1
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Udagawa C, Nakano MH, Yoshida T, Ohe Y, Kato K, Mushiroda T, Zembutsu H. Association between genetic variants and the risk of nivolumab-induced immune-related adverse events. Pharmacogenomics 2022; 23:887-901. [PMID: 36268685 DOI: 10.2217/pgs-2022-0113] [Citation(s) in RCA: 4] [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] [Indexed: 11/21/2022] Open
Abstract
Aim: We sought to identify the variants that could predict the risk of nivolumab-induced immune-related adverse events (irAEs) in patients with cancer. Patients & methods: We enrolled 622 Japanese patients and carried out a genome-wide association study. The associations for 507 single nucleotide polymorphisms (SNPs) showing p < 0.001 were further investigated using an independent cohort. Results: In the combined analysis, possible associations were found for a total of 90 SNPs. Although no SNPs were identified to be significantly associated with nivolumab-induced irAEs, the SNP most strongly associated with nivolumab-induced irAEs was rs469490. Conclusion: This study is an important hypothesis-generating study to guide future studies in larger and/or other ethnic cohorts.
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Affiliation(s)
- Chihiro Udagawa
- Department of Genetics Medicine & services, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Mari Hara Nakano
- Division of Breast & Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
| | - Teruhiko Yoshida
- Department of Genetics Medicine & services, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Science, Yokohama, 230-0045, Japan
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
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2
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Udagawa C, Kuah S, Shimoi T, Kato K, Yoshida T, Nakano MH, Shimo A, Kojima Y, Yoshie R, Tsugawa K, Mushiroda T, Tan EY, Zembutsu H. Replication Study for the Association of Five SNPs Identified by GWAS and Trastuzumab-Induced Cardiotoxicity in Japanese and Singaporean Cohorts. Biol Pharm Bull 2022; 45:1198-1202. [DOI: 10.1248/bpb.b22-00136] [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: 11/22/2022]
Affiliation(s)
- Chihiro Udagawa
- Department of Genetics Medicine and services, National Cancer Center Hospital
| | - Sherwin Kuah
- Department of General Surgery, Tan Tock Seng Hospital
| | | | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital
| | - Teruhiko Yoshida
- Department of Genetics Medicine and services, National Cancer Center Hospital
| | - Mari Hara Nakano
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine
| | - Arata Shimo
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine
| | - Yasuyuki Kojima
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine
| | - Reiko Yoshie
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine
| | - Koichiro Tsugawa
- Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Science
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute
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3
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Björn N, Jakobsen I, Udagawa C, Brandén E, Koyi H, Lewensohn R, De Petris L, Zembutsu H, Gréen H. The association of four genetic variants with myelosuppression in gemcitabine-treated Japanese is not evident in gemcitabine/carboplatin-treated Swedes. Basic Clin Pharmacol Toxicol 2022; 130:513-521. [PMID: 35132780 PMCID: PMC9303231 DOI: 10.1111/bcpt.13712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
Gemcitabine/carboplatin‐induced myelosuppressive adverse drug reactions (ADRs) are clinical problems leading to patient suffering and dose alterations. There is a need for personalised medicine to improve treatment effects and patients' well‐being. We tested four genetic variants, rs11141915, rs1901440, rs12046844 and rs11719165, previously suggested as potential biomarkers for gemcitabine‐induced leukopenia/neutropenia in Japanese patients, in 213 Swedish gemcitabine/carboplatin‐treated non‐small cell lung cancer (NSCLC) patients. DNA was genotyped using TaqMan probes and real‐time PCR. The relationships between the risk alleles and low toxicity (non‐ADR: Common Terminology Criteria for Adverse Events [CTCAE] grades 0) or high toxicity (ADR: CTCAE grades 3–4) of platelets, leukocytes and neutrophils were evaluated using Fisher's exact test. The risk alleles did not correlate with myelosuppression, and the strongest borderline significance (not withstanding adjustment for multiple testing) was for rs1901440 (neutropenia, p = 0.043) and rs11719165 (leukopenia, p = 0.049) where the risk alleles trended towards lower toxicity, contrasting with previous study findings. Risk alleles and higher risk scores were more common among our patients. We conclude that the genetic variants do not apply to Swedish patients treated with gemcitabine/carboplatin. However, they can still be important in other populations and cohorts, especially in a gemcitabine monotherapy setting, where the causal genetic variation might influence myelosuppressive ADRs.
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Affiliation(s)
- Niclas Björn
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ingrid Jakobsen
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden
| | - Chihiro Udagawa
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Eva Brandén
- Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Hirsh Koyi
- Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Rolf Lewensohn
- Thoracic Oncology Unit, Tema Cancer, Karolinska University Hospital, and Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Luigi De Petris
- Thoracic Oncology Unit, Tema Cancer, Karolinska University Hospital, and Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Henrik Gréen
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
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4
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Fukunaga K, Kato K, Okusaka T, Saito T, Ikeda M, Yoshida T, Zembutsu H, Iwata N, Mushiroda T. Functional Characterization of the Effects of N-acetyltransferase 2 Alleles on N-acetylation of Eight Drugs and Worldwide Distribution of Substrate-Specific Diversity. Front Genet 2021; 12:652704. [PMID: 33815485 PMCID: PMC8012690 DOI: 10.3389/fgene.2021.652704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Variability in the enzymatic activity of N-acetyltransferase 2 (NAT2) is an important contributor to interindividual differences in drug responses. However, there is little information on functional differences in N-acetylation activities according to NAT2 phenotypes, i.e., rapid, intermediate, slow, and ultra-slow acetylators, between different substrate drugs. Here, we estimated NAT2 genotypes in 990 Japanese individuals and compared the frequencies of different genotypes with those of different populations. We then calculated in vitro kinetic parameters of four NAT2 alleles (NAT2∗4, ∗5, ∗6, and ∗7) for N-acetylation of aminoglutethimide, diaminodiphenyl sulfone, hydralazine, isoniazid, phenelzine, procaineamide, sulfamethazine (SMZ), and sulfapyrizine. NAT2∗5, ∗6, and ∗7 exhibited significantly reduced N-acetylation activities with lower Vmax and CLint values of all drugs when compared with NAT2∗4. Hierarchical clustering analysis revealed that 10 NAT2 genotypes were categorized into three or four clusters. According to the results of in vitro metabolic experiments using SMZ as a substrate, the frequencies of ultra-slow acetylators were calculated to be 29.05–54.27% in Europeans, Africans, and South East Asians, whereas Japanese and East Asian populations showed lower frequencies (4.75 and 11.11%, respectively). Our findings will be helpful for prediction of responses to drugs primarily metabolized by NAT2.
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Affiliation(s)
- Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ken Kato
- Department of Head and Neck Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takeo Saito
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Zembutsu
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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5
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Udagawa C, Sasaki Y, Tanizawa Y, Suemizu H, Ohnishi Y, Nakamura Y, Tokino T, Zembutsu H. Whole-exome sequencing of 79 xenografts as a potential approach for the identification of genetic variants associated with sensitivity to cytotoxic anticancer drugs. PLoS One 2020; 15:e0239614. [PMID: 32986753 PMCID: PMC7521756 DOI: 10.1371/journal.pone.0239614] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Chemotherapy response remains unpredictable in most patients with cancer. In this study, we performed whole-exome sequencing of 79 cancer xenografts derived from human cancer tissues to identify genetic predictors of chemosensitivity to nine cytotoxic anticancer drugs. Xenografts were harvested from 12 organs with cancer and implanted into nude mice. The mice were exposed to one of nine cytotoxic anticancer drugs (5-fluorouracil, nimustine, adriamycin, cyclophosphamide, cisplatin, mitomycin C, methotrexate, vincristine, and vinblastine) to assess the correlation between chemosensitivity response and variant allele frequency. We found 162 candidate variants that were possibly associated with chemosensitivity to one or more of the nine anticancer drugs (P < 0.01). In a subgroup analysis of breast and gastric cancer xenografts, 78 and 67 variants, respectively, were possibly associated with chemosensitivity. This approach may help to contribute to the development of personalized treatments that may allow for the prescription of optimal chemotherapy regimens among patients with cancer.
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Affiliation(s)
- Chihiro Udagawa
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Sasaki
- Biology, Department of Liberal Arts and Sciences Center for Medical Education, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Suemizu
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Yasuyuki Ohnishi
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
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6
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Udagawa C, Zembutsu H. Pharmacogenetics for severe adverse drug reactions induced by molecular-targeted therapy. Cancer Sci 2020; 111:3445-3457. [PMID: 32780457 PMCID: PMC7540972 DOI: 10.1111/cas.14609] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/29/2022] Open
Abstract
Molecular-targeted drugs specifically interfere with molecules that are frequently overexpressed or mutated in cancer cells. As such, these drugs are generally considered to precisely attack cancer cells, thereby inducing fewer adverse drug reactions (ADRs). However, molecular-targeted drugs can still cause characteristic ADRs that, although rarely severe, can be life-threatening. Therefore, it is becoming increasingly important to be able to predict which patients are at risk of developing ADRs after treatment with molecular-targeted therapy. The emerging field of pharmacogenetics aims to better distinguish the genetic variants associated with drug toxicity and efficacy to improve the selection of therapeutic strategies for each genetic profile. Here, we provide an overview of the current reports on the relationship between genetic variants and molecular-targeted drug-induced severe ADRs in oncology.
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Affiliation(s)
- Chihiro Udagawa
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Hitoshi Zembutsu
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
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7
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Uesato Y, Sasahira N, Ozaka M, Sasaki T, Takatsuki M, Zembutsu H. Evaluation of circulating tumor DNA as a biomarker in pancreatic cancer with liver metastasis. PLoS One 2020; 15:e0235623. [PMID: 32614932 PMCID: PMC7332050 DOI: 10.1371/journal.pone.0235623] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Pancreatic cancer is an aggressive, solid tumor, with a grave prognosis. Despite surgical treatment in patients with pancreatic cancer, the rate of recurrence is high. In addition, although tumor biomarkers are frequently used to confirm advanced pancreatic cancer, this is not accurate and the biomarkers currently used cannot indicate prognosis. This study sought to evaluate circulating tumor DNA as a tumor biomarker to prognosticate pancreatic cancer. Patients with advanced pancreatic cancer and liver metastasis (N = 104) were included, and blood samples were collected from all patients. The mutant allele frequency was measured using amplicon-based deep sequencing on a cell-free DNA panel covering 14 genes with > 240 hot spots. In patients with advanced pancreatic cancer, 50% (N = 52) had detectable ctDNA levels, with TP53 (45%, N = 47) and KRAS (42.3%, N = 44) mutations the most common. Patients with detectable circulating tumor DNA levels also had significantly worse overall survival and progression free survival than ctDNA negative patients (8.4 vs 16 months, P<0.0001 for overall survival; 3.2 vs 7.9 months, P<0.0001 for progression-free survival). In a multivariate analysis, ctDNA status was independently associated with overall survival and progression-free survival (HR = 3.1, 95%CI = 1.9-5.0, P<0.0001; HR 2.6, 95%CI = 1.7-4.0, P<0.0001, respectively). Moreover, circulating tumor DNA significantly correlated with a higher number of liver metastases, the presence of lung and/or peritoneal metastases, tumor burden, and higher carbohydrate antigen 19-9 levels. This study supports the use of circulating tumor DNA as an independent prognostic marker for advanced pancreatic cancer.
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Affiliation(s)
- Yasunori Uesato
- Project of Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- * E-mail:
| | - Naoki Sasahira
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masato Ozaka
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Sasaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mitsuhisa Takatsuki
- Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hitoshi Zembutsu
- Project of Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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8
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Murahashi S, Akiyoshi T, Sano T, Fukunaga Y, Noda T, Ueno M, Zembutsu H. Serial circulating tumour DNA analysis for locally advanced rectal cancer treated with preoperative therapy: prediction of pathological response and postoperative recurrence. Br J Cancer 2020; 123:803-810. [PMID: 32565539 PMCID: PMC7462982 DOI: 10.1038/s41416-020-0941-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [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: 10/21/2019] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The "watch-and-wait" approach is a common treatment option amongst patients with locally advanced rectal cancer (LARC). However, the diagnostic sensitivity of clinical modalities, such as colonoscopy and magnetic resonance imaging to determine pathological response, is not high. We analysed the clinical utility of circulating tumour DNA (ctDNA) of patients with LARC to predict response to preoperative therapy and postoperative recurrence. METHODS A serial ctDNA analysis of 222 plasma samples from 85 patients with LARC was performed using amplicon-based deep sequencing on a cell-free DNA panel covering 14 genes with over 240 hotspots. RESULTS ctDNA was detected in 57.6% and 22.3% of samples at baseline and after preoperative treatment, respectively, which was significantly different (P = 0.0003). Change in ctDNA was an independent predictor of complete response to preoperative therapy (P = 0.0276). In addition, postoperative ctDNA and carcinoembryonic antigen (CEA) were independent prognostic markers for risk of recurrence after surgery (ctDNA, P = 0.0127 and CEA, P = 0.0105), with a combined analysis having cumulative effects on recurrence-free survival (P = 1.0 × 10-16). CONCLUSIONS Serial ctDNA analysis may offer clinically useful predictive and prognostic markers for response to preoperative therapy and postoperative recurrence in patients with LARC.
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Affiliation(s)
- Satoshi Murahashi
- Department of Gastrointestinal Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Akiyoshi
- Department of Gastrointestinal Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeshi Sano
- Department of Gastrointestinal Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yosuke Fukunaga
- Department of Gastrointestinal Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masashi Ueno
- Department of Gastrointestinal Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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9
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Zembutsu H, Osumi H, Shinozaki E, Yamaguchi K. Abstract A37: Early change in circulating tumor DNA as a potential predictor of response to chemotherapy in patients with metastatic colorectal cancer. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-a37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The impact of the change in ctDNA levels after chemotherapy on the clinical outcomes of patients with metastatic colorectal cancer (mCRC) remains unclear. The present study evaluated the clinical implications of the early change in ctDNA levels as a predictor of objective response and the clinical outcome in mCRC patients who received chemotherapy. We investigated the effects of after/before ratio of ctDNA levels 2 and 8 weeks after initiation of second-line chemotherapy on objective response rate (ORR), progression-free survival (PFS), and overall survival (OS). ctDNA was detected using amplicon-based deep sequencing with a molecular barcode that includes >240 hotspot mutations in 14 colon cancer-related genes. Patients with lower ctDNA level (≤ 50%) 8 weeks after initiation of chemotherapy compared to baseline showed significantly longer PFS and OS than the patients with higher (> 50%) ctDNA level in multivariate analysis. In patients achieving partial response or stable disease, the after/before ratio of ctDNA level 8 weeks after initiation of chemotherapy was significantly lower than those in patients with progressive disease. The present study suggests that an early change in the ctDNA level might serve as a biomarker to predict the chemotherapeutic efficacy and clinical outcomes in patients with mCRC.
Citation Format: Hitoshi Zembutsu, Hiroki Osumi, Eiji Shinozaki, Kensei Yamaguchi. Early change in circulating tumor DNA as a potential predictor of response to chemotherapy in patients with metastatic colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A37.
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Affiliation(s)
- Hitoshi Zembutsu
- 1Cancer Precision Medicine Center, Research Institute, Japanese Foundation for Cancer Research, Tokyo, Japan,
| | - Hiroki Osumi
- 2Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- 2Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- 2Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
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10
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Matsutani A, Udagawa C, Matsunaga Y, Nakamura S, Zembutsu H. Liquid biopsy for the detection of clinical biomarkers in early breast cancer: new insights and challenges. Pharmacogenomics 2020; 21:359-367. [PMID: 32284011 DOI: 10.2217/pgs-2019-0130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The widespread use of breast screening programs has contributed to the detection of early stage breast cancer, which is often asymptomatic. Early diagnosis is essential to avoid overtreatment and improve clinical outcomes, as early stage breast cancer is rarely life-threatening if detected quickly. Despite this, tissue biopsy remains the principle method for detecting these cancers. Liquid biopsy has been recently proposed as a promising detection method in oncology that is not only less invasive but also contributes to the early diagnosis of breast cancer. Here, we describe the clinical utility of liquid biopsy as a tool for the early detection of breast cancer.
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Affiliation(s)
- Akiko Matsutani
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan.,Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Chihiro Udagawa
- Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuki Matsunaga
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan
| | - Hitoshi Zembutsu
- Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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11
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Nakano MH, Udagawa C, Shimo A, Kojima Y, Yoshie R, Zaha H, Abe N, Motonari T, Unesoko M, Tamura K, Shimoi T, Yoshida M, Yoshida T, Sakamoto H, Kato K, Mushiroda T, Tsugawa K, Zembutsu H. A Genome-Wide Association Study Identifies Five Novel Genetic Markers for Trastuzumab-Induced Cardiotoxicity in Japanese Population. Biol Pharm Bull 2019; 42:2045-2053. [DOI: 10.1248/bpb.b19-00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Mari Hara Nakano
- Project for Development of Liquid Biopsy Diagnosis, Japanese Foundation for Cancer Research, Research Institute
- Division of Breast and Endocrine Surgery, Department of Surgery, St.Marianna University School of Medicine
| | - Chihiro Udagawa
- Project for Development of Liquid Biopsy Diagnosis, Japanese Foundation for Cancer Research, Research Institute
- New Business Development Life Science Group, Toyo Kohan Co., Ltd
| | - Arata Shimo
- Division of Breast and Endocrine Surgery, Department of Surgery, St.Marianna University School of Medicine
| | - Yasuyuki Kojima
- Division of Breast and Endocrine Surgery, Department of Surgery, St.Marianna University School of Medicine
| | - Reiko Yoshie
- Division of Breast and Endocrine Surgery, Department of Surgery, St.Marianna University School of Medicine
| | | | - Norie Abe
- Department of Breast Surgery, Nakagami Hospital
| | | | | | - Kenji Tamura
- Department of Breast and Medical Oncology, National Cancer Center Hospital
| | - Tatsunori Shimoi
- Department of Breast and Medical Oncology, National Cancer Center Hospital
| | - Masayuki Yoshida
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute
| | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital
| | | | - Koichiro Tsugawa
- Division of Breast and Endocrine Surgery, Department of Surgery, St.Marianna University School of Medicine
| | - Hitoshi Zembutsu
- Project for Development of Liquid Biopsy Diagnosis, Japanese Foundation for Cancer Research, Research Institute
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute
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12
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Udagawa C, Horinouchi H, Shiraishi K, Kohno T, Okusaka T, Ueno H, Tamura K, Ohe Y, Zembutsu H. Whole genome sequencing to identify predictive markers for the risk of drug-induced interstitial lung disease. PLoS One 2019; 14:e0223371. [PMID: 31584970 PMCID: PMC6777826 DOI: 10.1371/journal.pone.0223371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/19/2019] [Indexed: 01/13/2023] Open
Abstract
Drug-induced interstitial lung disease (DIILD) is a serious side effect of chemotherapy in cancer patients with an extremely high mortality rate. In this study, to identify genetic variants with greater risk of DIILD, we carried out whole genome sequencing (WGS) of germline DNA samples from 26 patients who developed DIILD, and conducted a case-control association study between these 26 cases and general Japanese population controls registered in the integrative Japanese Genome Variation Database (iJGVD) as a screening study. The associations of 42 single nucleotide variants (SNVs) showing P < 0.0001 were further validated using an independent cohort of 18 DIILD cases as a replication study. A further combined analysis of the screening and replication studies showed a possible association of two SNVs, rs35198919 in intron 1 of the chromosome 22 open reading frame 34 (C22orf34) and rs12625311 in intron 1 of the teashirt zinc finger homeobox 2 (TSHZ2), with DIILD (Pcombined = 1.87 × 10−5 and 5.16 × 10−5, respectively). Furthermore, in a subgroup analysis of epidermal growth factor receptor (EGFR)–tyrosine kinase inhibitor (TKI)-induced interstitial lung disease (ILD), we observed seven candidate SNVs that were possibly associated with ILD (P < 0.00001). This is the first study to identify genetic markers for the risk of DIILD using WGS. Collectively, our novel findings indicate that these SNVs may be applicable for predicting the risk of DIILD in patients receiving chemotherapy.
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Affiliation(s)
- Chihiro Udagawa
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Hideki Ueno
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kenji Tamura
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Hitoshi Zembutsu
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Project for Development of Liquid Biopsy Diagnosis, Japanese Foundation for Cancer Research, Research Institute, Tokyo, Japan
- * E-mail:
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Muramatsu M, Muramatsu M, Ito H, Zembutsu H. Abstract 1380: Clinical relevance of cell-free DNA analysis for bile juice assessed through amplicon-based deep sequencing in bile duct and pancreatic cancer patients with obstructive jaundice. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1380] [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
Personalized treatment for patients with pancreatic or bile duct cancer is limited because cancer cells could not be detected in some patient. Cell-free DNA (cfDNA) sequencing is expected to enable a precision oncology approach for these patients. The development of gene panel for cfDNA covering hundreds of mutation hotspots is important for the establishment of clinically practical cfDNA detection system. We enrolled 40 patients with bile duct or pancreatic cancer which caused obstructive jaundice. Amplicon-based genomic profiling of 14 genes, which are commonly mutated in digestive cancer, in preoperative bile juice by next-generation sequencing (NGS) was carried out to evaluate the feasibility of this assay, and was compared with their clinical parameters. One or more somatic mutation(s) of the 14 genes in bile cfDNA were detected in 25 patients (62.5%) with bile duct or pancreatic cancer. Mutations in TP53, KRAS and APC genes were detected in 19 (47.5%), 11 (27.5%) and 4 (10.0%) patients, respectively. Mutant allele frequencies in plasma were not associated with CEA nor CA19-9. Of the 40 patients with bile duct or pancreatic cancer, the cancer cells could be detected by cytology in 18 patients (45.0%). On the other hand, mutant alleles from cancer cells could be detected in 14 patients who showed negative cytology. Hence, 32 patients (80.0%) could be diagnosed as cancer before surgical operation by using the information from liquid biopsy (cfDNA analysis using bile juice) in addition to that from cytology. Our data confirmed that mutant allele in bile cfDNA could be sensitively detected by amplicon-based NGS system. These results suggest that the detection of cfDNA in bile juice using high-sensitive deep sequencing system could be a novel diagnostic tool, and these technologies could increase the ratio of definitive diagnosis of refractory cancer such as bile duct or pancreatic cancer.
Citation Format: Marie Muramatsu, Marie Muramatsu, Hiromichi Ito, Hitoshi Zembutsu. Clinical relevance of cell-free DNA analysis for bile juice assessed through amplicon-based deep sequencing in bile duct and pancreatic cancer patients with obstructive jaundice [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 1380.
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Affiliation(s)
| | | | - Hiromichi Ito
- Japanese Foundation For Cancer Research, Ariake,Koto, Japan
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14
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Nakamura N, Okamura H, Yamano H, Ito H, Zembutsu H. Abstract 2420: The development of novel detection system for circulating tumor DNA using DNA chip system. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2420] [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
Gene panels covering hundreds of mutation hotspots for detection of cell-free DNA (cfDNA) have been developed for the establishment of clinically practical circulating tumor (ctDNA) detection system. Although amplicon-based or capture-based genomic profiling of genes commonly mutated in cancer using next-generation sequencing (NGS) system have been developed, they are not sufficiently sensitive nor accurate to be used for clinical diagnosis in hospital. As a result of preliminary study using 87 advanced pancreatic cancer (stage lll/lV), we observed that one or more KRAS mutation(s) could be detected in 60.9% of patients with advanced pancreatic cancer by using the amplicon-based deep sequencing system. To develop more sensitive and accurate ctDNA detection system, we optimized conditions of our DNA chip system. We firstly used 100 synthetic DNA samples, whose KRAS mutant allele frequencies were from 0.1% to 10.0%, and investigated the quantitativity of our DNA chip system. We amplified target regions by PCR to obtain 2,000 copies of synthesized DNA. The PCR product was hybridized with the probe on the DNA chip. The fluorescence ratio (mutant allele fluorescence intensity / total fluorescence intensity) of 100 synthetic DNA samples were clearly distinguished to that of negative control by using the DNA chip system. We defined an appropriate cut-off values of small quantities (0.1%) of mutations. Furthermore, to confirm the accuracy and reliability of this method, we verified our DNA chip system using 15 plasma cfDNA samples from patients with mutant KRAS (0.1~10.0%) and 15 samples from patients without mutant KRAS as negative control. 10 ng of ctDNA which extracted from blood sample is used in PCR. We observed that detected mutant status by DNA chip was completely concordant (100%) with those by amplicon-based deep sequencing system. Our data confirmed that mutant allele in cfDNA can be sensitively and accurately detected by DNA chip system. These results suggest that the ctDNA detection system developed in this study could be a novel diagnostic tool for tumor burden, and could realize the ultra-early detection of refractory tumors including pancreatic cancer.
Citation Format: Noriaki Nakamura, Hiroshi Okamura, Hirofumi Yamano, Hiromichi Ito, Hitoshi Zembutsu. The development of novel detection system for circulating tumor DNA using DNA chip system [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 2420.
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Affiliation(s)
- Noriaki Nakamura
- 1New Business Development Life Science Group, Toyo Kohan Co., Ltd., Tokyo, Japan
| | - Hiroshi Okamura
- 1New Business Development Life Science Group, Toyo Kohan Co., Ltd., Tokyo, Japan
| | - Hirofumi Yamano
- 2Life Science Department, Toyo Kohan Co., Ltd., Yamaguchi, Japan
| | - Hiromichi Ito
- 3Department of Gastroenterology Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- 4Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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15
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Osumi H, Shinozaki E, Yamaguchi K, Zembutsu H. Clinical utility of circulating tumor DNA for colorectal cancer. Cancer Sci 2019; 110:1148-1155. [PMID: 30742729 PMCID: PMC6447957 DOI: 10.1111/cas.13972] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [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: 12/25/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is currently the most common type of cancer in Japan, and its prognosis has improved because of development of diagnosis and advancement in treatments including surgery and chemotherapy. However, because of intratumor heterogeneity and clonal evolution, tumors often develop resistance to treatment. Genotyping tumor tissue in search of somatic genetic alterations for actionable information has become routine examination in clinical practice. However, the inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens only. Circulating tumor DNA (ctDNA) carrying tumor‐specific genetic or epigenetic alterations is released into the circulation from tumor cells undergoing apoptosis or necrosis. Analysis of ctDNA has the potential to change clinical practice by exploiting blood rather than tissue, as a source of information. Here, we provide an overview of the characteristics of ctDNA and focus on detection methods for ctDNA, and the feasibility of use of ctDNA to monitor tumor dynamics for patients with colorectal cancer.
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Affiliation(s)
- Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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16
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Osumi H, Shinozaki E, Takeda Y, Wakatsuki T, Ichimura T, Saiura A, Yamaguchi K, Takahashi S, Noda T, Zembutsu H. Clinical relevance of circulating tumor DNA assessed through deep sequencing in patients with metastatic colorectal cancer. Cancer Med 2018; 8:408-417. [PMID: 30575318 PMCID: PMC6346227 DOI: 10.1002/cam4.1913] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Because circulating tumor DNA (ctDNA) studies focusing on only one or a few genes to monitor the disease progress or treatment response are unlikely to find its clinical significance, the development of cell‐free DNA (cfDNA) panel covering hundreds of mutation hot spots is important for the establishment of clinically practical ctDNA detection system. We enrolled 101 patients with metastatic colorectal cancer (mCRC) who received chemotherapy. Amplicon‐based genomic profiling of 14 genes, which are commonly mutated in CRC, in plasma by next‐generation sequencing (NGS) was carried out to evaluate the feasibility of this assay and was compared with their clinical parameters and RAS status in matched tissue samples. Somatic mutations of the 14 genes in plasma cfDNA were detected in 88 patients (87.1%) with mCRC. Mutations in TP53, KRAS, and APC genes were detected in 70 (69.3%), 39 (38.6%), and 24 (23.7%) patients, respectively. Mutant allele frequencies in plasma were significantly associated with metastasis (liver, P = 0.00004, lymph node, P = 0.008, number of metastatic organs, P = 0.0006), tumor markers (CEA, P = 0.000007, CA19‐9, P = 0.006, LDH, P = 0.00001), and tumor diameter (maximum, P = 0.00002, sum of diameter, P = 0.00009). The overall concordance rate of RAS status between ctDNA and matched tissue was 77.2% (78/101). Our data confirmed that mutant allele in cfDNA can be sensitively detected by amplicon‐based NGS system. These results suggest that ctDNA could be a novel diagnostic biomarker to monitor changes in mutational status and tumor burden in patients with mCRC.
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Affiliation(s)
- Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshinori Takeda
- Department of Hepato-Biliary-Pancreatic Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeru Wakatsuki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Ichimura
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akio Saiura
- Department of Hepato-Biliary-Pancreatic Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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17
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Osumi H, Shinozaki E, Zembutsu H, Takeda Y, Wakatsuki T, Ichimura T, Ota Y, Nakayama I, Ogura M, Suenaga M, Takahari D, Chin K, Saiura A, Takahashi S, Noda T, Yamaguchi K. Clinical relevance of circulating tumor DNA using amplicon-based deep sequencing panel in colorectal cancer patients with liver metastasis. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy281.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Onishi H, Udagawa C, Kubo M, Nakamura S, Akashi-Tanaka S, Kuwayama T, Watanabe C, Takamaru T, Takei H, Ishikawa T, Miyahara K, Matsumoto H, Hasegawa Y, Momozawa Y, Low SK, Kutomi G, Shima H, Satomi F, Okazaki M, Zaha H, Onomura M, Matsukata A, Sagara Y, Baba S, Yamada A, Shimada K, Shimizu D, Tsugawa K, Shimo A, Hartman M, Chan CW, Lee SC, Endo I, Zembutsu H. A genome-wide association study identifies three novel genetic markers for response to tamoxifen: A prospective multicenter study. PLoS One 2018; 13:e0201606. [PMID: 30161160 PMCID: PMC6116947 DOI: 10.1371/journal.pone.0201606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/03/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023] Open
Abstract
Purpose Although association studies of genetic variations with the clinical outcomes of breast cancer patients treated with tamoxifen have been reported, genetic factors which could determine individual response to tamoxifen are not fully clarified. We performed a genome-wide association study (GWAS) to identify novel genetic markers for response to tamoxifen. Experimental design We prospectively collected 347 blood samples from patients with hormone receptor-positive and human epidermal growth factor receptor 2-negative, invasive breast cancer receiving preoperative tamoxifen monotherapy for 14 to 28 days. We used Ki-67 response in breast cancer tissues after preoperative short-term tamoxifen therapy as a surrogate marker for response to tamoxifen. We performed GWAS and genotype imputation using 275 patients, and an independent set of 72 patients was used for replication study. Results The combined result of GWAS and the replication study, and subsequent imputation analysis indicated possible association of three loci with Ki-67 response after tamoxifen therapy (rs17198973 on chromosome 4q34.3, rs4577773 on 6q12, and rs7087428 on 10p13, Pcombined = 5.69 x 10−6, 1.64 x 10−5, and 9.77 x 10−6, respectively). When patients were classified into three groups by the scoring system based on the genotypes of the three SNPs, patients with higher scores showed significantly higher after/before ratio of Ki-67 compared to those with lower scores (P = 1.8 x 10−12), suggesting the cumulative effect of the three SNPs. Conclusion We identified three novel loci, which could be associated with clinical response to tamoxifen. These findings provide new insights into personalized hormonal therapy for the patients with breast cancer.
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Affiliation(s)
- Hiroshi Onishi
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chihiro Udagawa
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Sadako Akashi-Tanaka
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Takashi Kuwayama
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Chie Watanabe
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Tomoko Takamaru
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Hiroyuki Takei
- Department of Breast Surgery, Nippon Medical School, Tokyo, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery, Tokyo Medical University, Tokyo, Japan
| | - Kana Miyahara
- Department of Breast Surgery, Tokyo Medical University, Tokyo, Japan
| | | | - Yoshie Hasegawa
- Department of Breast Surgery, Hirosaki Municipal Hospital, Hirosaki, Japan
| | | | - Siew-Kee Low
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | - Goro Kutomi
- 1st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Hiroaki Shima
- 1st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Fukino Satomi
- 1st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Minoru Okazaki
- Department of Breast Surgery, Sapporo Breast Surgical Clinic, Sapporo, Japan
| | - Hisamitsu Zaha
- Department of Breast Surgery, Nakagami Hospital, Okinawa, Japan
| | - Mai Onomura
- Department of Breast Surgery, Nakagami Hospital, Okinawa, Japan
| | - Ayami Matsukata
- Department of Breast Surgery, Sagara Hospital, Kagoshima, Japan
| | - Yasuaki Sagara
- Department of Breast Surgery, Sagara Hospital, Kagoshima, Japan
| | - Shinichi Baba
- Department of Breast Surgery, Sagara Hospital, Kagoshima, Japan
| | - Akimitsu Yamada
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Japan
| | - Kazuhiro Shimada
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Japan
| | - Daisuke Shimizu
- Department of Breast Surgery, Yokohama Minato Red Cross Hospital, Yokohama, Japan
| | - Koichiro Tsugawa
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine Hospital, Kawasaki, Japan
| | - Arata Shimo
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine Hospital, Kawasaki, Japan
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Ching-Wan Chan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Soo Chin Lee
- Department of Hematology Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hitoshi Zembutsu
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
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Udagawa C, Nakamura H, Ohnishi H, Tamura K, Shimoi T, Yoshida M, Yoshida T, Okamura H, Totoki Y, Shibata T, Zembutsu H. Abstract 3887: Whole exome sequencing to identify genetic markers for trastuzumab-induced cardiotoxicity. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3887] [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
Although trastuzumab-induced cardiotoxicity is an important determinant to limit the use of this drug, the molecular mechanism of risk for this toxicity is not well understood. To identify a genetic marker(s) determining the risk of trastuzumab-induced cardiotoxicity, we performed whole exome sequencing of germline DNA samples from 9 patients with trastuzumab-induced cardiotoxicity, and conducted a case-control association study of 2,258 genetic variants between 9 cases (with trastuzumab-induced cardiotoxicity) and general Japanese population controls registered in Human Genetic Variation Database (HGVD). To further validate the result of the screening study, we carried out a replication study of 10 variants showing Pmin < 0.001 in the screening study using 234 independent patients treated with trastuzumab, including 10 cases and 224 controls (without trastuzumab-induced cardiotoxicity). In the replication study, we observed that three variants had effect in the same direction as in the screening study (SNV1 in exon 2 of HERADR1, SNV2 in exon 2 of HERADR2 and SNV3 in exon 44 of HERADR3). A combined result of the screening and the replication studies suggested an association of a locus on chromosome 6q12 with trastuzumab-induced cardiotoxicity (SNV3 in HERADR3, combined-Pmin = 0.00056, OR = 13.73). This finding provides new insights into personalized trastuzumab therapy for the patients with HER2 positive cancer.
Citation Format: Chihiro Udagawa, Hiromi Nakamura, Hiroshi Ohnishi, Kenji Tamura, Tatsunori Shimoi, Masayuki Yoshida, Teruhiko Yoshida, Hiroshi Okamura, Yasushi Totoki, Tatsuhiro Shibata, Hitoshi Zembutsu. Whole exome sequencing to identify genetic markers for trastuzumab-induced cardiotoxicity [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 3887.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yasushi Totoki
- 2National Cancer Center Research Institute, Tokyo, Japan
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Nakamura N, Hirayama K, Yamano H, Okamura H, Zembutsu H. Abstract 239: Development of DNA chip for detection of predictive SNPs for gemcitabine-induced adverse events. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-239] [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
[Introduction] Anticancer agent gemcitabine is one of the effective chemotherapies and has been widely used for the treatment of patients with various tumors. However, 13-35% of patients receiving gemcitabine experience severe leukopenia/neutropenia. In our previous studies, we identified four novel SNPs (rs11141915, rs1901440, rs11719165 and rs12046844) associated with this toxicity. To predict the risk of gemcitabine-induced myelosuppression, we developed a high accuracy DNA chip system for genotyping of these four SNPs.
[Methods] We used 17 and 170 germline DNA samples of patients who received gemcitabine therapy in the first stage and second stage respectively. For SNP genotyping using the DNA chip, we amplified target regions by PCR with 10 ng of DNA extracted from blood samples. The PCR product was hybridized with the probe on the DNA chip. Genotype was detected by genotyping score, which was calculated the ratio of risk allele fluorescence intensity to total fluorescence intensity. To confirm the accuracy and reliability of this method, TaqMan genotyping assay was performed for 187 samples.
[Results and Discussion] In the first stage, genotypes of 17 samples were clearly divided into 3 types (non-risk type homo, hetero type, risk type homo). We defined an appropriate cut off value of genotyping score for detection of genotype according to the results of first stage. In the second stage, 170 samples, whose genotype were unknown, were genotyped using the DNA chip. The genotype results were completely concordant (100%) with those using TaqMan genotyping assay. Our DNA chip system is extremely useful as a simple method that is capable of genotyping using DNAs extracted from small amount of blood samples in general hospitals. The development of our DNA chip system provides new insights into personalized anti-cancer drug therapy including gemcitabine for the patients with cancer.
Citation Format: Noriaki Nakamura, Koichi Hirayama, Hirofumi Yamano, Hiroshi Okamura, Hitoshi Zembutsu. Development of DNA chip for detection of predictive SNPs for gemcitabine-induced adverse events [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 239.
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Osumi H, Shinozaki E, Zembutsu H, Takeda Y, Wakatsuki T, Ichimura T, Ota Y, Nakayama I, Ogura M, Suenaga M, Takahari D, Chin K, Saiura A, Yamaguchi K. Abstract 2962: Clinical relevance of circulating cell-free DNA using amplicon-based next-generation sequencing panel in colorectal cancer patients with liver metastasis. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2962] [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: Recent advances in the next-generation sequencing technique (NGS) for the detection of cell-free DNA (cfDNA) will be possible to provide the utility as diagnostic and prognostic biomarkers of cancer. We conducted the study of feasibility to detect plasma cfDNA from patients with metastatic colorectal cancer (mCRC) using NGS panel and investigated their relationship with clinicopathological factors.
Methods: A total of 101 mCRC patients with liver metastasis, who had been treated with chemotherapy, were enrolled in this study from February to June in 2017. We investigated i) frequency of detectable mutations in plasma cfDNA, ii) concordance rate of RAS mutation between the DNA extracted from tissues and the plasma cfDNA, iii) relationship between the mutation allele frequencies (MAF) and clinicopathological factors including tumor location, metastatic site, number of metastatic organs, tumor marker (CEA and CA19-9), LDH level, D-dimer level and sum of the tumor diameter measured based on RECIST ver1.1 criteria. Sequencing of plasma cfDNA were performed using Ion Torrent™ Oncomine™ Colon cfDNA Assay.
Results: Mutations in plasma cfDNA were detected in 87.1% (88/101) of patients. The frequencies of plasma cfDNA mutation at TP53, KRAS, APC, and PIK3CA were 68.3%, 38.6%, 23.7%, and 14.8%, respectively. RAS mutational concordance rate between DNA extracted from tumor and cfDNA was 76.2% (77/101). MAF were significantly associated with CEA (P<0.0001), CA19-9 (P=0.006), LDH (P<0.0001) and number of metastatic organs (P<0.0001). Patients with liver or lymph node metastasis had significantly higher MAF compared with those without metastases (Liver: P<0.0001, Lymph node: P=0.008). Positive correlations between CEA level, CA19-9 level, LDH level, tumor diameter and MAF were observed. (CEA: r=0.52, CA19-9: r=0.34, LDH: r=0.55, tumor diameter: r=0.57)
Conclusions: Our results suggested that this cfDNA Assays could detect mutations at a high rate of mCRC patients undergoing chemotherapy and cfDNA analysis using NGS panel could be useful method of diagnostic biomarkers to monitor the change of RAS status and tumor burden. <!–EndFragment–>
Citation Format: Hiroki Osumi, Eiji Shinozaki, Hitoshi Zembutsu, Yoshinori Takeda, Takeru Wakatsuki, Takashi Ichimura, Yumiko Ota, Izuma Nakayama, Mariko Ogura, Mitsukuni Suenaga, Daisuke Takahari, Keisho Chin, Akio Saiura, Kensei Yamaguchi. Clinical relevance of circulating cell-free DNA using amplicon-based next-generation sequencing panel in colorectal cancer patients with liver metastasis [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 2962.
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Affiliation(s)
- Hiroki Osumi
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Yoshinori Takeda
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeru Wakatsuki
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Ichimura
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yumiko Ota
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Izuma Nakayama
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mariko Ogura
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mitsukuni Suenaga
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Daisuke Takahari
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisho Chin
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akio Saiura
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- 1Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
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22
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Taniguchi H, Hoshino D, Moriya C, Zembutsu H, Nishiyama N, Yamamoto H, Kataoka K, Imai K. Silencing PRDM14 expression by an innovative RNAi therapy inhibits stemness, tumorigenicity, and metastasis of breast cancer. Oncotarget 2018; 8:46856-46874. [PMID: 28423353 PMCID: PMC5564528 DOI: 10.18632/oncotarget.16776] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 11/11/2016] [Accepted: 03/22/2017] [Indexed: 12/11/2022] Open
Abstract
PR domain zinc finger protein 14 (PRDM14) maintains stemness in embryonic stem cells via epigenetic mechanisms. Although PRDM14 is elevated in several cancers, it is unclear if and how PRDM14 confers stem cell-like properties and epigenetic changes to cancer cells. Here, we examined the phenotypic characteristics and epigenetic and gene expression profiles of cancer cells that differentially express PRDM14, and assessed the potential of PRDM14-targeted cancer therapy. PRDM14 expression was markedly increased in many different cancer types and correlated with poor survival of breast cancer patients. PRDM14 conferred stem cell-like phenotypes to cancer cells and regulated the expression of genes involved in cancer stemness, metastasis, and chemoresistance. PRDM14 also reduced the methylation of proto-oncogene and stemness gene promoters and PRDM14-binding regions were primarily occupied by histone H3 Lys-4 trimethylation (H3K4me3), both of which are positively correlated with gene expression. Moreover, strong PRDM14 binding sites coincided with promoters containing both H3K4me3 and H3K27me3 histone marks. Using calcium phosphate hybrid micelles as an RNAi delivery system, silencing of PRDM14 expression by chimera RNAi reduced tumor size and metastasis in vivo without causing adverse effects. Conditional loss of PRDM14 function also improved survival of MMTV-Wnt-1 transgenic mice, a spontaneous model of murine breast cancer. Our findings suggest that PRDM14 inhibition may be an effective and novel therapy for cancer stem cells.
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Affiliation(s)
- Hiroaki Taniguchi
- The Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Daisuke Hoshino
- Cancer Biology Department, The Kanagawa Cancer Center Research Institute, Kanagawa 241-0815, Japan
| | - Chiharu Moriya
- The Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hitoshi Zembutsu
- Division of Genetics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Nobuhiro Nishiyama
- Polymer Chemistry Division, Chemical Resources Laboratory, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
| | - Hiroyuki Yamamoto
- Department of Gastroenterology and Hepatology, School of Medicine, St. Marianna Medical University, Kanagawa 216-0015, Japan
| | - Kazunori Kataoka
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Kohzoh Imai
- The Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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23
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Goetz MP, Sangkuhl K, Guchelaar HJ, Schwab M, Province M, Whirl-Carrillo M, Symmans WF, McLeod HL, Ratain MJ, Zembutsu H, Gaedigk A, van Schaik RH, Ingle JN, Caudle KE, Klein TE. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 and Tamoxifen Therapy. Clin Pharmacol Ther 2018; 103:770-777. [PMID: 29385237 DOI: 10.1002/cpt.1007] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/14/2017] [Accepted: 12/23/2017] [Indexed: 12/15/2022]
Abstract
Tamoxifen is biotransformed by CYP2D6 to 4-hydroxytamoxifen and 4-hydroxy N-desmethyl tamoxifen (endoxifen), both with greater antiestrogenic potency than the parent drug. Patients with certain CYP2D6 genetic polymorphisms and patients who receive strong CYP2D6 inhibitors exhibit lower endoxifen concentrations and a higher risk of disease recurrence in some studies of tamoxifen adjuvant therapy of early breast cancer. We summarize evidence from the literature and provide therapeutic recommendations for tamoxifen based on CYP2D6 genotype.
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Affiliation(s)
- Matthew P Goetz
- Department of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Michael Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Mark J Ratain
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
| | - Hitoshi Zembutsu
- Division of Human Genetics, National Cancer Center, Research Institute, Tokyo, Japan
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City and Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Ron H van Schaik
- International Expertcenter Pharmacogenetics, Dept Clinical Chemistry, Erasmus MC, Rotterdam, The Netherlands.,LKCH UMC Utrecht, The Netherlands
| | - James N Ingle
- Department of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
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24
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Udagawa C, Nakamura H, Ohnishi H, Tamura K, Shimoi T, Yoshida M, Yoshida T, Totoki Y, Shibata T, Zembutsu H. Whole exome sequencing to identify genetic markers for trastuzumab-induced cardiotoxicity. Cancer Sci 2018; 109:446-452. [PMID: 29247589 PMCID: PMC5797809 DOI: 10.1111/cas.13471] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/29/2017] [Accepted: 12/13/2017] [Indexed: 01/03/2023] Open
Abstract
Although trastuzumab‐induced cardiotoxicity is an important determinant to limit the use of this drug, the molecular mechanism of risk for this toxicity is not well understood. To identify genetic variants determining the risk of trastuzumab‐induced cardiotoxicity, we carried out whole exome sequencing of germline DNA samples from 9 patients with trastuzumab‐induced cardiotoxicity, and conducted a case‐control association study of 2258 genetic variants between 9 cases (with trastuzumab‐induced cardiotoxicity) and general Japanese population controls registered in the Human Genetic Variation Database (HGVD). The top variant which showed the lowest P‐value in the screening study was rs139503277 in PHD Finger Protein 3 (Pmin = .00012, odds ratio [OR] = 51.23). To further validate the result of screening study, we carried out a replication study of 10 variants showing Pmin < .001 in the screening study using 234 independent patients treated with trastuzumab, including 10 cases and 224 controls (without trastuzumab‐induced cardiotoxicity). In the replication study, we observed that three variants had an effect in the same direction as in the screening study (rs78272919 in exon 2 of Keratin 15, rs5762940 in exon 2 of zinc and ring finger 3, and rs139944387 in exon 44 of Eyes shut homologs [EYS]). A combined result of the screening and the replication studies suggested an association of a locus on chromosome 6q12 with trastuzumab‐induced cardiotoxicity (rs139944387 in EYS, combined Pmin = .00056, OR = 13.73). This finding provides new insights into personalized trastuzumab therapy for patients with human epidermal growth factor receptor 2 (HER2)‐positive cancer.
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Affiliation(s)
- Chihiro Udagawa
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan.,Pharmacogenomics Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroshi Ohnishi
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan.,Pharmacogenomics Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kenji Tamura
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsunori Shimoi
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Masayuki Yoshida
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Zembutsu
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan.,Pharmacogenomics Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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25
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Low SK, Zembutsu H, Nakamura Y. Breast cancer: The translation of big genomic data to cancer precision medicine. Cancer Sci 2017; 109:497-506. [PMID: 29215763 PMCID: PMC5834810 DOI: 10.1111/cas.13463] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/27/2022] Open
Abstract
Cancer is a complex genetic disease that develops from the accumulation of genomic alterations in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past 2 decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study and next-generation sequencing that contributes to big genomic data. International collaborative efforts have contributed to curating these data to identify clinically significant alterations that could be used in clinical settings. Focusing on breast cancer, the present review summarizes the identification of genomic alterations with high-throughput screening as well as the use of genomic information in clinical trials that match cancer patients to therapies, which further leads to cancer precision medicine. Furthermore, cancer screening and monitoring were enhanced greatly by the use of liquid biopsies. With the growing data complexity and size, there is much anticipation in exploiting deep machine learning and artificial intelligence to curate integrative "-omics" data to refine the current medical practice to be applied in the near future.
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Affiliation(s)
- Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Nakamura
- Department of Medicine, Center for Personalized Therapeutics, The University of Chicago, Chicago, IL, USA.,Department of Surgery, Center for Personalized Therapeutics, The University of Chicago, Chicago, IL, USA
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26
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Udagawa C, Sasaki Y, Suemizu H, Ohnishi Y, Ohnishi H, Tokino T, Zembutsu H. Targeted sequencing reveals genetic variants associated with sensitivity of 79 human cancer xenografts to anticancer drugs. Exp Ther Med 2017; 15:1339-1359. [PMID: 29434720 PMCID: PMC5774388 DOI: 10.3892/etm.2017.5533] [Citation(s) in RCA: 2] [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: 01/26/2017] [Accepted: 04/28/2017] [Indexed: 02/07/2023] Open
Abstract
Although there has been progress moving from a 'one-size-fits-all' cytotoxic approach to personalized molecular medicine, the majority of patients with cancer receive chemotherapy using cytotoxic anticancer drugs. The sequencing analysis of 409 genes associated with cancer was conducted in the present study using 59 DNA sequences extracted from human cancer xenografts implanted into nude mice, of which sensitivity to 9 cytotoxic anticancer drugs [5-fluorouracil, nimustine, adriamycin, cyclophosphamide, cisplatin, mitomycin C (MMC), methotrexate, vincristine (VCR), and vinblastine] was examined. The present study investigated the association between the sensitivities of the xenografts to the 9 anticancer drugs and the frequency of single nucleotide variants (SNV). The correlation between the expression level of the genes and sensitivities to the 9 drugs in the above xenografts was also estimated. In the screening study using 59 xenografts, 3 SNVs (rs1805321, rs62456182 in PMS1 Homolog 2, Mismatch Repair System Component and rs13382825 in LDL Receptor Related Protein 1B), were associated with sensitivity to VCR and MMC, respectively (P<0.001). A replication study of 596 SNVs was subsequently performed, which indicated P<0.05 in the screening study using independent samples of 20 xenografts. A combined result of the screening and replication studies indicated that 35 SNVs were potentially associated with sensitivities to one or more of the nine anticancer drugs (Pcombined=0.0011-0.035). Of the 35 SNVs, rs16903989 and rs201432181 in Leukemia Inhibitory Factor Receptor α and Adhesion G Protein-Coupled Receptor A2 were commonly associated with sensitivity to 2 or 4 anticancer drugs, respectively. These findings provide novel insights which may benefit the development of personalized anticancer therapy for patients with cancer in the future.
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Affiliation(s)
- Chihiro Udagawa
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.,Division of Genetics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yasushi Sasaki
- Department of Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Hokkaido 060-8556, Japan
| | - Hiroshi Suemizu
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
| | - Yasuyuki Ohnishi
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
| | - Hiroshi Ohnishi
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Takashi Tokino
- Department of Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Hokkaido 060-8556, Japan
| | - Hitoshi Zembutsu
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.,Division of Genetics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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27
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Udagawa C, Sasaki Y, Suemizu H, Ohnishi Y, Ohnishi H, Tokino T, Zembutsu H. Abstract 5027: Exome sequencing of cancer-related genes to identify genetic markers for sensitivity to cytotoxic anticancer drugs. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5027] [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
Although the progress in moving from a one-size-fits-all cytotoxic approach to personalized molecular medicine, majority of the patients with cancer receive chemotherapy with cytotoxic anticancer drugs. Exome sequencing of 409 cancer related genes was conducted using 59 DNAs extracted from human tumor xenografts implanted into nude mice, of which sensitivity to nine cytotoxic anticancer drugs (5-fluorouracil (5FU), Nimustine (ACNU), adriamycin (ADR), cyclophosphamide (CPM), cisplatin (DDP), mitomycin C (MMC), methotrexate (MTX), vincristine (VCR), and vinblastine (VLB)) had been examined. We investigated the relationship between the sensitivities of the xenografts to the nine anticancer drugs and single nucleotide variants (SNVs) by classifying them into three groups according to the allele frequency (≤10%, 10-90%, ≥90%). We further carried out replication study using additional set of 20 xenografts. We also estimated the correlation between the expression levels of the 409 genes and sensitivities to the nine drugs in the above xenografts. In the screening stage using 59 xenografts, three SNVs, which were associated with sensitivity to VCR or MMC, showed P < 0.001. We further carried out a replication study of 596 SNVs showing P < 0.05 in the screening stage using independent samples of 20 xenografts. A combined result of the screening and replication studies suggested possible associations of 35 SNVs with sensitivities to the nine anticancer drugs (Pcombined = 0.0011 - 0.035). A total of 35 SNVs showed possible association with sensitivity to at least one of the nine drugs. Of the 35 SNVs, SNV-1 and SNV-2 in a tumor suppressor gene and a oncogene were commonly associated with sensitivity to two or four anticancer drugs, respectively. These findings provide new insights into precision anticancer therapy for the patients with cancer.
Citation Format: Chihiro Udagawa, Yasushi Sasaki, Hiroshi Suemizu, Yasuyuki Ohnishi, Hiroshi Ohnishi, Takashi Tokino, Hitoshi Zembutsu. Exome sequencing of cancer-related genes to identify genetic markers for sensitivity to cytotoxic anticancer drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5027. doi:10.1158/1538-7445.AM2017-5027
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Affiliation(s)
| | - Yasushi Sasaki
- 2Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Hiroshi Suemizu
- 3Central Institute for Experimental Animals, Kawasaki, Japan
| | | | | | - Takashi Tokino
- 2Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
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28
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Shigemizu D, Iwase T, Yoshimoto M, Suzuki Y, Miya F, Boroevich KA, Katagiri T, Zembutsu H, Tsunoda T. The prediction models for postoperative overall survival and disease-free survival in patients with breast cancer. Cancer Med 2017; 6:1627-1638. [PMID: 28544536 PMCID: PMC5504310 DOI: 10.1002/cam4.1092] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/17/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
The goal of this study is to establish a method for predicting overall survival (OS) and disease‐free survival (DFS) in breast cancer patients after surgical operation. The gene expression profiles of cancer tissues from the patients, who underwent complete surgical resection of breast cancer and were subsequently monitored for postoperative survival, were analyzed using cDNA microarrays. We detected seven and three probes/genes associated with the postoperative OS and DFS, respectively, from our discovery cohort data. By incorporating these genes associated with the postoperative survival into MammaPrint genes, often used to predict prognosis of patients with early‐stage breast cancer, we constructed postoperative OS and DFS prediction models from the discovery cohort data using a Cox proportional hazard model. The predictive ability of the models was evaluated in another independent cohort using Kaplan–Meier (KM) curves and the area under the receiver operating characteristic curve (AUC). The KM curves showed a statistically significant difference between the predicted high‐ and low‐risk groups in both OS (log‐rank trend test P = 0.0033) and DFS (log‐rank trend test P = 0.00030). The models also achieved high AUC scores of 0.71 in OS and of 0.60 in DFS. Furthermore, our models had improved KM curves when compared to the models using MammaPrint genes (OS: P = 0.0058, DFS: P = 0.00054). Similar results were observed when our model was tested in publicly available datasets. These observations indicate that there is still room for improvement in the current methods of predicting postoperative OS and DFS in breast cancer.
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Affiliation(s)
- Daichi Shigemizu
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,CREST, Japan Science and Technology Agency, Tokyo, Japan.,Department for Medical Genome Sciences, Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Takuji Iwase
- Department of Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Yasuyo Suzuki
- First Department of Surgery, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keith A Boroevich
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan.,Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Zembutsu
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,CREST, Japan Science and Technology Agency, Tokyo, Japan
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29
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Hirata M, Nagai A, Kamatani Y, Ninomiya T, Tamakoshi A, Yamagata Z, Kubo M, Muto K, Kiyohara Y, Mushiroda T, Murakami Y, Yuji K, Furukawa Y, Zembutsu H, Tanaka T, Ohnishi Y, Nakamura Y, Matsuda K. Overview of BioBank Japan follow-up data in 32 diseases. J Epidemiol 2017; 27:S22-S28. [PMID: 28190660 PMCID: PMC5363789 DOI: 10.1016/j.je.2016.12.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 10/22/2016] [Accepted: 12/15/2016] [Indexed: 01/23/2023] Open
Abstract
Background We established a patient-oriented biobank, BioBank Japan, with information on approximately 200,000 patients, suffering from any of 47 common diseases. This follow-up survey focused on 32 diseases, potentially associated with poor vital prognosis, and collected patient survival information, including cause of death. We performed a survival analysis for all subjects to get an overview of BioBank Japan follow-up data. Methods A total of 141,612 participants were included. The survival data were last updated in 2014. Kaplan–Meier survival analysis was performed after categorizing subjects according to sex, age group, and disease status. Relative survival rates were estimated using a survival-rate table of the Japanese general population. Results Of 141,612 subjects (56.48% male) with 1,087,434 person-years and a 97.0% follow-up rate, 35,482 patients died during follow-up. Mean age at enrollment was 64.24 years for male subjects and 63.98 years for female subjects. The 5-year and 10-year relative survival rates for all subjects were 0.944 and 0.911, respectively, with a median follow-up duration of 8.40 years. Patients with pancreatic cancer had the least favorable prognosis (10-year relative survival: 0.184) and patients with dyslipidemia had the most favorable prognosis (1.013). The most common cause of death was malignant neoplasms. A number of subjects died from diseases other than their registered disease(s). Conclusions This is the first report to perform follow-up survival analysis across various common diseases. Further studies should use detailed clinical and genomic information to identify predictors of mortality in patients with common diseases, contributing to the implementation of personalized medicine. 141,612 participants with any of 32 diseases were included in the follow-up survey. Subject characteristics at enrollment for the follow-up survey were identified. The relative survival analysis showed the worst prognosis in pancreatic cancer. The most common cause of death in all subjects was malignant neoplasms.
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Affiliation(s)
- Makoto Hirata
- Laboratory of Genome Technology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akiko Nagai
- Department of Public Policy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akiko Tamakoshi
- Department of Public Health, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, University of Yamanashi, Yamanashi, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaori Muto
- Department of Public Policy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Kiyohara
- Hisayama Research Institute for Lifestyle Diseases, Fukuoka, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koichiro Yuji
- Project Division of International Advanced Medical Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Zembutsu
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihiro Tanaka
- SNP Research Center, RIKEN Yokohama Institute, Yokohama, Japan; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yozo Ohnishi
- SNP Research Center, RIKEN Yokohama Institute, Yokohama, Japan; Shinko Clinic, Medical Corporation Shinkokai, Tokyo, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, USA
| | | | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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Hirata M, Kamatani Y, Nagai A, Kiyohara Y, Ninomiya T, Tamakoshi A, Yamagata Z, Kubo M, Muto K, Mushiroda T, Murakami Y, Yuji K, Furukawa Y, Zembutsu H, Tanaka T, Ohnishi Y, Nakamura Y, Matsuda K. Cross-sectional analysis of BioBank Japan clinical data: A large cohort of 200,000 patients with 47 common diseases. J Epidemiol 2017; 27:S9-S21. [PMID: 28190657 PMCID: PMC5363792 DOI: 10.1016/j.je.2016.12.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [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: 10/22/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND To implement personalized medicine, we established a large-scale patient cohort, BioBank Japan, in 2003. BioBank Japan contains DNA, serum, and clinical information derived from approximately 200,000 patients with 47 diseases. Serum and clinical information were collected annually until 2012. METHODS We analyzed clinical information of participants at enrollment, including age, sex, body mass index, hypertension, and smoking and drinking status, across 47 diseases, and compared the results with the Japanese database on Patient Survey and National Health and Nutrition Survey. We conducted multivariate logistic regression analysis, adjusting for sex and age, to assess the association between family history and disease development. RESULTS Distribution of age at enrollment reflected the typical age of disease onset. Analysis of the clinical information revealed strong associations between smoking and chronic obstructive pulmonary disease, drinking and esophageal cancer, high body mass index and metabolic disease, and hypertension and cardiovascular disease. Logistic regression analysis showed that individuals with a family history of keloid exhibited a higher odds ratio than those without a family history, highlighting the strong impact of host genetic factor(s) on disease onset. CONCLUSIONS Cross-sectional analysis of the clinical information of participants at enrollment revealed characteristics of the present cohort. Analysis of family history revealed the impact of host genetic factors on each disease. BioBank Japan, by publicly distributing DNA, serum, and clinical information, could be a fundamental infrastructure for the implementation of personalized medicine.
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Affiliation(s)
- Makoto Hirata
- Laboratory of Genome Technology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akiko Nagai
- Department of Public Policy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Kiyohara
- Hisayama Research Institute for Lifestyle Diseases, Fukuoka, Japan
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akiko Tamakoshi
- Department of Public Health, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, University of Yamanashi, Yamanashi, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaori Muto
- Department of Public Policy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koichiro Yuji
- Project Division of International Advanced Medical Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Zembutsu
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihiro Tanaka
- SNP Research Center, RIKEN Yokohama Institute, Yokohama, Japan; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yozo Ohnishi
- SNP Research Center, RIKEN Yokohama Institute, Yokohama, Japan; Shinko Clinic, Medical Corporation Shinkokai, Tokyo, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, USA
| | | | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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Zembutsu H, Nakamura S, Akashi-Tanaka S, Kuwayama T, Watanabe C, Takamaru T, Takei H, Ishikawa T, Miyahara K, Matsumoto H, Hasegawa Y, Kutomi G, Shima H, Satomi F, Okazaki M, Zaha H, Onomura M, Matsukata A, Sagara Y, Baba S, Yamada A, Shimada K, Shimizu D, Tsugawa K, Shimo A, Tan EY, Hartman M, Chan CW, Lee SC, Nakamura Y. Significant Effect of Polymorphisms in CYP2D6 on Response to Tamoxifen Therapy for Breast Cancer: A Prospective Multicenter Study. Clin Cancer Res 2016; 23:2019-2026. [DOI: 10.1158/1078-0432.ccr-16-1779] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/09/2016] [Accepted: 09/28/2016] [Indexed: 11/16/2022]
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Zembutsu H, Nakamura S, Akashi-Tanaka S, Kuwayama T, Watanabe C, Takamaru T, Takei H, Miyahara K, Matsumoto H, Hasegawa Y, Kutomi G, Shima H, Satomi F, Maeda H, Okazaki M, Zaha H, Onomura M, Matsukata A, Sagara Y, Baba S, Yamada A, Shimada K, Shimizu D, Tsugawa K, Shimo A, Yu TE, Hartman M, Wang CC, Lee SC, Nakamura Y. Abstract 2031: Association between CYP2D6 genotype and response to tamoxifen in a prospective multicenter study in Japan. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2031] [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
Purpose:
CYP2D6 is key enzyme responsible for the generation of the potent active metabolite of tamoxifen, “endoxifen”. We previously reported that reduced- or null-function alleles of CYP2D6 were significantly associated with poor clinical outcome of breast cancer patients treated with tamoxifen. However, there are still discrepant reports questioning the association between CYP2D6 genotype and tamoxifen efficacy. Hence, we carried out prospective multicenter studies to evaluate the value of CYP2D6 genotyping in tamoxifen therapy.
Patients and Methods:
We studied 279 patients with hormone receptor-positive and Her-2 negative, invasive breast cancer receiving preoperative tamoxifen monotherapy for 14 - 28 days. Ki-67 response in breast cancer tissues after tamoxifen therapy was used as a surrogate marker of response to tamoxifen. We investigated the effects of allelic variants of CYP2D6 on Ki-67 change in breast cancer tissues, histological response, breast conservative operation and hot flash.
Results:
Ki-67 labeling index in breast cancer tissues significantly decreased after preoperative tamoxifen monotherapy for 14-28 days (P = 0.00000000024). Moreover, proportion of estrogen receptor positive cells in breast cancer tissues were significantly associated with Ki-67 change after tamoxifen therapy (P = 0.0099). CYP2D6 variants were not significantly associated with histological response, breast conservative operation and hot flash (P = 0.25, P = 0.28 and P = 0.34, respectively). However, CYP2D6 variants were significantly associated with Ki-67 decrease after the preoperative tamoxifen therapy (P = 0.000014; in patients with two variant alleles v patients carrying one or two wild-type alleles).
Conclusion:
Our result suggest that genetic variation in CYP2D6 is a key predictor for the prognosis of patients with breast cancer treated with tamoxifen.
Citation Format: Hitoshi Zembutsu, Seigo Nakamura, Sadako Akashi-Tanaka, Takashi Kuwayama, Chie Watanabe, Tomoko Takamaru, Hiroyuki Takei, Kana Miyahara, Hiroshi Matsumoto, Yoshie Hasegawa, Goro Kutomi, Hiroaki Shima, Fukino Satomi, Hideki Maeda, Minoru Okazaki, Hisamitsu Zaha, Mai Onomura, Ayami Matsukata, Yasuaki Sagara, Shinichi Baba, Akimitsu Yamada, Kazuhiro Shimada, Daisuke Shimizu, Koichiro Tsugawa, Arata Shimo, Tan Ern Yu, Mikael Hartman, Chan Ching Wang, Soo Chin Lee, Yusuke Nakamura. Association between CYP2D6 genotype and response to tamoxifen in a prospective multicenter study in Japan. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2031.
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Affiliation(s)
| | - Seigo Nakamura
- 2Department of Breast Surgery, Showa University, Tokyo, Japan
| | | | | | - Chie Watanabe
- 2Department of Breast Surgery, Showa University, Tokyo, Japan
| | - Tomoko Takamaru
- 2Department of Breast Surgery, Showa University, Tokyo, Japan
| | | | | | - Hiroshi Matsumoto
- 4Department of Breast Surgery, Saitama Cancer Center, Saitama, Japan
| | - Yoshie Hasegawa
- 5Department of Breast Surgery, Hirosaki Municipal Hospital, Hirosaki, Japan
| | - Goro Kutomi
- 61st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Hiroaki Shima
- 61st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Fukino Satomi
- 61st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Hideki Maeda
- 61st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Minoru Okazaki
- 7Department of Surgery, Sapporo Breast Surgical Clinic, Sapporo, Japan
| | | | | | | | | | | | - Akimitsu Yamada
- 10Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Japan
| | - Kazuhiro Shimada
- 10Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Japan
| | - Daisuke Shimizu
- 10Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Yokohama, Japan
| | - Koichiro Tsugawa
- 11Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine Hospital, Kawasaki, Japan
| | - Arata Shimo
- 11Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine Hospital, Kawasaki, Japan
| | - Tan Ern Yu
- 12Tan Tock Seng Hospital, Singapore, Singapore
| | - Mikael Hartman
- 13National University of Singapore, Singapore, Singapore
| | | | - Soo Chin Lee
- 13National University of Singapore, Singapore, Singapore
| | - Yusuke Nakamura
- 14Department of Medicine and Surgery, The University of Chicago, Chicago, IL
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Kato Y, Zembutsu H, Takata R, Matsuura T, Kato R, Kanehira M, Iwasaki K, Sugimura J, Omori S, Abe T, Nakamura Y, Obara W. MP49-13 SELECTIVE NEOADJUVANT CHEMOTHERAPY BY PREDICTION SYSTEMS IMPROVES THE CHEMO-SENSITIVITY OF THE MUSCLE INVASIVE BLADDER CANCERS. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.426] [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: 10/22/2022]
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Zembutsu H, Nakamura S, Akashi S, Kuwayama T, Watanabe C, Takei H, Ishikawa T, Hasegawa Y, Lee SC, Yu TE, Matsukata A, Matsumoto H, Kutomi G, Nakamura Y. Abstract 5482: CYP2D6 genotype and response to neoadjuvant tamoxifen therapy: a prospective study in Japan. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-5482] [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
Although lots of CYP2D6-Tamoxifen studies have been reported, the results of the association are still controversial. Because prospective studies are necessary to fully establish the value of CYP2D6 genotyping in tamoxifen therapy, we have initiated the prospective study to clarify the relationship between CYP2D6 genotype and response to preoperative Tamoxifen therapy using a surrogate marker of Ki-67 labeling index in cancer tissue (C-GENT study) since July, 2012. Of the 342 patients who have been recruited in this study, we analyzed 173 cases whose genotyping and measurement of Ki-67 Labeling Index were completed. We observed significant Ki-67 decrease after 2-4 weeks preoperative Tamoxifen therapy (P = 0.000052). Moreover, the patients with CYP2D6 *V/*V is unlikely to show Ki-67 decrease compared with those with CYP2D6 Wt/Wt or Wt/*V (P = 0.00046). Although further analysis should be continuing using a larger number of samples registered in this study, our results suggested that polymorphisms in CYP2D6 could be a key predictor for the prognosis of patients with breast cancer treated with tamoxifen.
Citation Format: Hitoshi Zembutsu, Seigo Nakamura, Sadako Akashi, Takashi Kuwayama, Chie Watanabe, Hiroyuki Takei, Takashi Ishikawa, Yoshie Hasegawa, Soo Chin Lee, Tan Ern Yu, Ayami Matsukata, Hiroshi Matsumoto, Goro Kutomi, Yusuke Nakamura. CYP2D6 genotype and response to neoadjuvant tamoxifen therapy: a prospective study in Japan. [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 5482. doi:10.1158/1538-7445.AM2015-5482
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Affiliation(s)
| | - Seigo Nakamura
- 2Department of Breast Surgery, Showa University, TOKYO, Japan
| | - Sadako Akashi
- 2Department of Breast Surgery, Showa University, TOKYO, Japan
| | | | - Chie Watanabe
- 2Department of Breast Surgery, Showa University, TOKYO, Japan
| | | | | | - Yoshie Hasegawa
- 5Department of Breast Surgery, Hirosaki Municipal Hospital, TOKYO, Japan
| | - Soo Chin Lee
- 6National University of Singapore, Singapore, Singapore
| | - Tan Ern Yu
- 7Breast Clinic, Tan Tock Seng Hospital, Singapore, Singapore
| | - Ayami Matsukata
- 8Department of Breast Surgery, Sagara Hospital, Kagoshima, Japan
| | - Hiroshi Matsumoto
- 9Department of Breast Surgery, Saitama Cancer Center, Saitama, Japan
| | - Goro Kutomi
- 101st Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Yusuke Nakamura
- 11Department of Medicine and Surgery, The University of Chicago, Chicago, IL
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Abstract
Tamoxifen has been used not only for the treatment or prevention of recurrence in patients with estrogen receptor positive breast cancers but also for recurrent breast cancer. Because CYP2D6 is known to be an important enzyme responsible for the generation of the potent tamoxifen metabolite, ‘endoxifen’, lots of studies reported that genetic variation which reduced its enzyme activity were associated with poor clinical outcome of breast cancer patients treated with tamoxifen. However, there are some discrepant reports questioning the association between CYP2D6 genotype and clinical outcome after tamoxifen therapy. Dose-adjustment study of tamoxifen based on CYP2D6 genotypes provides the evidence that dose adjustment is useful for the patients carrying reduced or null allele of CYP2D6 to maintain the effective endoxifen level. This review describes critical issues in pharmacogenomic studies as well as summarizes the results of the association of CYP2D6 genotype with tamoxifen efficacy.
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Kutomi G, Ohmura T, Satomi F, Takamaru T, Shima H, Suzuki Y, Otokozawa S, Zembutsu H, Mori M, Hirata K. Lymph node shape in computed tomography imaging as a predictor for axillary lymph node metastasis in patients with breast cancer. Exp Ther Med 2014; 8:681-685. [PMID: 25009640 PMCID: PMC4079443 DOI: 10.3892/etm.2014.1787] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/28/2014] [Indexed: 11/16/2022] Open
Abstract
The aim of the present study was to evaluate whether preoperative computed tomography (CT) is a useful modality for the diagnosis of axillary lymph node metastasis. The axillary lymph node status was examined in patients with primary breast cancer who had undergone surgery. In total, 75 patients were analyzed with preoperative contrast CT images, following which the patients underwent an intraoperative sentinel lymph node biopsy to determine possible predictors of axillary lymph node metastasis. The lymph node shape was classified into three groups, which included fat-, clear-and obscure-types. Multivariate analysis revealed that clear-type lymph nodes in preoperative contrast CT imaging may be an independent predictor of lymph node metastasis (odds ratio, 15; P=0.003). Therefore, the results indicated that preoperative CT examination is useful to predict axillary lymph node metastasis.
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Affiliation(s)
- Goro Kutomi
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Tousei Ohmura
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Fukino Satomi
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Tomoko Takamaru
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Hiroaki Shima
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Yasuyo Suzuki
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Seiko Otokozawa
- Department of Public Health, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Hitoshi Zembutsu
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
| | - Mitsuru Mori
- Department of Public Health, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Koichi Hirata
- First Department of Surgery, School of Medicine, Sapporo Medical University, Sapporo, Hokkaido 060-8543, Japan
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Aguilar H, Urruticoechea A, Halonen P, Kiyotani K, Mushiroda T, Barril X, Serra-Musach J, Islam A, Caizzi L, Di Croce L, Nevedomskaya E, Zwart W, Bostner J, Karlsson E, Pérez Tenorio G, Fornander T, Sgroi DC, Garcia-Mata R, Jansen MPHM, García N, Bonifaci N, Climent F, Soler MT, Rodríguez-Vida A, Gil M, Brunet J, Martrat G, Gómez-Baldó L, Extremera AI, Figueras A, Balart J, Clarke R, Burnstein KL, Carlson KE, Katzenellenbogen JA, Vizoso M, Esteller M, Villanueva A, Rodríguez-Peña AB, Bustelo XR, Nakamura Y, Zembutsu H, Stål O, Beijersbergen RL, Pujana MA. VAV3 mediates resistance to breast cancer endocrine therapy. Breast Cancer Res 2014; 16:R53. [PMID: 24886537 PMCID: PMC4076632 DOI: 10.1186/bcr3664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 05/16/2014] [Indexed: 02/07/2023] Open
Abstract
Introduction Endocrine therapies targeting cell proliferation and survival mediated by estrogen receptor α (ERα) are among the most effective systemic treatments for ERα-positive breast cancer. However, most tumors initially responsive to these therapies acquire resistance through mechanisms that involve ERα transcriptional regulatory plasticity. Herein we identify VAV3 as a critical component in this process. Methods A cell-based chemical compound screen was carried out to identify therapeutic strategies against resistance to endocrine therapy. Binding to ERα was evaluated by molecular docking analyses, an agonist fluoligand assay and short hairpin (sh)RNA–mediated protein depletion. Microarray analyses were performed to identify altered gene expression. Western blot analysis of signaling and proliferation markers, and shRNA-mediated protein depletion in viability and clonogenic assays, were performed to delineate the role of VAV3. Genetic variation in VAV3 was assessed for association with the response to tamoxifen. Immunohistochemical analyses of VAV3 were carried out to determine its association with therapeutic response and different tumor markers. An analysis of gene expression association with drug sensitivity was carried out to identify a potential therapeutic approach based on differential VAV3 expression. Results The compound YC-1 was found to comparatively reduce the viability of cell models of acquired resistance. This effect was probably not due to activation of its canonical target (soluble guanylyl cyclase), but instead was likely a result of binding to ERα. VAV3 was selectively reduced upon exposure to YC-1 or ERα depletion, and, accordingly, VAV3 depletion comparatively reduced the viability of cell models of acquired resistance. In the clinical scenario, germline variation in VAV3 was associated with the response to tamoxifen in Japanese breast cancer patients (rs10494071 combined P value = 8.4 × 10−4). The allele association combined with gene expression analyses indicated that low VAV3 expression predicts better clinical outcome. Conversely, high nuclear VAV3 expression in tumor cells was associated with poorer endocrine therapy response. Based on VAV3 expression levels and the response to erlotinib in cancer cell lines, targeting EGFR signaling may be a promising therapeutic strategy. Conclusions This study proposes VAV3 as a biomarker and a rationale for its use as a signaling target to prevent and/or overcome resistance to endocrine therapy in breast cancer.
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Hertz DL, Jiang C, Owzar K, Halabi S, Kelly WK, Mulkey F, Patel JN, Carducci MA, Kelley MJ, Stadler WM, Mohamed MK, Morris MJ, Nakamura Y, Zembutsu H, Ratain MJ, McLeod HL. A genome-wide association study (GWAS) of docetaxel-induced neutropenia in CALGB 90401/60404 (Alliance). J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.9612] [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: 11/20/2022] Open
Affiliation(s)
| | - Chen Jiang
- Duke University Medical Center, Durham, NC
| | | | | | | | | | | | | | | | | | | | - Michael J. Morris
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
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Zembutsu H, Sasa M, Kiyotani K, Mushiroda T, Nakamura Y. Should CYP2D6 inhibitors be administered in conjunction with tamoxifen? Expert Rev Anticancer Ther 2014; 11:185-93. [DOI: 10.1586/era.10.228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Low SK, Chung S, Takahashi A, Zembutsu H, Mushiroda T, Kubo M, Nakamura Y. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. Cancer Sci 2013; 104:1074-82. [PMID: 23648065 DOI: 10.1111/cas.12186] [Citation(s) in RCA: 41] [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] [Received: 03/21/2013] [Revised: 04/22/2013] [Accepted: 04/22/2013] [Indexed: 12/20/2022] Open
Abstract
Chemotherapeutic agents are notoriously known to have a narrow therapeutic range that often results in life-threatening toxicity. Hence, it is clinically important to identify the patients who are at high risk for severe toxicity to certain chemotherapy through a pharmacogenomics approach. In this study, we carried out multiple genome-wide association studies (GWAS) of 13 122 cancer patients who received different chemotherapy regimens, including cyclophosphamide- and platinum-based (cisplatin and carboplatin), anthracycline-based (doxorubicin and epirubicin), and antimetabolite-based (5-fluorouracil and gemcitabine) treatment, antimicrotubule agents (paclitaxel and docetaxel), and topoisomerase inhibitors (camptothecin and etoposide), as well as combination therapy with paclitaxel and carboplatin, to identify genetic variants that are associated with the risk of severe neutropenia/leucopenia in the Japanese population. In addition, we used a weighted genetic risk scoring system to evaluate the cumulative effects of the suggestive genetic variants identified from GWAS in order to predict the risk levels of individuals who carry multiple risk alleles. Although we failed to identify genetic variants that surpassed the genome-wide significance level (P < 5.0 × 10(-8) ) through GWAS, probably due to insufficient statistical power and complex clinical features, we were able to shortlist some of the suggestive associated loci. The current study is at the relatively preliminary stage, but does highlight the complexity and problematic issues associated with retrospective pharmacogenomics studies. However, we hope that verification of these genetic variants through local and international collaborations could improve the clinical outcome for cancer patients.
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Affiliation(s)
- Siew-Kee Low
- Laboratory for Statistical Analysis, Center for Genomic Medicine, RIKEN, Yokohama, Japan
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Hertz DL, Owzar K, Halabi S, Kelly WK, Zembutsu H, Jiang C, Patel JN, Watson D, Shterev I, Kroetz DL, Friedman PN, Mahoney JF, Carducci MA, Kelley MJ, Small EJ, Febbo PG, Nakamura Y, Kubo M, Ratain MJ, McLeod HL. A genome-wide association study (GWAS) of docetaxel-induced peripheral neuropathy in CALGB 90401 (Alliance). J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.11053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11053 Background: There are currently no effective methods for predicting, preventing, or treating chemotherapy-induced peripheral neuropathy. We performed a genome-wide association study in a clinical trial of castration-resistant prostate cancer (CRPC) to discover variants that may be useful for identifying patients at high risk of neuropathy during docetaxel treatment. Methods: Treatment and toxicity data were collected prospectively on the Cancer and Leukemia Group B (CALGB) 90401 trial of chemotherapy naïve CRPC patients treated with docetaxel and prednisone ± bevacizumab. Genotyping was performed by the RIKEN Institute using the Illumina HumanHap610-Quad platform. Genetically defined European subjects were included in the discovery analysis of all single nucleotide polymorphisms (SNPs) that passed quality control. The primary endpoint was the cumulative dose level triggering a grade 3+ sensory neuropathy. The inference was conducted within the framework of a competing risk model accounting for early treatment termination induced by death or progression, or other toxicities. SNPs that were highly associated with neuropathy were assessed for a broader taxane effect in a cohort of paclitaxel-treated patients from a breast cancer clinical trial, CALGB 40101. Results: 623 Caucasian patients and 498,022 SNPs were included in the discovery analysis. The incidence of grade 3 neuropathy was 8%. One intergenic SNP (rs11017056) was associated with increased risk of neuropathy (HR=2.83, p=4.7x10-7). This association surpassed the genome-wide significance threshold after covariate adjustment (p=7.2x10-8). However, none of the 7 SNPs selected for replication were associated with neuropathy in the paclitaxel-treated breast cancer cohort. Conclusions: Using a prospectively enrolled prostate cancer patient cohort we identified multiple SNPs that may identify risk of docetaxel-induced peripheral neuropathy, but not paclitaxel-induced neuropathy. However, since it is unknown whether the genetic factors that affect taxane neuropathy are drug-specific, further replication studies in docetaxel-treated cohorts are of great interest.
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Affiliation(s)
| | | | - Susan Halabi
- Alliance Statistical and Data Center/Duke University Medical Center, Durham, NC
| | | | | | - Chen Jiang
- Duke University Medical Center, Durham, NC
| | - Jai Narendra Patel
- University of North Carolina Institute for Pharmacogenomics and Individualized Therapy, Chapel Hill, NC
| | - Dorothy Watson
- Alliance Statistical and Data Center/Duke University Medical Center, Durham, NC
| | - Ivo Shterev
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC
| | | | | | | | | | | | - Eric Jay Small
- University of California, San Francisco, San Francisco, CA
| | - Phillip G. Febbo
- University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Yusuke Nakamura
- Human Genome Center, Institute of Medical Sciences, University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Genomic Medicine, RIKEN, Yokohama, Japan
| | | | - Howard L. McLeod
- University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC
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Kato Y, Zembutsu H, Takata R, Iwasaki K, Obara W, Nakamura Y, Fujioka T. 1439 A PROSPECTIVE STUDY TO EXAMINE THE AVAILABILITY OF THE PREDICTION SYSTEM OF NEOADJUVANT CHEMOTHERAPY FOR MUSCLE INVASIVE BLADDER CANCER. J Urol 2013. [DOI: 10.1016/j.juro.2013.02.2793] [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: 10/27/2022]
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Chung S, Low SK, Zembutsu H, Takahashi A, Kubo M, Sasa M, Nakamura Y. A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients. Breast Cancer Res 2013; 15:R81. [PMID: 24025145 PMCID: PMC3978764 DOI: 10.1186/bcr3475] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/18/2013] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Chemotherapy-induced alopecia is one of the most common adverse events caused by conventional cytotoxic chemotherapy, yet there has been very little progress in the prevention or treatment of this side effect. Although this is not a life-threatening event, alopecia is very psychologically difficult for many women to manage. In order to improve the quality of life for these women, it is important to elucidate the molecular mechanisms of chemotherapy-induced alopecia and develop ways to effectively prevent and/or treat it. To identify the genetic risk factors associated with chemotherapy-induced alopecia, we conducted a genome-wide association study (GWAS) using DNA samples from breast cancer patients who were treated with chemotherapy. METHODS We performed a case-control association study of 303 individuals who developed grade 2 alopecia, and compared them with 880 breast cancer patients who did not show hair loss after being treated with conventional chemotherapy. In addition, we separately analyzed a subset of patients who received specific combination therapies by GWASs and applied the weighted genetic risk scoring (wGRS) system to investigate the cumulative effects of the associated SNPs. RESULTS We identified an SNP significantly associated with drug-induced grade 2 alopecia (rs3820706 in CACNB4 (calcium channel voltage-dependent subunit beta 4) on 2q23, P = 8.13 × 10(-9), OR = 3.71) and detected several SNPs that showed some suggestive associations by subgroup analyses. We also classified patients into four groups on the basis of wGRS analysis and found that patients who classified in the highest risk group showed 443 times higher risk of antimicrotubule agents-induced alopecia than the lowest risk group. CONCLUSIONS Our study suggests several associated genes and should shed some light on the molecular mechanism of alopecia in chemotherapy-treated breast cancer patients and hopefully will contribute to development of interventions that will improve the quality of life (QOL) of cancer patients.
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Affiliation(s)
- Suyoun Chung
- Department of Medicine, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Siew-Kee Low
- Laboratory for Statistical Analysis, Center for Genomic Medicine, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hitoshi Zembutsu
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Genomic Medicine, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center of Genomic Medicine, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Sasa
- Tokushima Breast Care Clinic, 4-7-7, Nakashimada-cho, Tokushima 770-0052, Japan
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL 60637, USA
- Department of Surgery, The University of Chicago, A27 S Maryland Avenue, Chicago, IL 60637, USA
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 2012. [PMID: 23204130 DOI: 10.1158/1078-0432.ccr-12-2618] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE We sought to show the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results. EXPERIMENTAL DESIGN A GWAS of paclitaxel-induced cytotoxicity was conducted in 247 LCLs from the HapMap Project and compared with a GWAS of sensory peripheral neuropathy in patients with breast cancer (n = 855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis. RESULTS We observed an enrichment of LCL cytotoxicity-associated single-nucleotide polymorphisms (SNP) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTL), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of Neuroscreen-1(NS-1; rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel. CONCLUSIONS The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients.
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Affiliation(s)
- Heather E Wheeler
- Sections of Hematology/Oncology and Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Nyholt DR, Low SK, Anderson CA, Painter JN, Uno S, Morris AP, MacGregor S, Gordon SD, Henders AK, Martin NG, Attia J, Holliday EG, McEvoy M, Scott RJ, Kennedy SH, Treloar SA, Missmer SA, Adachi S, Tanaka K, Nakamura Y, Zondervan KT, Zembutsu H, Montgomery GW. Genome-wide association meta-analysis identifies new endometriosis risk loci. Nat Genet 2012; 44:1355-9. [PMID: 23104006 PMCID: PMC3527416 DOI: 10.1038/ng.2445] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [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: 05/16/2012] [Accepted: 09/24/2012] [Indexed: 12/18/2022]
Abstract
We conducted a genome-wide association (GWA) meta-analysis of 4,604 endometriosis cases and 9,393 controls of Japanese1 and European2 ancestry. We show that rs12700667 on chromosome 7p15.2, previously found in Europeans, replicates in Japanese (P = 3.6 × 10−3), and confirm association of rs7521902 on 1p36.12 near WNT4. In addition, we establish association of rs13394619 in GREB1 on 2p25.1 and identify a novel locus on 12q22 near VEZT (rs10859871). Excluding European cases with minimal or unknown severity, we identified additional novel loci on 2p14 (rs4141819), 6p22.3 (rs7739264) and 9p21.3 (rs1537377). All seven SNP effects were replicated in an independent cohort and produced P < 5 × 10−8 in a combined analysis. Finally, we found a significant overlap in polygenic risk for endometriosis between the European and Japanese GWA cohorts (P = 8.8 × 10−11), indicating that many weakly associated SNPs represent true endometriosis risk loci and risk prediction and future targeted disease therapy may be transferred across these populations.
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Affiliation(s)
- Dale R Nyholt
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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Nikolova DN, Doganov N, Dimitrov R, Angelov K, Low SK, Dimova I, Toncheva D, Nakamura Y, Zembutsu H. Genome-wide gene expression profiles of ovarian carcinoma: Identification of molecular targets for the treatment of ovarian carcinoma. Mol Med Rep 2012; 2:365-84. [PMID: 21475838 DOI: 10.3892/mmr_00000109] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study aimed to clarify the molecular mechanisms involved in ovarian carcinogenesis, and to identify candidate molecular targets for its diagnosis and treatment. The genome-wide gene expression profiles of 22 epithelial ovarian carcinomas were analyzed with a microarray representing 38,500 genes, in combination with laser microbeam microdissection. A total of 273 commonly up-regulated transcripts and 387 down-regulated transcripts were identified in the ovarian carcinoma samples. Of the 273 up-regulated transcripts, only 87 (31.9%) were previously reported as up-regulated in microarray studies using bulk cancer tissues and normal ovarian tissues for analysis. CHMP4C (chromatin-modifying protein 4C) was frequently overexpressed in ovarian carcinoma tissue, but not expressed in the normal human tissues used as a control. Our data should contribute to an improved understanding of tumorigenesis in ovarian cancer, and aid in the development of diagnostic tumor markers and molecular-targeting therapy for patients with the disease.
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Affiliation(s)
- Dragomira Nikolaeva Nikolova
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Baldwin RM, Owzar K, Zembutsu H, Chhibber A, Kubo M, Jiang C, Watson D, Eclov RJ, Mefford J, McLeod HL, Friedman PN, Hudis CA, Winer EP, Jorgenson EM, Witte JS, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL. A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101. Clin Cancer Res 2012; 18:5099-109. [PMID: 22843789 DOI: 10.1158/1078-0432.ccr-12-1590] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE Sensory peripheral neuropathy is a common and sometimes debilitating toxicity associated with paclitaxel therapy. This study aims to identify genetic risk factors for the development of this toxicity. EXPERIMENTAL DESIGN A prospective pharmacogenetic analysis of patients with primary breast cancer, randomized to the paclitaxel arm of CALGB 40101, was used to identify genetic predictors of the onset and severity of sensory peripheral neuropathy. A genome-wide association study in 855 subjects of European ancestry was conducted and findings were replicated in additional European (n = 154) and African American (n = 117) subjects. RESULTS A single nucleotide polymorphism in FGD4 was associated with the onset of sensory peripheral neuropathy in the discovery cohort [rs10771973; HR, 1.57; 95% confidence interval (CI), 1.30-1.91; P = 2.6 × 10(-6)] and in a European (HR, 1.72; 95% CI, 1.06-2.80; P = 0.013) and African American (HR, 1.93; 95% CI, 1.13-3.28; P = 6.7 × 10(-3)) replication cohort. There is also evidence that markers in additional genes, including EPHA5 (rs7349683) and FZD3 (rs10771973), were associated with the onset or severity of paclitaxel-induced sensory peripheral neuropathy. CONCLUSIONS A genome-wide association study has identified novel genetic markers of paclitaxel-induced sensory peripheral neuropathy, including a common polymorphism in FGD4, a congenital peripheral neuropathy gene. These findings suggest that genetic variation may contribute to variation in development of this toxicity. Validation of these findings may allow for the identification of patients at increased risk of peripheral neuropathy and inform the use of an alternative to paclitaxel and/or the clinical management of this toxicity.
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Affiliation(s)
- R Michael Baldwin
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th Street RH584E, San Francisco, CA 94158-2911, USA
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Cha PC, Zembutsu H, Takahashi A, Kubo M, Kamatani N, Nakamura Y. A genome-wide association study identifies SNP in DCC is associated with gallbladder cancer in the Japanese population. J Hum Genet 2012; 57:235-7. [PMID: 22318345 DOI: 10.1038/jhg.2012.9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 12/16/2022]
Abstract
Gallbladder cancer (GC) is a relatively uncommon cancer with higher incidence in certain areas including Japan. Because of the difficulty in diagnosis, prognosis of GC is very poor. To identify genetic determinants of GC, we conducted a genome-wide association study (GWAS) in 41 GC patients and 866 controls. Association between each single-nucleotide polymorphism (SNP) with GC susceptibility was evaluated by multivariate logistic regression analysis conditioned on age and gender of subjects. SNPs that showed suggestive association (P<1 × 10(-4)) with GC were further examined in 30 cases and 898 controls. SNP rs7504990 in the DCC (deleted in colorectal cancer, 18q21.3) that encodes a netrin 1 receptor achieved a combined P-value of 7.46 × 10(-8) (OR=6.95; 95% CI=3.43-14.08). Subsequent imputation analysis identified multiple SNPs with similarly strong associations in an adjacent genomic region, where loss of heterozygosity was reported in GC and other cancers. Reduced expression of DCC was indicated to be associated with the poorly differentiated histological type, increased proliferation and metastasis through loss of adhesiveness. However, due to the limited sample size investigated here, further replication study and functional analysis would be necessary to further confirm the result of the association.
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Affiliation(s)
- Pei-Chieng Cha
- Institute of Medical Science, Laboratory of Molecular Medicine, Human Genome Center, The University of Tokyo, Tokyo, Japan
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Low SK, Takahashi A, Cha PC, Zembutsu H, Kamatani N, Kubo M, Nakamura Y. Genome-wide association study for intracranial aneurysm in the Japanese population identifies three candidate susceptible loci and a functional genetic variant at EDNRA. Hum Mol Genet 2012; 21:2102-10. [PMID: 22286173 DOI: 10.1093/hmg/dds020] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aneurysmal subarachnoid hemorrhage (aSAH) is the most serious subtype of stroke. Genetic factors have been known to play an important role in the development of intracranial aneurysm (IA), some of which further progress to subarachnoid hemorrhage (SAH). In this study, we conducted a genome-wide association study (GWAS) to identify common genetic variants that are associated with the risk of IA, using 1383 aSAH subjects and 5484 control individuals in the Japanese population. We selected 36 single-nucleotide polymorphisms (SNPs) that showed suggestive association (P <1 × 10(-4)) in the GWAS as well as additional 7 SNPs that were previously reported to be associated with IA, and further genotyped an additional set of 1048 IA cases and 7212 controls. We identified an SNP, rs6842241, near EDNRA at chromosome 4q31.22 (combined P-value = 9.58 × 10(-9); odds ratio = 1.25), which was found to be significantly associated with IA. Additionally, we successfully replicated and validated rs10757272 on CDKN2BAS at chromosome 9p21.3 (combined P-value = 1.55 × 10(-7); odds ratio = 1.21) to be significantly associated with IA as previously reported. Furthermore, we performed functional analysis with the associated genetic variants on EDNRA, and identified two alleles of rs6841581 that have different binding affinities to a nuclear protein(s). The transcriptional activity of the susceptible allele of this variant was significantly lower than the other, suggesting that this functional variant might affect the expression of EDNRA and subsequently result in the IA susceptibility. Identification of genetic variants on EDNRA is of clinical significance probably due to its role in vessel hemodynamic stress. Our findings should contribute to a better understanding of physiopathology of IA.
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Affiliation(s)
- Siew-Kee Low
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Kiyotani K, Mushiroda T, Nakamura Y, Zembutsu H. Pharmacogenomics of Tamoxifen: Roles of Drug Metabolizing Enzymes and Transporters. Drug Metab Pharmacokinet 2012; 27:122-31. [DOI: 10.2133/dmpk.dmpk-11-rv-084] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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