic lupus erythematosus (NPSLE) is often difficult to diagnose and distinguish from those of other diseases, because no specific antibodies have yet been detected. [Methods]: We developed a novel proteomic strategy for identifying and profiling antigens in immune complexes (ICs) in the cerebrospinal fluid (CSF) of 26 NPSLE patients. We performed in vitro experiments using astrocytes and analyzed functional change by microarray. [Results]: We identified ICs of suprabasin (SBSN), a molecule which is thought to play a role in epidermal differentiation. Microarray data showed that the senescence and autophagy pathways were significantly changed in astrocytes with anti-SBSN antibody exposure compared to normal immunoglobulin G (IgG) exposure. [Conclusions]: These findings indicate that SBSN could be a novel autoantibody for the evaluation of suspected NPSLE, and may help elucidate the pathogenesis underlying this disease.
2016-09-01 | GSE79189 | GEO
Project description:Genome-wide alternative splice analysis of RNA from lupus and its severe form lupus nephritis We aimed to explore the genome-wide peripheral blood transcriptome of lupus (SLE) and its severe form lupus nephritis (LN) cases compared to healthy subjects (HC) using high density Affymetrix Human Exon1.0.ST arrays. Analysis revealed 15 splice variants that are differentially expressed between SLE/HC and 99 variants between LN/HC (pâ¤0.05,SI>orâ¤0.5,Benjamin Hochberg-False discovery rate correction). Comparison between LN/SLE revealed 7 variants that are differentially expressed with pâ¤0.05,SI>0.5,Benjamin Hochberg-FDR correction. Pathway analysis of differentially spliced genes revealed 11 significant pathways in SLE and 12 in LN (p<0.05). Analysis of peripheral blood transcriptome revealed signature causative genes that are alternatively spliced, signifying their clinical relevance in the pathophysiology of disease. The extent of differential splicing was found to be higher in LN than in SLE, signifying the need for further in-depth research in the same domain. Present study is the first to reveal the significance of alternative variants in susceptibility to SLE and LN. We analyzed blood from 11 female subjects (5 lupus, 3 lupus nephritis and 3 healthy control) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Alt Analyze and Genespring software. No techinical replicates were performed. One of the outiler sample (HC2) was excluded from further analysis.
2016-01-06 | E-GEOD-62764 | biostudies-arrayexpress
Project description:Cognitive impairment is a frequent manifestation of neuropsychiatric systemic lupus erythematosus (NPSLE), present in up to 80% of patients and leading to a diminished quality of life. We have developed a model of lupus-like cognitive impairment which is initiated when anti-DNA, anti-N-methyl D-aspartate receptor (NMDAR) cross- reactive antibodies, which are present in 30% of SLE patients, penetrate the hippocampus. This leads to immediate, self-limited excitotoxic death of CA1 pyramidal neurons followed by loss of dendritic arborization in the remaining CA1 pyramidal neurons and impaired spatial memory. Both microglia and C1q are required for dendritic loss. Here we show that this pattern of hippocampal injury creates a maladaptive homeostasis that is sustained for at least one year. It requires HMGB1 secretion by neurons to bind RAGE, a receptor for HMGB1 expressed on microglia, and leads to decreased expression of microglial LAIR-1, an inhibitory receptor for C1q. The angiotensin converting enzyme (ACE) inhibitor captopril, which can restore a healthy homeostasis, microglial quiescence, and intact spatial memory, leads to upregulation of LAIR-1. This paradigm highlights HMGB1:RAGE and C1q:LAIR-1 interactions as pivotal pathways in the microglial–neuronal interplay that defines a physiologic versus a maladaptive homeostasis.
2023-05-01 | GSE230077 | GEO