Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma

Lipika Goyal, Supriya K. Saha, Leah Y. Liu, Giulia Siravegna, Ignaty Leshchiner, Leanne G. Ahronian, Jochen K. Lennerz, Phuong Vu, Vikram Deshpande, Avinash Kambadakone, Benedetta Mussolin, Stephanie Reyes, Laura Henderson, Jiaoyuan Elisabeth Sun, Emily E. Van Seventer, Joseph M. Gurski, Sabrina Baltschukat, Barbara Schacher-Engstler, Louise Barys, Christelle StammPascal Furet, David P. Ryan, James R. Stone, A. John Iafrate, Gad Getz, Diana Graus Porta, Ralph Tiedt, Alberto Bardelli, Dejan Juric, Ryan B. Corcoran, Nabeel Bardeesy, Andrew X. Zhu

Research output: Contribution to journalArticle

Abstract

Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter-and intr alesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies. SIGNIFICANCE: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target.

Original languageEnglish
Pages (from-to)252-263
Number of pages12
JournalCancer Discovery
Volume7
Issue number3
DOIs
Publication statusPublished - Mar 1 2017

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Fibroblast Growth Factor Receptors
Cholangiocarcinoma
Mutation
Circulating Neoplastic Cells
Neoplasms
DNA
Point Mutation
Autopsy
Phosphotransferases
Therapeutics
Clone Cells
Neoplasm Metastasis
Biopsy
3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-(6-(4-(4-ethylpiperazin-1-yl)-phenylamino)pyrimidin-4-yl)-1-methylurea

ASJC Scopus subject areas

  • Oncology

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Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma. / Goyal, Lipika; Saha, Supriya K.; Liu, Leah Y.; Siravegna, Giulia; Leshchiner, Ignaty; Ahronian, Leanne G.; Lennerz, Jochen K.; Vu, Phuong; Deshpande, Vikram; Kambadakone, Avinash; Mussolin, Benedetta; Reyes, Stephanie; Henderson, Laura; Sun, Jiaoyuan Elisabeth; Van Seventer, Emily E.; Gurski, Joseph M.; Baltschukat, Sabrina; Schacher-Engstler, Barbara; Barys, Louise; Stamm, Christelle; Furet, Pascal; Ryan, David P.; Stone, James R.; John Iafrate, A.; Getz, Gad; Porta, Diana Graus; Tiedt, Ralph; Bardelli, Alberto; Juric, Dejan; Corcoran, Ryan B.; Bardeesy, Nabeel; Zhu, Andrew X.

In: Cancer Discovery, Vol. 7, No. 3, 01.03.2017, p. 252-263.

Research output: Contribution to journalArticle

Goyal, L, Saha, SK, Liu, LY, Siravegna, G, Leshchiner, I, Ahronian, LG, Lennerz, JK, Vu, P, Deshpande, V, Kambadakone, A, Mussolin, B, Reyes, S, Henderson, L, Sun, JE, Van Seventer, EE, Gurski, JM, Baltschukat, S, Schacher-Engstler, B, Barys, L, Stamm, C, Furet, P, Ryan, DP, Stone, JR, John Iafrate, A, Getz, G, Porta, DG, Tiedt, R, Bardelli, A, Juric, D, Corcoran, RB, Bardeesy, N & Zhu, AX 2017, 'Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma', Cancer Discovery, vol. 7, no. 3, pp. 252-263. https://doi.org/10.1158/2159-8290.CD-16-1000
Goyal, Lipika ; Saha, Supriya K. ; Liu, Leah Y. ; Siravegna, Giulia ; Leshchiner, Ignaty ; Ahronian, Leanne G. ; Lennerz, Jochen K. ; Vu, Phuong ; Deshpande, Vikram ; Kambadakone, Avinash ; Mussolin, Benedetta ; Reyes, Stephanie ; Henderson, Laura ; Sun, Jiaoyuan Elisabeth ; Van Seventer, Emily E. ; Gurski, Joseph M. ; Baltschukat, Sabrina ; Schacher-Engstler, Barbara ; Barys, Louise ; Stamm, Christelle ; Furet, Pascal ; Ryan, David P. ; Stone, James R. ; John Iafrate, A. ; Getz, Gad ; Porta, Diana Graus ; Tiedt, Ralph ; Bardelli, Alberto ; Juric, Dejan ; Corcoran, Ryan B. ; Bardeesy, Nabeel ; Zhu, Andrew X. / Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma. In: Cancer Discovery. 2017 ; Vol. 7, No. 3. pp. 252-263.
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abstract = "Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter-and intr alesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies. SIGNIFICANCE: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target.",
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T1 - Polyclonal secondary FGFR2 mutations drive acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive cholangiocarcinoma

AU - Goyal, Lipika

AU - Saha, Supriya K.

AU - Liu, Leah Y.

AU - Siravegna, Giulia

AU - Leshchiner, Ignaty

AU - Ahronian, Leanne G.

AU - Lennerz, Jochen K.

AU - Vu, Phuong

AU - Deshpande, Vikram

AU - Kambadakone, Avinash

AU - Mussolin, Benedetta

AU - Reyes, Stephanie

AU - Henderson, Laura

AU - Sun, Jiaoyuan Elisabeth

AU - Van Seventer, Emily E.

AU - Gurski, Joseph M.

AU - Baltschukat, Sabrina

AU - Schacher-Engstler, Barbara

AU - Barys, Louise

AU - Stamm, Christelle

AU - Furet, Pascal

AU - Ryan, David P.

AU - Stone, James R.

AU - John Iafrate, A.

AU - Getz, Gad

AU - Porta, Diana Graus

AU - Tiedt, Ralph

AU - Bardelli, Alberto

AU - Juric, Dejan

AU - Corcoran, Ryan B.

AU - Bardeesy, Nabeel

AU - Zhu, Andrew X.

PY - 2017/3/1

Y1 - 2017/3/1

N2 - Genetic alterations in the fibroblast growth factor receptor (FGFR) pathway are promising therapeutic targets in many cancers, including intrahepatic cholangiocarcinoma (ICC). The FGFR inhibitor BGJ398 displayed encouraging efficacy in patients with FGFR2 fusion-positive ICC in a phase II trial, but the durability of response was limited in some patients. Here, we report the molecular basis for acquired resistance to BGJ398 in three patients via integrative genomic characterization of cell-free circulating tumor DNA (cfDNA), primary tumors, and metastases. Serial analysis of cfDNA demonstrated multiple recurrent point mutations in the FGFR2 kinase domain at progression. Accordingly, biopsy of post-progression lesions and rapid autopsy revealed marked inter-and intr alesional heterogeneity, with different FGFR2 mutations in individual resistant clones. Molecular modeling and in vitro studies indicated that each mutation led to BGJ398 resistance and was surmountable by structurally distinct FGFR inhibitors. Thus, polyclonal secondary FGFR2 mutations represent an important clinical resistance mechanism that may guide the development of future therapeutic strategies. SIGNIFICANCE: We report the first genetic mechanisms of clinical acquired resistance to FGFR inhibition in patients with FGFR2 fusion-positive ICC. Our findings can inform future strategies for detecting resistance mechanisms and inducing more durable remissions in ICC and in the wide variety of cancers where the FGFR pathway is being explored as a therapeutic target.

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