DNA methylation of rhabdomyosarcoma
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ABSTRACT:
PROVIDER: PRJNA604271 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation of rhabdomyosarcoma
| PRJNA604272 | ENA
Project description:Many pediatric malignancies are embryonal in nature, and one hypothesis for the origin of embryonal tumors is that they arise from a defect in differentiation, either by an inability to terminally differentiate or a reversion to a pluripotent state. There is emerging evidence that epigenetic regulation plays an important role in the transition from embryonic stem cell to a more committed cell fate, utilizing both de novo DNA methylation and poised M-bM-^@M-^XbivalentM-bM-^@M-^Y chromatin domains (H3K27me3 and H3K4me3) to abolish pluripotency and gain lineage- and cell-type-specific characteristics as a cell differentiates. Thus inappropriate epigenetic silencing by aberrant DNA methylation of bivalent genes required for differentiation could lead to the uncontrolled cell growth observed in cancer. Our broad hypothesis is that aberrant DNA methylation in cancer is targeted to a non-random subset of critical pathways used in normal development. This dysregulation of the normal epigenetic program used in development promotes cellular proliferation and provides a mechanism to block differentiation in pediatric cancers, such as rhabdomyosarcoma. Examination of DNA methylation in fourteen human rhabdomyosarcoma patient samples using RRBS. In addition, RRBS was used to examine DNA methylation in one human rhabdomyosarcoma cell line (RD) forced to terminally differentiate by expression of the forced heterodimer MyoD~E12 (MDE). Lastly, RRBS was used to examine DNA methylation changes during normal differentiation in one primary human normal myoblast cell line
2014-10-22 | E-GEOD-61150 | biostudies-arrayexpress
Project description:In order to identify the specific DNA methylation pattern of different rhabdomyosarcoma (RMS) samples we performed a genome-wide study using Human DNA methylation platform (Agilent).
2016-09-01 | GSE67201 | GEO
Project description:In order to identify the specific DNA methylation pattern of different rhabdomyosarcoma (RMS) samples we performed a genome-wide study using Human DNA methylation platform (Agilent). DNA methylation profiling was carried out in 15 RMS tumor samples using the Human DNA methylation microarray (Agilent) consisting of about 244,000 (60-mer) probes design to interrogate about 27,000 known CpG islands. Enriched-methylated dsDNA for each sample was labeled with Cy5 dye and the control genomic DNA for each sample was labeled with Cy3 dye using Agilent Genomic DNA labeling kit PLUS (Agilent).
2016-09-01 | E-GEOD-67201 | biostudies-arrayexpress
Project description:Many pediatric malignancies are embryonal in nature, and one hypothesis for the origin of embryonal tumors is that they arise from a defect in differentiation, either by an inability to terminally differentiate or a reversion to a pluripotent state. There is emerging evidence that epigenetic regulation plays an important role in the transition from embryonic stem cell to a more committed cell fate, utilizing both de novo DNA methylation and poised ‘bivalent’ chromatin domains (H3K27me3 and H3K4me3) to abolish pluripotency and gain lineage- and cell-type-specific characteristics as a cell differentiates. Thus inappropriate epigenetic silencing by aberrant DNA methylation of bivalent genes required for differentiation could lead to the uncontrolled cell growth observed in cancer. Our broad hypothesis is that aberrant DNA methylation in cancer is targeted to a non-random subset of critical pathways used in normal development. This dysregulation of the normal epigenetic program used in development promotes cellular proliferation and provides a mechanism to block differentiation in pediatric cancers, such as rhabdomyosarcoma.
2014-10-22 | GSE61150 | GEO
Project description:DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells
| PRJNA641458 | ENA
Project description:DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells
| PRJNA641459 | ENA
Project description:The methylation enrichment was determined by MIRA-sequencing after MBD2-capture using the MethylCollector™ Ultra Kit (Active Motif) performed on DNA samples derived from rhabdomyosarcoma cells (RMS) TE671 cells. The cells expressing shRNA targeting ZNF555 (shZNF555) were compared to the control cells expressing non-targeting shRNA (shCtl). The signals of methylation-enriched DNA (ENR) were normalised to non-enriched input DNA (INP).
2022-07-28 | E-MTAB-10825 | biostudies-arrayexpress
Project description:Rhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both the pediatric and adult setting. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). Recent genomic sequencing studies have expanded the spectrum of RMS, with several new molecularly defined entities, including fusion-driven spindle cell/sclerosing rhabdomyosarcoma (SC/SRMS) and MYOD1-mutant SC/SRMS. Comprehensive genomic analysis has previously defined the mutational and copy number spectrum for the more common ERMS and ARMS, as well as revealed corresponding methylation signatures. In contrast, genetic and epigenetic correlates have not been defined for the rare SC/SRMS or PRMS histologic subtypes. Herein, we present genomic sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date. We identified two novel methylation subtypes, one having SC/SRMS histology and defined by MYOD1 p. L122R mutations and the other matching adult type PRMS. Selected tumors from adolescent patients grouped with the PRMS methylation class, expanding the age range of these rare tumors. Pediatric patients in the MYOD1-mutant group, as well as those clustering with PRMS, appear to have poor overall survival.
2021-11-24 | GSE167059 | GEO
Project description:Circulating Tumor DNA in Intermediate Risk Rhabdomyosarcoma
| PRJNA823798 | ENA