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Li J, Wang C, Zhao S, Qi L, Yu J, Hu X, Chen L, Sun Y, Wang D, Jiang Y, Du Y. Custom-Designed Probes for the Accurate Determination of Epidermal Growth Factor Receptor Mutations and Their Allelic Configuration. Anal Chem 2024; 96:10056-10063. [PMID: 38832555 DOI: 10.1021/acs.analchem.4c01771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The identification of single nucleotide polymorphisms (SNPs) is of paramount importance for disease diagnosis and clinical prognostication. In the context of nonsmall cell lung cancer (NSCLC), the emergence of resistance mutations, exemplified by the epidermal growth factor receptor (EGFR) T790 M and C797S, is intricately linked to the therapeutic efficacy of EGFR tyrosine kinase inhibitors (EGFR-TKIs). Herein, a highly efficient and specific SNP detection platform for T790 M and C797S mutations has been engineered through the integration of an asymmetric polymerase chain reaction (PCR) and an ingeniously tailored four-way junction (4WJ) probe. Notably, a molecular beacon (MB) probe was judiciously designed to discern the allelic configuration of these mutations. The administration of first- and third-generation EGFR-TKIs demonstrates therapeutic efficacy solely when the mutations are in the trans configuration, characterized by a low fluorescence signal. In contrast, significant fluorescence by the MB probe is indicative of the C797S mutation being in a cis arrangement with T790M, thereby rendering the cells refractory to the therapeutic interventions of both first- and third-generation EGFR-TKIs. The assay is capable of concurrently detecting two point-mutations and ascertaining their allelic positions in a single test within 1.5 h, enhancing both efficiency and simplicity. It also exhibits high accuracy in the identification of clinical samples, offering promising implications for therapeutic guidelines. By enabling tailored treatment plans based on specific genetic profiles, our approach not only advances the precision of NSCLC treatment strategies but also marks a significant contribution to personalized medicine.
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Affiliation(s)
- Jiaqi Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Songchen Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200000, China
| | - Lijuan Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jingyuan Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xintong Hu
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Liguo Chen
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yi Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Duo Wang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
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Wang L, Wen X, Yang Y, Hu Z, Jiang J, Duan L, Liao X, He Y, Liu Y, Wang J, Liang Z, Zhu X, Liu Q, Liu T, Luo D. CRISPR/Cas13a-based supersensitive circulating tumor DNA assay for detecting EGFR mutations in plasma. Commun Biol 2024; 7:657. [PMID: 38806596 PMCID: PMC11133305 DOI: 10.1038/s42003-024-06368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
Despite recent technological advancements in cell tumor DNA (ctDNA) mutation detection, challenges persist in identifying low-frequency mutations due to inadequate sensitivity and coverage of current procedures. Herein, we introduce a super-sensitivity and specificity technique for detecting ctDNA mutations, named HiCASE. The method utilizes PCR-based CRISPR, coupled with the restriction enzyme. In this work, HiCASE focuses on testing a series of EGFR mutations to provide enhanced detection technology for non-small cell lung cancer (NSCLC), enabling a detection sensitivity of 0.01% with 40 ng cell free DNA standard. When applied to a panel of 140 plasma samples from 120 NSCLC patients, HiCASE exhibits 88.1% clinical sensitivity and 100% specificity with 40 μL of plasma, higher than ddPCR and Super-ARMS assay. In addition, HiCASE can also clearly distinguish T790M/C797S mutations in different positions at a 1% variant allele frequency, offering valuable guidance for drug utilization. Indeed, the established HiCASE assay shows potential for clinical applications.
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Affiliation(s)
- Li Wang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaosha Wen
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China
- Shenzhen University Medical School, Shenzhen, 518060, PR China
| | - Yang Yang
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China
- Shenzhen University Medical School, Shenzhen, 518060, PR China
| | - Zheng Hu
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Chenzhou, 423000, PR China
| | - Jing Jiang
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Chenzhou, 423000, PR China
| | - Lili Duan
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Chenzhou, 423000, PR China
| | - Xiaofen Liao
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Chenzhou, 423000, PR China
| | - Yan He
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China
- Shenzhen University Medical School, Shenzhen, 518060, PR China
| | - Yaru Liu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China
- Shenzhen University Medical School, Shenzhen, 518060, PR China
| | - Jing Wang
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China
- Shenzhen University Medical School, Shenzhen, 518060, PR China
| | - Zhikun Liang
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, 510665, PR China
| | - Xiaoya Zhu
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, 510665, PR China
| | - Quan Liu
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China.
- Shenzhen University Medical School, Shenzhen, 518060, PR China.
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, PR China.
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, 518052, PR China.
- Shenzhen University Medical School, Shenzhen, 518060, PR China.
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Li YZ, Kong SN, Liu YP, Yang Y, Zhang HM. Can Liquid Biopsy Based on ctDNA/cfDNA Replace Tissue Biopsy for the Precision Treatment of EGFR-Mutated NSCLC? J Clin Med 2023; 12:jcm12041438. [PMID: 36835972 PMCID: PMC9966257 DOI: 10.3390/jcm12041438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
More and more clinical trials have explored the role of liquid biopsy in the diagnosis and treatment of EGFR-mutated NSCLC. In certain circumstances, liquid biopsy has unique advantages and offers a new way to detect therapeutic targets, analyze drug resistance mechanisms in advanced patients, and monitor MRD in patients with operable NSCLC. Although its potential cannot be ignored, more evidence is needed to support the transition from the research stage to clinical application. We reviewed the latest progress in research on the efficacy and resistance mechanisms of targeted therapy for advanced NSCLC patients with plasma ctDNA EGFR mutation and the evaluation of MRD based on ctDNA detection in perioperative and follow-up monitoring.
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Ogusu S, Ariyasu R, Akita T, Kiritani A, Tsugitomi R, Amino Y, Uchibori K, Kitazono S, Yanagitani N, Nishio M. EGFR-TKI re-administration after osimertinib failure in T790M mutation loss cases with re-biopsy. Invest New Drugs 2022; 40:1342-1349. [PMID: 36152107 DOI: 10.1007/s10637-022-01301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
Data on the re-administration of epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) after osimertinib failure in patients with T790M-positive non-small cell lung cancer (NSCLC) is limited. EGFR-TKI re-administration efficacy may vary between patients with T790M loss and those with T790M persistent with re-biopsy after osimertinib treatment. Patients who received EGFR-TKI re-administration (gefitinib, erlotinib, afatinib, dacomitinib, and osimertinib) after osimertinib failure were identified from our database. T790M mutation status before EGFR-TKI re-administration was analyzed via repeat biopsy. We retrospectively evaluated the efficacy of EGFR-TKI re-administration, especially differences according to the T790M mutation status, via repeat biopsy. Until June 2020, 28 patients received EGFR-TKI re-administration and 17 underwent repeat biopsy after osimertinib failure. Patients were divided into three groups, including the T790M loss group, where active mutation persisted and T790M was lost (13/17); T790M remaining group, where both the active mutation and T790M persisted (3/17); and active mutation loss group where both the active mutation and T790M were lost (1/17). The overall response rate (ORR) of EGFR-TKI re-administration in the T790M loss group was 31% and the disease control rate (DCR) was 54%, which were higher than the ORR of 21% and DCR of 43% in the entire patient population. ORR and DCR of the not re-biopsy group were low (9% and 27%, respectively). The therapeutic effect of EGFR-TKI re-administration in patients with T790M-positive NSCLC after osimertinib failure is limited. EGFR-TKI re-administration may be considered in cases of T790M loss after repeat biopsy.
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Affiliation(s)
- Shinsuke Ogusu
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Ryo Ariyasu
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takahiro Akita
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ayu Kiritani
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryosuke Tsugitomi
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshiaki Amino
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ken Uchibori
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoru Kitazono
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Noriko Yanagitani
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.
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Direct digital polymerase chain reaction chip for the detection of EGFR T790M mutation in plasma. Talanta 2022; 237:122977. [PMID: 34736699 DOI: 10.1016/j.talanta.2021.122977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/02/2023]
Abstract
Nucleic acid extraction and purification before amplification is considered an essential step for nucleic acid amplification testing. However, this may cause losses or introduce errors that can lead to inaccurate results, especially when using samples with a small nucleic acid concentration. Here, we developed a direct digital chip that enabled us to detect nucleic acid without DNA extraction and purification. We have developed a self-priming liquid-dispensing digital PCR chip that does not require any external power. This is a robust anti-evaporation digital PCR chip with fast sampling and accurate quantification performance. Using this chip, we have established an on-chip direct nucleic acid amplification method that does not require nucleic acid extraction and purification for liquid biopsy samples. In order to verify the feasibility of this chip for clinical samples, we detected the EGFR T790M mutation from plasma. Results showed that EGFR T790M mutation could be detected with an accuracy of 100% and a sensitivity of 0.01%. Without nucleic acid extraction and purification, the assay avoids complex pre-processing, thus saving time and achieving precise quantification. We expect our direct digital PCR chip to have practical applications in diagnosis, screening, and research, especially in resource-deprived regions.
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Palacín-Aliana I, García-Romero N, Asensi-Puig A, Carrión-Navarro J, González-Rumayor V, Ayuso-Sacido Á. Clinical Utility of Liquid Biopsy-Based Actionable Mutations Detected via ddPCR. Biomedicines 2021; 9:906. [PMID: 34440110 PMCID: PMC8389639 DOI: 10.3390/biomedicines9080906] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and remains a major public health challenge. The introduction of more sensitive and powerful technologies has permitted the appearance of new tumor-specific molecular aberrations with a significant cancer management improvement. Therefore, molecular pathology profiling has become fundamental not only to guide tumor diagnosis and prognosis but also to assist with therapeutic decisions in daily practice. Although tumor biopsies continue to be mandatory in cancer diagnosis and classification, several studies have demonstrated that liquid biopsies could be used as a potential tool for the detection of cancer-specific biomarkers. One of the main advantages is that circulating free DNA (cfDNA) provides information about intra-tumoral heterogeneity, reflecting dynamic changes in tumor burden. This minimally invasive tool has become an accurate and reliable instrument for monitoring cancer genetics. However, implementing liquid biopsies across the clinical practice is still ongoing. The main challenge is to detect genomic alterations at low allele fractions. Droplet digital PCR (ddPCR) is a powerful approach that can overcome this issue due to its high sensitivity and specificity. Here we explore the real-world clinical utility of the liquid biopsy ddPCR assays in the most diagnosed cancer subtypes.
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Affiliation(s)
- Irina Palacín-Aliana
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain
- Faculty of Science, Universidad de Alcalá, 28801 Madrid, Spain
| | - Noemí García-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | - Adrià Asensi-Puig
- Atrys Health, 08025 Barcelona, Spain; (I.P.-A.); (A.A.-P.); (V.G.-R.)
| | - Josefa Carrión-Navarro
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | | | - Ángel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; (N.G.-R.); (J.C.-N.)
- Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
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Ariyasu R, Uchibori K, Sasaki T, Tsukahara M, Kiyotani K, Yoshida R, Ono Y, Kitazono S, Ninomiya H, Ishikawa Y, Mizukami Y, Yanagitani N, Fujita N, Nishio M, Katayama R. Monitoring epidermal growth factor receptor C797S mutation in Japanese non-small cell lung cancer patients with serial cell-free DNA evaluation using digital droplet PCR. Cancer Sci 2021; 112:2371-2380. [PMID: 33686722 PMCID: PMC8177776 DOI: 10.1111/cas.14879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/13/2021] [Accepted: 03/07/2021] [Indexed: 12/25/2022] Open
Abstract
Osimertinib is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) that is effective in treating both naïve and T790M-mutated EGFR-TKI-resistant non-small cell lung cancer patients. The EGFR C797S mutation is the major osimertinib resistance mechanism. The present study monitored the EGFR C797S mutation during osimertinib treatment in Japanese patients using droplet digital PCR (ddPCR). In our first cohort, C797S detection was validated with tumor specimens and/or plasma samples from 26 patients using ddPCR with custom-designed probes detecting and discriminating T790M and C797S in cis and trans positions. In our second cohort, 18 patients with EGFR-T790M who were going to start osimertinib were analyzed using ddPCR by collecting the plasma samples every month from the beginning of the course of osimertinib. In the first cohort, C797S was detected in 15.4% of patients. C797S and T790M in cis and trans positions were distinguished using ddPCR. In the second cohort, serial cfDNA evaluation revealed that the rate of EGFR mutation changes with disease state. Increases of EGFR mutation were detected, including C797S several months before the diagnosis of disease progression. As with the first cohort, C797S and T790M in cis and trans position were distinguished by ddPCR at disease progression. Coincidentally, in the first cohort, next generation sequencing detected NRAS Q61K mutation and the resistance with NRAS Q61K mutation was overcome by trametinib. In the second cohort, serial cfDNA analysis was useful for evaluating bone oligo-progression and local radiation therapy.
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Affiliation(s)
- Ryo Ariyasu
- Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Department of Thoracic Medical OncologyThe Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Ken Uchibori
- Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Department of Thoracic Medical OncologyThe Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Takaaki Sasaki
- Respiratory CenterAsahikawa Medical University HospitalAsahikawaJapan
| | - Mika Tsukahara
- Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Kazuma Kiyotani
- Immunopharmacogenomics GroupCancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Ryohei Yoshida
- Respiratory CenterAsahikawa Medical University HospitalAsahikawaJapan
| | - Yusuke Ono
- Institute of Biomedical ResearchSapporo Higashi Tokushukai HospitalSapporoJapan
| | - Satoru Kitazono
- Department of Thoracic Medical OncologyThe Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Hironori Ninomiya
- Division of PathologyCancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yuichi Ishikawa
- Division of PathologyCancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yusuke Mizukami
- Institute of Biomedical ResearchSapporo Higashi Tokushukai HospitalSapporoJapan
| | - Noriko Yanagitani
- Department of Thoracic Medical OncologyThe Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Naoya Fujita
- Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Makoto Nishio
- Department of Thoracic Medical OncologyThe Cancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Ryohei Katayama
- Cancer Chemotherapy CenterJapanese Foundation for Cancer ResearchTokyoJapan
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