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. 2015 Jul 3;6:7557.
doi: 10.1038/ncomms8557.

Integrated Genetic and Epigenetic Analysis Defines Novel Molecular Subgroups in Rhabdomyosarcoma

Free PMC article

Integrated Genetic and Epigenetic Analysis Defines Novel Molecular Subgroups in Rhabdomyosarcoma

Masafumi Seki et al. Nat Commun. .
Free PMC article


Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in childhood. Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel the genetic/epigenetic basis of RMS. On the basis of methylation patterns, RMS is clustered into four distinct subtypes, which exhibits remarkable correlation with mutation/CN profiles, histological phenotypes and clinical behaviours. A1 and A2 subtypes, especially A1, largely correspond to alveolar histology with frequent PAX3/7 fusions and alterations in cell cycle regulators. In contrast, mostly showing embryonal histology, both E1 and E2 subtypes are characterized by high frequency of CN alterations and/or allelic imbalances, FGFR4/RAS/AKT pathway mutations and PTEN mutations/methylation and in E2, also by p53 inactivation. Despite the better prognosis of embryonal RMS, patients in the E2 are likely to have a poor prognosis. Our results highlight the close relationships of the methylation status and gene mutations with the biological behaviour in RMS.


Figure 1
Figure 1. Significantly altered pathways in rhabdomyosarcoma.
The FGFR4/RAS/AKT pathway (a), cell cycle, and p53 signalling (b) are frequently altered. Genes with genetic alterations are coloured in light orange. The types of alterations and their frequency in the population are indicated on the right side of each gene. The percentages of cases with alterations including copy-number alterations and/or gene mutations detected in embryonal and alveolar subgroups are separately indicated on the left side of each gene. PTEN methylation is also indicated below the gene name and coloured in orange.
Figure 2
Figure 2. Significant copy-number (CN) alterations detected in rhabdomyosarcoma.
(a) Statistically significant CN gains and losses detected by the GISTIC algorithm are shown in the left and right boxes, respectively. For each q-value peak, the putative gene targets are listed. A dashed line represents the centromere of each chromosome. Red and blue lines indicate the q-value for gains and losses, respectively. (bh) Heatmaps of significant CN alterations are shown for gene targets at 1p36.13 (b), 2p24.3 (c), 2q36.1 (d), 12q15 (e), 13q14.1 (f), 9p21.1 (g) and 17p13.1 (h).
Figure 3
Figure 3. Hierarchical clustering of DNA methylation profiles and significant PTEN hypermethylation in cluster E1/E2.
(a) The heatmap shows the DNA methylation profiles of 53 rhabdomyosarcoma (RMS) tumours based on unsupervised hierarchical clustering. Tumours were hierarchically clustered into four subgroups: E1, E2, A1 and A2. Clusters E1 and E2 were composed almost exclusively of embryonal RMS (95.5%), whereas all alveolar RMS were classified into clusters A1/A2. Red, high methylation; blue, low methylation. (b) Volcano plot comparing the number of significantly hypermethylated probes between clusters E1/E2 and A1/A2. Significantly hypermethylated probes showing >2-fold change are coloured in orange (P<1.0 × 10−8, Wilcoxon's rank-sum test). Red dots represent significantly hypermethylated probes in the promoter regions of PTEN in cluster E. (c) Difference in PTEN methylation intensities between clusters E1/E2 and A1/A2. Significantly higher methylation intensities were observed in cluster E1/E2 than in cluster A1/A2. The P-value was calculated using the Wilcoxon rank-sum test. β-values represent significantly hypermethylated eight promoter-associated probes (red dots in the Volcano plot) of PTEN. For the box and whisker plots, the bottom and top of the box are the first and third quartiles, the line inside the box is the median and the whiskers extend up to 1.5 times the interquartile range.
Figure 4
Figure 4. Correlations between DNA methylation clusters and additional parameters.
(a) Integrated view of DNA methylation clusters combined with histology, outcome, fusion status, gene alterations and copy-number changes. The horizontal axis represents each tumor. ARMS, alveolar rhabdomyosarcoma; ERMS, embryonal rhabdomyosarcoma; NOS, not otherwise specified; Mut, mutation; Met, methylation; CNA, copy-number alteration; Hetero., heterozygous; Com. Hetero., compound heterozygous mutation; CN, copy number; LOH, loss of heterozygosity; N, NRAS; K, KRAS; H, HRAS; P, detected in primary sample alone; R, Detected in relapse sample alone; F, PAX3–FOXO1 fusion-positive ERMS. (b) Kaplan–Meier curves of overall survival for each DNA methylation cluster. The P-value of the log-rank test is shown.

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