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Mobadersany P, Lucas J, Govind D, Aguilar-Bonavides C, McCarthy S, Brookman-May S, Yu MK, Tian K, Hutnick N, Zamalloa J, Greshock J, Khan N, Yip SS. Abstract 5053: Artificial intelligence (AI)-based multimodal framework predicts androgen-deprivation therapy (ADT) outcomes in non-metastatic castration resistant prostate cancer (nmCRPC) from SPARTAN. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5053] [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
Objective: AI has demonstrated great promise in learning sophisticated features and relations in data that would otherwise remain hidden to the human eye. Here, we developed a proprietary AI-based multimodal approach to integrate clinical, digitized hematoxylin-eosin (H&E), and radiology bone scan (rBS) data for outcome prediction in ADT-treated nmCRPC patients. Identifying prostate cancer patients who may not benefit from ADT could improve the medical management of this disease beyond current definitive therapy.
Methods: Patients in the ADT+placebo arm from SPARTAN clinical trial on nmCRPC with available clinical, H&E, and rBS were used (n=154). These patients were randomly divided into 70% (n=107) discovery and 30% (n=47) hold-out test datasets. Using the discovery set, we developed and trained a multimodal approach that combines survival convolutional neural networks (SCNNs1) and Cox proportional-hazards model (CPH) to learn ADT outcomes for overall survival (OS) and time to PSA progression (TTP) from the integration of imaging data and 11 traditional clinical features (e.g., tumor stage, Gleason score, PSA). The ability of the trained framework in predicting outcomes and risk stratification was evaluated on the hold-out set. Bootstrap analysis with Wilcoxon signed rank test was used to determine the significance of the multimodal framework’s performance improvement compared to clinical CPH.
Results: The multimodal framework was predictive of ADT outcomes for OS and TTP in nmCRPC patients. In SPARTAN’s hold-out set, the multimodal framework significantly improved the predictive power of clinical CPH by 14%—16% across both outcomes (Wilcoxon signed rank P<0.0001). In particular, the multimodal framework’s concordance index (c-index) was 0.72 for OS and 0.73 for TTP, while clinical CPH’s c-index was 0.62 for OS, and 0.64 for TTP. Further, multimodal framework significantly stratified high- from low-risk nmCRPC patients for OS and TTP (log-rank P= 0.0049-0.0072), while clinical CPH failed to stratify risk for OS (log-rank P= 0.2891).
Conclusion: AI-based framework that learns from the integration of different data types improves outcome prediction in ADT-treated nmCRPC. The multimodal approach demonstrates promise in treatment decision support for the early use of androgen receptor-directed therapy and patient selection for clinical trials with novel treatment combinations.
Reference:
1. Mobadersany, Pooya, et al. "Predicting cancer outcomes from histology and genomics using convolutional networks." Proceedings of the National Academy of Sciences 115.13 (2018): E2970-E2979.
Conflict of interest statement
P.M., J.L., D.G., C.A., S.M., S.B., M.K.Y., K.T., N.H., J.Z., J.G., N.K., and S.S.F.Y., are employees of Janssen Pharmaceutical, LLC.
Citation Format: Pooya Mobadersany, Justin Lucas, Darshana Govind, Clemente Aguilar-Bonavides, Sharon McCarthy, Sabine Brookman-May, Margaret K. Yu, Ken Tian, Natalie Hutnick, Jose Zamalloa, Joel Greshock, Najat Khan, Stephen S.F. Yip. Artificial intelligence (AI)-based multimodal framework predicts androgen-deprivation therapy (ADT) outcomes in non-metastatic castration resistant prostate cancer (nmCRPC) from SPARTAN [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5053.
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Affiliation(s)
- Pooya Mobadersany
- 1Janssen Pharmaceutical Research and Development, Data Sciences, Boston, MA
| | - Justin Lucas
- 2Janssen Pharmaceutical Research and Development, Oncology Translational Research, Spring House, PA
| | - Darshana Govind
- 1Janssen Pharmaceutical Research and Development, Data Sciences, Boston, MA
| | | | - Sharon McCarthy
- 3Janssen Pharmaceutical Research and Development, Oncology Clinical Development, Bridgewater, NJ
| | - Sabine Brookman-May
- 4Janssen Pharmaceutical Research and Development, Oncology Clinical Development, Los Angeles, CA
| | - Margaret K. Yu
- 5Janssen Pharmaceutical Research and Development, Disease Area Strongholds, Prostate, Los Angeles, CA
| | - Ken Tian
- 2Janssen Pharmaceutical Research and Development, Oncology Translational Research, Spring House, PA
| | - Natalie Hutnick
- 2Janssen Pharmaceutical Research and Development, Oncology Translational Research, Spring House, PA
| | - Jose Zamalloa
- 6Janssen Pharmaceutical Research and Development, Data Sciences, Titusville, NJ
| | - Joel Greshock
- 7Janssen Pharmaceutical Research and Development, Data Sciences, Wayne, PA
| | - Najat Khan
- 6Janssen Pharmaceutical Research and Development, Data Sciences, Titusville, NJ
| | - Stephen S.F. Yip
- 1Janssen Pharmaceutical Research and Development, Data Sciences, Boston, MA
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Ott PA, Hu-Lieskovan S, Chmielowski B, Govindan R, Naing A, Bhardwaj N, Margolin K, Awad MM, Hellmann MD, Lin JJ, Friedlander T, Bushway ME, Balogh KN, Sciuto TE, Kohler V, Turnbull SJ, Besada R, Curran RR, Trapp B, Scherer J, Poran A, Harjanto D, Barthelme D, Ting YS, Dong JZ, Ware Y, Huang Y, Huang Z, Wanamaker A, Cleary LD, Moles MA, Manson K, Greshock J, Khondker ZS, Fritsch E, Rooney MS, DeMario M, Gaynor RB, Srinivasan L. A Phase Ib Trial of Personalized Neoantigen Therapy Plus Anti-PD-1 in Patients with Advanced Melanoma, Non-small Cell Lung Cancer, or Bladder Cancer. Cell 2020; 183:347-362.e24. [PMID: 33064988 DOI: 10.1016/j.cell.2020.08.053] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/08/2020] [Accepted: 08/28/2020] [Indexed: 01/21/2023]
Abstract
Neoantigens arise from mutations in cancer cells and are important targets of T cell-mediated anti-tumor immunity. Here, we report the first open-label, phase Ib clinical trial of a personalized neoantigen-based vaccine, NEO-PV-01, in combination with PD-1 blockade in patients with advanced melanoma, non-small cell lung cancer, or bladder cancer. This analysis of 82 patients demonstrated that the regimen was safe, with no treatment-related serious adverse events observed. De novo neoantigen-specific CD4+ and CD8+ T cell responses were observed post-vaccination in all of the patients. The vaccine-induced T cells had a cytotoxic phenotype and were capable of trafficking to the tumor and mediating cell killing. In addition, epitope spread to neoantigens not included in the vaccine was detected post-vaccination. These data support the safety and immunogenicity of this regimen in patients with advanced solid tumors (Clinicaltrials.gov: NCT02897765).
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Affiliation(s)
- Patrick A Ott
- Dana Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
| | - Siwen Hu-Lieskovan
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bartosz Chmielowski
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Aung Naing
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine, New York, NY, USA
| | - Kim Margolin
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mark M Awad
- Dana Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Jessica J Lin
- Cancer Center, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
| | - Terence Friedlander
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Rana Besada
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | | | | | | | - Asaf Poran
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | | | | | | | - Jesse Z Dong
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | - Yvonne Ware
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | - Yuting Huang
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | | | | | | | | | | | | | | | - Ed Fritsch
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
| | | | - Mark DeMario
- Neon Therapeutics/BioNTech US, Cambridge, MA, USA
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Abelin JG, Harjanto D, Malloy M, Suri P, Colson T, Goulding SP, Creech AL, Serrano LR, Nasir G, Nasrullah Y, McGann CD, Velez D, Ting YS, Poran A, Rothenberg DA, Chhangawala S, Rubinsteyn A, Hammerbacher J, Gaynor RB, Fritsch EF, Greshock J, Oslund RC, Barthelme D, Addona TA, Arieta CM, Rooney MS. Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction. Immunity 2019; 51:766-779.e17. [PMID: 31495665 DOI: 10.1016/j.immuni.2019.08.012] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [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: 03/13/2019] [Revised: 06/19/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022]
Abstract
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II), hindering efforts to optimally target them therapeutically. Obstacles include inaccurate peptide-binding prediction and unsolved complexities of the HLA-II pathway. To address these challenges, we developed an improved technology for discovering HLA-II binding motifs and conducted a comprehensive analysis of tumor ligandomes to learn processing rules relevant in the tumor microenvironment. We profiled >40 HLA-II alleles and showed that binding motifs were highly sensitive to HLA-DM, a peptide-loading chaperone. We also revealed that intratumoral HLA-II presentation was dominated by professional antigen-presenting cells (APCs) rather than cancer cells. Integrating these observations, we developed algorithms that accurately predicted APC ligandomes, including peptides from phagocytosed cancer cells. These tools and biological insights will enable improved HLA-II-directed cancer therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Asaf Poran
- Neon Therapeutics, Cambridge, MA 02139, USA
| | | | | | - Alex Rubinsteyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeff Hammerbacher
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Bushway ME, Ting YS, Besada RH, Sciuto TE, Prabhakara J, Scherer J, Balogh KN, Lamb A, Kaplan JA, Cleary LD, Moles MA, Church SE, Ren Y, Ren X, Gaynor RB, Goldstein MJ, Brail LH, Greshock J, Srinivasan L. Abstract 5006: Comprehensive gene expression analysis of the tumor microenvironment in patients with advanced cancer treated with a personalized neoantigen vaccine, NEO-PV-01, in combination with anti-PD1. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5006] [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: Neoantigens arise from DNA mutations in cancer cells and are important targets for T cell mediated anti-tumor immunity. NEO-PV-01 is a personal neoantigen vaccine of up to 20 peptides designed based on a patient’s neoantigen and HLA profile that is directed at inducing tumor-specific T cell responses to neoantigens. Here we report comprehensive immune-related gene expression analysis of longitudinal tumor biopsies from patients with metastatic melanoma, bladder, and non-small cell lung cancer treated on our NT-001 trial with NEO-PV-01 + adjuvant in combination with nivolumab (NCT02897765) to correlate with clinical outcomes.
Methods: Tumor biopsies from all three tumor types were collected i) prior to treatment, ii) after 12 weeks of nivolumab monotherapy and iii) after completion of NEO-PV-01 vaccination. Targeted gene expression analysis on RNA extracted from FFPE blocks was performed using the NanoString™ nCounter platform. A custom set of 800 genes included markers for immune cell populations, cytolytic markers, immune activation and suppression, and the tumor microenvironment. Gene signatures of key immune features were calculated after normalization with housekeeping genes and used for subsequent analysis.
Results: Changes in the immune cell populations and the tumor microenvironment were detected after treatment with nivolumab and NEO-PV-01. Increases in various immune cell subsets, including T cells and B cells, as well as an increase in cytolytic phenotype were observed in tumor biopsies following treatment. Moreover, changes in the tumor microenvironment, consistent with the absence of tumor by histologic evaluation, were detected in many of the post-vaccination biopsies. In addition, these observations were consistent with data from peripheral blood that demonstrated durable de novo neoantigen-specific immune responses after vaccination. Additional exploratory analyses of the data demonstrate differential gene expression in patients’ tumors that align with tumor responses to therapy.
Conclusion: Treatment with nivolumab and NEO-PV-01 leads to changes in the tumor microenvironment that are consistent with cell types and phenotypes that could contribute to an anti-tumor response.
Citation Format: Meghan E. Bushway, Ying Sonia Ting, Rana H. Besada, Tracey E. Sciuto, Jasmina Prabhakara, Julian Scherer, Kristen N. Balogh, April Lamb, Jennifer A. Kaplan, Lisa D. Cleary, Melissa A. Moles, Sarah E. Church, Yuqi Ren, Xing Ren, Richard B. Gaynor, Matthew J. Goldstein, Les H. Brail, Joel Greshock, Lakshmi Srinivasan. Comprehensive gene expression analysis of the tumor microenvironment in patients with advanced cancer treated with a personalized neoantigen vaccine, NEO-PV-01, in combination with anti-PD1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5006.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Yuqi Ren
- 2NanoString Technologies, Inc, Seattle, WA
| | - Xing Ren
- 2NanoString Technologies, Inc, Seattle, WA
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Ott P, Govindan R, Naing A, Friedlander T, Margolin K, Lin J, Bhardwaj N, Hellman M, Srinivasan L, Greshock J, Moles M, Gaynor R, Goldstein M, Hu-Lieskovan S. A personal neoantigen vaccine, NEO-PV-01, with anti-PD1 induces broad de novo anti-tumor immunity in patients with metastatic melanoma, NSCLC, and bladder cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Naing A, Ott PA, Gates SJ, Martinez JG, Curran RR, Kohler VL, Bushway ME, Scherer J, Barthelme D, Dong JZ, Lamb A, Cleary LD, Moles M, Greshock J, Gaynor RB, Goldstein MJ, Srinivasan L. Abstract LB-147: Comprehensive immune and molecular analysis of two metastatic melanoma patients treated with a personal neoantigen vaccine, NEO-PV-01, in combination with anti-PD1: A case study. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-147] [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: Neoantigens arise from DNA mutations and are critical targets that are presented on the surface of cancer cells for tumor-specific T cell responses. Vaccines targeting neoantigens have the potential to induce de novo and amplify pre-existing anti-tumor T cell responses. NEO-PV-01, a personal neoantigen vaccine that is designed based on a patient's tumor-specific mutations, is comprised of up to 20 long peptides, and administered with the immune adjuvant Poly-ICLC. Here we report a comprehensive immune and molecular analysis observed in two metastatic melanoma patients treated with NEO-PV-01 in combination with nivolumab (ClinicalTrials.gov: NCT02897765).
Methods: Immune monitoring was performed from peripheral blood and tumor biopsies collected i) prior to any treatment, ii) after 12-weeks of nivolumab monotherapy and, iii) after NEO-PV-01 vaccination. Peripheral blood samples were evaluated for the presence of antigen-specific T cell responses by IFNγ ELISPOT, intracellular cytokine staining, multi-parameter surface and functional phenotyping by FACS, and presence of cytolytic properties. Tumor biopsies were analyzed for multiple immune and tumor markers by immunohistochemistry, gene expression, and whole exome sequencing.
Results: IFNγ ELISPOT analysis with PBMCs revealed neoantigen-specific CD4 and CD8 T cell responses that were predominantly observed following vaccination. Vaccine-induced, neoantigen-specific CD8 T cells had an effector memory and central memory phenotype, secreted IFNγ, TNFα and IL2, and were cytolytic. Finally, induction of neoantigen-specific immunity by NEO-PV-01 led to epitope spreading of the immune response to neoantigens not included in the vaccine. Assessment of pre- and post-treatment tumor biopsies with repeat exome sequencing, gene expression, as well as immunohistochemistry and pathologic analysis will be presented.
Conclusions: NEO-PV-01 is immunogenic and leads to multiple de novo neoantigen-specific immune responses in the peripheral blood. Furthermore, the detection of epitope spreading to additional neoantigen targets suggests vaccine-induced broadening of the immune response.
Citation Format: Aung Naing, Patrick A. Ott, Samantha J. Gates, Jose G. Martinez, Riley R. Curran, Victoria L. Kohler, Meghan E. Bushway, Julian Scherer, Dominik Barthelme, Jesse Z. Dong, April Lamb, Lisa D. Cleary, Melissa Moles, Joel Greshock, Richard B. Gaynor, Matthew J. Goldstein, Lakshmi Srinivasan. Comprehensive immune and molecular analysis of two metastatic melanoma patients treated with a personal neoantigen vaccine, NEO-PV-01, in combination with anti-PD1: A case study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-147.
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Longo T, McGinley KF, Freedman JA, Etienne W, Wu Y, Sibley A, Owzar K, Gresham J, Moy C, Szabo S, Greshock J, Zhou H, Bai Y, Inman BA. Targeted Exome Sequencing of the Cancer Genome in Patients with Very High-risk Bladder Cancer. Eur Urol 2016; 70:714-717. [PMID: 27520487 DOI: 10.1016/j.eururo.2016.07.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 12/20/2015] [Accepted: 07/20/2016] [Indexed: 11/27/2022]
Abstract
We completed targeted exome sequencing of the tumors of 50 patients with pTis-pT4b bladder cancer. Mutations were categorized by type, stratified against previously identified cancer loci in the Catalogue of Somatic Mutations in Cancer and The Cancer Genome Atlas databases, and evaluated in pathway analysis and comutation plots. We analyzed mutation associations with receipt of neoadjuvant chemotherapy, nodal involvement, metastatic disease development, and survival. Compared with The Cancer Genome Atlas, we found higher mutation rates in genes encoding products involved in epigenetic regulation and cell cycle regulation. Of the pathways examined, PI3K/mTOR and Cell Cycle/DNA Repair exhibited the greatest frequencies of mutation. RB1 and TP53, as well as NF1 and PIK3CA were frequently comutated. We identified no association between mutations in specific genes and key clinical outcomes of interest when corrected for multiple testing. Discovery phase analysis of the somatic mutations in 50 high-risk bladder cancer patients revealed novel mutations and mutational patterns, which may be useful for developing targeted therapy regimens or new biomarkers for patients at very high risk of disease metastasis and death. PATIENT SUMMARY In this report we found known, as well as previously unreported, genetic mutations in the tumors of patients with high-risk bladder cancer. These mutations, if validated, may serve as actionable targets for new trials.
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Affiliation(s)
- Thomas Longo
- Division of Urology, Department of Surgery, Duke University, Durham, NC, USA
| | - Kathleen F McGinley
- Division of Urology, Department of Surgery, Duke University, Durham, NC, USA
| | - Jennifer A Freedman
- Division of Oncology, Department of Medicine, Duke University, Durham, NC, USA
| | - Wiguins Etienne
- Division of Urology, Department of Surgery, Duke University, Durham, NC, USA
| | - Yuan Wu
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Alexander Sibley
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jeremy Gresham
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | | | | | | | - Hui Zhou
- GlaxoSmithKline, Zebulon, NC, USA
| | | | - Brant A Inman
- Division of Urology, Department of Surgery, Duke University, Durham, NC, USA.
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Horn T, Ferretti S, Ebel N, Tam A, Ho S, Harbinski F, Farsidjani A, Zubrowski M, Halilovic E, Morris E, Sellers WR, Schlegel R, Wuerthner J, Garraway LA, Jeay S, Greshock J, Caponigro G, Lehár J. Abstract LB-B04: Complex drug combinations can induce apoptotic killing in robust colorectal cancer cells. Mol Cancer Ther 2015. [DOI: 10.1158/1535-7163.targ-15-lb-b04] [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
Tumors are complex and robust biological systems that harbor the potential to proliferate against various drug treatments. Drug combinations provide a promising therapeutic strategy, but it is not clear which and how many drugs are required to overcome cancers.
Using image-based proliferation and apoptosis assays in colorectal cancer cells we systematically investigated complex treatments composed of two to six drugs targeting critical oncogenic pathways. Drug pairs targeting growth signaling resulted in synergies across a broad spectrum of genetic backgrounds, but often yielded cytostatic responses and failed to induce apoptosis. Enhanced, and sometimes genotype-specific cytotoxicity was seen after targeting additional mechanisms including apoptosis or cell cycle. Cells that resisted all tested drug pairs and drug triples were protected by a mechanism that prevented apoptosis. Targeted inhibition of this mechanism using combinations of up to four compounds induced cytotoxic responses in cells in vitro and in vivo.
Our results demonstrate that complex combinations of targeted drugs might be required to induce killing in cancers and show how the cells' genetic alterations and a molecular understanding of drug responses can guide their identification. The identification of resistance mechanisms that are pre-existing in subpopulations of tumor cells also opens the exciting avenue of sequenced treatments, with each drug or drug combination targeting and eradicating a specific cell population.
Citation Format: Thomas Horn, Stéphane Ferretti, Nicolas Ebel, Angela Tam, Samuel Ho, Fred Harbinski, Ali Farsidjani, Matthew Zubrowski, Ensar Halilovic, Erick Morris, William R. Sellers, Robert Schlegel, Jens Wuerthner, Levi A. Garraway, Sébastien Jeay, Joel Greshock, Giordano Caponigro, Joseph Lehár. Complex drug combinations can induce apoptotic killing in robust colorectal cancer cells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B04.
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Affiliation(s)
- Thomas Horn
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Nicolas Ebel
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Angela Tam
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Samuel Ho
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Fred Harbinski
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Ali Farsidjani
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | | | - Erick Morris
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | | | - Jens Wuerthner
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Sébastien Jeay
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Joel Greshock
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
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Jaeger S, Lee BH, Mosher R, Shebnova O, Wang Y, Yu Y, Yang D, Murakami M, Greshock J, Schlegel R, Boral A, Cao ZA. Abstract 1314: Evaluation of PD-L1 mRNA and protein expression in non-small cell lung and hepatocellular carcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1314] [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
SJ and BHL contributed equally to this work
BACKGROUND:
Tumor immunotherapy is a unique therapeutic modality against human cancers. The recent success of PD1 antibody treatments highlight the value and potential of this approach. While there is no definitive clinical biomarker that is prognostic of PD1 antibody efficacy, the presence of PD-L1 protein detected by immunohistochemistry has correlated positively to clinical responses to anti-PD1 and PD-L1 therapies. To enable broad examination of cancer indications for PD1/PD-L1 based therapies, we sought to evaluate PD-L1 expression at both the protein and mRNA level in lung and hepatic tumors.
MATERIALS & METHODS:
PD-L1 protein expression was evaluated in a set of formalin-fixed paraffin-embedded non-small cell lung (NSCLC) adenocarcinoma (ACA), NSCLC squamous cell carcinoma (SCC), and hepatocellular carcinoma (HCC) tumors by immunohistochemistry (IHC). PD-L1 expression was scored semi-quantitatively by a manual histo-score (H-score) methodology based on staining intensity and percentage of positive tumor cells. In our IHC analysis, PD-L1 positivity (PD-L1+) was defined as an H-score ≥ 20. In parallel, PD-L1 mRNA expression data was examined from The Cancer Genome Atlas (TCGA) in these same indications (503 NSCLC ACA, 489 NSCLC SCC, and 191 HCC) and analyzed by comparing the expression in matched normal tissues from TCGA.
RESULTS:
With RNAseq analysis, data was calculated as log2 (RPKM+0.1) after RSEM normalization, utilizing OmicSoft RNASeq pipelines across TCGA tumor indications. The expression of PD-L1 is elevated in NSCLC ACA and SCC, relative to that in HCC. By overlaying the distributions and comparing the expression levels across all indications in TCGA, we ranked overexpression profiles for PD-L1 and found the TCGA HCC cohort to have much reduced PD-L1 mRNA levels, with a median level of -0.8 compared to 1.3 for ACA and 1.5 for SCC, which amounts to more than a 2-fold change of median level expression. With RNAseq, our analysis defines 50% of NSCLC adenocarcinoma, 54% of NSCLC squamous cell carcinoma, and 6% of HCC as high expressers for PD-L1.
Tumor cell PD-L1 protein expression was measured in 45 lung adenocarcinoma, 47 lung squamous cell carcinoma, and 69 hepatocellular carcinoma. 16/45 (35.6%) lung ACA, 21/47 (44.7%) lung SCC were PD-L1 positive. In contrast, PD-L1 positivity was seen in only 5/69 (7.2%) HCC samples.
CONCLUSIONS:
In summary, with IHC and RNAseq analysis in large and independent human NSCLC and HCC sample sets, we have found PD-L1 expression to be more enriched in NSCLC than in HCC. Importantly, amongst the large number of samples (161 for IHC and 1183 for RNAseq) in the 3 indications, very good concordance is observed between protein- and mRNA-based analyses. Our finding thus establishes the basis for large scale mRNA-based data mining for indications and patient segments enriched for responses to PD1/PD-L1-based immune therapies.
Citation Format: Savina Jaeger, Benjamin H. Lee, Rebecca Mosher, Olga Shebnova, Yan Wang, Yenyen Yu, David Yang, Masato Murakami, Joel Greshock, Robert Schlegel, Anthony Boral, Zhu Alexander Cao. Evaluation of PD-L1 mRNA and protein expression in non-small cell lung and hepatocellular carcinoma. [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 1314. doi:10.1158/1538-7445.AM2015-1314
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Frampton GM, Ali SM, Rosenzweig M, Chmielecki J, Lu X, Bauer TM, Akimov M, Bufill JA, Lee C, Jentz D, Hoover R, Ou SHI, Salgia R, Brennan T, Chalmers ZR, Jaeger S, Huang A, Elvin JA, Erlich R, Fichtenholtz A, Gowen KA, Greenbowe J, Johnson A, Khaira D, McMahon C, Sanford EM, Roels S, White J, Greshock J, Schlegel R, Lipson D, Yelensky R, Morosini D, Ross JS, Collisson E, Peters M, Stephens PJ, Miller VA. Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. Cancer Discov 2015; 5:850-9. [PMID: 25971938 DOI: 10.1158/2159-8290.cd-15-0285] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/11/2015] [Indexed: 12/20/2022]
Abstract
UNLABELLED Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (METex14) that result in exon skipping and MET activation have been characterized, but their full diversity and prevalence across tumor types are unknown. Here, we report analysis of tumor genomic profiles from 38,028 patients to identify 221 cases with METex14 mutations (0.6%), including 126 distinct sequence variants. METex14 mutations are detected most frequently in lung adenocarcinoma (3%), but also frequently in other lung neoplasms (2.3%), brain glioma (0.4%), and tumors of unknown primary origin (0.4%). Further in vitro studies demonstrate sensitivity to MET inhibitors in cells harboring METex14 alterations. We also report three new patient cases with METex14 alterations in lung or histiocytic sarcoma tumors that showed durable response to two different MET-targeted therapies. The diversity of METex14 mutations indicates that diagnostic testing via comprehensive genomic profiling is necessary for detection in a clinical setting. SIGNIFICANCE Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors.
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Affiliation(s)
| | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Xinyuan Lu
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Todd M Bauer
- Sarah Cannon Research Institute/Tennessee Oncology, PLLC, Nashville, Tennessee
| | | | - Jose A Bufill
- Michiana Hematology-Oncology, PC, Mishawaka, Indiana
| | - Carrie Lee
- University of North Carolina School of Medicine, Clinical Research, Thoracic Oncology Program, Chapel Hill, North Carolina
| | - David Jentz
- South Bend Medical Foundation, South Bend, Indiana
| | - Rick Hoover
- South Bend Medical Foundation, South Bend, Indiana
| | - Sai-Hong Ignatius Ou
- Division of Hematology-Oncology, Department of Medicine, University of California Irvine School of Medicine, Irvine, California
| | - Ravi Salgia
- The University of Chicago School of Medicine, Chicago, Illinois
| | - Tim Brennan
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | - Savina Jaeger
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Alan Huang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | | | | | - Kyle A Gowen
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | | | | | | | - Steven Roels
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Jared White
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Joel Greshock
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Robert Schlegel
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Doron Lipson
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | | | - Eric Collisson
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
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Hu X, Feng Y, Zhang D, Zhao SD, Hu Z, Greshock J, Zhang Y, Yang L, Zhong X, Wang LP, Jean S, Li C, Huang Q, Katsaros D, Montone KT, Tanyi JL, Lu Y, Boyd J, Nathanson KL, Li H, Mills GB, Zhang L. A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell 2014; 26:344-357. [PMID: 25203321 PMCID: PMC4159613 DOI: 10.1016/j.ccr.2014.07.009] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 05/17/2014] [Accepted: 07/15/2014] [Indexed: 02/02/2023]
Abstract
In a genome-wide survey on somatic copy-number alterations (SCNAs) of long noncoding RNA (lncRNA) in 2,394 tumor specimens from 12 cancer types, we found that about 21.8% of lncRNA genes were located in regions with focal SCNAs. By integrating bioinformatics analyses of lncRNA SCNAs and expression with functional screening assays, we identified an oncogene, focally amplified lncRNA on chromosome 1 (FAL1), whose copy number and expression are correlated with outcomes in ovarian cancer. FAL1 associates with the epigenetic repressor BMI1 and regulates its stability in order to modulate the transcription of a number of genes including CDKN1A. The oncogenic activity of FAL1 is partially attributable to its repression of p21. FAL1-specific siRNAs significantly inhibit tumor growth in vivo.
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Affiliation(s)
- Xiaowen Hu
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Feng
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dongmei Zhang
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; State Key Laboratory of Biotherapy, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Sihai D Zhao
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - Zhongyi Hu
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joel Greshock
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Youyou Zhang
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lu Yang
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Xiaomin Zhong
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Stem Biology and Tissue Engineering, Department of Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Li-Ping Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Jean
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunsheng Li
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Dionyssios Katsaros
- Department of Obstetrics and Gynecology, University of Turin, Turin 10124, Italy
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janos L Tanyi
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yiling Lu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 7705, USA
| | - Jeff Boyd
- Cancer Genome Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gordon B Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX 7705, USA
| | - Lin Zhang
- Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Research on Reproduction & Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Cheng J, Greshock J, Shi L, Zheng S, Menius A, Lee K. Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis. BMC Syst Biol 2013; 7 Suppl 4:S2. [PMID: 24565120 PMCID: PMC3854673 DOI: 10.1186/1752-0509-7-s4-s2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Biomarker discovery holds the promise for advancing personalized medicine as the biomarkers can help match patients to optimal treatment to improve patient outcomes. However, serious concerns have been raised because very few molecular biomarkers or signatures discovered from high dimensional array data can be successfully validated and applied to clinical use. We propose good practice guidelines as well as a novel tool for biomarker discovery and use breast cancer prognosis as a case study to illustrate the proposed approach. Results We applied the proposed approach to a publicly available breast cancer prognosis dataset and identified small numbers of predictive markers for patient subpopulations stratified by clinical variables. Results from an independent cross-platform validation set show that our model compares favorably to other gene signature and clinical variable based prognostic tools. About half of the discovered candidate markers can individually achieve very good performance, which further demonstrate the high quality of feature selection. These candidate markers perform extremely well for young patient with estrogen receptor-positive, lymph node-negative early stage breast cancers, suggesting a distinct subset of these patients identified by these markers is actually at high risk of recurrence and may benefit from more aggressive treatment than cur-rent practice. Conclusion The results show that by following good practice guidelines, we can identify highly predictive genes in high dimensional breast cancer array data. These predictive genes have been successfully validated using an independent cross-platform dataset.
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13
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Billiard J, Dennison JB, Briand J, Annan RS, Chai D, Colón M, Dodson CS, Gilbert SA, Greshock J, Jing J, Lu H, McSurdy-Freed JE, Orband-Miller LA, Mills GB, Quinn CJ, Schneck JL, Scott GF, Shaw AN, Waitt GM, Wooster RF, Duffy KJ. Quinoline 3-sulfonamides inhibit lactate dehydrogenase A and reverse aerobic glycolysis in cancer cells. Cancer Metab 2013; 1:19. [PMID: 24280423 PMCID: PMC4178217 DOI: 10.1186/2049-3002-1-19] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [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: 05/31/2013] [Accepted: 08/27/2013] [Indexed: 12/13/2022] Open
Abstract
Background Most normal cells in the presence of oxygen utilize glucose for mitochondrial oxidative phosphorylation. In contrast, many cancer cells rapidly convert glucose to lactate in the cytosol, a process termed aerobic glycolysis. This glycolytic phenotype is enabled by lactate dehydrogenase (LDH), which catalyzes the inter-conversion of pyruvate and lactate. The purpose of this study was to identify and characterize potent and selective inhibitors of LDHA. Methods High throughput screening and lead optimization were used to generate inhibitors of LDHA enzymatic activity. Effects of these inhibitors on metabolism were evaluated using cell-based lactate production, oxygen consumption, and 13C NMR spectroscopy assays. Changes in comprehensive metabolic profile, cell proliferation, and apoptosis were assessed upon compound treatment. Results 3-((3-carbamoyl-7-(3,5-dimethylisoxazol-4-yl)-6-methoxyquinolin-4-yl) amino) benzoic acid was identified as an NADH-competitive LDHA inhibitor. Lead optimization yielded molecules with LDHA inhibitory potencies as low as 2 nM and 10 to 80-fold selectivity over LDHB. Molecules in this family rapidly and profoundly inhibited lactate production rates in multiple cancer cell lines including hepatocellular and breast carcinomas. Consistent with selective inhibition of LDHA, the most sensitive breast cancer cell lines to lactate inhibition in hypoxic conditions were cells with low expression of LDHB. Our inhibitors increased rates of oxygen consumption in hepatocellular carcinoma cells at doses up to 3 microM, while higher concentrations directly inhibited mitochondrial function. Analysis of more than 500 metabolites upon LDHA inhibition in Snu398 cells revealed that intracellular concentrations of glycolysis and citric acid cycle intermediates were increased, consistent with enhanced Krebs cycle activity and blockage of cytosolic glycolysis. Treatment with these compounds also potentiated PKM2 activity and promoted apoptosis in Snu398 cells. Conclusions Rapid chemical inhibition of LDHA by these quinoline 3-sulfonamids led to profound metabolic alterations and impaired cell survival in carcinoma cells making it a compelling strategy for treating solid tumors that rely on aerobic glycolysis for survival.
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Affiliation(s)
- Julia Billiard
- Cancer Metabolism DPU, GlaxoSmithKline, Collegeville PA, USA.
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14
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Nathanson KL, Martin AM, Wubbenhorst B, Greshock J, Letrero R, D'Andrea K, O'Day S, Infante JR, Falchook GS, Arkenau HT, Millward M, Brown MP, Pavlick A, Davies MA, Ma B, Gagnon R, Curtis M, Lebowitz PF, Kefford R, Long GV. Tumor genetic analyses of patients with metastatic melanoma treated with the BRAF inhibitor dabrafenib (GSK2118436). Clin Cancer Res 2013; 19:4868-78. [PMID: 23833299 DOI: 10.1158/1078-0432.ccr-13-0827] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE Dabrafenib is a selective inhibitor of V600-mutant BRAF kinase, which recently showed improved progression-free survival (PFS) as compared with dacarbazine, in metastatic melanoma patients. This study examined potential genetic markers associated with response and PFS in the phase I study of dabrafenib. EXPERIMENTAL DESIGN Baseline (pretreatment or archival) melanoma samples were evaluated in 41 patients using a custom genotyping melanoma-specific assay, sequencing of PTEN, and copy number analysis using multiplex ligation amplification and array-based comparative genomic hybridization. Nine patients had on-treatment and/or progression samples available. RESULTS All baseline patient samples had BRAF(V600E/K) confirmed. Baseline PTEN loss/mutation was not associated with best overall response to dabrafenib, but it showed a trend for shorter median PFS [18.3 (95% confidence interval, CI, 9.1-24.3) vs. 32.1 weeks (95% CI, 24.1-33), P=0.059]. Higher copy number of CCND1 (P=0.009) and lower copy number of CDKN2A (P=0.012) at baseline were significantly associated with decreased PFS. Although no melanomas had high-level amplification of BRAF, the two patients with progressive disease as their best response had BRAF copy gain in their tumors. CONCLUSIONS Copy number changes in CDKN2A, CCND1, and mutation/copy number changes in PTEN correlated with the duration of PFS in patients treated with dabrafenib. The results suggest that these markers should be considered in the design and interpretation of future trials with selective BRAF inhibitors in advanced melanoma patients.
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Affiliation(s)
- Katherine L Nathanson
- Department of Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Hou W, Qin X, Zhu X, Fei M, Liu P, Liu L, Moon H, Zhang P, Greshock J, Bachman KE, Ye BC, Wang H, Zang CYQ. Lapatinib inhibits the growth of esophageal squamous cell carcinoma and synergistically interacts with 5-fluorouracil in patient-derived xenograft models. Oncol Rep 2013; 30:707-14. [PMID: 23708506 DOI: 10.3892/or.2013.2500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/19/2013] [Indexed: 11/05/2022] Open
Abstract
Lapatinib is a dual tyrosine kinase inhibitor of epidermal growth factor receptor (EGFR) and human EGFR-2 (HER2) tyrosine kinase domains. To explore the potential utility of lapatinib for the treatment of esophageal squamous cell carcinoma (ESCC), we examined the expression profiles of EGFR and HER2 in tumor tissues and in paired adjacent non-neoplastic tissues from patients with ESCC. We evaluated the antitumor effects of lapatinib alone or in combination with oxaliplatin or 5-fluorouracil (5-FU) on a panel of primary ESCC cells in vitro with various levels of EGFR and HER2 expression. The in vivo effect of lapatinib alone or in combination with oxaliplatin or 5-FU was evaluated using a primary ESCC xenograft model. EGFR was overexpressed in 80.9% (76/94) of the ESCC samples, while 24.5% (23/94) of the samples overexpressed HER2. EGFR and HER2 co-overexpression was detected in 22.3% of samples (21/94). In vitro, the primary ESCC cells were more sensitive to lapatinib combined with 5-FU or oxaliplatin than to lapatinib alone. Lapatinib in combination with 5-FU had more potent antitumor effects in the primary ESCC xenograft model, and markedly reduced the phosphorylation of EGFR and HER2, compared with lapatinib alone or in combination with oxaliplatin. These data indicate that lapatinib has activity in EGFR- and/or HER2-expressing ESCC primary cells, and that lapatinib in combination with 5-FU may be a promising treatment strategy for patients with ESCC.
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Affiliation(s)
- Wenmin Hou
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, PR China
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16
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Abstract
Abstract
The phosphoinositide 3-kinase (PI3K) pathway is among the most commonly mutated pathways in human cancer. The majority of first-generation PI3K inhibitors currently in clinical trials inhibit multiple PI3K isoforms. The PIK3CB gene encodes p110β isoform, which has been reported to be required for pathway activation in phosphatase and tensin homolog (PTEN) deficient cancer cells. The observed dependence of PTEN-deficient tumors on p110β provides an opportunity for identification of a novel isoform-selective therapeutic with a synthetic lethal effect. During an extensive knowledge-based lead identification and optimization effort, we identified substituted benzimidazole GSK2636771 as a potent, orally bioavailable, PI3Kβ-selective inhibitor. The observed enzymatic potency for PI3Kβ is approximately 1000 and 10 fold higher than the potency against PI3Kα and PI3δ respectively. Pre-clinical data demonstrate the synthetic lethal relationship between PTEN deficiencies and PI3K-β inhibition. PTEN-deficient cells dosed with GSK2636771 show concentration dependent decreases in cellular levels of phosphorylated AKT (pAKT), and PRAS40 both in-vitro and in-vivo. A 3-day proliferation assay performed on a large panel of cell lines (n=80) grown in-vitro demonstrates selective growth inhibition in PTEN-deficient cells at lower concentrations of GSK2636771. In-vivo studies in PTEN-deficient prostate cancer models also show dose dependent tumor growth delay. PTEN is commonly mutated, deleted, or epigenetically silenced in a wide range of solid tumors. Loss of PTEN protein is particularly frequent in prostate (50%), endometrial (57%), and triple negative breast cancers (30%). Prospective selection of patients with this protein loss serves as a development path through the course of study P3B115717 (NCT01458067), a Phase I/IIa first-time-in-human study with GSK2363771. This study is currently in dose-escalation.β
Citation Format: Joel Greshock. Exploiting the synthetic lethal properties of selective PI3K-β inhibition in PTEN deficient cells with GSK2636771. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr IA17.
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Zhu X, Qin X, Fei M, Hou W, Greshock J, Bachman KE, Kang J, Qin CY. Loss and reduced expression of PTEN correlate with advanced-stage gastric carcinoma. Exp Ther Med 2012; 5:57-64. [PMID: 23251242 PMCID: PMC3524019 DOI: 10.3892/etm.2012.749] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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: 04/25/2012] [Accepted: 09/14/2012] [Indexed: 12/14/2022] Open
Abstract
Phosphatase and tensin homolog (PTEN) is a tumor suppressor involved in multiple cell processes. To investigate the role of PTEN in the development of gastric carcinoma, we determined the expression pattern of PTEN in primary gastric carcinoma and in paired adjacent non-neoplastic tissue. We also determined the correlation of PTEN expression with clinicopathological characteristics and patient survival. Overall, 159 gastric carcinomas and 151 paired adjacent non-neoplastic tissues were used in the present study. PTEN expression was determined using tissue microarrays and immunohistochemistry. The clinical sensitivity and specificity of PTEN expression were calculated using receiver operator characteristic curves. Results showed that the loss of cytoplasmic PTEN was significantly more frequent in carcinoma tissue compared with adjacent non-neoplastic tissue (62 vs. 5%, respectively; P<0.0001). PTEN expression was markedly downregulated in carcinoma tissues compared with adjacent non-neoplastic tissues. The loss of cytoplasmic PTEN expression was positively correlated with histological stage (P=0.016). The loss of nuclear or total PTEN, and downregulation of total PTEN expression, was significantly different between American Joint Committee on Cancer tumors of stage I and stages II-IV. A low cytoplasmic or total PTEN expression showed high clinical sensitivity and specificity for gastric carcinoma. However, PTEN expression was not significantly associated with overall or 3-year survival rates. The findings of the present study indicated that PTEN expression may be a molecular diagnostic marker for gastric cancer. Thus, the loss or reduced expression of PTEN potentially correlate with advanced stages of gastric carcinoma.
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Affiliation(s)
- Xuehua Zhu
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University
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18
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Hou W, Fei M, Qin X, Zhu X, Greshock J, Liu P, Zhou Y, Wang H, Ye BC, Qin CY. High overexpression of fatty acid synthase is associated with poor survival in Chinese patients with gastric carcinoma. Exp Ther Med 2012; 4:999-1004. [PMID: 23226763 PMCID: PMC3494127 DOI: 10.3892/etm.2012.727] [Citation(s) in RCA: 6] [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: 02/06/2012] [Accepted: 09/19/2012] [Indexed: 12/26/2022] Open
Abstract
Fatty acid synthase (FAS) is the key enzyme regulating de novo biosynthesis of fatty acids. FAS overexpression has been found in many types of tumors and is associated with poor survival. However, the expression of FAS and its relationship with prognosis in Chinese patients with gastric carcinoma are still unknown. Therefore, in this study, we examined the expression of FAS using tissue microarrays and determined its correlation with clinicopathological characteristics and prognosis of gastric carcinoma in Chinese patients. FAS overexpression was graded as S (T/A) <1, ≥1 to <2, ≥2 to <3 or ≥3 in 35 (38.9%), 20 (22.2%), 9 (10%) and 26 (28.9%) patients, respectively. High FAS overexpression [S (T/A) ≥3] was significantly correlated with poor prognosis (log-rank test, P= 0.0078) and with decreased 3-year survival rate (χ2 test, P=0.0023). FAS overexpression was not significantly associated with other clinicopathological characteristics. In conclusion, our results suggest that FAS expression might be a potential prognostic marker for gastric carcinoma in Chinese patients.
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Affiliation(s)
- Wenmin Hou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology; ; Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences
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Wang Y, Hu X, Greshock J, Shen L, Yang X, Shao Z, Liang S, Tanyi JL, Sood AK, Zhang L. Genomic DNA copy-number alterations of the let-7 family in human cancers. PLoS One 2012; 7:e44399. [PMID: 22970210 PMCID: PMC3435307 DOI: 10.1371/journal.pone.0044399] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 08/06/2012] [Indexed: 12/19/2022] Open
Abstract
In human cancer, expression of the let-7 family is significantly reduced, and this is associated with shorter survival times in patients. However, the mechanisms leading to let-7 downregulation in cancer are still largely unclear. Since an alteration in copy-number is one of the causes of gene deregulation in cancer, we examined copy number alterations of the let-7 family in 2,969 cancer specimens from a high-resolution SNP array dataset. We found that there was a reduction in the copy number of let-7 genes in a cancer-type specific manner. Importantly, focal deletion of four let-7 family members was found in three cancer types: medulloblastoma (let-7a-2 and let-7e), breast cancer (let-7a-2), and ovarian cancer (let-7a-3/let-7b). For example, the genomic locus harboring let-7a-3/let-7b was deleted in 44% of the specimens from ovarian cancer patients. We also found a positive correlation between the copy number of let-7b and mature let-7b expression in ovarian cancer. Finally, we showed that restoration of let-7b expression dramatically reduced ovarian tumor growth in vitro and in vivo. Our results indicate that copy number deletion is an important mechanism leading to the downregulation of expression of specific let-7 family members in medulloblastoma, breast, and ovarian cancers. Restoration of let-7 expression in tumor cells could provide a novel therapeutic strategy for the treatment of cancer.
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Affiliation(s)
- Yanling Wang
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xiaowen Hu
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel Greshock
- Abramson Family Cancer Research Institute; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Liang Shen
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xiaojun Yang
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhongjun Shao
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shun Liang
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Janos L. Tanyi
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anil K. Sood
- Department of Gynecologic Oncology, Division of Surgery, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lin Zhang
- Department of Obstetrics and Gynecology; University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Munster P, van der Noll R, Voest E, Specht J, Werner T, Dees E, Tan A, Daud A, Schellens J, Lolkema M, Griffin M, Agarwal N, Falchook G, Kleha J, Durante M, Smith D, Adams L, Greshock J, Morris S, Kurzrock R. PI3K Kinase Inhibitor GSK2126458 (GSK458): Clinical Activity in Select Patient (PT) Populations Defined by Predictive Markers (STUDY P3K112826). Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)33038-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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21
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Higgins MJ, Jelovac D, Barnathan E, Blair B, Slater S, Powers P, Zorzi J, Jeter SC, Oliver GR, Fetting J, Emens L, Riley C, Stearns V, Diehl F, Angenendt P, Huang P, Cope L, Argani P, Murphy KM, Bachman KE, Greshock J, Wolff AC, Park BH. Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin Cancer Res 2012; 18:3462-9. [PMID: 22421194 PMCID: PMC3533370 DOI: 10.1158/1078-0432.ccr-11-2696] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE We sought to evaluate the feasibility of detecting PIK3CA mutations in circulating tumor DNA (ctDNA) from plasma of patients with metastatic breast cancer using a novel technique called BEAMing. EXPERIMENTAL DESIGN In a retrospective analysis, 49 tumor and temporally matched plasma samples from patients with breast cancer were screened for PIK3CA mutations by BEAMing. We then prospectively screened the ctDNA of 60 patients with metastatic breast cancer for PIK3CA mutations by BEAMing and compared the findings with results obtained by screening corresponding archival tumor tissue DNA using both sequencing and BEAMing. RESULTS The overall frequency of PIK3CA mutations by BEAMing was similar in both patient cohorts (29% and 28.3%, respectively). In the retrospective cohort, the concordance of PIK3CA mutation status by BEAMing between formalin-fixed, paraffin-embedded (FFPE) samples and ctDNA from temporally matched plasma was 100% (34 of 34). In the prospective cohort, the concordance rate among 51 evaluable cases was 72.5% between BEAMing of ctDNA and sequencing of archival tumor tissue DNA. When the same archival tissue DNA was screened by both sequencing and BEAMing for PIK3CA mutations (n = 41 tissue samples), there was 100% concordance in the obtained results. CONCLUSIONS Analysis of plasma-derived ctDNA for the detection of PIK3CA mutations in patients with metastatic breast cancer is feasible. Our results suggest that PIK3CA mutational status can change upon disease recurrence, emphasizing the importance of reassessing PIK3CA status on contemporary (not archival) biospecimens. These results have implications for the development of predictive biomarkers of response to targeted therapies.
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Affiliation(s)
| | - Danijela Jelovac
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Evan Barnathan
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Brian Blair
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Shannon Slater
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Penny Powers
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Jane Zorzi
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Stacie C. Jeter
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - George R. Oliver
- Center for Clinical Innovation, Parkland Health and Hospital System
| | - John Fetting
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Leisha Emens
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Carol Riley
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Vered Stearns
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | | | | | - Peng Huang
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Pedram Argani
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | | | | | - Joel Greshock
- GlaxoSmithKline, Oncology R&D, Collegeville, Pennsylvania
| | - Antonio C. Wolff
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Ben H. Park
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
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Cheng J, Greshock J, Painter J, Lin X, Lee K, Zheng S, Menius A. Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis. J Integr Bioinform 2012. [DOI: 10.1515/jib-2012-209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Summary We developed a novel tool for microarray data analysis that can parsimoniously discover highly predictive genes by finding the optimal trade off between fold change and t-test p value through rigorous cross validation. In addition to find a small set of highly predictive genes, the tool also has a procedure that recursively discovers and removes predictive genes from the dataset until no such genes can be found. We applied our tool to a public breast cancer dataset with the goal to discover genes that can predict patient’s response to a preoperative chemotherapy. The results show that estrogen receptor (ER) gene is the most important gene to predict chemotherapeutic response and no gene signatures can add much clinical benefit for the whole patient population. We further identified a clinically homogenous subgroup of patients (ER-negative, PR-negative and HER2-negative) whose response to the chemotherapy can be reasonably predicted. Many of the discovered predictive markers for this subgroup of patients were successfully validated using a blinded validation set.
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Affiliation(s)
- Jie Cheng
- 1Quantitative Sciences, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Joel Greshock
- 2Cancer Research, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Jeffery Painter
- 1Quantitative Sciences, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Xiwu Lin
- 1Quantitative Sciences, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Kwan Lee
- 1Quantitative Sciences, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Shu Zheng
- 3Cancer Institute, Zhejiang University, Hangzhou, 310009, China
| | - Alan Menius
- 1Quantitative Sciences, GlaxoSmithKline, Collegeville, PA 19426, United States of America
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Kim N, He N, Kim C, Zhang F, Lu Y, Yu Q, Stemke-Hale K, Greshock J, Wooster R, Yoon S, Mills GB. Systematic analysis of genotype-specific drug responses in cancer. Int J Cancer 2012; 131:2456-64. [PMID: 22422301 DOI: 10.1002/ijc.27529] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 02/09/2012] [Indexed: 11/10/2022]
Abstract
A systematic understanding of genotype-specific sensitivity or resistance to anticancer agents is required to provide improved patient therapy. The availability of an expansive panel of annotated cancer cell lines enables comparative surveys of associations between genotypes and compounds of various target classes. Thus, one can better predict the optimal treatment for a specific tumor. Here, we present a statistical framework, cell line enrichment analysis (CLEA), to associate the response of anticancer agents with major cancer genotypes. Multilevel omics data, including transcriptome, proteome and phosphatome data, were integrated with drug data based on the genotypic classification of cancer cell lines. The results reproduced known patterns of compound sensitivity associated with particular genotypes. In addition, this approach reveals multiple unexpected associations between compounds and mutational genotypes. The mutational genotypes led to unique protein activation and gene expression signatures, which provided a mechanistic understanding of their functional effects. Furthermore, CLEA maps revealed interconnections between TP53 mutations and other mutations in the context of drug responses. The TP53 mutational status appears to play a dominant role in determining clustering patterns of gene and protein expression profiles for major cancer genotypes. This study provides a framework for the integrative analysis of mutations, drug responses and omics data in cancers.
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Affiliation(s)
- Nayoung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
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Jing J, Greshock J, Holbrook JD, Gilmartin A, Zhang X, McNeil E, Conway T, Moy C, Laquerre S, Bachman K, Wooster R, Degenhardt Y. Comprehensive predictive biomarker analysis for MEK inhibitor GSK1120212. Mol Cancer Ther 2012; 11:720-9. [PMID: 22169769 DOI: 10.1158/1535-7163.mct-11-0505] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [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
The MEK1 and MEK2 inhibitor GSK1120212 is currently in phase II/III clinical development. To identify predictive biomarkers, sensitivity to GSK1120212 was profiled for 218 solid tumor cell lines and 81 hematologic malignancy cell lines. For solid tumors, RAF/RAS mutation was a strong predictor of sensitivity. Among RAF/RAS mutant lines, co-occurring PIK3CA/PTEN mutations conferred a cytostatic response instead of a cytotoxic response for colon cancer cells that have the biggest representation of the comutations. Among KRAS mutant cell lines, transcriptomics analysis showed that cell lines with an expression pattern suggestive of epithelial-to-mesenchymal transition were less sensitive to GSK1120212. In addition, a proportion of cell lines from certain tissue types not known to carry frequent RAF/RAS mutations also seemed to be sensitive to GSK1120212. Among these were breast cancer cell lines, with triple negative breast cancer cell lines being more sensitive than cell lines from other breast cancer subtypes. We identified a single gene DUSP6, whose expression was associated with sensitivity to GSK1120212 and lack of expression associated with resistance irrelevant of RAF/RAS status. Among hematologic cell lines, acute myeloid leukemia and chronic myeloid leukemia cell lines were particularly sensitive. Overall, this comprehensive predictive biomarker analysis identified additional efficacy biomarkers for GSK1120212 in RAF/RAS mutant solid tumors and expanded the indication for GSK1120212 to patients who could benefit from this therapy despite the RAF/RAS wild-type status of their tumors.
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Affiliation(s)
- Junping Jing
- Cancer Research, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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Li N, Kaur S, Greshock J, Lassus H, Zhong X, Wang Y, Leminen A, Shao Z, Hu X, Liang S, Katsaros D, Huang Q, Bützow R, Weber BL, Coukos G, Zhang L. A combined array-based comparative genomic hybridization and functional library screening approach identifies mir-30d as an oncomir in cancer. Cancer Res 2011; 72:154-64. [PMID: 22058146 DOI: 10.1158/0008-5472.can-11-2484] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [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]
Abstract
Oncomirs are microRNAs (miRNA) that acts as oncogenes or tumor suppressor genes. Efficient identification of oncomirs remains a challenge. Here we report a novel, clinically guided genetic screening approach for the identification of oncomirs, identifying mir-30d through this strategy. mir-30d regulates tumor cell proliferation, apoptosis, senescence, and migration. The chromosomal locus harboring mir-30d was amplified in more than 30% of multiple types of human solid tumors (n = 1,283). Importantly, higher levels of mir-30d expression were associated significantly with poor clinical outcomes in ovarian cancer patients (n = 330, P = 0.0016). Mechanistic investigations suggested that mir-30d regulates a large number of cancer-associated genes, including the apoptotic caspase CASP3. The guided genetic screening approach validated by this study offers a powerful tool to identify oncomirs that may have utility as biomarkers or targets for drug development.
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Affiliation(s)
- Ning Li
- Ovarian Cancer Research Center and Department of Obstetrics & Gynecology, University of Pennsylvania, Wistar Institute, Philadelphia, Pennsylvania, USA
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Lin X, Parks DC, Greshock J, Wooster R, Lee KR. Effect of Predictive Performance of a Biomarker for the Sample Size of Targeted Designs for Randomized Clinical Trials. Stat Biopharm Res 2011. [DOI: 10.1198/sbr.2011.09047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Moy C, Oleykowski CA, Plant R, Greshock J, Jing J, Bachman K, Hardwicke MA, Wooster R, Degenhardt Y. High chromosome number in hematological cancer cell lines is a negative predictor of response to the inhibition of Aurora B and C by GSK1070916. J Transl Med 2011; 9:110. [PMID: 21762492 PMCID: PMC3146841 DOI: 10.1186/1479-5876-9-110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 04/06/2011] [Accepted: 07/15/2011] [Indexed: 01/02/2023] Open
Abstract
Background Aurora kinases play critical roles in mitosis and are being evaluated as therapeutic targets in cancer. GSK1070916 is a potent, selective, ATP competitive inhibitor of Aurora kinase B and C. Translation of predictive biomarkers to the clinic can benefit patients by identifying the tumors that are more likely to respond to therapies, especially novel inhibitors such as GSK1070916. Methods 59 Hematological cancer-derived cell lines were used as models for response where in vitro sensitivity to GSK1070916 was based on both time and degree of cell death. The response data was analyzed along with karyotype, transcriptomics and somatic mutation profiles to determine predictors of response. Results 20 cell lines were sensitive and 39 were resistant to treatment with GSK1070916. High chromosome number was more prevalent in resistant cell lines (p-value = 0.0098, Fisher Exact Test). Greater resistance was also found in cell lines harboring polyploid subpopulations (p-value = 0.00014, Unpaired t-test). A review of NOTCH1 mutations in T-ALL cell lines showed an association between NOTCH1 mutation status and chromosome number (p-value = 0.0066, Fisher Exact Test). Conclusions High chromosome number associated with resistance to the inhibition of Aurora B and C suggests cells with a mechanism to bypass the high ploidy checkpoint are resistant to GSK1070916. High chromosome number, a hallmark trait of many late stage hematological malignancies, varies in prevalence among hematological malignancy subtypes. The high frequency and relative ease of measurement make high chromosome number a viable negative predictive marker for GSK1070916.
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Affiliation(s)
- Christopher Moy
- GlaxoSmithKline Oncology Research, Cancer Metabolism, 1250 Collegeville Road, Collegeville, PA 19426, USA.
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28
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Huang J, Zhang L, Greshock J, Colligon TA, Wang Y, Ward R, Katsaros D, Lassus H, Butzow R, Godwin AK, Testa JR, Nathanson KL, Gimotty PA, Coukos G, Weber BL, Degenhardt Y. Frequent genetic abnormalities of the PI3K/AKT pathway in primary ovarian cancer predict patient outcome. Genes Chromosomes Cancer 2011. [PMID: 21563232 DOI: 10.1002/gcc.20883] [] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Identification and characterization of underlying genetic aberrations could facilitate diagnosis and treatment of ovarian cancer. Copy number analysis using array Comparative Genomic Hybridization (aCGH) on 93 primary ovarian tumors identified PI3K/AKT pathway as the most frequently altered cancer related pathway. Furthermore, survival analyses to correlate gene copy number and mutation data with patient outcome showed that copy number gains of PIK3CA, PIK3CB, and PIK3R4 in these tumors were associated with decreased survival. To confirm these findings at the protein level, immunohistochemistry (IHC) for PIK3CA product p110α and p-Akt was performed on tissue microarrays from 522 independent serous ovarian cancers. Overexpression of either of these two proteins was found to be associated with decreased survival. Multivariant analysis from these samples further showed that overexpression of p-AKT and/or p110α is an independent prognostic factor for these tumors. siRNAs targeting altered PI3K/AKT pathway genes inhibited proliferation and induced apoptosis in ovarian cancer cell lines. In addition, the effect of the siRNAs in different cell lines seemed to correlate with the particular genetic alterations that the cell line carries. These results strongly support the utilization of PI3K pathway inhibitors in ovarian cancer. They also suggest identifying the specific component in the PI3K pathway that is genetically altered has the potential to help select the most effective therapy. Both mutation as well as copy number changes can be used as predictive markers for this purpose.
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Affiliation(s)
- Jia Huang
- Department of Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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29
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Huang J, Zhang L, Greshock J, Colligon TA, Wang Y, Ward R, Katsaros D, Lassus H, Butzow R, Godwin AK, Testa JR, Nathanson KL, Gimotty PA, Coukos G, Weber BL, Degenhardt Y. Frequent genetic abnormalities of the PI3K/AKT pathway in primary ovarian cancer predict patient outcome. Genes Chromosomes Cancer 2011; 50:606-18. [PMID: 21563232 DOI: 10.1002/gcc.20883] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 03/24/2011] [Indexed: 11/10/2022] Open
Abstract
Identification and characterization of underlying genetic aberrations could facilitate diagnosis and treatment of ovarian cancer. Copy number analysis using array Comparative Genomic Hybridization (aCGH) on 93 primary ovarian tumors identified PI3K/AKT pathway as the most frequently altered cancer related pathway. Furthermore, survival analyses to correlate gene copy number and mutation data with patient outcome showed that copy number gains of PIK3CA, PIK3CB, and PIK3R4 in these tumors were associated with decreased survival. To confirm these findings at the protein level, immunohistochemistry (IHC) for PIK3CA product p110α and p-Akt was performed on tissue microarrays from 522 independent serous ovarian cancers. Overexpression of either of these two proteins was found to be associated with decreased survival. Multivariant analysis from these samples further showed that overexpression of p-AKT and/or p110α is an independent prognostic factor for these tumors. siRNAs targeting altered PI3K/AKT pathway genes inhibited proliferation and induced apoptosis in ovarian cancer cell lines. In addition, the effect of the siRNAs in different cell lines seemed to correlate with the particular genetic alterations that the cell line carries. These results strongly support the utilization of PI3K pathway inhibitors in ovarian cancer. They also suggest identifying the specific component in the PI3K pathway that is genetically altered has the potential to help select the most effective therapy. Both mutation as well as copy number changes can be used as predictive markers for this purpose.
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Affiliation(s)
- Jia Huang
- Department of Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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30
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Moy C, Aziz MU, Greshock J, Szabo S, McNeil E, Jing J, Conway T, Degenhardt Y, Wooster R, Bachman K. Mutation and copy number detection in human cancers using a custom genotyping assay. Genomics 2011; 98:296-301. [PMID: 21600279 DOI: 10.1016/j.ygeno.2011.04.008] [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] [Received: 01/28/2011] [Revised: 04/13/2011] [Accepted: 04/17/2011] [Indexed: 10/18/2022]
Abstract
Identification of biomarkers for positive and negative predictors of response to cancer therapeutics can help direct clinical strategies. However, challenges with tissue availability and costs are significant limiting factors for diagnostic assays. To address these challenges, we have customized a high-throughput single nucleotide polymorphism genotyping assay with the objective of simultaneously surveying known somatic mutations and copy number alterations for translational studies in cancer. As constructed, this assay can interrogate 376 known somatic mutations and quantify copy number alterations of genes commonly implicated in tumorigenesis or progression. Validation of this assay on a panel of 321 cell lines demonstrates sensitivity to accurately detect mutations, robust accuracy in the presence of infiltrating normal tissue, and the ability to detect both DNA copy number amplifications and deletions. This technology, with its high sensitivity, small DNA requirements, and low costs is an attractive platform for biomarker exploration in cancer.
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Affiliation(s)
- Christopher Moy
- GlaxoSmithKline Oncology Research, Cancer Metabolism, 1250 Collegeville Road, Collegeville, PA 19426, USA
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31
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Degenhardt Y, Greshock J, Laquerre S, Gilmartin AG, Jing J, Richter M, Zhang X, Bleam M, Halsey W, Hughes A, Moy C, Liu-Sullivan N, Powers S, Bachman K, Jackson J, Weber B, Wooster R. Sensitivity of cancer cells to Plk1 inhibitor GSK461364A is associated with loss of p53 function and chromosome instability. Mol Cancer Ther 2010; 9:2079-89. [PMID: 20571075 DOI: 10.1158/1535-7163.mct-10-0095] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Polo-like kinases are a family of serine threonine kinases that are critical regulators of cell cycle progression and DNA damage response. Predictive biomarkers for the Plk1-selective inhibitor GSK461364A were identified by comparing the genomics and genetics of a panel of human cancer cell lines with their response to a drug washout followed by an outgrowth assay. In this assay, cell lines that have lost p53 expression or carry mutations in the TP53 gene tended to be more sensitive to GSK461364A. These more sensitive cell lines also had increased levels of chromosome instability, a characteristic associated with loss of p53 function. Further mechanistic studies showed that p53 wild-type (WT) and not mutant cells can activate a postmitotic tetraploidy checkpoint and arrest at pseudo-G(1) state after GSK461364A treatment. RNA silencing of WT p53 increased the antiproliferative activity of GSK461364A. Furthermore, silencing of p53 or p21/CDKN1A weakened the tetraploidy checkpoint in cells that survived mitotic arrest and mitotic slippage. As many cancer therapies tend to be more effective in p53 WT patients, the higher sensitivity of p53-deficient tumors toward GSK461364A could potentially offer an opportunity to treat tumors that are refractory to other chemotherapies as well as early line therapy for these genotypes.
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Affiliation(s)
- Yan Degenhardt
- Cancer Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA.
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Greshock J, Bachman KE, Degenhardt YY, Jing J, Wen YH, Eastman S, McNeil E, Moy C, Wegrzyn R, Auger K, Hardwicke MA, Wooster R. Molecular target class is predictive of in vitro response profile. Cancer Res 2010; 70:3677-86. [PMID: 20406975 DOI: 10.1158/0008-5472.can-09-3788] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [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
Preclinical cellular response profiling of tumor models has become a cornerstone in the development of novel cancer therapeutics. As efforts to predict clinical efficacy using cohorts of in vitro tumor models have been successful, expansive panels of tumor-derived cell lines can recapitulate an "all comers" efficacy trial, thereby identifying which tumors are most likely to benefit from treatment. The response profile of a therapy is most often studied in isolation; however, drug treatment effect patterns in tumor models across a diverse panel of compounds can help determine the value of unique molecular target classes in specific tumor cohorts. To this end, a panel of 19 compounds was evaluated against a diverse group of cancer cell lines (n = 311). The primary oncogenic targets were a key determinant of concentration-dependent proliferation response, as a total of five of six, four of four, and five of five phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway, insulin-like growth factor-I receptor (IGF-IR), and mitotic inhibitors, respectively, clustered with others of that common target class. In addition, molecular target class was correlated with increased responsiveness in certain histologies. A cohort of PI3K/AKT/mTOR inhibitors was more efficacious in breast cancers compared with other tumor types, whereas IGF-IR inhibitors more selectively inhibited growth in colon cancer lines. Finally, specific phenotypes play an important role in cellular response profiles. For example, luminal breast cancer cells (nine of nine; 100%) segregated from basal cells (six of seven; 86%). The convergence of a common cellular response profile for different molecules targeting the same oncogenic pathway substantiates a rational clinical path for patient populations most likely to benefit from treatment. Cancer Res; 70(9); 3677-86. (c)2010 AACR.
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Affiliation(s)
- Joel Greshock
- Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA
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Degenhardt Y, Huang J, Greshock J, Horiates G, Nathanson K, Yang X, Herlyn M, Weber B. Distinct MHC gene expression patterns during progression of melanoma. Genes Chromosomes Cancer 2010; 49:144-54. [PMID: 19862823 DOI: 10.1002/gcc.20728] [Citation(s) in RCA: 19] [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] [Indexed: 11/10/2022] Open
Abstract
Abnormal expression of major histocompatibility complex (MHC) molecules in melanoma has been reported previously. However, the MHC molecule expression patterns in different growth phases of melanoma and the underlying mechanisms are not well understood. Here, we demonstrate that in vertical growth phase (VGP) melanomas, MHC genes are subject to increased rates of DNA copy number gains, accompanied by increased expression, in comparison to normal melanocytes. In contrast, MHC expression in metastatic melanomas drastically decreased compared to VGP melanomas, despite still prevalent DNA copy number gains. Subsequent investigations found that the master transactivator of MHC genes, CIITA, was also significantly downregulated in metastatic melanomas when compared to VGP melanomas. This could be one of the mechanisms accounting for the discrepancy between DNA copy number and expression level in metastatic melanomas, a potentially separate mechanism of gene regulation. These results infer a dynamic role of MHC function in melanoma progression. We propose potential mechanisms for the overexpression of MHC molecules in earlier stages of melanoma as well as for its downregulation in metastatic melanomas.
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Affiliation(s)
- Yan Degenhardt
- Cancer Metabolism DPU, Oncology, GlaxoSmithKline, King of Prussia, PA 19406, USA.
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34
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Degenhardt YY, Zhang X, Moy C, Conway T, Mcneil L, Jing J, Greshock J, Wegrzyn R, Yin H, Mousses S, Wooster R, Bachman K. Abstract B173: Synergistic interaction between CENP-E inhibitor GSK923295 and MEK inhibitor GSK1120212. Mol Cancer Ther 2009. [DOI: 10.1158/1535-7163.targ-09-b173] [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
Centromere protein-E (CENP-E) is a mitotic kinesin that is required during mitosis for metaphase chromosome alignment. GSK923295 (′295) is a potent and specific inhibitor of human CENP-E currently being developed as a next generation antimitotic drug for the treatment of cancer. It has shown a broad spectrum of anti-cancer activity in vitro and in vivo. A siRNA library screen targeting the ‘druggable genome’ identified multiple MAPK pathway genes as sensitizers to ′295, including BRAF and ERK1. Since the MEK protein plays an important role in the MAPK pathway, combination studies between GSK MEK inhibitor GSK1120212 (′212) and ′295 were performed in cancer cell lines from different tissue origins, and the combination effect was evaluated based on three different criteria: Excess over Single Highest Agent (EOHSA), Bliss, and Combination Index (CI).. Synergistic response was observed in 5/6 colon cancer cell lines, 5/15 lung cancer cell lines, and 6/8 pancreas cancer cell lines. Additionally, the combination of ′212 and ′295 treatment induced a much stronger apoptotic response than either drug alone in two colon cancer cell lines. These data suggest that combining MEK and CENP-E inhibitors might improve clinical efficacy over either as a single agent in selected tumors.
Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B173.
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Affiliation(s)
- Yan Y. Degenhardt
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Xiping Zhang
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Christopher Moy
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Theresa Conway
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Liz Mcneil
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Junping Jing
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Joel Greshock
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Ronald Wegrzyn
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Holy Yin
- 2 Pharmaceutical Genomics Division, Translational Genomics Research Institute, Scottsdale, AZ
| | - Spyro Mousses
- 2 Pharmaceutical Genomics Division, Translational Genomics Research Institute, Scottsdale, AZ
| | - Richard Wooster
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
| | - Kurtis Bachman
- 1 Cancer Metabolism Drug Discovery, GlaxoSmithKline, Collegeville, PA
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35
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Qian F, Engst S, Yamaguchi K, Yu P, Won KA, Mock L, Lou T, Tan J, Li C, Tam D, Lougheed J, Yakes FM, Bentzien F, Xu W, Zaks T, Wooster R, Greshock J, Joly AH. Inhibition of tumor cell growth, invasion, and metastasis by EXEL-2880 (XL880, GSK1363089), a novel inhibitor of HGF and VEGF receptor tyrosine kinases. Cancer Res 2009; 69:8009-16. [PMID: 19808973 DOI: 10.1158/0008-5472.can-08-4889] [Citation(s) in RCA: 266] [Impact Index Per Article: 17.7] [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
The Met receptor tyrosine kinase and its ligand, hepatocyte growth factor (HGF), are overexpressed and/or activated in a wide variety of human malignancies. Vascular endothelial growth factor (VEGF) receptors are expressed on the surface of vascular endothelial cells and cooperate with Met to induce tumor invasion and vascularization. EXEL-2880 (XL880, GSK1363089) is a small-molecule kinase inhibitor that targets members of the HGF and VEGF receptor tyrosine kinase families, with additional inhibitory activity toward KIT, Flt-3, platelet-derived growth factor receptor beta, and Tie-2. Binding of EXEL-2880 to Met and VEGF receptor 2 (KDR) is characterized by a very slow off-rate, consistent with X-ray crystallographic data showing that the inhibitor is deeply bound in the Met kinase active site cleft. EXEL-2880 inhibits cellular HGF-induced Met phosphorylation and VEGF-induced extracellular signal-regulated kinase phosphorylation and prevents both HGF-induced responses of tumor cells and HGF/VEGF-induced responses of endothelial cells. In addition, EXEL-2880 prevents anchorage-independent proliferation of tumor cells under both normoxic and hypoxic conditions. In vivo, these effects produce significant dose-dependent inhibition of tumor burden in an experimental model of lung metastasis. Collectively, these data indicate that EXEL-2880 may prevent tumor growth through a direct effect on tumor cell proliferation and by inhibition of invasion and angiogenesis mediated by HGF and VEGF receptors.
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Affiliation(s)
- Fawn Qian
- Exelixis, Inc, South San Francisco, California 94083, USA
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36
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Liu L, Greger J, Shi H, Liu Y, Greshock J, Annan R, Halsey W, Sathe GM, Martin AM, Gilmer TM. Novel mechanism of lapatinib resistance in HER2-positive breast tumor cells: activation of AXL. Cancer Res 2009; 69:6871-8. [PMID: 19671800 DOI: 10.1158/0008-5472.can-08-4490] [Citation(s) in RCA: 373] [Impact Index Per Article: 24.9] [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
HER2-directed therapies, such as trastuzumab and lapatinib, are important treatments for breast cancer. However, some tumors do not respond or develop resistance to these agents. We isolated and characterized multiple lapatinib-resistant, HER2-positive, estrogen receptor (ER)-positive breast cancer clones derived from lapatinib-sensitive BT474 cells by chronic exposure to lapatinib. We show overexpression of AXL as a novel mechanism of acquired resistance to HER2-targeted agents in these models. GSK1363089 (foretinib), a multikinase inhibitor of AXL, MET, and vascular endothelial growth factor receptor currently in phase II clinical trials, restores lapatinib and trastuzumab sensitivity in these resistant cells that exhibit increased AXL expression. Furthermore, small interfering RNA to AXL, estrogen deprivation, or fulvestrant, an ER antagonist, decreases AXL expression and restores sensitivity to lapatinib in these cells. Taken together, these data provide scientific evidence to assess the expression of AXL in HER2-positive, ER-positive patients who have progressed on either lapatinib or trastuzumab and to test the combination of HER2-targeted agents and GSK1363089 in the clinic.
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Affiliation(s)
- Li Liu
- Department of Translational Research, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
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37
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Greshock J, Nathanson K, Medina A, Ward MR, Herlyn M, Weber BL, Zaks TZ. Distinct patterns of DNA copy number alterations associate with BRAF mutations in melanomas and melanoma-derived cell lines. Genes Chromosomes Cancer 2009; 48:419-28. [PMID: 19226609 DOI: 10.1002/gcc.20651] [Citation(s) in RCA: 21] [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] [Indexed: 12/25/2022] Open
Abstract
A majority of malignant melanomas harbor an oncogenic mutation in either BRAF or NRAS. If BRAF and NRAS transform melanoma cells by a similar mechanism, then additional genetic aberrations would be similar (or random). Alternatively, distinct mutation-associated changes would suggest the existence of unique cooperating requirements for each mutation group. We first analyzed a panel of 52 melanoma cell lines (n = 35, 11, 6 for BRAF*, NRAS*, and BRAF/NRAS(wt/wt), respectively) by array-based comparative genomic hybridization for unique alterations that associate with each mutation subgroup. Subsequently, those DNA copy number changes that correlated with a mutation subgroup were used to predict the mutation status of an independent panel of 43 tumors (n = 17, 13, 13 for BRAF*, NRAS*, and BRAF/NRAS(wt/wt), respectively). BRAF mutant tumors were classified with a high rate of success (74.4%, P = 0.002), whereas NRAS mutants were not significantly distinguished from wild types (26/43, P = 0.12). Copy number gains of 7q32.1-36.3, 5p15.31, 8q21.11, and 8q24.11 were most strongly associated with BRAF* tumors and cell lines, as were losses of 11q24.2-24.3. BRAF* melanomas appear to be associated with a specific profile of DNA copy number aberrations that is distinct from those found in NRAS* and BRAF/NRAS(wt/wt) tumors. These findings suggest that although both BRAF and NRAS appear to function along the same signal transduction pathway, each may have different requirements for cooperating oncogenic events. The genetic loci that make up this profile may harbor therapeutic targets specific for tumors with BRAF mutations.
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Affiliation(s)
- J Greshock
- Translational Medicine Oncology, GlaxoSmithKline, King of Prussia, PA, USA
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38
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Yang N, Kaur S, Volinia S, Greshock J, Lassus H, Hasegawa K, Liang S, Leminen A, Deng S, Smith L, Johnstone CN, Chen XM, Liu CG, Huang Q, Katsaros D, Calin GA, Weber BL, Bützow R, Croce CM, Coukos G, Zhang L. MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer. Cancer Res 2009; 68:10307-14. [PMID: 19074899 DOI: 10.1158/0008-5472.can-08-1954] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNA) are approximately 22-nucleotide noncoding RNAs that negatively regulate protein-coding gene expression in a sequence-specific manner via translational inhibition or mRNA degradation. Our recent studies showed that miRNAs exhibit genomic alterations at a high frequency and their expression is remarkably deregulated in ovarian cancer, strongly suggesting that miRNAs are involved in the initiation and progression of this disease. In the present study, we performed miRNA microarray to identify the miRNAs associated with chemotherapy response in ovarian cancer and found that let-7i expression was significantly reduced in chemotherapy-resistant patients (n = 69, P = 0.003). This result was further validated by stem-loop real-time reverse transcription-PCR (n = 62, P = 0.015). Both loss-of-function (by synthetic let-7i inhibitor) and gain-of-function (by retroviral overexpression of let-7i) studies showed that reduced let-7i expression significantly increased the resistance of ovarian and breast cancer cells to the chemotherapy drug, cis-platinum. Finally, using miRNA microarray, we found that decreased let-7i expression was significantly associated with the shorter progression-free survival of patients with late-stage ovarian cancer (n = 72, P = 0.042). This finding was further validated in the same sample set by stem-loop real-time reverse transcription-PCR (n = 62, P = 0.001) and in an independent sample set by in situ hybridization (n = 53, P = 0.049). Taken together, our results strongly suggest that let-7i might be used as a therapeutic target to modulate platinum-based chemotherapy and as a biomarker to predict chemotherapy response and survival in patients with ovarian cancer.
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Affiliation(s)
- Nuo Yang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Abstract
Evolutionary conservation has become a powerful tool to identify functionally important genomic sequences/elements in the human genome. There are 481 genomic segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between human, mouse and rat genomes. Such segments are known as ultraconserved elements (UCEs). Although our knowledge of UCEs is limited, most recent studies suggest that UCEs play a functional role in vertebrate genomes, such as serving as long-range enhancers of flanking genes, regulating splicing and epigenetic modifications, and functioning as transcriptional coactivator. Most recent studies show that expression of UCEs is consistently altered in tumors, strongly suggesting these elements may also be involved in human disease such as cancer development.
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Affiliation(s)
- Eirini Baira
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Greshock J, Cheng J, Rusnak D, Martin AM, Wooster R, Gilmer T, Lee K, Weber BL, Zaks T. Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines. Mol Cancer Ther 2008; 7:935-43. [PMID: 18413807 DOI: 10.1158/1535-7163.mct-07-2072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [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
A common aim of pharmacogenomic studies that use genome-wide assays on panels of cancers is the unbiased discovery of genomic alterations that are associated with clinical outcome and drug response. Previous studies of lapatinib, a selective dual-kinase inhibitor of epidermal growth factor receptor (EGFR) and HER2 tyrosine kinases, have shown predictable relationships between the activity of these target genes and response. Under the hypothesis that additional genes may play a role in drug sensitivity, a predictive model for lapatinib response was constructed from genome-wide DNA copy number data from 24 cancer cell lines. An optimal predictive model which consists of aberrations at nine distinct genetic loci, includes gains of HER2, EGFR, and loss of CDKN2A. This model achieved an area under the receiver operating characteristic curve of approximately 0.85 (80% confidence interval, 0.70-0.98; P < 0.01), and correctly classified the sensitivity status of 8 of 10 head and neck cancer cell lines. This study shows that biomarkers predictive for lapatinib sensitivity, including the previously described copy number gains of EGFR and HER2, can be discovered using novel genomic assays in an unbiased manner. Furthermore, these results show the utility of DNA copy number profiles in pharmacogenomic studies.
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Affiliation(s)
- Joel Greshock
- Translational Medicine Oncology, GlaxoSmithKline, 1250 South Collegeville Road, UP 4W-4230, Collegeville, PA 19426, USA
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Greshock J, Weber BL, Feng B, Ivanova E, Perna I, Protopopov A, Nogueira C, Chin L, Nathanson K. Comment re: A Comparison of DNA Copy Number Profiling Platforms. Cancer Res 2008. [DOI: 10.1158/0008-5472.can-08-1006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Joel Greshock
- Discovery and Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Barbara L. Weber
- Discovery and Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Bin Feng
- Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science, Boston, Massachusetts
| | - Elena Ivanova
- Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science, Boston, Massachusetts
| | - Ilana Perna
- Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science, Boston, Massachusetts
| | - Alexei Protopopov
- Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science, Boston, Massachusetts
| | - Cristina Nogueira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynda Chin
- Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts and Department of Dermatology, Harvard Medical School, Boston, Massachusetts
| | - Katherine Nathanson
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
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42
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Tchou J, Greshock J, Bergey MR, Sonnad SS, Sargen M, Weinstein S, Czerniecki BJ, Boraas M, Fraker DL, Rosato E, Fox K, Weber B, Solin LJ. Method of Primary Tumor Detection as a Risk Factor for Local and Distant Recurrence After Breast-Conservation Treatment for Early-Stage Breast Cancer. Clin Breast Cancer 2008; 8:143-8. [DOI: 10.3816/cbc.2008.n.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Yang N, Huang J, Greshock J, Liang S, Barchetti A, Hasegawa K, Kim S, Giannakakis A, Li C, O'Brien-Jenkins A, Katsaros D, Bützow R, Coukos G, Zhang L. Transcriptional regulation of PIK3CA oncogene by NF-kappaB in ovarian cancer microenvironment. PLoS One 2008; 3:e1758. [PMID: 18335034 PMCID: PMC2258145 DOI: 10.1371/journal.pone.0001758] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 02/07/2008] [Indexed: 12/28/2022] Open
Abstract
PIK3CA upregulation, amplification and mutation have been widely reported in ovarian cancers and other tumors, which strongly suggests that PIK3CA is a promising therapeutic target. However, to date the mechanisms underlying PIK3CA regulation and activation in vivo is still unclear. During tumorigenesis, host-tumor interactions may play a critical role in editing the tumor. Here, we report a novel mechanism through which the tumor microenvironment activates the PIK3CA oncogene. We show that PIK3CA upregulation occurs in non-proliferating tumor regions in vivo. We identified and characterized the PIK3CA 5' upstream transcriptional regulatory region and confirmed that PIK3CA is transcriptionally regulated through NF-kappaB pathway. These results offer a new mechanism through which the tumor microenvironment directly activates oncogenic pathways in tumor cells.
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Affiliation(s)
- Nuo Yang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jia Huang
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joel Greshock
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Translational Medicine and Genetics at GlaxoSmithKline, King of Prussia, Pennsylvania, United States of America
| | - Shun Liang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Andrea Barchetti
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Kosei Hasegawa
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sarah Kim
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Antonis Giannakakis
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Laboratory of Gene Expression, Modern Diagnostic and Therapeutic Methods, Democritus University of Thrace, Alexandroupolis, Greece
| | - Chunsheng Li
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Anne O'Brien-Jenkins
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Ralf Bützow
- Department of Obstetrics, University of Helsinki, Helsinki, Finland
- Department of Gynecology, University of Helsinki, Helsinki, Finland
| | - George Coukos
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Lin Zhang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Giannakakis A, Sandaltzopoulos R, Greshock J, Liang S, Huang J, Hasegawa K, Li C, O'Brien-Jenkins A, Katsaros D, Weber BL, Simon C, Coukos G, Zhang L. miR-210 links hypoxia with cell cycle regulation and is deleted in human epithelial ovarian cancer. Cancer Biol Ther 2007; 7:255-64. [PMID: 18059191 PMCID: PMC3233968 DOI: 10.4161/cbt.7.2.5297] [Citation(s) in RCA: 275] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor growth results in hypoxia. Understanding the mechanisms of gene expression reprogramming under hypoxia may provide important clues to cancer pathogenesis. We studied miRNA genes that are regulated by hypoxia in ovarian cancer cell lines by TaqMan miRNA assay containing 157 mature miRNAs. MiR-210 was the most prominent miRNA consistently stimulated under hypoxic conditions. We provide evidence for the involvement of the HIF signaling pathway in miR-210 regulation. Biocomputational analysis and in vitro assays demonstrated that e2f transcription factor 3 (e2f3), a key protein in cell cycle, is regulated by miR-210. E2F3 was further confirmed to be downregulated at the protein level upon induction of miR-210. Importantly, we found remarkably high frequency of miR-210 gene copy deletions in ovarian cancer patients (64%, n = 114) and that gene copy number correlates with miR-210 expression levels. Taken together, our results indicate that miR-210 plays a crucial role in tumor onset as a key regulator of the hypoxia response and provide evidence for a link between hypoxia and the regulation of cell cycle.
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Affiliation(s)
- Antonis Giannakakis
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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45
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Greshock J, Feng B, Nogueira C, Ivanova E, Perna I, Nathanson K, Protopopov A, Weber BL, Chin L. A Comparison of DNA Copy Number Profiling Platforms. Cancer Res 2007; 67:10173-80. [DOI: 10.1158/0008-5472.can-07-2102] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [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 accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes. Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have emerged as a cornerstone technology in the genomic era. The diversity of commercially available platforms prompted a systematic comparison of five copy number profiling assays for their ability to detect 2-fold copy number gain and loss (4n or 1n, respectively) as well as focal high-amplitude CNAs. Here, using a collection of established human melanoma cell lines, we defined the reproducibility, absolute signals, signal to noise, and false-positive and false-negative rates for each of the five assays against ground truth defined by spectral karyotyping, in addition to comparing the concordance of CNA detection by two high-resolution Agilent and Affymetrix microarray platforms. Our analyses concluded that the Agilent's 60-mer oligonucleotide microarray with probe design optimized for genomic hybridization offers the highest sensitivity and specificity (area under receiver operator characteristic curve >0.99), whereas Affymetrix's single nucleotide polymorphism microarray seems to offer better detection of CNAs in gene-poor regions. Availability of these comparison results should guide study design decisions and facilitate further computational development. [Cancer Res 2007;67(21):10173–80]
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Affiliation(s)
- Joel Greshock
- 1Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Bin Feng
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | | | - Elena Ivanova
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Ilana Perna
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Katherine Nathanson
- 5Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Alexei Protopopov
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Barbara L. Weber
- 1Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Lynda Chin
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
- 3Department of Medical Oncology, Dana-Farber Cancer Institute
- 4Department of Dermatology, Harvard Medical School, Boston, Massachusetts; and
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46
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Zhang L, Huang J, Yang N, Greshock J, Liang S, Hasegawa K, Giannakakis A, Poulos N, O'Brien-Jenkins A, Katsaros D, Butzow R, Weber BL, Coukos G. Integrative genomic analysis of phosphatidylinositol 3'-kinase family identifies PIK3R3 as a potential therapeutic target in epithelial ovarian cancer. Clin Cancer Res 2007; 13:5314-21. [PMID: 17875760 DOI: 10.1158/1078-0432.ccr-06-2660] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PURPOSE The phosphatidylinositol 3'-kinase (PI3K) family plays a key regulatory role in various cancer-associated signal transduction pathways. Here, we investigated the genomic alterations and gene expression of most known PI3K family members in human epithelial ovarian cancer. EXPERIMENTAL DESIGN The DNA copy number of PI3K family genes was screened by a high-resolution array comparative genomic hybridization in 89 human ovarian cancer specimens. The mRNA expression level of PI3K genes was analyzed by microarray retrieval approach, and further validated by real-time reverse transcription-PCR. The expression of p55gamma protein in ovarian cancer was analyzed on tissue arrays. Small interfering RNA was used to study the function of PIK3R3 in ovarian cancer. RESULTS In ovarian cancer, 6 of 12 PI3K genes exhibited significant DNA copy number gains (>20%), including PIK3CA (23.6%), PIK3CB (27.0%), PIK3CG (25.8%), PIK3R2 (29.2%), PIK3R3 (21.3%), and PIK3C2B (40.4%). Among those, only PIK3R3 had significantly up-regulated mRNA expression level in ovarian cancer compared with normal ovary. Up-regulated PIK3R3 mRNA expression was also observed in liver, prostate, and breast cancers. The PIK3R3 mRNA expression level was significantly higher in ovarian cancer cell lines (n = 18) than in human ovarian surface epithelial cells (n = 6, P = 0.002). Overexpression of p55gamma protein in ovarian cancer was confirmed by tissue array analysis. In addition, we found that knockdown of PIK3R3 expression by small interfering RNA significantly increased the apoptosis in cultured ovarian cancer cell lines. CONCLUSION We propose that PIK3R3 may serve as a potential therapeutic target in human ovarian cancer.
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Affiliation(s)
- Lin Zhang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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Greshock J, Nathanson K, Martin AM, Zhang L, Coukos G, Weber BL, Zaks TZ. Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization. Cancer Res 2007; 67:3594-600. [PMID: 17440070 DOI: 10.1158/0008-5472.can-06-3674] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor-derived cell lines are used as in vitro cancer models, but their ability to accurately reflect the phenotype and genotype of the parental histology remains questionable, given the prevalence of documented cell line-specific cytogenetic changes. We have addressed the issue of whether copy number alterations seen in tumor-derived cell lines reflect those observed in studies of fresh tissue by carrying out a meta-analysis of array-based comparative genomic hybridization data that considers both copy number alteration frequencies and the occurrence of cancer gene amplifications and homozygous deletions. Pairwise correlation comparisons between the data sets of seven diagnosis-specific matched tumor and cell line groups indicate that the trends in aberration frequencies are highly correlated between tumors and cell line sets of matched cancer histology relative to unmatched pairings. Despite their similarities, cell lines showed uniformly higher locus-specific alteration frequencies (P = 0.004) and several recurring cell line-specific alterations emerged. These include the previously documented losses of 13q and 9p and gains of 20q, as well as additional undescribed cell line-specific gains of 5p, 7p, and 17q and losses of 18q and 4q. These results indicate that, on average, cell lines preserve in vitro the genetic aberrations that are unique to the parent histology from which they were derived while acquiring additional locus-specific alterations. These data may enable a more predictive understanding of individual cell lines as in vitro models of cancer biology and therapy.
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Affiliation(s)
- Joel Greshock
- Translational Medicine and Genetics, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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48
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Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ, Weber BL, Maris JM, Grant GR. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genes Dev 2006; 16:1149-58. [PMID: 16899652 PMCID: PMC1557772 DOI: 10.1101/gr.5076506] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regions of gain and loss of genomic DNA occur in many cancers and can drive the genesis and progression of disease. These copy number aberrations (CNAs) can be detected at high resolution by using microarray-based techniques. However, robust statistical approaches are needed to identify nonrandom gains and losses across multiple experiments/samples. We have developed a method called Significance Testing for Aberrant Copy number (STAC) to address this need. STAC utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach. We validate our method by using two published cancer data sets. STAC identifies genomic alterations known to be of clinical and biological significance and provides statistical support for 85% of previously reported regions. Moreover, STAC identifies numerous additional regions of significant gain/loss in these data that warrant further investigation. The P-values provided by STAC can be used to prioritize regions for follow-up study in an unbiased fashion. We conclude that STAC is a powerful tool for identifying nonrandom genomic amplifications and deletions across multiple experiments. A Java version of STAC is freely available for download at http://cbil.upenn.edu/STAC.
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Affiliation(s)
- Sharon J. Diskin
- Division of Oncology, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Penn Center for Bioinformatics (PCBI), University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Thomas Eck
- Penn Center for Bioinformatics (PCBI), University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joel Greshock
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Yael P. Mosse
- Division of Oncology, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Tara Naylor
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Christian J. Stoeckert
- Penn Center for Bioinformatics (PCBI), University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 19104, USA
| | - Barbara L. Weber
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - John M. Maris
- Division of Oncology, Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Gregory R. Grant
- Penn Center for Bioinformatics (PCBI), University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O’Brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A 2006; 103:9136-41. [PMID: 16754881 PMCID: PMC1474008 DOI: 10.1073/pnas.0508889103] [Citation(s) in RCA: 780] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous noncoding RNAs, which negatively regulate gene expression. To determine genomewide miRNA DNA copy number abnormalities in cancer, 283 known human miRNA genes were analyzed by high-resolution array-based comparative genomic hybridization in 227 human ovarian cancer, breast cancer, and melanoma specimens. A high proportion of genomic loci containing miRNA genes exhibited DNA copy number alterations in ovarian cancer (37.1%), breast cancer (72.8%), and melanoma (85.9%), where copy number alterations observed in >15% tumors were considered significant for each miRNA gene. We identified 41 miRNA genes with gene copy number changes that were shared among the three cancer types (26 with gains and 15 with losses) as well as miRNA genes with copy number changes that were unique to each tumor type. Importantly, we show that miRNA copy changes correlate with miRNA expression. Finally, we identified high frequency copy number abnormalities of Dicer1, Argonaute2, and other miRNA-associated genes in breast and ovarian cancer as well as melanoma. These findings support the notion that copy number alterations of miRNAs and their regulatory genes are highly prevalent in cancer and may account partly for the frequent miRNA gene deregulation reported in several tumor types.
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Affiliation(s)
- Lin Zhang
- *Center for Research on Reproduction and Women’s Health, Departments of
- Obstetrics and Gynecology and
| | - Jia Huang
- Abramson Family Cancer Research Institute
| | - Nuo Yang
- Cell and Molecular Biology Graduate Program and Department of Genetics
| | | | - Molly S. Megraw
- Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104
| | - Antonis Giannakakis
- *Center for Research on Reproduction and Women’s Health, Departments of
- **Laboratory of Gene Expression, Modern Diagnostic and Therapeutic Methods, Democritus University of Thrace, 69100 Alexandroupolis, Greece
| | - Shun Liang
- *Center for Research on Reproduction and Women’s Health, Departments of
| | | | - Andrea Barchetti
- *Center for Research on Reproduction and Women’s Health, Departments of
| | | | - George Yao
- *Center for Research on Reproduction and Women’s Health, Departments of
| | | | | | - Dionyssios Katsaros
- Department of Obstetrics and Gynecology, University of Turin, 10126 Turin, Italy; and
| | - Artemis Hatzigeorgiou
- Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | - George Coukos
- *Center for Research on Reproduction and Women’s Health, Departments of
- Obstetrics and Gynecology and
- Abramson Family Cancer Research Institute
- To whom correspondence should be addressed. E-mail:
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50
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Hoffman JD, Zhang Y, Greshock J, Ciprero KL, Emanuel BS, Zackai EH, Weber BL, Ming JE. Array based CGH and FISH fail to confirm duplication of 8p22-p23.1 in association with Kabuki syndrome. J Med Genet 2006; 42:49-53. [PMID: 15635075 PMCID: PMC1735911 DOI: 10.1136/jmg.2004.024372] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Kabuki (Niikawa-Kuroki) syndrome comprises a characteristic facial appearance, cleft palate, congenital heart disease, and developmental delay. Various cytogenetically visible chromosomal rearrangements have been reported in single cases, but the molecular genetic basis of the condition has not been established. A recent report described a duplication of 8p22-p23.1 in 13/13 patients. OBJECTIVE To determine the frequency of an 8p duplication in a cohort of patients with Kabuki syndrome. METHODS An 8p duplication was sought using two independent methods--array based comparative genomic hybridisation (aCGH) and fluorescence in situ hybridisation (FISH)--in 15 patients with a definitive clinical diagnosis of Kabuki syndrome. RESULTS No evidence for a duplication of 8p was obtained by FISH or aCGH in any of the 15 patients. CONCLUSIONS 8p22-p23.1 duplication may not be a common mechanism for Kabuki syndrome. Another genetic abnormality may be responsible for the aetiology in many patients.
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Affiliation(s)
- J D Hoffman
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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