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Tamura D, Abe M, Hiraki H, Sasaki N, Yashima‐Abo A, Ikarashi D, Kato R, Kato Y, Maekawa S, Kanehira M, Takata R, Maejima K, Sasagawa S, Fujita M, Suzuki Y, Nakagawa H, Iwaya T, Nishizuka SS, Obara W. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma. Cancer Sci 2024; 115:529-539. [PMID: 38083992 PMCID: PMC10859621 DOI: 10.1111/cas.16025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 02/13/2024] Open
Abstract
Biomarkers that could detect the postoperative recurrence of upper tract urothelial carcinoma (UTUC) have not been established. In this prospective study, we aim to evaluate the utility of individualized circulating tumor DNA (ctDNA) monitoring using digital PCR (dPCR) as a tumor recurrence biomarker for UTUC in the perioperative period. Twenty-three patients who underwent radical nephroureterectomy (RNU) were included. In each patient, whole exome sequencing by next-generation sequencing and TERT promoter sequencing of tumor DNA were carried out. Case-specific gene mutations were selected from sequencing analysis to examine ctDNA by dPCR analysis. We also prospectively collected plasma and urine ctDNA from each patient. The longitudinal variant allele frequencies of ctDNA during the perioperative period were plotted. Case-specific gene mutations were detected in 22 cases (96%) from ctDNA in the preoperative samples. Frequently detected genes were TERT (39%), FGFR3 (26%), TP53 (22%), and HRAS (13%). In all cases, we obtained plasma and urine samples for 241 time points and undertook individualized ctDNA monitoring for 2 years after RNU. Ten patients with intravesical recurrence had case-specific ctDNA detected in urine at the time of recurrence. The mean lead time of urinary ctDNA in intravesical recurrence was 60 days (range, 0-202 days). Two patients with distal metastasis had case-specific ctDNA in plasma at the time of metastasis. In UTUC, tumor-specific gene mutations can be monitored postoperatively as ctDNA in plasma and urine. Individualized ctDNA might be a minimally invasive biomarker for the early detection of postoperative recurrence.
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Affiliation(s)
- Daichi Tamura
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Masakazu Abe
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Hayato Hiraki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Noriyuki Sasaki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Akiko Yashima‐Abo
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Daiki Ikarashi
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Renpei Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Yoichiro Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Shigekatsu Maekawa
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Mitsugu Kanehira
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Ryo Takata
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Kazuhiro Maejima
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Shota Sasagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Masashi Fujita
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical SciencesThe University of TokyoKashiwaJapan
| | - Hidewaki Nakagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Takeshi Iwaya
- Department of Clinical OncologyIwate Medical University School of MedicineYahabaJapan
| | - Satoshi S. Nishizuka
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Wataru Obara
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
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2
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Okawa Y, Sasagawa S, Kato H, Johnson TA, Nagaoka K, Kobayashi Y, Hayashi A, Shibayama T, Maejima K, Tanaka H, Miyano S, Shibahara J, Nishizuka S, Hirano S, Seto Y, Iwaya T, Kakimi K, Yasuda T, Nakagawa H. Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas. Cancer Lett 2024; 581:216499. [PMID: 38013050 DOI: 10.1016/j.canlet.2023.216499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Most of esophageal squamous cell carcinoma (ESCC) develop in smoking males in Japan, but the genomic etiology and immunological characteristics of rare non-smoking female ECSS remain unclear. To elucidate the genomic and immunological features of ESCC in non-smoking females, we analyzed whole-genome or transcriptome sequencing data from 94 ESCCs, including 20 rare non-smoking female cases. In addition, 31,611 immune cells were extracted from four ESCC tissues and subject to single-cell RNA-seq. We compared their immuno-genomic and microbiome profiles between non-smoking female and smoking ESCCs. Non-smoking females showed much better prognosis. Whole-genome sequencing analysis showed no significant differences in driver genes or copy number alterations depending on smoking status. The mutational signatures specifically observed in non-smoking females ESCC could be attributed to aging. Immune profiling from RNA-seq revealed that ESCC in non-smoking females had high tumor microenvironment signatures and a high abundance of eosinophils with a favorable prognosis. Single-cell RNA-sequencing of intratumor immune cells revealed gender differences of eosinophils and their activation in female cases. ESCCs in non-smoking females have age-related mutational signatures and gender-specific tumor immune environment with eosinophils, which is likely to contribute to their favorable prognosis.
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Affiliation(s)
- Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Kato
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koji Nagaoka
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Yukari Kobayashi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Akimasa Hayashi
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Takahiro Shibayama
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroko Tanaka
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Mitaka, Japan
| | - Satoshi Nishizuka
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Yasuyuki Seto
- Department of GI Surgery, Graduate of School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Iwaya
- Department of Clinical Oncology, Iwate Medical University School of Medicine, Yahaba, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; Department of Immunology, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Takushi Yasuda
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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3
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Kanazashi Y, Maejima K, Johnson TA, Sasagawa S, Jikuya R, Hasumi H, Matsumoto N, Maekawa S, Obara W, Nakagawa H. Mitochondrial DNA Variants at Low-Level Heteroplasmy and Decreased Copy Numbers in Chronic Kidney Disease (CKD) Tissues with Kidney Cancer. Int J Mol Sci 2023; 24:17212. [PMID: 38139039 PMCID: PMC10743237 DOI: 10.3390/ijms242417212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The human mitochondrial genome (mtDNA) is a circular DNA molecule with a length of 16.6 kb, which contains a total of 37 genes. Somatic mtDNA mutations accumulate with age and environmental exposure, and some types of mtDNA variants may play a role in carcinogenesis. Recent studies observed mtDNA variants not only in kidney tumors but also in adjacent kidney tissues, and mtDNA dysfunction results in kidney injury, including chronic kidney disease (CKD). To investigate whether a relationship exists between heteroplasmic mtDNA variants and kidney function, we performed ultra-deep sequencing (30,000×) based on long-range PCR of DNA from 77 non-tumor kidney tissues of kidney cancer patients with CKD (stages G1 to G5). In total, this analysis detected 697 single-nucleotide variants (SNVs) and 504 indels as heteroplasmic (0.5% ≤ variant allele frequency (VAF) < 95%), and the total number of detected SNVs/indels did not differ between CKD stages. However, the number of deleterious low-level heteroplasmic variants (pathogenic missense, nonsense, frameshift and tRNA) significantly increased with CKD progression (p < 0.01). In addition, mtDNA copy numbers (mtDNA-CNs) decreased with CKD progression (p < 0.001). This study demonstrates that mtDNA damage, which affects mitochondrial genes, may be involved in reductions in mitochondrial mass and associated with CKD progression and kidney dysfunction.
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Affiliation(s)
- Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Todd A. Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Ryosuke Jikuya
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Shigekatsu Maekawa
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Wataru Obara
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
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4
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Shima Y, Sasagawa S, Ota N, Oyama R, Tanaka M, Kubota-Sakashita M, Kawakami H, Kobayashi M, Takubo N, Ozeki AN, Sun X, Kim YJ, Kamatani Y, Matsuda K, Maejima K, Fujita M, Noda K, Kamiyama H, Tanikawa R, Nagane M, Shibahara J, Tanaka T, Rikitake Y, Mataga N, Takahashi S, Kosaki K, Okano H, Furihata T, Nakaki R, Akimitsu N, Wada Y, Ohtsuka T, Kurihara H, Kamiguchi H, Okabe S, Nakafuku M, Kato T, Nakagawa H, Saito N, Nakatomi H. Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms. Sci Transl Med 2023; 15:eabq7721. [PMID: 37315111 DOI: 10.1126/scitranslmed.abq7721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2023] [Indexed: 06/16/2023]
Abstract
Intracranial aneurysms (IAs) are a high-risk factor for life-threatening subarachnoid hemorrhage. Their etiology, however, remains mostly unknown at present. We conducted screening for sporadic somatic mutations in 65 IA tissues (54 saccular and 11 fusiform aneurysms) and paired blood samples by whole-exome and targeted deep sequencing. We identified sporadic mutations in multiple signaling genes and examined their impact on downstream signaling pathways and gene expression in vitro and an arterial dilatation model in mice in vivo. We identified 16 genes that were mutated in at least one IA case and found that these mutations were highly prevalent (92%: 60 of 65 IAs) among all IA cases examined. In particular, mutations in six genes (PDGFRB, AHNAK, OBSCN, RBM10, CACNA1E, and OR5P3), many of which are linked to NF-κB signaling, were found in both fusiform and saccular IAs at a high prevalence (43% of all IA cases examined). We found that mutant PDGFRBs constitutively activated ERK and NF-κB signaling, enhanced cell motility, and induced inflammation-related gene expression in vitro. Spatial transcriptomics also detected similar changes in vessels from patients with IA. Furthermore, virus-mediated overexpression of a mutant PDGFRB induced a fusiform-like dilatation of the basilar artery in mice, which was blocked by systemic administration of the tyrosine kinase inhibitor sunitinib. Collectively, this study reveals a high prevalence of somatic mutations in NF-κB signaling pathway-related genes in both fusiform and saccular IAs and opens a new avenue of research for developing pharmacological interventions.
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Affiliation(s)
- Yasuyuki Shima
- Biomedical Neural Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
- Neurodegenerative Disorders Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Nakao Ota
- Biomedical Neural Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
- Department of Neurosurgery, Sapporo Teishinkai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Rieko Oyama
- Biomedical Neural Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Minoru Tanaka
- Biomedical Neural Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
- Division of Innovative Cancer Therapy and Department of Surgical Neuro-Oncology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Mie Kubota-Sakashita
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Hirochika Kawakami
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Mika Kobayashi
- Isotope Science Center, University of Tokyo, Tokyo 113-0032, Japan
| | - Naoko Takubo
- Isotope Science Center, University of Tokyo, Tokyo 113-0032, Japan
| | | | - Xiaoning Sun
- Isotope Science Center, University of Tokyo, Tokyo 113-0032, Japan
| | - Yeon-Jeong Kim
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kosumo Noda
- Department of Neurosurgery, Sapporo Teishinkai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Hiroyasu Kamiyama
- Department of Neurosurgery, Sapporo Teishinkai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Rokuya Tanikawa
- Department of Neurosurgery, Sapporo Teishinkai Hospital, Sapporo, Hokkaido 065-0033, Japan
| | - Motoo Nagane
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan
| | - Junji Shibahara
- Department of Pathology, Faculty of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan
| | - Toru Tanaka
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Kobe, Hyogo 658-8558, Japan
| | - Yoshiyuki Rikitake
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Kobe, Hyogo 658-8558, Japan
| | - Nobuko Mataga
- Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-0005, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University Faculty of Medicine, Tokyo 160-0016, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo 160-0016, Japan
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, Wako, Saitama 351-0198, Japan
- International Center for Brain Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Tomomi Furihata
- Laboratory of Clinical Pharmacy and Experimental Therapeutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | | | | | - Youichiro Wada
- Isotope Science Center, University of Tokyo, Tokyo 113-0032, Japan
| | - Toshihisa Ohtsuka
- Department of Biochemistry, Faculty of Medicine and Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Hiroki Kurihara
- Department of Molecular Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Tokyo 113-8654, Japan
| | - Hiroyuki Kamiguchi
- Laboratory for Neural Cell Dynamics, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Tokyo 113-8654, Japan
- Brain Medical Science Collaboration Division, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Masato Nakafuku
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo 113-8654, Japan
| | - Hirofumi Nakatomi
- Biomedical Neural Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
- Department of Neurosurgery, Faculty of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan
- Department of Neurosurgery, Graduate School of Medicine, University of Tokyo, Tokyo 113-8654, Japan
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5
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Jikuya R, Johnson TA, Maejima K, An J, Ju YS, Lee H, Ha K, Song W, Kim Y, Okawa Y, Sasagawa S, Kanazashi Y, Fujita M, Imoto S, Mitome T, Ohtake S, Noguchi G, Kawaura S, Iribe Y, Aomori K, Tatenuma T, Komeya M, Ito H, Ito Y, Muraoka K, Furuya M, Kato I, Fujii S, Hamanoue H, Tamura T, Baba M, Suda T, Kodama T, Makiyama K, Yao M, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nakagawa H, Hasumi H. Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma. EBioMedicine 2023; 92:104596. [PMID: 37182269 DOI: 10.1016/j.ebiom.2023.104596] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/21/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Birt-Hogg-Dubé (BHD) syndrome, caused by germline alteration of folliculin (FLCN) gene, develops hybrid oncocytic/chromophobe tumour (HOCT) and chromophobe renal cell carcinoma (ChRCC), whereas sporadic ChRCC does not harbor FLCN alteration. To date, molecular characteristics of these similar histological types of tumours have been incompletely elucidated. METHODS To elucidate renal tumourigenesis of BHD-associated renal tumours and sporadic renal tumours, we conducted whole genome sequencing (WGS) and RNA-sequencing (RNA-seq) of sixteen BHD-associated renal tumours from nine unrelated BHD patients, twenty-one sporadic ChRCCs and seven sporadic oncocytomas. We then compared somatic mutation profiles with FLCN variants and RNA expression profiles between BHD-associated renal tumours and sporadic renal tumours. FINDINGS RNA-seq analysis revealed that BHD-associated renal tumours and sporadic renal tumours have totally different expression profiles. Sporadic ChRCCs were clustered into two distinct clusters characterized by L1CAM and FOXI1 expressions, molecular markers for renal tubule subclasses. Increased mitochondrial DNA (mtDNA) copy number with fewer variants was observed in BHD-associated renal tumours compared to sporadic ChRCCs. Cell-of-origin analysis using WGS data demonstrated that BHD-associated renal tumours and sporadic ChRCCs may arise from different cells of origin and second hit FLCN alterations may occur in early third decade of life in BHD patients. INTERPRETATION These data further our understanding of renal tumourigenesis of these two different types of renal tumours with similar histology. FUNDING This study was supported by JSPS KAKENHI Grants, RIKEN internal grant, and the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research.
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Affiliation(s)
- Ryosuke Jikuya
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan; Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young-Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hwajin Lee
- Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyungsik Ha
- UPPThera, Inc. BRC Laboratory 1-204 9, Songdomirae-ro, Yeonsu-gu, Incheon, Republic of Korea
| | - WooJeung Song
- UPPThera, Inc. BRC Laboratory 1-204 9, Songdomirae-ro, Yeonsu-gu, Incheon, Republic of Korea
| | - Youngwook Kim
- National Cancer Center Korea, 323 Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do, Republic of Korea
| | - Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Seiya Imoto
- Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Taku Mitome
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Shinji Ohtake
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Go Noguchi
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Sachi Kawaura
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yasuhiro Iribe
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kota Aomori
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomoyuki Tatenuma
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mitsuru Komeya
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hiroki Ito
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yusuke Ito
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kentaro Muraoka
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Mitsuko Furuya
- Pathology Center, GeneticLab Co., Ltd., 28-196, N9, W15, Chuo-ku, Sapporo, 060-0009, Japan
| | - Ikuma Kato
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Satoshi Fujii
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Haruka Hamanoue
- Clinical Genetics Department, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan; Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
| | - Masaya Baba
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Toshio Suda
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, 153-8904, Japan
| | - Kazuhide Makiyama
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Masahiro Yao
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Brian M Shuch
- Institute of Urologic Oncology, UCLA School of Medicine, Los Angeles, CA90095, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD20892, USA
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University Graduate School of Medicine, 3-9 Fuku-ura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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6
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Sun C, Nagaoka K, Kobayashi Y, Maejima K, Nakagawa H, Nakajima J, Kakimi K. Immunotherapies targeting neoantigens are effective in PD-1 blockade-resistant tumors. Int J Cancer 2023; 152:1463-1475. [PMID: 36451303 DOI: 10.1002/ijc.34382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022]
Abstract
Only a small fraction of tumor-infiltrating lymphocytes can specifically recognize and attack cancer cells in PD-1/PD-L1 blockade therapy. Here, we investigate approaches to expand the neoantigen-specific CD8+ T cells to overcome the difficulties in treating PD-1/PD-L1 blockade-resistant tumors. Mutation-associated neoepitopes of murine nonsmall cell lung cancer ASB-XIV were estimated by whole-exome and RNA sequencing and predicted by MHC-I binding affinity (FPKM >1) in silico. Using ASB-XIV-specific CD8+ T cells, we screened a panel of 257 neoepitope peptides derived from ASB-XIV missense and indel mutations. Mutated Phf3 peptide (mPhf3) was successfully identified as an immunogenic neoepitope. Prophylactic mPhf3-DC vaccination inhibited ASB-XIV tumor growth through CD8+ T cell-mediated antitumor immunity. Combining the mPhf3-DC vaccine and anti-PD-1 treatment elicited robust antitumor activity through the induction of mPhf3-specific CD8+ T cells in the tumor microenvironment. Furthermore, the adoptive transfer of mPhf3-specific CD8+ T cells eradicated ASB-XIV tumors. Likewise, the combination of mutated Cdt1 peptide (mCdt1)-DC vaccine and anti-PD-1 treatment or adoptive transfer of mCdt1-specific CD8+ T cells also led to significant regression of PD-1 blockade-resistant murine gastric YTN16 tumors. In conclusion, a novel immunogenic neoepitope of ASB-XIV was identified for immunotherapy targeting neoantigens. Identification of immunogenic neoantigens can extend the therapeutic strategies by increasing the frequency of neoantigen-specific T cells, even for PD-1/PD-L1 blockade-resistant tumors.
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Affiliation(s)
- Changbo Sun
- Department of Immunotherapeutics, University of Tokyo Hospital, Tokyo, Japan.,Department of Thoracic Surgery, University of Tokyo Hospital, Tokyo, Japan.,Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Koji Nagaoka
- Department of Immunotherapeutics, University of Tokyo Hospital, Tokyo, Japan
| | - Yukari Kobayashi
- Department of Immunotherapeutics, University of Tokyo Hospital, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Jun Nakajima
- Department of Thoracic Surgery, University of Tokyo Hospital, Tokyo, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, University of Tokyo Hospital, Tokyo, Japan
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7
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Tamura K, Kanazashi Y, Kawada C, Sekine Y, Maejima K, Ashida S, Karashima T, Kojima S, Parrish NF, Kosugi S, Terao C, Sasagawa S, Fujita M, Johnson TA, Momozawa Y, Inoue K, Shuin T, Nakagawa H. Variant Spectrum of von Hippel-Lindau (VHL) disease and its genomic heterogeneity in Japan. Hum Mol Genet 2023:7076181. [PMID: 36905328 DOI: 10.1093/hmg/ddad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant, inherited syndrome with variants in the VHL gene, causing predisposition to multi-organ neoplasms with vessel abnormality. Germline variants in VHL can be detected in 80-90% of patients clinically diagnosed with VHL disease. Here, we summarize the results of genetic tests for 206 Japanese VHL families, and elucidate the molecular mechanisms of VHL disease, especially in variant-negative unsolved cases. Of the 206 families, genetic diagnosis was positive in 175 families (85%), including 134 families (65%) diagnosed by exon sequencing (15 novel variants) and 41 (20%) diagnosed by MLPA (one novel variant). The deleterious variants were significantly enriched in VHL disease Type 1. Interestingly, five synonymous or non-synonymous variants within exon 2 caused exon 2 skipping, which is the first report of exon 2 skipping caused by several missense variants. Whole genome and target deep sequencing analysis were performed for 22 unsolved cases with no variant identified (NVI) and found three cases with VHL mosaicism (VAF: 2.5-22%), one with mobile element insertion in the VHL promoter region, and two with a pathogenic variant of BAP1 or SDHB. The variants associated with VHL disease are heterogeneous, and for more accuracy of the genetic diagnosis of VHL disease, comprehensive genome and RNA analyses are required to detect VHL mosaicism, complicated structure variants, and other related gene variants.
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Affiliation(s)
- Kenji Tamura
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Yuki Kanazashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chiaki Kawada
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Yuya Sekine
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Urology, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | | | - Shingo Ashida
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Takashi Karashima
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Shohei Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Shunichi Kosugi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shota Sasagawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Todd A Johnson
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Keiji Inoue
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Taro Shuin
- Department of Urology, Kochi Medical School, Kochi University, Nankoku, Japan
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8
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Johnson TA, Maekawa S, Fujita M, An J, Ju YS, Maejima K, Kanazashi Y, Jikuya R, Okawa Y, Sasagawa S, Yagi K, Okazaki Y, Kuroda N, Takata R, Obara W, Nakagawa H. Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis. Hum Mol Genet 2023; 32:290-303. [PMID: 35981075 DOI: 10.1093/hmg/ddac180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 07/28/2022] [Indexed: 01/18/2023] Open
Abstract
Patients with end-stage renal disease (ESRD) or receiving dialysis have a much higher risk for renal cell carcinoma (RCC), but carcinogenic mechanisms and genomic features remain little explored and undefined. This study's goal was to identify the genomic features of ESRD RCC and characterize them for associations with tumor histology and dialysis exposure. In this study, we obtained 33 RCCs, with various histological subtypes, that developed in ESRD patients receiving dialysis and performed whole-genome sequencing and transcriptome analyses. Driver events, copy-number alteration (CNA) analysis and mutational signature profiling were performed using an analysis pipeline that integrated data from germline and somatic SNVs, Indels and structural variants as well as CNAs, while transcriptome data were analyzed for differentially expressed genes and through gene set enrichment analysis. ESRD related clear cell RCCs' driver genes and mutations mirrored those in sporadic ccRCCs. Longer dialysis periods significantly correlated with a rare mutational signature SBS23, whose etiology is unknown, and increased mitochondrial copy number. All acquired cystic disease (ACD)-RCCs, which developed specifically in ESRD patients, showed chromosome 16q amplification. Gene expression analysis suggests similarity between certain ACD-RCCs and papillary RCCs and in TCGA papillary RCCs with chromosome 16 gain identified enrichment for genes related to DNA repair, as well as pathways related to reactive oxygen species, oxidative phosphorylation and targets of Myc. This analysis suggests that ESRD or dialysis could induce types of cellular stress that impact some specific types of genomic damage leading to oncogenesis.
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Affiliation(s)
- Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shigekatsu Maekawa
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Young-Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ryosuke Jikuya
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Urology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ken Yagi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Naoto Kuroda
- Department of Diagnostic Pathology, Kochi Red Cross Hospital, Kochi 780-8562, Japan
| | - Ryo Takata
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Wataru Obara
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Iwate, 028-3694, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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9
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, 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Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, 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Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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11
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Fujita M, Chen MJM, Siwak DR, Sasagawa S, Oosawa-Tatsuguchi A, Arihiro K, Ono A, Miura R, Maejima K, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Lee JS, Lu Y, Mills GB, Liang H, Nishizuka SS, Nakagawa H. Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets. Nat Commun 2022; 13:6481. [PMID: 36309506 PMCID: PMC9617926 DOI: 10.1038/s41467-022-34249-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 10/19/2022] [Indexed: 12/25/2022] Open
Abstract
Primary liver cancer is a heterogeneous disease in terms of its etiology, histology, and therapeutic response. Concurrent proteomic and genomic characterization of a large set of clinical liver cancer samples can help elucidate the molecular basis of heterogeneity and thus serve as a valuable resource for personalized liver cancer treatment. In this study, we perform proteomic profiling of ~300 proteins on 259 primary liver cancer tissues with reverse-phase protein arrays, mutational analysis using whole genome sequencing and transcriptional analysis with RNA-Seq. Patients are of Japanese ethnic background and mainly HBV or HCV positive, providing insight into this important liver cancer subtype. Unsupervised classification of tumors based on protein expression profiles reveal three proteomic subclasses R1, R2, and R3. The R1 subclass is immunologically hot and demonstrated a good prognosis. R2 contains advanced proliferative tumor with TP53 mutations, high expression of VEGF receptor 2 and the worst prognosis. R3 is enriched with CTNNB1 mutations and elevated mTOR signaling pathway activity. Twenty-two proteins, including CDK1 and CDKN2A, are identified as potential prognostic markers. The proteomic classification presented in this study can help guide therapeutic decision making for liver cancer treatment.
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Affiliation(s)
- Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mei-Ju May Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Doris Rieko Siwak
- Department of Systems Biology to Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ayako Oosawa-Tatsuguchi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University Hospital, Hiroshima, Japan
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryoichi Miura
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ju-Seog Lee
- Department of Systems Biology to Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiling Lu
- Department of Systems Biology to Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology to Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Satoshi S Nishizuka
- Division of Biomedical Research and Development, Institute of Biomedical Sciences, Iwate Medical University, Morioka, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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12
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Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, Takata S, Inai C, Aoi T, Mizukoshi M, Maejima K, Hirata M, Murakami Y, Kamatani Y, Kubo M, Akagi K, Matsuda K, Nakagawa H, Momozawa Y. Population-based Screening for Hereditary Colorectal Cancer Variants in Japan. Clin Gastroenterol Hepatol 2022; 20:2132-2141.e9. [PMID: 33309985 DOI: 10.1016/j.cgh.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) is one of the most common cancers in the world. A small proportion of CRCs can be attributed to recognizable hereditary germline variants of known CRC susceptibility genes. To better understand cancer risk, it is necessary to explore the prevalence of hereditary CRC and pathogenic variants of multiple cancer-predisposing genes in non-European populations. METHODS We analyzed the coding regions of 27 cancer-predisposing genes in 12,503 unselected Japanese CRC patients and 23,705 controls by target sequencing and genome-wide SNP chip. Their clinical significance was assessed using ClinVar and the guidelines by ACMG/AMP. RESULTS We identified 4,804 variants in the 27 genes and annotated them as pathogenic in 397 and benign variants in 941, of which 43.6% were novel. In total, 3.3% of the unselected CRC patients and 1.5% of the controls had a pathogenic variant. The pathogenic variants of MSH2 (odds ratio (OR) = 18.1), MLH1 (OR = 8.6), MSH6 (OR = 4.9), APC (OR = 49.4), BRIP1 (OR=3.6), BRCA1 (OR = 2.6), BRCA2 (OR = 1.9), and TP53 (OR = 1.7) were significantly associated with CRC development in the Japanese population (P-values<0.01, FDR<0.05). These pathogenic variants were significantly associated with diagnosis age and personal/family history of cancer. In total, at least 3.5% of the Japanese CRC population had a pathogenic variant or CNV of the 27 cancer-predisposing genes, indicating hereditary cancers. CONCLUSIONS This largest study of CRC heredity in Asia can contribute to the development of guidelines for genetic testing and variant interpretation for heritable CRCs.
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Affiliation(s)
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | | | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program, RIKEN, Yokohama; Artificial intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba
| | | | - Chihiro Inai
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Tomomi Aoi
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | - Makoto Hirata
- Institute of Medical Science, University of Tokyo, Tokyo
| | | | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama
| | - Koichi Matsuda
- Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan
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13
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Sasagawa S, Kato H, Nagaoka K, Sun C, Imano M, Sato T, Johnson TA, Fujita M, Maejima K, Okawa Y, Kakimi K, Yasuda T, Nakagawa H. Immuno-genomic profiling of biopsy specimens predicts neoadjuvant chemotherapy response in esophageal squamous cell carcinoma. Cell Rep Med 2022; 3:100705. [PMID: 35944530 PMCID: PMC9418738 DOI: 10.1016/j.xcrm.2022.100705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/23/2021] [Revised: 04/15/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers and is primarily treated with platinum-based neoadjuvant chemotherapy (NAC). Some ESCCs respond well to NAC. However, biomarkers to predict NAC sensitivity and their response mechanism in ESCC remain unclear. We perform whole-genome sequencing and RNA sequencing analysis of 141 ESCC biopsy specimens before NAC treatment to generate a machine-learning-based diagnostic model to predict NAC reactivity in ESCC and analyzed the association between immunogenomic features and NAC response. Neutrophil infiltration may play an important role in ESCC response to NAC. We also demonstrate that specific copy-number alterations and copy-number signatures in the ESCC genome are significantly associated with NAC response. The interactions between the tumor genome and immune features of ESCC are likely to be a good indicator of therapeutic capability and a therapeutic target for ESCC, and machine learning prediction for NAC response is useful. Four different immune subtypes from RNA-seq of ESCC biopsy specimen Neutrophils within tumors are associated with tumor sensitivity to NAC Specific copy-number changes and signatures in ESCC are associated with NAC response Machine learning prediction for NAC response using immunogenomics of ESCC is useful
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Affiliation(s)
- Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hiroaki Kato
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka 577-8502, Japan
| | - Koji Nagaoka
- Department of Immuno-therapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan
| | - Changbo Sun
- Department of Immuno-therapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan
| | - Motohiro Imano
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka 577-8502, Japan
| | - Takao Sato
- Department of Pathology, Kindai University Faculty of Medicine, Osaka 577-8502, Japan
| | - Todd A Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kazuhiro Kakimi
- Department of Immuno-therapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan
| | - Takushi Yasuda
- Department of Surgery, Graduate School of Medicine, Kindai University, Osaka 577-8502, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
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14
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Jikuya R, Murakami K, Nishiyama A, Kato I, Furuya M, Nakabayashi J, Ramilowski JA, Hamanoue H, Maejima K, Fujita M, Mitome T, Ohtake S, Noguchi G, Kawaura S, Odaka H, Kawahara T, Komeya M, Shinoki R, Ueno D, Ito H, Ito Y, Muraoka K, Hayashi N, Kondo K, Nakaigawa N, Hatano K, Baba M, Suda T, Kodama T, Fujii S, Makiyama K, Yao M, Shuch BM, Schmidt LS, Linehan WM, Nakagawa H, Tamura T, Hasumi H. Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers. iScience 2022; 25:104463. [PMID: 35874919 PMCID: PMC9301876 DOI: 10.1016/j.isci.2022.104463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/05/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
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15
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Oshima K, Kato K, Ito Y, Daiko H, Nozaki I, Nakagawa S, Shibuya Y, Kojima T, Toh Y, Okada M, Hironaka S, Akiyama Y, Komatsu Y, Maejima K, Nakagawa H, Onuki R, Nagai M, Kato M, Kanato K, Kuchiba A, Nakamura K, Kitagawa Y. A prognostic biomarker study in patients with clinical stage I esophageal squamous cell carcinoma: JCOG0502-A1. Cancer Sci 2021; 113:1018-1027. [PMID: 34962019 PMCID: PMC8898710 DOI: 10.1111/cas.15251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/03/2022] Open
Abstract
We conducted genomic analyses of Japanese patients with stage I esophageal squamous cell carcinoma (ESCC) to investigate the frequency of genomic alterations and the association with survival outcomes. Biomarker analysis was conducted for patients with clinical stage T1bN0M0 ESCC enrolled in JCOG0502 (UMIN000000551). Whole-exome sequencing (WES) was performed using DNA extracted from formalin-fixed, paraffin-embedded tissue of ESCC and normal tissue or blood sample. Single nucleotide variants (SNVs), insertions/deletions (indels), and copy number alterations (CNAs) were identified. We then evaluated the associations between each gene alteration with a frequency ≥10% and progression-free survival (PFS) using a Cox regression model. We controlled for family-wise errors at 0.05 using the Bonferroni method. Among the 379 patients who were enrolled in JCOG0502, 127 patients were successfully analyzed using WES. The median patient age was 63 years (IQR, 57-67 years), and 78.0% of the patients ultimately underwent surgery. The 3-year PFS probability was 76.3%. We detected 20 genes with SNVs, indels, or amplifications with a frequency of ≥10%. Genomic alterations in FGF19 showed the strongest association with PFS with a borderline level of statistical significance of p = 0.00252 (Bonferroni-adjusted significance level is 0.0025). Genomic alterations in FGF4, MYEOV, CTTN, and ORAOV1 showed a marginal association with PFS (p < 0.05). These genomic alterations were all CNAs at chromosome 11q13.3. We have identified new genomic alterations associated with the poor efficacy of ESCC (T1bN0M0). These findings open avenues for the development of new potential treatments for patients with ESCC.
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Affiliation(s)
- Kotoe Oshima
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo
| | - Ken Kato
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, Tokyo
| | - Yoshinori Ito
- Department of Radiation Oncology, Showa University School of Medicine, Tokyo
| | - Hiroyuki Daiko
- Esophageal Surgery Division, National Cancer Center Hospital, Tokyo
| | - Isao Nozaki
- Department of Gastroenterological Surgery, National Hospital Organization Shikoku Cancer Center, Matsuyama
| | - Satoru Nakagawa
- Department of Gastroenterological Surgery, Niigata Cancer Center Hospital, Niigata
| | - Yuichi Shibuya
- Department of Gastroenterology Surgery, Kochi Health Sciences Center, Kochi
| | - Takashi Kojima
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa
| | - Yasushi Toh
- Department of Gastroenterological Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka
| | | | - Shuichi Hironaka
- Clinical Trial Promotion Department, Chiba Cancer Center, Chiba.,Department of Medical Oncology and Hematology, Oita University Faculty of Medicine, Yufu
| | - Yuji Akiyama
- Department of Surgery, Iwate Medical University, Iwate
| | - Yoshito Komatsu
- Cancer Chemotherapy, Hokkaido University Hospital Cancer Center, Sapporo
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for integrative Medical Sciences, Yokohama
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for integrative Medical Sciences, Yokohama
| | - Ritsuko Onuki
- Division of Bioinformatics, Research Institute, National Cancer Center, Tokyo
| | - Momoko Nagai
- Division of Bioinformatics, Research Institute, National Cancer Center, Tokyo
| | - Mamoru Kato
- Division of Bioinformatics, Research Institute, National Cancer Center, Tokyo
| | - Keisuke Kanato
- Research Management Division, Clinical Research Support Office, National Cancer Center Hospital, Tokyo
| | - Aya Kuchiba
- Biostatistics Division, Center for Research Administration and Support, National Cancer Center, Tokyo.,Graduate School of Health Innovation, Kanagawa University of Human Services, Kanagawa
| | - Kenichi Nakamura
- Research Management Division, Clinical Research Support Office, National Cancer Center Hospital, Tokyo
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo
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16
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Nagaoka K, Sun C, Kobayashi Y, Kanaseki T, Tokita S, Komatsu T, Maejima K, Futami J, Nomura S, Udaka K, Nakagawa H, Torigoe T, Kakimi K. Identification of Neoantigens in Two Murine Gastric Cancer Cell Lines Leading to the Neoantigen-Based Immunotherapy. Cancers (Basel) 2021; 14:cancers14010106. [PMID: 35008270 PMCID: PMC8750027 DOI: 10.3390/cancers14010106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Despite the success of immune checkpoint inhibitors (ICI) for treating a variety of solid cancers, most gastric cancer patients are resistant to ICI monotherapies. Combinations of ICI with other therapies may be able to overcome this resistance. In order to develop combination immunotherapies, immunologically well-characterized preclinical gastric cancer models are required. To this end, in the present study, we characterized two murine gastric cancer cell lines, namely, YTN2 which spontaneously regresses, and YTN16 which grows progressively. Although anti-CTLA-4 monotherapy eradicated most YTN16 tumors, these were resistant to either anti-PD-1 or anti-PD-L1 treatment. Furthermore, we identified neoantigens in YTN2 and YTN16 tumors and conducted neoantigen-based immunotherapy for these tumors. In addition, the information on neoantigens facilitates the evaluation of tumor-specific immune responses induced by the combination therapies. These immunologically well-characterized gastric cancer models will contribute to the development of novel combination immunotherapies. Abstract To develop combination immunotherapies for gastric cancers, immunologically well-characterized preclinical models are crucial. Here, we leveraged two transplantable murine gastric cancer cell lines, YTN2 and YTN16, derived from the same parental line but differing in their susceptibility to immune rejection. We established their differential sensitivity to immune checkpoint inhibitors (ICI) and identified neoantigens. Although anti-CTLA-4 mAbs eradicated YTN16 tumors in 4 of 5 mice, anti-PD-1 and anti-PD-L1 mAbs failed to eradicate YTN16 tumors. Using whole-exome and RNA sequencing, we identified two and three neoantigens in YTN2 and YTN16, respectively. MHC class I ligandome analysis detected the expression of only one of these neoantigens, mutated Cdt1, but the exact length of MHC binding peptide was determined. Dendritic cell vaccine loaded with neoepitope peptides and adoptive transfer of neoantigen-specific CD8+ T cells successfully inhibited the YTN16 tumor growth. Targeting mutated Cdt1 had better efficacy for controlling the tumor. Therefore, mutated Cdt1 was the dominant neoantigen in these tumor cells. More mCdt1 peptides were bound to MHC class I and presented on YTN2 surface than YTN16. This might be one of the reasons why YTN2 was rejected while YTN16 grew in immune-competent mice.
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Affiliation(s)
- Koji Nagaoka
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan; (K.N.); (C.S.); (Y.K.)
| | - Changbo Sun
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan; (K.N.); (C.S.); (Y.K.)
| | - Yukari Kobayashi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan; (K.N.); (C.S.); (Y.K.)
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan; (T.K.); (S.T.); (T.T.)
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan; (T.K.); (S.T.); (T.T.)
- Sapporo Dohto Hospital, Sapporo 065-0017, Japan
| | - Toshihiro Komatsu
- Department of Immunology, Kochi University, Kochi 783-8505, Japan; (T.K.); (K.U.)
| | - Kazuhiro Maejima
- RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics, Yokohama 230-0045, Japan; (K.M.); (H.N.)
| | - Junichiro Futami
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan;
| | - Sachiyo Nomura
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan;
| | - Keiko Udaka
- Department of Immunology, Kochi University, Kochi 783-8505, Japan; (T.K.); (K.U.)
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, Laboratory for Cancer Genomics, Yokohama 230-0045, Japan; (K.M.); (H.N.)
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan; (T.K.); (S.T.); (T.T.)
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo 113-8655, Japan; (K.N.); (C.S.); (Y.K.)
- Correspondence: ; Tel./Fax: +81-3-5805-3161
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17
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Nagaoka K, Shirai M, Taniguchi K, Hosoi A, Sun C, Kobayashi Y, Maejima K, Fujita M, Nakagawa H, Nomura S, Kakimi K. Deep immunophenotyping at the single-cell level identifies a combination of anti-IL-17 and checkpoint blockade as an effective treatment in a preclinical model of data-guided personalized immunotherapy. J Immunother Cancer 2021; 8:jitc-2020-001358. [PMID: 33093158 PMCID: PMC7583806 DOI: 10.1136/jitc-2020-001358] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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] [Accepted: 09/27/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Although immune checkpoint blockade is effective for several malignancies, a substantial number of patients remain refractory to treatment. The future of immunotherapy will be a personalized approach adapted to each patient's cancer-immune interactions in the tumor microenvironment (TME) to prevent suppression of antitumor immune responses. To demonstrate the feasibility of this kind of approach, we developed combination therapy for a preclinical model guided by deep immunophenotyping of the TME. METHODS Gastric cancer cell lines YTN2 and YTN16 were subcutaneously inoculated into C57BL/6 mice. YTN2 spontaneously regresses, while YTN16 grows progressively. Bulk RNA-Seq, single-cell RNA-Seq (scRNA-Seq) and flow cytometry were performed to investigate the immunological differences in the TME of these tumors. RESULTS Bulk RNA-Seq demonstrated that YTN16 tumor cells produced CCL20 and that CD8+ T cell responses were impaired in these tumors relative to YTN2. We have developed a vertical flow array chip (VFAC) for targeted scRNA-Seq to identify unique subtypes of T cells by employing a panel of genes reflecting T cell phenotypes and functions. CD8+ T cell dysfunction (cytotoxicity, proliferation and the recruitment of interleukin-17 (IL-17)-producing cells into YTN16 tumors) was identified by targeted scRNA-Seq. The presence of IL-17-producing T cells in YTN16 tumors was confirmed by flow cytometry, which also revealed neutrophil infiltration. IL-17 blockade suppressed YTN16 tumor growth, while tumors were rejected by the combination of anti-IL-17 and anti-PD-1 (Programmed cell death protein 1) mAb treatment. Reduced neutrophil activation and enhanced expansion of neoantigen-specific CD8+ T cells were observed in tumors of the mice receiving the combination therapy. CONCLUSIONS Deep phenotyping of YTN16 tumors identified a sequence of events on the axis CCL20->IL-17-producing cells->IL-17-neutrophil-angiogenesis->suppression of neoantigen-specific CD8+ T cells which was responsible for the lack of tumor rejection. IL-17 blockade together with anti-PD-1 mAb therapy eradicated these YTN16 tumors. Thus, the deep immunological phenotyping can guide immunotherapy for the tailored treatment of each individual patient's tumor.
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Affiliation(s)
- Koji Nagaoka
- Department of Immunotherapeutics, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Masataka Shirai
- Research and Development Group, Hitachi Ltd, Chiyoda-ku, Tokyo, Japan
| | - Kiyomi Taniguchi
- Research and Development Group, Hitachi Ltd, Chiyoda-ku, Tokyo, Japan
| | - Akihiro Hosoi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Changbo Sun
- Department of Immunotherapeutics, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan.,Department of Thoracic Surgery, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yukari Kobayashi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Sachiyo Nomura
- Department of Gastrointestinal Surgery, The University of Tokyo Graduate School of Medicine Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan .,Cancer Immunology Data Multi-Level Integration Unit, Medical Sciences Innovation Hub Program (MIH), RIKEN, Chuo-ku, Tokyo, Japan
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18
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Nagae G, Yamamoto S, Fujita M, Fujita T, Nonaka A, Umeda T, Fukuda S, Tatsuno K, Maejima K, Hayashi A, Kurihara S, Kojima M, Hishiki T, Watanabe K, Ida K, Yano M, Hiyama Y, Tanaka Y, Inoue T, Ueda H, Nakagawa H, Aburatani H, Hiyama E. Genetic and epigenetic basis of hepatoblastoma diversity. Nat Commun 2021; 12:5423. [PMID: 34538872 PMCID: PMC8450290 DOI: 10.1038/s41467-021-25430-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 09/17/2020] [Accepted: 08/06/2021] [Indexed: 02/08/2023] Open
Abstract
Hepatoblastoma (HB) is the most common pediatric liver malignancy; however, hereditary predisposition and acquired molecular aberrations related to HB clinicopathological diversity are not well understood. Here, we perform an integrative genomic profiling of 163 pediatric liver tumors (154 HBs and nine hepatocellular carcinomas) based on the data acquired from a cohort study (JPLT-2). The total number of somatic mutations is precious low (0.52/Mb on exonic regions) but correlated with age at diagnosis. Telomerase reverse transcriptase (TERT) promoter mutations are prevalent in the tween HBs, selective in the transitional liver cell tumor (TLCT, > 8 years old). DNA methylation profiling reveals that classical HBs are characterized by the specific hypomethylated enhancers, which are enriched with binding sites for ASCL2, a regulatory transcription factor for definitive endoderm in Wnt-pathway. Prolonged upregulation of ASCL2, as well as fetal-liver-like methylation patterns of IGF2 promoters, suggests their "cell of origin" derived from the premature hepatoblast, similar to intestinal epithelial cells, which are highly proliferative. Systematic molecular profiling of HB is a promising approach for understanding the epigenetic drivers of hepatoblast carcinogenesis and deriving clues for risk stratification.
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Affiliation(s)
- Genta Nagae
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Masashi Fujita
- grid.509459.40000 0004 0472 0267Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takanori Fujita
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Aya Nonaka
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Takayoshi Umeda
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Shiro Fukuda
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Kenji Tatsuno
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Kazuhiro Maejima
- grid.509459.40000 0004 0472 0267Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akimasa Hayashi
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan ,grid.411205.30000 0000 9340 2869Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Sho Kurihara
- grid.470097.d0000 0004 0618 7953Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Masato Kojima
- grid.470097.d0000 0004 0618 7953Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Tomoro Hishiki
- grid.136304.30000 0004 0370 1101Chiba University Graduate School of Medicine, Chiba, Japan
| | - Kenichiro Watanabe
- grid.415798.60000 0004 0378 1551Shizuoka Children’s Hospital, Shizuoka, Japan
| | - Kohmei Ida
- grid.412305.10000 0004 1769 1397Department of Pediatrics, Teikyo University Mizonokuchi Hospital, Kawasaki, Japan
| | - Michihiro Yano
- grid.411403.30000 0004 0631 7850Department of Pediatrics, Akita University Hospital, Akita, Japan
| | - Yoko Hiyama
- grid.257022.00000 0000 8711 3200Department of Biomedical Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan 734-8551, 1-2-3, Kasumi, Minami-ku, Hiroshima
| | - Yukichi Tanaka
- grid.414947.b0000 0004 0377 7528Department of Pathology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Takeshi Inoue
- grid.416948.60000 0004 1764 9308Department of Pathology, Osaka City General Hospital, Osaka, Japan
| | - Hiroki Ueda
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Hidewaki Nakagawa
- grid.509459.40000 0004 0472 0267Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroyuki Aburatani
- grid.26999.3d0000 0001 2151 536XGenome Science Laboratory, Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo, Japan
| | - Eiso Hiyama
- grid.470097.d0000 0004 0618 7953Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan ,grid.257022.00000 0000 8711 3200Department of Biomedical Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan 734-8551, 1-2-3, Kasumi, Minami-ku, Hiroshima
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19
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Okawa Y, Ebata N, Kim NKD, Fujita M, Maejima K, Sasagawa S, Nakamura T, Park WY, Hirano S, Nakagawa H. Actionability evaluation of biliary tract cancer by genome transcriptome analysis and Asian cancer knowledgebase. Oncotarget 2021; 12:1540-1552. [PMID: 34316332 PMCID: PMC8310666 DOI: 10.18632/oncotarget.28021] [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: 04/30/2021] [Accepted: 06/14/2021] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Treatment options for biliary tract cancer (BTC) are very limited. It is necessary to investigate actionable genes and candidate drugs using a sophisticated knowledgebase (KB) and characterize BTCs immunologically for evaluating the actionability of molecular and immune therapies. MATERIALS AND METHODS The genomic and transcriptome data of 219 patients with BTC who underwent surgery were analyzed. Actionable mutations and candidate drugs were annotated using the largest available KB of the Asian population (CancerSCAN®). Predictive biomarkers of immune checkpoint inhibitors were analyzed using DNA and RNA sequencing data. RESULTS Twenty-two actionable genes and 43 candidate drugs were annotated in 74 patients (33.8%). The most frequent actionable genes were PTEN (7.3%), CDKN2A (6.8%), KRAS (6.4%). BRCA2, CDKN2A, and FGFR2 mutations were most frequently identified in case of intrahepatic cholangiocarcinoma. PTEN and CDKN2A mutations were associated with significantly shorter overall survival. PD-L1 and PD-1 expression was significantly higher in case of extrahepatic cholangiocarcinoma and T-cell-high expression. In total, 49.7% of cases were evaluated as having actionability for molecular therapy or immune checkpoint inhibitors. CONCLUSIONS Identifying actionable genes and candidate drugs using the KB contribute to the development of therapeutic drugs and personalized treatment for BTC.
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Affiliation(s)
- Yuki Okawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Nobutaka Ebata
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Nayoung K D Kim
- Geninus Inc., Seoul, Republic of Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toru Nakamura
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Woong-Yang Park
- Geninus Inc., Seoul, Republic of Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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20
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Yanagimichi M, Nishino K, Sakamoto A, Kurodai R, Kojima K, Eto N, Isoda H, Ksouri R, Irie K, Kambe T, Masuda S, Akita T, Maejima K, Nagao M. Analyses of putative anti-cancer potential of three STAT3 signaling inhibitory compounds derived from Salvia officinalis. Biochem Biophys Rep 2020; 25:100882. [PMID: 33392396 PMCID: PMC7772785 DOI: 10.1016/j.bbrep.2020.100882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 08/14/2020] [Revised: 11/17/2020] [Accepted: 12/13/2020] [Indexed: 12/05/2022] Open
Abstract
The extract of Salvia officinalis (Common Sage) exhibited inhibitory activity of STAT3 signal after screening of several plants extracts using the STAT3-responsive reporter system. Cirsiliol, luteolin, and carnosol were identified from the methanol extract of Silvia officinalis as inhibitors of STAT3 signaling and the effects of these three compounds on STAT3 protein or growth inhibition on cancer cells was compared. Luteolin at the dose of 90 μM clearly suppressed the phosphorylation of STAT3 induced by IL-6, while carnosol was prone to decrease total STAT3 proteins at high doses (>90 μM). Cirsiliol had almost no effect. Since the three compounds exhibited similar concentration-dependent suppression patterns in the reporter assay except for cirsiliol became plateau beyond 30 μM, these compounds appeared to function as STAT3 inhibitory factors in different ways. The direct anti-proliferative activity of three compounds was examined with or without the anti-cancer drug gefitinib using HepG2 and A549 cells. The anti-proliferative effect of the three compounds was additively enhanced by gefitinib. At the doses of 3.6 μM, statistically significant suppression of proliferation was observed in HepG2 cells only by cirsiliol among the three compounds in the absence of gefitinib but all three compounds were prone to suppress the proliferation of HepG2 cells and A549 cells dose-dependently although cirsiliol showed a modest dose-dependency and this suppression of proliferation was enhanced by the addition of gefitinib. Cirsiliol, a dimethyoxylated flavone, activated the natural killer activity of KHYG-1 cells against erythroleukemia K562 cells like a hexamethoxylated flavone, nobiletin, suggesting that it may also have an indirect anti-cancer potential through activation of NK cells. These results shed light on the putative anti-cancer potential of Salvia officinalis. Carnosol, luteolin and cirsiliol were identified as STAT3 signal inhibitors in S. officinalis. Cirsiliol inhibited the STAT3-responsive reporter expression at 7.5 μM but showed low dose-dependency at higher doses. Cirsiliol at 90 μM showed almost no effect on phosphorylation of STAT3 and weakly suppressed total STAT3. Cirsiliol exhibited anti-proliferative activity at 3.6 μM against HepG2 cells and A549 cells but showed low dose-dependency. Cirsiliol activated NK cells by stimulating exocytosis of granules for cytolysis.
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Affiliation(s)
- Maho Yanagimichi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Akiho Sakamoto
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryusei Kurodai
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Kojima
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Nozomu Eto
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hiroko Isoda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan.,Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Riadh Ksouri
- Centre de Biotechnologie à la Technopole de Borj Cédria (CBBC), BP 901, 2050, Hammam-lif, Tunisia
| | - Kazuhiro Irie
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Taiho Kambe
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Seiji Masuda
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Toru Akita
- Nippon Shinyaku CO., LTD., Kyoto, 601-8550, Japan
| | | | - Masaya Nagao
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
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21
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Kawasaki K, Toshimitsu K, Matano M, Fujita M, Fujii M, Togasaki K, Ebisudani T, Shimokawa M, Takano A, Takahashi S, Ohta Y, Nanki K, Igarashi R, Ishimaru K, Ishida H, Sukawa Y, Sugimoto S, Saito Y, Maejima K, Sasagawa S, Lee H, Kim HG, Ha K, Hamamoto J, Fukunaga K, Maekawa A, Tanabe M, Ishihara S, Hamamoto Y, Yasuda H, Sekine S, Kudo A, Kitagawa Y, Kanai T, Nakagawa H, Sato T. An Organoid Biobank of Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping. Cell 2020; 183:1420-1435.e21. [PMID: 33159857 DOI: 10.1016/j.cell.2020.10.023] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 01/11/2023]
Abstract
Gastroenteropancreatic (GEP) neuroendocrine neoplasm (NEN) that consists of neuroendocrine tumor and neuroendocrine carcinoma (NEC) is a lethal but under-investigated disease owing to its rarity. To fill the scarcity of clinically relevant models of GEP-NEN, we here established 25 lines of NEN organoids and performed their comprehensive molecular characterization. GEP-NEN organoids recapitulated pathohistological and functional phenotypes of the original tumors. Whole-genome sequencing revealed frequent genetic alterations in TP53 and RB1 in GEP-NECs, and characteristic chromosome-wide loss of heterozygosity in GEP-NENs. Transcriptome analysis identified molecular subtypes that are distinguished by the expression of distinct transcription factors. GEP-NEN organoids gained independence from the stem cell niche irrespective of genetic mutations. Compound knockout of TP53 and RB1, together with overexpression of key transcription factors, conferred on the normal colonic epithelium phenotypes that are compatible with GEP-NEN biology. Altogether, our study not only provides genetic understanding of GEP-NEN, but also connects its genetics and biological phenotypes.
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Affiliation(s)
- Kenta Kawasaki
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kohta Toshimitsu
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mami Matano
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masayuki Fujii
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Deparment of Surgical Oncology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Kazuhiro Togasaki
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshiki Ebisudani
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Pulmonary Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mariko Shimokawa
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ai Takano
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Sirirat Takahashi
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yuki Ohta
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kosaku Nanki
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ryo Igarashi
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuhiro Ishimaru
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Deparment of Surgical Oncology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Hiroki Ishida
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yasutaka Sukawa
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shinya Sugimoto
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yoshimasa Saito
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan; Division of Pharmacotherapeutics, Keio University Faculty of Pharmacy, Tokyo 105-8512, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hwajin Lee
- Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul 08826, South Korea
| | - Hong-Gee Kim
- Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul 08826, South Korea
| | - Kyungsik Ha
- Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul 08826, South Korea
| | - Junko Hamamoto
- Department of Pulmonary Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Koichi Fukunaga
- Department of Pulmonary Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Aya Maekawa
- Department of Hepatobiliary and Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Minoru Tanabe
- Department of Hepatobiliary and Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Soichiro Ishihara
- Deparment of Surgical Oncology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Yasuo Hamamoto
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroyuki Yasuda
- Department of Pulmonary Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Atsushi Kudo
- Department of Hepatobiliary and Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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22
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Oshima K, Kato K, Ito Y, Daiko H, Nozaki I, Nakagawa S, Shibuya Y, Kojima T, Toh Y, Okada M, Hironaka S, Akiyama Y, Komatsu Y, Maejima K, Nakagawa H, Kato M, Kanato K, Kuchiba A, Nakamura K, Kitagawa Y. 1488P A prognostic biomarker study in patients who underwent surgery or received chemoradiotherapy for clinical stage I esophageal squamous cell carcinoma. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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23
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Nagaoka K, Kanaseki T, Sun C, Hosoi A, Tokita S, Maejima K, Fujita M, Nakagawa H, Torigoe T, Kakimi K. Abstract 6610: To identify neoantigens relevant to anti-tumor activity is challenging even with NGS-based prediction combined with MHC ligandome profiling. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6610] [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 T cells that target neoantigens, which are mutant peptides encoded by tumor-specific mutations in cancer cells, have a pivotal role in response to immunotherapy. Current affordable NGS and bioinformatics have facilitated neoantigen research. However, the prediction of neoantigens in silico analysis lacks actual proof that the predicted neoantigens are indeed relevant to anti-tumor immune response. In this study, immunogenicity and anti-tumor activity of in silico predicted neoepitopes of gastric cancer cell lines, YTN2 and YTN16, were evaluated in vitro and in vivo. Besides, MHC ligandome profiling was performed on whether predicted neoantigens were presented by cancer cells.
Methods YTN2 and YTN16 are subclones established from a chemically induced murine gastric cancer (Cancer Sci. 2018;109:1480-1492). Whole-exome sequencing and microarray analysis were performed. Binding affinities of peptides with MHC-I were predicted using NetMHCpan. Peptides with IC50≤250 nM were considered as candidate neoantigen.
Results Exome sequencing identified 3329 and 3347 missense mutations in YTN2 and YTN16 tumors, respectively. Most of the mutations (3007) were common in YTN2 and YTN16. Among them, 2356 and 2166 mutations were expressed in YTN2 and YTN16, respectively. Candidate neoantigen peptides were 263 and 250 in YTN2 and YTN16, respectively. Although we detected 75 neoantigen-peptide-specific T cell responses, only six neoantigens (Cdt1, Cers4, Nlrp1a, Scarb2, Vmn2r121, and Zfp106)-specific T cells could recognize YTN2 or YTN16 cell line and produced IFNγ. To evaluate in vivo anti-tumor effects of neoantigen-specific T cells, we expanded four neoantigens (Cdt1, Nlrp1a, Vmn2r121, and Zfp106)-specific CD8+ T cell lines and injected them into YTN16 tumor-bearing mice. Only Cdt1-specific T cells completely eradicated the tumor, and Nlrp1a-specific T cells partially inhibited tumor growth. However, Vmn2r121- or Zfp106-specific CD8+ T cell lines could not inhibit the tumor growth. MHC ligandome profiling identified 424 Db-binding peptides and 228 Kb-binding peptides in YTN2, while 317 Db-binding peptides and 228 Kb-binding peptides were detected in YTN16. Almost all MHC-binding peptides had wild type sequences. Only one mutated peptide, Cdt1, was detected in YTN2 but not YTN16. Although Cdt1-specific CD8+ T cells recognized both YTN2 and YTN16. Other neoantigens, Cers4, Nlrp1a, Scarb2, Vmn2r121, and Zfp106, were not detected by MHC ligandome profiling, though T cells specific to these neoantigens responded to cancer cells.
Conclusion Currently available technologies anyhow identified neoantigens that are relevant to anti-tumor immune response. However, any single methodology is not sufficient to identify real neoantigens. Detection of neoantigen-specific T cells is still important.
Citation Format: Koji Nagaoka, Takayuki Kanaseki, Changbo Sun, Akihiro Hosoi, Serina Tokita, Kazuhiro Maejima, Masashi Fujita, Hidewaki Nakagawa, Toshihiko Torigoe, Kazuhiro Kakimi. To identify neoantigens relevant to anti-tumor activity is challenging even with NGS-based prediction combined with MHC ligandome profiling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6610.
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Affiliation(s)
| | | | - Changbo Sun
- 1The University of Tokyo Hospital, Tokyo, Japan
| | | | | | | | - Masashi Fujita
- 3RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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24
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Dutta M, Nakagawa H, Kato H, Maejima K, Sasagawa S, Nakano K, Sasaki-Oku A, Fujimoto A, Mateos RN, Patil A, Tanaka H, Miyano S, Yasuda T, Nakai K, Fujita M. Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma. PeerJ 2020; 8:e9294. [PMID: 32617189 PMCID: PMC7323713 DOI: 10.7717/peerj.9294] [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: 10/07/2019] [Accepted: 05/14/2020] [Indexed: 12/17/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant type of esophageal cancer in the Asian region, including Japan. A previous study reported mutational landscape of Japanese ESCCs by using exome sequencing. However, somatic structural alterations were yet to be explored. To provide a comprehensive mutational landscape, we performed whole genome sequencing (WGS) analysis of biopsy specimens from 20 ESCC patients in a Japanese population. WGS analysis identified non-silent coding mutations of TP53, ZNF750 and FAT1 in ESCC. We detected six mutational signatures in ESCC, one of which showed significant association with smoking status. Recurrent structural variations, many of which were chromosomal deletions, affected genes such as LRP1B, TTC28, CSMD1, PDE4D, SDK1 and WWOX in 25%–30% of tumors. Somatic copy number amplifications at 11q13.3 (CCND1), 3q26.33 (TP63/SOX2), and 8p11.23 (FGFR1) and deletions at 9p21.3 (CDKN2A) were identified. Overall, these multi-dimensional view of genomic alterations improve the understanding of the ESCC development at molecular level and provides future prognosis and therapeutic implications for ESCC in Japan.
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Affiliation(s)
- Munmee Dutta
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroaki Kato
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aya Sasaki-Oku
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Raúl Nicolás Mateos
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ashwini Patil
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takushi Yasuda
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate school of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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25
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Fujimoto A, Fujita M, Hasegawa T, Wong JH, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, Nakagawa H. Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. Genome Res 2020; 30:gr.255026.119. [PMID: 32209592 PMCID: PMC7111525 DOI: 10.1101/gr.255026.119] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/25/2020] [Indexed: 01/08/2023]
Abstract
Microsatellites are repeats of 1- to 6-bp units, and approximately 10 million microsatellites have been identified across the human genome. Microsatellites are vulnerable to DNA mismatch errors and have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of microsatellite repeat regions at the genome level, we analyzed approximately 20.1 billion microsatellites in 2717 whole genomes of pan-cancer samples across 21 tissue types. First, we developed a new insertion and deletion caller (MIMcall) that takes into consideration the error patterns of different types of microsatellites. Among the 2717 pan-cancer samples, our analysis identified 31 samples, including colorectal, uterus, and stomach cancers, with a higher proportion of mutated microsatellite (≥0.03), which we defined as microsatellite instability (MSI) cancers of genome-wide level. Next, we found 20 highly mutated microsatellites that can be used to detect MSI cancers with high sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of microsatellites. Last, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impacts than germline mutations and structural variations. Our analysis provides a comprehensive picture of mutations in the microsatellite regions and reveals possible causes of mutations, as well as provides a useful marker set for MSI detection.
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Affiliation(s)
- Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo 113-0033, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Takanori Hasegawa
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jing Hao Wong
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo 113-0033, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Aya Oku-Sasaki
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
| | - Yuichi Shiraishi
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Satoru Miyano
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
- Human Genome Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Go Yamamoto
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Seiya Imoto
- Health Intelligence Center, Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 230-0045, Japan
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26
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Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H. Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. EBioMedicine 2020; 53:102659. [PMID: 32113157 PMCID: PMC7048625 DOI: 10.1016/j.ebiom.2020.102659] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" tumors based on the infiltration of cytotoxic immune cells. Previous studies on liver cancer have reported a superior prognosis for inflamed tumors compared to non-inflamed tumors. However, liver cancer is highly heterogeneous immunologically and genetically, and a finer classification of the liver cancer microenvironment may improve our understanding of its immunological diversity and response to immune therapy. METHODS We characterized the immune gene signatures of 234 primary liver cancers, mainly virus-related, from a Japanese population using RNA-Seq of tumors and matched non-tumorous hepatitis livers. We then compared them with the somatic alterations detected using the whole-genome sequencing. FINDINGS Liver cancers expressed lower levels of immune marker genes than non-tumorous hepatitis livers, indicating immunosuppression in the tumor microenvironment. Several immunosuppression mechanisms functioned actively and mutually exclusively, resulting in four immune subclasses of liver cancer: tumor-associated macrophage (TAM), CTNNB1, cytolytic activity (CYT), and regulatory T cell (Treg). The CYT and Treg subclasses represented inflamed tumors, while the TAM and CTNNB1 subclasses represented non-inflamed tumors. The TAM subclass, which comprised 31% of liver cancers, showed a poor survival, expressed elevated levels of extracellular matrix genes, and was associated with somatic mutations of chromatin regulator ARID2. The results of cell line experiments suggested a functional link between ARID2 and chemokine production by liver cancer cells. INTERPRETATION Primary liver cancer was classified into four subclasses based on mutually exclusive mechanisms for immunosuppression. This classification indicate the importance of immunosuppression mechanisms, such as TAM and Treg, as therapeutic targets for liver cancer. FUNDING The Japan Agency for Medical Research and Development (AMED).
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Affiliation(s)
- Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Rui Yamaguchi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Takanori Hasegawa
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Shu Shimada
- Department of Molecular Oncology Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University, Hiroshima, Japan.
| | - Shuto Hayashi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Hiroko Tanaka
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Kazuhiro Kakimi
- Department of Immuno-therapeutics, The University of Tokyo Hospital, Japan; Cancer Immunology Data Multi-level Integration Unit, RIKEN Medical Innovation Hub Program, Tokyo, Japan.
| | - Shinji Tanaka
- Department of Molecular Oncology Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Seiya Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H. Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. EBioMedicine 2020. [PMID: 32113157 DOI: 10.1016/j.ebiom.2020.102659.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" tumors based on the infiltration of cytotoxic immune cells. Previous studies on liver cancer have reported a superior prognosis for inflamed tumors compared to non-inflamed tumors. However, liver cancer is highly heterogeneous immunologically and genetically, and a finer classification of the liver cancer microenvironment may improve our understanding of its immunological diversity and response to immune therapy. METHODS We characterized the immune gene signatures of 234 primary liver cancers, mainly virus-related, from a Japanese population using RNA-Seq of tumors and matched non-tumorous hepatitis livers. We then compared them with the somatic alterations detected using the whole-genome sequencing. FINDINGS Liver cancers expressed lower levels of immune marker genes than non-tumorous hepatitis livers, indicating immunosuppression in the tumor microenvironment. Several immunosuppression mechanisms functioned actively and mutually exclusively, resulting in four immune subclasses of liver cancer: tumor-associated macrophage (TAM), CTNNB1, cytolytic activity (CYT), and regulatory T cell (Treg). The CYT and Treg subclasses represented inflamed tumors, while the TAM and CTNNB1 subclasses represented non-inflamed tumors. The TAM subclass, which comprised 31% of liver cancers, showed a poor survival, expressed elevated levels of extracellular matrix genes, and was associated with somatic mutations of chromatin regulator ARID2. The results of cell line experiments suggested a functional link between ARID2 and chemokine production by liver cancer cells. INTERPRETATION Primary liver cancer was classified into four subclasses based on mutually exclusive mechanisms for immunosuppression. This classification indicate the importance of immunosuppression mechanisms, such as TAM and Treg, as therapeutic targets for liver cancer. FUNDING The Japan Agency for Medical Research and Development (AMED).
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Affiliation(s)
- Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Rui Yamaguchi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Takanori Hasegawa
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Shu Shimada
- Department of Molecular Oncology Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University, Hiroshima, Japan.
| | - Shuto Hayashi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Hiroko Tanaka
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoru Miyano
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan.
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Kazuhiro Kakimi
- Department of Immuno-therapeutics, The University of Tokyo Hospital, Japan; Cancer Immunology Data Multi-level Integration Unit, RIKEN Medical Innovation Hub Program, Tokyo, Japan.
| | - Shinji Tanaka
- Department of Molecular Oncology Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Seiya Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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29
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Mateos RN, Nakagawa H, Hirono S, Takano S, Fukasawa M, Yanagisawa A, Yasukawa S, Maejima K, Oku-Sasaki A, Nakano K, Dutta M, Tanaka H, Miyano S, Enomoto N, Yamaue H, Nakai K, Fujita M. Genomic analysis of pancreatic juice DNA assesses malignant risk of intraductal papillary mucinous neoplasm of pancreas. Cancer Med 2019; 8:4565-4573. [PMID: 31225717 PMCID: PMC6712468 DOI: 10.1002/cam4.2340] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 01/16/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Intraductal papillary mucinous neoplasm (IPMN) of pancreas has a high risk to develop into invasive cancer or co‐occur with malignant lesion. Therefore, it is important to assess its malignant risk by less‐invasive approach. Pancreatic juice cell‐free DNA (PJD) would be an ideal material in this purpose, but genetic biomarkers for predicting malignant risk from PJD are not yet established. We here performed deep exome sequencing analysis of PJD from 39 IPMN patients with or without malignant lesion. Somatic alterations and copy number alterations (CNAs) detected in PJD were compared with the histologic grade of IPMN to evaluate their potential as a malignancy marker. Somatic mutations of KRAS, GNAS, TP53, and RNF43 were commonly detected in PJD of IPMNs, but no association with the histologic grades of IPMN was found. Instead, mutation burden was positively correlated with the histologic grade (r = 0.427, P = 0.015). We also observed frequent copy number deletions in 17p13 (TP53) and amplifications in 7q21 and 8q24 (MYC) in PJDs. The amplifications in 7q21 and 8q24 were positively correlated with the histologic grade and most prevalent in the cases of invasive carcinoma (P = 0.002 and 7/11; P = 0.011 and 6/11, respectively). We concluded that mutation burden and CNAs detected in PJD may have potential to assess the malignant progression risk of IPMNs.
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Affiliation(s)
- Raúl N Mateos
- Department of Computational Biology and Medical Science, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Seiko Hirono
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinichi Takano
- First Department of Internal Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mitsuharu Fukasawa
- First Department of Internal Medicine, University of Yamanashi, Yamanashi, Japan
| | - Akio Yanagisawa
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoru Yasukawa
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aya Oku-Sasaki
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Munmee Dutta
- Department of Computational Biology and Medical Science, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Science, The University of Tokyo, Chiba, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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30
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Yamamoto Y, Uemura M, Fujita M, Maejima K, Koh Y, Matsushita M, Nakano K, Hayashi Y, Wang C, Ishizuya Y, Kinouchi T, Hayashi T, Matsuzaki K, Jingushi K, Kato T, Kawashima A, Ujike T, Nagahara A, Fujita K, Imamura R, Nakagawa H, Nonomura N. Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma. Cancer Sci 2019; 110:617-628. [PMID: 30536551 PMCID: PMC6361573 DOI: 10.1111/cas.13906] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
Reliable biomarkers for renal cell carcinoma (RCC) have yet to be determined. Circulating tumor DNA (ctDNA) is an emerging resource to detect and monitor molecular characteristics of various tumors. The present study aims to clarify the clinical utility of ctDNA for RCC. Fifty-three patients histologically diagnosed with clear cell RCC were enrolled. Targeted sequencing was carried out using plasma cell-free DNA (cfDNA) and tumor DNA. We applied droplet digital PCR (ddPCR) to validate detected mutations. cfDNA fragment size was also evaluated using a microfluidics-based platform and sequencing. Proportion of cfDNA fragments was defined as the ratio of small (50-166 bp) to large (167-250 bp) cfDNA fragments. Association of mutant allele frequency of ctDNA with clinical course was analyzed. Prognostic potential was evaluated using log-rank test. A total of 38 mutations across 16 (30%) patients were identified from cfDNA, including mutations in TP53 (n = 6) and VHL (n = 5), and median mutant allele frequency of ctDNA was 10%. We designed specific ddPCR probes for 11 mutations and detected the same mutations in both cfDNA and tumor DNA. Positive ctDNA was significantly associated with a higher proportion of cfDNA fragments (P = .033), indicating RCC patients with ctDNA had shorter fragment sizes of cfDNA. Interestingly, the changes of mutant allele frequency in ctDNA concurrently correlated with clinical course. Positive ctDNA and fragmentation of cfDNA were significantly associated with poor cancer-specific survival (P < .001, P = .011). In conclusion, our study shows the clinical utility of ctDNA status and cfDNA fragment size as biomarkers for prognosis and disease monitoring in RCC.
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Affiliation(s)
- Yoshiyuki Yamamoto
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Motohide Uemura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Therapeutic Urologic Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yoko Koh
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Matsushita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kosuke Nakano
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yujiro Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Cong Wang
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yu Ishizuya
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshiro Kinouchi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takuji Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyosuke Matsuzaki
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kentaro Jingushi
- Department of Therapeutic Urologic Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Taigo Kato
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Atsunari Kawashima
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takeshi Ujike
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akira Nagahara
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazutoshi Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryoichi Imamura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
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31
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Nguyen DT, Nguyen HH, Nguyen TD, Nguyen TTH, Nakano K, Maejima K, Sasaki-Oku A, Nguyen VB, Nguyen DB, Le BQ, Wong JH, Tsunoda T, Nakagawa H, Fujimoto A, Nong VH. Whole Genome Sequencing of a Vietnamese Family from a Dioxin Contamination Hotspot Reveals Novel Variants in the Son with Undiagnosed Intellectual Disability. Int J Environ Res Public Health 2018; 15:ijerph15122629. [PMID: 30477169 PMCID: PMC6313569 DOI: 10.3390/ijerph15122629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 11/24/2022]
Abstract
Although it has been a half-century since dioxin-contaminated herbicides were used to defoliate the landscape during the Vietnam War, dioxin contamination “hotspots” still remain in Vietnam. Environmental and health impacts of these hotspots need to be evaluated. Intellectual disability (ID) is one of the diseases found in the children of people exposed to the herbicides. This study aims to identify genetic alterations of a patient whose family lived in a dioxin hotspot. The patient’s father had a highly elevated dioxin concentration. He was affected with undiagnosed moderate ID. To analyze de novo mutations and genetic variations, and to identify causal gene(s) for ID, we performed whole genome sequencing (WGS) of the proband and his parents. Two de novo missense mutations were detected, each one in ETS2 and ZNF408 genes, respectively. Compound heterozygosity was identified in CENPF and TTN genes. Existing knowledge on the genes and bioinformatics analyses suggest that EST2, ZNF408, and CENPF might be promising candidates for ID causative genes.
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Affiliation(s)
- Dang Ton Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
| | - Hai Ha Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.
| | - Thuy Duong Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.
| | - Thi Thanh Hoa Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.
| | - Kaoru Nakano
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
| | - Kazuhiro Maejima
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
| | - Aya Sasaki-Oku
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
| | - Van Ba Nguyen
- Vietnam Military Medical University, Ha Dong, Hanoi 100000, Vietnam.
| | - Duy Bac Nguyen
- Vietnam Military Medical University, Ha Dong, Hanoi 100000, Vietnam.
| | - Bach Quang Le
- Vietnam Military Medical University, Ha Dong, Hanoi 100000, Vietnam.
| | - Jing Hao Wong
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.
| | - Tatsuhiko Tsunoda
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.
| | - Hidewaki Nakagawa
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
| | - Akihiro Fujimoto
- RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.
| | - Van Hai Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.
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32
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Ton ND, Nakagawa H, Ha NH, Duong NT, Nhung VP, Hien LTT, Hue HTT, Hoang NH, Wong JH, Nakano K, Maejima K, Sasaki-Oku A, Tsunoda T, Fujimoto A, Van Hai N. Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure. Hum Mutat 2018; 39:1384-1392. [PMID: 29969170 DOI: 10.1002/humu.23585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/14/2018] [Accepted: 06/29/2018] [Indexed: 11/12/2022]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or dioxin, is commonly considered the most toxic man-made substance. Dioxin exposure impacts human health and diseases, birth defects and teratogenesis were frequently observed in children of persons who have been exposed to dioxin. However, the impact of dioxin on human mutation rate in trios has not yet been elucidated at the whole genome level. To identify and characterize the genetic alterations in the individuals exposed to dioxin, we performed whole genome sequencing (WGS) of nine Vietnamese trios whose fathers were exposed to dioxin. In total, 846 de novo point mutations, 26 de novo insertions and deletions, 4 de novo structural variations, and 1 de novo copy number variation were identified. The number of point mutations and dioxin concentrations were positively correlated (P-value < 0.05). Considering the substitution pattern, the number of A > T/T > A mutation and the dioxin concentration was positively correlated (P-value < 0.05). Our analysis also identified one possible disease-related mutation in LAMA5 in one trio. These findings suggested that dioxin exposure might affect father genomes of trios leading to de novo mutations in their children. Further analysis with larger sample sizes would be required to better clarify mutation rates and substitution patterns in trios caused by dioxin.
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Affiliation(s)
- Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam.,Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Vu Phuong Nhung
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Le Thi Thu Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Huynh Thi Thu Hue
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Nguyen Huy Hoang
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Jing Hao Wong
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Aya Sasaki-Oku
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
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33
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Furuta M, Tanaka H, Shiraishi Y, Unida T, Imamura M, Fujimoto A, Fujita M, Sasaki-Oku A, Maejima K, Nakano K, Kawakami Y, Arihiro K, Aikata H, Ueno M, Hayami S, Ariizumi SI, Yamamoto M, Gotoh K, Ohdan H, Yamaue H, Miyano S, Chayama K, Nakagawa H. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected livers. Oncotarget 2018; 9:25075-25088. [PMID: 29861854 PMCID: PMC5982772 DOI: 10.18632/oncotarget.25308] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 12/05/2017] [Accepted: 04/06/2018] [Indexed: 12/17/2022] Open
Abstract
Integration of Hepatitis B virus (HBV) into the human genome can cause genetic instability, leading to selective advantages for HBV-induced liver cancer. Despite the large number of studies for HBV integration into liver cancer, little is known about the mechanism of initial HBV integration events owing to the limitations of materials and detection methods. We conducted an HBV sequence capture, followed by ultra-deep sequencing, to screen for HBV integrations in 111 liver samples from human-hepatocyte chimeric mice with HBV infection and human clinical samples containing 42 paired samples from non-tumorous and tumorous liver tissues. The HBV infection model using chimeric mice verified the efficiency of our HBV-capture analysis and demonstrated that HBV integration could occur 23 to 49 days after HBV infection via microhomology-mediated end joining and predominantly in mitochondrial DNA. Overall HBV integration sites in clinical samples were significantly enriched in regions annotated as exhibiting open chromatin, a high level of gene expression, and early replication timing in liver cells. These data indicate that HBV integration in liver tissue was biased according to chromatin accessibility, with additional selection pressures in the gene promoters of tumor samples. Moreover, an integrative analysis using paired non-tumorous and tumorous samples and HBV-related transcriptional change revealed the involvement of TERT and MLL4 in clonal selection. We also found frequent and non-tumorous liver-specific HBV integrations in FN1 and HBV-FN1 fusion transcript. Extensive survey of HBV integrations facilitates and improves the understanding of the timing and biology of HBV integration during infection and HBV-related hepatocarcinogenesis.
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Affiliation(s)
- Mayuko Furuta
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takuro Unida
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Masahi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Aya Sasaki-Oku
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Yoshiiku Kawakami
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shun-Ichi Ariizumi
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Masakazu Yamamoto
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Kunihito Gotoh
- Department of Surgery, Osaka International Cancer Institute, Osaka 537-8511, Japan
| | - Hideki Ohdan
- Department of Gastroenterological Surgery, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
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34
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Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K, Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H. Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations. J Hepatol 2018; 68:959-969. [PMID: 29360550 DOI: 10.1016/j.jhep.2018.01.009] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous and respond poorly to treatment. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed large-scale genome sequencing analyses on BTCs to investigate their somatic and germline driver events and characterize their genomic landscape. METHODS We analyzed 412 BTC samples from Japanese and Italian populations, 107 by whole-exome sequencing (WES), 39 by whole-genome sequencing (WGS), and a further 266 samples by targeted sequencing. The subtypes were 136 intrahepatic cholangiocarcinomas (ICCs), 101 distal cholangiocarcinomas (DCCs), 109 peri-hilar type cholangiocarcinomas (PHCs), and 66 gallbladder or cystic duct cancers (GBCs/CDCs). We identified somatic alterations and searched for driver genes in BTCs, finding pathogenic germline variants of cancer-predisposing genes. We predicted cell-of-origin for BTCs by combining somatic mutation patterns and epigenetic features. RESULTS We identified 32 significantly and commonly mutated genes including TP53, KRAS, SMAD4, NF1, ARID1A, PBRM1, and ATR, some of which negatively affected patient prognosis. A novel deletion of MUC17 at 7q22.1 affected patient prognosis. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes such as BRCA1, BRCA2, RAD51D, MLH1, or MSH2 were detected in 11% (16/146) of BTC patients. CONCLUSIONS BTCs have distinct genetic features including somatic events and germline predisposition. These findings could be useful to establish treatment and diagnostic strategies for BTCs based on genetic information. LAY SUMMARY We here analyzed genomic features of 412 BTC samples from Japanese and Italian populations. A total of 32 significantly and commonly mutated genes were identified, some of which negatively affected patient prognosis, including a novel deletion of MUC17 at 7q22.1. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes were detected in 11% of patients with BTC. BTCs have distinct genetic features including somatic events and germline predisposition.
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Affiliation(s)
- Christopher P Wardell
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Toru Yamada
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Michele Simbolo
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Matteo Fassan
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Rosa Karlic
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Paz Polak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yutaka Hatanaka
- Research Division of Companion Diagnostics, Hokkaido University Hospital, Sapporo 060-8648, Japan
| | - Kazuhiro Maejima
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Rita T Lawlor
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Yoshitsugu Nakanishi
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Tomoko Mitsuhashi
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo 060-8648, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Andrea Ruzzenente
- Department of Surgery, General and Hepatobiliary Surgery, University Hospital G.B. Rossi, University and Hospital Trust of Verona, Verona, Italy
| | - Simone Conci
- Department of Surgery, General and Hepatobiliary Surgery, University Hospital G.B. Rossi, University and Hospital Trust of Verona, Verona, Italy
| | - Ayako Oosawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Aya Sasaki-Oku
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kaoru Nakano
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yujiro Yamamoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan; Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kubo Michiaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoshiiku Kawakami
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Kunihito Gotoh
- Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka 537-8511, Japan
| | - Shun-Ichi Ariizumi
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Masakazu Yamamoto
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aldo Scarpa
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Toru Nakamura
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
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Fujita M, Matsubara N, Matsuda I, Maejima K, Oosawa A, Yamano T, Fujimoto A, Furuta M, Nakano K, Oku-Sasaki A, Tanaka H, Shiraishi Y, Mateos RN, Nakai K, Miyano S, Tomita N, Hirota S, Ikeuchi H, Nakagawa H. Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling. Oncotarget 2018; 9:969-981. [PMID: 29416670 PMCID: PMC5787528 DOI: 10.18632/oncotarget.22867] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) increases the risk of colorectal cancer, known as colitis-associated cancer (CAC). It is still unclear what driver mutations are caused by chronic inflammation and lead to CAC development. To get insight into this issue, we investigated somatic alterations in CAC. We performed exome sequencing of 22 fresh CACs and targeted sequencing of 43 genes on 90 archive specimens from Japanese CAC patients, of which 58 were ulcerative colitis (UC) and 32 were Crohn's disease (CD). Consistently with the previous reports, TP53 was commonly mutated (66%) whereas APC, KRAS and SMAD4 were mutated less frequently (16%, 11% and 11%, respectively). Mucinous CD-CACs in the anus, an Asian-specific subtype of CD-CAC, had less somatic mutations in our target genes. We also found that RNF43, a negative regulator of the Wnt signaling, was somatically mutated in a significant fraction of CACs (10 of 90; 11%). Two lines of evidence indicated that somatic mutations of RNF43 were related to chronic inflammation. First, somatic mutations of RNF43 were significantly associated with longer duration of IBD. Second, clinico-pathological features suggested many of the APC-mutated CACs were actually sporadic colorectal cancer whereas RNF43-mutated CACs did not have this tendency. RNA-Seq analysis showed that RNF43-mutated CACs had elevated expression of c-Myc and its target genes, suggesting that RNF43 is a bona fide driver of CAC development. This study provides evidence that somatic mutation of RNF43 is the driver genetic alteration that links chronic inflammation and cancer development in about 10% of CACs.
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Affiliation(s)
- Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nagahide Matsubara
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Ikuo Matsuda
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Kazuhiro Maejima
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Ayako Oosawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tomoki Yamano
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kaoru Nakano
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Aya Oku-Sasaki
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
- Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
- Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naohiro Tomita
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Seiichi Hirota
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Hiroki Ikeuchi
- Department of Inflammatory Bowel Disease Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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Fujita M, Matsubara N, Maejima K, Yamano T, Matsuda I, Hirota S, Ikeuchi H, Tomita N, Nakagawa H. Abstract 1439: Genetic profiling of colitis-associated cancer indicates de novo carcinogenesis and the impact of chronic inflammation. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1439] [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: Chronic inflammation is one of the major causes of carcinogenesis. Ulcerative colitis (UC) and Crohn’s disease (CD) increase the risk of colitis-associated cancer (CAC) development, and its biological and pathological characters are also distinct. However, the genetic mechanism of how chronic inflammation leads to CACs is still unclear.
Methods: We obtained frozen tumor tissues from 21 CAC patients and performed exome or whole-genome sequencing of the matched tumor-normal samples. We enumerated recurrently mutated genes and selected 43 genes among them for target capture. We then performed targeted resequencing of 84 FFPE specimens from CAC tissues. Totally, we made genomic profiles of 105 CACs.
Results: The most frequently mutated gene was TP53, whose mutation was found in 70 of 105 samples (67%), which is more prevalent in CACs than common colorectal cancers (CRCs). Somatic mutations of APC and KRAS were less prevalent (17 and 13 samples, respectively). Genes in the Wnt signaling pathway (APC, FBXW7, TCF7L2, and RNF43) were mutated in 31 samples, whereas those in the TGFβ pathway (TGFBR2, ACVR1B, SMAD2, SMAD4, LTBP4) were mutated in 25 samples. Mutational signature of CACs shows some differences from common CRCs.
Conclusion: Our results confirmed genetic differences for cancer development between CACs and common CRCs. Frequent TP53 mutations and less frequent APC mutations are consistent with the idea of “de novo” carcinogenesis than adenoma-carcinoma sequence. The association between the mutations and clinical information are also discussed.
Citation Format: Masashi Fujita, Nagahide Matsubara, Kazuhiro Maejima, Tomoki Yamano, Ikuo Matsuda, Seiichi Hirota, Hiroki Ikeuchi, Naohiro Tomita, Hidewaki Nakagawa. Genetic profiling of colitis-associated cancer indicates de novo carcinogenesis and the impact of chronic inflammation [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 1439. doi:10.1158/1538-7445.AM2017-1439
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Affiliation(s)
- Masashi Fujita
- 1RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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Itoh K, Mitsuoka T, Maejima K, Hiraga C, Nakano K. Comparison of faecal flora of cats based on different housing conditions with special reference to Bifidobacterium. Lab Anim 2016. [DOI: 10.1258/002367784780958303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Faecal flora of cats was compared in different colonies. In conventional cats there were no significant qualitative differences in composition of faecal flora in 3 colonies but there was variation in numbers of enterobacteriaceae, streptococci, bifidobacteria and clostridia, Bacteroidaceae and eubacteria were the most predominant nora followed by clostridia, streptococci and lactobacilli. In SPF cats produced by hysterectomy, the numbers of clostridia and enterobacteriaceae and the frequency of occurrence of staphylococci were higher than in conventional cats, and the numbers of bacterioidaceae and lactobacilli were much lower. 44 strains of bifidobacteria isolated from the faeces of cats were identified as Bifidobacterium adolescentis biovar b and d.
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Affiliation(s)
| | - T. Mitsuoka
- Animal Physiology Laboratory, The Institute of Physical and Chemical Research, Wako-shi, Saitama, 351, Japan; Department of Biomedical Science, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo, 113, Japan
| | - K. Maejima
- Laboratory Animal Centre, Keio University School of Medicine, Shinanomachi 35, Shinjuku, Tokyo 160, Japan
| | - C. Hiraga
- Department of Bacteriology, Saitama Medical School, Moroyama, Iruma-gun, Saitama,350-04, Japan
| | - K. Nakano
- Department of Laboratory Animal Science, School of Medicine, Kitasato University, 1-15-1, Kitasato, Sagamihara-shi, Kanagawa, 228, Japan
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Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi SI, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, Ohsawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Ohashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusaka T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamaue H, Chayama K, Miyano S, Aburatani H, Shibata T, Nakagawa H. Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet 2016; 48:700. [PMID: 27230686 DOI: 10.1038/ng0616-700a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ohtera A, Miyamae Y, Yoshida K, Maejima K, Akita T, Kakizuka A, Irie K, Masuda S, Kambe T, Nagao M. Identification of a New Type of Covalent PPARγ Agonist using a Ligand-Linking Strategy. ACS Chem Biol 2015; 10:2794-804. [PMID: 26414848 DOI: 10.1021/acschembio.5b00628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor that plays an important role in adipogenesis and glucose metabolism. The ligand-binding pocket (LBP) of PPARγ has a large Y-shaped cavity with multiple subpockets where multiple ligands can simultaneously bind and cooperatively activate PPARγ. Focusing on this unique property of the PPARγ LBP, we describe a novel two-step cell-based strategy to develop PPARγ ligands. First, a combination of ligands that cooperatively activates PPARγ was identified using a luciferase reporter assay. Second, hybrid ligands were designed and synthesized. For proof of concept, we focused on covalent agonists, which activate PPARγ through a unique activation mechanism regulated by a covalent linkage with the Cys285 residue in the PPARγ LBP. Despite their biological significance and pharmacological potential, few covalent PPARγ agonists are known except for endogenous fatty acid metabolites. With our strategy, we determined that plant-derived cinnamic acid derivatives cooperatively activated PPARγ by combining with GW9662, an irreversible antagonist. GW9662 covalently reacts with the Cys285 residue. A docking study predicted that a cinnamic acid derivative can bind to the open cavity in GW9662-bound PPARγ LBP. On the basis of the putative binding mode, structures of both ligands were linked successfully to create a potent PPARγ agonist, which enhanced the transactivation potential of PPARγ at submicromolar levels through covalent modification of Cys285. Our approach could lead to the discovery of novel high-potency PPARγ agonists.
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Affiliation(s)
| | | | | | | | - Toru Akita
- Nippon Shinyaku CO., LTD., Kyoto 601-8550, Japan
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Yoshimura M, Ninomiya K, Tagashira Y, Maejima K, Yoshida T, Amakura Y. Polyphenolic Constituents of the Pericarp of Mangosteen (Garcinia mangostana L.). J Agric Food Chem 2015; 63:7670-7674. [PMID: 26023815 DOI: 10.1021/acs.jafc.5b01771] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three new polyphenols, together with 14 known compounds, were isolated from a hot water extract of mangosteen (Garcinia mangostana L.) pericarp, a plant that has been used medicinally in Southeast Asia. The three new polyphenols were characterized as a 4-aryl-2-flavanylbenzopyran derivative (tentatively named GM-1), 1, 3,4,3',5'-tetrahydroxy-5-methoxybenzophenone (GM-2), 2, and 2,3-dihydrochromone derivative (GM-3), 3 on the basis of NMR and MS data. The relative stereostructure of GM-1 was assigned to have 2,3-cis-3,4-trans- and 2″,3″-cis configurations on the basis of the coupling constants of heterocyclic ring protons in the (1)H NMR spectrum along with nuclear Overhauser effect correlations. The HPLC analysis indicated that major polyphenolic components in the hot water extract of mangosteen pericarp were epicatechin and procyanidin B2 (epicatechin dimer).
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Affiliation(s)
- Morio Yoshimura
- College of Pharmaceutical Sciences, Matsuyama University , 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Kana Ninomiya
- College of Pharmaceutical Sciences, Matsuyama University , 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Yukari Tagashira
- Food Development Laboratory, Nippon Shinyaku Company, Ltd. , 14 Nishinosho-monguchi-cho, Kisshoin, Minami-ku, Kyoto 601-8550, Japan
| | - Kazuhiro Maejima
- Food Development Laboratory, Nippon Shinyaku Company, Ltd. , 14 Nishinosho-monguchi-cho, Kisshoin, Minami-ku, Kyoto 601-8550, Japan
| | - Takashi Yoshida
- College of Pharmaceutical Sciences, Matsuyama University , 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Yoshiaki Amakura
- College of Pharmaceutical Sciences, Matsuyama University , 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
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Ohno RI, Moroishi N, Sugawa H, Maejima K, Saigusa M, Yamanaka M, Nagai M, Yoshimura M, Amakura Y, Nagai R. Mangosteen pericarp extract inhibits the formation of pentosidine and ameliorates skin elasticity. J Clin Biochem Nutr 2015; 57:27-32. [PMID: 26236097 PMCID: PMC4512896 DOI: 10.3164/jcbn.15-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 01/22/2023] Open
Abstract
The inhibition of advanced glycation end-products (AGEs) by daily meals is believed to become an effective prevention for lifestyle-related diseases. In the present study, the inhibitory effect of hot water extracts of mangosteen (Garcinia mangostana L.) pericarp (WEM) on the formation of pentosidine, one of AGEs, in vitro and in vivo and the remedial effect on skin conditions were measured. WEM significantly inhibited pentosidine formation during gelatin incubation with ribose. Several compounds purified from WEM, such as garcimangosone D and rhodanthenone B, were identified as inhibitors of pentosidine formation. Oral administration of WEM at 100 mg/day to volunteer subjects for 3 months reduced the serum pentosidine contents. Because obtaining skin biopsies from healthy volunteers is ethically difficult, AGE accumulation in the skin was estimated by a fluorescence detector. The oral administration of WEM significantly reduced the skin autofluorescence intensity, demonstrating that WEM also reduced AGE accumulation in the skin. Furthermore, the elasticity and moisture content of the skin was also improved by WEM. These results demonstrate that intakes of WEM reduces the glycation stress and results in the improvement of skin conditions.
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Affiliation(s)
- Rei-Ichi Ohno
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan
| | - Narumi Moroishi
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan
| | - Hikari Sugawa
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan
| | - Kazuhiro Maejima
- Food Development Laboratories, Nippon Shinyaku Co., Ltd., 14 Nishinosho-monguchi-cho, Kisshoin, Minami-ku, Kyoto 601-8550, Japan
| | - Musashi Saigusa
- Food Development Laboratories, Nippon Shinyaku Co., Ltd., 14 Nishinosho-monguchi-cho, Kisshoin, Minami-ku, Kyoto 601-8550, Japan
| | - Mikihiro Yamanaka
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan ; Engineering Department 2, Product Development Center, New Business Development Division, SHARP Corporation, 2613-1 Ichinomoto-cho, Tenri, Nara 632-8567, Japan
| | - Mime Nagai
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan
| | - Morio Yoshimura
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama-shi, Ehime 790-8578, Japan
| | - Yoshiaki Amakura
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama-shi, Ehime 790-8578, Japan
| | - Ryoji Nagai
- Laboratory of Food and Regulation Biology, Graduate School of Agriculture, Tokai University, Kumamoto 869-1404, Japan
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Ohtera A, Miyamae Y, Nakai N, Kawachi A, Kawada K, Han J, Isoda H, Neffati M, Akita T, Maejima K, Masuda S, Kambe T, Mori N, Irie K, Nagao M. Identification of 6-octadecynoic acid from a methanol extract of Marrubium vulgare L. as a peroxisome proliferator-activated receptor γ agonist. Biochem Biophys Res Commun 2013; 440:204-9. [PMID: 24025677 DOI: 10.1016/j.bbrc.2013.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 10/26/2022]
Abstract
6-Octadecynoic acid (6-ODA), a fatty acid with a triple bond, was identified in the methanol extract of Marrubium vulgare L. as an agonist of peroxisome proliferator-activated receptor γ (PPARγ). Fibrogenesis caused by hepatic stellate cells is inhibited by PPARγ whose ligands are clinically used for the treatment of diabetes. Plant extracts of Marrubium vulgare L., were screened for activity to inhibit fibrosis in the hepatic stellate cell line HSC-T6 using Oil Red-O staining, which detects lipids that typically accumulate in quiescent hepatic stellate cells. A methanol extract with activity to stimulate accumulation of lipids was obtained. This extract was found to have PPARγ agonist activity using a luciferase reporter assay. After purification using several chromatographic methods, 6-ODA, a fatty acid with a triple bond, was identified as a candidate of PPARγ agonist. Synthesized 6-ODA and its derivative 9-octadecynoic acid (9-ODA), which both have a triple bond but in different positions, activated PPARγ in a luciferase reporter assay and increased lipid accumulation in 3T3-L1 adipocytes in a PPARγ-dependent manner. There is little information about the biological activity of fatty acids with a triple bond, and to our knowledge, this is the first report that 6-ODA and 9-ODA function as PPARγ agonists.
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Affiliation(s)
- Anna Ohtera
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Cho HS, Toyokawa G, Daigo Y, Hayami S, Masuda K, Ikawa N, Yamane Y, Maejima K, Tsunoda T, Field HI, Kelly JD, Neal DE, Ponder BAJ, Maehara Y, Nakamura Y, Hamamoto R. The JmjC domain-containing histone demethylase KDM3A is a positive regulator of the G1/S transition in cancer cells via transcriptional regulation of the HOXA1 gene. Int J Cancer 2012; 131:E179-89. [PMID: 22020899 DOI: 10.1002/ijc.26501] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/28/2011] [Indexed: 11/08/2022]
Abstract
A number of histone demethylases have been identified and biochemically characterized, yet their biological functions largely remain uncharacterized, particularly in the context of human diseases such as cancer. In this study, we describe important roles for the histone demethylase KDM3A, also known as JMJD1A, in human carcinogenesis. Expression levels of KDM3A were significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p < 0.0001), when assessed by real-time PCR. We confirmed that some other cancers including lung cancer also overexpressed KDM3A, using cDNA microarray analysis. Treatment of cancer cell lines with small interfering RNA targeting KDM3A significantly knocked down its expression and resulted in the suppression of proliferation. Importantly, we found that KDM3A activates transcription of the HOXA1 gene through demethylating histone H3 at lysine 9 di-methylation by binding to its promoter region. Indeed, expression levels of KDM3A and HOXA1 in several types of cancer cell lines and bladder cancer samples were statistically correlated. We observed the down-regulation of HOXA1 as well as CCND1 after treatment with KDM3A siRNA, indicating G(1) arrest of cancer cells. Together, our results suggest that elevated expression of KDM3A plays a critical role in the growth of cancer cells, and further studies may reveal a cancer therapeutic potential in KDM3A inhibition.
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Affiliation(s)
- Hyun-Soo Cho
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
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Takawa M, Cho HS, Hayami S, Toyokawa G, Kogure M, Yamane Y, Iwai Y, Maejima K, Ueda K, Masuda A, Dohmae N, Field HI, Tsunoda T, Kobayashi T, Akasu T, Sugiyama M, Ohnuma SI, Atomi Y, Ponder BAJ, Nakamura Y, Hamamoto R. Histone lysine methyltransferase SETD8 promotes carcinogenesis by deregulating PCNA expression. Cancer Res 2012; 72:3217-27. [PMID: 22556262 DOI: 10.1158/0008-5472.can-11-3701] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the physiologic significance of lysine methylation of histones is well known, whether lysine methylation plays a role in the regulation of nonhistone proteins has not yet been examined. The histone lysine methyltransferase SETD8 is overexpressed in various types of cancer and seems to play a crucial role in S-phase progression. Here, we show that SETD8 regulates the function of proliferating cell nuclear antigen (PCNA) protein through lysine methylation. We found that SETD8 methylated PCNA on lysine 248, and either depletion of SETD8 or substitution of lysine 248 destabilized PCNA expression. Mechanistically, lysine methylation significantly enhanced the interaction between PCNA and the flap endonuclease FEN1. Loss of PCNA methylation retarded the maturation of Okazaki fragments, slowed DNA replication, and induced DNA damage, and cells expressing a methylation-inactive PCNA mutant were more susceptible to DNA damage. An increase of methylated PCNA was found in cancer cells, and the expression levels of SETD8 and PCNA were correlated in cancer tissue samples. Together, our findings reveal a function for lysine methylation on a nonhistone protein and suggest that aberrant lysine methylation of PCNA may play a role in human carcinogenesis.
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Affiliation(s)
- Masashi Takawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, and National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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Cho HS, Hayami S, Toyokawa G, Maejima K, Yamane Y, Suzuki T, Dohmae N, Kogure M, Kang D, Neal DE, Ponder BAJ, Yamaue H, Nakamura Y, Hamamoto R. RB1 methylation by SMYD2 enhances cell cycle progression through an increase of RB1 phosphorylation. Neoplasia 2012; 14:476-86. [PMID: 22787429 PMCID: PMC3394190 DOI: 10.1593/neo.12656] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/05/2012] [Accepted: 05/07/2012] [Indexed: 12/13/2022]
Abstract
It is well known that RB functions are regulated by posttranslational modifications such as phosphorylation and acetylation, but the significance of lysine methylation on RB has not been fully elucidated. Our expression analysis of SMYD2 by quantitative real-time polymerase chain reaction showed that expression levels of SMYD2 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (P < .0001), and its expression levels in tumor tissues were much higher than those of any other normal tissues. SMYD2 knockdown resulted in the suppression of cancer cell growth, and cell cycle analysis indicated that SMYD2 might play a crucial role in the G(1)/S transition. According to an in vitro methyltransferase assay, we found that SMYD2 methylates RB1 protein, and liquid chromatography-tandem mass spectrometry analysis revealed lysine 810 of RB1 to be methylated by SMYD2. Importantly, this methylation enhanced Ser 807/811 phosphorylation of RB1 both in vitro and in vivo. Furthermore, we demonstrated that methylated RB1 accelerates E2F transcriptional activity and promotes cell cycle progression. SMYD2 is an important oncoprotein in various types of cancer, and SMYD2-dependent RB1 methylation at lysine 810 promotes cell cycle progression of cancer cells. Further study may explore SMYD2-dependent RB1 methylation as a potential therapeutic target in human cancer.
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Affiliation(s)
- Hyun-Soo Cho
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinya Hayami
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Gouji Toyokawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuka Yamane
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Naoshi Dohmae
- Biomolecular Characterization Team, RIKEN, Saitama, Japan
| | - Masaharu Kogure
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daechun Kang
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - David E Neal
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Bruce AJ Ponder
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Hiroki Yamaue
- Second Department of Surgery, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ryuji Hamamoto
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
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Toyokawa G, Cho HS, Iwai Y, Yoshimatsu M, Takawa M, Hayami S, Maejima K, Shimizu N, Tanaka H, Tsunoda T, Field HI, Kelly JD, Neal DE, Ponder BAJ, Maehara Y, Nakamura Y, Hamamoto R. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Cancer Prev Res (Phila) 2011; 4:2051-61. [PMID: 21930796 DOI: 10.1158/1940-6207.capr-11-0290] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Histone methyltransferases and demethylases are known to regulate transcription by altering the epigenetic marks on histones, but the pathologic roles of their dysfunction in human diseases, such as cancer, still remain to be elucidated. Herein, we show that the histone demethylase JMJD2B is involved in human carcinogenesis. Quantitative real-time PCR showed notably elevated levels of JMJD2B expression in bladder cancers, compared with corresponding nonneoplastic tissues (P < 0.0001), and elevated protein expression was confirmed by immunohistochemistry. In addition, cDNA microarray analysis revealed transactivation of JMJD2B in lung cancer, and immunohistochemical analysis showed protein overexpression in lung cancer. siRNA-mediated reduction of expression of JMJD2B in bladder and lung cancer cell lines significantly suppressed the proliferation of cancer cells, and suppressing JMJD2B expression lead to a decreased population of cancer cells in S phase, with a concomitant increase of cells in G(1) phase. Furthermore, a clonogenicity assay showed that the demethylase activity of JMJD2B possesses an oncogenic activity. Microarray analysis after knockdown of JMJD2B revealed that JMJD2B could regulate multiple pathways which contribute to carcinogenesis, including the cell-cycle pathway. Of the downstream genes, chromatin immunoprecipitation showed that CDK6 (cyclin-dependent kinase 6), essential in G(1)-S transition, was directly regulated by JMJD2B, via demethylation of histone H3-K9 in its promoter region. Expression levels of JMJD2B and CDK6 were significantly correlated in various types of cell lines. Deregulation of histone demethylation resulting in perturbation of the cell cycle, represents a novel mechanism for human carcinogenesis and JMJD2B is a feasible molecular target for anticancer therapy.
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Affiliation(s)
- Gouji Toyokawa
- 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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Takawa M, Masuda K, Kunizaki M, Daigo Y, Takagi K, Iwai Y, Cho HS, Toyokawa G, Yamane Y, Maejima K, Field HI, Kobayashi T, Akasu T, Sugiyama M, Tsuchiya E, Atomi Y, Ponder BAJ, Nakamura Y, Hamamoto R. Validation of the histone methyltransferase EZH2 as a therapeutic target for various types of human cancer and as a prognostic marker. Cancer Sci 2011; 102:1298-305. [PMID: 21539681 DOI: 10.1111/j.1349-7006.2011.01958.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The emphasis in anticancer drug discovery has always been on finding a drug with great antitumor potential but few side-effects. This can be achieved if the drug is specific for a molecular site found only in tumor cells. Here, we find the enhancer of zeste homolog 2 (EZH2) to be highly overexpressed in lung and other cancers, and show that EZH2 is integral to proliferation in cancer cells. Quantitative real-time PCR analysis revealed higher expression of EZH2 in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P < 0.0001), and we confirmed that a wide range of cancers also overexpress EZH2, using cDNA microarray analysis. Immunohistochemical analysis showed positive staining for EZH2 in 14 of 29 cases of bladder cancer, 135 of 292 cases of non-small-cell lung cancer (NSCLC), and 214 of 245 cases of colorectal cancer, whereas no significant staining was observed in various normal tissues. We found elevated expression of EZH2 to be associated with poor prognosis for patients with NSCLC (P = 0.0239). In lung and bladder cancer cells overexpressing EZH2, suppression of EZH2 using specific siRNAs inhibited incorporation of BrdU and resulted in significant suppression of cell growth, even though no significant effect was observed in the normal cell strain CCD-18Co, which has undetectable EZH2. Because EZH2 expression was scarcely detectable in all normal tissues we examined, EZH2 shows promise as a tumor-specific therapeutic target. Furthermore, as elevated levels of EZH2 are associated with poor prognosis of patients with NSCLC, its overexpression in resected specimens could prove a useful molecular marker, indicating the necessity for a more extensive follow-up in some lung cancer patients after surgical treatment.
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Affiliation(s)
- Masashi Takawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
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Toyokawa G, Masuda K, Daigo Y, Cho HS, Yoshimatsu M, Takawa M, Hayami S, Maejima K, Chino M, Field HI, Neal DE, Tsuchiya E, Ponder BAJ, Maehara Y, Nakamura Y, Hamamoto R. Minichromosome Maintenance Protein 7 is a potential therapeutic target in human cancer and a novel prognostic marker of non-small cell lung cancer. Mol Cancer 2011; 10:65. [PMID: 21619671 PMCID: PMC3125391 DOI: 10.1186/1476-4598-10-65] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 05/28/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The research emphasis in anti-cancer drug discovery has always been to search for a drug with the greatest antitumor potential but fewest side effects. This can only be achieved if the drug used is against a specific target located in the tumor cells. In this study, we evaluated Minichromosome Maintenance Protein 7 (MCM7) as a novel therapeutic target in cancer. RESULTS Immunohistochemical analysis showed that MCM7 was positively stained in 196 of 331 non-small cell lung cancer (NSCLC), 21 of 29 bladder tumor and 25 of 70 liver tumor cases whereas no significant staining was observed in various normal tissues. We also found an elevated expression of MCM7 to be associated with poor prognosis for patients with NSCLC (P = 0.0055). qRT-PCR revealed a higher expression of MCM7 in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P < 0.0001), and we confirmed that a wide range of cancers also overexpressed MCM7 by cDNA microarray analysis. Suppression of MCM7 using specific siRNAs inhibited incorporation of BrdU in lung and bladder cancer cells overexpressing MCM7, and suppressed the growth of those cells more efficiently than that of normal cell strains expressing lower levels of MCM7. CONCLUSIONS Since MCM7 expression was generally low in a number of normal tissues we examined, MCM7 has the characteristics of an ideal candidate for molecular targeted cancer therapy in various tumors and also as a good prognostic biomarker for NSCLC patients.
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Affiliation(s)
- Gouji Toyokawa
- 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
- Department of Surgery and Science, Graduate School of Medical Science, Kyusyu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ken Masuda
- 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
| | - Yataro Daigo
- 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
- Department of Medical Oncology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Hyun-Soo Cho
- 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
| | - Masanori Yoshimatsu
- 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
- Department of Surgery and Science, Graduate School of Medical Science, Kyusyu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masashi Takawa
- 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
| | - Shinya Hayami
- 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
| | - Kazuhiro Maejima
- 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
| | - Makoto Chino
- Specialty Chemicals & International Division Pharmaceuticals Group, Nippon Kayaku Co., Ltd., 11-2, Fujimi 1 Chome, Chiyoda-ku, Tokyo, 102-8172, Japan
| | - Helen I Field
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - David E Neal
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eiju Tsuchiya
- Department of Pathology, Saitama Cancer Center, Saitama 362-0806, Japan
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa 241-0815, Japan
| | - Bruce AJ Ponder
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Science, Kyusyu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Nakamura
- 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
| | - Ryuji Hamamoto
- 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
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
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Uheda E, Maejima K. Inhibition of nitrogen-fixing activity of the cyanobiont affects the localization of glutamine synthetase in hair cells of Azolla. J Plant Physiol 2009; 166:1705-1709. [PMID: 19464754 DOI: 10.1016/j.jplph.2009.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 04/14/2009] [Accepted: 04/14/2009] [Indexed: 05/27/2023]
Abstract
In the Azolla-Anabaena association, the host plant Azolla efficiently incorporates and assimilates ammonium ions that are released from the nitrogen-fixing cyanobiont, probably via glutamine synthetase (GS; EC 6.3.1.2) in hair cells, which are specialized cells protruding into the leaf cavity. In order to clarify the regulatory mechanism underlying ammonium assimilation in the Azolla-Anabaena association, Azolla plants were grown under an argon environment (Ar), in which the nitrogen-fixing activity of the cyanobiont was inhibited specifically and completely. The localization of GS in hair cells was determined by immunoelectron microscopy and quantitative analysis of immunogold labeling. Azolla plants grew healthily under Ar when nitrogen sources, such as NO(3)(-) and NH(4)(+), were provided in the growth medium. Both the number of cyanobacterial cells per leaf and the heterocyst frequency of the plants under Ar were similar to those of plants in a nitrogen environment (N(2)). In hair cells of plants grown under Ar, regardless of the type of nitrogen source provided, only weak labeling of GS was observed in the cytoplasm and in chloroplasts. In contrast, in hair cells of plants grown under N(2), abundant labeling of GS was observed in both sites. These findings indicate that specific inhibition of the nitrogen-fixing activity of the cyanobiont affects the localization of GS isoenzymes. Ammonium fixed and released by the cyanobiont could stimulate GS synthesis in hair cells. Simultaneously, the abundant GS, probably GS1, in these cells, could assimilate ammonium rapidly.
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Affiliation(s)
- Eiji Uheda
- Department of Biological Sciences, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-2, Minami-ku, Sakai, Osaka 599-8570, Japan.
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Maejima K, Himeno M, Komatsu K, Kakizawa S, Yamaji Y, Hamamoto H, Namba S. Complete nucleotide sequence of a new double-stranded RNA virus from the rice blast fungus, Magnaporthe oryzae. Arch Virol 2007; 153:389-91. [DOI: 10.1007/s00705-007-1101-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Accepted: 09/28/2007] [Indexed: 10/22/2022]
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