Melanoma whole-exome sequencing identifies V600E B-RAF amplification-mediated acquired B-RAF inhibitor resistance

Hubing Shi; Gatien Moriceau; Xiangju Kong; Mi Kyung Lee; Hane Lee; Richard C. Koya; Charles Ng; Thinle Chodon; Richard A. Scolyer; Kimberly B. Dahlman; Jeffrey A. Sosman; Richard F. Kefford; Georgina V. Long; Stanley F. Nelson; Antoni Ribas; Roger S. Lo

doi:10.1038/ncomms1727

Melanoma whole-exome sequencing identifies ^V600E B-RAF amplification-mediated acquired B-RAF inhibitor resistance

Hubing Shi, Gatien Moriceau, Xiangju Kong, Mi Kyung Lee, Hane Lee, Richard C. Koya, Charles Ng, Thinle Chodon, Richard A. Scolyer, Kimberly B. Dahlman, Jeffrey A. Sosman, Richard F. Kefford, Georgina V. Long, Stanley F. Nelson, Antoni Ribas, Roger S. Lo^*

^*Corresponding author for this work

Medicine, Hematology Oncology Division

Research output: Contribution to journal › Article › peer-review

545 Scopus citations

Abstract

The development of acquired drug resistance hampers the long-term success of B-RAF inhibitor therapy for melanoma patients. Here we show ^V600E B-RAF copy-number gain as a mechanism of acquired B-RAF inhibitor resistance in 4 out of 20 (20%) patients treated with B-RAF inhibitor. In cell lines, ^V600E B-RAF overexpression and knockdown conferred B-RAF inhibitor resistance and sensitivity, respectively. In ^V600E B-RAF amplification-driven (versus mutant N-RAS-driven) B-RAF inhibitor resistance, extracellular signal-regulated kinase reactivation is saturable, with higher doses of vemurafenib down-regulating phosho-extracellular signal-regulated kinase and re-sensitizing melanoma cells to B-RAF inhibitor. These two mechanisms of extracellular signal-regulated kinase reactivation are sensitive to the MEK1/2 inhibitor AZD6244/selumetinib or its combination with the B-RAF inhibitor vemurafenib. In contrast to mutant N-RAS-mediated ^V600E B-RAF bypass, which is sensitive to C-RAF knockdown, ^V600E B-RAF amplification-mediated resistance functions largely independently of C-RAF. Thus, alternative clinical strategies may potentially overcome distinct modes of extracellular signal-regulated kinase reactivation underlying acquired B-RAF inhibitor resistance in melanoma.

Original language	English (US)
Article number	724
Journal	Nature communications
Volume	3
DOIs	https://doi.org/10.1038/ncomms1727
State	Published - Mar 6 2012

Funding

We are grateful to G. Bollag (Plexxikon Inc.) for providing PLX4032, J. S. Economou for biopsies, N. Doan for immunohistochemistry, B. Chmielowski and J. Glaspy for coordinated patient care, T.L. Toy for technical help with library generation for deep sequencing, and B. Harry for help with analysis of whole-exome sequence data. R.S.L. acknowledges funding from the following: Burroughs Wellcome Fund, National Cancer Institute (K22CA151638), V Foundation for Cancer Research, Melanoma Research Foundation, Melanoma Research Alliance, American Skin Association, Joint Center for Translational Medicine, Sidney Kimmel Foundation, Stand Up to Cancer, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, the Wesley Coyle Memorial Fund, Ian Copeland Melanoma Fund, Ruby Family Foundation, Louis Belley and Richard Schnarr Fund, and The Seaver Institute. R.F.K. and G.V.L. are supported by Program Grant No. 402761 from the National Health and Medical Research Council of Australia, Translational Research Program Grant No. 05/TPG/1-01 from the Cancer Institute New South Wales (CINSW). J.A.S. is supported by National Cancer Institute (K24CA097588) and American Cancer Society Melanoma Professorship. We are grateful to every patient volunteer who donated tissue(s) for this study.

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

Access to Document

10.1038/ncomms1727

Cite this

Shi, H., Moriceau, G., Kong, X., Lee, M. K., Lee, H., Koya, R. C., Ng, C., Chodon, T., Scolyer, R. A., Dahlman, K. B., Sosman, J. A., Kefford, R. F., Long, G. V., Nelson, S. F., Ribas, A., & Lo, R. S. (2012). Melanoma whole-exome sequencing identifies ^V600E B-RAF amplification-mediated acquired B-RAF inhibitor resistance. Nature communications, 3, Article 724. https://doi.org/10.1038/ncomms1727

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title = "Melanoma whole-exome sequencing identifies V600E B-RAF amplification-mediated acquired B-RAF inhibitor resistance",

abstract = "The development of acquired drug resistance hampers the long-term success of B-RAF inhibitor therapy for melanoma patients. Here we show V600E B-RAF copy-number gain as a mechanism of acquired B-RAF inhibitor resistance in 4 out of 20 (20%) patients treated with B-RAF inhibitor. In cell lines, V600E B-RAF overexpression and knockdown conferred B-RAF inhibitor resistance and sensitivity, respectively. In V600E B-RAF amplification-driven (versus mutant N-RAS-driven) B-RAF inhibitor resistance, extracellular signal-regulated kinase reactivation is saturable, with higher doses of vemurafenib down-regulating phosho-extracellular signal-regulated kinase and re-sensitizing melanoma cells to B-RAF inhibitor. These two mechanisms of extracellular signal-regulated kinase reactivation are sensitive to the MEK1/2 inhibitor AZD6244/selumetinib or its combination with the B-RAF inhibitor vemurafenib. In contrast to mutant N-RAS-mediated V600E B-RAF bypass, which is sensitive to C-RAF knockdown, V600E B-RAF amplification-mediated resistance functions largely independently of C-RAF. Thus, alternative clinical strategies may potentially overcome distinct modes of extracellular signal-regulated kinase reactivation underlying acquired B-RAF inhibitor resistance in melanoma.",

author = "Hubing Shi and Gatien Moriceau and Xiangju Kong and Lee, {Mi Kyung} and Hane Lee and Koya, {Richard C.} and Charles Ng and Thinle Chodon and Scolyer, {Richard A.} and Dahlman, {Kimberly B.} and Sosman, {Jeffrey A.} and Kefford, {Richard F.} and Long, {Georgina V.} and Nelson, {Stanley F.} and Antoni Ribas and Lo, {Roger S.}",

note = "Funding Information: We are grateful to G. Bollag (Plexxikon Inc.) for providing PLX4032, J. S. Economou for biopsies, N. Doan for immunohistochemistry, B. Chmielowski and J. Glaspy for coordinated patient care, T.L. Toy for technical help with library generation for deep sequencing, and B. Harry for help with analysis of whole-exome sequence data. R.S.L. acknowledges funding from the following: Burroughs Wellcome Fund, National Cancer Institute (K22CA151638), V Foundation for Cancer Research, Melanoma Research Foundation, Melanoma Research Alliance, American Skin Association, Joint Center for Translational Medicine, Sidney Kimmel Foundation, Stand Up to Cancer, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, the Wesley Coyle Memorial Fund, Ian Copeland Melanoma Fund, Ruby Family Foundation, Louis Belley and Richard Schnarr Fund, and The Seaver Institute. R.F.K. and G.V.L. are supported by Program Grant No. 402761 from the National Health and Medical Research Council of Australia, Translational Research Program Grant No. 05/TPG/1-01 from the Cancer Institute New South Wales (CINSW). J.A.S. is supported by National Cancer Institute (K24CA097588) and American Cancer Society Melanoma Professorship. We are grateful to every patient volunteer who donated tissue(s) for this study.",

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AU - Shi, Hubing

AU - Moriceau, Gatien

AU - Kong, Xiangju

AU - Lee, Mi Kyung

AU - Lee, Hane

AU - Koya, Richard C.

AU - Ng, Charles

AU - Chodon, Thinle

AU - Scolyer, Richard A.

AU - Dahlman, Kimberly B.

AU - Sosman, Jeffrey A.

AU - Kefford, Richard F.

AU - Long, Georgina V.

AU - Nelson, Stanley F.

AU - Ribas, Antoni

AU - Lo, Roger S.

N1 - Funding Information: We are grateful to G. Bollag (Plexxikon Inc.) for providing PLX4032, J. S. Economou for biopsies, N. Doan for immunohistochemistry, B. Chmielowski and J. Glaspy for coordinated patient care, T.L. Toy for technical help with library generation for deep sequencing, and B. Harry for help with analysis of whole-exome sequence data. R.S.L. acknowledges funding from the following: Burroughs Wellcome Fund, National Cancer Institute (K22CA151638), V Foundation for Cancer Research, Melanoma Research Foundation, Melanoma Research Alliance, American Skin Association, Joint Center for Translational Medicine, Sidney Kimmel Foundation, Stand Up to Cancer, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, the Wesley Coyle Memorial Fund, Ian Copeland Melanoma Fund, Ruby Family Foundation, Louis Belley and Richard Schnarr Fund, and The Seaver Institute. R.F.K. and G.V.L. are supported by Program Grant No. 402761 from the National Health and Medical Research Council of Australia, Translational Research Program Grant No. 05/TPG/1-01 from the Cancer Institute New South Wales (CINSW). J.A.S. is supported by National Cancer Institute (K24CA097588) and American Cancer Society Melanoma Professorship. We are grateful to every patient volunteer who donated tissue(s) for this study.

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N2 - The development of acquired drug resistance hampers the long-term success of B-RAF inhibitor therapy for melanoma patients. Here we show V600E B-RAF copy-number gain as a mechanism of acquired B-RAF inhibitor resistance in 4 out of 20 (20%) patients treated with B-RAF inhibitor. In cell lines, V600E B-RAF overexpression and knockdown conferred B-RAF inhibitor resistance and sensitivity, respectively. In V600E B-RAF amplification-driven (versus mutant N-RAS-driven) B-RAF inhibitor resistance, extracellular signal-regulated kinase reactivation is saturable, with higher doses of vemurafenib down-regulating phosho-extracellular signal-regulated kinase and re-sensitizing melanoma cells to B-RAF inhibitor. These two mechanisms of extracellular signal-regulated kinase reactivation are sensitive to the MEK1/2 inhibitor AZD6244/selumetinib or its combination with the B-RAF inhibitor vemurafenib. In contrast to mutant N-RAS-mediated V600E B-RAF bypass, which is sensitive to C-RAF knockdown, V600E B-RAF amplification-mediated resistance functions largely independently of C-RAF. Thus, alternative clinical strategies may potentially overcome distinct modes of extracellular signal-regulated kinase reactivation underlying acquired B-RAF inhibitor resistance in melanoma.

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