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Methylation profiling reveals novel molecular classes of rhabdomyosarcoma

ABSTRACT: Methylation profiling reveals novel molecular classes of rhabdomyosarcoma

PROVIDER: PRJNA702806 | ENA |

REPOSITORIES: ENA

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Methylation profiling reveals novel molecular classes of rhabdomyosarcoma

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

Methylation profiling reveals novel molecular classes of rhabdomyosarcoma.

Project description:Rhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both children and adults. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and the adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). 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 and revealed corresponding methylation signatures. Comparatively, less is known about epigenetic correlates for the rare SC/SRMS or PRMS histologic subtypes. Herein, we present exome and RNA sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date. In addition to ARMS and ERMS, we identify 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. Limited follow-up data suggest that pediatric tumors with MYOD1-mutations are associated with an aggressive clinical course.

| S-EPMC8592993 | biostudies-literature

Genomic characterization of DICER1-associated neoplasms uncovers novel molecular classes

Project description:Genomic characterization of DICER1-associated neoplasms uncovers novel molecular classes

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Genomic characterization of DICER1-associated neoplasms uncovers novel molecular classes

Project description:DNA methylation data of a novel group of mesenchymal tumors with DICER1 alteration which includes two novel classes designated “low-grade mesenchymal tumor with DICER1 alteration” (LGMT DICER1) and “high-grade sarcoma with DICER1 alteration” (HGS DICER1), as well as the recently described class of primary intracranial sarcoma, DICER1-mutant (PIS DICER1)

2023-02-08 | GSE214568 | GEO

DNA methylation of rhabdomyosarcoma

Project description:DNA methylation of rhabdomyosarcoma

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DNA methylation of rhabdomyosarcoma

Project description:DNA methylation of rhabdomyosarcoma

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NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

Project description:Purpose:Up to 80% of the human genome produces “dark matter” RNAs, most of which are noncapped RNAs (napRNAs). However, determining the functional impacts and metabolism of napRNAs requires the identification of their full-length sequences. Method:Here, by developing a novel method, NAP-seq, to globally profile the full-length sequences of napRNAs at single-nucleotide resolution, we revealed several novel classes of exceptionally structured noncoding RNAs (ncRNAs). Results:We discovered stably expressed linear intron RNAs (sliRNAs), a novel class of snoRNA-intron RNAs (snotrons), a new class of RNAs embedded in miRNA spacers (misRNAs) and thousands of new structured ncRNAs in humans and mice. These new napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we showed that the novel napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Conclusion:Our approach establishes a paradigm for discovering novel classes of ncRNAs with regulatory potency.

2024-02-19 | GSE192632 | GEO

NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

Project description:NAP-seq Reveals Novel Classes of Structured Noncoding RNAs with Regulatory Functions

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MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma [RMS_GEMM_tumors]

Project description:We have developed a new conditional genetically engineered mouse model of rhabdomyosarcoma (RMS) with homologous molecular signature to human RMS that provides valuable pre-clinical models for evaluating novel therapies

2022-02-04 | GSE195922 | GEO

MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma [RMS_GEMM_cell_lines]

2022-02-04 | GSE195921 | GEO