Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy

Luca Zammataro, Salvatore Lopez, Stefania Bellone, Francesca Pettinella, Elena Bonazzoli, Emanuele Perrone, Siming Zhao, Gulden Menderes, Gary Altwerger, Chanhee Han, Burak Zeybek, Anna Bianchi, Aranzazu Manzano, Paola Manara, Emiliano Cocco, Natalia Buza, Pei Hui, Serena Wong, Antonella Ravaggi, Eliana BignottiChiara Romani, Paola Todeschini, Laura Zanotti, Franco Odicino, Sergio Pecorelli, Carla Donzelli, Laura Ardighieri, Roberto Angioli, Francesco Raspagliesi, Giovanni Scambia, Jungmin Choi, Weilai Dong, Kaya Bilguvar, Ludmil B. Alexandrov, Dan Arin Silasi, Gloria S. Huang, Elena Ratner, Masoud Azodi, Peter E. Schwartz, Valentina Pirazzoli, Amy L. Stiegler, Titus J. Boggon, Richard P. Lifton, Joseph Schlessinger, Alessandro D. Santin

Research output: Contribution to journalArticle

Abstract

The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirustype-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/ AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.

Original languageEnglish
Pages (from-to)22730-22736
Number of pages7
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number45
DOIs
Publication statusPublished - Jan 1 2019

Fingerprint

Exome
Uterine Cervical Neoplasms
Carcinoma
Mutation
Phosphatidylinositol 3-Kinases
Neoplasms
Heterografts
Nucleotides
Cytidine Deaminase
Therapeutics
Chromatin Assembly and Disassembly
Missense Mutation
Tumor Cell Line
Mutagenesis
Squamous Cell Carcinoma
Cell Cycle
Adenocarcinoma
Apoptosis
Cell Line
DNA

Keywords

  • Cervical cancer
  • Copanlisib
  • HER2/neu
  • Neratinib
  • PIK3CA

ASJC Scopus subject areas

  • General

Cite this

Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy. / Zammataro, Luca; Lopez, Salvatore; Bellone, Stefania; Pettinella, Francesca; Bonazzoli, Elena; Perrone, Emanuele; Zhao, Siming; Menderes, Gulden; Altwerger, Gary; Han, Chanhee; Zeybek, Burak; Bianchi, Anna; Manzano, Aranzazu; Manara, Paola; Cocco, Emiliano; Buza, Natalia; Hui, Pei; Wong, Serena; Ravaggi, Antonella; Bignotti, Eliana; Romani, Chiara; Todeschini, Paola; Zanotti, Laura; Odicino, Franco; Pecorelli, Sergio; Donzelli, Carla; Ardighieri, Laura; Angioli, Roberto; Raspagliesi, Francesco; Scambia, Giovanni; Choi, Jungmin; Dong, Weilai; Bilguvar, Kaya; Alexandrov, Ludmil B.; Silasi, Dan Arin; Huang, Gloria S.; Ratner, Elena; Azodi, Masoud; Schwartz, Peter E.; Pirazzoli, Valentina; Stiegler, Amy L.; Boggon, Titus J.; Lifton, Richard P.; Schlessinger, Joseph; Santin, Alessandro D.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 116, No. 45, 01.01.2019, p. 22730-22736.

Research output: Contribution to journalArticle

Zammataro, L, Lopez, S, Bellone, S, Pettinella, F, Bonazzoli, E, Perrone, E, Zhao, S, Menderes, G, Altwerger, G, Han, C, Zeybek, B, Bianchi, A, Manzano, A, Manara, P, Cocco, E, Buza, N, Hui, P, Wong, S, Ravaggi, A, Bignotti, E, Romani, C, Todeschini, P, Zanotti, L, Odicino, F, Pecorelli, S, Donzelli, C, Ardighieri, L, Angioli, R, Raspagliesi, F, Scambia, G, Choi, J, Dong, W, Bilguvar, K, Alexandrov, LB, Silasi, DA, Huang, GS, Ratner, E, Azodi, M, Schwartz, PE, Pirazzoli, V, Stiegler, AL, Boggon, TJ, Lifton, RP, Schlessinger, J & Santin, AD 2019, 'Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 45, pp. 22730-22736. https://doi.org/10.1073/pnas.1911385116
Zammataro, Luca ; Lopez, Salvatore ; Bellone, Stefania ; Pettinella, Francesca ; Bonazzoli, Elena ; Perrone, Emanuele ; Zhao, Siming ; Menderes, Gulden ; Altwerger, Gary ; Han, Chanhee ; Zeybek, Burak ; Bianchi, Anna ; Manzano, Aranzazu ; Manara, Paola ; Cocco, Emiliano ; Buza, Natalia ; Hui, Pei ; Wong, Serena ; Ravaggi, Antonella ; Bignotti, Eliana ; Romani, Chiara ; Todeschini, Paola ; Zanotti, Laura ; Odicino, Franco ; Pecorelli, Sergio ; Donzelli, Carla ; Ardighieri, Laura ; Angioli, Roberto ; Raspagliesi, Francesco ; Scambia, Giovanni ; Choi, Jungmin ; Dong, Weilai ; Bilguvar, Kaya ; Alexandrov, Ludmil B. ; Silasi, Dan Arin ; Huang, Gloria S. ; Ratner, Elena ; Azodi, Masoud ; Schwartz, Peter E. ; Pirazzoli, Valentina ; Stiegler, Amy L. ; Boggon, Titus J. ; Lifton, Richard P. ; Schlessinger, Joseph ; Santin, Alessandro D. / Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy. In: Proceedings of the National Academy of Sciences of the United States of America. 2019 ; Vol. 116, No. 45. pp. 22730-22736.
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T1 - Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy

AU - Zammataro, Luca

AU - Lopez, Salvatore

AU - Bellone, Stefania

AU - Pettinella, Francesca

AU - Bonazzoli, Elena

AU - Perrone, Emanuele

AU - Zhao, Siming

AU - Menderes, Gulden

AU - Altwerger, Gary

AU - Han, Chanhee

AU - Zeybek, Burak

AU - Bianchi, Anna

AU - Manzano, Aranzazu

AU - Manara, Paola

AU - Cocco, Emiliano

AU - Buza, Natalia

AU - Hui, Pei

AU - Wong, Serena

AU - Ravaggi, Antonella

AU - Bignotti, Eliana

AU - Romani, Chiara

AU - Todeschini, Paola

AU - Zanotti, Laura

AU - Odicino, Franco

AU - Pecorelli, Sergio

AU - Donzelli, Carla

AU - Ardighieri, Laura

AU - Angioli, Roberto

AU - Raspagliesi, Francesco

AU - Scambia, Giovanni

AU - Choi, Jungmin

AU - Dong, Weilai

AU - Bilguvar, Kaya

AU - Alexandrov, Ludmil B.

AU - Silasi, Dan Arin

AU - Huang, Gloria S.

AU - Ratner, Elena

AU - Azodi, Masoud

AU - Schwartz, Peter E.

AU - Pirazzoli, Valentina

AU - Stiegler, Amy L.

AU - Boggon, Titus J.

AU - Lifton, Richard P.

AU - Schlessinger, Joseph

AU - Santin, Alessandro D.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirustype-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/ AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.

AB - The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirustype-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/ AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.

KW - Cervical cancer

KW - Copanlisib

KW - HER2/neu

KW - Neratinib

KW - PIK3CA

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