Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Immunoglobulin-producing AT2-like cells secrete IgA into the extracellular matrix in pulmonary fibrosis

ABSTRACT: Mouse of SiO2 group were instilled with silica suspension, and mouse of control group were instilled with NS. The mouse mouse were raised for 56 d, and then the ECM was harvest. We found out the main protein deposited in fabrotic lung ECM. By spatial transcriptomics, we analyzed the distribution pattern of transcripts in space. Using sc-RNA sequencing, we investigated the cell resource of IgA.

ORGANISM(S): Mus Musculus

SUBMITTER: Jie Chao

PROVIDER: PXD028194 | iProX | Tue Aug 31 00:00:00 BST 2021

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

A missing piece of the puzzle in pulmonary fibrosis: anoikis resistance promotes fibroblast activation.

Yin Juan J Wang Jing J Zhang Xinxin X Liao Yan Y Luo Wei W Wang Sha S Ding Jiawei J Huang Jie J Chen Mengling M Wang Wei W Fang Shencun S Chao Jie J

Cell & bioscience 20220225 1

<h4>Background</h4>Pulmonary fibrosis initiates a pneumonic cascade that leads to fibroblast dysfunction characterized by excess proliferation. Anoikis is a physiological process that ensures tissue development and homeostasis. Researchers have not clearly determined whether disruption of anoikis is involved in pulmonary fibrosis.<h4>Results</h4>Here, we investigated the mechanism by which silica induces fibroblast activation via anoikis resistance and subsequent fibrosis. Anoikis of lung fibrob ...[more]

PMID: 35216634

Similar Datasets

Impact on Arabidopsis thaliana transcriptome of multifunctional silica nanoparticles based on metal atom clusters

Project description:au14-09_silice - clustop transcriptomics. - Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication. - Phytotoxicity of Cs2[Mo6Br14]@SiO2 nanoparticles and their components, i.e. Cs2[Mo6Br14] clusters and SiO2 nanoparticles, has been studied usign Arabidopsis thaliana cell suspension culture. Cs2[Mo6Br14]@SiO2 nanoparticles used here are composed of 7,5% clusters and 92,5% SiO2. Thus, to compare to the impact of a 100 mg/L Cs2[Mo6Br14]@SiO2 nanoparticle treatment (CS), we also treated Arabidopsis cells with clusters at 7,5 mg/L (C), SiO2 at 92,5 mg/L (S), and combined 7,5 mgCMB/L plus 92,5 mgSiO2/L (C+S).

2017-02-01 | GSE93182 | GEO

Nano-silica particles synergistically IgE-mediated mast cell activation

Project description:To deeply investigate the details of the nano-SiO2 effects, we examined the gene expression profile alterations after nano-SiO2 treatment in BMMCs. The difference analysis between the groups showed that 285 genes were significantly expressed after treatment with nano-SiO2. Compared with the blank group, both nano-SiO2 exposure and DNP-HSA stimulation increased the expression of genes related to the MAPK signaling pathway in mast cells to varying degrees.

2022-07-05 | GSE206630 | GEO

Metabolomics of immunoglobulin-producing cells in IgA nephropathy

Project description:IgA nephropathy (IgAN), the most common primary glomerulonephritis, is characterized by deposits of IgA-containing immune complexes in the kidney glomeruli, as first described by Berger and Hinglais in 1968. IgAN is a major cause of end-stage renal disease with its associated cardio-renal morbidity and mortality. Analyses of the IgA deposits revealed that the IgA is exclusively of the IgA1 subclass and that this IgA1 is aberrantly glycosylated, deficient in galactose in some O-glycans (Gd-IgA1). Patients with IgAN have elevated serum levels of Gd-IgA1 bound by anti-glycan autoantibodies in circulating immune complexes (CIC) that are fundamental in driving disease pathology in an autoimmune process. We have recently shown that elevated serum levels of Gd-IgA1 in patients with IgAN predict disease progression. Thus, understanding the mechanisms behind Gd-IgA1 production will improve future treatment options, as there is presently no disease-specific therapy. A total of 24 cell pellets (4 replicates from 6 cell lines) were analyzed by LCMS metabolomics. Immortalized immunoglobulin-producing cell lines were generated from peripheral-blood lymphocytes from patients with IgAN and healthy controls as described in Suzuki, H., Moldoveanu, Z., Hall, S., et al. IgA1-secreting cell lines from patients with IgA nephropathy produce aberrantly glycosylated IgA1. J Clin Invest. 2008, 118, 629-639.

2017-02-17 | ST000560 | MetabolomicsWorkbench

Analysis of three kinds of tumors gene expression by RNA microarray

Project description:In order to detect the difference of tumorigenicity induced by different cell lines in nude mice. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of genes expression. 10 week old 44 thymus-free nude mice were randomly divided into four groups, control group, A549 group, H1299 group and A549+H1299 group. 0.2ml saline suspension containing 5×10^6 cells were implanted subcutaneously in the flanks of each nude mouse in the control group. A549+H1299 group means 0.2ml saline suspension containing 2.5×10^6 A549 cells and 2.5×10^6 H1299 cells. After 30 days, Tumor tissue in each nude mouse Tumor tissue was taken out and detected with Agilent Human 4x44K Gene Expression Microarrays.

2018-12-20 | GSE124112 | GEO

Expression data from Rat neuronal Schwann cells (SCs) that under different extracellular matrix (ECM) conditions

Project description:Post peripheral injuries, Schwann cells express certain regenerative genes to promote nerve regeneration. The expression of regenerative genes can be regulated by ECM cues such as stiffness and cell shape. We used microarray to illustrate the interplays between SC regenerative gene expression and different ECM conditions.

2021-05-01 | GSE165206 | GEO

Global proteomics to study silica nanoparticle-induced cytotoxicity and its mechanisms in HepG2 cells

Project description:Silica nanoparticles (SiO2 NPs) are commonly used in medical and pharmaceutical fields. Research into the cytotoxicity and overall proteomic changes occurring during initial exposure to SiO2 NPs is limited. We investigated the mechanism of toxicity in human liver cells according to exposure time [0, 4, 10, and 16 hours (h)] to SiO2 NPs through proteomic analysis using mass spectrometry. SiO2 NP-induced cytotoxicity through various pathways in HepG2 cells. Interestingly, when cells were exposed to SiO2 NPs for 4 h, the morphology of the cells remained intact, while the expression of proteins involved in mRNA splicing, cell cycle, and mitochondrial function was significantly downregulated. These results show that the toxicity of the nanoparticles affects protein expression even if there is no change in cell morphology at the beginning of exposure to SiO2 NPs. The levels of reactive oxygen species changed significantly after 10 h of exposure to SiO2 NPs, and the expression of proteins associated with oxidative phosphorylation, and the immune system was upregulated. Eventually, these changes in protein expression induced HepG2 cell death. This study provides insights into cytotoxicity evaluation at early stages of exposure to SiO2 NPs through in vitro experiments.

2021-09-10 | PXD024206 | Pride

Gene expression response to silica treatment in wild-type C57 black 6 mice vs Rag1 knockout, NK-depleted mice

Project description:The lung is constantly exposed to potentially pathogenic particles and microorganisms. It has recently become evident that not only innate, but also adaptive immune responses to particulates such as crystalline silica (SiO2) entering the respiratory tract are complex and dynamic events. Although the cellular mechanisms and anatomical consequences involved in the development of silicosis have been extensively studied, they still remain poorly understood. Based on their capacity for immune regulation, lymphocytes may play a role in determining the respiratory response to environmental challenge by SiO2. The objective of this study was to characterize the impact of SiO2 exposure on respiratory immune processes, with particular emphasis on evaluating the importance of lymphocytes in the murine silicosis model. Therefore, we utilized lymphopenic mice including NK deficient, Rag1-/- or a combination (Rag1-/- NK depleted) and demonstrated that SiO2-induced fibrosis and inflammation occur independently of T, B, NK T, and NK cells. Studies in Rag1-/- mice further suggest that lymphocytes may participate in controlling SiO2-induced inflammation through modulation of the Nalp3 inflammasome. This observation may have clinical relevance in the treatment of inflammatory and fibrotic lung diseases that are either refractory or respond sub-optimally to current therapeutics.

2009-12-19 | GSE19563 | GEO

Gene expression profiles of the EBV-induced lymphomas against ‘normal’ human PBL

Project description:Peripheral blood lymphocytes (PBLs) were isolated from the fresh blood samples of six healthy donors and intraperitoneally grafted into SCID mice at 8~10 × 107 PBLs/mouse. PBLs from each donor were grafted into 3~4 SCID mice. EBV was isolated from the supernatant of B95-8 cells cultured in vitro under starvation conditions. EBV infection was not required for SCID mice that were grafted with PBLs from donors who were positive for EBV viral capsid antigen (VCA)-IgG and IgA. On the other hand, 0.4 mL of EBV suspension was intraperitoneally injected into SCID mice that were grafted with PBLs from donors who were VCA-IgA negative on day 3 post-grafting. All surviving mice were euthanized on day 135 post-PBL grafting. Total RNA was extracted from the six EBV-induced lymphomas (tumor group) and normal human lymphocytes (normal group) using TRIZOL reagent, and labelled as per the instructions of the Agilent Quick Amp Labeling Kit. First-strand cDNA was synthesized from purified total RNA (template) using the T7 promoter primer and Moloney murine leukemia virus reverse transcriptase, followed by the synthesis of the second-strand cDNA. Both cDNA strands were then synthesized into cRNA using transcription master mix and labelled with cyanine-3-cytidine-5'-triphosphate. Gene expression profiles of the normal and tumor groups were detected using Agilent whole genome microarray containing 41,000 known human gene transcripts. The microarrays were scanned with the Agilent Microarray Scanner and the raw data were recorded and normalized using Agilent Feature Extraction Software to calculate the signal fold change between the tumor and normal groups. A ≥2-fold change in gene expression, as determined by the t-test, was considered as up-regulated, and a ≤0.5-fold change in gene expression was considered as down-regulated.

2022-06-30 | E-MTAB-11857 | biostudies-arrayexpress

Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

Project description:The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). To investigate the effect of matrix cues on phenotypic plasticity, we embedded triple negative DU4475 cells from suspension culture into mechanically tunable fibrin gels or basement membrane extract (Matrigel). Cells in suspension culture and matrix cultures showed divergent gene expression profiles, with specific gene expression signatures depending on the biochemical composition and stiffness of the matrix.

2023-04-05 | GSE228939 | GEO

Transcription profiling of mouse blood from native and Plasmodium berghei induced experimental cerebral malaria untreated or treated with activated charcoal.

Project description:We found that oral activated charcoal (oAC) provided significant protection against P. berghei ANKA-induced ECM, significantly increasing overall survival time compared to untreated mice. Protection from ECM by oAC was associated with a reduced numbers of splenic TNF+ CD4+ T cells and multifunctional IFNy+TNF+ CD4+ and CD8+ T cells. Furthermore, we identified a whole blood gene expression signature (68 genes) associated with protection from ECM. To evaluate whether oAC might affect current best available anti-malarial treatment, a group of female C57BL/6 mice infected with PbA received Activated Charcoal. At day 6 p.i., and prior to the first deaths of untreated PbA-infected mice, 5 untreated PbA-infected mice (Group 1) and 5 AC-treated PbA-infected mice (Group 2) were killed and fresh blood (300-500�l per mouse) was collected and processed into RNA. Blood was also taken from uninfected control mice (�baseline�- Group 3).

2010-04-01 | E-MEXP-2594 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data