Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation in sarcoma patients

ABSTRACT: We retrospectively identified adult patients who had received anti-PD-1 ICI therapy for recurrent sarcoma and performed DNA methylation profiling using Infinium MethylationEPIC microarrays. Response to anti-PD-1 ICI therapy was correlated with DNA methylation profiles.

ORGANISM(S): Homo sapiens

PROVIDER: GSE172468 | GEO | 2021/04/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA methylation analysis of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney and Ewing's sarcoma family of tumors

Project description:Genome wide DNA methylation profiling of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney, Ewing's sarcoma family of tumors and non-neoplastic kidney. The Illumina Infinium HumanMethylation 27 BeadChip was used to obtain DNA methylation profiles across approximately 27000 CpGs . Samples included 3 Rhabdoid tumor of the kidney, 3 Clear cell sarcoma of the kidney, 3 Ewing's sarcoma family of tumor and 3 non-neoplastic kidney. Bisulfite converted DNA from the 12 samples were hybridized to the Illumina Infinium HumanMethylation27 Beadchip.

2015-06-12 | E-GEOD-44847 | biostudies-arrayexpress

Epigenome analysis of primary intracranial sarcoma

Project description:Genome wide DNA methylation profiling of DNA extracted from formalin-fixed parffin embedded tumor samples from patients with primary intracranial sarcoma from Peru. The Illumina MethylationEPIC array was used to obtain DNA methylation profiles of 850.000 CpG sides

2021-09-12 | GSE155660 | GEO

Methylation profiling (450K and EPIC array) for sarcoma classification

Project description:Infinium® HumanMethylation450 BeadChip and EPIC arrays were run with the aim of using the methylation profiles (n=986 in total) for sarcoma subtype classification (Paper: Lyskjær et al, 2021, DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the ‘DKFZ sarcoma Classifier’ ). 500ng of DNA from fresh frozen (FT) or formalin-fixed paraffin-embedded (FFPE) tumour samples were bisulfite converted using the Zymo EZ DNA methylation Gold kit (Zymo Research Corp. Irvine, USA) before hybridisation to the Infinium HumanMethylation450 or EPIC beadchip arrays (Illumina, San Diego, CA) by UCL Genomics. All bisulfite-converted FFPE samples were restored with the Infinium FFPE DNA Restore kit (Illumina).

2021-05-01 | E-MTAB-9875 | biostudies-arrayexpress

Sarcoma Classification by DNA-methylation profiling

Project description:DNA methylation classification reference set (1077) and validation set (428) of 1505 sarcoma samples using Illumina HumanMethylation450 BeadChips or Illumina Infinium HumanMethylation850 BeadChips

2020-03-01 | GSE140686 | GEO

DNA methylation analysis of Rhabdoid tumor of the kidney, Clear cell sarcoma of the kidney and Ewing's sarcoma family of tumors

2015-06-12 | GSE44847 | GEO

Exploration of exhausted CD8 T cell markers to predict response to immune checkpoint inhibitor therapy for hepatocellular carcinoma

Project description:This study sought to identify transcriptomic and protein markers of T cell exhaustion that may predict response to anti-program cell death-1 (anti-PD-1) / anti-PD-L1-based ICI therapy for patients with advanced/metastatic hepatocellular carcinoma (HCC).

2021-05-18 | GSE140901 | GEO

Epigenome wide association study of response to methotrexate in early rheumatoid arthritis patients

Project description:The aim of the study is to identify differentially methylated positions (DMPs) and regions (DMRs) that predict response to Methotrexate (MTX) in early rheumatoid arthritis (RA) patients. DNA from baseline peripheral blood mononuclear cells was extracted from treatment naive RA patients. DNA methylation, quantified using the Infinium MethylationEPIC, was assessed in relation to response to MTX (combination) therapy (deltaDAS28) over the first 3 months in 69 RA patients.

2021-02-07 | E-MTAB-10159 | biostudies-arrayexpress

Murine MHC-Deficient Nonobese Diabetic Mice Carrying Human HLA-DQ8 Develop Severe Myocarditis and Myositis in Response to Anti–PD-1 Immune Checkpoint Inhibitor Cancer Therapy

Project description:Myocarditis has emerged as an immune-related adverse event of immune-checkpoint inhibitor (ICI) cancer therapy associated with significant mortality. Our new NOD-cMHCI/II-/-.DQ8 mouse strain expresses human HLA-DQ8 in the absence of classical murine MHC class I and II. These mice are highly susceptible to myocarditis and acute heart failure following anti-PD-1 ICI-induced treatment. Additionally, anti-PD-1 administration accelerates skeletal muscle myositis development. Using RNA sequencing analyses we performed a thorough characterization of cardiac and skeletal muscle infiltrating T-cells, identifying shared and unique characteristics of both populations.

2024-02-02 | GSE248625 | GEO

Human derived and patient derived xenografts epigenome analysis of primary and metastasis colorectal cancer

Project description:Genome wide DNA methylation profiling of primary (PR) and liver metastasis (LM) colorectal cancer (CRC). The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in human and xenogratfs derived samples. Raw data were processed using R minfi package. The main goal of this study is to develop a methylation-based classifier and predictor for metastatic CRC (mCRC), in order to find specific patients stratification for anti-EGFR targeted therapy (cetuximab) and bring the promise to shed new light on the role of methylation in driving colorectal cancer progression in different groups of patients.

2023-01-31 | GSE208713 | GEO

MEK inhibition overcomes chemoimmunotherapy resistance by inducing CXCL10 in cancer cells [France3]

Project description:Chemotherapy with anti PD-1/PD-L1 mAb has become the standard of care for patients with metastatic non-small cell lung cancer (NSCLC). Using lung tumor models, where pemetrexed-platinum chemotherapy (PEM/CDDP) remains unable to synergize with immune checkpoint inhibitors (ICI), we linked failure of this treatment with its inability to induce CXCL10 expression and CD8+ T cell recruitment. Using drug screening, we showed that combining a MEK inhibitor (MEKi) with PEM/CDDP triggers CXCL10 secretion by cancer cells and CD8+ T cell recruitment, and restores ICI efficacy. PEM/CDDP plus MEKi promotes optineurin (OPTN)-dependent mitophagy, resulting in CXCL10 production in a mitochondrial DNA and TLR9-dependent manner. TLR9 or autophagy/mitophagy processes genetic inactivation of abort the antitumor efficacy of PEM/CDDP plus MEKi/anti PD-L1 therapy. In human NSCLC, high OPTN, TLR9 and CXCL10 expression is associated with better response to ICI. Our results underline the role of TLR9 and OPTN-dependent mitophagy in enhancing chemoimmunotherapy efficacy.

2021-12-08 | GSE190265 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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