Genomic landscape of liposarcoma

Deepika Kanojia, Yasunobu Nagata, Manoj Garg, Dhong Hyun Lee, Aiko Sato, Kenichi Yoshida, Yusuke Sato, Masashi Sanada, Anand Mayakonda, Christoph Bartenhagen, Hans Ulrich Klein, Ngan B. Doan, Jonathan W. Said, S. Mohith, Swetha Gunasekar, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Ola MyklebostHenry Yang, Martin Dugas, Leonardo A. Meza-Zepeda, Allan W. Silberman, Charles Forscher, Jeffrey Tyner, Seishi Ogawa, H. Phillip Koeffler

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate <0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.

Original languageEnglish (US)
Pages (from-to)42429-42444
Number of pages16
JournalOncotarget
Volume6
Issue number40
DOIs
StatePublished - 2015

Fingerprint

Liposarcoma
Neurofibromin 1
Exome
Chromosomes
Sarcoma
Genes
Single Nucleotide Polymorphism
Neoplasms
Genetic Association Studies
Oncogenes
DNA Repair
DNA Damage
Cell Cycle
Therapeutics
Genome
Apoptosis
Mutation

Keywords

  • Exome sequencing
  • Intra-tumor heterogeneity
  • Liposarcoma
  • SNP array
  • Therapeutics

ASJC Scopus subject areas

  • Oncology

Cite this

Kanojia, D., Nagata, Y., Garg, M., Lee, D. H., Sato, A., Yoshida, K., ... Phillip Koeffler, H. (2015). Genomic landscape of liposarcoma. Oncotarget, 6(40), 42429-42444. https://doi.org/10.18632/oncotarget.6464

Genomic landscape of liposarcoma. / Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans Ulrich; Doan, Ngan B.; Said, Jonathan W.; Mohith, S.; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A.; Silberman, Allan W.; Forscher, Charles; Tyner, Jeffrey; Ogawa, Seishi; Phillip Koeffler, H.

In: Oncotarget, Vol. 6, No. 40, 2015, p. 42429-42444.

Research output: Contribution to journalArticle

Kanojia, D, Nagata, Y, Garg, M, Lee, DH, Sato, A, Yoshida, K, Sato, Y, Sanada, M, Mayakonda, A, Bartenhagen, C, Klein, HU, Doan, NB, Said, JW, Mohith, S, Gunasekar, S, Shiraishi, Y, Chiba, K, Tanaka, H, Miyano, S, Myklebost, O, Yang, H, Dugas, M, Meza-Zepeda, LA, Silberman, AW, Forscher, C, Tyner, J, Ogawa, S & Phillip Koeffler, H 2015, 'Genomic landscape of liposarcoma', Oncotarget, vol. 6, no. 40, pp. 42429-42444. https://doi.org/10.18632/oncotarget.6464
Kanojia D, Nagata Y, Garg M, Lee DH, Sato A, Yoshida K et al. Genomic landscape of liposarcoma. Oncotarget. 2015;6(40):42429-42444. https://doi.org/10.18632/oncotarget.6464
Kanojia, Deepika ; Nagata, Yasunobu ; Garg, Manoj ; Lee, Dhong Hyun ; Sato, Aiko ; Yoshida, Kenichi ; Sato, Yusuke ; Sanada, Masashi ; Mayakonda, Anand ; Bartenhagen, Christoph ; Klein, Hans Ulrich ; Doan, Ngan B. ; Said, Jonathan W. ; Mohith, S. ; Gunasekar, Swetha ; Shiraishi, Yuichi ; Chiba, Kenichi ; Tanaka, Hiroko ; Miyano, Satoru ; Myklebost, Ola ; Yang, Henry ; Dugas, Martin ; Meza-Zepeda, Leonardo A. ; Silberman, Allan W. ; Forscher, Charles ; Tyner, Jeffrey ; Ogawa, Seishi ; Phillip Koeffler, H. / Genomic landscape of liposarcoma. In: Oncotarget. 2015 ; Vol. 6, No. 40. pp. 42429-42444.
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AU - Kanojia, Deepika

AU - Nagata, Yasunobu

AU - Garg, Manoj

AU - Lee, Dhong Hyun

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AU - Yoshida, Kenichi

AU - Sato, Yusuke

AU - Sanada, Masashi

AU - Mayakonda, Anand

AU - Bartenhagen, Christoph

AU - Klein, Hans Ulrich

AU - Doan, Ngan B.

AU - Said, Jonathan W.

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AU - Gunasekar, Swetha

AU - Shiraishi, Yuichi

AU - Chiba, Kenichi

AU - Tanaka, Hiroko

AU - Miyano, Satoru

AU - Myklebost, Ola

AU - Yang, Henry

AU - Dugas, Martin

AU - Meza-Zepeda, Leonardo A.

AU - Silberman, Allan W.

AU - Forscher, Charles

AU - Tyner, Jeffrey

AU - Ogawa, Seishi

AU - Phillip Koeffler, H.

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