Integrated genetic and epigenetic analysis of myxofibrosarcoma

Koichi Ogura, Fumie Hosoda, Yasuhito Arai, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Momoko Nagai, Mamoru Kato, Erika Arakawa, Wakako Mukai, Hirofumi Rokutan, Akira Kawai, Sakae Tanaka and Tatsuhiro Shibata ()
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Koichi Ogura: National Cancer Center Research Institute
Fumie Hosoda: National Cancer Center Research Institute
Yasuhito Arai: National Cancer Center Research Institute
Hiromi Nakamura: National Cancer Center Research Institute
Natsuko Hama: National Cancer Center Research Institute
Yasushi Totoki: National Cancer Center Research Institute
Akihiko Yoshida: National Cancer Center Hospital
Momoko Nagai: National Cancer Center Research Institute
Mamoru Kato: National Cancer Center Research Institute
Erika Arakawa: National Cancer Center Research Institute
Wakako Mukai: National Cancer Center Research Institute
Hirofumi Rokutan: National Cancer Center Research Institute
Akira Kawai: National Cancer Center Hospital
Sakae Tanaka: The University of Tokyo
Tatsuhiro Shibata: National Cancer Center Research Institute

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high local recurrence rate. Here we report the genetic and epigenetic landscape of MFS based on the results of whole-exome sequencing (N = 41), RNA sequencing (N = 29), and methylation analysis (N = 41), using 41 MFSs as a discovery set, and subsequent targeted sequencing of 140 genes in the entire cohort of 99 MFSs and 17 MFSs' data from TCGA. Fourteen driver genes are identified, including potentially actionable therapeutic targets seen in 37% of cases. There are frequent alterations in p53 signaling (51%) and cell cycle checkpoint genes (43%). Other conceivably actionable driver genes including ATRX, JAK1, NF1, NTRK1, and novel oncogenic BRAF fusion gene are identified. Methylation patterns cluster into three subtypes associated with unique combinations of driver mutations, clinical outcomes, and immune cell compositions. Our results provide a valuable genomic resource to enable the design of precision medicine for MFS.

Date: 2018
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DOI: 10.1038/s41467-018-03891-9

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