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Zaimoku Y, Katagiri T, Nakagawa N, Imi T, Maruyama H, Takamatsu H, Ishiyama K, Yamazaki H, Miyamoto T, Nakao S. HLA Class I Allele Loss and Bone Marrow Transplantation Outcomes in Immune Aplastic Anemia. Transplant Cell Ther 2024; 30:281.e1-281.e13. [PMID: 37972732 DOI: 10.1016/j.jtct.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/23/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
In patients with immune-mediated acquired aplastic anemia (AA), HLA class I alleles often disappear from the surface of hematopoietic progenitor cells, potentially enabling evasion from cytotoxic T lymphocyte-mediated pathogenesis. Although HLA class I allele loss has been studied in AA patients treated with immunosuppressive therapy (IST), its impact on allogeneic bone marrow transplantation (BMT) has not been thoroughly investigated. The purpose of this study was to evaluate the clinical implications of HLA class I allele loss in patients with acquired AA undergoing allogeneic BMT. The study enrolled acquired AA patients who underwent initial BMT from unrelated donors through the Japan Marrow Donor Program between 1993 and 2011. The presence of HLA class I allele loss due to loss of heterozygosity (HLA-LOH) was assessed using pretransplantation blood DNA and correlated with clinical data obtained from the Japanese Transplant Registry Unified Management Program. A total of 432 patients with acquired AA were included in the study, and HLA-LOH was detected in 20 of the 178 patients (11%) available for analysis. Patients with HLA-LOH typically presented with more severe AA at diagnosis (P = .017) and underwent BMT earlier (P < .0001) compared to those without HLA-LOH. They also showed a slight but significant recovery in platelet count from the time of diagnosis to BMT (P = .00085). However, HLA-LOH status had no significant effect on survival, engraftment, graft failure, chimerism status, graft-versus-host disease, or other complications following BMT, even when the 20 HLA-LOH+ patients were compared with the 40 propensity score-matched HLA-LOH- patients. Nevertheless, patients lacking HLA-A*02:06 or HLA-B*40:02, the alleles most frequently lost and associated with a better IST response, showed higher survival rates compared to those lacking other alleles, with estimated 5-year overall survival (OS) rates of 100% and 44%, respectively (P = .0042). In addition, in a specific subset of HLA-LOH- patients showing clinical features similar to HLA-LOH+ patients, the HLA-A*02:06 and HLA-B*40:02 allele genotypes correlated with better survival rates compared with other allele genotypes, with estimated 5-year OS rates of 100% and 43%, respectively (P = .0096). However, this genotype correlation did not extend to all patients, suggesting that immunopathogenic mechanisms linked to the loss of certain HLA alleles, rather than the HLA genotypes themselves, influence survival outcomes. The survival benefit associated with the loss of these two alleles was confirmed in a multivariable Cox regression model. The observed correlations between HLA loss and the pretransplantation clinical manifestations and between loss of specific HLA class I alleles and survival outcomes in AA patients may improve patient selection for unrelated BMT and facilitate further investigations into the immune pathophysiology of the disease.
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Affiliation(s)
- Yoshitaka Zaimoku
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan; Department of Infection Control and Prevention, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan.
| | - Takamasa Katagiri
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Noriharu Nakagawa
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Tatsuya Imi
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Maruyama
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Takamatsu
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan; Faculty of Transdisciplinary Sciences for Innovation, Institute of Transdisciplinary Sciences for Innovation, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ken Ishiyama
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Hirohito Yamazaki
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan; Division of Transfusion Medicine, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Toshihiro Miyamoto
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Shinji Nakao
- Department of Hematology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan; Japanese Red Cross Ishikawa Blood Center, Kanazawa, Ishikawa, Japan
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2
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Djos A, Treis D, Fransson S, Gordon Murkes L, Wessman S, Ásmundsson J, Markström A, Kogner P, Martinsson T. Multifocal Neuroblastoma and Central Hypoventilation in An Infant with Germline ALK F1174I Mutation. Diagnostics (Basel) 2022; 12:diagnostics12092260. [PMID: 36140661 PMCID: PMC9498070 DOI: 10.3390/diagnostics12092260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
A preterm infant with central hypoventilation was diagnosed with multifocal neuroblastoma. Congenital anomalies of the autonomic nervous system in association with neuroblastoma are commonly associated with germline mutations in PHOX2B. Further, the ALK gene is frequently mutated in both familial and sporadic neuroblastoma. Sanger sequencing of ALK and PHOX2B, SNP microarray of three tumor samples and whole genome sequencing of tumor and blood were performed. Genetic testing revealed a germline ALK F1174I mutation that was present in all tumor samples as well as in normal tissue samples from the patient. Neither of the patient’s parents presented the ALK variant. Array profiling of the three tumor samples showed that two of them had only numerical aberrations, whereas one sample displayed segmental alterations, including a gain at chromosome 2p, resulting in two copies of the ALK-mutated allele. Whole genome sequencing confirmed the presence of the ALK variant and did not detect any aberrations in the coding or promotor region of PHOX2B. This study is to our knowledge the first to report a de novoALK F1174I germline mutation. This may not only predispose to congenital multifocal neuroblastoma but may also contribute to the respiratory dysfunction seen in this patient.
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Affiliation(s)
- Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Diana Treis
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lena Gordon Murkes
- Department of Pediatric Radiology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Sandra Wessman
- Department of Clinical Pathology, Karolinska University Hospital, 141 86 Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Jurate Ásmundsson
- Pathology Department, Landspitali University Hospital, 101 Reykjavík, Iceland
| | - Agneta Markström
- Pediatric Neurology, Department of Women’s and Children’s Health, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 141 86 Stockholm, Sweden
- Correspondence: (P.K.); (T.M.)
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence: (P.K.); (T.M.)
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3
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Bokhari A, Lai W, Le A, Gabre J, Chung TP, Fransson S, Bergman B, Djos A, Chen N, Martinsson T, Van den Eynden J, Doebele R, Palmer R, Hallberg B, Umapathy G. Novel Human-derived EML4-ALK Fusion Cell Lines identify ribonucleotide reductase RRM2 as a target of activated ALK in NSCLC. Lung Cancer 2022; 171:103-114. [DOI: 10.1016/j.lungcan.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022]
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4
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In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations. Eur J Cancer 2022; 170:27-41. [DOI: 10.1016/j.ejca.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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Honda T, Yamaoka M, Terao YM, Hasegawa D, Kumamoto T, Takagi M, Yoshida K, Ogawa S, Goto H, Akiyama M. Successful treatment of hepatosplenic T-cell lymphoma with fludarabine, high-dose cytarabine and subsequent unrelated umbilical cord blood transplantation. Int J Hematol 2022; 115:140-145. [PMID: 34591292 DOI: 10.1007/s12185-021-03229-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Hepatosplenic T-cell lymphoma (HSTCL) is a rare subtype of peripheral T-cell lymphoma that occurs most often in adolescents and young adults and is rare in children. Because of the aggressive clinical course, resistance to conventional chemotherapy and poor prognosis of HSTCL, an effective treatment has not been established. We report the case of a 3-year-old girl with HSTCL presenting with trilineage myelodysplasia. Although the HSTCL was refractory to conventional chemotherapy, remission was achieved with salvage chemotherapy that included fludarabine and cytarabine, which were shown to be effective in the drug sensitivity assay. After undergoing umbilical cord blood transplantation with a conditioning regimen consisting of etoposide, cyclophosphamide and total body irradiation, the patient has remained in complete remission for 8 years. Single-nucleotide polymorphism array analysis revealed heterozygous deletions of PAX5 (9p), ETV6 (12p) and homozygous deletions of CDKN2A (9p). Exome analysis showed a heterozygous nonsense c.2961C>G (p.Tyr987Ter) variant of the KMT2C gene. To improve the poor prognosis of HSTCL, the chemotherapeutic regimen can be selected for each patient on the basis of drug sensitivity and molecular genetic characteristics.
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Affiliation(s)
- Takaya Honda
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Masayoshi Yamaoka
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Yoko Mikami Terao
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Tadashi Kumamoto
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan.
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7
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Aoki K, Suzuki H, Yamamoto T, Yamamoto KN, Maeda S, Okuno Y, Ranjit M, Motomura K, Ohka F, Tanahashi K, Hirano M, Nishikawa T, Shimizu H, Kitano Y, Yamaguchi J, Yamazaki S, Nakamura H, Takahashi M, Narita Y, Nakada M, Deguchi S, Mizoguchi M, Momii Y, Muragaki Y, Abe T, Akimoto J, Wakabayashi T, Saito R, Ogawa S, Haeno H, Natsume A. Mathematical Modeling and Mutational Analysis Reveal Optimal Therapy to Prevent Malignant Transformation in Grade II IDH-Mutant Gliomas. Cancer Res 2021; 81:4861-4873. [PMID: 34333454 PMCID: PMC9635454 DOI: 10.1158/0008-5472.can-21-0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/10/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023]
Abstract
Isocitrate dehydrogenase-mutant low-grade gliomas (IDHmut-LGG) grow slowly but frequently undergo malignant transformation, which eventually leads to premature death. Chemotherapy and radiotherapy treatments prolong survival, but can also induce genetic (or epigenetic) alterations involved in transformation. Here, we developed a mathematical model of tumor progression based on serial tumor volume data and treatment history of 276 IDHmut-LGGs classified by chromosome 1p/19q codeletion (IDHmut/1p19qcodel and IDHmut/1p19qnoncodel) and performed genome-wide mutational analyses, including targeted sequencing and longitudinal whole-exome sequencing data. These analyses showed that tumor mutational burden correlated positively with malignant transformation rate, and chemotherapy and radiotherapy significantly suppressed tumor growth but increased malignant transformation rate per cell by 1.8 to 2.8 times compared with before treatment. This model revealed that prompt adjuvant chemoradiotherapy prolonged malignant transformation-free survival in small IDHmut-LGGs (≤ 50 cm3). Furthermore, optimal treatment differed according to genetic alterations for large IDHmut-LGGs (> 50 cm3); adjuvant therapies delayed malignant transformation in IDHmut/1p19qnoncodel but often accelerated it in IDHmut/1p19qcodel. Notably, PI3K mutation was not associated with malignant transformation but increased net postoperative proliferation rate and decreased malignant transformation-free survival, prompting the need for adjuvant therapy in IDHmut/1p19qcodel. Overall, this model uncovered therapeutic strategies that could prevent malignant transformation and, consequently, improve overall survival in patients with IDHmut-LGGs. SIGNIFICANCE: A mathematical model successfully estimates malignant transformation-free survival and reveals a link between genetic alterations and progression, identifying precision medicine approaches for optimal treatment of IDH-mutant low-grade gliomas.
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Affiliation(s)
- Kosuke Aoki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Hiromichi Suzuki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Yamamoto
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kimiyo N. Yamamoto
- Departments of General and Gastroenterological Surgery, Osaka Medical College Hospital, Takatsuki-shi, Osaka, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,Department of Virology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Melissa Ranjit
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Kuniaki Tanahashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Masaki Hirano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Tomohide Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hiroyuki Shimizu
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Shintaro Yamazaki
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan.,Department of Neurosurgery, Kurume University, Kurume, Fukuoka, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shoichi Deguchi
- Division of Neurosurgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences Kyushu University, Fukuoka, Japan
| | - Yasutomo Momii
- Department of Neurosurgery, Oita University, Yufu, Oita, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Tatsuya Abe
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Jiro Akimoto
- Department of Neurosurgery, Tokyo Medical University, Tokyo, Japan
| | - Toshihiko Wakabayashi
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Haeno
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
| | - Atsushi Natsume
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi, Japan.,Corresponding Authors: Kosuke Aoki, Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Nagoya 4668550, Japan. Phone: 815-2744-2353; E-mail: ; Hiroshi Haeno, ; and Atsushi Natsume,
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8
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Fujii Y, Sato Y, Suzuki H, Kakiuchi N, Yoshizato T, Lenis AT, Maekawa S, Yokoyama A, Takeuchi Y, Inoue Y, Ochi Y, Shiozawa Y, Aoki K, Yoshida K, Kataoka K, Nakagawa MM, Nannya Y, Makishima H, Miyakawa J, Kawai T, Morikawa T, Shiraishi Y, Chiba K, Tanaka H, Nagae G, Sanada M, Sugihara E, Sato TA, Nakagawa T, Fukayama M, Ushiku T, Aburatani H, Miyano S, Coleman JA, Homma Y, Solit DB, Kume H, Ogawa S. Molecular classification and diagnostics of upper urinary tract urothelial carcinoma. Cancer Cell 2021; 39:793-809.e8. [PMID: 34129823 PMCID: PMC9110171 DOI: 10.1016/j.ccell.2021.05.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/11/2020] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Upper urinary tract urothelial carcinoma (UTUC) is one of the common urothelial cancers. Its molecular pathogenesis, however, is poorly understood, with no useful biomarkers available for accurate diagnosis and molecular classification. Through an integrated genetic study involving 199 UTUC samples, we delineate the landscape of genetic alterations in UTUC enabling genetic/molecular classification. According to the mutational status of TP53, MDM2, RAS, and FGFR3, UTUC is classified into five subtypes having discrete profiles of gene expression, tumor location/histology, and clinical outcome, which is largely recapitulated in an independent UTUC cohort. Sequencing of urine sediment-derived DNA has a high diagnostic value for UTUC with 82.2% sensitivity and 100% specificity. These results provide a solid basis for better diagnosis and management of UTUC.
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Affiliation(s)
- Yoichi Fujii
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Andrew T Lenis
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shigekatsu Maekawa
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Akira Yokoyama
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhide Takeuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yoshikage Inoue
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Aoki
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Masahiro M Nakagawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Jimpei Miyakawa
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Taketo Kawai
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Teppei Morikawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Eiji Sugihara
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8550, Japan
| | - Taka-Aki Sato
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8550, Japan
| | - Tohru Nakagawa
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Urology, Teikyo University School of Medicine, Tokyo 173-8606, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Urology, Japanese Red Cross Medical Center, Tokyo 150-8935, Japan
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 17177, Sweden.
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9
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Siaw JT, Javanmardi N, Van den Eynden J, Lind DE, Fransson S, Martinez-Monleon A, Djos A, Sjöberg RM, Östensson M, Carén H, Trøen G, Beiske K, Berbegall AP, Noguera R, Lai WY, Kogner P, Palmer RH, Hallberg B, Martinsson T. 11q Deletion or ALK Activity Curbs DLG2 Expression to Maintain an Undifferentiated State in Neuroblastoma. Cell Rep 2021; 32:108171. [PMID: 32966799 DOI: 10.1016/j.celrep.2020.108171] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/09/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
High-risk neuroblastomas typically display an undifferentiated or poorly differentiated morphology. It is therefore vital to understand molecular mechanisms that block the differentiation process. We identify an important role for oncogenic ALK-ERK1/2-SP1 signaling in the maintenance of undifferentiated neural crest-derived progenitors through the repression of DLG2, a candidate tumor suppressor gene in neuroblastoma. DLG2 is expressed in the murine "bridge signature" that represents the transcriptional transition state when neural crest cells or Schwann cell precursors differentiate to chromaffin cells of the adrenal gland. We show that the restoration of DLG2 expression spontaneously drives neuroblastoma cell differentiation, highlighting the importance of DLG2 in this process. These findings are supported by genetic analyses of high-risk 11q deletion neuroblastomas, which identified genetic lesions in the DLG2 gene. Our data also suggest that further exploration of other bridge genes may help elucidate the mechanisms underlying the differentiation of NC-derived progenitors and their contribution to neuroblastomas.
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Affiliation(s)
- Joachim Tetteh Siaw
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Niloufar Javanmardi
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden
| | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, 9000 Ghent, Belgium
| | - Dan Emil Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden
| | - Angela Martinez-Monleon
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden
| | - Rose-Marie Sjöberg
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden
| | - Malin Östensson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gunhild Trøen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Klaus Beiske
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia/CIBER of Cancer, Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia/CIBER of Cancer, Madrid, Spain
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530 Gothenburg, Sweden.
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10
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Haruta M, Arai Y, Okita H, Tanaka Y, Takimoto T, Kamijo T, Oue T, Souzaki R, Taguchi T, Kuwahara Y, Chin M, Nakadate H, Hiyama E, Ishida Y, Koshinaga T, Kaneko Y. Frequent breakpoints of focal deletion and uniparental disomy in 22q11.1 or 11.2 segmental duplication region reveal distinct tumorigenesis in rhabdoid tumor of the kidney. Genes Chromosomes Cancer 2021; 60:546-558. [PMID: 33896058 DOI: 10.1002/gcc.22952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
SMARCB1 is mutated in most rhabdoid tumors (RTs) developing in the kidney (RTK) and various other organs. Focal deletions found in patients with 22q11.2 deletion syndrome show breakpoints within clusters of segmental duplications (SDs), and those in some RTs show breakpoints in the 22q11-q12 region. SDs are known to cause focal deletion mediated by non-allelic homologous recombination. The present study identified SMARCB1 alterations in all 30 RTKs, using SNP array CGH, MLPA, and sequence analyses. Twenty-eight tumors had a total of 51 breakpoints forming focal 22q deletion and/or uniparental disomy (22qUPD), and the other two had compound mutation with no breakpoints in 22q. Twenty-four (47.1%) of the 51 breakpoints were within SDs, and occurred in 16 (53.3%) of the 30 tumors. The association of breakpoints with SDs was found not only in focal deletion, but also in 22qUPD, indicating that SDs mediate the first and second hits (focal deletion) and the second hit (22qUPD) of SMARCB1 alteration. Of the 51 breakpoints, 14 were recurrent, and 10 of the 14 were within SDs, suggesting the presence of hotspots in the 22q11.2 region. One recurrent breakpoint outside SDs resided in SMARCB1, suggesting inactivation of the gene by out-of-frame fusion. The association between SDs and focal deletion has been reported in two other types of cancer. RTKs may be the third example of SD-associated tumors. Thus, the present study indicated that RTKs exploit genomic instability in the 22q11.1-11.2 SDs region, and 22qUPD caused by mitotic recombination may also be mediated by SDs.
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Affiliation(s)
- Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Yasuhito Arai
- Cancer Genomics Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Tetsuya Takimoto
- Department of Childhood Cancer Data Management, Childhood Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Takaharu Oue
- Department of Pediatric Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Ryota Souzaki
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Motoaki Chin
- Department of Pediatrics, Nihon University School of Medicine, Tokyo, Japan
| | - Hisaya Nakadate
- Division of Hematology, National Center for Child Health and Development, Tokyo, Japan
| | - Eiso Hiyama
- Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Yasushi Ishida
- Pediatric Medical Center, Ehime Prefectural Central Hospital, Matsuyama, Ehime, Japan
| | - Tsugumichi Koshinaga
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Yasuhiko Kaneko
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
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11
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Inagaki-Kawata Y, Yoshida K, Kawaguchi-Sakita N, Kawashima M, Nishimura T, Senda N, Shiozawa Y, Takeuchi Y, Inoue Y, Sato-Otsubo A, Fujii Y, Nannya Y, Suzuki E, Takada M, Tanaka H, Shiraishi Y, Chiba K, Kataoka Y, Torii M, Yoshibayashi H, Yamagami K, Okamura R, Moriguchi Y, Kato H, Tsuyuki S, Yamauchi A, Suwa H, Inamoto T, Miyano S, Ogawa S, Toi M. Genetic and clinical landscape of breast cancers with germline BRCA1/2 variants. Commun Biol 2020; 3:578. [PMID: 33067557 PMCID: PMC7567851 DOI: 10.1038/s42003-020-01301-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/15/2020] [Indexed: 12/24/2022] Open
Abstract
The genetic and clinical characteristics of breast tumors with germline variants, including their association with biallelic inactivation through loss-of-heterozygosity (LOH) and second somatic mutations, remain elusive. We analyzed germline variants of 11 breast cancer susceptibility genes for 1,995 Japanese breast cancer patients, and identified 101 (5.1%) pathogenic variants, including 62 BRCA2 and 15 BRCA1 mutations. Genetic analysis of 64 BRCA1/2-mutated tumors including TCGA dataset tumors, revealed an association of biallelic inactivation with more extensive deletions, copy neutral LOH, gain with LOH and younger onset. Strikingly, TP53 and RB1 mutations were frequently observed in BRCA1- (94%) and BRCA2- (9.7%) mutated tumors with biallelic inactivation. Inactivation of TP53 and RB1 together with BRCA1 and BRCA2, respectively, involved LOH of chromosomes 17 and 13. Notably, BRCA1/2 tumors without biallelic inactivation were indistinguishable from those without germline variants. Our study highlights the heterogeneity and unique clonal selection pattern in breast cancers with germline variants. Yukiko Inagaki-Kawata et al. report an analysis of germline variants in breast cancer susceptibility genes in 1,995 Japanese breast cancer patients. They find that 5.1% of the patients carry germline variants in cancer-linked genes and investigate the characteristics of patients with germline mutations in BRCA1/2.
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Affiliation(s)
- Yukiko Inagaki-Kawata
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | | | - Tomomi Nishimura
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Noriko Senda
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yasuhide Takeuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Diagnostic Pathology, Kyoto University, Kyoto, Japan
| | - Yoshikage Inoue
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Aiko Sato-Otsubo
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Masahiro Takada
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Centre, 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
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuki Kataoka
- Hospital Care Research Unit/Department of Respiratory Medicine, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Masae Torii
- Department of Breast Surgery, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | - Hiroshi Yoshibayashi
- Department of Breast Surgery, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | | | - Ryuji Okamura
- Department of Breast Surgery, Yamatotakada Municipal Hospital, Yamatotakada, Japan
| | | | - Hironori Kato
- Department of Breast Surgery, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Shigeru Tsuyuki
- Department of Breast Surgery, Osaka Red Cross Hospital, Osaka, Japan
| | - Akira Yamauchi
- Department of Breast Surgery, Kitano Hospital, Osaka, Japan
| | - Hirofumi Suwa
- Department of Breast Surgery, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | | | - Satoru Miyano
- Laboratory of Sequence Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan. .,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan. .,Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Masakazu Toi
- Department of Breast Surgery, Kyoto University, Kyoto, Japan.
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12
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Sekiguchi M, Seki M, Kawai T, Yoshida K, Yoshida M, Isobe T, Hoshino N, Shirai R, Tanaka M, Souzaki R, Watanabe K, Arakawa Y, Nannya Y, Suzuki H, Fujii Y, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Sato Y, Sato-Otsubo A, Kimura S, Kubota Y, Hiwatari M, Koh K, Hayashi Y, Kanamori Y, Kasahara M, Kohashi K, Kato M, Yoshioka T, Matsumoto K, Oka A, Taguchi T, Sanada M, Tanaka Y, Miyano S, Hata K, Ogawa S, Takita J. Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets. NPJ Precis Oncol 2020; 4:20. [PMID: 32656360 PMCID: PMC7341754 DOI: 10.1038/s41698-020-0125-y] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although hepatoblastoma is the most common pediatric liver cancer, its genetic heterogeneity and therapeutic targets are not well elucidated. Therefore, we conducted a multiomics analysis, including mutatome, DNA methylome, and transcriptome analyses, of 59 hepatoblastoma samples. Based on DNA methylation patterns, hepatoblastoma was classified into three clusters exhibiting remarkable correlation with clinical, histological, and genetic features. Cluster F was largely composed of cases with fetal histology and good outcomes, whereas clusters E1 and E2 corresponded primarily to embryonal/combined histology and poor outcomes. E1 and E2, albeit distinguishable by different patient age distributions, were genetically characterized by hypermethylation of the HNF4A/CEBPA-binding regions, fetal liver-like expression patterns, upregulation of the cell cycle pathway, and overexpression of NQO1 and ODC1. Inhibition of NQO1 and ODC1 in hepatoblastoma cells induced chemosensitization and growth suppression, respectively. Our results provide a comprehensive description of the molecular basis of hepatoblastoma and rational therapeutic strategies for high-risk cases.
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Affiliation(s)
- Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Misa Yoshida
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Hoshino
- Department of Pediatric Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Ryota Shirai
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Mio Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Ryota Souzaki
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Department of Systems Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | | | - Yutaka Kanamori
- Division of Surgery, Department of Surgical Specialties, National Center for Child Health and Development, Tokyo, Japan
| | - Mureo Kasahara
- Transplantation Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takako Yoshioka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Satoru Miyano
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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13
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Invariant phenotype and molecular association of biallelic TET2 mutant myeloid neoplasia. Blood Adv 2020; 3:339-349. [PMID: 30709865 DOI: 10.1182/bloodadvances.2018024216] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022] Open
Abstract
Somatic TET2 mutations (TET2 MT) are frequent in myeloid neoplasia (MN), particularly chronic myelomonocytic leukemia (CMML). TET2 MT includes mostly loss-of-function/hypomorphic hits. Impaired TET2 activity skews differentiation of hematopoietic stem cells toward proliferating myeloid precursors. This study was prompted by the observation of frequent biallelic TET2 gene inactivations (biTET2 i ) in CMML. We speculated that biTET2 i might be associated with distinct clinicohematological features. We analyzed TET2 MT in 1045 patients with MN. Of 82 biTET2 i cases, 66 were biTET2 MT, 13 were hemizygous TET2 MT, and 3 were homozygous TET2 MT (uniparental disomy); the remaining patients (denoted biTET2 - hereafter) were either monoallelic TET2 MT (n = 96) or wild-type TET2 (n = 823). Truncation mutations were found in 83% of biTET2 i vs 65% of biTET2 - cases (P = .02). TET2 hits were founder lesions in 72% of biTET2 i vs 38% of biTET2 - cases (P < .0001). In biTET2 i , significantly concurrent hits included SRSF2 MT (33%; P < .0001) and KRAS/NRAS MT (16%; P = .03) as compared with biTET2 - When the first TET2 hit was ancestral in biTET2 i , the most common subsequent hits affected a second TET2 MT, followed by SRSF2 MT, ASXL1 MT, RAS MT, and DNMT3A MT BiTET2 i patients without any monocytosis showed an absence of SRSF2 MT BiTET2 i patients were older and had monocytosis, CMML, normal karyotypes, and lower-risk disease compared with biTET2 - patients. Hence, while a second TET2 hit occurred frequently, biTET2 i did not portend faster progression but rather determined monocytic differentiation, consistent with its prevalence in CMML. Additionally, biTET2 i showed lower odds of cytopenias and marrow blasts (≥5%) and higher odds of myeloid dysplasia and marrow hypercellularity. Thus, biTET2 i might represent an auxiliary assessment tool in MN.
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14
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OGAWA S. Genetic basis of myelodysplastic syndromes. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:107-121. [PMID: 32161209 PMCID: PMC7167367 DOI: 10.2183/pjab.96.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/15/2020] [Indexed: 05/06/2023]
Abstract
During the past decade, substantial progress has been made in the field of the genetics of myelodysplastic syndromes (MDS). These comprise a group of chronic myeloid neoplasms with abnormal cell morphology and progression to acute myeloid leukemia (AML), where revolutionary sequencing technologies have played a major role. Through extensive sequencing of a large number of MDS genomes, a comprehensive registry of driver mutations involved in the pathogenesis of MDS has been revealed, along with their impacts on clinical phenotype and prognosis. The most frequently affected molecules are involved in DNA methylations, chromatin modification, RNA splicing, transcription, signal transduction, cohesin regulation, and DNA repair. These mutations show strong positive and negative correlations with each other, suggesting the presence of functional interactions between mutations, which dictate disease progression. Because these mutations are associated with disease phenotype, drug response, and clinical outcomes, it is essential to be familiar with MDS genetics not only for better understanding of MDS pathogenesis but also for management of patients.
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Affiliation(s)
- Seishi OGAWA
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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15
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Stahel P, Nahmias A, Sud SK, Lee SJ, Pucci A, Yousseif A, Youseff A, Jackson T, Urbach DR, Okrainec A, Allard JP, Sockalingam S, Yao T, Barua M, Jiao H, Magi R, Bassett AS, Paterson AD, Dahlman I, Batterham RL, Dash S. Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease. Diabetes 2019; 68:2235-2246. [PMID: 31506345 DOI: 10.2337/db18-1254] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 08/27/2019] [Indexed: 11/13/2022]
Abstract
Extreme obesity (EO) (BMI >50 kg/m2) is frequently associated with neuropsychiatric disease (NPD). As both EO and NPD are heritable central nervous system disorders, we assessed the prevalence of protein-truncating variants (PTVs) and copy number variants (CNVs) in genes/regions previously implicated in NPD in adults with EO (n = 149) referred for weight loss/bariatric surgery. We also assessed the prevalence of CNVs in patients referred to University College London Hospital (UCLH) with EO (n = 218) and obesity (O) (BMI 35-50 kg/m2; n = 374) and a Swedish cohort of participants from the community with predominantly O (n = 161). The prevalence of variants was compared with control subjects in the Exome Aggregation Consortium/Genome Aggregation Database. In the discovery cohort (high NPD prevalence: 77%), the cumulative PTV/CNV allele frequency (AF) was 7.7% vs. 2.6% in control subjects (odds ratio [OR] 3.1 [95% CI 2-4.1]; P < 0.0001). In the UCLH EO cohort (intermediate NPD prevalence: 47%), CNV AF (1.8% vs. 0.9% in control subjects; OR 1.95 [95% CI 0.96-3.93]; P = 0.06) was lower than the discovery cohort. CNV AF was not increased in the UCLH O cohort (0.8%). No CNVs were identified in the Swedish cohort with no NPD. These findings suggest that PTV/CNVs, in genes/regions previously associated with NPD, may contribute to NPD in patients with EO.
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Affiliation(s)
- Priska Stahel
- Department of Medicine, Banting & Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
| | - Avital Nahmias
- Department of Medicine, Banting & Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shawn K Sud
- Department of Medicine, Banting & Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
| | - So Jeong Lee
- Department of Medicine, Banting & Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Pucci
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College London, London, U.K
- UCLH Bariatric Centre for Weight Management and Metabolic Surgery, University College London Hospital, London, U.K
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust and University College London, London, U.K
| | - Ahmed Yousseif
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College London, London, U.K
- UCLH Bariatric Centre for Weight Management and Metabolic Surgery, University College London Hospital, London, U.K
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust and University College London, London, U.K
| | - Alaa Youseff
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Timothy Jackson
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of General Surgery, University Health Network, Toronto, Ontario, Canada
| | - David R Urbach
- Division of General Surgery, University Health Network, Toronto, Ontario, Canada
| | - Allan Okrainec
- Division of General Surgery, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Johane P Allard
- Bariatric Surgery Department, Toronto Western Hospital, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sanjeev Sockalingam
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Centre for Mental Health, University Health Network, Toronto, Ontario, Canada
| | - Tony Yao
- Division of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Moumita Barua
- Division of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Hong Jiao
- Division of Nephrology, Department of Medicine, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Reedik Magi
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anne S Bassett
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University Health Network, Toronto, Ontario, Canada
- Division of Cardiology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Andrew D Paterson
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Ingrid Dahlman
- Division of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Rachel L Batterham
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College London, London, U.K
- UCLH Bariatric Centre for Weight Management and Metabolic Surgery, University College London Hospital, London, U.K
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust and University College London, London, U.K
| | - Satya Dash
- Department of Medicine, Banting & Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
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16
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Nagata Y, Makishima H, Kerr CM, Przychodzen BP, Aly M, Goyal A, Awada H, Asad MF, Kuzmanovic T, Suzuki H, Yoshizato T, Yoshida K, Chiba K, Tanaka H, Shiraishi Y, Miyano S, Mukherjee S, LaFramboise T, Nazha A, Sekeres MA, Radivoyevitch T, Haferlach T, Ogawa S, Maciejewski JP. Invariant patterns of clonal succession determine specific clinical features of myelodysplastic syndromes. Nat Commun 2019; 10:5386. [PMID: 31772163 PMCID: PMC6879617 DOI: 10.1038/s41467-019-13001-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 09/16/2019] [Indexed: 02/07/2023] Open
Abstract
Myelodysplastic syndromes (MDS) arise in older adults through stepwise acquisitions of multiple somatic mutations. Here, analyzing 1809 MDS patients, we infer clonal architecture by using a stringent, the single-cell sequencing validated PyClone bioanalytic pipeline, and assess the position of the mutations within the clonal architecture. All 3,971 mutations are grouped based on their rank in the deduced clonal hierarchy (dominant and secondary). We evaluated how they affect the resultant morphology, progression, survival and response to therapies. Mutations of SF3B1, U2AF1, and TP53 are more likely to be dominant, those of ASXL1, CBL, and KRAS are secondary. Among distinct combinations of dominant/secondary mutations we identified 37 significant relationships, of which 12 affect clinical phenotypes, 5 cooperatively associate with poor prognosis. They also predict response to hypomethylating therapies. The clonal hierarchy has distinct ranking and the resultant invariant combinations of dominant/secondary mutations yield novel insights into the specific clinical phenotype of MDS.
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Affiliation(s)
- Yasunobu Nagata
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Cassandra M Kerr
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej P Przychodzen
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mai Aly
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Abhinav Goyal
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hassan Awada
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohammad Fahad Asad
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Teodora Kuzmanovic
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, 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
| | - Yuichi Shiraishi
- 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
| | - Sudipto Mukherjee
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department ofGenetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Aziz Nazha
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mikkael A Sekeres
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Tomas Radivoyevitch
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology & Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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17
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Matsumoto Y, Chinen Y, Shimura Y, Nagoshi H, Sasaki N, Muramatsu A, Kuriyama K, Ohshiro M, Hirakawa Y, Iwai T, Uchiyama H, Taki T, Horiike S, Kuroda J, Taniwaki M. Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma. Int J Hematol 2019; 111:75-83. [PMID: 31686349 DOI: 10.1007/s12185-019-02766-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022]
Abstract
Expression of intragenic exon rearrangements (IERs) has reportedly been detected in both normal and cancer cells. However, there have been few reports of occurrence of these rearrangements specific to neoplasms including malignant lymphoma. In this study, we detected IERs of ten genes (NBPF8, SOBP, AUTS2, RAB21, SPATA13, ABCC4, WDR7, PHLPP1, NFATC1 and MAGED1) in non-Hodgkin B cell lymphoma (B-NHL) cell line KPUM-UH1 using a high-resolution single nucleotide polymorphism array and reverse transcription polymerase chain reaction using reversely directed divergent primers within exons involved in genomic intragenic gains followed by sequencing analysis. Among them, the IERs involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in B-NHL samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers.
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Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan.
| | - Yoshiaki Chinen
- Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan.,Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Ayako Muramatsu
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Kodai Kuriyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Muneo Ohshiro
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Yoshiko Hirakawa
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Toshiki Iwai
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University, Faculty of Health Science, Tokyo, Japan.,Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
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18
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Piaggio F, Tozzo V, Bernardi C, Croce M, Puzone R, Viaggi S, Patrone S, Barla A, Coviello D, Jager MJ, van der Velden PA, Zeschnigk M, Cangelosi D, Eva A, Pfeffer U, Amaro A. Secondary Somatic Mutations in G-Protein-Related Pathways and Mutation Signatures in Uveal Melanoma. Cancers (Basel) 2019; 11:cancers11111688. [PMID: 31671564 PMCID: PMC6896012 DOI: 10.3390/cancers11111688] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/17/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Uveal melanoma (UM), a rare cancer of the eye, is characterized by initiating mutations in the genes G-protein subunit alpha Q (GNAQ), G-protein subunit alpha 11 (GNA11), cysteinyl leukotriene receptor 2 (CYSLTR2), and phospholipase C beta 4 (PLCB4) and by metastasis-promoting mutations in the genes splicing factor 3B1 (SF3B1), serine and arginine rich splicing factor 2 (SRSF2), and BRCA1-associated protein 1 (BAP1). Here, we tested the hypothesis that additional mutations, though occurring in only a few cases ("secondary drivers"), might influence tumor development. METHODS We analyzed all the 4125 mutations detected in exome sequencing datasets, comprising a total of 139 Ums, and tested the enrichment of secondary drivers in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that also contained the initiating mutations. We searched for additional mutations in the putative secondary driver gene protein tyrosine kinase 2 beta (PTK2B) and we developed new mutational signatures that explain the mutational pattern observed in UM. RESULTS Secondary drivers were significantly enriched in KEGG pathways that also contained GNAQ and GNA11, such as the calcium-signaling pathway. Many of the secondary drivers were known cancer driver genes and were strongly associated with metastasis and survival. We identified additional mutations in PTK2B. Sparse dictionary learning allowed for the identification of mutational signatures specific for UM. CONCLUSIONS A considerable part of rare mutations that occur in addition to known driver mutations are likely to affect tumor development and progression.
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Affiliation(s)
- Francesca Piaggio
- Tumor Epigenetics; IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
| | | | - Cinzia Bernardi
- Tumor Epigenetics; IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
| | - Michela Croce
- Biotherapy; IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
| | - Roberto Puzone
- Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
| | - Silvia Viaggi
- DISTAV, University of Genova, 16132 Genova, Italy.
- IRCCS Istituto G. Gaslini, 16147 Genova, Italy.
| | | | | | | | - Martine J Jager
- Laboratory of Human Genetics, Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | - Pieter A van der Velden
- Laboratory of Human Genetics, Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | - Michael Zeschnigk
- Institute of Human Genetics, University Clinics Essen, University Duisburg-Essen, 45147 Essen, Germany.
| | - Davide Cangelosi
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy.
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy.
| | - Ulrich Pfeffer
- Tumor Epigenetics; IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
| | - Adriana Amaro
- Tumor Epigenetics; IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy.
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19
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Kubota Y, Arakawa Y, Sekiguchi M, Watanabe K, Hiwatari M, Kishimoto H, Nakazawa A, Yoshida A, Ogawa S, Hanada R, Oka A, Takita J, Koh K. A case of malignant rhabdoid tumor mimicking yolk sac tumor. Pediatr Blood Cancer 2019; 66:e27784. [PMID: 31034722 DOI: 10.1002/pbc.27784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Malignant rhabdoid tumors (MRTs) are rare, highly aggressive embryonal neoplasms caused by biallelic alterations of the SMARCB1 gene. MRTs may occur in any soft tissue, but extracranial extrarenal MRTs are extremely rare. Diagnosis of MRTs in unusual locations and with an uncharacteristic cytomorphology that mimics other tumors is difficult. This was an atypical case of MRT in a 15-year-old female with tumors that closely resembled yolk sac tumors. It was extremely challenging to diagnose the tumors without confirming the SMARCB1 status.
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Affiliation(s)
- Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Cell Therapy and Transplantation Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroshi Kishimoto
- Department of Pathology, Saitama Children's Medical Center, Saitama, Japan
| | - Atsuko Nakazawa
- Department of Pathology, Saitama Children's Medical Center, Saitama, Japan
| | - Akihiko Yoshida
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryoji Hanada
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
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20
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Aoki K, Nakamura H, Suzuki H, Matsuo K, Kataoka K, Shimamura T, Motomura K, Ohka F, Shiina S, Yamamoto T, Nagata Y, Yoshizato T, Mizoguchi M, Abe T, Momii Y, Muragaki Y, Watanabe R, Ito I, Sanada M, Yajima H, Morita N, Takeuchi I, Miyano S, Wakabayashi T, Ogawa S, Natsume A. Prognostic relevance of genetic alterations in diffuse lower-grade gliomas. Neuro Oncol 2019; 20:66-77. [PMID: 29016839 DOI: 10.1093/neuonc/nox132] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Diffuse lower-grade gliomas (LGGs) are genetically classified into 3 distinct subtypes based on isocitrate dehydrogenase (IDH) mutation status and codeletion of chromosome 1p and 19q (1p/19q). However, the subtype-specific effects of additional genetic lesions on survival are largely unknown. Methods Using Cox proportional hazards regression modeling, we investigated the subtype-specific effects of genetic alterations and clinicopathological factors on survival in each LGG subtype, in a Japanese cohort of LGG cases fully genotyped for driver mutations and copy number variations associated with LGGs (n = 308). The results were validated using a dataset from 414 LGG cases available from The Cancer Genome Atlas (TCGA). Results In Oligodendroglioma, IDH-mutant and 1p/19q codeleted, NOTCH1 mutations (P = 0.0041) and incomplete resection (P = 0.0019) were significantly associated with shorter survival. In Astrocytoma, IDH-mutant, PIK3R1 mutations (P = 0.0014) and altered retinoblastoma pathway genes (RB1, CDKN2A, and CDK4) (P = 0.013) were independent predictors of poor survival. In IDH-wildtype LGGs, co-occurrence of 7p gain, 10q loss, mutation in the TERT promoter (P = 0.024), and grade III histology (P < 0.0001) independently predicted poor survival. IDH-wildtype LGGs without any of these factors were diagnosed at a younger age (P = 0.042), and were less likely to have genetic lesions characteristic of glioblastoma, in comparison with other IDH-wildtype LGGs, suggesting that they likely represented biologically different subtypes. These results were largely confirmed in the cohort of TCGA. Conclusions Subtype-specific genetic lesions can be used to stratify patients within each LGG subtype. enabling better prognostication and management.
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Affiliation(s)
- Kosuke Aoki
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideo Nakamura
- Department of Neurosurgery, School of Medicine, Kumamoto University, Kumamoto, Japan
| | - Hiromichi Suzuki
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University School of Medicine, Nagoya, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Satoshi Shiina
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Takashi Yamamoto
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsuichi Yoshizato
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuya Abe
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasutomo Momii
- Department of Neurosurgery, School of Medicine, Oita University, Oita, Japan
| | - Yoshihiro Muragaki
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Reiko Watanabe
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Ichiro Ito
- Division of Diagnostic Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Yajima
- Department of Scientific and Engineering Simulation, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Naoya Morita
- Department of Scientific and Engineering Simulation, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Ichiro Takeuchi
- Department of Computer Science/Research Institute for Information Science, Nagoya Institute of Technology, Nagoya, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.,Center for Materials Research by Information Integration, National Institute for Materials Science, Tsukuba, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
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21
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Abstract
Our knowledge about the genetics of myelodysplastic syndromes (MDS) and related myeloid disorders has been dramatically improved during the past decade, in which revolutionized sequencing technologies have played a major role. Through intensive efforts of sequencing of a large number of MDS genomes, a comprehensive registry of driver mutations recurrently found in a recognizable fraction of MDS patients has been revealed, and ongoing efforts are being made to clarify their impacts on clinical phenotype and prognosis, as well as their role in the pathogenesis of MDS. Among major mutational targets in MDS are the molecules involved in DNA methylations, chromatin modification, RNA splicing, transcription, signal transduction, cohesin regulation, and DNA repair. Showing substantial overlaps with driver mutations seen in acute myeloid leukemia (AML), as well as age-related clonal hematopoiesis in healthy individuals, these mutations are presumed to have a common clonal origin. Mutations are thought to be acquired and positively selected in a well-organized manner to allow for expansion of the initiating clone to compromise normal hematopoiesis, ultimately giving rise to MDS and subsequent transformation to AML in many patients. Significant correlations between mutations suggest the presence of functional interactions between mutations, which dictate disease progression. Mutations are frequently associated with specific disease phenotype, drug response, and clinical outcomes, and thus, it is essential to be familiar with MDS genetics for better management of patients. This review aims to provide a brief overview of the recent progresses in MDS genetics.
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22
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Yokoyama A, Kakiuchi N, Yoshizato T, Nannya Y, Suzuki H, Takeuchi Y, Shiozawa Y, Sato Y, Aoki K, Kim SK, Fujii Y, Yoshida K, Kataoka K, Nakagawa MM, Inoue Y, Hirano T, Shiraishi Y, Chiba K, Tanaka H, Sanada M, Nishikawa Y, Amanuma Y, Ohashi S, Aoyama I, Horimatsu T, Miyamoto S, Tsunoda S, Sakai Y, Narahara M, Brown JB, Sato Y, Sawada G, Mimori K, Minamiguchi S, Haga H, Seno H, Miyano S, Makishima H, Muto M, Ogawa S. Age-related remodelling of oesophageal epithelia by mutated cancer drivers. Nature 2019; 565:312-317. [DOI: 10.1038/s41586-018-0811-x] [Citation(s) in RCA: 346] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
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23
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Haruta M, Arai Y, Okita H, Tanaka Y, Takimoto T, Sugino RP, Yamada Y, Kamijo T, Oue T, Fukuzawa M, Koshinaga T, Kaneko Y. Combined Genetic and Chromosomal Characterization of Wilms Tumors Identifies Chromosome 12 Gain as a Potential New Marker Predicting a Favorable Outcome. Neoplasia 2018; 21:117-131. [PMID: 30530054 PMCID: PMC6288985 DOI: 10.1016/j.neo.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 11/26/2022] Open
Abstract
To identify prognostic factors, array CGH (aCGH) patterns and mutations in WT1 and 9 other genes were analyzed in 128 unilateral Wilms tumors (WTs). Twenty patients had no aCGH aberrations, and 31 had WT1 alterations [silent and WT1 types: relapse-free survival (RFS), 95% and 83%, respectively]. Seventy-seven patients had aCGH changes without WT1 alterations (nonsilent/non-WT1 type) and were subtyped into those with or without +12, 11q-, 16q-, or HACE1 loss. RFS was better for those with than those without +12 (P = .010) and worse for those with than those without 11q-, 16q-, or HACE1 loss (P = .001, .025, or 1.2E-04, respectively). Silent and WT1 type and 8 subtype tumors were integrated and classified into 3 risk groups: low risk for the silent type and +12 subgroup; high risk for the no +12 plus 11q-, 16q-, or HACE1 loss subgroup; intermediate risk for the WT1 type and no +12 plus no 11q-, 16q-, or HACE1 loss subgroup. Among the 27 WTs examined, the expression of 146 genes on chromosome 12 was stronger in +12 tumors than in no +12 tumors, while that of 10 genes on 16q was weaker in 16q- tumors than in no 16q- tumors. Overexpression in 75 out of 146 upregulated genes and underexpression in 7 out of 10 downregulated genes correlated with better and worse overall survival, respectively, based on the public database. +12 was identified as a potential new marker predicting a favorable outcome, and chromosome abnormalities may be related to altered gene expression associated with these abnormalities.
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Affiliation(s)
- Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Yasuhito Arai
- Cancer Genomics Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hajime Okita
- Department of Pathology, Keio University, Tokyo 157-8535, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa 232-8555, Japan
| | - Tetsuya Takimoto
- Clinical Research Center, National Center for Child Health and Development, Tokyo 157-8535, Japan
| | - Ryuichi P Sugino
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Yasuhiro Yamada
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Takaharu Oue
- Department of Pediatric Surgery, Hyogo College of Medicine, Hyogo 663-8501, Japan
| | | | - Tsugumichi Koshinaga
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yasuhiko Kaneko
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama 362-0806, Japan.
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24
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Takimoto-Shimomura T, Nagoshi H, Maegawa S, Fujibayashi Y, Tsukamoto T, Matsumura-Kimoto Y, Mizuno Y, Chinen Y, Mizutani S, Shimura Y, Horiike S, Taniwaki M, Kobayashi T, Kuroda J. Establishment and Characteristics of a Novel Mantle Cell Lymphoma-derived Cell Line and a Bendamustine-resistant Subline. Cancer Genomics Proteomics 2018; 15:213-223. [PMID: 29695404 DOI: 10.21873/cgp.20080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/AIM Bendamustine hydrochloride (BH) is a key therapeutic agent for mantle cell lymphoma (MCL), while the mechanism underlying BH-resistance has not been verified. MATERIALS AND METHODS We compared molecular/biological characteristics of a newly-generated MCL-derived cell line KPUM-YY1 and its BH-resistant subline KPUM-YY1R. RESULTS The growth-inhibitory IC50 for BH was 20 μM in KPUM-YY1 cells, while cell proliferation was not inhibited by up to 60 μM BH in KPUM-YY1R cells. Compared to KPUM-YY1 cells, gene expression profiling in KPUM-YY1R cells revealed up-regulation of 312 genes, including ABCB1 encoding P-glycoprotein (P-gp), and microsomal glutathione S-transferase 1 (MGST1). Addition of either a P-gp inhibitor or a GST inhibitor, at least partly, restored sensitivity to BH in KPUM-YY1R cells. In addition, KPUM-YY1R cells showed cross-resistance against various anti-MCL chemotherapeutics. CONCLUSION BH resistance is mediated by overlapping mechanisms with overexpression of ABCB1 and MGST1, and is potentially accompanied by multidrug resistance in MCL.
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Affiliation(s)
- Tomoko Takimoto-Shimomura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisao Nagoshi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Saori Maegawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsuke Mizutani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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25
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Xiao JF, Sun QY, Ding LW, Chien W, Liu XY, Mayakonda A, Jiang YY, Loh XY, Ran XB, Doan NB, Castor B, Chia D, Said JW, Tan KT, Yang H, Fu XY, Lin DC, Koeffler HP. The c-MYC-BMI1 axis is essential for SETDB1-mediated breast tumourigenesis. J Pathol 2018; 246:89-102. [PMID: 29926931 DOI: 10.1002/path.5126] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 05/26/2018] [Accepted: 06/11/2018] [Indexed: 12/21/2022]
Abstract
Characterising the activated oncogenic signalling that leads to advanced breast cancer is of clinical importance. Here, we showed that SET domain, bifurcated 1 (SETDB1), a histone H3 lysine 9 methyltransferase, is aberrantly expressed and behaves as an oncogenic driver in breast cancer. SETDB1 enhances c-MYC and cyclin D1 expression by promoting the internal ribosome entry site (IRES)-mediated translation of MYC/CCND1 mRNA, resulting in prominent signalling of c-MYC to promote cell cycle progression, and provides a growth/self-renewal advantage to breast cancer cells. The activated c-MYC-BMI1 axis is essential for SETDB1-mediated breast tumourigenesis, because silencing of either c-MYC or BMI1 profoundly impairs the enhanced growth/colony formation conferred by SETDB1. Furthermore, c-MYC directly binds to the SETDB1 promoter region and enhances its transcription, suggesting a positive regulatory interplay between SETDB1 and c-MYC. In this study, we identified SETDB1 as a prominent oncogene and characterised the underlying mechanism whereby SETDB1 drives breast cancer, providing a therapeutic rationale for targeting SETDB1-BMI1 signalling in breast cancer. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wenwen Chien
- Division of Hematology/Oncology, Cedar-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - Xin-Yu Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xin-Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xue-Bin Ran
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ngan B Doan
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Brandon Castor
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - David Chia
- Departments of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Jonathan W Said
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedar-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Division of Hematology/Oncology, Cedar-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA
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26
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Tsujimoto SI, Nakano Y, Osumi T, Okada K, Ouchi-Uchiyama M, Kataoka K, Fujii Y, Ohki K, Seki M, Tamagawa N, Takita J, Ogawa S, Kiyokawa N, Hara J, Kato M. A Cryptic NUP214-ABL1 Fusion in B-cell Precursor Acute Lymphoblastic Leukemia. J Pediatr Hematol Oncol 2018; 40:e397-e399. [PMID: 29219890 DOI: 10.1097/mph.0000000000001007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fluorescent in situ hybridization (FISH) analysis is the standard methods for screening ABL1 fusions, which is recurrently translocated in pediatric acute lymphoblastic leukemia (ALL), and potentially targetable by kinase inhibitors. Here we demonstrated a case of B-cell precursor ALL with NUP214-ABL1 fusion, which break-apart FISH assay for ABL1 failed to detect. The cryptic fusion was generated by small duplication from ABL1 to NUP214, which was detected by copy number analysis using genomic microarray and confirmed by PCR. In the context of precision medicine, we should establish how to screen targetable abnormalities for minimizing risk of false-negative.
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Affiliation(s)
- Shin-Ichi Tsujimoto
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development.,Department of Pediatrics, Yokohama City University, Kanagawa
| | - Yoshiko Nakano
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development.,Children's Cancer Center, National Center for Child Health and Development
| | - Keiko Okada
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital
| | - Meri Ouchi-Uchiyama
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development
| | - Masafumi Seki
- Department of Pediatrics, University of Tokyo, Tokyo
| | | | - Junko Takita
- Department of Pediatrics, University of Tokyo, Tokyo
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development.,Children's Cancer Center, National Center for Child Health and Development
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27
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Amaro A, Angelini G, Mirisola V, Esposito AI, Reverberi D, Matis S, Maffei M, Giaretti W, Viale M, Gangemi R, Emionite L, Astigiano S, Cilli M, Bachmeier BE, Killian PH, Albini A, Pfeffer U. A highly invasive subpopulation of MDA-MB-231 breast cancer cells shows accelerated growth, differential chemoresistance, features of apocrine tumors and reduced tumorigenicity in vivo. Oncotarget 2018; 7:68803-68820. [PMID: 27626697 PMCID: PMC5356591 DOI: 10.18632/oncotarget.11931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/13/2016] [Indexed: 11/28/2022] Open
Abstract
The acquisition of an invasive phenotype is a prerequisite for metastasization, yet it is not clear whether or to which extent the invasive phenotype is linked to other features characteristic of metastatic cells. We selected an invasive subpopulation from the triple negative breast cancer cell line MDA-MB-231, performing repeated cycles of preparative assays of invasion through Matrigel covered membranes. The invasive sub-population of MDA-MB-231 cells exhibits stronger migratory capacity as compared to parental cells confirming the highly invasive potential of the selected cell line. Prolonged cultivation of these cells did not abolish the invasive phenotype. ArrayCGH, DNA index quantification and karyotype analyses confirmed a common genetic origin of the parental and invasive subpopulations and revealed discrete structural differences of the invasive subpopulation including increased ploidy and the absence of a characteristic amplification of chromosome 5p14.1-15.33. Gene expression analyses showed a drastically altered expression profile including features of apocrine breast cancers and of invasion related matrix-metalloproteases and cytokines. The invasive cells showed accelerated proliferation, increased apoptosis, and an altered pattern of chemo-sensitivity with lower IC50 values for drugs affecting the mitotic apparatus. However, the invasive cell population is significantly less tumorigenic in orthotopic mouse xenografts suggesting that the acquisition of the invasive capacity and the achievement of metastatic growth potential are distinct events.
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Affiliation(s)
- Adriana Amaro
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Giovanna Angelini
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Valentina Mirisola
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Alessia Isabella Esposito
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Daniele Reverberi
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Serena Matis
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Massimo Maffei
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Walter Giaretti
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Maurizio Viale
- Biotherapy, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Rosaria Gangemi
- Biotherapy, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Laura Emionite
- Animal Facility, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Simonetta Astigiano
- Immunology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Michele Cilli
- Animal Facility, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Beatrice E Bachmeier
- Institute of Laboratory Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Peter H Killian
- Institute of Laboratory Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Adriana Albini
- Scientific and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Ulrich Pfeffer
- Molecular Pathology, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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28
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Isobe T, Seki M, Yoshida K, Sekiguchi M, Shiozawa Y, Shiraishi Y, Kimura S, Yoshida M, Inoue Y, Yokoyama A, Kakiuchi N, Suzuki H, Kataoka K, Sato Y, Kawai T, Chiba K, Tanaka H, Shimamura T, Kato M, Iguchi A, Hama A, Taguchi T, Akiyama M, Fujimura J, Inoue A, Ito T, Deguchi T, Kiyotani C, Iehara T, Hosoi H, Oka A, Sanada M, Tanaka Y, Hata K, Miyano S, Ogawa S, Takita J. Integrated Molecular Characterization of the Lethal Pediatric Cancer Pancreatoblastoma. Cancer Res 2018; 78:865-876. [PMID: 29233928 DOI: 10.1158/0008-5472.can-17-2581] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/24/2017] [Accepted: 12/07/2017] [Indexed: 11/16/2022]
Abstract
Pancreatoblastoma is a rare pediatric pancreatic malignancy for which the molecular pathogenesis is not understood. In this study, we report the findings of an integrated multiomics study of whole-exome and RNA sequencing as well as genome-wide copy number and methylation analyses of ten pancreatoblastoma cases. The pancreatoblastoma genome was characterized by a high frequency of aberrant activation of the Wnt signaling pathway, either via somatic mutations of CTNNB1 (90%) and copy-neutral loss of heterozygosity (CN-LOH) of APC (10%). In addition, imprinting dysregulation of IGF2 as a consequence of CN-LOH (80%), gain of paternal allele (10%), and gain of methylation (10%) was universally detected. At the transcriptome level, pancreatoblastoma exhibited an expression profile characteristic of early pancreas progenitor-like cells along with upregulation of the R-spondin/LGR5/RNF43 module. Our results offer a comprehensive description of the molecular basis for pancreatoblastoma and highlight rational therapeutic targets for its treatment.Significance: Molecular genetic analysis of a rare untreatable pediatric tumor reveals Wnt/IGF2 aberrations and features of early pancreas progenitor-like cells, suggesting cellular origins and rational strategies for therapeutic targeting. Cancer Res; 78(4); 865-76. ©2017 AACR.
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Affiliation(s)
- Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Shiozawa
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Misa Yoshida
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshikage Inoue
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Yokoyama
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, 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
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Iguchi
- Department of Pediatrics, Hokkaido University, Sapporo, Japan
| | - Asahito Hama
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Graduate School of Medicine, Kyushu University, Fukuoka, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Junya Fujimura
- Department of Pediatrics, Juntendo University School of Medicine, Tokyo, Japan
| | - Akiko Inoue
- Department of Pediatrics, Osaka Medical College, Osaka, Japan
| | - Tsuyoshi Ito
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Japan
| | - Takao Deguchi
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Chikako Kiyotani
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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29
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Identification of the genetic and clinical characteristics of neuroblastomas using genome-wide analysis. Oncotarget 2017; 8:107513-107529. [PMID: 29296183 PMCID: PMC5746085 DOI: 10.18632/oncotarget.22495] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/28/2017] [Indexed: 12/12/2022] Open
Abstract
To provide better insight into the genetic signatures of neuroblastomas, we analyzed 500 neuroblastomas (included specimens from JNBSG) using targeted-deep sequencing for 10 neuroblastoma-related genes and SNP arrays analysis. ALK expression was evaluated using immunohistochemical analysis in 259 samples. Based on genetic alterations, the following 6 subgroups were identified: groups A (ALK abnormalities), B (other gene mutations), C (MYCN amplification), D (11q loss of heterozygosity [LOH]), E (at least 1 copy number variants), and F (no genetic changes). Groups A to D showed advanced disease and poor prognosis, whereas groups E and F showed excellent prognosis. Intriguingly, in group A, MYCN amplification was not a significant prognostic marker, while high ALK expression was a relevant indicator for prognosis (P = 0.033). Notably, the co-existence of MYCN amplification and 1p LOH, and the co-deletion of 3p and 11q were significant predictors of relapse (P = 0.043 and P = 0.040). Additionally, 6q/8p LOH and 17q gain were promising indicators of survival in patients older than 5 years, and 1p, 4p, and 11q LOH potentially contributed to outcome prediction in the intermediate-risk group. Our genetic overview clarifies the clinical impact of genetic signatures and aids in the better understanding of genetic basis of neuroblastoma.
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30
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Prognostic relevance of integrated genetic profiling in adult T-cell leukemia/lymphoma. Blood 2017; 131:215-225. [PMID: 29084771 DOI: 10.1182/blood-2017-01-761874] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATL) is a heterogeneous group of peripheral T-cell malignancies characterized by human T-cell leukemia virus type-1 infection, whose genetic profile has recently been fully investigated. However, it is still poorly understood how these alterations affect clinical features and prognosis. We investigated the effects of genetic alterations commonly found in ATL on disease phenotypes and clinical outcomes, based on genotyping data obtained from 414 and 463 ATL patients using targeted-capture sequencing and single nucleotide polymorphism array karyotyping, respectively. Aggressive (acute/lymphoma) subtypes were associated with an increased burden of genetic and epigenetic alterations, higher frequencies of TP53 and IRF4 mutations, and many copy number alterations (CNAs), including PD-L1 amplifications and CDKN2A deletions, compared with indolent (chronic/smoldering) subtypes. By contrast, STAT3 mutations were more characteristic of indolent ATL. Higher numbers of somatic mutations and CNAs significantly correlated with worse survival. In a multivariate analysis incorporating both clinical factors and genetic alterations, the Japan Clinical Oncology Group prognostic index high-risk, older age, PRKCB mutations, and PD-L1 amplifications were independent poor prognostic factors in aggressive ATL. In indolent ATL, IRF4 mutations, PD-L1 amplifications, and CDKN2A deletions were significantly associated with shorter survival, although the chronic subtype with unfavorable clinical factors was only marginally significant. Thus, somatic alterations characterizing aggressive diseases predict worse prognosis in indolent ATL, among which PD-L1 amplifications are a strong genetic predictor in both aggressive and indolent ATL. ATL subtypes are further classified into molecularly distinct subsets with different prognosis. Genetic profiling might contribute to improved prognostication and management of ATL patients.
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31
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Chari R, Lockwood WW, Lam WL. Computational Methods for the Analysis of Array Comparative Genomic Hybridization. Cancer Inform 2017. [DOI: 10.1177/117693510600200007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
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Affiliation(s)
- Raj Chari
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - William W. Lockwood
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - Wan L. Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
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32
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Maruyama K, Aotsuka N, Kumano Y, Sato N, Kawashima N, Onda Y, Maruyama H, Katagiri T, Zaimoku Y, Nakagawa N, Hosomichi K, Ogawa S, Nakao S. Immune-Mediated Hematopoietic Failure after Allogeneic Hematopoietic Stem Cell Transplantation: A Common Cause of Late Graft Failure in Patients with Complete Donor Chimerism. Biol Blood Marrow Transplant 2017; 24:43-49. [PMID: 28860001 DOI: 10.1016/j.bbmt.2017.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/15/2017] [Indexed: 10/19/2022]
Abstract
Late graft failure (LGF) without evidence of residual recipient cells is a serious complication after allogeneic hematopoietic stem cell transplantation (allo-SCT) and often requires stem cell infusion from the same donor when the patient fails to respond to conventional therapies. We screened the peripheral blood (PB) of 14 patients who developed donor-type LGF at 2 to 132 months after allo-SCT for the presence of the markers for immune-mediated bone marrow (BM) failure. Increased glycosylphosphatidyl inositol-anchored protein-deficient (GPI-AP-) leukocytes, which accounted for .009% to 0.147% of the total granulocytes, were detected in 5 patients (severe aplastic anemia, n = 2; follicular lymphoma, n = 1; acute lymphoblastic leukemia, n = 1; myelodysplastic syndromes; n = 1) and 4.7% to 81.2% HLA-allele-lacking leukocytes (HLA-LLs) were detected in 2 patients (acute myelogenous leukemia, n = 1; and myelodysplastic syndromes, n = 1). Three of the 5 patients with increased GPI-AP- leukocytes were treated with antithymocyte globulin (ATG), and 2 patients achieved transfusion independence. These results suggest that immune mechanisms that are similar to acquired aplastic anemia underlie condition of approximately one-half of the patients with donor-type LGF, and that in patients with increased GPI-AP- cells, donor-derived hematopoiesis may be restored by ATG therapy alone without donor stem cell infusion.
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Affiliation(s)
- Kana Maruyama
- Department of Hematology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Nobuyuki Aotsuka
- Department of Hematology, Japanese Red Cross Narita Hospital, Narita, Japan
| | - Yoshihisa Kumano
- Department of Internal Medicine, Keiju Kanazawa Hospital, Kanazawa, Japan
| | - Naoko Sato
- Department of Hematology, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Naomi Kawashima
- Department of Hematology, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Yoshiyuki Onda
- Department of Hematology, Takatsuki Red Cross Hospital, Takatsuki, Japan
| | - Hiroyuki Maruyama
- Department of Internal Medicine, Keiju Kanazawa Hospital, Kanazawa, Japan
| | - Takamasa Katagiri
- Clinical Laboratory Science, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yoshitaka Zaimoku
- Department of Hematology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Noriharu Nakagawa
- Department of Hematology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Nakao
- Department of Hematology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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Knijnenburg J, Uytdewilligen ME, van Hassel DA, Oostenbrink R, Eussen BH, de Klein A, Brooks AS, van Zutven LJ. Postzygotic telomere capture causes segmental UPD, duplication and deletion of chromosome 8p in a patient with intellectual disability and obesity. Eur J Med Genet 2017; 60:445-450. [DOI: 10.1016/j.ejmg.2017.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/13/2017] [Accepted: 06/06/2017] [Indexed: 01/30/2023]
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Development and Function of Immune Cells in an Adolescent Patient With a Deficiency in the Interleukin-10 Receptor. J Pediatr Gastroenterol Nutr 2017. [PMID: 28644354 DOI: 10.1097/mpg.0000000000001559] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Monogenic defects in the interleukin-10 (IL-10) pathway are extremely rare and cause infantile-onset inflammatory bowel disease (IBD)-like pathology. Understanding how immune responses are dysregulated in monogenic IBD-like diseases can provide valuable insight in "classical" IBD pathogenesis. Here, we studied long-term immune cell development and function in an adolescent IL-10 receptor (IL10RA)-deficient patient who presented in infancy with severe colitis and fistulizing perianal disease and is currently treated with immune suppressants. METHODS Biomaterial was collected from the IL10RA-deficient patient, pediatric patients with IBD, and healthy controls. The frequency and phenotype of immune cells were determined in peripheral blood and intestinal biopsies by flow cytometry and immunohistochemistry. Functional changes in monocyte-derived dendritic cells and T cells were assessed by in vitro activation assays. RESULTS The IL10RA-deficient immune system developed normally with respect to numbers and phenotype of circulating immune cells. Despite normal co-stimulatory molecule expression, bacterial lipopolysaccharide-stimulated monocyte-derived dendritic cells from the IL10RA-deficient patient released increased amounts of tumor necrosis factor α compared to healthy controls. Upon T-cell receptor ligation, IL10RA-deficient peripheral blood mononuclear cells released increased amounts of T-cell cytokines interferon γ and IL-17 agreeing with high numbers of T-bet and IL-17 cells in intestinal biopsies taken at disease onset. In vitro, the immunosuppressive drug thalidomide used to treat the patient's decreased peripheral blood mononuclear cell-derived tumor necrosis factor production. CONCLUSIONS With time and during immunosuppressive treatment the IL10RA-deficient immune system develops relatively normally. Upon activation, IL-10 is crucial for controlling excessive inflammatory cytokine release by dendritic cells and preventing interferon γ and IL-17-mediated T-cell responses.
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Takada M, Nagai S, Haruta M, Sugino RP, Tozuka K, Takei H, Ohkubo F, Inoue K, Kurosumi M, Miyazaki M, Sato-Otsubo A, Sato Y, Ogawa S, Kaneko Y. BRCA1 alterations with additional defects in DNA damage response genes may confer chemoresistance to BRCA-like breast cancers treated with neoadjuvant chemotherapy. Genes Chromosomes Cancer 2017; 56:405-420. [PMID: 28124401 DOI: 10.1002/gcc.22445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/15/2017] [Accepted: 01/18/2017] [Indexed: 12/30/2022] Open
Abstract
The BRCA-like phenotype is a feature that some sporadic breast cancers share with those occurring in BRCA1 or BRCA2 mutation carriers. As tumors with the phenotype have defects in the DNA damage response pathway, which may increase sensitivity to drugs such as DNA cross-linking agents and PARP inhibitors, a method to identify this phenotype is important. The prediction of chemoresistance, which frequently develops in these tumors, is also crucial for improving therapy. We examined genomic aberrations and BRCA1 promoter methylation in tumors of 73 breast cancer (20 HR-/HER2- and 53 HR+/HER2-) patients, who received neoadjuvant chemotherapy with anthracycline, cyclophosphamide, and taxane, using SNP array CGH and quantitative PCR. The methylation and/or loss or uniparental disomy (UPD) of BRCA1 (BRCA1 alterations) and the loss or UPD of BRCA2 (BRCA2 alterations) were detected in 27 (37%) and 21 (29%), respectively, of the 73 tumors. Tumors with BRCA1 or BRCA2 alterations were associated with a higher number of genomic aberrations (P < 0.001 and P < 0.001) and higher percentage of TP53 alterations (P < 0.001 and P < 0.001) than those without. Overall survival (OS) rates were similar between patients with or without BRCA1 or BRCA2 alterations. However, when 27 patients with BRCA1-altered tumors were classified into those with or without the loss or UPD of PALB2, PAGR1, RAD51B, FANCM, MLL4, or ERCC1/2 in tumors, patients with additional defects in DNA damage response genes had worse OS (P = 0.037, 0.045, 0.038, 0.044, 0.041, or 0.019) than those without. These defects may confer chemoresistance and predict poor outcomes in patients with BRCA1-altered breast cancer.
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Affiliation(s)
- Mamoru Takada
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigenori Nagai
- Divisions of Breast Oncology, Saitama Cancer Center, Saitama, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Ryuichi P Sugino
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Katsunori Tozuka
- Divisions of Breast Surgery, Saitama Cancer Center, Ina, Saitama, Japan
| | - Hiroyuki Takei
- Divisions of Breast Surgery, Saitama Cancer Center, Ina, Saitama, Japan
| | - Fumie Ohkubo
- Divisions of Breast Oncology, Saitama Cancer Center, Saitama, Japan
| | - Kenichi Inoue
- Divisions of Breast Oncology, Saitama Cancer Center, Saitama, Japan
| | | | - Masaru Miyazaki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Aiko Sato-Otsubo
- Division of Tumor Biology, Department of Pathology, Kyoto University School of Medicine, Kyoto, Japan
| | - Yusuke Sato
- Division of Tumor Biology, Department of Pathology, Kyoto University School of Medicine, Kyoto, Japan
| | - Seishi Ogawa
- Division of Tumor Biology, Department of Pathology, Kyoto University School of Medicine, Kyoto, Japan
| | - Yasuhiko Kaneko
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
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Ohta S, Isojima T, Mizuno Y, Kato M, Mimaki M, Seki M, Sato Y, Ogawa S, Takita J, Kitanaka S, Oka A. Partial monosomy of 10p and duplication of another chromosome in two patients. Pediatr Int 2017; 59:99-102. [PMID: 28102624 DOI: 10.1111/ped.13181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 07/16/2016] [Accepted: 09/23/2016] [Indexed: 11/30/2022]
Abstract
Partial monosomy of 10p is a rare chromosomal abnormality. Common features are hypoparathyroidism, deafness, renal anomalies, distinctive facies, and mental retardation, with phenotypic variability. We report two patients with chromosomal abnormalities identified on single-nucleotide polymorphism (SNP) array analysis. Although patient 1 had common features of monosomy10p, G-banding indicated a normal karyotype. SNP array and fluorescence in situ hybridization (FISH), however, indicated unbalanced translocation of a 10p terminal deletion of 11.7 Mb and a 15q terminal duplication of 8.2 Mb. In patient 2, SNP array and FISH indicated a 10p terminal deletion of 12.6 Mb and a 7q terminal duplication of 1.9 Mb. This is the first case report of monosomy 10p combined with trisomy 15q (patient 1). Because the clinical heterogeneity of the 10p deletion syndrome would be affected by duplication of another chromosome, we emphasize that SNP/microarray analysis is necessary to confirm genotype-phenotype correlation.
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Affiliation(s)
- Sayaka Ohta
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Isojima
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoko Mizuno
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masakazu Mimaki
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Sachiko Kitanaka
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Dynamics of clonal evolution in myelodysplastic syndromes. Nat Genet 2016; 49:204-212. [PMID: 27992414 DOI: 10.1038/ng.3742] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
To elucidate differential roles of mutations in myelodysplastic syndromes (MDS), we investigated clonal dynamics using whole-exome and/or targeted sequencing of 699 patients, of whom 122 were analyzed longitudinally. Including the results from previous reports, we assessed a total of 2,250 patients for mutational enrichment patterns. During progression, the number of mutations, their diversity and clone sizes increased, with alterations frequently present in dominant clones with or without their sweeping previous clones. Enriched in secondary acute myeloid leukemia (sAML; in comparison to high-risk MDS), FLT3, PTPN11, WT1, IDH1, NPM1, IDH2 and NRAS mutations (type 1) tended to be newly acquired, and were associated with faster sAML progression and a shorter overall survival time. Significantly enriched in high-risk MDS (in comparison to low-risk MDS), TP53, GATA2, KRAS, RUNX1, STAG2, ASXL1, ZRSR2 and TET2 mutations (type 2) had a weaker impact on sAML progression and overall survival than type-1 mutations. The distinct roles of type-1 and type-2 mutations suggest their potential utility in disease monitoring.
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Okuda T, Taki T, Nishida K, Chinen Y, Nagoshi H, Sakakura C, Taniwaki M. Molecular heterogeneity in the novel fusion gene APIP-FGFR2: Diversity of genomic breakpoints in gastric cancer with high-level amplifications at 11p13 and 10q26. Oncol Lett 2016; 13:215-221. [PMID: 28123544 PMCID: PMC5244987 DOI: 10.3892/ol.2016.5386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/28/2016] [Indexed: 01/14/2023] Open
Abstract
Several novel fusion transcripts were identified by next-generation sequencing in gastric cancer; however, the breakpoint junctions have yet to be characterized. The present study characterized a plethora of APIP-FGFR2 genomic breakpoints in the SNU-16 gastric cancer cell line, which harbored homogeneously staining regions (hsrs) and double minute chromosomes. Oligonucleotide microarrays revealed high-level amplifications at chromosomes 8q24.1 (0.8 Mb region), 10q26 (1.1 Mb) and 11p13 (1.1 Mb). These amplicons contained MYC and PVT1 at chromosome 8q24.1, BRWD2, FGFR2 and ATE1 at chromosome 10q26, and 24 genes, including APIP, CD44, RAG1 and RAG2, at chromosome 11p13. Based on these findings, reverse transcription-polymerase chain reaction (PCR) was performed using various candidate gene primers to detect possible fusion transcripts, and several products using primer sets for the APIP and FGFR2 genes were detected. Eventually, three in-frame and two out-of-frame fusion transcripts were detected. Notably, PCR analysis of the entire genomic DNA detected three distinct genomic junctions. The breakpoints were within intron 5 of APIP, which contained three distinct breakpoints, and introns 5, 7 and 9 of FGFR2. Fluorescence in situ hybridization showed several fusion signals within hsrs using two short probes (~10-kb segments of a bacterial artificial chromosome clone) containing exons 2–5 of APIP or exons 11–13 of FGFR2. Although, for any given fusion, a multiplicity of transcripts is thought to be created by alternative splicing of one rearranged allele, the results of the present study suggested that genomic fusions of APIP and FGFR2 are generated in hsrs with a diversity of breakpoints that are then faithfully transcribed.
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Affiliation(s)
- Takashi Okuda
- Department of Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan; Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Tomohiko Taki
- Department of Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Kazuhiro Nishida
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Yoshiaki Chinen
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Chouhei Sakakura
- Department of Digestive Surgery, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Masafumi Taniwaki
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
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Primary Carcinoid Tumor of the Renal Pelvis Arising From Intestinal Metaplasia: An Unusual Histogenetic Pathway? Appl Immunohistochem Mol Morphol 2016; 25:e49-e57. [PMID: 27753663 DOI: 10.1097/pai.0000000000000445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Primary carcinoid tumor of the renal pelvis is a rare neoplasm with few cases reported in the literature. Here we present the clinical and histopathologic findings of a primary carcinoid tumor arising in the left renal pelvis of a horseshoe kidney in a 61-year-old female patient. MATERIALS AND METHODS Pathologic features were evaluated with standard hematoxylin and eosin sections and immunohistochemical studies. A literature review was performed to place our case in context to previous reports. RESULTS The tumor was associated with intestinal metaplasia with high-grade dysplasia and neuroendocrine hyperplasia. Molecular testing for microsatellite instability and loss of heterozygosity were negative. CONCLUSIONS This report portrays a unique presentation of carcinoid tumor arising from intestinal metaplasia of the pelvic urothelium, and supports its histogenesis from urothelial intestinal metaplasia and neuroendocrine hyperplasia.
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40
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Long-term outcome of 6-month maintenance chemotherapy for acute lymphoblastic leukemia in children. Leukemia 2016; 31:580-584. [PMID: 27698447 DOI: 10.1038/leu.2016.274] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/29/2016] [Accepted: 09/06/2016] [Indexed: 12/27/2022]
Abstract
In the treatment of childhood acute lymphoblastic leukemia (ALL), excess shortening of maintenance therapy resulted in high relapse rate, as shown by our previous trial, TCCSG L92-13, in which maintenance therapy was terminated at 1 year from initiation of treatment. In this study, we aimed to confirm the long-term outcome of L92-13, and to identify who can or cannot be cured by shorter duration of maintenance therapy. To obtain sentinel cytogenetics information that had been missed before, we performed genetic analysis with genomic microarray and target intron-capture sequencing from diagnostic bone marrow smear. Disease-free survival (DFS) at 10 years from the end of therapy was 66.0±2.8%. Females (n=138) had better DFS (74.6±3.7%) than males (n=142, 57.5±4.2%, P=0.002). Patients with TCF3-PBX1 (n=11) and ETV6-RUNX1 (n=16) had excellent DFS (90.9±8.7% and 93.8±6.1%, respectively), whereas high hyperdiploidy (n=23) was the most unfavorable subgroup, with 56.6±10.3% of DFS. Short duration of therapy can cure more than half of pediatric ALL, especially females, TCF3-PBX1 and ETV6-RUNX1. Our retrospective observations suggest a gender/karyotype inhomogeneity on the impact of brief therapy.
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Maruyama H, Katagiri T, Kashiwase K, Shiina T, Sato-Otsubo A, Zaimoku Y, Maruyama K, Hosokawa K, Ishiyama K, Yamazaki H, Inoko H, Ogawa S, Nakao S. Clinical significance and origin of leukocytes that lack HLA-A allele expression in patients with acquired aplastic anemia. Exp Hematol 2016; 44:931-939.e3. [DOI: 10.1016/j.exphem.2016.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/24/2016] [Accepted: 05/23/2016] [Indexed: 01/10/2023]
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Srilekha S, Rao B, Rao DM, Sudha D, Chandrasekar SP, Pandian AJ, Soumittra N, Sripriya S. Strategies for Gene Mapping in Inherited Ophthalmic Diseases. Asia Pac J Ophthalmol (Phila) 2016; 5:282-92. [PMID: 27488070 DOI: 10.1097/apo.0000000000000228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Gene mapping of inherited ophthalmic diseases such as congenital cataracts, retinal degeneration, glaucoma, age-related macular degeneration, myopia, optic atrophy, and eye malformations has shed more light on the disease pathology, identified targets for research on therapeutics, earlier detection, and treatment options for disease management and patient care. This article details the different approaches to gene identification for both Mendelian and complex eye disorders.
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Affiliation(s)
- Sundar Srilekha
- From the SNONGC Department of Genetics and Molecular Biology, Kamal Nayan Bajaj Institute for Research in Vision and Ophthalmology (KNBIRVO), Chennai, Tamil Nadu, India
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Kataoka K, Shiraishi Y, Takeda Y, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S, Tanaka H, Chiba K, Ito S, Watatani Y, Kakiuchi N, Suzuki H, Yoshizato T, Yoshida K, Sanada M, Itonaga H, Imaizumi Y, Totoki Y, Munakata W, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Masuda K, Minato N, Kashiwase K, Izutsu K, Takaori-Kondo A, Miyazaki Y, Takahashi S, Shibata T, Kawamoto H, Akatsuka Y, Shimoda K, Takeuchi K, Seya T, Miyano S, Ogawa S. Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. Nature 2016; 534:402-6. [PMID: 27281199 DOI: 10.1038/nature18294] [Citation(s) in RCA: 468] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/29/2016] [Indexed: 12/13/2022]
Abstract
Successful treatment of many patients with advanced cancer using antibodies against programmed cell death 1 (PD-1; also known as PDCD1) and its ligand (PD-L1; also known as CD274) has highlighted the critical importance of PD-1/PD-L1-mediated immune escape in cancer development. However, the genetic basis for the immune escape has not been fully elucidated, with the exception of elevated PD-L1 expression by gene amplification and utilization of an ectopic promoter by translocation, as reported in Hodgkin and other B-cell lymphomas, as well as stomach adenocarcinoma. Here we show a unique genetic mechanism of immune escape caused by structural variations (SVs) commonly disrupting the 3' region of the PD-L1 gene. Widely affecting multiple common human cancer types, including adult T-cell leukaemia/lymphoma (27%), diffuse large B-cell lymphoma (8%), and stomach adenocarcinoma (2%), these SVs invariably lead to a marked elevation of aberrant PD-L1 transcripts that are stabilized by truncation of the 3'-untranslated region (UTR). Disruption of the Pd-l1 3'-UTR in mice enables immune evasion of EG7-OVA tumour cells with elevated Pd-l1 expression in vivo, which is effectively inhibited by Pd-1/Pd-l1 blockade, supporting the role of relevant SVs in clonal selection through immune evasion. Our findings not only unmask a novel regulatory mechanism of PD-L1 expression, but also suggest that PD-L1 3'-UTR disruption could serve as a genetic marker to identify cancers that actively evade anti-tumour immunity through PD-L1 overexpression.
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Affiliation(s)
- Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yohei Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Seiji Sakata
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Misako Matsumoto
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Seiji Nagano
- Department of Immunology, Institute for Frontier Medical Science, Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Maeda
- Department of Immunology, Institute for Frontier Medical Science, Kyoto University, Kyoto 606-8507, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Akira Kitanaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center and Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Satoshi Ito
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yosaku Watatani
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Hidehiro Itonaga
- Department of Hematology, Sasebo City General Hospital, Sasebo 857-8511, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki 852-8523, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Wataru Munakata
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kotaro Shide
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yoko Kubuki
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Tomonori Hidaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Takuro Kameda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kyoko Masuda
- Department of Immunology, Institute for Frontier Medical Science, Kyoto University, Kyoto 606-8507, Japan
| | - Nagahiro Minato
- Department of Immunology and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Koichi Kashiwase
- Department of HLA Laboratory, Japanese Red Cross Kanto-Koshinetsu Block Blood Center, Tokyo 135-8639, Japan
| | - Koji Izutsu
- Department of Hematology, Toranomon Hospital, Tokyo 105-8470, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki 852-8523, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center and Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Kawamoto
- Department of Immunology, Institute for Frontier Medical Science, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshiki Akatsuka
- Department of Hematology, Fujita Health University School of Medicine, Toyoake 470-1192, Japan.,Division of Immunology, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Kazuya Shimoda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Tsukasa Seya
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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45
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Cutcutache I, Wu AY, Suzuki Y, McPherson JR, Lei Z, Deng N, Zhang S, Wong WK, Soo KC, Chan WH, Ooi LL, Welsch R, Tan P, Rozen SG. Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma. Gastric Cancer 2016; 19. [PMID: 26205786 PMCID: PMC4824836 DOI: 10.1007/s10120-015-0514-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas. METHODS We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted. RESULTS The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene. CONCLUSIONS The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.
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Affiliation(s)
- Ioana Cutcutache
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Alice Yingting Wu
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
| | - Yuka Suzuki
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - John Richard McPherson
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Zhengdeng Lei
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niantao Deng
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Shenli Zhang
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wai Keong Wong
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - Khee Chee Soo
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Hoong Chan
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
| | - London Lucien Ooi
- />Department of General Surgery, Singapore General Hospital, Singapore, Singapore
- />Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Roy Welsch
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Engineering Systems Division and Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Patrick Tan
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
- />Duke-NUS Genome Biology Facility, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Genome Institute of Singapore, A* STAR, Singapore, Singapore
| | - Steven G. Rozen
- />Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
- />Computation and Systems Biology, Singapore-MIT Alliance, Singapore, Singapore
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46
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Variegated RHOA mutations in adult T-cell leukemia/lymphoma. Blood 2015; 127:596-604. [PMID: 26574607 DOI: 10.1182/blood-2015-06-644948] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/02/2015] [Indexed: 12/24/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATLL) is a distinct form of peripheral T-cell lymphoma with poor prognosis, which is caused by the human T-lymphotropic virus type 1 (HTLV-1). In contrast to the unequivocal importance of HTLV-1 infection in the pathogenesis of ATLL, the role of acquired mutations in HTLV-1 infected T cells has not been fully elucidated, with a handful of genes known to be recurrently mutated. In this study, we identified unique RHOA mutations in ATLL through whole genome sequencing of an index case, followed by deep sequencing of 203 ATLL samples. RHOA mutations showed distinct distribution and function from those found in other cancers. Involving 15% (30/203) of ATLL cases, RHOA mutations were widely distributed across the entire coding sequence but almost invariably located at the guanosine triphosphate (GTP)-binding pocket, with Cys16Arg being most frequently observed. Unexpectedly, depending on mutation types and positions, these RHOA mutants showed different or even opposite functional consequences in terms of GTP/guanosine diphosphate (GDP)-binding kinetics, regulation of actin fibers, and transcriptional activation. The Gly17Val mutant did not bind GTP/GDP and act as a dominant negative molecule, whereas other mutants (Cys16Arg and Ala161Pro) showed fast GTP/GDP cycling with enhanced transcriptional activation. These findings suggest that both loss- and gain-of-RHOA functions could be involved in ATLL leukemogenesis. In summary, our study not only provides a novel insight into the molecular pathogenesis of ATLL but also highlights a unique role of variegation of heterologous RHOA mutations in human cancers.
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47
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Liao B, Jiang Y, Liang W, Peng L, Peng L, Hanyurwimfura D, Li Z, Chen M. On Efficient Feature Ranking Methods for High-Throughput Data Analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1374-1384. [PMID: 26684461 DOI: 10.1109/tcbb.2015.2415790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Efficient mining of high-throughput data has become one of the popular themes in the big data era. Existing biology-related feature ranking methods mainly focus on statistical and annotation information. In this study, two efficient feature ranking methods are presented. Multi-target regression and graph embedding are incorporated in an optimization framework, and feature ranking is achieved by introducing structured sparsity norm. Unlike existing methods, the presented methods have two advantages: (1) the feature subset simultaneously account for global margin information as well as locality manifold information. Consequently, both global and locality information are considered. (2) Features are selected by batch rather than individually in the algorithm framework. Thus, the interactions between features are considered and the optimal feature subset can be guaranteed. In addition, this study presents a theoretical justification. Empirical experiments demonstrate the effectiveness and efficiency of the two algorithms in comparison with some state-of-the-art feature ranking methods through a set of real-world gene expression data sets.
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48
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Li MM, Monzon FA, Biegel JA, Jobanputra V, Laffin JJ, Levy B, Leon A, Miron P, Rossi MR, Toruner G, Alvarez K, Doho G, Dougherty MJ, Hu X, Kash S, Streck D, Znoyko I, Hagenkord JM, Wolff DJ. A multicenter, cross-platform clinical validation study of cancer cytogenomic arrays. Cancer Genet 2015; 208:525-36. [DOI: 10.1016/j.cancergen.2015.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 01/31/2023]
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49
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Ruffalo M, Husseinzadeh H, Makishima H, Przychodzen B, Ashkar M, Koyutürk M, Maciejewski JP, LaFramboise T. Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J Biomed Inform 2015; 58:104-113. [PMID: 26453823 DOI: 10.1016/j.jbi.2015.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/14/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
PURPOSE To date the standard nosology and prognostic schemes for myeloid neoplasms have been based on morphologic and cytogenetic criteria. We sought to test the hypothesis that a comprehensive, unbiased analysis of somatic mutations may allow for an improved classification of these diseases to predict outcome (overall survival). EXPERIMENTAL DESIGN We performed whole-exome sequencing (WES) of 274 myeloid neoplasms, including myelodysplastic syndrome (MDS, N=75), myelodysplastic/myeloproliferative neoplasia (MDS/MPN, N=33), and acute myeloid leukemia (AML, N=22), augmenting the resulting mutational data with public WES results from AML (N=144). We fit random survival forests (RSFs) to the patient survival and clinical/cytogenetic data, with and without gene mutation information, to build prognostic classifiers. A targeted sequencing assay was used to sequence predictor genes in an independent cohort of 507 patients, whose accompanying data were used to evaluate performance of the risk classifiers. RESULTS We show that gene mutations modify the impact of standard clinical variables on patient outcome, and therefore their incorporation hones the accuracy of prediction. The mutation-based classification scheme robustly predicted patient outcome in the validation set (log rank P=6.77 × 10(-21); poor prognosis vs. good prognosis categories HR 10.4, 95% CI 3.21-33.6). The RSF-based approach also compares favorably with recently-published efforts to incorporate mutational information for MDS prognosis. CONCLUSION The results presented here support the inclusion of mutational information in prognostic classification of myeloid malignancies. Our classification scheme is implemented in a publicly available web-based tool (http://myeloid-risk. CASE edu/).
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Affiliation(s)
- Matthew Ruffalo
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA
| | - Holleh Husseinzadeh
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohamed Ashkar
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, OH, USA.
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50
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Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse. Blood 2015; 126:2491-501. [PMID: 26438511 DOI: 10.1182/blood-2015-05-646240] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/22/2015] [Indexed: 01/15/2023] Open
Abstract
Acute myeloid leukemia (AML) with an FLT3 internal tandem duplication (FLT3-ITD) mutation is an aggressive hematologic malignancy with a grave prognosis. To identify the mutational spectrum associated with relapse, whole-exome sequencing was performed on 13 matched diagnosis, relapse, and remission trios followed by targeted sequencing of 299 genes in 67 FLT3-ITD patients. The FLT3-ITD genome has an average of 13 mutations per sample, similar to other AML subtypes, which is a low mutation rate compared with that in solid tumors. Recurrent mutations occur in genes related to DNA methylation, chromatin, histone methylation, myeloid transcription factors, signaling, adhesion, cohesin complex, and the spliceosome. Their pattern of mutual exclusivity and cooperation among mutated genes suggests that these genes have a strong biological relationship. In addition, we identified mutations in previously unappreciated genes such as MLL3, NSD1, FAT1, FAT4, and IDH3B. Mutations in 9 genes were observed in the relapse-specific phase. DNMT3A mutations are the most stable mutations, and this DNMT3A-transformed clone can be present even in morphologic complete remissions. Of note, all AML matched trio samples shared at least 1 genomic alteration at diagnosis and relapse, suggesting common ancestral clones. Two types of clonal evolution occur at relapse: either the founder clone recurs or a subclone of the founder clone escapes from induction chemotherapy and expands at relapse by acquiring new mutations. Relapse-specific mutations displayed an increase in transversions. Functional assays demonstrated that both MLL3 and FAT1 exert tumor-suppressor activity in the FLT3-ITD subtype. An inhibitor of XPO1 synergized with standard AML induction chemotherapy to inhibit FLT3-ITD growth. This study clearly shows that FLT3-ITD AML requires additional driver genetic alterations in addition to FLT3-ITD alone.
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