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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [methylation]

ABSTRACT: DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [methylation]

PROVIDER: PRJNA801865 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17818769_1.fastq.gz	Fastqsanger.gz
	SRR17818769_2.fastq.gz	Fastqsanger.gz
	SRR17818770_1.fastq.gz	Fastqsanger.gz
	SRR17818770_2.fastq.gz	Fastqsanger.gz
	SRR17818771_1.fastq.gz	Fastqsanger.gz

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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients.

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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [RNA-seq]

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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [methylation]

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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients.

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The diagnostic and prognostic value of hsa_circ_0084927 in colon adenocarcinoma and its ceRNA network construction (miRNA-Seq)

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DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [RNA-seq]

Project description:We performed RNA-seq to characterize the transcriptome of tumor-associated macrophages (TAMs), bone marrow-derived monocytes from healthy and tumor-bearing mice (BMDM-Ts/BMDM-Hs) and, macrophages from healthy mammary fat pad (MGMs).

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DNA methylation adds prognostic value to minimal residual disease status in pediatric T-cell acute lymphoblastic leukemia

Project description:Background: Despite increased knowledge about genetic aberrations in pediatric T-cell acute lymphoblastic leukemia (T-ALL), no clinically feasible treatment-stratifying marker exists at diagnosis. Instead patients are enrolled in intensive induction therapies with substantial side effects. In modern protocols, therapy response is monitored by minimal residual disease (MRD) analysis, and used for post-induction risk group stratification. DNA methylation profiling is a candidate for subtype discrimination at diagnosis and we investigated its role as a prognostic marker in pediatric T-ALL. Procedure: Sixty-five diagnostic T-ALL samples from Nordic pediatric patients treated according to the NOPHO-ALL2008 protocol were analyzed by HumMeth450K genome wide DNA methylation arrays. Methylation status was analyzed in relation to clinical data and early T-cell precursor (ETP) phenotype. Results: Two distinct CpG Island Methylator Phenotype (CIMP) groups were identified. Patients with a CIMP negative profile had an inferior response to treatment compared to CIMP positive patients (3-year cumulative incidence of relapse (CIR3y) rate: 29% vs. 6%, p=0.01). Most importantly, CIMP classification at diagnosis allowed subgrouping of high risk T-ALL patients (MRD â?¥0.1% at day 29) into two groups with significant differences in outcome (CIR3y rates: CIMP negative 50% vs CIMP positive 12%; p=0.02). These groups did not differ regarding ETP-phenotype, but the CIMP negative group was younger (p=0.02) and had higher white blood cell count at diagnosis (p=0.004) compared with the CIMP positive group. Conclusions: CIMP classification at diagnosis in combination with MRD during induction therapy is a strong candidate for further risk classification and could confer important information in treatment decision-making. Bisulphite converted DNA from T-ALL samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2016-03-30 | E-GEOD-69954 | biostudies-arrayexpress

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