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Makino T, Miyata H, Yasuda T, Kitagawa Y, Muro K, Park JH, Hikichi T, Hasegawa T, Igarashi K, Iguchi M, Masaoka Y, Yano M, Doki Y. A phase 3, randomized, double-blind, multicenter, placebo-controlled study of S-588410, a five-peptide cancer vaccine as an adjuvant therapy after curative resection in patients with esophageal squamous cell carcinoma. Esophagus 2024:10.1007/s10388-024-01072-w. [PMID: 38990441 DOI: 10.1007/s10388-024-01072-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND S-588410, a cancer peptide vaccine (CPV), comprises five HLA-A*24:02-restricted peptides from five cancer-testis antigens. In a phase 2 study, S-588410 was well-tolerated and exhibited antitumor efficacy in patients with urothelial cancer. Therefore, we aimed to evaluate the efficacy, immune response, and safety of S-588410 in patients with completely resected esophageal squamous cell carcinoma (ESCC). METHODS This phase 3 study involved patients with HLA-A*24:02-positive and lymph node metastasis-positive ESCC who received neoadjuvant therapy followed by curative resection. After randomization, patients were administered S-588410 and placebo (both emulsified with Montanide™ ISA 51VG) subcutaneously. The primary endpoint was relapse-free survival (RFS). The secondary endpoints were overall survival (OS), cytotoxic T-lymphocyte (CTL) induction, and safety. Statistical significance was tested using the one-sided weighted log-rank test with the Fleming-Harrington class of weights. RESULTS A total of 276 patients were randomized (N = 138/group). The median RFS was 84.3 and 84.1 weeks in the S-588410 and placebo groups, respectively (P = 0.8156), whereas the median OS was 236.3 weeks and not reached, respectively (P = 0.6533). CTL induction was observed in 132/134 (98.5%) patients who received S-588410 within 12 weeks. Injection site reactions (137/140 patients [97.9%]) were the most frequent treatment-emergent adverse events in the S-588410 group. Prolonged survival was observed in S-588410-treated patients with upper thoracic ESCC, grade 3 injection-site reactions, or high CTL intensity. CONCLUSIONS S-588410 induced immune response and had acceptable safety but failed to reach the primary endpoint. A high CTL induction rate and intensity may be critical for prolonging survival during future CPV development.
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Affiliation(s)
- Tomoki Makino
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiroshi Miyata
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Takushi Yasuda
- Department of Surgery, Kindai University Faculty of Medicine, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi, Japan
| | - Jae-Hyun Park
- OncoTherapy Science, Inc., Kawasaki, Kanagawa, Japan
| | - Tetsuro Hikichi
- Laboratory Department, Cancer Precision Medicine, Inc., Kawasaki, Kanagawa, Japan
| | | | | | - Motofumi Iguchi
- Medical Affairs Department, Shionogi & Co., Ltd, Osaka, Japan
| | | | - Masahiko Yano
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, Osaka, Japan
- Kyowakai Hospital, Osaka, Japan
| | - Yuichiro Doki
- Department of Surgery, Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
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Murai A, Kubo T, Ohkuri T, Yanagawa J, Yajima Y, Kosaka A, Li D, Nagato T, Murata K, Kanaseki T, Tsukahara T, Nagasaki T, Hirohashi Y, Kobayashi H, Torigoe T. NF9 peptide specific cytotoxic T lymphocyte clone cross react to Y453F mutation of SARS-CoV-2 virus spike protein. Immunol Med 2024; 47:93-99. [PMID: 38236134 DOI: 10.1080/25785826.2024.2304363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
The recognition by cytotoxic T cells (CTLs) is essential for the clearance of SARS-CoV-2 virus-infected cells. Several viral proteins have been described to be recognized by CTLs. Among them, the spike (S) protein is one of the immunogenic proteins. The S protein acts as a ligand for its receptors, and several mutants with different affinities for its cognate receptors have been reported, and certain mutations in the S protein, such as L452R and Y453F, have been found to inhibit the HLA-A24-restricted CTL response. In this study, we conducted a screening of candidate peptides derived from the S protein, specifically targeting those carrying the HLA-A24 binding motif. Among these peptides, we discovered that NF9 (NYNYLYRLF) represents an immunogenic epitope. CTL clones specific to the NF9 peptide were successfully established. These CTL clones exhibited the ability to recognize endogenously expressed NF9 peptide. Interestingly, the CTL clone demonstrated cross-reactivity with the Y453F peptide (NYNYLFRLF) but not with the L452R peptide (NYNYRYRLF). The CTL clone was able to identify the endogenously expressed Y453F mutant peptide. These findings imply that the NF9-specific CTL clone possesses the capability to recognize and respond to the Y453F mutant peptide.
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Affiliation(s)
- Aiko Murai
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Terufumi Kubo
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takayuki Ohkuri
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Junko Yanagawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuki Yajima
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
- Department of Oral and Maxillofacial Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Akemi Kosaka
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Dongliang Li
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd, Ina, Japan
| | - Toshihiro Nagato
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Kenji Murata
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | | | - Takeshi Nagasaki
- Tsukuba Laboratory, Medical & Biological Laboratories Co., Ltd, Ina, Japan
| | - Yoshihiko Hirohashi
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroya Kobayashi
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
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3
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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4
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Liu X, Matsunami M, Horikoshi M, Ito S, Ishikawa Y, Suzuki K, Momozawa Y, Niida S, Kimura R, Ozaki K, Maeda S, Imamura M, Terao C. Natural Selection Signatures in the Hondo and Ryukyu Japanese Subpopulations. Mol Biol Evol 2023; 40:msad231. [PMID: 37903429 PMCID: PMC10615566 DOI: 10.1093/molbev/msad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20-150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.
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Affiliation(s)
- Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kunihiko Suzuki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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5
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Donne R, Lujambio A. The liver cancer immune microenvironment: Therapeutic implications for hepatocellular carcinoma. Hepatology 2023; 77:1773-1796. [PMID: 35989535 PMCID: PMC9941399 DOI: 10.1002/hep.32740] [Citation(s) in RCA: 141] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/26/2022] [Accepted: 08/18/2022] [Indexed: 12/19/2022]
Abstract
The liver is the sixth most common site of primary cancer in humans and the fourth leading cause of cancer-related death in the world. Hepatocellular carcinoma (HCC) accounts for 90% of liver cancers. HCC is a prevalent disease with a progression that is modulated by the immune system. Half of the patients with HCC receive systemic therapies, traditionally sorafenib or lenvatinib, as a first-line therapy. In the last few years, immune-checkpoint inhibitors (ICIs) have revolutionized cancer therapy and have gained an increased interest in the treatment of HCC. In 2020, the combination of atezolizumab (anti-programmed death-ligand 1) and bevacizumab (anti-vascular endothelial growth factor) improved overall survival over sorafenib, resulting in Food and Drug Administration (FDA) approval as a first-line treatment for patients with advanced HCC. Despite these major advances, a better molecular and cellular characterization of the tumor microenvironment is still needed because it has a crucial role in the development and progression of HCC. Inflamed (hot) and noninflamed (cold) HCC tumors and genomic signatures have been associated with response to ICIs. However, there are no additional biomarkers to guide clinical decision-making. Other immune-targeting strategies, such as adoptive T-cell transfer, vaccination, and virotherapy, are currently under development. This review provides an overview on the HCC immune microenvironment, different cellular players, current available immunotherapies, and potential immunotherapy modalities.
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Affiliation(s)
- Romain Donne
- Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York , USA
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai , Tisch Cancer Institute , New York , New York , USA
- Icahn School of Medicine at Mount Sinai , The Precision Immunology Institute , New York , New York , USA
| | - Amaia Lujambio
- Department of Oncological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York , USA
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai , Tisch Cancer Institute , New York , New York , USA
- Icahn School of Medicine at Mount Sinai , The Precision Immunology Institute , New York , New York , USA
- Graduate School of Biomedical Sciences , Icahn School of Medicine at Mount Sinai , New York , New York , USA
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6
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Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes. Hum Genome Var 2022; 9:49. [PMID: 36543786 PMCID: PMC9772353 DOI: 10.1038/s41439-022-00226-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on 'The Current Landscape of HLA Genomics and Genetics', we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases.
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7
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Iwasaki M, Kanda J, Tanaka H, Shindo T, Sato T, Doki N, Fukuda T, Ozawa Y, Eto T, Uchida N, Katayama Y, Kataoka K, Ara T, Ota S, Onizuka M, Kanda Y, Ichinohe T, Atsuta Y, Morishima S. Impact of HLA Epitope Matching on Outcomes After Unrelated Bone Marrow Transplantation. Front Immunol 2022; 13:811733. [PMID: 35309307 PMCID: PMC8928463 DOI: 10.3389/fimmu.2022.811733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/14/2022] [Indexed: 11/26/2022] Open
Abstract
The significance of antibody-identified epitopes stimulating humoral alloimmunity is not well understood in the identification of non-permissive human leukocyte antigen (HLA) mismatching patterns in hematopoietic stem cell transplantation (HSCT). This was a retrospective study in a cohort of 9,991 patients who underwent their first HSCT for hematologic malignancies from unrelated bone marrow donors in the Transplant Registry Unified Management Program (TRUMP). HLA eplet mismatches (EMM) were quantified using HLAMatchmaker (HLAMM). The median age of patients was 48 years (range, 16 to 77). The number of EMM in recipient-donor pairs in our study population ranged from 0 to 37 in HLA class I (median, 0) and 0 to 60 in HLA class II (median, 1). In addition to the known high-risk mismatch patterns in the Japanese cohort, HLA-C EMM in the GVH direction was associated with a significantly higher risk for grade III-IV aGVHD, leading to a higher risk of non-relapse mortality and lower overall survival (compared with HLA-C matched patients, HR 1.67, 95% CI 1.44–1.95; HR 1.39, 95% CI 1.25–1.54; HR 1.20, 95% CI 1.10–1.30, respectively). HLAMM-based epitope matching might be useful for identifying patients who are at high risk for serious complications after HSCT from HLA mismatched unrelated donors.
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Affiliation(s)
- Makoto Iwasaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junya Kanda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Takero Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiko Sato
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Noriko Doki
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Takahiro Fukuda
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Yukiyasu Ozawa
- Department of Hematology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Naoyuki Uchida
- Department of Hematology, Federation of National Public Service Personnel Mutual Aid Associations, Toranomon Hospital, Tokyo, Japan
| | - Yuta Katayama
- Department of Hematology, Hiroshima Red Cross Hospital and Atomic-bomb Survivors Hospital, Hiroshima, Japan
| | - Keisuke Kataoka
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takahide Ara
- Department of Hematology, Hokkaido University Hospital, Sapporo, Japan
| | - Shuichi Ota
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Makoto Onizuka
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Yoshinobu Kanda
- Division of Hematology, Jichi Medical University, Tochigi, Japan
| | - Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Nagoya, Japan.,Department of Registry Science for Transplant and Cellular Therapy, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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8
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Huang C, Chen J, Ding F, Yang L, Zhang S, Wang X, Shi Y, Zhu Y. Related parameters of affinity and stability prediction of HLA-A*2402 restricted antigen peptides based on molecular docking. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:673. [PMID: 33987371 PMCID: PMC8106073 DOI: 10.21037/atm-21-630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Major histocompatibility complex class I (MHC-I) plays an important role in cell immune response, and stable interaction between polypeptides and MHC-I ensures efficient presentation of polypeptide-MHC-I (pMHC-I) molecular complexes to T cells. The aim of this study was to explore ways to improve the affinity and stability of the p-Human Leukocyte Antigen (HLA)-A*2402 complex. Methods The peptide sequences of the restricted antigen peptides for HLA-A*2402 and the results of the in vitro competitive binding test were retrieved from the literature. The affinity values were predicted using NetMHCpan v4.1 server, and the stability values were predicted using the NetMHCstab v1.0 server. Auto Vina was used to dock peptides to HLA-A*2402 protein in a flexible docking manner, while Flexpepdock was employed to optimize the docking morphology. Maestro was used to analyze the intermolecular forces and the binding affinity of the complex, while MM-GBSA was used to calculate the binding free energy values. Results The intermolecular interactions that maintained the affinity and stability of peptide-HLA-A*2402 complex relied mainly on HB, followed by pi stack. The binding affinity values of molecular docking were associated with the predicted values of affinity and stability, the binding affinity and the binding free energy, as well as the intermolecular force pi-stack. The pi stack had a significant negative correlation with binding affinity and binding free energy. The replacement of the residues of the polypeptides that did not form pi-stack interactions with HLA-A*2402 improved the affinity and/or stability compared to before replacement. Conclusions The generation and increase in the number of pi-stacks between peptides and HLA-A*2402 molecules may help improve the affinity and stability of p-HLA-A*2402 complexes. The prediction of intermolecular forces and binding affinity of peptide-HLA by means of molecular docking is a supplement to the current commonly used prediction databases.
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Affiliation(s)
- Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Fei Ding
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Lili Yang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Siyu Zhang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xuechun Wang
- Zhejiang Chinese Medical University 4th School of Clinical Medicine, Hangzhou, China
| | - Yanfei Shi
- Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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9
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T-cell receptor repertoire of cytomegalovirus-specific cytotoxic T-cells after allogeneic stem cell transplantation. Sci Rep 2020; 10:22218. [PMID: 33335252 PMCID: PMC7747720 DOI: 10.1038/s41598-020-79363-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Cytomegalovirus (CMV) infection is a major complication during allogeneic stem cell transplantation (allo-SCT). However, mechanisms of adaptive immunity that drive this remain unclear. To define early immunological responses to CMV after transplantation, we using next-generation sequencing to examine the repertoire of T-cell receptors in CD8+/CMV pp65 tetramer+ cells (CMV-CTLs) in peripheral blood samples obtained from 16 allo-SCT recipients with HLA-A*24:02 at the time of CMV reactivation. In most patients, TCR beta repertoire of CMV-CTLs was highly skewed (median Inverse Simpson's index: 1.595) and, 15 of 16 patients shared at least one TCR-beta clonotype with ≥ 2 patients. The shared TCRs were dominant in 12 patients and, two clonotypes were shared by about half of the patients. Similarity analysis showed that CDR3 sequences of shared TCRs were more similar than unshared TCRs. TCR beta repertoires of CMV-CTLs in 12 patients were also analyzed after 2-4 weeks to characterize the short-term dynamics of TCR repertoires. In ten patients, we observed persistence of prevailing clones. In the other two patients, TCR repertoires became more diverse, major clones declined, and new private clones subsequently emerged. These results provided the substantive clue to understand the immunological behavior against CMV reactivation after allo-SCT.
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10
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Li Z, Gong H, Liu Q, Wu W, Cheng J, Mei Y, Chen Y, Zheng H, Yu X, Zhong S, Li Y. Identification of an HLA-A*24:02-restricted α-fetoprotein signal peptide-derived antigen and its specific T-cell receptor for T-cell immunotherapy. Immunology 2020; 159:384-392. [PMID: 31849039 DOI: 10.1111/imm.13168] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver cancer with limited treatments. Asia has the highest HCC incidence rates; China accounts for over 50% of all HCC cases worldwide. T-cell receptor (TCR) -engineered T-cell immunotherapies specific for human leukocyte antigen (HLA) -A*02:01-restricted α-fetoprotein (AFP) peptide have shown encouraging results in clinics. HLA-A*24:02 is more common than HLA-A*02:01 in Asian countries, including China. Here we identified a novel HLA-A*24:02-restricted peptide KWVESIFLIF (AFP2-11 ) located in AFP signal peptide domain by mass spectrometric analysis of HLA-bound peptides from HepG2 cells. A TCR (KWV3.1) specific for AFP2-11 -HLA-A*24:02 was isolated from peripheral blood mononuclear cells of a healthy donor. The binding affinity of soluble KWV3.1 to its antigen was determined to be ~55 μm, within the affinity range of native TCRs for self-antigens. KWV3.1-transfected T cells could specifically activate and kill AFP2-11 pulsed T2-A24 cells and AFP+ HLA-A*24:02+ tumor cell lines, demonstrating that AFP2-11 can be naturally presented on the surface of AFP+ tumor cell lines. The newly identified antigenic peptide can provide a novel target for immunotherapeutic strategies for patients with AFP+ HLA-A*24:02+ HCC.
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Affiliation(s)
- Zhenjuan Li
- School of Life Sciences, University of Science and Technology of China, Hefei, China.,Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haiping Gong
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Qiuping Liu
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Wanli Wu
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Jianting Cheng
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Yingyi Mei
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Yaolong Chen
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Hongjun Zheng
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Xiaohong Yu
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Shi Zhong
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China
| | - Yi Li
- Guangdong Xiangxue Life Sciences, Ltd., Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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11
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Inaba H, Ariyasu H, Iwakura H, Ueda Y, Kurimoto C, Uraki S, Takeshima K, Yamaoka H, Furukawa Y, Morita S, Nishi M, Akamizu T. Comparative analysis of human leucocyte antigen between idiopathic and anti-PD-1 antibody induced isolated adrenocorticotropic hormone deficiency: A pilot study. Clin Endocrinol (Oxf) 2019; 91:786-792. [PMID: 31468541 DOI: 10.1111/cen.14082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND Adult-onset idiopathic isolated adrenocorticotropic hormone deficiency (id-IAD) is a rare disease with unknown aetiology. Recently, numerous cases of anti-PD-1 antibody-induced IAD (PD1-IAD) have been reported, but the clinical course, predictive factors and relationship to id-IAD have not been clarified. Moreover, associations of id-IAD and PD1-IAD with human leucocyte antigen (HLA) require elucidation. METHODS Clinical characteristics of 13 Japanese patients with id-IAD and eight Japanese patients with PD1-IAD were analysed, and HLA-typing test was performed for each patient. Allele and haplotype frequencies of the patients were compared to those of healthy Japanese controls. RESULTS In the HLA allele and haplotype analyses of id-IAD, the frequencies of HLA-C*14:02, HLA-DPB1*05:01, HLA-DRB1*04:05-DQB1*04:01-DPB1*05:01 and HLA-DRB1*09:01-DQB1*03:03-DPB1*05:01 were significantly increased. On the other hand, HLA alleles account for PD1-IAD susceptibility as follows: HLA-DQB1*06:01, HLA-DPB1*09:01 and HLA-DRB5*01:02. Moreover, protective effect for HLA-C*03:03 was suggested in combined id-IAD and PD1-IAD patients. Comparison of the effects of HLA on id-IAD and PD1-IAD revealed some differences. Alleles or haplotypes frequencies increased in id-IAD group were as follows: HLA-DPB1*05:01, HLA-DRB1*09:01, HLA-DRB4*01:03:02, HLA-DQB1*03:03 and HLA-DRB1*09:01-DQB1*03:03. In clinical settings, hyponatremia, disturbance of consciousness and hypoglycaemia were less frequently seen in patients with PD1-IAD than in patients with id-IAD. CONCLUSIONS Distinct clinical characteristics and predisposing HLA allele contributions were proposed between id-IAD and PD1-IAD. Further investigations with greater number of cases are warranted to clarify the detailed mechanisms of id-IAD and PD1-IAD.
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Affiliation(s)
- Hidefumi Inaba
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Hiroyuki Ariyasu
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Hiroshi Iwakura
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yoko Ueda
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Chiaki Kurimoto
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shinsuke Uraki
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Ken Takeshima
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Hiroyuki Yamaoka
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yasushi Furukawa
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shuhei Morita
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Masahiro Nishi
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Takashi Akamizu
- The First Department of Medicine, Wakayama Medical University, Wakayama, Japan
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12
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Mimori T, Yasuda J, Kuroki Y, Shibata TF, Katsuoka F, Saito S, Nariai N, Ono A, Nakai-Inagaki N, Misawa K, Tateno K, Kawai Y, Fuse N, Hozawa A, Kuriyama S, Sugawara J, Minegishi N, Suzuki K, Kinoshita K, Nagasaki M, Yamamoto M. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. THE PHARMACOGENOMICS JOURNAL 2019; 19:136-146. [PMID: 29352165 PMCID: PMC6462828 DOI: 10.1038/s41397-017-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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Affiliation(s)
- Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko F Shibata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naoki Nariai
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, USA
| | - Akira Ono
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Kazuharu Misawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Keiko Tateno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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13
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Tsuchiya N, Ohashi J. Human immune system diversity and its implications in diseases. J Hum Genet 2015; 60:655-6. [PMID: 26601708 DOI: 10.1038/jhg.2015.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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