title: NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma.
abstract: Rhabdomyosarcoma (RMS), which represents the most frequent soft tissue sarcoma in pediatric populations, is classified into two major subtypes: embryonal RMS (ERMS) and alveolar RMS (ARMS). ARMS subtype, which shows greater aggressiveness and proneness to metastasis with respect to ERMS, are characterized, in about 75% of cases, by specific chromosomal translocations that involve PAX and FOXO1 genes. Many findings have demonstrated that PAX/FOXO1-positive ARMS have a worse prognosis than PAX/FOXO1-negative ones and that distinct molecular features characterize RMS with different gene fusion statuses. DNA methylation, which presently represents a challenging research area, is involved in the modulation of gene expression.We performed a genome-wide DNA methylation analysis using reduced-representation bisulfite sequencing (RRBS) in RMS samples and we found that fusion-positive alveolar and embryonal subgroups have different DNA methylation signatures and that ARMS fusion-positive subtypes are characterized by overall hypomethylation levels. While NELL1 was found to be hypomethylated and transcriptionally enhanced in RMS alveolar subtypes, high NELL1 expression levels, which proved to be correlated with negative RMS prognostic factors such as fusion status and histology (P < 0.0001), were found to discriminate between RMS patients with different outcomes (P < 0.05).In conclusion, our results demonstrated that different DNA methylation patterns distinguish between different RMS subgroups and they suggest that epigenetic signatures could be useful for risk stratification of patients.
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.|Department of Women's and Children's Health, Oncology Hematology Division, University of Padova, Padova, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Tombolan
authors.affiliation: Department of Women's and Children's Health, Oncology Hematology Division, University of Padova, Padova, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Poli
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Martini
authors.affiliation: Institute of Pediatric Research, Padova, Italy.
authors.forename: Angelica
authors.initials: A
authors.lastname: Zin
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
authors.affiliation: Department of Women's and Children's Health, Oncology Hematology Division, University of Padova, Padova, Italy.
authors.forename: Gianni
authors.initials: G
authors.lastname: Bisogno
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.|Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative, University of Padova, Padova, Italy.
authors.forename: Gerolamo
authors.initials: G
authors.lastname: Lanfranchi
mesh_terms: D002135:Calcium-Binding Proteins; D045744:Cell Line, Tumor; D002648:Child; D002675:Child, Preschool; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D009419:Nerve Tissue Proteins / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D011379:Prognosis; D018232:Rhabdomyosarcoma, Alveolar / Q000235:genetics*; D018233:Rhabdomyosarcoma, Embryonal / Q000235:genetics*; D014178:Translocation, Genetic; D015854:Up-Regulation
chemical_list: D002135:Calcium-Binding Proteins; C104144:NELL1 protein, human; D009419:Nerve Tissue Proteins; D015514:Oncogene Proteins, Fusion
keywords: DNA methylation; NELL1; RRBS; rhabdomyosarcoma; sequencing