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Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma (single-cell RNA-seq analysis)

ABSTRACT: A single-cell analysis (10x) of p53/MCA induced sarcomas tumors with and without radiation and CpG treatment. p53/MCA induced sarcomes are induced by intramuscular injection of adenovirus expressing Cas9 and sgRNA targeting Trp53 (Adeno-p53-sgRNA; Viraquest) at gastrucnemius muscle site. We used scRNA-seq to analyze the differences in immune cells after treatment with CpG+RT

ORGANISM(S): Mus musculus

PROVIDER: GSE252143 | GEO | 2024/01/01

REPOSITORIES: GEO

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Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma

Project description:p53/MCA sarcomas are induced by intramuscular injection of adenovirus expressing Cas9 and sgRNA targeting Trp53 (Adeno-p53-sgRNA; Viraquest) at gastrucnemius muscle site. We used bulk tumor RNAseq to analyze the differences in tumor cells and immune cells after treatment with CpG+RT

2024-01-01 | GSE252213 | GEO

mRNA-seq of Myc and Yap1-activated mouse lung tumors and controls

Project description:mRNA-seq for expression profiling of Myc and Yap1 activated mouse lung tumors and controls. 4 cohorts of lung tumors induced through nasal instillation of Cre/sgRNA(MS2)-encoding lentivirus in mice carrying conditional P53 loss (P53 F/F), oncogenic Kras (Kras LSL-G12D/+), and CRISPRa/SAM construct (Rosa26(LSL-SAM) or YFP reporter (Rosa26(LSL-YFP): 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Myc) (PPKS/M); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Yap1) (PPKS/Y); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKS/NT); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-YFP) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKY/NT)

2022-08-30 | E-MTAB-11122 | biostudies-arrayexpress

TLR9-activated B cells imprint adoptively transferred CD8+ T cells with potent tumor immunity and persistence

Project description:Here we report a new way to reverse the tolerant state of adoptively transferred CD8+ T cells against melanoma through ex vivo expansion with the TLR9 agonist CpG. CpG-generated T cells elicited potent immunity without co-administration of high dose IL-2 or vaccination, which are adjuvants classically required to effectively treat solid tumors. CpG-expanded T cells exhibited an IL-2RhighICOShighCD39low phenotype ex vivo and engrafted robustly in vivo. In culture, B cells were the only cell type essential for imprinting T cells with this phenotype and potent tumor immunity. CpG agonists targeting B cells, but not dendritic cells, generated CD8+ T cell products with remarkable antitumor properties. Purified B cells were sufficient to mediate the CpG-associated changes in T cells. These findings reveal a vital role for B cells in the generation of effective antitumor T cells and have immediate implications for profoundly improving immunotherapy for patients.

2022-02-22 | PXD022909 | Pride

ABL Tyrosine Kinase Phosphorylates DGCR8 to Stimulate MicroRNA Processing in DNA Damage Response

Project description:miR-seq to find miRs that are induced by DNA damage and whose induction requires ABL kinase activity Use p53-inactive HEK293T cells. Use doxorubicin to induce DNA damage. Use imatinib co-treatment to inhibit ABL kinase activity

2015-07-01 | E-GEOD-59028 | biostudies-arrayexpress

RNA-seq to compare gene expression profiles between Asf1a WT and Asf1a KO cells

Project description:KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 or ctrl-sgRNA-3 and then selected by using 5ug/ml Blasticidin, to get the 4 ctrl lines; KP-Cas9 single clone was transfected with Asf1a sgRNA-1, sgRNA-2, sgRNA-3 and new sgRNA-1 and then selected by using 5ug/ml Blasticidin, and then picked up single clones with Asf1a KO. For each Asf1a sgRNA, we selected one clone for RNA seq, so totally we have 4 Asf1a KO clones for RNA seq.

2019-11-26 | GSE127205 | GEO

Mechansisms of resistance to decitabine in myelodysplastic syndrome

Project description:Investiage global methylation changes between patients at diagnosis and after relapse by CpG island methylation microarray analysis and determine the role of gene-specific methylation associated with relapse of cancer patients. Two-condition experiment, Biological replicates: 2 biological replicates and 2 samples from the same methylated CpG island amplification (MCA).

2011-04-08 | E-GEOD-28459 | biostudies-arrayexpress

Short and long-term changes in gene expression mediated by the activation of TLR9

Project description:CpG DNA binds to Toll-like receptor 9 to stimulate a strong innate immune response. Despite extensive studies of TLR9 mediated signal transduction, the scope of CpG-induced changes in gene expression is incompletely understood. In particular, the prolonged effects of CpG ODN (oligodeoxynucleotide) on gene activation have not been investigated despite evidence that a single dose of CpG ODN alters immune reactivity for several weeks. This study used gene expression analysis to monitor changes in mRNA levels for 14 days, and identified the genes, pathways, functional groups and regulatory networks triggered in vivo following CpG ODN administration. Two discrete peaks of gene activation (at 3 hr and 5 days) were observed after CpG administration. Both the regulation and function of genes activated during the second peak differed from those triggered shortly after CpG administration. Initial gene up-regulation corresponded to a period when TLR9 ligation stimulated genes functionally associated with the generation of innate and adaptive immune responses (e.g. the NF-kB and B-cell receptor pathways). The second peak reflected processes associated with cell division (e.g., cell cycle and DNA replication & repair). Whereas TNF and IFNG played central roles regulating the first peak of activation, E2F1, E2F2, BRCA1, and HRAS had major impact on the networks controlling the second peak. The complex bimodal pattern of gene expression elicited by CpG ODN administration provides novel insights into the long term effects of CpG DNA on genes associated with immunity and cell proliferation.

2010-01-08 | GSE16465 | GEO

Short and long-term changes in gene expression mediated by the activation of TLR9

2010-05-16 | E-GEOD-16465 | biostudies-arrayexpress

Genome-wide copy number aberrations and methylation profiles in human colorectal lesions

Project description:This SuperSeries is composed of the following subset Series: GSE35476: Array CGH analysis of human colorectal tumors GSE35508: Methylated CpG island amplification (MCA) microarray analysis of human colorectal tumors Refer to individual Series

2012-08-31 | E-GEOD-35534 | biostudies-arrayexpress

CNS-endogenous TLR7 and TLR9 induce different immune responses and effects on experimental autoimmune encephalomyelitis

Project description:Innate receptors, including Toll like receptors (TLRs), are implicated in pathogenesis of CNS inflammatory diseases such as multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). TLR response to pathogens or endogenous signals includes production of immunoregulatory mediators. One of these, interferon (IFN)β, a Type I IFN, plays a protective role in MS and EAE. We have previously shown that intrathecal administration of selected TLR ligands induced IFNβ and infiltration of blood-derived myeloid cells into the CNS, and suppressed EAE in mice. We have now extended these studies to evaluate a potential therapeutic role for CNS-endogenous TLR7 and TLR9. Intrathecal application of Imiquimod (TLR7 ligand) or CpG oligonucleotide (TLR9 ligand) into CNS of otherwise unmanipulated mice induced IFNβ expression, with greater magnitude in response to CpG. CNS extraparenchymal CD45+ cells were identified as source of IFNβ. Intrathecal CpG induced infiltration of monocytes, neutrophils, CD4+ T cells and NK cells whereas Imiquimod did not recruit blood-derived CD45+ cells. CpG, but not Imiquimod, had a beneficial effect on EAE, when given at time of disease onset. This therapeutic effect of CpG on EAE was not seen in mice lacking the Type I IFN receptor. In mice with EAE treated with CpG, the proportion of monocytes was significantly increased in the CNS. Infiltrating cells were predominantly localized to spinal cord meninges and demyelination was significantly reduced compared to non-treated mice with EAE. Our findings show that TLR7 and TLR9 signaling induce distinct inflammatory responses in the CNS with different outcome in EAE and point to recruitment of blood-derived cells and IFNβ induction as possible mechanistic links between TLR9 stimulation and amelioration of EAE. The protective role of TLR9 signaling in the CNS may have application in treatment of diseases such as MS.

2021-04-15 | GSE172083 | GEO

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