ScRNA-seq Analysis of Whole Skin Cells from Irradiated and Naïve Mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE201447 | GEO | 2022/05/04
REPOSITORIES: GEO
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Project description:CEA_SGF:E00006# This set of experiments was performed in order to identify radiation responsive genes. For this, differentiated cultures derived from a single donor were irradiated at either 1 cGy, 2 Gy or sham-irradiated at T0 and total RNA extracts were prepared at 6 time points post-irradiation. Irradiated samples for each dose were hybridized seperately with sham-irradiated samples at the same time point. Each time point for each individual dose was assessed with two independent dye-swap hybridizations. Keywords: time-course
2004-11-01 | GSE1370 | GEO
Project description:Background: The brain undergoes ionizing radiation exposure in many clinical situations, particularly during radiotherapy for brain tumors. The critical role of hippocampus in the pathogenesis of radiation-induced neurocognitive dysfunction is well recognized. Aim: The goal of this study is to test the potential contribution of non-targeted effects in the detrimental response of hippocampus to irradiation and to elucidate the mechanisms involved. Material and Methods: C57Bl/6 mice were whole body (WBI) or partial body (PBI) irradiated with 0.1 or 2.0 Gy of X-rays or sham irradiated. PBI consisted in the exposure of the lower third of the mouse body, whilst the upper two thirds were shielded. Hippocampi were collected 15 days or 6 months post-irradiation and a multi-omics approach was adopted to assess the molecular changes in non-coding RNAs, proteins and metabolic levels, as well as histological changes in the rate of hippocampal neurogenesis. Results: Notably, at 2.0 Gy the pattern of early molecular and histopathological changes induced in the hippocampus at 15 days following PBI was similar in quality and quantity to the effects induced by WBI, thus providing a proof of principle of the existence of out-of-target radiation response in the hippocampus of conventional mice. We detected major alterations in DAG/IP3 and TGF- signaling pathways as well as in the expression of proteins involved in the regulation of long-term neuronal synaptic plasticity and synapse organization, coupled with defects in NSCs self-renewal in the hippocampal dentate gyrus. However, compared to the persistence of the WBI effects, most of the PBI effects were only transient and tended to decrease at 6 months post-irradiation, indicating important mechanistic difference. On the contrary, at low dose we identified a progressive accumulation of molecular defects that tended to manifest at later post-irradiation times. These data, indicating that both targeted and non-targeted radiation effects might contribute to the pathogenesis of hippocampal radiation-damage, have general implications for human health
2021-09-10 | PXD024975 | Pride
Project description:One murine lung was irradiated using 6Gyx5 X-ray exposure. Following irradiation, CD45+ (immune) were sorted from the ipsilateral (irradiated) and contralateral (non-irradiated) lung. Cells from non-irradiated controls were also collected. Proteins from the immune cells were extracted using the MPLEx method. Proteins were reduced with DTT, alkylated with Iodoacetamide, and digested using trypsin. 5 ul of 0.1 ug/ul of peptides were analyzed by LC-MS/MS on a Thermo Q Exactive Orbitrap instrument.
| MSV000090379 | MassIVE
Project description:To examine whether the local carbon ion radiotherapy affects the characteristics of the metastatic tumors, the expression profiles of the primary tumors and the lung metastases were studied in a mouse squamous cell carcinoma model by applying local radiotherapy with no irradiation (negative control), gamma-ray irradiation (reference beam), and carbon-ion irradiation. Keywords: mouse, squamous cell carcinoma, primary tumor, lung metastases, radiotherapy, carbon ion, gamma ray A highly metastatic mouse squamous cell carcinoma NR-S1 was implanted into the hind leg of synergetic C3H/HeNrs mice and irradiated with 5 Gy of carbon ion beam. 8 Gy of gamma ray was used as a reference beam. At 2 weeks after the irradiation, the lung tissue was sampled. In order to collect samples of primary tumors, the tumors were implanted in other mice and irradiated in the same manner, and the primary tumors were collected at 1 week after the irradiation. The tumor cells of the primary and metastatic tumors were collected by laser microdissection, and oligonucleotide microarray analysis of the irradiated primary tumors and the metastatic tumors were all performed in comparison to the non-irradiated primary tumor by two-color methods.
2009-04-22 | E-GEOD-9305 | biostudies-arrayexpress
Project description:Gamma knife surgery (GKS) is used for treatment of various brain disorders. The effects of gamma irradiation to targeted and un-targeted regions were evaluated by monitoring gene expression changes in the unilateral irradiated (60 Gy) and contralateral un-irradiated striata in the rat. Striata of irradiated and control brains were dissected 16 h post-irradiation for analysis by rat whole genome 44K DNA oligo microarray. Results revealed 230 induced and 144 repressed genes in the irradiated striatum and 432 induced and 239 repressed genes in the un-irradiated striatum. The number of altered genes in un-irradiated striatum was more than that in irradiated striatum. Results of RT-PCR and western analyses suggested that gamma-irradiation caused cellular damage, including oxidative stress, in both striata of both hemispheres. Our present results indicate that unilateral irradiation during GKS produce bilateral effects as early as 16 h, the time-period analyzed, and these molecular changes in the un-irradiated striatum are ample proof.
2008-10-18 | GSE13220 | GEO
Project description:To further study and understand the DNA damage responses, we developed aniFOUND, a new method for capturing under native conditions the repaired DNA and the proteins associated with it after UVC irradiation. hTert-immortalised human skin fibroblasts were irradiated with 20 J/m2 UVC and the nascent DNA that resulted from the Unscheduled DNA Synthesis was specifically labeled with nucleotide analogues (EdU). This newly repaired/synthesized DNA together with the bound proteins were pulled-down with streptavidin beads. For negative controls we used both irradiated, but non-labelled samples (+UV/-EdU) and labelled, but not irradiated cells (-UV/+EdU). The pulldowns were eluted from the beads by boiling in 0.1 % SDS.
2021-03-10 | PXD012997 | Pride
Project description:Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation. In both groups, mice were treated for 5 consecutive days with either IGF1 or vehicle via mini-pumps (Alzet 1007D, IGF1 at 10mg/ml) implanted subcutaneously immediately following radiation. 4 distinct cell populations FACS-isolated based on levels of expression of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells). 4 conditions: Non-irradiated/vehicle vs Non-irradiated/IGF1 vs Irradiated/vehicle vs Irradiated/IGF1. Biological replicates: 7 independent non-irradiated mice treated with vehicle - 3 independent non-irradiated mice treated for 5 days with IGF1 - 3 independent irradiated mice studied at day 5 post-irradiation treated with vehicle - 3 independent irradiated mice studied at day 5 post-irradiation treated for 5 days with IGF1.
2015-04-14 | E-GEOD-42817 | biostudies-arrayexpress
Project description:Whole brain irradiation remains important in the management of brain tumors. Although necessary for improving survival outcomes, cranial irradiation also results in cognitive decline in long-term survivors. A chronic inflammatory state characterized by microglial activation has been implicated in radiation-induced brain injury, and here we present a comprehensive transcriptional profile of irradiated microglia. Fluorescence-activated cell sorting (FACS) was used to isolate CD11b+ microglia from the hippocampi of C57BL/6 and Balb/c mice 1 month after 10Gy cranial irradiation. Affymetrix gene expression profiles were evaluated using linear modeling and rank product analyses. A conserved signature of irradiation was identified across strains, and gene set enrichment analysis was employed to functionally compare our signature to publically available mouse and human datasets.
2014-12-31 | GSE55968 | GEO
Project description:Radiotherapy can act as in situ vaccine activating preventive tumor-specific immune responses in treated patients. While carbon ion radiotherapy holds superior biophysical properties over conventional photon irradiation, little is known about the immunological effects induced by this radiation type. Multiple strategies combining radiotherapy with immune checkpoint inhibition (radioimmunotherapy) to enhance anti-tumor immunity have been described, however, results on the immune cell composition in tumors following radioimmunotherapy with carbon ions are lacking. Here, we present a bilateral tumor model based on time-shifted transplantation of murine, Her2+ EO771 tumor cells onto the flanks of immune competent mice followed by selective irradiation of the primal tumor. αCTLA4- but not αPD-L1-based radioimmunotherapy induced complete tumor rejection and mediated eradication of even non-irradiated, distant tumors. Cured mice were protected against EO771 rechallenge indicative of long lasting, tumor-specific immunological memory. Single cell RNA-sequencing and flow cytometric analyses of irradiated tumors revealed activation of NK cells and distinct tumor-associated macrophage clusters with upregulated expression of TNF and IL1 responsive genes. Distant tumors of irradiated mice showed higher frequencies of naïve T cells, which were activated upon combination with CTLA4 blockade. Thus, radioimmunotherapy with carbon ions plus CTLA4 inhibition reshapes the tumor-infiltrating immune cell composition and can induce complete rejection even of non-irradiated tumors. Our data suggest to combine radiotherapy approaches with CTLA4 blockade to achieve durable anti-tumor immunity. Furthermore, evaluation of future radioimmunotherapy approaches should not be restricted to immunological impacts at the irradiation site, but should also consider systemic immunological effects on non-irradiated tumors.
2022-09-30 | GSE214524 | GEO
Project description:Electron beam irradiation is an efficient cold sterilization technique that has been widely utilized in food preservation. To understand the biological and morphological changes of microorganisms by electron beam irradiation, the D10 value, growth curve, and morphological characterization by scanning electron microscope (SEM) of Staphylococcus aureus were studied. Furthermore, Tandem mass tag (TMT)-based quantitative proteomic was performed to investigate the responses of Staphylococcus aureus to electron beam. The results showed that electron beam sensitized the irradiated strain and prolonged the lag phase of bacterial growth. There were 53, 96, 1055, and 431 differentially expressed proteins (DEPs) detected in 1-kGy irradiated strain (0 h-1-kGy), 2-kGy irradiated strain (0 h-2-kGy), 1-kGy irradiated strain after 24 h cultivation (24 h-1-kGy), and 2-kGy irradiated strain after 24 h cultivation (24 h-2-kGy) groups compared to unirradiated strain (control) group, respectively. Most of DEPs involved in DNA repair were found to be up-regulated. However, DEPs involved in biofilm formation and staphylococcal enterotoxin production were down-regulated. There were no noticeable morphological changes observed in irradiated S. aureus. These findings provided valuable information in the responses of S. aureus to electron beam irradiation, leading to a better understanding of the effects of electron beam irradiation on food pathogens.
2023-03-31 | PXD041285 | iProX