1
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Suzuki T, Sato Y, Okuno Y, Torii Y, Fukuda Y, Haruta K, Yamaguchi M, Kawamura Y, Hama A, Narita A, Muramatsu H, Yoshikawa T, Takahashi Y, Kimura H, Ito Y, Kawada JI. Single-Cell Transcriptomic Analysis of Epstein-Barr Virus-Associated Hemophagocytic Lymphohistiocytosis. J Clin Immunol 2024; 44:103. [PMID: 38642164 DOI: 10.1007/s10875-024-01701-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
Epstein-Barr virus (EBV) infection can lead to infectious mononucleosis (EBV-IM) and, more rarely, EBV-associated hemophagocytic lymphohistiocytosis (EBV-HLH), which is characterized by a life-threatening hyperinflammatory cytokine storm with immune dysregulation. Interferon-gamma (IFNγ) has been identified as a critical mediator for primary HLH; however, the detailed role of IFNγ and other cytokines in EBV-HLH is not fully understood. In this study, we used single-cell RNA sequencing to characterize the immune landscape of EBV-HLH and compared it with EBV-IM. Three pediatric patients with EBV-HLH with different backgrounds, one with X-linked lymphoproliferative syndrome type 1 (XLP1), two with chronic active EBV disease (CAEBV), and two patients with EBV-IM were enrolled. The TUBA1B + STMN1 + CD8 + T cell cluster, a responsive proliferating cluster with rich mRNA detection, was explicitly observed in EBV-IM, and the upregulation of SH2D1A-the gene responsible for XLP1-was localized in this cluster. This proliferative cluster was scarcely observed in EBV-HLH cases. In EBV-HLH cases with CAEBV, upregulation of LAG3 was observed in EBV-infected cells, which may be associated with an impaired response by CD8 + T cells. Additionally, genes involved in type I interferon (IFN) signaling were commonly upregulated in each cell fraction of EBV-HLH, and activation of type II IFN signaling was observed in CD4 + T cells, natural killer cells, and monocytes but not in CD8 + T cells in EBV-HLH. In conclusion, impaired responsive proliferation of CD8 + T cells and upregulation of type I IFN signaling were commonly observed in EBV-HLH cases, regardless of the patients' background, indicating the key features of EBV-HLH.
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Affiliation(s)
- Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Departments of Pediatrics, Aichi Medical University, Nagakute, Aichi, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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2
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Noda T, Takeichi T, Tanahashi K, Ogawa Y, Takeuchi S, Yoshikawa T, Toriyama E, Ashida M, Imakado S, Tsuchihashi H, Okamoto T, Okuno Y, Ogi T, Sugiura K, Kubo A, Muro Y, Suga Y, Ishida-Yamamoto A, Akiyama M. Updated mutational spectrum and genotype-phenotype correlations in ichthyosis patients with ABCA12 pathogenic variants. Exp Dermatol 2024; 33:e15072. [PMID: 38576105 DOI: 10.1111/exd.15072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
Autosomal recessive congenital ichthyoses (ARCI) is a genetically heterogeneous condition that can be caused by pathogenic variants in at least 12 genes, including ABCA12. ARCI mainly consists of congenital ichthyosiform erythroderma (CIE), lamellar ichthyosis (LI) and harlequin ichthyosis (HI). The objective was to determine previously unreported pathogenic variants in ABCA12 and to update genotype-phenotype correlations for patients with pathogenic ABCA12 variants. Pathogenic variants in ABCA12 were detected using Sanger sequencing or a combination of Sanger sequencing and whole-exome sequencing. To verify the pathogenicity of a previously unreported large deletion and intron variant, cDNA analysis was performed using total RNA extracted from hair roots. Genetic analyses were performed on the patients with CIE, LI, HI and non-congenital ichthyosis with unusual phenotypes (NIUP), and 11 previously unreported ABCA12 variants were identified. Sequencing of cDNA confirmed the aberrant splicing of the variant ABCA12 in the patients with the previously unreported large deletion and intron variant. Our findings expand the phenotype spectrum of ichthyosis patients with ABCA12 pathogenic variants. The present missense variants in ABCA12 are considered to be heterogenous in pathogenicity, and they lead to varying disease severities in patients with ARCI and non-congenital ichthyosis with unusual phenotypes (NIUP).
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Affiliation(s)
- Tatsuhiro Noda
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Nagoya University Institute for Advanced Research, Nagoya, Japan
| | - Kana Tanahashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasushi Ogawa
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - So Takeuchi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takenori Yoshikawa
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Erika Toriyama
- Department of Dermatology, Japanese Red Cross Aichi Medical Center Nagoya Daini Hospital, Nagoya, Japan
| | - Miwa Ashida
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Sumihisa Imakado
- Department of Dermatology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Hitoshi Tsuchihashi
- Department of Dermatology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Takashi Okamoto
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazumitsu Sugiura
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasushi Suga
- Department of Dermatology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | | | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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3
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Kato S, Hamada M, Okamoto A, Yamashita D, Miyoshi H, Arai H, Satou A, Gion Y, Sato Y, Tsuyuki Y, Miyata-Takata T, Takata K, Asano N, Takahashi E, Ohshima K, Tomita A, Hosoda W, Nakamura S, Okuno Y. EBV+ nodal T/NK-cell lymphoma associated with clonal hematopoiesis and structural variations of the viral genome. Blood Adv 2024:bloodadvances.2023012019. [PMID: 38429084 DOI: 10.1182/bloodadvances.2023012019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 03/03/2024] Open
Abstract
Epstein-Barr virus (EBV)+ nodal T- and NK-cell lymphoma (EBV+ nPTCL) is a peripheral T-cell lymphoma (PTCL) that presents as a primary nodal disease with T-cell phenotype and EBV harboring on tumor cells. To date, the genetic aspect of EBV+ nPTCL has not been fully investigated. In this study, whole-exome and/or genome sequencing was performed on 22 cases of EBV+ nPTCL. TET2 (68%) and DNMT3A (32%) were observed to be the most frequently mutated genes whose presence was associated with poor overall survival (p = 0.004). The RHOA p.Gly17Val mutation was identified in two patients who had TET2 and/or DNMT3A mutations. In four patients with TET2/DNMT3A alterations, blood cell-rich tissues (bone marrow [BM] or spleen) were available as paired normal samples. Three out of these four cases had at least one identical TET2/DNMT3A mutation in the BM or spleen. Additionally, the whole part of the EBV genome was sequenced and structural variations (SVs) were found frequent among the EBV genomes (63%). The most frequently identified type of SV was deletion. In one patient, four pieces of human chromosome 9, including PD-L1 were identified to be tandemly incorporated into the EBV genome. The 3'-untranslated region of PD-L1 was truncated, causing a high-level of PD-L1 protein expression. Overall, the frequent TET2 and DNMT3A mutations in EBV+ nPTCL seem to be closely associated with clonal hematopoiesis and, together with the EBV genome deletions, may contribute to the pathogenesis of this intractable lymphoma.
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Affiliation(s)
| | - Motoharu Hamada
- Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | | | | | | | - Haruto Arai
- Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akira Satou
- Aichi Medical University School of Medicine, Nagakute, Japan
| | - Yuka Gion
- Ehime Prefectural University of Health Sciences, Japan
| | - Yasuharu Sato
- Okayama University Graduate School of Medicine, Japan
| | | | - Tomoko Miyata-Takata
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Katsuyoshi Takata
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naoko Asano
- Nagano Prefectural Shinshu Medical Center, Suzaka, Japan, Suzaka, Japan
| | | | | | - Akihiro Tomita
- Fujita Health University School of Medicine, Toyoake, Japan
| | | | | | - Yusuke Okuno
- Nagoya City University Graduate School of Medical Sciences, Nagoya-shi, Japan
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4
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Suzuki K, Hama A, Okuno Y, Xu Y, Narita A, Yoshida N, Muramatsu H, Nishio N, Kato K, Kojima S, Yoo KH, Takahashi Y. A retrospective analysis of gene fusions and treatment outcomes in pediatric acute megakaryoblastic leukemia without Down syndrome. Haematologica 2024. [PMID: 38299674 DOI: 10.3324/haematol.2023.283760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Indexed: 02/02/2024] Open
Abstract
Not available.
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Affiliation(s)
- Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Asahito Hama
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Aichi
| | - Yinyan Xu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Nao Yoshida
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Aichi
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Nobuhiro Nishio
- Department of Advanced Medicine, Nagoya University Hospital, Aichi
| | - Koji Kato
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Aichi
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Aichi.
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5
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Sagou K, Sato Y, Okuno Y, Watanabe T, Inagaki T, Motooka Y, Toyokuni S, Murata T, Kiyoi H, Kimura H. Epstein-Barr virus lytic gene BNRF1 promotes B-cell lymphomagenesis via IFI27 upregulation. PLoS Pathog 2024; 20:e1011954. [PMID: 38300891 PMCID: PMC10833513 DOI: 10.1371/journal.ppat.1011954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous human lymphotropic herpesvirus that is causally associated with several malignancies. In addition to latent factors, lytic replication contributes to cancer development. In this study, we examined whether the lytic gene BNRF1, which is conserved among gamma-herpesviruses, has an important role in lymphomagenesis. We found that lymphoblastoid cell lines (LCLs) established by BNRF1-knockout EBV exhibited remarkably lower pathogenicity in a mice xenograft model than LCLs produced by wild-type EBV (LCLs-WT). RNA-seq analyses revealed that BNRF1 elicited the expression of interferon-inducible protein 27 (IFI27), which promotes cell proliferation. IFI27 knockdown in LCLs-WT resulted in excessive production of reactive oxygen species, leading to cell death and significantly decreased their pathogenicity in vivo. We also confirmed that IFI27 was upregulated during primary infection in B-cells. Our findings revealed that BNRF1 promoted robust proliferation of the B-cells that were transformed by EBV latent infection via IFI27 upregulation both in vitro and in vivo.
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Affiliation(s)
- Ken Sagou
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoki Inagaki
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yashiro Motooka
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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6
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Yamashita D, Muramatsu H, Narita A, Wakamatsu M, Tsumura Y, Sajiki D, Maemura R, Yamamori A, Imaya M, Narita K, Kataoka S, Taniguchi R, Nishio N, Okuno Y, Fujita N, Koh K, Umeda K, Morihana E, Iwafuchi H, Ito M, Kojima S, Hama A, Takahashi Y. Hematological abnormalities in Jacobsen syndrome: cytopenia of varying severities and morphological abnormalities in peripheral blood and bone marrow. Haematologica 2023; 108:3438-3443. [PMID: 37317839 PMCID: PMC10690895 DOI: 10.3324/haematol.2022.282513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
Not available.
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Affiliation(s)
- Daiki Yamashita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Yusuke Tsumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Daichi Sajiki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Ryo Maemura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Ayako Yamamori
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Masayuki Imaya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - Naoto Fujita
- Department of Pediatrics, Hiroshima Red Cross Hospital and Atomic-Bomb Survivors Hospital, Hiroshima
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto
| | - Eiji Morihana
- Department of Pediatric Cardiology, Aichi Children's Health and Medical Center, Obu
| | - Hideto Iwafuchi
- Department of Pathology, Shizuoka Children's Hospital, Shizuoka
| | - Masafumi Ito
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
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7
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Yoshida T, Muramatsu H, Wakamatsu M, Sajiki D, Murakami N, Kitazawa H, Okamoto Y, Taniguchi R, Kataoka S, Narita A, Hama A, Okuno Y, Takahashi Y. Clinical and molecular features of CBL-mutated juvenile myelomonocytic leukemia. Haematologica 2023; 108:3115-3119. [PMID: 37226702 PMCID: PMC10620587 DOI: 10.3324/haematol.2022.282385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/15/2023] [Indexed: 05/26/2023] Open
Affiliation(s)
- Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Daichi Sajiki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Yasuhiro Okamoto
- Department of Pediatrics, Kagoshima University Graduate school of Medical and Dental Sciences, Kagoshima
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
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8
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Okuno Y, Clore GM. Extending the Experimentally Accessible Range of Spin Dipole-Dipole Spectral Densities for Protein-Cosolute Interactions by Temperature-Dependent Solvent Paramagnetic Relaxation Enhancement Measurements. J Phys Chem B 2023; 127:7887-7898. [PMID: 37681752 DOI: 10.1021/acs.jpcb.3c05301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Longitudinal (Γ1) and transverse (Γ2) solvent paramagnetic relaxation enhancement (sPRE) yields field-dependent information in the form of spectral densities that provides unique information related to cosolute-protein interactions and electrostatics. A typical protein sPRE data set can only sample a few points on the spectral density curve, J(ω), within a narrow frequency window (500 MHz to ∼1 GHz). However, complex interactions and dynamics of paramagnetic cosolutes around a protein make it difficult to directly interpret the few experimentally accessible points of J(ω). In this paper, we show that it is possible to significantly extend the experimentally accessible frequency range (corresponding to a range from ∼270 MHz to 1.8 GHz) by acquiring a series of sPRE experiments at different temperatures. This approach is based on the scaling property of J(ω) originally proposed by Melchior and Fries for small molecules. Here, we demonstrate that the same scaling property also holds for geometrically far more complex systems such as proteins. Using the extended spectral densities derived from the scaling property as the reference dataset, we demonstrate that our previous approach that makes use of a non-Lorentzian Ansatz spectral density function to fit only J(0) and one to two J(ω) points allows one to obtain accurate values for the concentration-normalized equilibrium average of the electron-proton interspin separation ⟨r-6⟩norm and the correlation time τC, which provide quantitative information on the energetics and timescale, respectively, of local cosolute-protein interactions. We also show that effective near-surface potentials, ϕENS, obtained from ⟨r-6⟩norm provide a reliable and quantitative measure of intermolecular interactions including electrostatics, while ϕENS values obtained from only Γ1 or Γ2 sPRE rates can have significant artifacts as a consequence of potential variations and changes in the diffusive properties of the cosolute around the protein surface. Finally, we discuss the experimental feasibility and limitations of extracting the high-frequency limit of J(ω) that is related to ⟨r-8⟩norm and report on the extremely local intermolecular potential.
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Affiliation(s)
- Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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9
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Sugimoto A, Watanabe T, Matsuoka K, Okuno Y, Yanagi Y, Narita Y, Mabuchi S, Nobusue H, Sugihara E, Hirayama M, Ide T, Onouchi T, Sato Y, Kanda T, Saya H, Iwatani Y, Kimura H, Murata T. Growth Transformation of B Cells by Epstein-Barr Virus Requires IMPDH2 Induction and Nucleolar Hypertrophy. Microbiol Spectr 2023; 11:e0044023. [PMID: 37409959 PMCID: PMC10433962 DOI: 10.1128/spectrum.00440-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The in vitro growth transformation of primary B cells by Epstein-Barr virus (EBV) is the initial step in the development of posttransplant lymphoproliferative disorder (PTLD). We performed electron microscopic analysis and immunostaining of primary B cells infected with wild-type EBV. Interestingly, the nucleolar size was increased by two days after infection. A recent study found that nucleolar hypertrophy, which is caused by the induction of the IMPDH2 gene, is required for the efficient promotion of growth in cancers. In the present study, RNA-seq revealed that the IMPDH2 gene was significantly induced by EBV and that its level peaked at day 2. Even without EBV infection, the activation of primary B cells by the CD40 ligand and interleukin-4 increased IMPDH2 expression and nucleolar hypertrophy. Using EBNA2 or LMP1 knockout viruses, we found that EBNA2 and MYC, but not LMP1, induced the IMPDH2 gene during primary infections. IMPDH2 inhibition by mycophenolic acid (MPA) blocked the growth transformation of primary B cells by EBV, leading to smaller nucleoli, nuclei, and cells. Mycophenolate mofetil (MMF), which is a prodrug of MPA that is approved for use as an immunosuppressant, was tested in a mouse xenograft model. Oral MMF significantly improved the survival of mice and reduced splenomegaly. Taken together, these results indicate that EBV induces IMPDH2 expression through EBNA2-dependent and MYC-dependent mechanisms, leading to the hypertrophy of the nucleoli, nuclei, and cells as well as efficient cell proliferation. Our results provide basic evidence that IMPDH2 induction and nucleolar enlargement are crucial for B cell transformation by EBV. In addition, the use of MMF suppresses PTLD. IMPORTANCE EBV infections cause nucleolar enlargement via the induction of IMPDH2, which are essential for B cell growth transformation by EBV. Although the significance of IMPDH2 induction and nuclear hypertrophy in the tumorigenesis of glioblastoma has been reported, EBV infection brings about the change quickly by using its transcriptional cofactor, EBNA2, and MYC. Moreover, we present here, for the novel, basic evidence that an IMPDH2 inhibitor, namely, MPA or MMF, can be used for EBV-positive posttransplant lymphoproliferative disorder (PTLD).
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Affiliation(s)
- Atsuko Sugimoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yusuke Yanagi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yohei Narita
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Seiyo Mabuchi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Hiroyuki Nobusue
- Division of Gene Regulation, Cancer Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Eiji Sugihara
- Division of Gene Regulation, Cancer Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
- Open Facility Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Masaya Hirayama
- Department of Morphology and Diagnostic Pathology, School of Medical Sciences, Fujita Health University, Toyoake, Japan
- Department of Biomedical Molecular Sciences, Graduate School of Medicine, Fujita Health University, Toyoake, Japan
| | - Tomihiko Ide
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
- Open Facility Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Takanori Onouchi
- Open Facility Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teru Kanda
- Department of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Hideyuki Saya
- Division of Gene Regulation, Cancer Center, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayuki Murata
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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10
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Takeichi T, Ito Y, Lee JYW, Murase C, Okuno Y, Muro Y, McGrath JA, Akiyama M. KLK11 ichthyosis: large truncal hyperkeratotic pigmented plaques underscore a distinct autosomal dominant disorder of cornification. Br J Dermatol 2023; 189:134-136. [PMID: 37212630 DOI: 10.1093/bjd/ljad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/07/2023] [Accepted: 03/15/2023] [Indexed: 05/23/2023]
Abstract
Recently, Gong et al. reported two substitutions, p.(Gly50Glu) and p.(Gly50Arg), located at the last amino acid of the estimated signal peptide in kallikrein11 (KLK11) in three independent ichthyosiform erythroderma or erythrokeratoderma pedigrees (Gong et al., Br J Dermatol, 2023). Here, we present a further case of autosomal dominant congenital ichthyosiform erythroderma caused by the p.(Gly50Glu) substitution in KLK11; the patient had sharply demarcated pigmented hyperkeratotic lesions. Thus, p.(Gly50Glu) in KLK11 might represent a recurrent variant underlying this recently reported autosomal dominant disorder of cornification, and the large hyperkeratotic pigmented plaques seen in all patients may represent a pathognomonic part of the phenotype.
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Affiliation(s)
- Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasutoshi Ito
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - John Y W Lee
- St John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Chiaki Murase
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - John A McGrath
- St John's Institute of Dermatology, King's College London, Guy's Hospital, London, UK
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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11
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Al-Kzayer LFY, Saeed RM, Ghali HH, Tanaka M, Al-Jadiry MF, Faraj SA, Al-Hadad SA, Al Abdullah HMS, Majeed AA, Qadir AO, Abdullah DA, Noori KD, Hama ZM, Muhsin AA, Al-Doski AA, Al-Agele YS, Malallah AH, Al-Badrani KS, Khaleel AMA, Kamata M, Hamada M, Kojima S, Nakazawa Y, Okuno Y. Comprehensive genetic analyses of childhood acute leukemia in Iraq using next-generation sequencing. Transl Pediatr 2023; 12:827-844. [PMID: 37305720 PMCID: PMC10248931 DOI: 10.21037/tp-22-512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background Molecular analyses in hematological malignancies provide insights about genetic makeup. Probable etiological factors in leukemogenesis could also be disclosed. Since genetic analyses are still primitive in Iraq, a country of repeated wars, we conceived of performing next-generation sequencing (NGS), to disclose the genomic landscape of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) among a cohort of Iraqi children. Methods Dried blood samples were collected from Iraqi children with ALL (n=55), or AML (n=11), and transferred to Japan where NGS was done. Whole-exome, whole-genome, and targeted gene sequencings were performed. Results Somatic point mutations and the copy number variations among Iraqi children with acute leukemia were comparable with those in other countries, and cytosine-to-thymine nucleotide alterations were dominant. Strikingly, TCF3-PBX1 was the most recurrent fusion gene (22.4%) in B-cell precursor ALL (B-ALL), and acute promyelocytic leukemia (AML-M3) was subtyped in 5 AML cases. Additionally, a high frequency of RAS signaling pathway mutations was detected in children with B-ALL (38.8%), along with 3 AML cases that carried oncogenic RAS. Conclusions Apart from disclosing the high frequency of TCF3-PBX1, NGS confirmed our previous finding of recurrent RAS mutations in Iraqi childhood acute leukemia. Our results suggest that the biology of Iraqi childhood acute leukemia is in part characteristic, where the war-aftermath environment or geography might play a role.
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Affiliation(s)
| | - Raghad M. Saeed
- Department of Pediatric Oncology, Children Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Hasanein Habeeb Ghali
- Department of Pediatric Oncology, Children Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq
| | - Miyuki Tanaka
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mazin F. Al-Jadiry
- Department of Pediatric Oncology, Children Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq
| | - Safa A. Faraj
- Department of Pediatric Oncology, Children Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
- Department of Pediatrics, College of Medicine, Wasit University, Al Kut, Iraq
| | - Salma A. Al-Hadad
- Department of Pediatric Oncology, Children Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq
| | | | - Athar A. Majeed
- Department of Pediatric Oncology, Basra Children’s Specialty Hospital, Basra, Iraq
| | - Ali Omer Qadir
- Department of Pediatric Hematology and Oncology, Hiwa Cancer Hospital, Sulaymaniyah, Iraq
| | - Dana Ahmed Abdullah
- Department of Hematopathology, Hiwa Cancer Hospital, Sulaymaniyah, Iraq
- Department of Pathology, College of Medicine, University of Sulaimani, Sulaymaniyah, Iraq
| | - Kani Dlawar Noori
- Department of Hematopathology, Hiwa Cancer Hospital, Sulaymaniyah, Iraq
| | | | - Abdulrahman A. Muhsin
- Department of Medical Laboratories, College of Health Science, University of Duhok, Duhok, Iraq
| | - Adnan Anwer Al-Doski
- Department of Hematopathology, College of Medicine, University of Duhok, Duhok, Iraq
| | - Yasir S. Al-Agele
- Department of Pediatric Oncology, Ibn Al-Atheer Hospital for Children, Mosul, Iraq
| | | | | | - Asmaa M. A. Khaleel
- Department of Hematopathology, Ibn Al-Atheer Hospital for Children, Mosul, Iraq
| | - Minoru Kamata
- Japan Chernobyl Foundation (JCF) NPO, Matsumoto, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Medical Genomics Centre, Nagoya University Hospital, Nagoya, Japan
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12
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Oshima K, Hinoki A, Uchida H, Tanaka Y, Okuno Y, Go Y, Shirota C, Tainaka T, Sumida W, Yokota K, Makita S, Takimoto A, Kano Y, Sawa S. Single-cell RNA sequencing of intestinal immune cells in neonatal necrotizing enterocolitis. Pediatr Surg Int 2023; 39:179. [PMID: 37041419 DOI: 10.1007/s00383-023-05461-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/03/2023] [Indexed: 04/13/2023]
Abstract
PURPOSE Necrotizing enterocolitis (NEC) causes fatal intestinal necrosis in neonates, but its etiology is unknown. We analyzed the intestinal immune response to NEC. METHODS Using single-cell RNA sequencing (scRNA-seq), we analyzed the gene expression profiles of intestinal immune cells from four neonates with intestinal perforation (two with NEC and two without NEC). Target mononuclear cells were extracted from the lamina propria of the resected intestines. RESULTS In all four cases, major immune cells, such as T cells (15.1-47.7%), B cells (3.1-19.0%), monocytes (16.5-31.2%), macrophages (1.6-17.4%), dendritic cells (2.4-12.2%), and natural killer cells (7.5-12.8%), were present in similar proportions to those in the neonatal cord blood. Gene set enrichment analysis showed that the MTOR, TNF-α, and MYC signaling pathways were enriched in T cells of the NEC patients, suggesting upregulated immune responses related to inflammation and cell proliferation. In addition, all four cases exhibited a bias toward cell-mediated inflammation, based on the predominance of T helper 1 cells. CONCLUSION Intestinal immunity in NEC subjects exhibited stronger inflammatory responses compared to non-NEC subjects. Further scRNA-seq and cellular analysis may improve our understanding of the pathogenesis of NEC.
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Affiliation(s)
- Kazuo Oshima
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatric Surgery, Saitama Medical University, Saitama, Japan
| | - Akinari Hinoki
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroo Uchida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yujiro Tanaka
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatric Surgery, Saitama Medical University, Saitama, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- Department of System Neuroscience, National Institute for Physiological Science, Okazaki, Japan
- Department of Physiological Science, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Chiyoe Shirota
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahisa Tainaka
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wataru Sumida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuki Yokota
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Makita
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Aitaro Takimoto
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoko Kano
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichiro Sawa
- Division of Mucosal Immunology, Research Center for Systems Immunology, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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13
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Yamamori A, Hamada M, Muramatsu H, Wakamatsu M, Hama A, Narita A, Tsumura Y, Yoshida T, Doi T, Terada K, Higa T, Yamamoto N, Miura H, Shiota M, Watanabe K, Yoshida N, Maemura R, Imaya M, Miwata S, Narita K, Kataoka S, Taniguchi R, Suzuki K, Kawashima N, Nishio N, Iwafuchi H, Ito M, Kojima S, Okuno Y, Takahashi Y. Germline and somatic RUNX1 variants in a pediatric bone marrow failure cohort. Am J Hematol 2023; 98:E102-E105. [PMID: 36740830 DOI: 10.1002/ajh.26874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/07/2023]
Affiliation(s)
- Ayako Yamamori
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Tsumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takehiko Doi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology, Japanese Red Cross Narita Hospital, Narita, Japan
| | - Takeshi Higa
- Division of Pediatric Hematology/Oncology, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Okinawa, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Mitsutaka Shiota
- Department of Pediatrics, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Nao Yoshida
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Ryo Maemura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masayuki Imaya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Miwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideto Iwafuchi
- Department of Pathology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Masafumi Ito
- Department of Pathology, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Science and Medical School, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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14
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Murata T, Iwahori S, Okuno Y, Nishitsuji H, Yanagi Y, Watashi K, Wakita T, Kimura H, Shimotohno K. N6-methyladenosine Modification of Hepatitis B Virus RNA in the Coding Region of HBx. Int J Mol Sci 2023; 24:ijms24032265. [PMID: 36768585 PMCID: PMC9917364 DOI: 10.3390/ijms24032265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
N6-methyladenosine (m6A) is a post-transcriptional modification of RNA involved in transcript transport, degradation, translation, and splicing. We found that HBV RNA is modified by m6A predominantly in the coding region of HBx. The mutagenesis of methylation sites reduced the HBV mRNA and HBs protein levels. The suppression of m6A by an inhibitor or knockdown in primary hepatocytes decreased the viral RNA and HBs protein levels in the medium. These results suggest that the m6A modification of HBV RNA is needed for the efficient replication of HBV in hepatocytes.
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Affiliation(s)
- Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake 470-1192, Japan
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Correspondence:
| | - Satoko Iwahori
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake 470-1192, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Hironori Nishitsuji
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake 470-1192, Japan
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
| | - Yusuke Yanagi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kunitada Shimotohno
- Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan
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15
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Sakai T, Okuno Y, Murakami N, Shimoyama Y, Imagama S, Nishida Y. Case report: Novel NIPBL-BEND2 fusion gene identified in osteoblastoma-like phosphaturic mesenchymal tumor of the fibula. Front Oncol 2023; 12:956472. [PMID: 36686800 PMCID: PMC9850095 DOI: 10.3389/fonc.2022.956472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/29/2022] [Indexed: 01/07/2023] Open
Abstract
Phosphaturic mesenchymal tumor (PMT) is a rare tumor that secretes fibroblast growth factor 23 (FGF23) and causes hypophosphatemia and tumor-induced osteomalacia (TIO). Fusion genes FN1-FGFR1 and FN1-FGF1 have been detected in some PMTs, but the pathogenesis of PMTs without these fusion genes remains unclear. Here, we report a 12-year-old boy with persistent muscle weakness and gait disturbance. Roentgenographic examination revealed a radiolucent lesion with endosteal scalloping in the left fibula, while his serum level of FGF23 was markedly increased. Combined with simple X-ray findings of other body parts, we suspected that TIO was caused by PMT, and resected the tumor. After resection, the serum level of FGF23 started to decrease immediately and normalized within 3 hours after resection, with this being earlier than normalization of the serum phosphorus level. In RNA sequencing, FN1-FGFR1 and FN1-FGF1 were not detected, but a novel NIPBL-BEND2 fusion gene was identified. When we forcedly expressed this fusion gene in HEK293T cells and MG63 cells, cell proliferation was enhanced in both cell lines. Furthermore, Gene set enrichment analysis of HEK293T cells showed significant upregulation of MYC-target genes. Our results suggest that this novel NIPBL-BEND2 fusion gene promotes cell proliferation possibly via the MYC pathway and might be one of the etiologies of PMTs other than FN1-FGFR1 or FN1-FGF1.
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Affiliation(s)
- Tomohisa Sakai
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan,Rare Cancer Center, Nagoya University Hospital, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshie Shimoyama
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Shiro Imagama
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nishida
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan,Rare Cancer Center, Nagoya University Hospital, Nagoya, Japan,Department of Rehabilitation, Nagoya University Hospital, Nagoya, Japan,*Correspondence: Yoshihiro Nishida,
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16
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Maemura R, Wakamatsu M, Matsumoto K, Sakaguchi H, Yoshida N, Hama A, Yoshida T, Miwata S, Kitazawa H, Narita K, Kataoka S, Ichikawa D, Hamada M, Taniguchi R, Suzuki K, Kawashima N, Nishikawa E, Narita A, Okuno Y, Nishio N, Kato K, Kojima S, Morita K, Muramatsu H, Takahashi Y. Clinical Impact of Melphalan Pharmacokinetics on Transplantation Outcomes in Children Undergoing Hematopoietic Stem Cell Transplantation. Cell Transplant 2022; 31:9636897221143364. [PMID: 36537564 PMCID: PMC9772935 DOI: 10.1177/09636897221143364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Melphalan is widely used for hematopoietic stem cell transplantation (HSCT) conditioning. However, the relationship between its pharmacokinetic (PK) and transplantation outcomes in children has not been thoroughly investigated. We prospectively analyzed the relationship between melphalan area under the curve (AUC) and transplantation outcome and examined the development of a predictive model for melphalan clearance in children. This study included 43 children aged 0 to 19 years who underwent HSCT following a melphalan-based conditioning regimen from 2017 to 2021. In univariable analysis, high-melphalan AUC resulted in a significantly lower cumulative incidence of acute graft-versus-host disease and a higher cumulative incidence of thrombotic microangiopathy, although no significant difference was observed in survival. Regression analysis of a randomly selected derivation cohort (n = 21) revealed the following covariate PK model: predicted melphalan clearance (mL/min) = 6.47 × 24-h urinary creatinine excretion rate (CER, g/day) × 24-h creatinine clearance rate (CCR, mL/min) + 92.8. In the validation cohort (n = 22), the measured melphalan clearance values were significantly correlated with those calculated based on the prediction equation (R2 = 0.663). These results indicate that melphalan exposure may be optimized by adjusting the melphalan dose according to CER and CCR.
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Affiliation(s)
- Ryo Maemura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan,Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan,Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Kana Matsumoto
- Department of Clinical Pharmaceutics, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe, Japan
| | - Hirotoshi Sakaguchi
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Nao Yoshida
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Miwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Koji Kato
- Department of Hematology and Oncology, Children’s Medical Center, Japanese Red Cross Aichi Medical Center Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kunihiko Morita
- Department of Clinical Pharmaceutics, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan,Hideki Muramatsu, Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Aichi, Japan.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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17
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Tugarinov V, Okuno Y, Torricella F, Karamanos TK, Clore GM. A "Steady-State" Relaxation Dispersion Nuclear Magnetic Resonance Experiment for Studies of Chemical Exchange in Degenerate 1H Transitions of Methyl Groups. J Phys Chem Lett 2022; 13:11271-11279. [PMID: 36449372 DOI: 10.1021/acs.jpclett.2c02937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Degenerate spin-systems consisting of magnetically equivalent nuclear spins, such as a 1H3 spin-system in selectively 13CH3-labeled proteins, present considerable challenges for the design of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments to characterize chemical exchange on the micro-to-millisecond time-scale. Several approaches have been previously proposed for the elimination of deleterious artifacts observed in methyl 1H CPMG relaxation dispersion profiles obtained for (13C)1H3 groups. We describe an alternative, experimentally simple solution and design a "steady-state" methyl 1H CPMG scheme, where 90° or acute-angle (<90°) 1H radiofrequency pulses are applied after each CPMG echo in-phase with methyl 1H magnetization, resulting in the establishment of a "steady-state" for effective rates of magnetization decay. A simple computational procedure for quantitative analysis of the "steady-state" CPMG relaxation dispersion profiles is developed. The "steady-state" CPMG methodology is applied to two protein systems where exchange between major and minor species occurs in different regimes on the chemical shift time-scale.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Francesco Torricella
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Theodoros K Karamanos
- The Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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18
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Okuno Y, Schwieters CD, Yang Z, Clore GM. Theory and Applications of Nitroxide-based Paramagnetic Cosolutes for Probing Intermolecular and Electrostatic Interactions on Protein Surfaces. J Am Chem Soc 2022; 144:21371-21388. [DOI: 10.1021/jacs.2c10035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Charles D. Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Zhilin Yang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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19
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Imaizumi T, Meyer J, Wakamatsu M, Kitazawa H, Murakami N, Okuno Y, Yoshida T, Sajiki D, Hama A, Kojima S, Takahashi Y, Loh M, Stieglitz E, Muramatsu H. Clinical parameter-based prediction of DNA methylation classification generates a prediction model of prognosis in patients with juvenile myelomonocytic leukemia. Sci Rep 2022; 12:14753. [PMID: 36042365 PMCID: PMC9427938 DOI: 10.1038/s41598-022-18733-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/18/2022] [Indexed: 11/11/2022] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare heterogeneous hematological malignancy of early childhood characterized by causative RAS pathway mutations. Classifying patients with JMML using global DNA methylation profiles is useful for risk stratification. We implemented machine learning algorithms (decision tree, support vector machine, and naïve Bayes) to produce a DNA methylation-based classification according to recent international consensus definitions using a well-characterized pooled cohort of patients with JMML (n = 128). DNA methylation was originally categorized into three subgroups: high methylation (HM), intermediate methylation (IM), and low methylation (LM), which is a trichotomized classification. We also dichotomized the subgroups as HM/IM and LM. The decision tree model showed high concordances with 450k-based methylation [82.3% (106/128) for the dichotomized and 83.6% (107/128) for the trichotomized subgroups, respectively]. With an independent cohort (n = 72), we confirmed that these models using both the dichotomized and trichotomized classifications were highly predictive of survival. Our study demonstrates that machine learning algorithms can generate clinical parameter-based models that predict the survival outcomes of patients with JMML and high accuracy. These models enabled us to rapidly and effectively identify candidates for augmented treatment following diagnosis.
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Affiliation(s)
- Takahiro Imaizumi
- Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Daichi Sajiki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan
| | - Mignon Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, USA
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8560, Japan.
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20
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Narita K, Muramatsu H, Narumi S, Nakamura Y, Okuno Y, Suzuki K, Hamada M, Yamaguchi N, Suzuki A, Nishio Y, Shiraki A, Yamamori A, Tsumura Y, Sawamura F, Kawaguchi M, Wakamatsu M, Kataoka S, Kato K, Asada H, Kubota T, Muramatsu Y, Kidokoro H, Natsume J, Mizuno S, Nakata T, Inagaki H, Ishihara N, Yonekawa T, Okumura A, Ogi T, Kojima S, Kaname T, Hasegawa T, Saitoh S, Takahashi Y. Whole-exome analysis of 177 pediatric patients with undiagnosed diseases. Sci Rep 2022; 12:14589. [PMID: 36028527 PMCID: PMC9418234 DOI: 10.1038/s41598-022-14161-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Recently, whole-exome sequencing (WES) has been used for genetic diagnoses of patients who remain otherwise undiagnosed. WES was performed in 177 Japanese patients with undiagnosed conditions who were referred to the Tokai regional branch of the Initiative on Rare and Undiagnosed Diseases (IRUD) (TOKAI-IRUD). This study included only patients who had not previously received genome-wide testing. Review meetings with specialists in various medical fields were held to evaluate the genetic diagnosis in each case, which was based on the guidelines of the American College of Medical Genetics and Genomics. WES identified diagnostic single-nucleotide variants in 66 patients and copy number variants (CNVs) in 11 patients. Additionally, a patient was diagnosed with Angelman syndrome with a complex clinical phenotype upon detection of a paternally derived uniparental disomy (UPD) [upd(15)pat] wherein the patient carried a homozygous DUOX2 p.E520D variant in the UPD region. Functional analysis confirmed that this DUOX2 variant was a loss-of-function missense substitution and the primary cause of congenital hypothyroidism. A significantly higher proportion of genetic diagnoses was achieved compared to previous reports (44%, 78/177 vs. 24-35%, respectively), probably due to detailed discussions and the higher rate of CNV detection.
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Affiliation(s)
- Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health, Tokyo, Japan.,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yuji Nakamura
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Naoya Yamaguchi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Atsushi Suzuki
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yosuke Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Anna Shiraki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Ayako Yamamori
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Tsumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Fumi Sawamura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Masahiro Kawaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Hideyuki Asada
- Department of Pediatrics, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Tetsuo Kubota
- Department of Pediatrics, Anjo Kosei Hospital, Anjo, Japan
| | - Yukako Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroyuki Kidokoro
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun Natsume
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Aichi Developmental Disability Center Central Hospital, Kasugai, Japan
| | - Tomohiko Nakata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takahiro Yonekawa
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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21
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Wakamatsu M, Kojima D, Muramatsu H, Okuno Y, Kataoka S, Nakamura F, Sakai Y, Tsuge I, Ito T, Ueda K, Saito A, Morihana E, Ito Y, Ohashi N, Tanaka M, Tanaka T, Kojima S, Nakajima Y, Ito T, Takahashi Y. TREC/KREC Newborn Screening followed by Next-Generation Sequencing for Severe Combined Immunodeficiency in Japan. J Clin Immunol 2022; 42:1696-1707. [PMID: 35902420 DOI: 10.1007/s10875-022-01335-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/15/2022] [Indexed: 10/16/2022]
Abstract
PURPOSE The aim of this study is to evaluate the usefulness of T cell receptor excision circle (TREC) and/or kappa-deleting recombination excision circle (KREC) measurements integrated with diagnostic next-generation sequencing (NGS) analysis using a severe combined immunodeficiency (SCID) newborn screening (NBS) program. METHODS TREC and/or KREC values were measured in 137,484 newborns between April 2017 and December 2021 using EnLite TREC (n = 80,791) or TREC/KREC kits (n = 56,693). For newborns with positive screening results, diagnostic NGS analysis was performed with a 349-gene panel to detect genetic mutations associated with primary immunodeficiencies (PIDs). RESULTS A total of 145 newborns (0.11%) had abnormal TREC and/or KREC values, and a genetic diagnosis was established in 2 patients with SCID (1 in 68,742 newborns) (IL2RG-SCID and reticular dysgenesis) and 10 with non-SCID PIDs with T and/or B cell deficiencies (1 in 13,748 newborns) using NGS analysis. Furthermore, TREC values of 2849 newborns were measured and confirmed the significant correlation between the results of both TREC and TREC/KREC kits (P < 0.001) and naïve T cell counts. CONCLUSIONS We performed the first large-scale TREC and TREC/KREC NBS programs in Japan. Our NBS programs followed by the diagnostic NGS analysis for newborns with abnormal TREC and/or KREC values are useful for the early identification and rapid molecular evaluation of not only SCID but also different non-SCID PIDs.
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Affiliation(s)
- Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daiei Kojima
- Department of Pediatrics, Ogaki Municipal Hospital, Ogaki, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiko Nakamura
- Department of Clinical Laboratory, Aichi Health Promotion Foundation, Nagoya, Japan
| | - Yoshimi Sakai
- Department of Clinical Laboratory, Aichi Health Promotion Foundation, Nagoya, Japan
| | - Ikuya Tsuge
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Tsuyoshi Ito
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Japan
| | - Kazuto Ueda
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Akiko Saito
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya, Japan
| | - Eiji Morihana
- Department of Neonatology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Yasuhiko Ito
- Department of Pediatrics, Nagoya City University West Medical Center, Nagoya, Japan
| | - Naoki Ohashi
- Department of Paediatric Cardiology, Chukyo Children Heart Centre, Japan, Community Health Care Organization Chukyo Hospital, Nagoya, Japan
| | - Makito Tanaka
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Taihei Tanaka
- Department of Pediatrics, Japanese Red Cross Aichi Medical Center Nagoya Daini Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoko Nakajima
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Tetsuya Ito
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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22
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Sato Y, Yaguchi M, Okuno Y, Ishimaru H, Sagou K, Ozaki S, Suzuki T, Inagaki T, Umeda M, Watanabe T, Fujimuro M, Murata T, Kimura H. Epstein-Barr virus tegument protein BGLF2 in exosomes released from virus-producing cells facilitates de novo infection. Cell Commun Signal 2022; 20:95. [PMID: 35729616 PMCID: PMC9210680 DOI: 10.1186/s12964-022-00902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background Viruses must adapt to the environment of their host cells to establish infection and persist. Diverse mammalian cells, including virus-infected cells, release extracellular vesicles such as exosomes containing proteins and miRNAs, and use these vesicles to mediate intercellular communication. However, the roles of exosomes in viral infection remain unclear. Results We screened viral proteins to identify those responsible for the exosome-mediated enhancement of Epstein–Barr virus (EBV) infection. We identified BGLF2 protein encapsulated in exosomes, which were released by EBV-infected cells. BGLF2 protein is a tegument protein that exists in the space between the envelope and nucleocapsid, and it is released into the cytoplasm shortly after infection. BGLF2 protein-containing exosomes enhanced viral gene expression and repressed innate immunity, thereby supporting the EBV infection. Conclusions The EBV tegument protein BGLF2 is encapsulated in exosomes and released by infected cells to facilitate the establishment of EBV infection. These findings suggest that tegument proteins support viral infection not only between the envelope and nucleocapsid, as well as in extraviral particles such as exosomes. Graphical abstract ![]()
Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00902-7.
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Affiliation(s)
- Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan. .,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
| | - Masahiro Yaguchi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Virology, Graduate School of Medicine, Nagoya City University, Nagoya, Japan
| | - Hanako Ishimaru
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan.,Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ken Sagou
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Somi Ozaki
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Suzuki
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoki Inagaki
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Dermatology, School of Medicine, University of California Davis (UC Davis), Sacramento, CA, USA
| | - Miki Umeda
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Takayuki Murata
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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23
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Narita S, Unno K, Kato K, Okuno Y, Sato Y, Tsumura Y, Fujikawa Y, Shimizu Y, Hayashida R, Kondo K, Shibata R, Murohara T. Direct reprogramming of adult adipose-derived regenerative cells toward cardiomyocytes using six transcriptional factors. iScience 2022; 25:104651. [PMID: 35811849 PMCID: PMC9263527 DOI: 10.1016/j.isci.2022.104651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 04/30/2022] [Accepted: 06/16/2022] [Indexed: 10/29/2022] Open
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24
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Nishikubo M, Hiramoto N, Yamashita D, Imoto H, Sato Y, Okuno Y, Haga H, Nannya Y, Ogawa S, Kimura H, Ishikawa T. Elderly-onset systemic Epstein-Barr virus-positive T-cell lymphoma of childhood. Pathol Int 2022; 72:376-378. [PMID: 35611496 PMCID: PMC9542217 DOI: 10.1111/pin.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Masashi Nishikubo
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Nobuhiro Hiramoto
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Daisuke Yamashita
- Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Hiroharu Imoto
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,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
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
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25
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Kondo S, Okuno Y, Murata T, Dochi H, Wakisaka N, Mizokami H, Moriyama-Kita M, Kobayashi E, Kano M, Komori T, Hirai N, Ueno T, Nakanishi Y, Endo K, Sugimoto H, Kimura H, Yoshizaki T. EBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region. Cancer Sci 2022; 113:2446-2456. [PMID: 35485636 PMCID: PMC9277247 DOI: 10.1111/cas.15381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is caused by infection with Epstein–Barr virus (EBV) and endemic in certain geographic regions. EBV lytic gene, BALF2, closely associates with viral reactivation and BALF2 gene variation, the H‐H‐H strain, causes NPC in endemic region, southern China. Here, we investigate whether such EBV variations also affect NPC in a non‐endemic region, Japan. Viral genome sequencing with 47 EBV isolates of Japanese NPC were performed and compared with those of other EBV‐associated diseases from Japan or NPC in Southern China. EBV genomes of Japanese NPC are different from those of other diseases in Japan or endemic NPC; Japanese NPC was not affected by the endemic strain (the BALF2 H‐H‐H) but frequently carried the type 2 EBV or the strain with intermediate risk of endemic NPC (the BALF2 H‐H‐L). Seven single nucleotide variations were specifically associated with Japanese NPC, of which six were present in both type 1 and 2 EBV genomes, suggesting the contribution of the type 2 EBV‐derived haplotype. This observation was supported by a higher viral titer and stronger viral reactivation in NPC with either type 2 or H‐H‐L strains. Our results highlight the importance of viral strains and viral reactivation in the pathogenesis of non‐endemic NPC.
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Affiliation(s)
- Satoru Kondo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan.,These authors contributed equally to this work
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan.,Pediatric Cancer Treatment Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,These authors contributed equally to this work
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hirotomo Dochi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Naohiro Wakisaka
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Harue Mizokami
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Eiji Kobayashi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makoto Kano
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takeshi Komori
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Nobuyuki Hirai
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takayoshi Ueno
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Yosuke Nakanishi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Kazuhira Endo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hisashi Sugimoto
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University, Graduate school of Medicine, Nagoya, Aichi, Japan
| | - Tomokazu Yoshizaki
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
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26
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Takeichi T, Lee JYW, Okuno Y, Miyasaka Y, Murase Y, Yoshikawa T, Tanahashi K, Nishida E, Okamoto T, Ito K, Muro Y, Sugiura K, Ohno T, McGrath JA, Akiyama M. Autoinflammatory Keratinization Disease With Hepatitis and Autism Reveals Roles for JAK1 Kinase Hyperactivity in Autoinflammation. Front Immunol 2022; 12:737747. [PMID: 35046931 PMCID: PMC8761858 DOI: 10.3389/fimmu.2021.737747] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/06/2021] [Indexed: 01/20/2023] Open
Abstract
Heterozygous mutations in JAK1 which result in JAK-STAT hyperactivity have been implicated in an autosomal dominant disorder that features multi-organ immune dysregulation. This study identifies another previously unreported heterozygous missense JAK1 mutation, H596D, in an individual with a unique autoinflammatory keratinization disease associated with early-onset liver dysfunction and autism. Using CRISPR-Cas9 gene targeting, we generated mice with an identical Jak1 knock-in missense mutation (Jak1H595D/+;I596I/+;Y597Y/+ mice) that recapitulated key aspects of the human phenotype. RNA sequencing of samples isolated from the Jak1H595D/+;I596I/+;Y597Y/+ mice revealed the upregulation of genes associated with the hyperactivation of tyrosine kinases and NF-κB signaling. Interestingly, there was a strong correlation between genes downregulated in Jak1H595D/+;I596I/+;Y597Y/+ mice and those downregulated in the brain of model mice with 22q11.2 deletion syndrome that showed cognitive and behavioral deficits, such as autism spectrum disorders. Our findings expand the phenotypic spectrum of JAK1-associated disease and underscore how JAK1 dysfunction contributes to this autoinflammatory disorder.
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Affiliation(s)
- Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - John Y W Lee
- St John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuya Murase
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takenori Yoshikawa
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kana Tanahashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Emi Nishida
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tatsuya Okamoto
- Division of Pediatric Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Komei Ito
- Department of Allergology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazumitsu Sugiura
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - John A McGrath
- St John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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27
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Pongphitcha P, Okuno Y, Vilaiyuk S, Tunlayadechanont P, Sasanakul W, Kadegasem P, Songdej D, Sirachainan N. Report on effective treatment and genetic predisposition in two children with refractory probable catastrophic antiphospholipid syndrome. Thromb Res 2021; 208:117-120. [PMID: 34749043 DOI: 10.1016/j.thromres.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Pongpak Pongphitcha
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Soamarat Vilaiyuk
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Padcha Tunlayadechanont
- Department of Diagnostic and Therapeutic Radiology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Werasak Sasanakul
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Praguywan Kadegasem
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duantida Songdej
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nongnuch Sirachainan
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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28
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Takeuchi S, Takeichi T, Koike Y, Takama H, Tanahashi K, Okuno Y, Ishii N, Muro Y, Ogi T, Suga Y, Akiyama M. Mutations in SAM syndrome and palmoplantar keratoderma patients suggest genotype/phenotype correlations in DSG1 mutations. J Eur Acad Dermatol Venereol 2021; 36:e215-e218. [PMID: 34657339 DOI: 10.1111/jdv.17752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/21/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- S Takeuchi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Koike
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H Takama
- Department of Dermatology, Aichi Medical University, Nagakute, Japan
| | - K Tanahashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - N Ishii
- Department of Dermatology, Kurume University School of Medicine, Fukuoka, Japan
| | - Y Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Y Suga
- Department of Dermatology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - M Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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29
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Miwata S, Narita A, Okuno Y, Suzuki K, Hamada M, Yoshida T, Imaya M, Yamamori A, Wakamatsu M, Narita K, Kitazawa H, Ichikawa D, Taniguchi R, Kawashima N, Nishikawa E, Nishio N, Kojima S, Muramatsu H, Takahashi Y. Clinical diagnostic value of telomere length measurement in inherited bone marrow failure syndromes. Haematologica 2021; 106:2511-2515. [PMID: 33882640 PMCID: PMC8409025 DOI: 10.3324/haematol.2021.278334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 01/14/2023] Open
Affiliation(s)
- Shunsuke Miwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Masayuki Imaya
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Ayako Yamamori
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya.
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31
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Kimura H, Okuno Y, Sato Y, Watanabe T, Murata T. Deletion of Viral microRNAs in the Oncogenesis of Epstein-Barr Virus-Associated Lymphoma. Front Microbiol 2021; 12:667968. [PMID: 34305835 PMCID: PMC8297563 DOI: 10.3389/fmicb.2021.667968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Epstein–Barr virus (EBV), which encodes >80 genes and nearly 50 non-coding RNAs, is a double-stranded DNA virus. EBV is associated with various types of lymphomas and lymphoproliferative disorders not only of B-cell but also T/NK-cell origin. However, the oncogenic mechanism remains poorly understood, including the EBV receptors expressed on T/NK cells, relationship of EBV with host genes, and epigenetic regulation of EBV and host genes. The roles of host and viral non-coding RNAs during tumorigenesis have been elucidated. EBV encodes at least 49 mature microRNAs (miRNAs), of which 44 are located in BamHI-A rightward transcripts (BARTs) region, and the remaining five are located in BamHI-H rightward fragment 1. BART miRNAs modulate cell differentiation, proliferation, apoptosis, and the cell cycle, and they are considered positive regulators of oncogenesis. We and others have recently reported that EBV-positive lymphomas frequently possess large deletions in BART miRNA clusters, suggesting that some viral miRNAs have suppressive effects on oncogenesis, and that deletion of these miRNAs may aid lymphoma formation.
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Affiliation(s)
- Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayuki Murata
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan
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32
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Taniguchi R, Muramatsu H, Okuno Y, Yoshida T, Wakamatsu M, Hamada M, Shirota C, Sumida W, Hinoki A, Tainaka T, Gotoh Y, Tsuzuki T, Tanaka Y, Kojima S, Uchida H, Takahashi Y. A patient with very early onset FH-deficient renal cell carcinoma diagnosed at age seven. Fam Cancer 2021; 21:337-341. [PMID: 34156580 DOI: 10.1007/s10689-021-00268-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/13/2021] [Indexed: 12/20/2022]
Abstract
Hereditary leiomyomatosis and renal cell cancer (HLRCC) is caused by heterozygous germline variants in the fumarate hydratase (FH) gene and is associated with increased susceptibility to cutaneous leiomyomas, uterine leiomyomas, and renal cell carcinoma (RCC). HLRCC-associated RCC usually occurs in the middle age, with the median age being 40-44 years. This report describes a seven-year-old (84-month-old) male who developed a large right kidney tumor with multiple cystic lesions that contained enhanced solid components. There was no evidence of distant metastasis. The male patient underwent right nephrectomy and has been recovering well without metastasis or recurrence. Pathological examination revealed that tumor cells with relatively prominent nucleoli and surrounded by halos, were located in a limited area. Immunohistochemical staining was negative for FH. Whole-exome sequencing identified his germline variant in the FH gene and its loss of heterozygosity in the tumor. At nine years (114 months) of age, the male patient showed no recurrence of the tumor. This was the youngest-onset case of HLRCC-associated RCC to date. This report may affect the starting age for future RCC-surveillance programs for patients with HLRCC.
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Affiliation(s)
- Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Taro Yoshida
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Chiyoe Shirota
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wataru Sumida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akinari Hinoki
- Department of Rare/ Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahisa Tainaka
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshimitsu Gotoh
- Department of Pediatric Nephrology, Japanese Red Cross Nagoya Daini Hospital, Nagoya, Japan
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroo Uchida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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33
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Ichikawa D, Yamashita K, Okuno Y, Muramatsu H, Murakami N, Suzuki K, Kojima D, Kataoka S, Hamada M, Taniguchi R, Nishikawa E, Kawashima N, Narita A, Nishio N, Hama A, Kasai K, Mizuno S, Shimoyama Y, Nakaguro M, Okita H, Kojima S, Nakazawa A, Takahashi Y. Integrated diagnosis based on transcriptome analysis in suspected pediatric sarcomas. NPJ Genom Med 2021; 6:49. [PMID: 34131151 PMCID: PMC8206218 DOI: 10.1038/s41525-021-00210-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/09/2021] [Indexed: 12/24/2022] Open
Abstract
Pediatric solid tumors are a heterogeneous group of neoplasms with over 100 subtypes. Clinical and histopathological diagnosis remains challenging due to the overlapping morphological and immunohistochemical findings and the presence of atypical cases. To evaluate the potential utility of including RNA-sequencing (RNA-seq) in the diagnostic process, we performed RNA-seq in 47 patients with suspected pediatric sarcomas. Histopathologists specialized in pediatric cancer re-evaluated pathological specimens to reach a consensus diagnosis; 42 patients were diagnosed with known subtypes of solid tumors whereas 5 patients were diagnosed with undifferentiated sarcoma. RNA-seq analysis confirmed and refined consensus diagnoses and further identified diagnostic genetic variants in four of the five patients with undifferentiated sarcoma. Genetic lesions were detected in 23 patients, including the novel SMARCA4-THOP1 fusion gene and 22 conventional or recently reported genetic events. Unsupervised clustering analysis of the RNA-seq data identified a distinct cluster defined by the overexpression of rhabdomyosarcoma-associated genes including MYOG and CHRNG. These findings suggest that RNA-seq-based genetic analysis may aid in the diagnosis of suspected pediatric sarcomas, which would be useful for the development of stratified treatment strategies.
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Affiliation(s)
- Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyoko Yamashita
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daiei Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Advanced Medicine, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Asahito Hama
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Kasai
- Department of Pathology, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Yoshie Shimoyama
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Masato Nakaguro
- Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Hajime Okita
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan.,Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsuko Nakazawa
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan.,Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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34
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Narita A, Muramatsu H, Ichikawa D, Hamada M, Nishikawa E, Suzuki K, Kawashima N, Okuno Y, Nishio N, Hama A, Yamazaki H, Nakao S, Kojima S, Takahashi Y. Relationship between plasma rabbit anti-thymocyte globulin concentration and immunosuppressive therapy response in patients with severe aplastic anemia. Eur J Haematol 2021; 107:255-264. [PMID: 33949001 DOI: 10.1111/ejh.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Patients with acquired aplastic anemia (AA) without HLA-matched sibling donors or aged >40 years receive immunosuppressive therapy (IST) with anti-thymocyte globulin (ATG). We investigated the relationship between plasma rabbit ATG (r-ATG) concentration and IST response. METHODS From May 2012 to October 2017, 81 patients with severe AA who required initial IST were included. A 1:1 block randomization was employed for 2.5 and 3.5 mg/kg doses of r-ATG. RESULTS No significant difference in response rates was observed between the 2.5 and 3.5 mg/kg groups (63% vs. 58%, P = .894). Median r-ATG concentrations on days 14 and 28 after IST were 15.2 (0.0-97.7) and 1.8 (0.0-74.9 µg/mL), respectively. According to r-ATG concentration, response rates were significantly higher in the group with higher r-ATG concentration than in those with lower r-ATG concentration (day 14, 88% vs. 52%; P = .006 and day 28, 79% vs. 46%; P = .005). In multivariate analysis, higher r-ATG concentrations at day 28 were independent predictors of favorable response to IST at 6 months (odds ratio, 0.29; 95% confidence interval, 0.09-0.93; P = .037). CONCLUSIONS The present data indicate that higher r-ATG concentration at day 28 resulted in improved IST response.
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Affiliation(s)
- Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahito Hama
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Hirohito Yamazaki
- Division of Transfusion Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Shinji Nakao
- Department of Hematology and Respirology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Kawashima N, Fukasawa Y, Nishikawa E, Ohta-Ogo K, Ishibashi-Ueda H, Hamada M, Ichikawa D, Narita A, Okuno Y, Muramatsu H, Nishio N, Kojima S, Kato T, Takahashi Y. Echocardiography Monitoring of Pulmonary Hypertension after Pediatric Hematopoietic Stem Cell Transplantation: Pediatric Pulmonary Arterial Hypertension and Pulmonary Veno-Occlusive Disease after Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2021; 27:786.e1-786.e8. [PMID: 34058426 DOI: 10.1016/j.jtct.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/15/2021] [Accepted: 05/23/2021] [Indexed: 10/21/2022]
Abstract
Pulmonary hypertension (PH) is associated with high morbidity in children undergoing hematopoietic stem cell transplantation (HSCT). However, owing to the lack of sequential echocardiography, the nature of the condition is not fully understood. This study was conducted to investigate whether routine echocardiography performed after HSCT could detect patients with PH at an earlier stage and elucidate the role of intervention using tadalafil. The study population comprised 93 consecutive children age <18 years who underwent a total of 109 HSCTs. All patients underwent routine transthoracic echocardiography during HSCT. Four children (4%) with a median age of 4 years (range, 0.7 to 6 years) were found to have PH, and their median tricuspid regurgitation peak velocity (TRV) was 4.1 m/s (range, 3.5 to 4.2 m/s). PH was diagnosed at a median of 52 days (range, 21 to 118 days) after HSCT. Three of them were diagnosed with neuroblastoma, and 1 was diagnosed with infantile leukemia. One patient developed PH after autologous HSCT, and 3 received killer immunoglobulin-like receptor ligand-mismatched cord blood. Busulfan was used for conditioning in all patients, and the proportion of patients receiving this medication was significantly higher in the PH group compared with the non-PH group (100% versus 30%; P = .011). Three of the 4 patients had a durable response (TRV ≤2.8 m/s) at a median of 46 days (range, 14 to 79 days) after starting treatment with tadalafil. No patient experienced exacerbation of PH, and treatment was completed at median of 96 days (range, 46 to 212 days). Our data suggest that routine echocardiography monitoring after HSCT should be considered in children receiving busulfan, although the precise follow-up timing needs further study. In addition, safe and effective administration of tadalafil must be ensured by close monitoring.
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Affiliation(s)
- Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshie Fukasawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Ohta-Ogo
- Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Japan
| | | | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Genome Medical Center, Nagoya University Hospital, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Center for Advanced Medicine and Clinical Research, Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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36
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Yamanaka M, Iwata H, Masuda K, Araki M, Okuno Y, Okamura M, Koiwa J, Tanaka T. A novel orexin antagonist from a natural plant was discovered using zebrafish behavioural analysis. Eur Rev Med Pharmacol Sci 2021; 24:5127-5139. [PMID: 32432777 DOI: 10.26355/eurrev_202005_21207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Phenotypic screening is one of the most practical approaches to the identification of mediators of behaviour, since it is difficult to model brain function in vitro, at a cellular level. We used a zebrafish (Danio rerio) behavioural assay to discover novel, natural, neuroactive compounds. MATERIALS AND METHODS A zebrafish behavioural assay was performed for seven natural compounds, obtained from plants. The behavioural profiles were compared to those of known psychoactive drugs. We characterised a natural compound exhibiting a behaviour profile similar to that of suvorexant, using in silico, in vitro and microarray expression analysis. RESULTS The behavioural analysis performed in this study classified central nervous system drugs according to their mechanism. Zebrafish treated with a natural compound, 8b-(4'-Hydroxytigloyloxy) costunolide (8b), showed behaviour profiles similar to those of zebrafish treated with suvorexant, a known orexin antagonist. This behavioural assay was validated using in silico and in vitro assays, which revealed that the new compound was a dual orexin receptor antagonist. In addition, transcriptome analysis suggested that 8b might regulate the nuclear factor-κB (NF-κB) related pathway. CONCLUSIONS We conclude that zebrafish phenotypic screening, combined with in silico assays and gene expression profiling, is a useful strategy to discover and characterize novel therapeutic compounds, including natural products.
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Affiliation(s)
- M Yamanaka
- Department of Systems Pharmacology, Mie University, Graduate School of Medicine, Tsu, Mie, Japan.
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37
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Kataoka S, Kawashima N, Okuno Y, Muramatsu H, Miwata S, Narita K, Hamada M, Murakami N, Taniguchi R, Ichikawa D, Kitazawa H, Suzuki K, Nishikawa E, Narita A, Nishio N, Yamamoto H, Fukasawa Y, Kato T, Yamamoto H, Natsume J, Kojima S, Nishino I, Taketani T, Ohnishi H, Takahashi Y. Successful treatment of a novel type I interferonopathy due to a de novo PSMB9 gene mutation with a Janus kinase inhibitor. J Allergy Clin Immunol 2021; 148:639-644. [PMID: 33727065 DOI: 10.1016/j.jaci.2021.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Type I interferonopathies are a recently established subgroup of autoinflammatory diseases caused by mutations in genes associated with proteasome degradation or cytoplasmic RNA- and DNA-sensing pathways. OBJECTIVE This study aimed to unveil the molecular pathogenesis of a patient with novel type I interferonopathy, for which no known genetic mutations have been identified. METHODS We performed the whole-exome sequencing of a 1-month-old boy with novel type I interferonopathy. We also investigated proteasome activities using patient-derived B lymphoblastoid cell lines (LCLs) and normal LCLs transduced with the mutant gene. RESULTS Whole-exome sequencing identified a de novo proteasome 20S subunit beta 9 (PSMB9) p.G156D mutation in the patient who developed fever, a chilblain-like skin rash, myositis, and severe pulmonary hypertension due to the hyperactivation of IFN-α. Patient-derived LCLs revealed reduced proteasome activities, and exogenous transduction of mutant PSMB9 p.G156D into normal LCLs significantly suppressed proteasome activities, and the endogenous PSMB9 protein was lost along with the reduction of other immunoproteasome subunits, PSMB8 and PSMB10 proteins. He responded to the administration of a Janus kinase inhibitor, tofacitinib, and he was successfully withdrawn from venoarterial extracorporeal membranous oxygenation. At age 7 months, he received an unrelated cord blood transplantation. At 2 years posttransplantation, he no longer required tofacitinib and experienced no disease recurrence. CONCLUSIONS We present the case of a patient with a novel type I interferonopathy caused by a de novo PSMB9 p.G156D mutation that suppressed the wild-type PSMB9 protein expression. Janus kinase inhibitor and stem cell transplantation could be curative therapies in patients with severe interferonopathies.
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Affiliation(s)
- Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nozomu Kawashima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Miwata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Taniguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Ichikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hironobu Kitazawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Nishikawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Hidenori Yamamoto
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshie Fukasawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Yamamoto
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun Natsume
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takeshi Taketani
- Department of Pediatrics, Shimane University Faculty of Medicine, Shimane, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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38
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Yanagi Y, Okuno Y, Narita Y, Masud HMAA, Watanabe T, Sato Y, Kanda T, Kimura H, Murata T. RNAseq analysis identifies involvement of EBNA2 in PD-L1 induction during Epstein-Barr virus infection of primary B cells. Virology 2021; 557:44-54. [PMID: 33639481 DOI: 10.1016/j.virol.2021.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and several types of malignancy. RNAseq of peripheral blood primary B cell samples infected with wild-type EBV revealed that expression of programmed cell death ligand-1 (PD-L1) is markedly induced by infection. This induction of PD-L1 was alleviated by knockout of the EBNA2 gene, but knockout of LMP1 had little effect. ChIPseq, ChIA-PET, and reporter assays further confirmed that EBNA2-binding sites in the promoter region and at 130 kb downstream of the PD-L1 gene played important roles in PD-L1 induction. Our results indicate that EBV mainly utilizes the EBNA2 gene for induction of PD-L1 and to evade host immunity on infection of primary B cells. Furthermore, pathway analysis revealed that genes involved in the cell cycle, metabolic processes, membrane morphogenesis, and vesicle regulation were induced by EBNA2, and that EBNA2 suppressed genes related to immune signaling.
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Affiliation(s)
- Yusuke Yanagi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Yohei Narita
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - H M Abdullah Al Masud
- Department of Microbiology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teru Kanda
- Department of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Takayuki Murata
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan.
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39
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Inagaki T, Sato Y, Ito J, Takaki M, Okuno Y, Yaguchi M, Masud HMAA, Watanabe T, Sato K, Iwami S, Murata T, Kimura H. Direct Evidence of Abortive Lytic Infection-Mediated Establishment of Epstein-Barr Virus Latency During B-Cell Infection. Front Microbiol 2021; 11:575255. [PMID: 33613459 PMCID: PMC7888302 DOI: 10.3389/fmicb.2020.575255] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022] Open
Abstract
Viral infection induces dynamic changes in transcriptional profiles. Virus-induced and antiviral responses are intertwined during the infection. Epstein-Barr virus (EBV) is a human gammaherpesvirus that provides a model of herpesvirus latency. To measure the transcriptome changes during the establishment of EBV latency, we infected EBV-negative Akata cells with EBV-EGFP and performed transcriptome sequencing (RNA-seq) at 0, 2, 4, 7, 10, and 14 days after infection. We found transient downregulation of mitotic division-related genes, reflecting reprogramming of cell growth by EBV, and a burst of viral lytic gene expression in the early phase of infection. Experimental and mathematical investigations demonstrate that infectious virions were not produced in the pre-latent phase, suggesting the presence of an abortive lytic infection. Fate mapping using recombinant EBV provided direct evidence that the abortive lytic infection in the pre-latent phase converges to latent infection during EBV infection of B-cells, shedding light on novel roles of viral lytic gene(s) in establishing latency. Furthermore, we find that the BZLF1 protein, which is a key regulator of reactivation, was dispensable for abortive lytic infection in the pre-latent phase, suggesting the divergent regulation of viral gene expressions from a productive lytic infection.
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Affiliation(s)
- Tomoki Inagaki
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshitaka Sato
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuaki Takaki
- Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Masahiro Yaguchi
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H. M. Abdullah Al Masud
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Microbiology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Takahiro Watanabe
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shingo Iwami
- Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Japan
- MIRAI, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Takayuki Murata
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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40
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Dingler FA, Wang M, Mu A, Millington CL, Oberbeck N, Watcham S, Pontel LB, Kamimae-Lanning AN, Langevin F, Nadler C, Cordell RL, Monks PS, Yu R, Wilson NK, Hira A, Yoshida K, Mori M, Okamoto Y, Okuno Y, Muramatsu H, Shiraishi Y, Kobayashi M, Moriguchi T, Osumi T, Kato M, Miyano S, Ito E, Kojima S, Yabe H, Yabe M, Matsuo K, Ogawa S, Göttgens B, Hodskinson MRG, Takata M, Patel KJ. Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mice and Humans. Mol Cell 2020; 80:996-1012.e9. [PMID: 33147438 PMCID: PMC7758861 DOI: 10.1016/j.molcel.2020.10.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/20/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023]
Abstract
Reactive aldehydes arise as by-products of metabolism and are normally cleared by multiple families of enzymes. We find that mice lacking two aldehyde detoxifying enzymes, mitochondrial ALDH2 and cytoplasmic ADH5, have greatly shortened lifespans and develop leukemia. Hematopoiesis is disrupted profoundly, with a reduction of hematopoietic stem cells and common lymphoid progenitors causing a severely depleted acquired immune system. We show that formaldehyde is a common substrate of ALDH2 and ADH5 and establish methods to quantify elevated blood formaldehyde and formaldehyde-DNA adducts in tissues. Bone-marrow-derived progenitors actively engage DNA repair but also imprint a formaldehyde-driven mutation signature similar to aging-associated human cancer mutation signatures. Furthermore, we identify analogous genetic defects in children causing a previously uncharacterized inherited bone marrow failure and pre-leukemic syndrome. Endogenous formaldehyde clearance alone is therefore critical for hematopoiesis and in limiting mutagenesis in somatic tissues.
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Affiliation(s)
- Felix A Dingler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Meng Wang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anfeng Mu
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | | | - Nina Oberbeck
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sam Watcham
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Lucas B Pontel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET, Polo Científico Tecnológico, Godoy Cruz 2390, C1425FQD Buenos Aires, Argentina
| | | | - Frederic Langevin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Camille Nadler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rebecca L Cordell
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Paul S Monks
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Rui Yu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Asuka Hira
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minako Mori
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Shiraishi
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Hematology, Kyoto Katsura Hospital, Kyoto, Japan
| | | | - Tomoo Osumi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiromasa Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Miharu Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of Analytical Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Sweden; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | | | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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Oka Y, Hamada M, Nakazawa Y, Muramatsu H, Okuno Y, Higasa K, Shimada M, Takeshima H, Hanada K, Hirano T, Kawakita T, Sakaguchi H, Ichimura T, Ozono S, Yuge K, Watanabe Y, Kotani Y, Yamane M, Kasugai Y, Tanaka M, Suganami T, Nakada S, Mitsutake N, Hara Y, Kato K, Mizuno S, Miyake N, Kawai Y, Tokunaga K, Nagasaki M, Kito S, Isoyama K, Onodera M, Kaneko H, Matsumoto N, Matsuda F, Matsuo K, Takahashi Y, Mashimo T, Kojima S, Ogi T. Digenic mutations in ALDH2 and ADH5 impair formaldehyde clearance and cause a multisystem disorder, AMeD syndrome. Sci Adv 2020; 6:6/51/eabd7197. [PMID: 33355142 DOI: 10.1126/sciadv.abd7197] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Rs671 in the aldehyde dehydrogenase 2 gene (ALDH2) is the cause of Asian alcohol flushing response after drinking. ALDH2 detoxifies endogenous aldehydes, which are the major source of DNA damage repaired by the Fanconi anemia pathway. Here, we show that the rs671 defective allele in combination with mutations in the alcohol dehydrogenase 5 gene, which encodes formaldehyde dehydrogenase (ADH5FDH ), causes a previously unidentified disorder, AMeD (aplastic anemia, mental retardation, and dwarfism) syndrome. Cellular studies revealed that a decrease in the formaldehyde tolerance underlies a loss of differentiation and proliferation capacity of hematopoietic stem cells. Moreover, Adh5-/-Aldh2 E506K/E506K double-deficient mice recapitulated key clinical features of AMeDS, showing short life span, dwarfism, and hematopoietic failure. Collectively, our results suggest that the combined deficiency of formaldehyde clearance mechanisms leads to the complex clinical features due to overload of formaldehyde-induced DNA damage, thereby saturation of DNA repair processes.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Honoka Takeshima
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- School of Medicine, Nagoya University, Nagoya, Japan
| | - Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, Yufu, Japan
| | - Taichi Hirano
- Department of Hematology, National Hospital Organization, Kumamoto Medical Center, Kumamoto, Japan
| | - Toshiro Kawakita
- Department of Hematology, National Hospital Organization, Kumamoto Medical Center, Kumamoto, Japan
| | - Hirotoshi Sakaguchi
- Department of Hematology and Oncology, Children Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Takuya Ichimura
- Department of Pediatrics, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Shuichi Ozono
- Department of Pediatrics and Child Health, School of Medicine, Kurume University, Kurume, Japan
| | - Kotaro Yuge
- Department of Pediatrics and Child Health, School of Medicine, Kurume University, Kurume, Japan
| | - Yoriko Watanabe
- Department of Pediatrics and Child Health, School of Medicine, Kurume University, Kurume, Japan
| | - Yuko Kotani
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
- Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mutsumi Yamane
- Center for Animal Research and Education, Nagoya University, Nagoya, Japan
| | - Yumiko Kasugai
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Miyako Tanaka
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Norisato Mitsutake
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Yuichiro Hara
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Aichi Developmental Disability Center, Kasugai, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Seiji Kito
- Center for Animal Research and Education, Nagoya University, Nagoya, Japan
| | - Keiichi Isoyama
- Department of Pediatrics, Showa University Fujigaoka Hospital, Yokohama, Japan
| | - Masafumi Onodera
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Hideo Kaneko
- Department of Clinical Research, National Hospital Organization, Nagara Medical Center, Gifu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoji Mashimo
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
- Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan.
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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42
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Schönung M, Meyer J, Nöllke P, Olshen AB, Hartmann M, Murakami N, Wakamatsu M, Okuno Y, Plass C, Loh ML, Niemeyer CM, Muramatsu H, Flotho C, Stieglitz E, Lipka DB. International Consensus Definition of DNA Methylation Subgroups in Juvenile Myelomonocytic Leukemia. Clin Cancer Res 2020; 27:158-168. [PMID: 33139265 DOI: 10.1158/1078-0432.ccr-20-3184] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/01/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML on the basis of DNA methylation patterns are lacking. We, therefore, sought to define an international consensus for DNA methylation subgroups in JMML and develop classification methods for clinical implementation. EXPERIMENTAL DESIGN Published DNA methylation data from 255 patients with JMML were used to develop and internally validate a classifier model. Accuracy across platforms (EPIC-arrays and MethylSeq) was tested using a technical validation cohort (32 patients). The suitability of both methods for single-patient classification was demonstrated using an independent cohort (47 patients). RESULTS Analysis of pooled, published data established three DNA methylation subgroups as a de facto standard. Unfavorable prognostic parameters (PTPN11 mutation, elevated fetal hemoglobin, and older age) were significantly enriched in the high methylation (HM) subgroup. A classifier was then developed that predicted subgroups with 98% accuracy across different technological platforms. Applying the classifier to an independent validation cohort confirmed an association of HM with secondary mutations, high relapse incidence, and inferior overall survival (OS), while the low methylation subgroup was associated with a favorable disease course. Multivariable analysis established DNA methylation subgroups as the only significant factor predicting OS. CONCLUSIONS This study provides an international consensus definition for DNA methylation subgroups in JMML. We developed and validated methods which will facilitate the design of risk-stratified clinical trials in JMML.
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Affiliation(s)
- Maximilian Schönung
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam B Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Mark Hartmann
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Christoph Plass
- Division Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
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Nishiwaki S, Kim JH, Ito M, Maeda M, Okuno Y, Koyama D, Ozawa Y, Gunji M, Osaki M, Kitamura K, Ushijima Y, Ishikawa Y, Miyamura K, Sugiura I, Kiyoi H. Multi-Lineage BCR-ABL Expression in Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Is Associated With Improved Prognosis but No Specific Molecular Features. Front Oncol 2020; 10:586567. [PMID: 33194739 PMCID: PMC7646258 DOI: 10.3389/fonc.2020.586567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/30/2020] [Indexed: 01/09/2023] Open
Abstract
Background Recently, various blood cell lineages expressing the BCR-ABL fusion gene in Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL) have been reported. However, the biological and clinical significance of these BCR-ABL lineages has not been established; therefore, we aimed to clarify the impacts of these different BCR-ABL-expressing lineages. Patients Multi-lineage BCR-ABL expression (multi-Ph) was defined as BCR-ABL expression outside of the B-lineage compartment, as determined by fluorescence in situ hybridization (FISH) in peripheral blood neutrophils and bone marrow clots, and flow cytometry-sorted polymerase chain reaction (PCR). We analyzed IKZF1 deletion patterns by PCR, examined gene expression profiles using RNA sequencing, and compared treatment outcomes across different BCR-ABL-expressing lineages. Results Among the 21 multi-Ph patients in our 59-patient cohort (36%), BCR-ABL expression was detected at the multipotential progenitor level. However, no IKZF1 deletion patterns or gene expression profiles were identified that were specific for multi-Ph. However, multi-Ph patients were found to have better survival rates than patients with uni-lineage BCR-ABL expression [event-free survival (EFS): 74 vs. 33%, P = 0.01; overall survival (OS): 79 vs. 44% at 4 years, P = 0.01]. In multivariate analyses, multi-Ph was identified as a good prognostic factor for both EFS and OS. Conclusion We confirmed that more than one-third of Ph+ALL patients could be classified as mutli-Ph. Although no specific molecular characteristics were identified for multi-Ph, this phenotype was associated with better treatment outcomes.
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Affiliation(s)
- Satoshi Nishiwaki
- Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Jeong Hui Kim
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masafumi Ito
- Department of Pathology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Matsuyoshi Maeda
- Division of Pathology, Toyohashi Municipal Hospital, Toyohashi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Daisuke Koyama
- Division of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, Japan
| | - Yukiyasu Ozawa
- Department of Hematology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Masaharu Gunji
- Department of Pathology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Masahide Osaki
- Department of Hematology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Kunio Kitamura
- Division of Hematology, Ichinomiya Municipal Hospital, Ichinomiya, Japan
| | - Yoko Ushijima
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Ishikawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koichi Miyamura
- Department of Hematology, Japanese Red Cross Nagoya Daiichi Hospital, Nagoya, Japan
| | - Isamu Sugiura
- Division of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Yamamoto H, Hayano S, Okuno Y, Onoda A, Kato K, Nagai N, Fukasawa Y, Saitoh S, Takahashi Y, Kato T. Phosphorylated proteome analysis of a novel germline ABL1 mutation causing an autosomal dominant syndrome with ventricular septal defect. Int J Cardiol 2020; 326:81-87. [PMID: 33075386 DOI: 10.1016/j.ijcard.2020.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND A gain-of-function mutation in germline ABL1 causes a syndrome including congenital heart defects. However, the molecular mechanisms of this syndrome remain unknown. In this study, we found a novel ABL1 mutation in a Japanese family with ventricular septal defect, finger contracture, skin abnormalities and failure to thrive, and the molecular mechanisms of these phenotypes were investigated. METHODS AND RESULTS Whole-exome sequencing on several family members revealed a novel mutation (c.1522A > C, p.I508L) in the tyrosine kinase domain of ABL1, and complete co-segregation with clinical presentations was confirmed in all members. Wild-type and mutant ABL1 were transfected into human embryonic kidney 293 cells for functional analysis. Western blotting confirmed that tyrosine phosphorylation in STAT5, a substrate of ABL1, was enhanced, and the novel mutation was proved to be a gain-of-function mutation. Since this novel mutation in ABL1 enhances tyrosine kinase activity, phosphorylated proteome analysis was used to elucidate the molecular pathology. The proteome analysis showed that phosphorylation in proteins such as UFD1, AXIN1, ATRX, which may be involved in the phenotypes, was enhanced in the mutant group. CONCLUSIONS The onset of congenital heart defects associated with this syndrome appears to involve a mechanism caused by UFD1 common to 22q.11.2 deletion syndrome. On the other hand, AXIN1 and ATRX may be important in elucidating the mechanisms of other phenotypes, such as finger contracture and failure to thrive. Verification of these hypotheses would lead to further understanding of the pathophysiology and the development of treatment methods.
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Affiliation(s)
- Hidenori Yamamoto
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan.
| | - Satoshi Hayano
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan; Department of Pediatrics, Chutoen General Medical Center, 1-1 Shobugaike, Kakegawa, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Atsuto Onoda
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan; Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Japan.
| | - Kohji Kato
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Noriko Nagai
- Department of Pediatrics, Okazaki City Hospital, 3-1 Goshoai, Koryuji-cho, Okazaki, Japan.
| | - Yoshie Fukasawa
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Japan.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan.
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan.
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45
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Torii Y, Horiba K, Hayano S, Kato T, Suzuki T, Kawada JI, Takahashi Y, Kojima S, Okuno Y, Ogi T, Ito Y. Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study. BMC Pediatr 2020; 20:482. [PMID: 33059644 PMCID: PMC7557310 DOI: 10.1186/s12887-020-02380-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.
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Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Hayano
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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46
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Sugaya M, Funamizu K, Kono M, Okuno Y, Kondo T, Ono R, Akiyama M, Nishigori C, Sato S. Whole-exome sequencing and host cell reactivation assay lead to a diagnosis of xeroderma pigmentosum group D with mild ultraviolet radiation sensitivity. J Dermatol 2020; 48:96-100. [PMID: 32974964 DOI: 10.1111/1346-8138.15617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 11/27/2022]
Abstract
A case of xeroderma pigmentosum (XP) group D in a 39-year-old Japanese man is reported. The patient had suffered from moderate to severe solar sensitivity and freckle-like pigmented macules in sun-exposed areas since 6 years of age, and developed skin malignancies such as squamous cell carcinoma, actinic keratosis, Bowen's disease and basal cell carcinoma. The minimal erythema dose for ultraviolet (UV) radiation was decreased with a delayed peak reaction. The level of unscheduled DNA synthesis of fibroblasts from the patient was 70% of normal, while they expressed POLH, a gene product responsible for the XP variant. Whole-exome sequencing indicated that the patient harbored a homozygous mutation of c.1802G>T, p.Arg601Leu in ERCC2. A genetic complementation test was carried out by host cell reactivation assay, which showed that the patient's fibroblasts recovered only when they were transfected with XPD cDNA, confirming the diagnosis of XP-D. Arg601Leu mutation in ERCC2 may be related to mild UV radiation sensitivity and moderate skin lesions.
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Affiliation(s)
- Makoto Sugaya
- Department of Dermatology, International University of Health and Welfare, Chiba, Japan.,Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kaoru Funamizu
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Michihiro Kono
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Dermatology and Plastic Surgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Taisuke Kondo
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryusuke Ono
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinichi Sato
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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47
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Takeichi T, Hirabayashi T, Miyasaka Y, Kawamoto A, Okuno Y, Taguchi S, Tanahashi K, Murase C, Takama H, Tanaka K, Boeglin WE, Calcutt MW, Watanabe D, Kono M, Muro Y, Ishikawa J, Ohno T, Brash AR, Akiyama M. SDR9C7 catalyzes critical dehydrogenation of acylceramides for skin barrier formation. J Clin Invest 2020; 130:890-903. [PMID: 31671075 DOI: 10.1172/jci130675] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023] Open
Abstract
The corneocyte lipid envelope, composed of covalently bound ceramides and fatty acids, is important to the integrity of the permeability barrier in the stratum corneum, and its absence is a prime structural defect in various skin diseases associated with defective skin barrier function. SDR9C7 encodes a short-chain dehydrogenase/reductase family 9C member 7 (SDR9C7) recently found mutated in ichthyosis. In a patient with SDR9C7 mutation and a mouse Sdr9c7-KO model, we show loss of covalent binding of epidermal ceramides to protein, a structural fault in the barrier. For reasons unresolved, protein binding requires lipoxygenase-catalyzed transformations of linoleic acid (18:2) esterified in ω-O-acylceramides. In Sdr9c7-/- epidermis, quantitative liquid chromatography-mass spectometry (LC-MS) assays revealed almost complete loss of a species of ω-O-acylceramide esterified with linoleate-9,10-trans-epoxy-11E-13-ketone; other acylceramides related to the lipoxygenase pathway were in higher abundance. Recombinant SDR9C7 catalyzed NAD+-dependent dehydrogenation of linoleate 9,10-trans-epoxy-11E-13-alcohol to the corresponding 13-ketone, while ichthyosis mutants were inactive. We propose, therefore, that the critical requirement for lipoxygenases and SDR9C7 is in producing acylceramide containing the 9,10-epoxy-11E-13-ketone, a reactive moiety known for its nonenzymatic coupling to protein. This suggests a mechanism for coupling of ceramide to protein and provides important insights into skin barrier formation and pathogenesis.
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Affiliation(s)
- Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Hirabayashi
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akane Kawamoto
- Biological Science Research Laboratories, Kao Corporation, Haga, Tochigi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Shijima Taguchi
- Division of Dermatology, Mito Kyodo General Hospital, Mito, Ibaraki, Japan
| | - Kana Tanahashi
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chiaki Murase
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Takama
- Department of Dermatology, Aichi Medical University, Nagakute, Japan
| | - Kosei Tanaka
- Analytical Science Research Laboratories, Kao Corporation, Haga, Tochigi, Japan
| | | | - M Wade Calcutt
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Daisuke Watanabe
- Department of Dermatology, Aichi Medical University, Nagakute, Japan
| | - Michihiro Kono
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinao Muro
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Junko Ishikawa
- Biological Science Research Laboratories, Kao Corporation, Haga, Tochigi, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Alan R Brash
- Departments of Pharmacology and Biochemistry and
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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48
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Affiliation(s)
- Takuya Takeichi
- Department of Dermatology, Nagoya University Graduate School of Medicine, 466-8550 Nagoya, Japan. E-mail:
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49
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Shinjo K, Hara K, Nagae G, Umeda T, Katsushima K, Suzuki M, Murofushi Y, Umezu Y, Takeuchi I, Takahashi S, Okuno Y, Matsuo K, Ito H, Tajima S, Aburatani H, Yamao K, Kondo Y. A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer. PLoS One 2020; 15:e0233782. [PMID: 32520974 PMCID: PMC7286528 DOI: 10.1371/journal.pone.0233782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD–ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD–ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD–ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.
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Affiliation(s)
- Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Hara
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Genta Nagae
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Umeda
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miho Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Umezu
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Ichiro Takeuchi
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroyuki Aburatani
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan.,Department of Gastroenterology, Narita Memorial Hospital, Toyohashi, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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50
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Schmidt T, Jeon J, Okuno Y, Chiliveri SC, Clore GM. Submillisecond Freezing Permits Cryoprotectant-Free EPR Double Electron-Electron Resonance Spectroscopy. Chemphyschem 2020; 21:1224-1229. [PMID: 32383308 DOI: 10.1002/cphc.202000312] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/06/2020] [Indexed: 01/22/2023]
Abstract
Double electron-electron resonance (DEER) EPR spectroscopy is a powerful method for obtaining distance distributions between pairs of engineered nitroxide spin-labels in proteins and other biological macromolecules. These measurements require the use of cryogenic temperatures (77 K or less) to prolong the phase memory relaxation time (Tm ) sufficiently to enable detection of a DEER echo curve. Generally, a cryoprotectant such as glycerol is added to protein samples to facilitate glass formation and avoid protein clustering (which can result in a large decrease in Tm ) during relatively slow flash freezing in liquid N2 . However, cryoprotectants are osmolytes and can influence protein folding/unfolding equilibria, as well as species populations in weak multimeric systems. Here we show that submillisecond rapid freezing, achieved by high velocity spraying of the sample onto a rapidly spinning, liquid nitrogen cooled copper disc obviates the requirement for cryoprotectants and permits high quality DEER data to be obtained in absence of glycerol. We demonstrate this approach on five different protein systems: protein A, the metastable drkN SH3 domain, urea-unfolded drkN SH3, HIV-1 reverse transcriptase, and the transmembrane domain of HIV-1 gp41 in lipid bicelles.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Yusuke Okuno
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Sai C Chiliveri
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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