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Tabata M, Sato Y, Kogure Y, McClure MB, Oshikawa-Kumade Y, Saito Y, Shingaki S, Ito Y, Yuasa M, Koya J, Yoshida K, Kohno T, Miyama Y, Morikawa T, Chiba K, Okada A, Ogawa S, Ushiku T, Shiraishi Y, Kume H, Kataoka K. Inter- and intra-tumor heterogeneity of genetic and immune profiles in inherited renal cell carcinoma. Cell Rep 2023; 42:112736. [PMID: 37405915 DOI: 10.1016/j.celrep.2023.112736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/04/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Patients with von Hippel-Lindau disease (vHL) are at risk of developing spatially and temporally multiple clear cell renal cell carcinomas (ccRCCs), which offers a valuable opportunity to analyze inter- and intra-tumor heterogeneity of genetic and immune profiles within the same patient. Here, we perform whole-exome and RNA sequencing, digital gene expression, and immunohistochemical analyses for 81 samples from 51 ccRCCs of 10 patients with vHL. Inherited ccRCCs are clonally independent and have less genomic alterations than sporadic ccRCCs. Hierarchical clustering of transcriptome profiles shows two clusters with distinct immune signatures: immune hot and cold clusters. Interestingly, not only samples from the same tumors but also different tumors from the same patients tend to show a similar immune signature, whereas samples from different patients frequently exhibit different signatures. Our findings reveal the genetic and immune landscape of inherited ccRCCs, demonstrating the relevance of host factors in shaping anti-tumor immunity.
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Affiliation(s)
- Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuji Oshikawa-Kumade
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima 771-0182, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Mitsuhiro Yuasa
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kazushi Yoshida
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yu Miyama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo 141-8625, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 17177, Sweden
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan.
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2
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Yoshikawa Y, Yamada Y, Emi M, Atanesyan L, Smout J, de Groot K, Savola S, Nakanishi-Shinkai Y, Kanematsu A, Nojima M, Ohmuraya M, Hashimoto-Tamaoki T, Yamamoto S. Risk prediction for metastasis of clear cell renal cell carcinoma using digital multiplex ligation-dependent probe amplification. Cancer Sci 2021; 113:297-307. [PMID: 34687579 PMCID: PMC8748218 DOI: 10.1111/cas.15170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022] Open
Abstract
Precise quantification of copy‐number alterations (CNAs) in a tumor genome is difficult. We have applied a comprehensive copy‐number analysis method, digital multiplex ligation‐dependent probe amplification (digitalMLPA), for targeted gene copy‐number analysis in clear cell renal cell carcinoma (ccRCC). Copy‐number status of all chromosomal arms and 11 genes was determined in 60 ccRCC samples. Chromosome 3p loss and 5q gain, known as early changes in ccRCC development, as well as losses at 9p and 14q were detected in 56/60 (93.3%), 31/60 (51.7%), 11/60 (18.3%), and 33/60 (55%), respectively. Through gene expression analysis, a significant positive correlation was detected in terms of 14q loss determined using digitalMLPA and downregulation of mRNA expression ratios with HIF1A and L2HGDH (P = .0253 and .0117, respectively). Patients with early metastasis (<1 y) (n = 18) showed CNAs in 6 arms (in median), whereas metastasis‐free patients (n = 34) showed those in significantly less arms (3 arms in median) (P = .0289). In particular, biallelic deletion of CDKN2A/2B was associated with multiple CNAs (≥7 arms) in 3 tumors. Together with sequence‐level mutations in genes VHL, PBRM1, SETD2, and BAP1, we performed multiple correspondence analysis, which identified the association of 9p loss and 4q loss with early metastasis (both P < .05). This analysis indicated the association of 4p loss and 1p loss with poor survival (both, P < .05). These findings suggest that CNAs have essential roles in aggressiveness of ccRCC. We showed that our approach of measuring CNA through digitalMLPA will facilitate the selection of patients who may develop metastasis.
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Affiliation(s)
- Yoshie Yoshikawa
- Department of Genetics, Hyogo College of Medicine, Nishinomiya, Japan
| | - Yusuke Yamada
- Department of Urology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Mitsuru Emi
- Department of Genetics, Hyogo College of Medicine, Nishinomiya, Japan
| | - Lilit Atanesyan
- Oncogenetics Department, MRC Holland, Amsterdam, The Netherlands
| | - Jan Smout
- Oncogenetics Department, MRC Holland, Amsterdam, The Netherlands
| | - Karel de Groot
- Bioinformatics Department, MRC Holland, Amsterdam, The Netherlands
| | - Suvi Savola
- Oncogenetics Department, MRC Holland, Amsterdam, The Netherlands
| | | | - Akihiro Kanematsu
- Department of Urology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Michio Nojima
- Department of Urology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo College of Medicine, Nishinomiya, Japan
| | | | - Shingo Yamamoto
- Department of Urology, Hyogo College of Medicine, Nishinomiya, Japan
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3
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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4
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Gonzales F, Cheok MH. Impact of CNA on AML prognosis. Oncotarget 2018; 9:12540-12541. [PMID: 29560083 PMCID: PMC5849147 DOI: 10.18632/oncotarget.23404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/16/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- Fanny Gonzales
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JParc-Centre de Recherche, Jean-Pierre Aubert Neurosciences and Cancer Research Center, Lille, France
| | - Meyling H Cheok
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JParc-Centre de Recherche, Jean-Pierre Aubert Neurosciences and Cancer Research Center, Lille, France
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5
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Kato M, Vasco DA, Sugino R, Narushima D, Krasnitz A. Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. R Soc Open Sci 2017; 4:171060. [PMID: 28989791 PMCID: PMC5627131 DOI: 10.1098/rsos.171060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Single-cell sequencing is a promising technology that can address cancer cell evolution by identifying genetic alterations in individual cells. In a recent study, genome-wide DNA copy numbers of single cells were accurately quantified by single-cell sequencing in breast cancers. Phylogenetic-tree analysis revealed genetically distinct populations, each consisting of homogeneous cells. Bioinformatics methods based on population genetics should be further developed to quantitatively analyse the single-cell sequencing data. We developed a bioinformatics framework that was combined with molecular-evolution theories to analyse copy-number losses. This analysis revealed that most deletions in the breast cancers at the single-cell level were generated by simple stochastic processes. A non-standard type of coalescent theory, the multiple-merger coalescent model, aided by approximate Bayesian computation fit well with the data, allowing us to estimate the population-genetic parameters in addition to false-positive and false-negative rates. The estimated parameters suggest that the cancer cells underwent sweepstake evolution, where only one or very few parental cells produced a descendent cell population. We conclude that breast cancer cells successively substitute in a tumour mass, and the high reproduction of only a portion of cancer cells may confer high adaptability to this cancer.
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Affiliation(s)
- Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Daniel A. Vasco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Ryuichi Sugino
- School of Advanced Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Daichi Narushima
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Alexander Krasnitz
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
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6
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Gao J, Shi LZ, Zhao H, Chen J, Xiong L, He Q, Chen T, Roszik J, Bernatchez C, Woodman SE, Chen PL, Hwu P, Allison JP, Futreal A, Wargo JA, Sharma P. Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy. Cell 2016; 167:397-404.e9. [PMID: 27667683 PMCID: PMC5088716 DOI: 10.1016/j.cell.2016.08.069] [Citation(s) in RCA: 875] [Impact Index Per Article: 109.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 08/26/2016] [Indexed: 02/07/2023]
Abstract
Antibody blockade of the inhibitory CTLA-4 pathway has led to clinical benefit in a subset of patients with metastatic melanoma. Anti-CTLA-4 enhances T cell responses, including production of IFN-γ, which is a critical cytokine for host immune responses. However, the role of IFN-γ signaling in tumor cells in the setting of anti-CTLA-4 therapy remains unknown. Here, we demonstrate that patients identified as non-responders to anti-CTLA-4 (ipilimumab) have tumors with genomic defects in IFN-γ pathway genes. Furthermore, mice bearing melanoma tumors with knockdown of IFN-γ receptor 1 (IFNGR1) have impaired tumor rejection upon anti-CTLA-4 therapy. These data highlight that loss of the IFN-γ signaling pathway is associated with primary resistance to anti-CTLA-4 therapy. Our findings demonstrate the importance of tumor genomic data, especially IFN-γ related genes, as prognostic information for patients selected to receive treatment with immune checkpoint therapy.
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Affiliation(s)
- Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lewis Zhichang Shi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hao Zhao
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfeng Chen
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liangwen Xiong
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qiuming He
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tenghui Chen
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chantale Bernatchez
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pei-Ling Chen
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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7
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Serizawa M, Kusuhara M, Zangiacomi V, Urakami K, Watanabe M, Takahashi T, Yamaguchi K, Yamamoto N, Koh Y. Identification of metabolic signatures associated with erlotinib resistance of non-small cell lung cancer cells. Anticancer Res 2014; 34:2779-2787. [PMID: 24922639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND/AIM The acquisition of resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) remains a major challenge in lung cancer medicine. We sought to identify biomarkers for the early detection of resistance to TKIs. MATERIALS AND METHODS Capillary electrophoresis time-of-flight mass spectrometry analysis was performed to identify the metabolic signatures associated with erlotinib resistance in erlotinib-resistant PC-9ER NSCLC cells established from the EGFR-mutant NSCLC cell line PC-9. RESULTS PC-9ER cells showed metabolic signatures indicative of enhanced glutamine metabolism. Copy number gains in v-myc avian myelocytomatosis viral oncogene homolog (MYC), glutathione-S-transferase theta 2 (GSTT2), gamma-glutamyltransferase 1 (GGT1), and GGT5 were also detected, suggesting that amplification of these genes confers glutamine addiction in PC-9ER cells. CONCLUSION Enhanced glutamine metabolism may be a surrogate marker that can be used to predict the likelihood of patients to respond to EGFR-TKIs.
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MESH Headings
- Adenocarcinoma/drug therapy
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- DNA Copy Number Variations/genetics
- Drug Resistance, Neoplasm
- Electrophoresis, Capillary
- Erlotinib Hydrochloride
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Metabolome/drug effects
- Polymerase Chain Reaction
- Protein Kinase Inhibitors/pharmacology
- Quinazolines/pharmacology
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tumor Cells, Cultured
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Affiliation(s)
- Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center, Shizuoka, Japan
| | | | | | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center, Shizuoka, Japan
| | - Masaru Watanabe
- Drug Discovery and Development Division, Shizuoka Cancer Center, Shizuoka, Japan
| | | | - Ken Yamaguchi
- Region Resources Division, Shizuoka Cancer Center, Shizuoka, Japan
| | - Nobuyuki Yamamoto
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shizuoka, Japan Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yasuhiro Koh
- Drug Discovery and Development Division, Shizuoka Cancer Center, Shizuoka, Japan
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8
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Serizawa M, Takahashi T, Yamamoto N, Koh Y. Genomic aberrations associated with erlotinib resistance in non-small cell lung cancer cells. Anticancer Res 2013; 33:5223-5233. [PMID: 24324054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND/AIM Mechanisms of resistance to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) are not fully-understood. In this study we aimed to elucidate remaining unknown mechanisms using erlotinib-resistant NSCLC cells. MATERIALS AND METHODS We performed array comparative genomic hybridization (aCGH) to identify genomic aberrations associated with EGFR-TKI resistance in erlotinib-resistant PC-9ER cells. Real-time polymerase chain reaction (PCR) and immunoblot analyses were performed to confirm the results of aCGH. RESULTS Among the five regions with copy number gain detected in PC-9ER cells, we focused on 22q11.2-q12.1 including v-crk avian sarcoma virus CT10 oncogene homolog-like (CRKL), the overexpression of which seemed to be associated with EGFR-TKI resistance. Blockade of downstream phosphatidylinositol 3-kinase (PI3K)/v-akt murine thymoma viral oncogene homolog (AKT) signaling using NVP-BEZ235 suppressed the proliferation of PC-9ER cells, implying the involvement of acquired CRKL amplification in EGFR-TKI resistance. CONCLUSION Acquired CRKL amplification was identified as contributing to EGFR-TKI resistance; this cell line model can be utilized to study this resistance mechanism.
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Affiliation(s)
- Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo Nagaizumi-cho Sunto-gun, Shizuoka, 411-8777, Japan.
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