Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

Jinghui Zhang, Gang Wu, Claudia P. Miller, Ruth G. Tatevossian, James D. Dalton, Bo Tang, Wilda Orisme, Chandanamali Punchihewa, Matthew Parker, Ibrahim Qaddoumi, Frederick Boop, Charles Lu, Cyriac Kandoth, Li Ding, Ryan Lee, Robert Huether, Xiang Chen, Erin Hedlund, Panduka Nagahawatte, Michael RuschKristy Boggs, Jinjun Cheng, Jared Becksfort, Jing Ma, Guangchun Song, Yongjin Li, Lei Wei, Jianmin Wang, Sheila Shurtleff, John Easton, David Zhao, Robert S. Fulton, Lucinda L. Fulton, David J. Dooling, Bhavin Vadodaria, Heather L. Mulder, Chunlao Tang, Kerri Ochoa, Charles G. Mullighan, Amar Gajjar, Richard Kriwacki, Denise Sheer, Richard J. Gilbertson, Elaine R. Mardis, Richard K. Wilson, James R. Downing, Suzanne J. Baker, David W. Ellison

Research output: Contribution to journalArticle

343 Citations (Scopus)

Abstract

The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.

Original languageEnglish (US)
Pages (from-to)602-612
Number of pages11
JournalNature Genetics
Volume45
Issue number6
DOIs
StatePublished - Jun 1 2013

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Glioma
Genome
Pediatrics
Neoplasms
Receptor, Fibroblast Growth Factor, Type 1
Penetrance
MAP Kinase Signaling System
Astrocytoma
Phosphatidylinositol 3-Kinases
Nude Mice
Brain Neoplasms
Astrocytes
Histones
Protein-Tyrosine Kinases
Up-Regulation
Transplantation
Brain
Genes
Therapeutics

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Zhang, J., Wu, G., Miller, C. P., Tatevossian, R. G., Dalton, J. D., Tang, B., ... Ellison, D. W. (2013). Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nature Genetics, 45(6), 602-612. https://doi.org/10.1038/ng.2611

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. / Zhang, Jinghui; Wu, Gang; Miller, Claudia P.; Tatevossian, Ruth G.; Dalton, James D.; Tang, Bo; Orisme, Wilda; Punchihewa, Chandanamali; Parker, Matthew; Qaddoumi, Ibrahim; Boop, Frederick; Lu, Charles; Kandoth, Cyriac; Ding, Li; Lee, Ryan; Huether, Robert; Chen, Xiang; Hedlund, Erin; Nagahawatte, Panduka; Rusch, Michael; Boggs, Kristy; Cheng, Jinjun; Becksfort, Jared; Ma, Jing; Song, Guangchun; Li, Yongjin; Wei, Lei; Wang, Jianmin; Shurtleff, Sheila; Easton, John; Zhao, David; Fulton, Robert S.; Fulton, Lucinda L.; Dooling, David J.; Vadodaria, Bhavin; Mulder, Heather L.; Tang, Chunlao; Ochoa, Kerri; Mullighan, Charles G.; Gajjar, Amar; Kriwacki, Richard; Sheer, Denise; Gilbertson, Richard J.; Mardis, Elaine R.; Wilson, Richard K.; Downing, James R.; Baker, Suzanne J.; Ellison, David W.

In: Nature Genetics, Vol. 45, No. 6, 01.06.2013, p. 602-612.

Research output: Contribution to journalArticle

Zhang, J, Wu, G, Miller, CP, Tatevossian, RG, Dalton, JD, Tang, B, Orisme, W, Punchihewa, C, Parker, M, Qaddoumi, I, Boop, F, Lu, C, Kandoth, C, Ding, L, Lee, R, Huether, R, Chen, X, Hedlund, E, Nagahawatte, P, Rusch, M, Boggs, K, Cheng, J, Becksfort, J, Ma, J, Song, G, Li, Y, Wei, L, Wang, J, Shurtleff, S, Easton, J, Zhao, D, Fulton, RS, Fulton, LL, Dooling, DJ, Vadodaria, B, Mulder, HL, Tang, C, Ochoa, K, Mullighan, CG, Gajjar, A, Kriwacki, R, Sheer, D, Gilbertson, RJ, Mardis, ER, Wilson, RK, Downing, JR, Baker, SJ & Ellison, DW 2013, 'Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas', Nature Genetics, vol. 45, no. 6, pp. 602-612. https://doi.org/10.1038/ng.2611
Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B et al. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nature Genetics. 2013 Jun 1;45(6):602-612. https://doi.org/10.1038/ng.2611
Zhang, Jinghui ; Wu, Gang ; Miller, Claudia P. ; Tatevossian, Ruth G. ; Dalton, James D. ; Tang, Bo ; Orisme, Wilda ; Punchihewa, Chandanamali ; Parker, Matthew ; Qaddoumi, Ibrahim ; Boop, Frederick ; Lu, Charles ; Kandoth, Cyriac ; Ding, Li ; Lee, Ryan ; Huether, Robert ; Chen, Xiang ; Hedlund, Erin ; Nagahawatte, Panduka ; Rusch, Michael ; Boggs, Kristy ; Cheng, Jinjun ; Becksfort, Jared ; Ma, Jing ; Song, Guangchun ; Li, Yongjin ; Wei, Lei ; Wang, Jianmin ; Shurtleff, Sheila ; Easton, John ; Zhao, David ; Fulton, Robert S. ; Fulton, Lucinda L. ; Dooling, David J. ; Vadodaria, Bhavin ; Mulder, Heather L. ; Tang, Chunlao ; Ochoa, Kerri ; Mullighan, Charles G. ; Gajjar, Amar ; Kriwacki, Richard ; Sheer, Denise ; Gilbertson, Richard J. ; Mardis, Elaine R. ; Wilson, Richard K. ; Downing, James R. ; Baker, Suzanne J. ; Ellison, David W. / Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. In: Nature Genetics. 2013 ; Vol. 45, No. 6. pp. 602-612.
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abstract = "The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62{\%}) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53{\%} of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100{\%} penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.",
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AU - Punchihewa, Chandanamali

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