Single-cell RNA sequencing in Kawasaki disease
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE200743 | GEO | 2022/09/06
REPOSITORIES: GEO
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Project description:We performed single-cell RNA sequencing (using Cell Ranger Single Cell Pipeline v.4.0.0 to process data de-multiplexing, barcode processing, and single cell 3' gene counting generated by the 10X Chromium platform) in KD patients (within 24 hours before IVIG treatment) and age-matched fever controls.
2024-06-01 | GSE254657 | GEO
Project description:The goals of this study are to determine tissue composition of human lung organoids (hLOs) when maintained long-term (day 230). hLOs consist of alveolar epithelial cells, mesenchymal/endothelial cells, smooth muscle cells and immune cells. After dissociated hLOs, a target capture of 1x 104 cells was performed using the 10X Genomics Chromium Single Cell RNA sequencing. Briefly, single cell gel bead-in-emulsions(GEMs) are generated by passing cells with enzyme mix, partitioning oil, and barcoded gel beads by 10X Chromium chip. After GEM formation, the gel bead is dissolved and co-partitioned cell is lysed. Subsequently, reverse transcription (RT) occurs inside GEMs and barcoded full-length cDNA is generated. After RT, amplified cDNAs with barcode sequences (cell index and UMI) are pooled and single cell library is constructed using the Single Cell 3` Reagent Kit (v3 chemistry). The resulting library was sequenced on illumina HiseqX platform with 150bp paired end. Raw base calling files generated by illumine sequencing were demultiplexed based on the sample index read to generate FASTQ files using the 10X Genomics Cell Ranger (v3.0.2) pipeline. The raw reads were trimmed from the 3’ end to get the recommended number of cycle for read pairs (read1: 28bp; read2 : 91bp). The trimmed reads were mapped to the hg38 reference human genome with subsequent analysis, including filtering, barcode counting, and UMI counting. The resulting data were used to generate the multidimensional feature-barcode matrix using the CellRanger count with default parameters.
2020-01-03 | GSE142838 | GEO
Project description:Human synovial Single cell RNA-seq was performed on three tissue samples from healthy donors. This experiment was done to explore the heterogeneity of cells in healthy human synovial joint and enabled the comparison of cellular states and composition to those of publicly available single cell RNA-seq datasets from psoriatic arthritis and rheumatoid arthritis patients. Human synovial cells were loaded immediately after tissue dissociation with up to 25,000 cells in a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as paired end (PE) 150 bp by Illumina sequencing to 65-80% saturation. Reads were mapped to the GRCh38 human genome (GENCODE) using the 10x Genomics Cell Ranger pipeline (7.2.0).
2024-08-06 | E-MTAB-14339 | biostudies-arrayexpress
Project description:Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone. Intravenous immunoglobulin (IVIG) treatment-resistant patients are high risk of developing coronary artery lesions (CALs) with Kawasaki disease (KD). The IVIG-responsive (Group A; n = 6) and -resistant patients (Group B) were predicted before starting the initial treatment using the Egami scoring system, and randomly allocated a single-IVIG treatment group (Group B1; n = 6) or a IVIG-plus-methylprednisolone (IVMP) combined therapy group (Group B2; n = 5). We investigated transcript abundance in the leukocytes of those patients using microarray analysis. Results: five patients in Group A and 1 patient in Group B1 responded to initial IVIG treatment. All Group B2 patients responded to IVIP-plus-IVMP combined therapy. Prior to performing these treatments, those transcripts related to IVIG-resistance and to the development of CALs, such as IL1R, IL18R, oncostatin M, suppressor of cytokine signaling-3, S100A12 protein, carcinoembryonic antigen-related cell adhesion molecule-1, matrix metallopeptidase-9 and polycythemia rubra vera-1 were more abundant in Group B patients in comparison to Group A patients. Moreover, those transcripts in Group B2 patients were more profoundly and broadly suppressed than Group B1 patients after treatment. Conclusion: this study elucidated the molecular mechanism of the effectiveness of IVIG-plus-IVMP combined therapy. 34 samples of pre- and post-treatment in three groups consisting of predicted as IVIG-responsive patients, given single-IVIG treatment patients and IVIG-plus-IVMP combined therapy group in predicted as IVIG-resistant patients.
2010-07-08 | E-GEOD-16797 | biostudies-arrayexpress
Project description:Background: Kawasaki disease (KD) is an acute self-limited vasculitis and the leading cause of acquired heart disease in children in developed countries. No etiologic agent(s) has been identified, and the processes that mediate formation of coronary artery aneurysms and abatement of fever following treatment with intravenous immunoglobulin (IVIG) remain poorly understood. Results: In an initial survey, we used DNA microarrays to examine patterns of gene expression in peripheral whole blood from 20 children with KD; each was sampled during the acute, subacute, and convalescent phases of the illness. Acute KD was characterized by increased relative abundance of gene transcripts associated with innate immune and proinflammatory responses and decreased abundance of transcripts associated with natural killer cells and CD8+ lymphocytes. There was significant temporal variation in transcript levels during the acute disease phase and stabilization thereafter. We confirmed these temporal patterns in a second cohort of 64 patients, and identified additional inter-individual differences in transcript abundance. Notably, higher levels of transcripts of the gene for carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) were associated with an increased percentage of unsegmented neutrophils, fewer days of illness, higher levels of C-reactive protein, and subsequent non-response to IVIG; this last association was confirmed by quantitative reverse transcription PCR in a third cohort of 33 patients, and was independent of day of illness. Conclusions: Acute KD is characterized by dynamic and variable gene-expression programs that highlight the importance of neutrophil activation state and apoptosis in KD pathogenesis. Our findings also support the feasibility of extracting biomarkers associated with clinical prognosis from gene-expression profiles of individuals with systemic inflammatory illnesses. Whole blood (PAXgene tubes) was obtained from 64 Kawasaki disease patients prior to treatment. RNA was amplified using the MessageAmp kit (Ambion), and reverse transcribed. Each sample was labelled with Cy5, and hybridized to a Lymphochip cDNA array along with amplified human reference RNA labelled with Cy3(Universal Human Reference RNA, Stratagene). Analysis was restricted to those array elements (LUIDs) with signal intensity/background of at least 2.5 in either channel for at least 80% of the samples, and a regression correlation of 0.6. Patterns of gene expression were correlated with clinical parameters, including subsequent response to treatment with intravenous immunoglobulin (IVIG). A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Phenotype: Patient responded (R) or not (NR) to IVIG therapy. Some patients were not classified because they were treated more than 10 days after onset of fever Keywords: disease_state_design
2007-12-13 | GSE9864 | GEO
Project description:Infliximab (IFX) has been reported as the further therapy in intravenous immunoglobulin G (IVIG)-resistant Kawasaki disease (KD) patients. IFX is a monoclonal antibody that blocks the pro-inflammatory cytokine tumor necrosis factor (TNF)-α, but how IFX affect KD vasculitis is unknown. We investigated expression profiling of whole blood cells to elucidate the molecular mechanisms of the effectiveness of IFX therapy and to find characteristic biomarker and an important target in refractory KD. Methods: Refractory KD patients who failed to respond to repeated intravenous immunoglobulin G (IVIG) infusions had received a single infusion of IFX as third therapy. To validate specifically transcripts abundance for IFX therapy, we detected the altered transcripts expression and signaling pathways of whole blood mRNA in these IFX-responsive patients (n=8) using Affymetrix array, comparing initial IVIG-responsive patients (n=6).Results: A total of 1,388 transcripts abundance were significantly altered before and after IFX treatment. These transcripts abundance in IFX had Nucleotide-binding oligomerization domain pathway that play a role in activation of NFκB and IL-1 signaling pathway outside the field of TNF-α signaling pathway. Fifty transcripts including Peptidase inhibitor-3 (PI3), Matrix metalloproteinase-8 (MMP8), Chemokine (C-C motif) receptor-2 (CCR2) and Pentraxin-3 (PTX3) were significantly down-regulated in IFX. Conclusion: We demonstrated that the inhibition of TNF-α by IFX have affected various molecular mechanism materially for IVIG-resistant KD patients. 28 samples of pre- and post-treatment in IFX-responsive patients (n=8) and IVIG-responsive patients (n=6).
2014-04-30 | E-GEOD-48498 | biostudies-arrayexpress
Project description:Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone. Intravenous immunoglobulin (IVIG) treatment-resistant patients are high risk of developing coronary artery lesions (CALs) with Kawasaki disease (KD). The IVIG-responsive (Group A; n = 6) and -resistant patients (Group B) were predicted before starting the initial treatment using the Egami scoring system, and randomly allocated a single-IVIG treatment group (Group B1; n = 6) or a IVIG-plus-methylprednisolone (IVMP) combined therapy group (Group B2; n = 5). We investigated transcript abundance in the leukocytes of those patients using microarray analysis. Results: five patients in Group A and 1 patient in Group B1 responded to initial IVIG treatment. All Group B2 patients responded to IVIP-plus-IVMP combined therapy. Prior to performing these treatments, those transcripts related to IVIG-resistance and to the development of CALs, such as IL1R, IL18R, oncostatin M, suppressor of cytokine signaling-3, S100A12 protein, carcinoembryonic antigen-related cell adhesion molecule-1, matrix metallopeptidase-9 and polycythemia rubra vera-1 were more abundant in Group B patients in comparison to Group A patients. Moreover, those transcripts in Group B2 patients were more profoundly and broadly suppressed than Group B1 patients after treatment. Conclusion: this study elucidated the molecular mechanism of the effectiveness of IVIG-plus-IVMP combined therapy.
2010-06-17 | GSE16797 | GEO
Project description:Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. To evaluate methods for demultiplexing barcode-multiplexed data, we generated a dataset by labeling samples separately with barcode-tagged antibodies, mixing those samples, and progressively overloading a droplet-based scRNA-seq system.
2021-12-01 | GSE181862 | GEO
Project description:In this study, 7530 newborn pancreatic β-cells were analyzed by single-cell sequencing. Cell Ranger was used to compare the original sequencing data, count the genome, filter background cells and cell transcript UMI, and use cell barcode to generate gene-barcode matrix. Then the samples were grouped, gene expression analysis, etc., and the statistical results of each sample sequencing data were output
2024-12-18 | GSE267867 | GEO
Project description:We compared the abundance of gene transcripts of whole blood RNA between IVIG-resistant and –responsive KD patients to identify biomarkers that might differentiate between these two groups and to generate new targets for therapies in IVIG-resistant KD patients.
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