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Ubhi T, Zaslaver O, Quaile AT, Plenker D, Cao P, Pham NA, Békési A, Jang GH, O'Kane GM, Notta F, Moffat J, Wilson JM, Gallinger S, Vértessy BG, Tuveson DA, Röst HL, Brown GW. Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. Nat Cancer 2024:10.1038/s43018-024-00742-z. [PMID: 38448522 DOI: 10.1038/s43018-024-00742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-scale CRISPR-Cas9 chemical-genetic screens in PDAC cells and found selective loss of cell fitness upon disruption of the cytidine deaminases APOBEC3C and APOBEC3D. Following gemcitabine treatment, APOBEC3C and APOBEC3D promote DNA replication stress resistance and cell survival by deaminating cytidines in the nuclear genome to ensure DNA replication fork restart and repair in PDAC cells. We provide evidence that the chemical-genetic interaction between APOBEC3C or APOBEC3D and gemcitabine is absent in nontransformed cells but is recapitulated across different PDAC cell lines, in PDAC organoids and in PDAC xenografts. Thus, we uncover roles for APOBEC3C and APOBEC3D in DNA replication stress resistance and offer plausible targets for improving gemcitabine-based therapies for PDAC.
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Affiliation(s)
- Tajinder Ubhi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Plenker
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Xilis Inc., Durham, NC, USA
| | - Pinjiang Cao
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Angéla Békési
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - David A Tuveson
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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2
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Moghal N, Li Q, Stewart EL, Navab R, Mikubo M, D'Arcangelo E, Martins-Filho SN, Raghavan V, Pham NA, Li M, Shepherd FA, Liu G, Tsao MS. Single-Cell Analysis Reveals Transcriptomic Features of Drug-Tolerant Persisters and Stromal Adaptation in a Patient-Derived EGFR-Mutated Lung Adenocarcinoma Xenograft Model. J Thorac Oncol 2023; 18:499-515. [PMID: 36535627 DOI: 10.1016/j.jtho.2022.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/11/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Targeted therapies require life-long treatment, as drug discontinuation invariably leads to tumor recurrence. Recurrence is mainly driven by minor subpopulations of drug-tolerant persister (DTP) cells that survive the cytotoxic drug effect. In lung cancer, DTP studies have mainly been conducted with cell line models. METHODS We conducted an in vivo DTP study using a lung adenocarcinoma patient-derived xenograft tumor driven by an EGFR mutation. Daily treatment of tumor-bearing mice for 5 to 6 weeks with the EGFR inhibitor erlotinib markedly shrunk tumors and generated DTPs, which were analyzed by whole exome, bulk population transcriptome, and single-cell RNA sequencing. RESULTS The DTP tumors maintained the genomic clonal architecture of untreated baseline (BL) tumors but had reduced proliferation. Single-cell RNA sequencing identified a rare (approximately 4%) subpopulation of BL cells (DTP-like) with transcriptomic similarity to DTP cells and intermediate activity of pathways that are up-regulated in DTPs. Furthermore, the predominant transforming growth factor-β activated cancer-associated fibroblast (CAF) population in BL tumors was replaced by a CAF population enriched for IL6 production. In vitro experiments indicate that these populations interconvert depending on the levels of transforming growth factor-β versus NF-κB signaling, which is modulated by tyrosine kinase inhibitor presence. The DTPs had signs of increased NF-κB and STAT3 signaling, which may promote their survival. CONCLUSIONS The DTPs may arise from a specific preexisting subpopulation of cancer cells with partial activation of specific drug resistance pathways. Tyrosine kinase inhibitor treatment induces DTPs revealing greater activation of these pathways while converting the major preexisting CAF population into a new state that may further promote DTP survival.
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Affiliation(s)
- Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Erin L Stewart
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Roya Navab
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Masashi Mikubo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Thoracic Surgery, Kitasato University School of Medicine, Kanagawa, Japan
| | - Elisa D'Arcangelo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sebastiao N Martins-Filho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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3
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Mirhadi S, Zhang W, Pham NA, Karimzadeh F, Pintilie M, Tong J, Taylor P, Krieger J, Pitcher B, Sykes J, Wybenga-Groot L, Fladd C, Xu J, Wang T, Cabanero M, Li M, Weiss J, Sakashita S, Zaslaver O, Yu M, Caudy AA, St-Pierre J, Hawkins C, Kislinger T, Liu G, Shepherd FA, Tsao MS, Moran MF. Mitochondrial Aconitase ACO2 Links Iron Homeostasis with Tumorigenicity in Non-Small Cell Lung Cancer. Mol Cancer Res 2023; 21:36-50. [PMID: 36214668 PMCID: PMC9808373 DOI: 10.1158/1541-7786.mcr-22-0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/08/2022] [Accepted: 10/03/2022] [Indexed: 02/03/2023]
Abstract
The ability of a patient tumor to engraft an immunodeficient mouse is the strongest known independent indicator of poor prognosis in early-stage non-small cell lung cancer (NSCLC). Analysis of primary NSCLC proteomes revealed low-level expression of mitochondrial aconitase (ACO2) in the more aggressive, engrafting tumors. Knockdown of ACO2 protein expression transformed immortalized lung epithelial cells, whereas upregulation of ACO2 in transformed NSCLC cells inhibited cell proliferation in vitro and tumor growth in vivo. High level ACO2 increased iron response element binding protein 1 (IRP1) and the intracellular labile iron pool. Impaired cellular proliferation associated with high level ACO2 was reversed by treatment of cells with an iron chelator, whereas increased cell proliferation associated with low level ACO2 was suppressed by treatment of cells with iron. Expression of CDGSH iron-sulfur (FeS) domain-containing protein 1 [CISD1; also known as mitoNEET (mNT)] was modulated by ACO2 expression level and inhibition of mNT by RNA interference or by treatment of cells with pioglitazone also increased iron and cell death. Hence, ACO2 is identified as a regulator of iron homeostasis and mNT is implicated as a target in aggressive NSCLC. IMPLICATIONS FeS cluster-associated proteins including ACO2, mNT (encoded by CISD1), and IRP1 (encoded by ACO1) are part of an "ACO2-Iron Axis" that regulates iron homeostasis and is a determinant of a particularly aggressive subset of NSCLC.
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Affiliation(s)
- Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Wen Zhang
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul Taylor
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bethany Pitcher
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jenna Sykes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Christopher Fladd
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jing Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tao Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Man Yu
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amy A. Caudy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie St-Pierre
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Québec, Canada.,Department of Biochemistry, Microbiology, and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cynthia Hawkins
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Frances A. Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Michael F. Moran, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada. Phone: 647-235-6435; E-mail: ; and Ming-Sound Tsao, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-340-4737; E-mail:
| | - Michael F. Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada.,Corresponding Authors: Michael F. Moran, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada. Phone: 647-235-6435; E-mail: ; and Ming-Sound Tsao, Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-340-4737; E-mail:
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4
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Hinzpeter R, Kulanthaivelu R, Kohan A, Avery L, Pham NA, Ortega C, Metser U, Haider M, Veit-Haibach P. CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling. Cancers (Basel) 2022; 14:cancers14246224. [PMID: 36551709 PMCID: PMC9776865 DOI: 10.3390/cancers14246224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
We investigate whether computed tomography (CT) derived radiomics may correlate with driver gene mutations in patients with pancreatic ductal adenocarcinoma (PDAC). In this retrospective study, 47 patients (mean age 64 ± 11 years; range: 42-86 years) with PDAC, who were treated surgically and who underwent preoperative CT imaging at our institution were included in the study. Image segmentation and feature extraction was performed semi-automatically with a commonly used open-source software platform. Genomic data from whole genome sequencing (WGS) were collected from our institution's web-based resource. Two statistical models were then built, in order to evaluate the predictive ability of CT-derived radiomics feature for driver gene mutations in PDAC. 30/47 of all tumor samples harbored 2 or more gene mutations. Overall, 81% of tumor samples demonstrated mutations in KRAS, 68% of samples had alterations in TP53, 26% in SMAD4 and 19% in CDKN2A. Extended statistical analysis revealed acceptable predictive ability for KRAS and TP53 (Youden Index 0.56 and 0.67, respectively) and mild to acceptable predictive signal for SMAD4 and CDKN2A (Youden Index 0.5, respectively). Our study establishes acceptable correlation of radiomics features and driver gene mutations in PDAC, indicating an acceptable prognostication of genomic profiles using CT-derived radiomics. A larger and more homogenous cohort may further enhance the predictive ability.
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Affiliation(s)
- Ricarda Hinzpeter
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
- Correspondence: ; Tel.: +1-416-340-4800
| | - Roshini Kulanthaivelu
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
| | - Andres Kohan
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
| | - Lisa Avery
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Claudia Ortega
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
| | - Ur Metser
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
| | - Masoom Haider
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
| | - Patrick Veit-Haibach
- Joint Department of Medical Imaging, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON M5G 2C1, Canada
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5
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Mirhadi S, Tam S, Li Q, Moghal N, Pham NA, Tong J, Golbourn BJ, Krieger JR, Taylor P, Li M, Weiss J, Martins-Filho SN, Raghavan V, Mamatjan Y, Khan AA, Cabanero M, Sakashita S, Huo K, Agnihotri S, Ishizawa K, Waddell TK, Zadeh G, Yasufuku K, Liu G, Shepherd FA, Moran MF, Tsao MS. Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies distinct proteotypes associated with patient outcomes. Nat Commun 2022; 13:1811. [PMID: 35383171 PMCID: PMC8983714 DOI: 10.1038/s41467-022-29444-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/17/2022] [Indexed: 12/24/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. Only a fraction of NSCLC harbor actionable driver mutations and there is an urgent need for patient-derived model systems that will enable the development of new targeted therapies. NSCLC and other cancers display profound proteome remodeling compared to normal tissue that is not predicted by DNA or RNA analyses. Here, we generate 137 NSCLC patient-derived xenografts (PDXs) that recapitulate the histology and molecular features of primary NSCLC. Proteome analysis of the PDX models reveals 3 adenocarcinoma and 2 squamous cell carcinoma proteotypes that are associated with different patient outcomes, protein-phosphotyrosine profiles, signatures of activated pathways and candidate targets, and in adenocarcinoma, stromal immune features. These findings portend proteome-based NSCLC classification and treatment and support the PDX resource as a viable model for the development of new targeted therapies. With non-small cell lung cancer (NSCLC) being the leading cause of cancer deaths worldwide, the development of targeted therapies remains crucial. Here, the generation and multi-omics characterization of 137 NSCLC patient-derived xenografts provides a resource for potential classifications and targets.
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Affiliation(s)
- Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shirley Tam
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Brian J Golbourn
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, and Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Paul Taylor
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jessica Weiss
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Sebastiao N Martins-Filho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yasin Mamatjan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aafaque A Khan
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kugeng Huo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sameer Agnihotri
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, and Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kota Ishizawa
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Thomas K Waddell
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada.,Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Kazuhiro Yasufuku
- Division of Thoracic Surgery, Toronto General Hospital, University Health Network, Toronto, ON, Canada.,Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
| | - Michael F Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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6
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Weiss J, Pham NA, Pintilie M, Li M, Liu G, Shepherd FA, Tsao MS, Xu W. Optimizing Drug Response Study Design in Patient-Derived Tumor Xenografts. Cancer Inform 2022; 21:11769351221136056. [DOI: 10.1177/11769351221136056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022] Open
Abstract
Patient-derived tumor xenograft (PDX) models were used to evaluate the effectiveness of preclinical anticancer agents. A design using 1 mouse per patient per drug (1 × 1 × 1) was considered practical for large-scale drug efficacy studies. We evaluated modifiable parameters that could increase the statistical power of this design based on our consolidated PDX experiments. Real studies were used as a reference to investigate the relationship between statistical power with treatment effect size, inter-mouse variation, and tumor measurement frequencies. Our results showed that large effect sizes could be detected at a significance level of .2 or .05 under a 1 × 1 × 1 design. We found that the minimum number of mice required to achieve 80% power at an alpha level of .05 under all situations explored was 21 mice per group for a small effect size and 5 mice per group for a medium effect size.
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Affiliation(s)
- Jessica Weiss
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Melania Pintilie
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
- Department of Biostatistics, Dalla Lana School of Public Health, Toronto, ON, Canada
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7
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Ortmann J, Rampášek L, Tai E, Mer AS, Shi R, Stewart EL, Mascaux C, Fares A, Pham NA, Beri G, Eeles C, Tkachuk D, Ho C, Sakashita S, Weiss J, Jiang X, Liu G, Cescon DW, O'Brien CA, Guo S, Tsao MS, Haibe-Kains B, Goldenberg A. Assessing therapy response in patient-derived xenografts. Sci Transl Med 2021; 13:eabf4969. [PMID: 34788078 DOI: 10.1126/scitranslmed.abf4969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Janosch Ortmann
- Département AOTI, Université du Québec à Montréal, Montréal, QC H2X3X2, Canada.,Group for Research in Decision Analysis (GERAD), Montreal, QC H3T1J4, Canada
| | - Ladislav Rampášek
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Elijah Tai
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Ruoshi Shi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Erin L Stewart
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Celine Mascaux
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Pulmonology Department, Hôpitaux Universitaires de Strasbourg, 67200 Strasbourg, France.,Laboratory of Molecular Mechanisms of the Stress Response and Pathologies, INSERM U1113, 3 Avenue Molière, 67200 Strasbourg, France
| | - Aline Fares
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Gangesh Beri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Denis Tkachuk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Chantal Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Xiaoqian Jiang
- Crown Bioscience Taicang Inc., No.6 Beijing West Road, Taicang, Jiangsu 215400, P. R. China
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Catherine A O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S1A8, Canada.,Department of Physiology, University of Toronto, Toronto, ON M5G1L7, Canada.,Department of Surgery, Toronto General Hospital, Toronto, ON M5G2C4, Canada
| | - Sheng Guo
- Crown Bioscience Taicang Inc., No.6 Beijing West Road, Taicang, Jiangsu 215400, P. R. China
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada
| | - Benjamin Haibe-Kains
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON M5G1L7, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada.,Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada.,Hospital for Sick Children, Toronto, ON M5G1X8, Canada.,CIFAR, Toronto, ON M5G1M1, Canada
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8
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Huo KG, Notsuda H, Fang Z, Liu NF, Gebregiworgis T, Li Q, Pham NA, Li M, Liu N, Shepherd FA, Marshall CB, Ikura M, Moghal N, Tsao MS. Lung cancer driven by BRAF G469V mutation is targetable by EGFR kinase inhibitors. J Thorac Oncol 2021; 17:277-288. [PMID: 34648945 DOI: 10.1016/j.jtho.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Mutations in BRAF occur in 2-4% of lung adenocarcinoma (LUAD) patients. Combination dabrafenib/trametinib or single-agent vemurafenib is approved only for patients with cancers driven by the V600E BRAF mutation. Targeted therapy is not currently available for patients harboring non-V600 BRAF mutations. METHODS An LUAD patient-derived xenograft (PDX) model (PHLC12) with wild-type and non-amplified epidermal growth factor receptor (EGFR) was tested for response to EGFR tyrosine kinase inhibitors (TKI). A cell line derived from this model (X12CL) was also used to evaluate drug sensitivity and to identify potential drivers by siRNA knockdown. Kinase assays were used to test direct targeting of the candidate driver by the EGFR TKIs. Structural modeling including, molecular dynamics (MD) simulations, and binding assays were conducted to explore the mechanism of off-target inhibition by EGFR TKIs on the model 12 driver. RESULTS Both PDX PHLC12 and the X12CL cell line were sensitive to multiple EGFR TKIs. The BRAFG469V mutation was found to be the only known oncogenic mutation in this model. siRNA knockdown of BRAF, but not the EGFR, killed X12CL, confirming BRAFG469V as the oncogenic driver. Kinase activity of the BRAF protein isolated from X12CL was inhibited by treatment with the EGFR TKIs gefitinib and osimertinib, and expression of BRAFG469V in non-EGFR-expressing NR6 cells promoted growth in low serum, which was also sensitive to EGFR TKIs. . Structural modeling, MD simulations, and in vitro binding assays support BRAFG469V being a direct target of the TKIs. CONCLUSION Clinically approved EGFR TKIs can be repurposed to treat NSCLC patients harboring the BRAFG469V mutation.
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Affiliation(s)
- Ku-Geng Huo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hirotsugu Notsuda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Thoracic Surgery Institute of Development, Aging and Cancer, Tohoku University. Sendai, Japan
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ningdi Feng Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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9
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Rosen JC, Weiss J, Pham NA, Li Q, Martins-Filho SN, Wang Y, Tsao MS, Moghal N. Antitumor efficacy of XPO1 inhibitor Selinexor in KRAS-mutant lung adenocarcinoma patient-derived xenografts. Transl Oncol 2021; 14:101179. [PMID: 34284202 PMCID: PMC8313753 DOI: 10.1016/j.tranon.2021.101179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Gain-of-function Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations occur in 25% of lung adenocarcinomas, and these tumors are challenging to treat. Some preclinical work, largely based on cell lines, suggested KRASmut lung cancers are especially dependent on the nuclear export protein exportin-1 (XPO1), while other work supports XPO1 being a broader cancer dependency. To investigate the sensitivity of KRASmut lung cancers to XPO1 inhibition in models that more closely match clinical tumors, we treated 10 independently established lung cancer patient-derived tumor xenografts (PDXs) with the clinical XPO1 inhibitor, Selinexor. Monotherapy with Selinexor reduced tumor growth in all KRASmut PDXs, which included 4 different codon mutations, and was more effective than the clinical MEK1/2 inhibitor, Trametinib. Selinexor was equally effective in KRASG12C and KRASG12D tumors, with TP53 mutations being a biomarker for a weaker drug response. By mining genome-wide dropout datasets, we identified XPO1 as a universal cancer cell dependency and confirmed this functionally in two KRASWT PDX models harboring kinase drivers. However, targeted kinase inhibitors were more effective than Selinexor in these models. Our findings support continued investigation of XPO1 inhibitors in KRASmut lung adenocarcinoma, regardless of the codon alteration.
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Affiliation(s)
- Joshua C Rosen
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jessica Weiss
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5T 3M7, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Sebastiao N Martins-Filho
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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10
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Pham NA, Radulovich N, Ibrahimov E, Martins-Filho SN, Li Q, Pintilie M, Weiss J, Raghavan V, Cabanero M, Denroche RE, Wilson JM, Metran-Nascente C, Borgida A, Hutchinson S, Dodd A, Begora M, Chadwick D, Serra S, Knox JJ, Gallinger S, Hedley DW, Muthuswamy L, Tsao MS. Patient-derived tumor xenograft and organoid models established from resected pancreatic, duodenal and biliary cancers. Sci Rep 2021; 11:10619. [PMID: 34011980 PMCID: PMC8134568 DOI: 10.1038/s41598-021-90049-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patient-derived xenograft (PDX) and their xenograft-derived organoid (XDO) models that recapitulate the genotypic and phenotypic landscape of patient cancers could help to advance research and lead to improved clinical management. PDX models were established from 276 pancreato-duodenal and biliary cancer resections. Initial, passage 0 (P0) engraftment rates were 59% (118/199) for pancreatic, 86% (25/29) for duodenal, and 35% (17/48) for biliary ductal tumors. Pancreatic ductal adenocarcinoma (PDAC), had a P0 engraftment rate of 62% (105/169). KRAS mutant and wild-type PDAC models were molecularly profiled, and XDO models were generated to perform initial drug response evaluations. Subsets of PDAC PDX models showed global copy number variants and gene expression profiles that were retained with serial passaging, and they showed a spectrum of somatic mutations represented in patient tumors. PDAC XDO models were established, with a success rate of 71% (10/14). Pathway activation of KRAS-MAPK in PDXs was independent of KRAS mutational status. Four wild-type KRAS models were characterized by one with EGFR (L747-P753 del), two with BRAF alterations (N486_P490del or V600E), and one with triple negative KRAS/EGFR/BRAF. Model OCIP256, characterized by BRAF (N486-P490 del), had activated phospho-ERK. A combination treatment of a pan-RAF inhibitor (LY3009120) and a MEK inhibitor (trametinib) effectively suppressed phospho-ERK and inhibited growth of OCIP256 XDO and PDX models. PDAC/duodenal adenocarcinoma have high success rates forming PDX/organoid and retaining their phenotypic and genotypic features. These models may be effective tools to evaluate novel drug combination therapies.
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Affiliation(s)
- Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Emin Ibrahimov
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jessica Weiss
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Julie M Wilson
- Ontario Institute of Cancer Research (OICR), Toronto, ON, Canada
| | | | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Shawn Hutchinson
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anna Dodd
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Begora
- Department of Pathology, UHN Program in BioSpecimen Sciences, University Health Network, Toronto, ON, Canada
| | - Dianne Chadwick
- Department of Pathology, UHN Program in BioSpecimen Sciences, University Health Network, Toronto, ON, Canada
| | - Stefano Serra
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jennifer J Knox
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Steven Gallinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of General Surgery, University of Toronto, Toronto, ON, Canada
| | - David W Hedley
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lakshmi Muthuswamy
- Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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11
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Chia PL, Parakh S, Tsao MS, Pham NA, Gan HK, Cao D, Burvenich IJG, Rigopoulos A, Reilly EB, John T, Scott AM. Targeting and Efficacy of Novel mAb806-Antibody-Drug Conjugates in Malignant Mesothelioma. Pharmaceuticals (Basel) 2020; 13:E289. [PMID: 33023139 PMCID: PMC7601847 DOI: 10.3390/ph13100289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 11/30/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is highly overexpressed in malignant mesothelioma (MM). MAb806 is a novel anti-EGFR antibody that selectively targets a tumor-selective epitope. MAb806-derived antibody drug conjugates (ADCs), ABT-414, ABBV-221 and ABBV-322, may represent a novel therapeutic strategy in MM. EGFR and mAb806 epitope expressions in mesothelioma cell lines were evaluated using an array of binding assays, and the in vitro cell effects of ABT-414 and ABBV-322 were determined. In vivo therapy studies were conducted in mesothelioma xenograft and patient-derived xenograft (PDX) tumor models. We also performed biodistribution and imaging studies to allow the quantitative targeting of MM by mAb806 using a 89Zr-labeled immunoconjugate-ch806. A high EGFR expression was present in all mesothelioma cell lines evaluated and mAb806 binding present in all cell lines, except NCIH-2452. ABT-414 and ABBV-322 resulted in significant tumor growth inhibition in MM models with high EGFR and mAb806 epitope expressions. In contrast, in an EGFR-expressing PDX model that was negative for the mAb806 epitope, no growth inhibition was observed. We demonstrated the specific targeting of the mAb806 epitope expressing MM tumors using 89Zr-based PET imaging. Our data suggest that targeting EGFR in MM using specific ADCs is a valid therapeutic strategy and supports further investigation of the mAb806 epitope expression as a predictive biomarker.
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Affiliation(s)
- Puey-Ling Chia
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Faculty of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria 3084, Australia
| | - Sagun Parakh
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Department of Medical Oncology, Austin Health, Melbourne, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Victoria 3086, Australia
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.-S.T.); (N.-A.P.)
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; (M.-S.T.); (N.-A.P.)
| | - Hui K. Gan
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Faculty of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Victoria 3086, Australia
| | - Diana Cao
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
| | - Ingrid J. G. Burvenich
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Faculty of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Angela Rigopoulos
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
| | | | - Thomas John
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Faculty of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Victoria 3086, Australia
| | - Andrew M. Scott
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia; (P.-L.C.); (S.P.); (H.K.G.); (D.C.); (I.J.G.B.); (A.R.)
- Faculty of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia
- School of Cancer Medicine, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Victoria 3086, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria 3084, Australia
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12
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Shi R, Filho SNM, Li M, Fares A, Weiss J, Pham NA, Ludkovski O, Raghavan V, Li Q, Ravi D, Cabanero M, Moghal N, Leighl NB, Bradbury P, Sacher A, Shepherd FA, Yasufuku K, Tsao MS, Liu G. BRAF V600E mutation and MET amplification as resistance pathways of the second-generation anaplastic lymphoma kinase (ALK) inhibitor alectinib in lung cancer. Lung Cancer 2020; 146:78-85. [PMID: 32521388 DOI: 10.1016/j.lungcan.2020.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/02/2020] [Accepted: 05/12/2020] [Indexed: 01/28/2023]
Abstract
BACKGROUND Anaplastic lymphoma kinase (ALK) targeted therapies have demonstrated remarkable efficacy in ALK-positive lung adenocarcinomas. However, patients inevitably develop resistance to such therapies. To investigate novel mechanisms of resistance to second generation ALK inhibitors, we characterized and modeled ALK inhibitor resistance of ALK-positive patient-derived xenograft (PDX) models established from advanced-stage lung adenocarcinoma patients who have progressed on one or more ALK inhibitors. METHODS Whole exome sequencing was performed to identify resistance mechanisms to ALK inhibitors in PDXs generated from biopsies at the time of relapse. ALK fusion status was confirmed using fluorescent in situ hybridization, immunohistochemistry, RNA-sequencing, RT-qPCR and western blot. Targeted therapies to overcome acquired resistance were then tested on the PDX models. RESULTS Three PDX models were successfully established from biopsies of two patients who had progressed on crizotinib and/or alectinib. The PDX models recapitulated the histology and ALK status of their patient tumors, as well as their matched patients' clinical treatment outcome to ALK inhibitors. Whole exome sequencing identified MET amplification and previously unreported BRAF V600E mutation as independent mechanisms of resistance to alectinib. Importantly, PDX treatment of inhibitors specific for these targets combined with ALK inhibitor overcame resistance. CONCLUSIONS Bypass signaling pathway through c-MET and BRAF are independent mechanisms of resistance to alectinib. Individualized intervention against these resistance pathways could be viable therapeutic options in alectinib-refractory lung adenocarcinoma.
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Affiliation(s)
- Ruoshi Shi
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sebastiao N Martins Filho
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ming Li
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Aline Fares
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Weiss
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga Ludkovski
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Vibha Raghavan
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Quan Li
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Deepti Ravi
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Cabanero
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Natasha B Leighl
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Penelope Bradbury
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kazuhiro Yasufuku
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Geoffrey Liu
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Dalla Lana School of Public Health and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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13
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Fares AF, Martins-Filho SN, Li Q, Seto A, Stewart EL, Zhang T, Lau SCM, Ravi D, Weiss J, Patel D, Pham NA, Sacher AG, Bradbury PA, Stockley T, Leighl NB, Shepherd FA, Tsao MS, Liu G. Genomic analysis of driver-negative lung adenocarcinoma (LA) in lifetime never smokers. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3571 Background: Genomic events giving rise to driver negative LA in never smokers remain elusive. Here we report results of whole exome sequencing (WES) and targeted RNA sequencing in NS who had no mutation drivers found on routine clinical testing by targeted next generation sequencing (NGS). Methods: The cohort of never smokers with EGFR/ALK negative LA by clinical biomarker testing at Princess Margaret Cancer Centre, were first subjected to various clinical NGS profiling platforms (table). Where tissue was available, those negative for potential drivers in the clinical NGS then underwent WES (mean coverage > 200x) and Oncomine comprehensive v.3 RNA sequencing. We analyzed mutational signatures (MS) of the driver negative cohort based on the COSMIC catalog and assessed the median tumor mutation burden (mTMB mut/Mb -Megabase) in cases without a smoking MS, to avoid confounders. Results: Of 159 never smokers profiled with clinical NGS, potential drivers were found in 86 (54%): 75 (87%) with mutations in known LA driver genes and 11 (13%) with fusions. Among the remaining never smokers that tested negative by clinical NGS, 35 (48%) had available tissue for further testing. The Oncomine panel identified 9 cases (25%) with fusions or MET exon14 mutation (n = 7). Within the driver negative group, 24 (92%) underwent WES. Three tumors had WES base substitution patterns that were consistent with a smoking-related MS (MS4). Twenty-one patients exhibited signatures found common across all cancer types (MS 5), associated with DNA mismatch repair (MS 6, MS 20) or APOBEC over-activation (MS 2, MS13). In the driver-negative group, we identified 7 pts with somatic mutations in the KMT2 family (4 KMT2C, 4 KMT2A, 1 KMT2D), known for putative tumor suppressors and histone methyltransferases. mTMB on the driver negative group was 1.92, while one outlier with APOBEC MS and KMT2C/A mutations had a TMB of 16.8. Conclusions: Never smokers with driver negative LA are a heterogeneous group, with different MS and a wide TMB range. Mutations on KMT2 family are frequently found in driver negative LA in never smokers and warrant further investigations. [Table: see text]
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Affiliation(s)
| | | | - Quan Li
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Andrew Seto
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Tong Zhang
- Ontario Cancer Institute, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Sally CM Lau
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Deepti Ravi
- University Health Network, Toronto, ON, Canada
| | - Jessica Weiss
- University Hospital Network (UHN) Biostatistics Department, Toronto, ON, Canada
| | | | - Nhu-An Pham
- University Health Network, University of Toronto, Toronto, ON, Canada
| | | | | | - Tracy Stockley
- University Health Network, Genome Diagnostics, Laboratory Medicine Program, Toronto, ON, Canada
| | | | - Frances A. Shepherd
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Ming Sound Tsao
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
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14
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Saraon P, Snider J, Kalaidzidis Y, Wybenga-Groot LE, Weiss K, Rai A, Radulovich N, Drecun L, Vučković N, Vučetić A, Wong V, Thériault B, Pham NA, Park JH, Datti A, Wang J, Pathmanathan S, Aboualizadeh F, Lyakisheva A, Yao Z, Wang Y, Joseph B, Aman A, Moran MF, Prakesch M, Poda G, Marcellus R, Uehling D, Samaržija M, Jakopović M, Tsao MS, Shepherd FA, Sacher A, Leighl N, Akhmanova A, Al-Awar R, Zerial M, Stagljar I. A drug discovery platform to identify compounds that inhibit EGFR triple mutants. Nat Chem Biol 2020; 16:577-586. [PMID: 32094923 DOI: 10.1038/s41589-020-0484-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease. Historically, therapeutics targeting RTKs have been identified using in vitro kinase assays. Due to frequent development of drug resistance, however, there is a need to identify more diverse compounds that inhibit mutated but not wild-type RTKs. Here, we describe MaMTH-DS (mammalian membrane two-hybrid drug screening), a live-cell platform for high-throughput identification of small molecules targeting functional protein-protein interactions of RTKs. We applied MaMTH-DS to an oncogenic epidermal growth factor receptor (EGFR) mutant resistant to the latest generation of clinically approved tyrosine kinase inhibitors (TKIs). We identified four mutant-specific compounds, including two that would not have been detected by conventional in vitro kinase assays. One of these targets mutant EGFR via a new mechanism of action, distinct from classical TKI inhibition. Our results demonstrate how MaMTH-DS is a powerful complement to traditional drug screening approaches.
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Affiliation(s)
- Punit Saraon
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Konstantin Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nika Vučković
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adriana Vučetić
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Brigitte Thériault
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jin H Park
- Department of Pharmacology and Cancer Biology Institute, Yale University, New Haven, CT, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Jenny Wang
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Shivanthy Pathmanathan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Babu Joseph
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael F Moran
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Miroslav Samaržija
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. .,Mediterranean Institute for Life Sciences, Split, Croatia.
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15
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Shi R, Radulovich N, Ng C, Liu N, Notsuda H, Cabanero M, Martins-Filho SN, Raghavan V, Li Q, Mer AS, Rosen JC, Li M, Wang YH, Tamblyn L, Pham NA, Haibe-Kains B, Liu G, Moghal N, Tsao MS. Organoid Cultures as Preclinical Models of Non-Small Cell Lung Cancer. Clin Cancer Res 2019; 26:1162-1174. [PMID: 31694835 DOI: 10.1158/1078-0432.ccr-19-1376] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/19/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide. There is an unmet need to develop novel clinically relevant models of NSCLC to accelerate identification of drug targets and our understanding of the disease. EXPERIMENTAL DESIGN Thirty surgically resected NSCLC primary patient tissue and 35 previously established patient-derived xenograft (PDX) models were processed for organoid culture establishment. Organoids were histologically and molecularly characterized by cytology and histology, exome sequencing, and RNA-sequencing analysis. Tumorigenicity was assessed through subcutaneous injection of organoids in NOD/SCID mice. Organoids were subjected to drug testing using EGFR, FGFR, and MEK-targeted therapies. RESULTS We have identified cell culture conditions favoring the establishment of short-term and long-term expansion of NSCLC organoids derived from primary lung patient and PDX tumor tissue. The NSCLC organoids recapitulated the histology of the patient and PDX tumor. They also retained tumorigenicity, as evidenced by cytologic features of malignancy, xenograft formation, preservation of mutations, copy number aberrations, and gene expression profiles between the organoid and matched parental tumor tissue by whole-exome and RNA sequencing. NSCLC organoid models also preserved the sensitivity of the matched parental tumor to targeted therapeutics, and could be used to validate or discover biomarker-drug combinations. CONCLUSIONS Our panel of NSCLC organoids closely recapitulates the genomics and biology of patient tumors, and is a potential platform for drug testing and biomarker validation.
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Affiliation(s)
- Ruoshi Shi
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Christine Ng
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ni Liu
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hirotsugu Notsuda
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Michael Cabanero
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sebastiao N Martins-Filho
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Vibha Raghavan
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Quan Li
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Arvind Singh Mer
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Joshua C Rosen
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ming Li
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Yu-Hui Wang
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Laura Tamblyn
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Geoffrey Liu
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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16
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Ishizawa K, Yamanaka M, Saiki Y, Miyauchi E, Fukushige S, Akaishi T, Asao A, Mimori T, Saito R, Tojo Y, Yamashita R, Abe M, Sakurada A, Pham NA, Li M, Okada Y, Ishii T, Ishii N, Kobayashi S, Nagasaki M, Ichinose M, Tsao MS, Horii A. CD45 +CD326 + Cells are Predictive of Poor Prognosis in Non-Small Cell Lung Cancer Patients. Clin Cancer Res 2019; 25:6756-6763. [PMID: 31383733 DOI: 10.1158/1078-0432.ccr-19-0545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/06/2019] [Accepted: 07/31/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE The epithelial-to-mesenchymal transition, the major process by which some cancer cells convert from an epithelial phenotype to a mesenchymal one, has been suggested to drive chemo-resistance and/or metastasis in patients with cancer. However, only a few studies have demonstrated the presence of CD45/CD326 doubly-positive cells (CD45/CD326 DPC) in cancer. We deployed a combination of cell surface markers to elucidate the phenotypic heterogeneity in non-small cell lung cancer (NSCLC) cells and identified a new subpopulation that is doubly-positive for epithelial and non-epithelial cell-surface markers in both NSCLC cells and patients' malignant pleural effusions. EXPERIMENTAL DESIGN We procured a total of 39 patients' samples, solid fresh lung cancer tissues from 21 patients and malignant pleural effusion samples from 18 others, and used FACS and fluorescence microscopy to check their surface markers. We also examined the EGFR mutations in patients with known acquired EGFR mutations. RESULTS Our data revealed that 0.4% to 17.9% of the solid tumor tissue cells and a higher percentage of malignant pleural effusion cells harbored CD45/CD326 DPC expressing both epithelial and nonepithelial surface markers. We selected 3 EGFR mutation patients and genetically confirmed that the newly identified cell population really originated from cancer cells. We also found that higher proportions of CD45/CD326 DPC are significantly associated with poor prognosis. CONCLUSIONS In conclusion, varying percentages of CD45/CD326 DPC exist in both solid cancer tissue and malignant pleural effusion in patients with NSCLC. This CD45/CD326 doubly-positive subpopulation can be an important key to clinical management of patients with NSCLC.
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Affiliation(s)
- Kota Ishizawa
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan. .,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Education and Support for Regional Medicine, Tohoku University Hospital, Sendai, Japan
| | - Mie Yamanaka
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan
| | - Yuriko Saiki
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan
| | - Eisaku Miyauchi
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinichi Fukushige
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan
| | - Tetsuya Akaishi
- Department of Education and Support for Regional Medicine, Tohoku University Hospital, Sendai, Japan
| | - Atsuko Asao
- Department of Microbiology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ryota Saito
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yutaka Tojo
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Michiaki Abe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Education and Support for Regional Medicine, Tohoku University Hospital, Sendai, Japan
| | - Akira Sakurada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Yoshinori Okada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tadashi Ishii
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Education and Support for Regional Medicine, Tohoku University Hospital, Sendai, Japan
| | - Naoto Ishii
- Department of Microbiology and Immunology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiichi Kobayashi
- Department of Respiratory Medicine, Japanese Red Cross Ishinomaki Hospital, Ishinomaki, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masakazu Ichinose
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ming-Sound Tsao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Akira Horii
- Department of Molecular Pathology, Tohoku University School of Medicine, Sendai, Japan.
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17
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Martins-Filho SN, Weiss J, Pham NA, Cabanero M, Fares AF, Stewart EL, Patel D, McConnell J, Bradbury PA, Sacher AG, Leighl NB, Grindlay A, Allison F, LI M, Yasufuku K, Shepherd FA, Moghal N, Tsao MS, Liu G. Clinical, pathological and genetic predictors of patient-derived xenograft (PDX) engraftment in EGFR-mutated lung adenocarcinoma (LUAD). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.3110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3110 Background: PDX are useful preclinical models to study drug response and resistance. Different specimen types have been used to generate PDX models including histological (surgery and CT-guided biopsy) and cytological preparations (EBUS and pleural effusions). We hypothesize that engraftment is not stochastic and is affected by many factors including sample type and tumor pathological and molecular properties. To improve sample selection and cost-effectiveness of PDX experiments, we investigated clinical, histological and genetic correlates of engraftment in EGFR-mutated LUAD. Methods: We assessed PDX engraftment from 96 surgical resections, 13 CT-guided biopsies, 21 EBUS and 14 pleural effusions of EGFR-mutated LUAD. Sixty-five samples, including 6 engrafted (XG) and 54 non-engrafted (noXG) were evaluated by exome sequencing. Results: Engraftment was successful in 9/96 (9%) surgical resections, 6/13 (46%) CT-guided biopsies, and 0/35 cytological samples. Biopsies taken at time of treatment failure (compared to treatment naive biopsies) correlated with greater engraftment (p=0.007, AUC = 0.68). Multivariable regression analysis of clinical variables at the time of sampling identified advanced (vs early) stage (p = 0.003) and histological (vs cytological) preparations (p < 0.001) as the strongest predictors of engraftment (AUC = 0.79). Among tumor histologic features, solid (vs lepidic, acinar and papillary) pattern was associated with greater engraftment (p < 0.001). Presence of EGFR-T790M (p = 0.004) and TP53 (p = 0.009) mutations were associated with greater engraftment; all XG samples carried TP53 mutations. EGFR-Ex19del (p = 0.076) showed a trend towards engraftment whereas EGFR-L858R (p = 0.086) trended towards non-engraftment. Conclusions: Advanced stage, post-therapy tumors, T790M+ and TP53+ EGFR-mutated LUAD samples obtained for histological processing are more likely to engraft as PDXs. Despite low engraftment rates, these models are useful to study novel therapeutic strategy and elucidation of resistance mechanisms.
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Affiliation(s)
| | - Jessica Weiss
- University Hospital Network (UHN) Biostatistics Department, Toronto, ON, Canada
| | - Nhu-An Pham
- University Health Network, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Devalben Patel
- Princess Margaret Cancer Centre, University Health Network, Ontario Cancer Institute, Toronto, ON, Canada
| | | | | | - Adrian G. Sacher
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Ming LI
- University Health Network, Toronto, ON, Canada
| | | | - Frances A. Shepherd
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Ming Sound Tsao
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
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18
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Yao J, Ly D, Dervovic D, Fang L, Lee JB, Kang H, Wang YH, Pham NA, Pan H, Tsao MS, Zhang L. Human double negative T cells target lung cancer via ligand-dependent mechanisms that can be enhanced by IL-15. J Immunother Cancer 2019; 7:17. [PMID: 30670085 PMCID: PMC6343266 DOI: 10.1186/s40425-019-0507-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/13/2019] [Indexed: 12/25/2022] Open
Abstract
Background The advents of novel immunotherapies have revolutionized the treatment of cancer. Adoptive cellular therapies using chimeric antigen receptor T (CAR-T) cells have achieved remarkable clinical responses in B cell leukemia and lymphoma but the effect on solid tumors including lung cancer is limited. Here we present data on the therapeutic potential of allogeneic CD3+CD4−CD8− double negative T (DNT) cells as a new cellular therapy for the treatment of lung cancer and underlying mechanisms. Methods DNTs were enriched and expanded ex vivo from healthy donors and phenotyped by flow cytometry. Functionally, their cytotoxicity was determined against primary and established non-small-cell lung cancer (NSCLC) cell lines in vitro or through in vivo adoptive transfer into xenograft models. Mechanistic analysis was performed using blocking antibodies against various cell surface and soluble markers. Furthermore, the role of IL-15 on DNT function was determined. Results We demonstrated that ex vivo expanded DNTs can effectively lyse various human NSCLC cells in vitro and inhibit tumor growth in xenograft models. Expanded DNTs have a cytotoxic phenotype, as they express NKp30, NKG2D, DNAM-1, membrane TRAIL (mTRAIL), perforin and granzyme B, and secrete IFNγ and soluble TRAIL (sTRAIL). DNT-mediated cytotoxicity was dependent on a combination of tumor-expressed ligands for NKG2D, DNAM-1, NKp30 and/or receptors for TRAIL, which differ among different NSCLC cell lines. Furthermore, stimulation of DNTs with IL-15 increased expression of effector molecules on DNTs, their TRAIL production and cytotoxicity against NSCLC in vitro and in vivo. Conclusion Healthy donor-derived DNTs can target NSCLC in vitro and in vivo. DNTs recognize tumors via innate receptors which can be up-regulated by IL-15. DNTs have the potential to be used as a novel adoptive cell therapy for lung cancer either alone or in combination with IL-15. Electronic supplementary material The online version of this article (10.1186/s40425-019-0507-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junlin Yao
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Present address: Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Dalam Ly
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Dzana Dervovic
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Present address: Department of Systems Biology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Linan Fang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jong Bok Lee
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Hyeonjeong Kang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Yu-Hui Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hongming Pan
- Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Li Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada. .,Department of Immunology, University of Toronto, Toronto, Ontario, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. .,University Health Network, Princess Margaret Cancer Research Tower, 101 College St. Rm 2-807, Toronto, Ontario, M5G 1L7, Canada.
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19
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Lheureux S, Tinker A, Clarke B, Ghatage P, Welch S, Weberpals JI, Dhani NC, Butler MO, Tonkin K, Tan Q, Tan DSP, Brooks K, Ramsahai J, Wang L, Pham NA, Shaw PA, Tsao MS, Garg S, Stockley T, Oza AM. A Clinical and Molecular Phase II Trial of Oral ENMD-2076 in Ovarian Clear Cell Carcinoma (OCCC): A Study of the Princess Margaret Phase II Consortium. Clin Cancer Res 2018; 24:6168-6174. [PMID: 30108107 DOI: 10.1158/1078-0432.ccr-18-1244] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/05/2018] [Accepted: 08/09/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with recurrent ovarian clear cell carcinoma (OCCC) have limited effective options due to chemoresistance. A phase II study was designed to assess the activity of ENMD-2076, an oral multitarget kinase selective against Aurora A and VEGFR. PATIENTS AND METHODS This multicenter phase II study included patients with recurrent OCCC who received prior platinum-based chemotherapy. Primary endpoints were objective response and 6-month progression-free survival (PFS) rates. Correlative analyses include ARID1A and PTEN expression by IHC and gene sequencing with a targeted custom capture next-generation sequencing panel. RESULTS Forty patients were enrolled with a median age of 54, of which 38 patients were evaluable. ENMD-2076 was well tolerated with main related grade 3 toxicities being hypertension (28%), proteinuria (10%), and diarrhea (10%). Best response was partial response for 3 patients (1 unconfirmed) and stable disease for 26 patients. The overall 6-month PFS rate was 22% and differed according to ARID1A expression (ARIDIA- vs. ARID1A+; 33% vs. 12%, P = 0.023). PTEN-positive expression was observed in 20 of 36 patients, and there was no correlation with outcome. Median PFS in patients with PI3KCA wild-type versus PI3KCA-mutated group was 5 versus 3.7 months (P = 0.049). Molecular profiling showed variants in PI3KCA (27%), ARID1A (26%), and TP53 (7%). The patient with the longest treatment duration (22 months) was PTEN wild-type, diploid PTEN with putative biallelic inactivation of ARID1A. CONCLUSIONS Single-agent ENMD-2076 did not meet the preset bar for efficacy. Loss of ARID1A correlated with better PFS on ENMD-2076 and warrants further investigation as a potential predictive biomarker.
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Affiliation(s)
- Stephanie Lheureux
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - Anna Tinker
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Blaise Clarke
- University Health Network, Department of Pathology and Laboratory Medicine, Toronto, Canada
| | - Prafull Ghatage
- Arnie Charbonneau Cancer Institute, Calgary, Alberta, Canada
| | - Stephen Welch
- London Regional Cancer Program, London, Ontario, Canada
| | | | - Neesha C Dhani
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - Marcus O Butler
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - Katia Tonkin
- Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Qian Tan
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - David S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Kelly Brooks
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - Janelle Ramsahai
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada
| | - Lisa Wang
- Princess Margaret Cancer Centre, Department of Biostatistics, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Department of Pathology and Laboratory Medicine, Toronto, Canada
| | - Patricia A Shaw
- University Health Network, Department of Pathology and Laboratory Medicine, Toronto, Canada
| | - Ming S Tsao
- University Health Network, Department of Pathology and Laboratory Medicine, Toronto, Canada
| | - Swati Garg
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Tracey Stockley
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, The University of Toronto, Ontario, Canada.,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Amit M Oza
- Princess Margaret Cancer Centre, Division of Medical Oncology and Hematology, Toronto, Ontario, Canada.
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20
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Shi R, Li M, Raghavan V, Tam S, Cabanero M, Pham NA, Shepherd FA, Moghal N, Tsao MS. Targeting the CDK4/6-Rb Pathway Enhances Response to PI3K Inhibition in PIK3CA-Mutant Lung Squamous Cell Carcinoma. Clin Cancer Res 2018; 24:5990-6000. [PMID: 30093452 DOI: 10.1158/1078-0432.ccr-18-0717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/18/2018] [Accepted: 07/30/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Lung squamous cell carcinoma (LUSC) is a major subtype of non-small cell lung cancer characterized by multiple genetic alterations, particularly PI3K pathway alterations which have been identified in over 50% of LUSC cases. Despite being an attractive target, single-agent PI3K inhibitors have demonstrated modest response in LUSC. Thus, novel combination therapies targeting LUSC are needed. EXPERIMENTAL DESIGN PI3K inhibitors alone and in combination with CDK4/6 inhibitors were evaluated in previously established LUSC patient-derived xenografts (PDX) using an in vivo screening method. Screening results were validated with in vivo expansion to 5 to 8 mice per arm. Pharmacodynamics studies were performed to confirm targeted inhibition of compounds. RESULTS Consistent with results from The Cancer Genome Atlas analysis of LUSC, genomic profiling of our large cohort of LUSC PDX models identified PI3K pathway alterations in over 50% of the models. In vivo screening using PI3K inhibitors in 12 of these models identified PIK3CA mutation as a predictive biomarker of response (<20% tumor growth compared with baseline/vehicle). Combined inhibition of PI3K and CDK4/6 in models with PIK3CA mutation resulted in greater antitumor effects compared with either monotherapy alone. In addition, the combination of the two drugs achieved targeted inhibition of the PI3K and cell-cycle pathways. CONCLUSIONS PIK3CA mutations predict response to PI3K inhibitors in LUSC. Combined PI3K and CDK4/6 inhibition enhances response to either single agents alone. Our findings provide a rationale for clinical testing of combined PI3K and CDK4/6 inhibitors in PIK3CA-mutant LUSC.
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Affiliation(s)
- Ruoshi Shi
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ming Li
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Vibha Raghavan
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Shirley Tam
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Michael Cabanero
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Frances A Shepherd
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Oncology and Hematology, University of Toronto, Toronto, Ontario, Canada
| | - Nadeem Moghal
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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21
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Lheureux S, Butler MO, Clarke B, Cristea MC, Martin LP, Tonkin K, Fleming GF, Tinker AV, Hirte HW, Tsoref D, Mackay H, Dhani NC, Ghatage P, Weberpals J, Welch S, Pham NA, Motta V, Sotov V, Wang L, Karakasis K, Udagani S, Kamel-Reid S, Streicher HZ, Shaw P, Oza AM. Association of Ipilimumab With Safety and Antitumor Activity in Women With Metastatic or Recurrent Human Papillomavirus-Related Cervical Carcinoma. JAMA Oncol 2018; 4:e173776. [PMID: 29145543 DOI: 10.1001/jamaoncol.2017.3776] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Importance Based on evidence of human papillomavirus (HPV)-induced immune evasion, immunotherapy may be an attractive strategy in cervical cancer. Ipilimumab is a fully humanized monoclonal antibody that blocks cytotoxic T-lymphocyte antigen-4 (CTLA-4), which acts to downregulate the T-cell immune response. Objective To assess the safety and antitumor activity of ipilimumab in recurrent cervical cancer. Design, Setting, and Participants A multicenter trial was designed for patients with metastatic cervical cancer (squamous cell carcinoma or adenocarcinoma) with measurable disease and progression after at least 1 line of platinum chemotherapy. A run-in safety cohort using ipilimumab, 3 mg/kg, every 21 days for 4 cycles in 6 patients was followed by a phase II cohort of ipilimumab, 10 mg/kg, every 21 days for 4 cycles and then 4 cycles of maintenance therapy every 12 weeks for patients demonstrating radiologic response or stabilization. Immune correlative studies were performed on peripheral blood before and after therapy on archival tissue and fresh tumor obtained prior to registration and 7 days after cycle 2. The study was conducted from December 3, 2012, to September 15, 2014. The data were analyzed from April 2016 to June 2016 and in July 2017. Main Outcomes and Measures The primary end points were safety and objective response rate. Immune analyses were performed on blood and tumor tissue. Results A total of 42 women (median age, 49 years; range, 23-78 years) were enrolled (29 [69%] squamous cell cervical cancer and 13 [31%] adenocarcinoma; 37 [93%] of 40 patients with tissue available for analysis had HPV-positive confirmation; there was no archival tissue for 2 women). Grade 3 toxic effects included diarrhea in 4 patients, 3 of whom had colitis. Of 34 patients evaluated for best response (Response Evaluation Criteria in Solid Tumors, version 1.1), 1 patient had partial response and 10 had stable disease. The median progression-free survival and overall survival were 2.5 months (95% CI, 2.1-3.2 months) and 8.5 months (95% CI, 3.6-not reached; 1 patient was still alive), respectively. Intratumoral pretreatment CD3, CD4, CD8, FoxP3, indoleamine 2,3-dioxygenase, and programmed cell death ligand 1 (PD-L1) expression was not predictive of benefit and did not significantly change with treatment. Multicolor flow cytometry on peripheral lymphocytes revealed a treatment-dependent increase of inducible T-cell costimulator, human leukocyte antigen-antigen D related, and PD-1 during initial treatment, which returned to baseline during maintenance. Conclusions and Relevance Ipilimumab was tolerable in this population but did not show significant single-agent activity. Immune changes were induced by anti-CTLA-4 therapy but did not correlate with clinical activity. Changes in these markers may guide further treatment strategies.
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Affiliation(s)
- Stephanie Lheureux
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Marcus O Butler
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Blood Immune Monitoring Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Blaise Clarke
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Lainie P Martin
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pensylvania
| | - Katia Tonkin
- Department of Medical Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Gini F Fleming
- Department of Medical Oncology, University of Chicago Medical Center, Chicago, Illinois
| | - Anna V Tinker
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hal W Hirte
- Department of Medical Oncology, Juravinski Cancer Center, Hamilton, Ontario, Canada
| | - Daliah Tsoref
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Helen Mackay
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Neesha C Dhani
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Prafull Ghatage
- Department of Gynecology Oncology, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Johanne Weberpals
- Division of Gynecology Oncology, Ottawa Hospital, Ottawa, Ontario, Canada
| | - Stephen Welch
- Department of Medical Oncology, London Hospital, London, Ontario, Canada
| | - Nhu-An Pham
- Department of Laboratory Medicine and Pathobiology, Drug Development Program, Toronto, Ontario, Canada
| | - Vinicius Motta
- Blood Immune Monitoring Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Valentin Sotov
- Blood Immune Monitoring Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Lisa Wang
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Katherine Karakasis
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Smitha Udagani
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Suzanne Kamel-Reid
- Cancer Genomics Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Howard Z Streicher
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | - Patricia Shaw
- Blood Immune Monitoring Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Amit M Oza
- Drug Development Program, Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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22
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Brana I, Pham NA, Kim L, Sakashita S, Li M, Ng C, Wang Y, Loparco P, Sierra R, Wang L, Clarke BA, Neel BG, Siu LL, Tsao MS. Novel combinations of PI3K-mTOR inhibitors with dacomitinib or chemotherapy in PTEN-deficient patient-derived tumor xenografts. Oncotarget 2017; 8:84659-84670. [PMID: 29156674 PMCID: PMC5689564 DOI: 10.18632/oncotarget.19109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022] Open
Abstract
PTEN inactivation occurs commonly in human cancers and putatively activates the PI3K/AKT/ mTOR pathway. Activation of this pathway has been involved in resistance to chemotherapy or anti-EGFR/HER2 therapies. We evaluated the combination of PI3K-mTOR inhibitors with chemotherapy or the pan-HER inhibitor dacomitinib in PTEN-deficient patient-derived tumor xenografts (PDX). Three PDXs were selected for their lack of PTEN expression by immunohistochemistry: a triple-negative breast cancer (TNBC), a KRAS G12R low-grade serous ovarian cancer (LGSOC), and KRAS G12C and TP53 R181P lung adenocarcinoma (LADC). Two dual PI3K-mTOR inhibitors were evaluated-PF-04691502 and PF-05212384-in combination with cisplatin, paclitaxel, or dacomitinib. The addition of PI3K-mTOR inhibitors to cisplatin or paclitaxel increased the activity of chemotherapy in the TNBC and LGSOC models; whereas no added activity was observed in the LADC model. Pharmacodynamic modulation of pS6 and pAKT was observed in the group treated with PI3K-mTOR inhibitor. Our research suggests that the addition of a PI3K-mTOR inhibitor may enhance tumor growth inhibition when compared to chemotherapy alone in certain PTEN-deficient PDXs. However, this benefit was absent in the KRAS and TP53 mutant LADC model. The role of PTEN deficiency in the antitumor activity of these combinations should be further investigated in the clinic.
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Affiliation(s)
- Irene Brana
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Christine Ng
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loparco
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Rafael Sierra
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L Siu
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
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23
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Stewart E, Cabanero M, Pham NA, Shen SY, Li T, Bruce J, Li M, Leighl N, Shepherd F, Pugh T, De Carvalho D, Lupien M, Liu G, Tsao M. P3.02b-028 Characterizing Residual Erlotinib-Tolerant Population Using EGFR-Mutated NSCLC Primary Derived Xenografts: The Last Holdouts. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.1695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Shi R, Li M, Cabanero M, Pham NA, Ng C, Shepherd F, Moghal N, Tsao M. P2.03b-071 Therapeutic Targeting of the Phosphatidylinositol-3 Kinase Pathway in Lung Squamous Cell Carcinoma. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.1352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Cabanero M, Pham NA, Stewart E, Patel D, Mcconnell J, Grindlay A, Allison F, Wang Y, Li M, Shepherd F, Tsao M, Yasufuku K, Liu G. P2.03b-077 EGFR/ALK+ Patient-Derived Xenografts from Advanced NSCLC for TKI Drug Selection & Resistance Development: The REAL-PDX Study. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.1359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Shi R, Radulovich N, Ng C, Akshinthala D, Cabanero M, Li M, Pham NA, Tsao M. P2.03b-070 Establishment of Organoid Cell Lines from Lung Squamous Cell Carcinoma. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.1351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Raghavan V, Tam S, Pham NA, Li M, Shepherd F, Liu G, Tsao M. MA17.06 Landscape of Somatic Mutations Involving Lung Cancer Associated Genes in Non-Small Cell Lung Cancer (NSCLC) Patient-Derived Xenografts. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Tam S, Pham NA, Sakashita S, Kaufman E, Pintilie M, Liu N, Liu G, Shepherd F, Tsao M. P1.05-006 Identification of miRNAs and mRNAs Associated with Metastasis in Early-Stage Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Wang D, Pham NA, Tong J, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei Y, To C, Trinh QM, Starmans MHW, Chan-Seng-Yue MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson JD, Muthuswamy L, Moran MF, Tsao MS. Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors. Int J Cancer 2016; 140:662-673. [PMID: 27750381 DOI: 10.1002/ijc.30472] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
Abstract
Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were in NOD SCID mice. A subset of matched patient and PDX tumors and non-neoplastic lung tissues were profiled by whole exome sequencing, single nucleotide polymorphism (SNP) and methylation arrays, and phosphotyrosine (pY)-proteome by mass spectrometry. The data were compared to published NSCLC datasets of NSCLC primary and cell lines. 127 stable PDXs were established from 441 lung carcinomas representing all major histological subtypes: 52 adenocarcinomas, 62 squamous cell carcinomas, one adeno-squamous carcinoma, five sarcomatoid carcinomas, five large cell neuroendocrine carcinomas, and two small cell lung cancers. Somatic mutations, gene copy number and expression profiles, and pY-proteome landscape of 36 PDXs showed greater similarity with patient tumors than with established cell lines. Novel somatic mutations on cancer associated genes were identified but only in PDXs, likely due to selective clonal growth in the PDXs that allows detection of these low allelic frequency mutations. The results provide the strongest evidence yet that PDXs established from lung cancers closely mimic the characteristics of patient primary tumors.
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Affiliation(s)
- Dennis Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK, S1O 2HQ
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jiefei Tong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ghassan Allo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Naoki Yanagawa
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yuhong Wei
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Christine To
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | | | | | - Dianne Chadwick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lei Li
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sharon Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Dan Strumpf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul Taylor
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Lakshmi Muthuswamy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael F Moran
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada.,Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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30
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Shi R, Varella-Garcia M, Li M, Ludkovski O, Danesh A, Ng C, Pham NA, Pugh T, Shepherd FA, Tsao MS. An Anaplastic Lymphoma Kinase Immunohistochemistry-Negative but Fluorescence In Situ Hybridization-Positive Lung Adenocarcinoma Is Resistant to Crizotinib. J Thorac Oncol 2016; 11:2248-2252. [PMID: 27613526 DOI: 10.1016/j.jtho.2016.08.139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Oncogenic fusion of anaplastic lymphoma kinase (ALK) with echinoderm microtubule associated protein like 4 protein or other partner genes occurs in 3% to 6% of lung adenocarcinomas. Although fluorescence in situ hybridization (FISH) is the accepted standard for detecting anaplastic lymphoma receptor tyrosine kinase gene (ALK) gene rearrangement that gives rise to new fusion genes, not all ALK FISH-positive patients respond to ALK inhibitor therapies. We report here an ALK FISH-positive patient-derived xenograft (PDX) that was nonresponsive to crizotinib therapy. METHODS The PDX patient human lung cancer (PHLC402) was established in NOD/SCID mice from a patient with resected pT4N1M0 lung adenocarcinoma. ALK gene status was investigated using the standard FISH break-apart assay, reverse-transcriptase quantitative polymerase chain reaction, RNA sequencing and immunohistochemical assay using the 5A4 antibody. PHLC402 was treated with crizotinib (50 mg/kg) by daily oral gavage. RESULTS ALK FISH assay was positive in both the primary patient tumor and PDX, which were negative for ALK protein expression by immunohistochemical analysis. ALK fusion product was not detected by RNA sequencing and reverse-transcriptase quantitative polymerase chain reaction comparing the 5' and 3' ALK transcript levels. Crizotinib treatment of PHLC402 grown in mice resulted in no tumor response. CONCLUSION ALK protein expression may be necessary for ALK FISH-positive lung cancer to be responsive to ALK inhibitor therapy.
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Affiliation(s)
- Ruoshi Shi
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ming Li
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga Ludkovski
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Christine Ng
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Trevor Pugh
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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31
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Radulovich N, Ibrahimov E, Holt C, Raghavan V, Zhao T, Denroch R, Pham NA, Gallinger S, Pintilie M, Stein L, McPherson J, Muthuswamy L, Tsao MS. Abstract B31: Establishment and molecular characterization of patient-derived tumor xenografts from resected tumors or ascites fluids of patients with pancreatic/ampullary/bile duct carcinomas. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic adenocarcinoma (PDAC) is the 4th most common cause of cancer deaths in North America, for both men and women with a 5-year survival rate of less than 5%. The poor prognosis rate is attributed to late presentation of the disease and the lack of effective treatment options. Large-scale genome sequencing efforts on PDAC tumors show evidence of high mutational burden and revealed a number of mutated genes affecting multiple oncogenic pathways. While there are significant endeavors in developing specific targeted agents against “driver” mutations, tumor diversity within and across patient population remains a key factor affecting therapeutic efficacy. In this context, the availability of large cohorts of genomically characterized patient-derived xenograft (PDX) tumor models may help to accelerate the development of novel therapies against this lethal cancer.
PDX models provide a renewable resource to maintain a patient's tumor ex vivo for pre-clinical or co-clinical studies. As part of The International Cancer Genome Consortium (ICGC), our laboratory has established 93 PDX models in non-obese diabetic and severe combined immune-deficient (NOD-SCID) mice from Whipple resection specimens. These tumors represent a heterogeneous group of neoplasms arising from the head, body and tail of pancreas, bile duct and Ampulla of Vater. All implantations including in the subcutaneous pocket at the flank or at the orthotopic pancreas site, were performed using 4-8 weeks old NOD-SCID mice. Successful growth and serial transplant to multiple mouse generations were observed in in 74 PDX models of the 93 implanted PDAC specimens, achieving an 80% engraftment rate, one of the highest reported in any type of cancer. Histology fidelity was preserved in the PDX models compared to corresponding patient tumors. Failed implants were due to specimens characterized by borderline malignancy and absence of tumor cells.
Whole exome sequencing and copy number aberration profiling was completed for 61 PDXs and blood from the matched patients. Cancer-specific single nucleotide variation (SNV) load varied widely from 38 to 305 in PDXs. The most recurrent activating mutation was observed in KRAS with 77% of PDX models showing alterations at codon G12 (65%), G13 (8%) and Q61 (4%); in addition, 26% PDXs had a copy number gain in KRAS. Molecular comparisons of the 21 PDX models and their matched patient tumors showed that alternate allele frequency of KRAS mutation from exome sequencing of primary tumor is a strong indicator of the tumor cellularity; a higher tumor cellularity results in a larger overlap of cancer specific alterations between xenografts and corresponding patient tumors.
We have demonstrated a successful establishment of PDX models that represent genomic architecture of major subclonal populations of patient PDAC primary tumors.
Citation Format: Nikolina Radulovich, Emin Ibrahimov, Carson Holt, Vibha Raghavan, Tracy Zhao, Rob Denroch, Nhu-An Pham, Steve Gallinger, Melania Pintilie, Lincoln Stein, John McPherson, Lakshmi Muthuswamy, Ming Sound Tsao. Establishment and molecular characterization of patient-derived tumor xenografts from resected tumors or ascites fluids of patients with pancreatic/ampullary/bile duct carcinomas. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B31.
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Affiliation(s)
| | | | | | | | - Tracy Zhao
- 3Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Rob Denroch
- 3Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Nhu-An Pham
- 1University Health Network, Toronto, ON, Canada,
| | | | | | - Lincoln Stein
- 3Ontario Institute for Cancer Research, Toronto, ON, Canada,
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Pham NA, Wang D, Tong J, Zhu CQ, Li L, Zhang W, Shi R, Sakashita S, Pintilie M, Moran MF, Liu G, Tsao MS. Abstract B32: Fidelity of genomic and proteomic features of patient-derived xenografts of lung cancers. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The establishment of valid lung carcinoma preclinical models for testing new cancer therapies is necessary, as existing cell lines and mouse models may not recapitulate the full spectrum of heterogeneity of patient tumors. Studies suggest lung cancer patient-derived xenograft (PDX) models recapitulate well gene copy number variation, gene expression profiles, and metabolic states of corresponding patient tumors. However, an understanding of mechanisms linking cancer-associated genome, transcriptome, and proteome alterations with driver mutations and dysregulated signal transduction networks in primary and PDX models is lacking. We report a large (>150) resource of lung cancer PDX models, derived from surgically resected tumors, and endobronchial ultrasound-guided (EBUS) and CT-guided biopsies. Tumor specimens were grown and serially passaged in the subcutaneous pocket at the flanks of NSG mice (NOD SCID gamma) at initial implant, and following passages in NOD SCID (non-obese diabetic severe combined immunodeficiency) mice. Among 127 established PDX models from 441 surgically derived tumor specimens, all major histological subtypes were included: 52 adenocarcinomas, 62 squamous cell carcinomas, 1 adeno-squamous cell carcinomas, 5 sarcomatoid carcinomas, 5 large cell neuroendocrine carcinomas, and 2 small cell lung cancers. Over 100 PDX models have been profiled by next-generation exome sequencing (SureSelect Human 50Mbp kit), and array-based assays for copy number variant (HumanOmni 2.5-Quad BeadChip), DNA methylation (Infinium HumanMethylation450 BeadChip) and mRNA (DASL HumanHT-12 v4 BeadChip) profiles. Smaller subsets of PDXs have been characterized by mass spectrometry (MS)-based comprehensive proteome and protein-phosphotyrosine characterization.
Genome/transcriptome/proteome profiles of 36 non-small cell lung carcinoma (NSCLC) PDX models correlated with patient primary tumors but to a much lesser extent with established NSCLC cell lines. A number of PDX models have genetic abnormalities linked to targeted therapies including mutations in EGFR (6), PIK3CA (13), and KRAS (21), and amplifications in FGFR1 (7) and CDK4 (6). This study provides the most solid evidence as yet that PDXs established from lung cancers mimic closely the genomic and proteomic characteristics of patient primary tumors and retain driver genetic abnormalities.
Citation Format: Nhu-An Pham, Dennis Wang, Jiefei Tong, Chang-Qi Zhu, Lei Li, Wen Zhang, Ruoshi Shi, Shingo Sakashita, Melania Pintilie, Michael F. Moran, Geoffrey Liu, Ming-Sound Tsao. Fidelity of genomic and proteomic features of patient-derived xenografts of lung cancers. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B32.
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Affiliation(s)
- Nhu-An Pham
- 1University Health Network, Toronto, ON, Canada,
| | - Dennis Wang
- 1University Health Network, Toronto, ON, Canada,
| | - Jiefei Tong
- 2Hospital for Sick Children, Toronto, ON, Canada
| | - Chang-Qi Zhu
- 1University Health Network, Toronto, ON, Canada,
| | - Lei Li
- 2Hospital for Sick Children, Toronto, ON, Canada
| | - Wen Zhang
- 2Hospital for Sick Children, Toronto, ON, Canada
| | - Ruoshi Shi
- 1University Health Network, Toronto, ON, Canada,
| | | | | | | | - Geoffrey Liu
- 1University Health Network, Toronto, ON, Canada,
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Martin P, Stewart E, Pham NA, Mascaux C, Panchal D, Li M, Kim L, Sakashita S, Wang D, Sykes J, Friess T, Shepherd FA, Liu G, Tsao MS. Cetuximab Inhibits T790M-Mediated Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor in a Lung Adenocarcinoma Patient-Derived Xenograft Mouse Model. Clin Lung Cancer 2016; 17:375-383.e2. [PMID: 26926157 DOI: 10.1016/j.cllc.2016.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 01/28/2023]
Abstract
BACKGROUND The epidermal growth factor receptor (EGFR) kinase domain T790M (amino acid substitution at position 790 in EGFR from threonine [T] to methionine [M]) mutation in non-small-cell lung cancer (NSCLC) results in resistance to EGFR tyrosine kinase inhibitors (TKIs). We used a patient-derived tumor xenograft (PDX) model containing an EGFR exon 19 deletion/T790M mutation to assess response to the EGFR-directed antibody cetuximab. Changes in the EGFR signaling pathway and ligand expression after treatment were investigated. METHODS PDX were randomized into control and treatment arms. Pharmacodynamic studies were performed at 2 and 24 hours and at 4 days after a single administration of cetuximab, erlotinib, or dacomitinib. Changes in the EGFR signaling pathway were assessed using Western blot analysis, and baseline mRNA expression of EGFR ligands using microarray analysis. Relative changes after treatment were assessed using quantitative polymerase chain reaction. RESULTS The xenograft showed a dramatic response to cetuximab. A complete reduction of total EGFR and phosphorylated EGFR occurred after cetuximab treatment. The PDX had increased baseline levels of heparin-binding epidermal growth factor-like growth factor (HB-EGF) compared with other PDX models with or without EGFR mutations. Amphiregulin was significantly reduced 2 hours after treatment with cetuximab. Compared with control mice, cetuximab- and EGFR-TKI-treated mice had significantly reduced HB-EGF gene expression at 2 hours, however, by day 4 the level of HB-EGF expression was higher. The effect of cetuximab compared with EGFR TKI on HB-EGF gene expression levels differed significantly at 2 and 24 hours but not at 4 days. CONCLUSION We showed a dramatic tumor response with cetuximab in an exon 19 deletion/T790M EGFR mutant lung adenocarcinoma PDX model, which suggests a role for the autocrine feedback loop in the mutant EGFR signaling pathway. Further investigation using cetuximab in NSCLC with T790M mutation is warranted.
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Affiliation(s)
- Petra Martin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erin Stewart
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Celine Mascaux
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Devang Panchal
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jenna Sykes
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Thomas Friess
- Department of Pharmacology, Roche Diagnostics GmbH, Mannheim, Germany
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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Nakajima T, Geddie W, Anayama T, Ko HM, da Cunha Santos G, Boerner S, Wang T, Wang YH, Li M, Pham NA, Tsao MS, Yasufuku K. Patient-derived tumor xenograft models established from samples obtained by endobronchial ultrasound-guided transbronchial needle aspiration. Lung Cancer 2015; 89:110-4. [DOI: 10.1016/j.lungcan.2015.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 05/06/2015] [Accepted: 05/19/2015] [Indexed: 12/25/2022]
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Zhang W, Taylor P, Li L, Wei Y, Tong J, Ignatchenko V, Pham NA, Kislinger T, Tsao MS, Moran M. Abstract 1822: Proteome signatures distinguish lung cancer subtypes, define metabolism states, and have prognostic impact. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung cancer is one of the most common cancers worldwide, and is the number one cause of cancer death in both men and women. Non-small cell lung cancer (NSCLC) accounts for 85% of lung cancers and is subdivided into two major histological subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). There is an unmet need to better understand and stratify NSCLC according to distinctive molecular features that may help develop diagnostic and therapeutic strategies to improve patient outcomes. The proteome is expected to have a pronounced and direct effect on cancer phenotypes. Therefore, proteomic approaches hold promise as superior methods to characterize cancers, with the ultimate goal to translate research results into clinical utilities. Mass spectrometry (MS)-based quantitative comprehensive proteome analysis resolved the proteomes of human lung ADC and SCC primary tumor-derived xenografts. A multi-protein signature able to distinguish between ADC and SCC was identified and validated in an independent cohort of samples. The signature is comprised of various components of the epithelial barrier and metabolism enzymes. Signatures composed of metabolism proteins were found to be highly recapitulated between primary and matched xenograft tumors, and when extrapolated to DNA alterations in the encoding genes, to have prognostic impact for overall patient survival. The ability of NSCLC primary tumors to engraft in severely immune deficient mice is an independent predictor of shorter disease-free survival in early-stage NSCLC patients. Therefore, we sought to identify proteome signatures of engraftment, which would then be tested for prognostic impact. The proteomes of a series of >50 NSCLC primary tumors that engrafted or not were quantitatively compared by using the so-called super-SILAC method, in which a mixture of metabolically-labeled, stable-isotope-encoded NSCLC-derived cell lines were used as an internal standard. ADC and SCC tumors were analyzed, and a signature of proteins including enzymes involved in central carbon metabolism were identified as differentially expressed between engrafting and non-engrafting tumors. These results highlight the significance of metabolic remodeling as a feature that might be a determinant of more aggressive cancer phenotypes. These results support the further development of proteome signatures to diagnose, stratify, and precisely treat NSCLC.
Citation Format: Wen Zhang, Paul Taylor, Lei Li, Yuhong Wei, Jiefei Tong, Vladimir Ignatchenko, Nhu-An Pham, Thomas Kislinger, Ming-sound Tsao, Michael Moran. Proteome signatures distinguish lung cancer subtypes, define metabolism states, and have prognostic impact. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1822. doi:10.1158/1538-7445.AM2015-1822
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Affiliation(s)
- Wen Zhang
- 1University of Toronto, Toronto, Ontario, Canada
| | - Paul Taylor
- 2The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Lei Li
- 2The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Yuhong Wei
- 2The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jiefei Tong
- 2The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | | | - Nhu-An Pham
- 3Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Moran MF, Li L, Wei Y, Taylor P, To C, Tong J, Ignatchenko V, Pintilie M, Pham NA, Zhang W, Muthuswamy L, Shepherd FA, Kislinger T, Tsao MS. Abstract SY33-04: Integrated omic analysis of lung cancer reveals metabolism-proteome signatures with prognostic impact. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-sy33-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer results from processes prone to selective pressure and dysregulation acting along the sequence-to- phenotype continuum DNA→RNA→Protein→Disease. An Omics Array integrating DNA gene copy number, mRNA transcriptome, and quantified proteome was assembled into a genetic map representing non-small cell lung carcinoma (NSCLC). Data were collected from patient-matched normal lung, primary tumors, and patient tumor-derived xenograft (PDX) tumors. Dysregulated proteins not previously implicated as cancer drivers were found encoded throughout the genome including but not limited to regions of recurrent DNA amplification/deletion in NSCLC. Unsupervised clustering revealed signatures comprising metabolism proteins particularly highly recapitulated between matched primary and PDX tumors, and which distinguished between the major NSCLC histological subtypes adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Interrogation of The Cancer Genome Atlas (TCGA) revealed sizeable cohorts of NSCLC patients with DNA alterations in genes encoding the metabolism proteome signatures, and accompanied by differences in survival. Similar to the proteome signatures from which they were extrapolated, the gene mutation signatures with prognostic impact discriminated between the lung ADC and SCC subtypes. Serine hydroxymethyltransferase 2 (SHMT2), a key enzyme in serine/glycine and folate- dependent one-carbon metabolism, is upregulated in the proteomes of NSCLC primary and PDX tumours, and is implicated as a driver of recurrent chromosome 12q14.1 amplification in NSCLC. SHMT2, along with other enzymes implicated as anti-folate targets, is also part of a metabolism proteome signature associated with poor outcome in lung ADC. The interrogation of cancer genomes and proteomes for alterations that are related products of selective pressures driving the cancer phenotype may be a general approach to uncover and group together cryptic, polygenic cancer drivers, which might represent new anti-cancer therapeutic targets.
Citation Format: Michael F. Moran, Lei Li, Yuhong Wei, Paul Taylor, Christine To, Jiefei Tong, Vladimir Ignatchenko, Melania Pintilie, Nhu-An Pham, Wen Zhang, Lakshmi Muthuswamy, Frances A. Shepherd, Thomas Kislinger, Ming S. Tsao. Integrated omic analysis of lung cancer reveals metabolism-proteome signatures with prognostic impact. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY33-04. doi:10.1158/1538-7445.AM2015-SY33-04
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Affiliation(s)
| | - Lei Li
- 1Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yuhong Wei
- 1Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul Taylor
- 1Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine To
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jiefei Tong
- 1Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Nhu-An Pham
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Wen Zhang
- 3University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Ming S. Tsao
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Stewart EL, Mascaux C, Pham NA, Sakashita S, Sykes J, Kim L, Yanagawa N, Allo G, Ishizawa K, Wang D, Zhu CQ, Li M, Ng C, Liu N, Pintilie M, Martin P, John T, Jurisica I, Leighl NB, Neel BG, Waddell TK, Shepherd FA, Liu G, Tsao MS. Clinical Utility of Patient-Derived Xenografts to Determine Biomarkers of Prognosis and Map Resistance Pathways in EGFR-Mutant Lung Adenocarcinoma. J Clin Oncol 2015; 33:2472-80. [PMID: 26124487 DOI: 10.1200/jco.2014.60.1492] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Although epidermal growth factor receptor (EGFR) -mutated adenocarcinomas initially have high response rates to EGFR tyrosine kinase inhibitors (TKIs), most patients eventually develop resistance. Patient-derived xenografts (PDXs) are considered preferred preclinical models to study the biology of patient tumors. EGFR-mutant PDX models may be valuable tools to study the biology of these tumors and to elucidate mechanisms of resistance to EGFR-targeted therapies. METHODS Surgically resected early-stage non-small-cell lung carcinoma (NSCLC) tumors were implanted into nonobese diabetic severe combined immune deficient (NOD-SCID) mice. EGFR TKI treatment was initiated at tumor volumes of 150 μL. Gene expression analysis was performed using a microarray platform. RESULTS Of 33 lung adenocarcinomas with EGFR activating mutations, only 6 (18%) engrafted and could be propagated beyond passage one. Engraftment was associated with upregulation of genes involved in mitotic checkpoint and cell proliferation. A differentially expressed gene set between engrafting and nonengrafting patients could identify patients harboring EGFR-mutant tumor with significantly different prognoses in The Cancer Genome Atlas Lung Adenocarcinoma datasets. The PDXs included models with variable sensitivity to first- and second-generation EGFR TKIs and the monoclonal antibody cetuximab. All EGFR-mutant NSCLC PDXs studied closely recapitulated their corresponding patient tumor phenotype and clinical course, including response pattern to EGFR TKIs. CONCLUSION PDX models closely recapitulate primary tumor biology and clinical outcome. They may serve as important laboratory models to investigate mechanisms of resistance to targeted therapies, and for preclinical testing of novel treatment strategies.
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Affiliation(s)
- Erin L Stewart
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Celine Mascaux
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Nhu-An Pham
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Shingo Sakashita
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Jenna Sykes
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Lucia Kim
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Naoki Yanagawa
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ghassan Allo
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Kota Ishizawa
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Dennis Wang
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Chang-Qi Zhu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ming Li
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Christine Ng
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ni Liu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Melania Pintilie
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Petra Martin
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Tom John
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Igor Jurisica
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Natasha B Leighl
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Benjamin G Neel
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Thomas K Waddell
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Frances A Shepherd
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Geoffrey Liu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ming-Sound Tsao
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia.
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Lheureux S, Butler MO, Clarke B, Cristea MC, Martin LP, Tonkin KS, Fleming GF, Tinker A, Hirte HW, Tsoref D, Mackay H, Dhani NC, Ghatage P, Pham NA, Motta V, Wang L, Karakasis K, Udagani S, Streicher H, Oza AM. A phase I/II study of ipilimumab in women with metastatic or recurrent cervical carcinoma: A study of the Princess Margaret and Chicago N01 Consortia. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.3061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Blaise Clarke
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
| | - Mihaela C. Cristea
- City of Hope, Department of Medical Oncology and Therapeutics Research, Duarte, CA
| | | | | | | | - Anna Tinker
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | | | - Helen Mackay
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neesha C. Dhani
- Princess Margaret Cancer Centre, University Health Network, Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Nhu-An Pham
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Lisa Wang
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | | | - Howard Streicher
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | - Amit M. Oza
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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Wei Y, Vellanki RN, Coyaud É, Ignatchenko V, Li L, Krieger JR, Taylor P, Tong J, Pham NA, Liu G, Raught B, Wouters BG, Kislinger T, Tsao MS, Moran MF. CHCHD2 Is Coamplified with EGFR in NSCLC and Regulates Mitochondrial Function and Cell Migration. Mol Cancer Res 2015; 13:1119-29. [DOI: 10.1158/1541-7786.mcr-14-0165-t] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 03/07/2015] [Indexed: 11/16/2022]
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Li L, Wei Y, To C, Zhu CQ, Tong J, Pham NA, Taylor P, Ignatchenko V, Ignatchenko A, Zhang W, Wang D, Yanagawa N, Li M, Pintilie M, Liu G, Muthuswamy L, Shepherd FA, Tsao MS, Kislinger T, Moran MF. Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact. Nat Commun 2014; 5:5469. [DOI: 10.1038/ncomms6469] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/03/2014] [Indexed: 11/09/2022] Open
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Zhang W, Wei Y, Ignatchenko V, Li L, Sakashita S, Pham NA, Taylor P, Tsao MS, Kislinger T, Moran MF. Proteomic profiles of human lung adeno and squamous cell carcinoma using super-SILAC and label-free quantification approaches. Proteomics 2014; 14:795-803. [PMID: 24453208 DOI: 10.1002/pmic.201300382] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/29/2013] [Accepted: 12/26/2013] [Indexed: 01/07/2023]
Abstract
Nonsmall cell lung cancer (NSCLC) accounts for 85% of lung cancers, and is subdivided into two major histological subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). There is an unmet need to further subdivide NSCLC according to distinctive molecular features that may be associated with responsiveness to therapies. Four primary tumor-derived xenograft proteomes (two-each ADC and SCC) were quantitatively compared by using a super-SILAC labeling approach together with ultrahigh-resolution MS. Proteins highly differentially expressed in the two subtypes were identified, including 30 that were validated in an independent cohort of 12 NSCLC primary tumor-derived xenograft tumors whose proteomes were quantified by an alternative, label-free shotgun MS methodology. The 30-protein signature contains metabolism enzymes including phosphoglycerate dehydrogenase, which is more highly expressed in SCC, as well as a comprehensive set of cytokeratins and other components of the epithelial barrier, which is therefore distinctly different between ADC and SCC. These results demonstrate the utility of the super-SILAC method for the characterization of primary tissues, and compatibility with datasets derived from different MS-based platforms. The validation of proteome signatures of NSCLC subtypes supports the further development and application of MS-based quantitative proteomics as a basis for precision classifications and treatments of tumors. All MS data have been deposited in the ProteomeXchange with identifier PXD000438 (http://proteomecentral.proteomexchange.org/dataset/PXD000438).
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Affiliation(s)
- Wen Zhang
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Stewart EL, Mascaux C, Shakashita S, Panchal D, Wang D, Li M, Pham NA, Leighl N, Liu G, Shepherd FA, Tsao MS. Abstract 1184: Modeling mechanisms of resistance of epidermal growth factor receptor (EGFR) mutations to targeted drugs through patient-derived xenografts (PDX) of non-small cell lung cancer (NSCLC). Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-1184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Resistance to small molecule EGFR tyrosine kinase inhibitors (TKIs) is seen in some NSCLC patients with activating EGFR mutations. We evaluated in vivo PDX models for their utility in studying EGFR-targeted drug resistance mechanisms.
Methods: Surgically resected early stage NSCLC tumors were implanted into non-obese diabetic severe combined immune deficient (NOD-SCID) mice. Tumors were passaged and expanded in new mouse hosts once the humane endpoint of 1.5 cm maximum diameter was reached. EGFR TKI treatment was initiated at an average tumor volume of 150mm3. Treatments included daily oral gavage with first and second generation EGFR TKIs, and with weekly intraperitoneally administered cetuximab.
Results: Of the 55 NSCLC tumors with EGFR activating mutations, only 6 engrafted (11%) and could be propagated beyond the first passage, and 4 have been studied for their responsiveness to EGFR-targeted agents. Model 148, developed from a patient who received pre-operative erlotinib, showed intrinsic pan-resistance to all EGFR-targeted therapies despite having an L858R mutation. The corresponding patient did not respond to erlotinib, relapsed after surgery and did not receive additional TKI therapy. Model 137, with an exon19 E746-A750 deletion, recapitulated the patient's response to gefitinib at relapse; this model was sensitive to first and second generation EGFR TKIs. Model 192 also has the exon19 E746-A750 deletion, however it did not recapitulate the patient's observed sensitivity to erlotinib. Selection for a MET amplified population during engraftment may be the cause for the disparate drug sensitivities. Model 164 has a double exon19 L747-T751 deletion and T790M EGFR mutation. Neither patient nor xenograft responded to erlotinib; the xenograft responded to cetuximab. Resistance developed over time to a second generation EGFR TKI; this resistant phenotype was not stable as each subsequent passage of the ‘resistant’ tumor exhibited the same initial response pattern. Two potential mechanisms for this transient sensitivity are currently being investigated: epigenetic mechanisms and intratumoural mutational heterogeneity.
Conclusions: PDX models may provide important insight into biomarkers and mechanisms of resistance to targeted therapies, and provide a means to test novel treatment strategies to improve future treatment efficacies.
Citation Format: Erin L. Stewart, Celine Mascaux, Shingo Shakashita, Devang Panchal, Dennis Wang, Ming Li, Nhu-An Pham, Natasha Leighl, Geoffrey Liu, Frances A. Shepherd, Ming-Sound Tsao. Modeling mechanisms of resistance of epidermal growth factor receptor (EGFR) mutations to targeted drugs through patient-derived xenografts (PDX) of non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1184. doi:10.1158/1538-7445.AM2014-1184
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Affiliation(s)
| | - Celine Mascaux
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Devang Panchal
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Dennis Wang
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ming Li
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Natasha Leighl
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Geoffrey Liu
- 2Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Brana I, Pham NA, Kim L, Sakashita S, Li M, Ng C, Wang Y, Loparco P, Sierra JR, Wang L, Siu LL, Tsao MS. Abstract 3121: Evaluation of novel combinations of PI3K-mTOR inhibitors with dacomitinib (dac) or chemotherapy in PTEN-deficient genomically characterized patient-derived tumor xenografts (gPTX). Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Activation of the PI3K pathway has been associated with resistance to anti-human epidermal growth factor receptor (HER) therapy providing a rationale to combine PI3K-mTOR inhibitors and the pan-HER inhibitor dac. Loss of PTEN function may be associated with sensitivity to PI3K-mTOR inhibitors. The objectives of these experiments are to evaluate the combination of PI3K-mTOR inhibitors with chemotherapy or dac in PTEN-deficient gPTX models.
Material and Methods: Three gPTX models [triple-negative breast cancer (TNBC), low-grade serous ovarian cancer (LGSOC), and non-small cell lung cancer (NSCLC)] were selected based on their deficient expression of PTEN by immunohistochemistry. Two dual PI3K-mTOR inhibitors were evaluated: PF-04691502 (5 mg/kg, daily, oral gavage) and PF-05212384 (10 mg/kg, twice weekly, intravenously). Three different combinations were evaluated: PI3K-mTOR inhibitor with 1) cisplatin (3 mg/kg, once weekly, intraperitoneally -IP); 2) with paclitaxel (10 mg/kg, twice weekly, IP); 3) with dac (3 mg/kg daily, oral gavage). This last experiment contained an acute dose component to evaluate target modulation by collecting tumor samples at 1 hr and 24 hr post dosing.
Results: The percentages of tumor growth inhibition (TGI%) induced by the different treatment arms and daily tumor volume change (ΔV) for each arm compared to the control arm (p-value) are summarized in Table 1. Pharmacodynamic modulation of pS6 and pAKT was observed in the acute dose experiment in the arms of PI3K-mTOR inhibitor with or without dac.
Conclusions: In gPTX with PTEN loss, the addition of a PI3K-mTOR inhibitor may improve the TGI% when compared to chemotherapy or dac alone. This benefit was largely offset in the NSCLC gPTX harboring KRAS G12C and/or TP53 mutations. The role of PTEN deficiency in the antitumor activity of these combinations should be further investigated in the clinic.
Table 1gPTX tumor typeTNBCLGSOCNSCLCMolecular profilePTEN nullKRAS G12RPTEN lowKRAS G12CTP53 R181PPTEN lowTGI%ΔVp-valueTGI%ΔVp-valueTGI%ΔVp-valueExperiment 1PF-0521238432%0.0739%0.19-1%0.78Cis42%<0.05**43%0.0397%<0.05**PF-05212384 + Cis96%<0.05**68%<0.05**92%<0.05**Experiment 2PF-0521238422%0.6440%0.21PF-0469150233%<0.05**Pac84%<0.05**38%0.2079%<0.05**PF-05212384 + Pac110%^<0.05**56%<0.05**PF-04691502 + Pac45%<0.05**Experiment 3PF-0521238422%0.6140%0.26PF-0469150233%<0.05**Dac15%0.998%0.5323%0.35PF-05212384 + Dac55%0.0945%0.47PF-04691502 + Dac32%0.055Cis = cisplatin; Pac = paclitaxel; Dac = dacomitinib; TNBC = triple negative breast cancer; LGSOC = low grade serous ovarian cancer; NSCLC = non-small cell lung cancerTGI%: percentages of tumor growth inhibition; ΔV: differences between daily tumor volume change of each treatment arm and the control arm^ Tumor regression; ** statistically significant
Citation Format: Irene Brana, Nhu-An Pham, Lucia Kim, Shingo Sakashita, Ming Li, Christine Ng, Yuhui Wang, Peter Loparco, Jose Rafael Sierra, Lisa Wang, Lillian L. Siu, Ming S. Tsao. Evaluation of novel combinations of PI3K-mTOR inhibitors with dacomitinib (dac) or chemotherapy in PTEN-deficient genomically characterized patient-derived tumor xenografts (gPTX). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3121. doi:10.1158/1538-7445.AM2014-3121
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Affiliation(s)
- Irene Brana
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Ming Li
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Christine Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Peter Loparco
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Lisa Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ming S. Tsao
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Brana I, She D, Chau NG, Pham NA, Kim L, Sakashita S, Ng C, Zhu C, Razak ARA, Chen E, Wang L, Perz-Ordonez B, Winquist E, Hotte SJ, Tsao MS, Siu LL. Preoperative window-of-opportunity (WOO) study of dacomitinib (Dac) in patients (Pts) with resectable oral cavity squamous cell carcinoma (OCC): Generation of a gene expression signature (DGS) as a predictor of Dac activity. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.6041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Irene Brana
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Desmond She
- Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Nhu-An Pham
- Princess Margaret Cancer Centre - University Health Network, Toronto, ON, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre - University Health Network, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Hospital - University Health Network, Toronto, ON, Canada
| | - Christine Ng
- Princess Margaret Cancer Centre - University Health Network, Toronto, ON, Canada
| | - ChangQi Zhu
- Princess Margaret Cancer Centre - University Health Network, Toronto, ON, Canada
| | | | - Eric Chen
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Lisa Wang
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | | | - Sebastien J. Hotte
- Escarpment Cancer Research Institute, Juravinski Cancer Centre, Hamilton, ON, Canada
| | - Ming-Sound Tsao
- Princess Margaret Hospital-University Health Network and University of Toronto, Toronto, ON, Canada
| | - Lillian L. Siu
- Drug Development Program, Princess Margaret Cancer Center, Toronto, ON, Canada
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To C, Strumpf D, Panchal D, Li M, Pham NA, Xie W, Yanagawa N, Bandarchi B, Chui MH, Der S, Shepherd FA, Kislinger T, Moran M, Jurisica I, Muthuswamy L, Tsao MS. Abstract 5069: Genomic profiles of primary non-small cell lung cancer (NSCLC) xenograft tumors identify distinct gene signatures associated with histological subtypes. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Xenografts established directly from patient tumors mirror closely the histology of the primary tumors. Therefore, primary tumor xenografts (PTXG) may serve as important preclinical models to evaluate novel anti-cancer drugs. We previously reported that the ability of resected tumors to engraft in NOD-scid mice is a strong predictor of relapse after surgery and poorer prognosis in NSCLC patients, and thus may represent biologically more aggressive cancers (Clin Cancer Res 2011;17:134-41). Genomic characterization of PTXG would help identify genetic aberrations that drive malignant oncogenic pathways in NSCLC. We characterized the somatic copy number alterations (CNA) of 36 PTGX, consisting of 15 adenocarcinoma (ADC), 18 squamous cell carcinoma (SCC), 2 large cell neuroendocrine carcinoma (LCNEC) and 1 large cell carcinoma (LC), along with 34 patient normal samples as controls using Illumina Omni-1 Quad SNP arrays. The gene expression profiles of the 36 PTGX were analyzed using Illumina Omni-1 Quad HT-12 v4 arrays. Histology-specific recurrent regions of CNA observed in PTGX are concordant with the published and publicly available primary NSCLC CNAs. We identified 1053 genes with somatic copy number gains and 932 genes with somatic copy number losses that distinguish between SCC and ADC. From integrative analysis of mRNA expression and somatic CNAs, we identified 325 genes specific to ADC and 2232 specific to SCC that are well correlated. Gene candidates that are deregulated in ADC include WRN, STK35, SIX1; and genes that are over-expressed in SCC include SOX2, RNF13, WNK1, PIK3CA, TFRC, TP63, PAK2 suggesting there is differential deregulation of signaling pathways between these two subtypes of lung cancer. We have identified candidate gene signatures that distinguish between ADC and SCC from PTXG, suggesting these xenograft models can provide a valuable resource to study cancer biology and preclinical drug target evaluation in vivo.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5069. doi:1538-7445.AM2012-5069
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Affiliation(s)
- Christine To
- 1University Health Network, Toronto, Ontario, Canada
| | - Dan Strumpf
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Ming Li
- 1University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- 1University Health Network, Toronto, Ontario, Canada
| | - Wing Xie
- 1University Health Network, Toronto, Ontario, Canada
| | | | | | | | - Sandy Der
- 1University Health Network, Toronto, Ontario, Canada
| | | | | | - Michael Moran
- 2The Hospital For Sick Children, Toronto, Ontario, Canada
| | - Igor Jurisica
- 1University Health Network, Toronto, Ontario, Canada
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Wei Y, Taylor P, Tong J, Pham NA, Li M, Panchal D, To C, Chui MH, Tsao MS, Kislinger T, Moran MF. Abstract 4805: Distinctive phospho-proteome signatures in non-small cell lung carcinoma tumors. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-small cell lung carcinoma (NSCLC) is a major, lethal cancer worldwide. Various molecular and cellular abnormalities are found in NSCLC, and an established theme is the alteration of protein phosphotyrosine (pY), as exemplified by elevated epidermal growth factor receptor (EGFR) activity recognized in a subset of NSCLC. In order to gain a broad perspective of pY-mediated signaling networks in NSCLC, mass spectrometry was used to analyze pY-containing peptides affinity purified from protease-digested xenograft tumors. Seventeen tumors representing the major NSCLC subtypes adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were characterized. The major classes of pY proteins detected were cytoskeletal, protein kinases, and adhesion proteins. Pathways and cellular functions enriched in the data set included focal adhesion, adherens junction, and ErbB signaling. Five receptor tyrosine kinases (RTKs) were detected, with EGFR and EPHA2 most prevalent. Src-family kinases (YES, LYN, FRK and LCK) and focal adhesion kinase (FAK) comprised the majority of non-receptor tyrosine kinases measured. Analysis of individual pY sites on 14 tyrosine kinases indicates their activation by kinase domain activation loop phosphorylation, but also revealed additional pY sites suggestive of regulation by trafficking/endocytosis and inter- and intra-molecular protein-protein interactions involving, for example, SH2 and SH3 domains, and extra-kinase domain regions. Analysis of tumors based on protein-pY suggested subtypes distinguished by their activated tyrosine kinase networks. Genetic analysis of 3 tumors that displayed EGFR-associated phospho-proteome signatures confirmed that they carried either EGFR activating mutations (in two ADCs) or increased gene copy number (in one SCC). Western blot analysis of protein pY confirmed different patterns of cellular protein pY among the tumor phospho-types in agreement with the phospho-proteomic analysis. Quantification of kinase and substrate pY sites, according to their integrated extracted ion currents, revealed a set of phosphorylations that constituted a molecular signature that differentiated between the ADC and SCC subtypes. In summary, quantitative phospho-proteomic profiling of NSCLC tumors is feasible and may have utility in the categorization of individual tumors according to their networks of activated tyrosine kinases and substrates.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4805. doi:1538-7445.AM2012-4805
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Affiliation(s)
- Yuhong Wei
- 1Hospital for Sick Children, Program in Molecular Structure & Function, Toronto, Ontario, Canada
| | - Paul Taylor
- 1Hospital for Sick Children, Program in Molecular Structure & Function, Toronto, Ontario, Canada
| | - Jiefei Tong
- 1Hospital for Sick Children, Program in Molecular Structure & Function, Toronto, Ontario, Canada
| | - Nhu-An Pham
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Ming Li
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Devang Panchal
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Christine To
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Michael H. Chui
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Thomas Kislinger
- 2Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Michael F. Moran
- 1Hospital for Sick Children, Program in Molecular Structure & Function, Toronto, Ontario, Canada
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Moran MF, To C, Wei Y, Li L, Taylor P, Ignatchenko V, Strumpf D, Tong J, Pham NA, Jurisica I, Muthuswamy L, Kislinger T, Kislinger T, Tsao MS. Abstract 5127: Characterization of lung cancers by integrated genomic and proteomic analysis. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-small cell lung carcinoma (NSCLC) represents 80% of lung cancers, the deadliest cancer worldwide. The genomic profiling of DNA and mRNA, and characterization of proteomes have begun to address the objective to stratify and treat tumors according to their molecular features. However, these data sets have largely been used independently and typically have not been integrated. Hence most cancers including NSCLC continue to be classified largely based on histology. Our aim for this study was to integrate a set of comprehensive functional genomics data sets in order to stratify a set of NSCLC primary tumors and establish that primary tumor xenografts mirror closely the primary tumors, and hence may serve as validated pre-clinical models. Our preliminary analyses indicated that engraftment is prognostic of poor clinical outcome (John et al., 2011, Clin Cancer Res, 17:134-41), and that the major NSCLC subtypes adenocarcinoma and squamous cell carcinoma are readily resolved according to their distinctive proteomes (Wei et al., 2011, J Proteome Res 10:161-74). Herein we characterized a collection of 12 each primary tumor (T), primary tumor xenograft (X), and patient-matched normal lung (N) by using mass spectrometry for proteome analysis, Illumina 1M Omni-Quad for somatic copy number alterations (SCNAs), and Illumina Omni-1 Quad HT-12 v4 for mRNA expression. Unsupervised hierarchical clustering of protein abundances and SCNAs independently revealed that primary tumor and xenografts are highly correlated with each other. This correlation was significantly enhanced in the proteome data when a small number of highly abundant blood-associated proteins were systematically identified and subtracted. We identified tumor-specific dysregulated proteins and SCNAs in T and X using N as a reference. Two thirds of T and X matched pairs could be identified based on Pearson Correlation Coefficients of the dysregulated proteins. This clearly demonstrates that the xenografts accurately recapitulated tumor proteomes. Proteins upregulated in tumors were expressed to a significant extent from regions of SCNA gain, and we found a high degree of concordance between mRNA expression levels and SCNAs. Some primary tumors had very highly correlated proteomic profiles, suggesting they may be effectively stratified according to their proteome signatures. In conclusion, our integrated analysis has validated the primary xenograft model, provided an initial systems level perspective on the central dogma in cancer, and reinforces the proteome as a distinctive molecular feature for lung tumor stratification.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5127. doi:1538-7445.AM2012-5127
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Affiliation(s)
| | - Christine To
- 2Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Yuhong Wei
- 1Hospital For Sick Children, Toronto, Ontario, Canada
| | - Lei Li
- 1Hospital For Sick Children, Toronto, Ontario, Canada
| | - Paul Taylor
- 1Hospital For Sick Children, Toronto, Ontario, Canada
| | | | - Dan Strumpf
- 2Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Jeifei Tong
- 1Hospital For Sick Children, Toronto, Ontario, Canada
| | - Nhu-An Pham
- 2Ontario Cancer Institute, Toronto, Ontario, Canada
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Razak ARA, Bedard PL, You B, Panchal D, Chen EX, Ivy SP, Zhang WJ, Kamel-Reid S, Pham NA, Zhang T, Hotte SJ, Reedijk M, Shimizu M, Ailles L, Haines C, Oza A, Tsao M, Siu LL. Abstract B50: A phase I study of various administration schedules for RO4929097 (R) with multi-parameter assessment (pharmacokinetics [PK] and primary tumor xenograft [XG]) in patients (pts) with advanced solid cancers. Mol Cancer Ther 2011. [DOI: 10.1158/1535-7163.targ-11-b50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Dysregulated Notch signalling has been implicated in a variety of cancers. R is a potent and selective inhibitor of -secretase, a key enzyme in Notch signalling. Phase I data demonstrated R to be tolerable but PK profile revealed auto-induction with repeated dosing at high doses (Tolcher et al. ASCO 2010). The primary aim of this study is to determine the optimal regimen of R using alternative dosing schedules. Its secondary aim is to establish mouse XG from tumor biopsies to enable correlative biomarker research.
Methods: Pts with advanced solid tumors were enrolled in one of 6 different schedules and starting doses of R. Serial PK samples were collected on Day 1 and at steady state. Mandatory pre and post treatment tumor biopsies were procured if medically safe and implanted subcutaneously into NOD-SCID mice for propagation in up to 4 serial generations. Tumor DNA from second XG passage was analyzed using the Sequenom OncoCarta Panel v1.0 (SOCP).
Results: To date, 24 pts have been enrolled. PK data are available for 21 pts, summarized in Table 1. The maximum tolerable dose for schedules C-F has not been reached. Commonest adverse events (AE) of all grades with at least possible attribution to R were fatigue (n=14), nausea (13), hypophosphatemia (11), anorexia (9) and diarrhoea (8). Grade 3/4 AEs consisted of hypophosphatemia (n=2), lymphopenia (2), vomiting (1) and QTc prolongation (1). Data on engraftment are available from biopsies of 18 pts (18 pre and 16 post treatment samples). Primary tumor sites included gastrointestinal (n=6), breast (4), melanoma (2), ovarian (2), pancreatic (1), neuroendocrine (1), parotid (1) and lung cancers (1). In pre treatment biopsies, the rate of initial engraftment was 12/18 (67%); while in post treatment biopsies, the rate of initial engraftment was 14/16 (88%). Further passages (2nd and 3rd) from viable engrafted cancers demonstrated a 100% engraftment rate. The SOCP analyses were carried out in 9 different XG models with mutations detected in 4 (KRAS [n=3] and BRAF mutations), all of which were from metastatic colon cancers.
Conclusions: Preliminary PK evaluation demonstrated auto-induction of R in schedules A and B (concordant with prior data), but to a lesser degree in schedules C, D & E. It is unclear whether this observation was due to the lower administered doses of R or the alternative schedules employed. This study demonstrated the ability to generate mouse XG models from different tumor histologies using core biopsies, with a mean engraftment rate of 78% at first implantation. We also confirmed the feasibility of detecting point mutations in cancers using SOCP platform on XG specimens.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B50.
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Affiliation(s)
| | | | - Benoit You
- 1Princess Margaret Hospital, Toronto, ON, Canada
| | | | - Eric X. Chen
- 1Princess Margaret Hospital, Toronto, ON, Canada
| | | | | | | | - Nhu-An Pham
- 1Princess Margaret Hospital, Toronto, ON, Canada
| | - Tong Zhang
- 1Princess Margaret Hospital, Toronto, ON, Canada
| | | | | | | | | | | | - Amit Oza
- 1Princess Margaret Hospital, Toronto, ON, Canada
| | - Ming Tsao
- 1Princess Margaret Hospital, Toronto, ON, Canada
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Hembrough T, Thyparambil S, Krizman D, Darfler M, Wei Y, Taylor P, Tong J, Pham NA, Jasani B, Adams R, Tsao MS, Moran M, Burrows J. Abstract 4919: Multiplexed EGFR signaling pathway analysis in FFPE tissue using quantitative mass spectrometry. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The epidermal growth factor receptor (EGFR) is a drug target for both small molecule and antibody therapeutics and has been approved in non small-cell lung carcinoma (NSCLC) and colorectal carcinoma (CRC) among other indications. These drugs block receptor signaling though blockade of the tyrosine kinase domain, or through inhibition of ligand binding. Current genomic tests measure receptor amplification, RNA levels, the mutation status of receptor or pathway molecules (EGFR or kRAS mutations) but no current assay can directly assess the activation state of the EGFR or its downstream signaling pathway components. Indeed, the EGFR mutation positive NSCLC tumors (thought to be constitutively active) show a high response rate to TKI therapy, but the many non responders (50% or more) demonstrate the limitation of genomic analysis.
Since activation of EGFR is necessary for the response to these targeted agents, it is critical to measure what levels of receptor activation and downstream signaling determines tumor responsiveness to EGFR targeted therapies in these patients. For this reason, we have developed a panel of new diagnostic assays which measure the activation of the EGFR and key downstream signaling proteins through quantitation of the phosphorylation state of these proteins. These assays are based on the Liquid Tissue®-SRM technology platform. This approach enables relative and absolute quantification of proteins and their phosphorylation status directly in formalin fixed paraffin embedded (FFPE) tissue.
We preclinically validated the multiplexed Liquid Tissue® phospho-SRM assay on formalin fixed EGF stimulated A431 cells. We followed up these in vitro studies with phospho-SRM analysis of FFPE NSCLC xenograft explants where extensive independent histopathologic and molecular characterization had been performed, allowing us to benchmark our phospho-SRM analysis with standard diagnostic analyses.
We have now extended these quantitation studies by measuring the expression of EGFR and phospho-EGFR in FFPE tissues obtained from relevant human clinical trial cohorts – Gefitinib treated NSCLC and Cetuximab treated CRC. It is hoped that we will be able to correlate EGFR expression, activation and signaling in these tumors with responsiveness to EGFR targeted therapy, and to validate this assay for use as a companion diagnostic to guide therapy in both NSCLC and CRC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4919. doi:10.1158/1538-7445.AM2011-4919
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Affiliation(s)
| | | | | | | | - Yuhong Wei
- 2Hospital for Sick Kids, Toronto, Ontario, Canada
| | - Paul Taylor
- 2Hospital for Sick Kids, Toronto, Ontario, Canada
| | - Jiefei Tong
- 2Hospital for Sick Kids, Toronto, Ontario, Canada
| | - Nhu-An Pham
- 3Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Ming-Sound Tsao
- 3Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
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Chau NG, Perez-Ordonez B, Zhang K, Pham NA, Ho J, Zhang T, Ludkovski O, Wang L, Chen EX, Tsao MS, Kamel-Reid S, Siu LL. The association between EGFR variant III, HPV, p16, c-MET, EGFR gene copy number and response to EGFR inhibitors in patients with recurrent or metastatic squamous cell carcinoma of the head and neck. Head Neck Oncol 2011; 3:11. [PMID: 21352589 PMCID: PMC3052237 DOI: 10.1186/1758-3284-3-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 02/27/2011] [Indexed: 12/31/2022]
Abstract
Background We examine the potential prognostic and predictive roles of EGFR variant III mutation, EGFR gene copy number (GCN), human papillomavirus (HPV) infection, c-MET and p16INK4A protein expression in recurrent or metastatic squamous cell carcinoma of the head and neck (R/M SCCHN). Methods We analyzed the archival tumor specimens of 53 patients who were treated in 4 phase II trials for R/M SCCHN. Two trials involved the EGFR inhibitor erlotinib, and 2 trials involved non-EGFR targeted agents. EGFRvIII mutation was determined by quantitative RT-PCR, HPV DNA by Linear Array Genotyping, p16 and c-MET protein expression by immunohistochemistry, and EGFR GCN by FISH. Results EGFRvIII mutation, detected in 22 patients (42%), was associated with better disease control, but no difference was seen between erlotinib-treated versus non-erlotinib treated patients. EGFRvIII was not associated with TTP or OS. The presence of HPV DNA (38%), p16 immunostaining (32%), c-MET high expression (58%) and EGFR amplification (27%), were not associated with response, TTP or OS. Conclusion EGFRvIII mutation, present in about 40% of SCCHN, appears to be an unexpected prognostic biomarker associated with better disease control in R/M SCCHN regardless of treatment with erlotinib. Larger prospective studies are required to validate its significance.
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Affiliation(s)
- Nicole G Chau
- Division of Medical Oncology and Hematology, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
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