Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors.

Abstract

UNLABELLED:

Despite gains in survival, outcomes for patients with metastatic or recurrent rhabdomyosarcoma remain dismal. In a collaboration between the National Cancer Institute, Children's Oncology Group, and Broad Institute, we performed whole-genome, whole-exome, and transcriptome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs. Two genotypes are evident in rhabdomyosarcoma tumors: those characterized by the PAX3 or PAX7 fusion and those that lack these fusions but harbor mutations in key signaling pathways. The overall burden of somatic mutations in rhabdomyosarcoma is relatively low, especially in tumors that harbor a PAX3/7 gene fusion. In addition to previously reported mutations in NRAS, KRAS, HRAS, FGFR4, PIK3CA, and CTNNB1, we found novel recurrent mutations in FBXW7 and BCOR, providing potential new avenues for therapeutic intervention. Furthermore, alteration of the receptor tyrosine kinase/RAS/PIK3CA axis affects 93% of cases, providing a framework for genomics-directed therapies that might improve outcomes for patients with rhabdomyosarcoma.

SIGNIFICANCE:

This is the most comprehensive genomic analysis of rhabdomyosarcoma to date. Despite a relatively low mutation rate, multiple genes were recurrently altered, including NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1, FBXW7, and BCOR. In addition, a majority of rhabdomyosarcoma tumors alter the receptor tyrosine kinase/RAS/PIK3CA axis, providing an opportunity for genomics-guided intervention.

• Authors: Jack F Shern, Li Chen, Juliann Chmielecki, Jun S Wei, Rajesh Patidar, Mara Rosenberg, Lauren Ambrogio, Daniel Auclair, Jianjun Wang, Young K Song, Catherine Tolman, Laura Hurd, Hongling Liao, Shile Zhang, Dominik Bogen, Andrew S Brohl, Sivasish Sindiri, Daniel Catchpoole, Thomas Badgett, Gad Getz, Jaume Mora, James R Anderson, Stephen X Skapek, Frederic G Barr, Matthew Meyerson, Douglas S Hawkins, Javed Khan
• Journal: Cancer discovery (Cancer Discov) Vol. 4 Issue 2 Pg. 216-31 (Feb 2014) ISSN: 2159-8290 [Electronic] United States
• PMID: 24436047 (Publication Type: Journal Article, Research Support, N.I.H., Intramural, Research Support, Non-U.S. Gov't)
• Copyright: 2014 AACR

Chemical References

• Cell Cycle Proteins
• Oncogene Proteins, Fusion
• PAX3-FOXO1A fusion protein, human
• Paired Box Transcription Factors
• Receptors, Fibroblast Growth Factor
• Phosphatidylinositol 3-Kinases
• Class I Phosphatidylinositol 3-Kinases
• PIK3CA protein, human
• Proto-Oncogene Proteins p21(ras)

Topics

• Animals
• Cell Cycle Proteins (genetics)
• Chromosome Aberrations
• Class I Phosphatidylinositol 3-Kinases
• Cluster Analysis
• DNA Copy Number Variations
• Exome
• Gene Expression Regulation, Neoplastic
• Gene Rearrangement
• Gene Regulatory Networks
• Genome-Wide Association Study
• Genomics
• Genotype
• Humans
• Mice
• Mutation
• Oncogene Proteins, Fusion (genetics, metabolism)
• Paired Box Transcription Factors (genetics, metabolism)
• Phosphatidylinositol 3-Kinases (metabolism)
• Proto-Oncogene Proteins p21(ras) (metabolism)
• Receptors, Fibroblast Growth Factor (metabolism)
• Rhabdomyosarcoma (genetics, metabolism)
• Signal Transduction