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Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Reference Cell-type MCC-seq]

ABSTRACT: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Reference Cell-type MCC-seq]

PROVIDER: PRJNA823567 | ENA |

REPOSITORIES: ENA

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Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Reference Cell-type MCC-seq]

Project description:Radiation therapy is an effective cancer treatment although damage to healthy tissues is common. Here we establish sequencing-based, cell-type specific DNA methylation reference maps of human and mouse tissues to infer the origins of cell-free DNA fragments released from dying cells into the circulation. We find cell-type specific DNA blocks mostly hypomethylated and located within genes intrinsic to cellular identity. In a mouse model, thoracic radiation-induced tissue damages were reflected by dose-dependent increases in lung endothelial, cardiomyocyte and hepatocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation indicating the impact on liver tissues. Thus, cell-free methylated DNA in serum can uncover cell-type specific effects of radiation on healthy tissues and inform treatment.

2023-07-24 | GSE200185 | GEO

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type MCC-seq]

2023-07-24 | GSE200093 | GEO

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type MCC-seq]

Project description:Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type MCC-seq]

| PRJNA823031 | ENA

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Serum MCC-seq]

2023-07-24 | GSE200094 | GEO

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Serum MCC-seq]

2023-07-24 | GSE200092 | GEO

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Serum MCC-seq]

Project description:Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Serum MCC-seq]

| PRJNA823032 | ENA

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Serum MCC-seq]

Project description:Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Serum MCC-seq]

| PRJNA823030 | ENA

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type RNA-seq]

2023-07-24 | GSE200095 | GEO

Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment

Project description:Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment

| PRJNA823570 | ENA

Microarray analysis of Merkel cell carcinoma (MCC) tumors, small cell lung cancer (SCLC) tumors, and MCC cell lines

Project description:When using cell lines to study cancer, phenotypic similarity to the original tumor is paramount. Yet, little has been done to characterize how closely Merkel cell carcinoma (MCC) cell lines model native tumors. To determine their similarity to MCC tumor samples, we characterized MCC cell lines via gene expression microarrays. Using whole transcriptome gene expression signatures and a computational bioinformatic approach, we identified significant differences between variant cell lines (UISO, MCC13, and MCC26) and fresh frozen MCC tumors. Conversely, the classic WaGa and Mkl-1 cell lines more closely represented the global transcriptome of MCC tumors. When compared to publicly available cancer lines, WaGa and Mkl-1 cells were similar to other neuroendocrine tumors, but the variant cell lines were not. WaGa and Mkl-1 cells grown as xenografts in mice had histological and immunophenotypical features consistent with MCC, while UISO xenograft tumors were atypical for MCC. Spectral karyotyping and short tandem repeat analysis of the UISO cells matched the original cell line's description, ruling out contamination. Our results validate the use of transcriptome analysis to assess the cancer cell line representativeness and indicate that UISO, MCC13, and MCC26 cell lines are not representative of MCC tumors, whereas WaGa and Mkl-1 more closely model MCC. RNA was extracted from MCC cell lines and MCC and SCLC tumor samples and hybridized to Affymetrix microarrays for transcriptome profiling.

2014-12-23 | E-GEOD-50451 | biostudies-arrayexpress

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