1
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Sugio T, Uchida N, Miyawaki K, Ohno Y, Eto T, Mori Y, Yoshimoto G, Kikushige Y, Kunisaki Y, Mizuno S, Nagafuji K, Iwasaki H, Kamimura T, Ogawa R, Miyamoto T, Taniguchi S, Akashi K, Kato K. Prognostic impact of HLA supertype mismatch in single-unit cord blood transplantation. Bone Marrow Transplant 2024; 59:466-472. [PMID: 38238452 DOI: 10.1038/s41409-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 04/06/2024]
Abstract
The "human leukocyte antigen (HLA) supertype" is a functional classification of HLA alleles, which was defined by structural features and peptide specificities, and has been reportedly associated with the clinical outcomes of viral infections and autoimmune diseases. Although the disparity in each HLA locus was reported to have no clinical significance in single-unit cord blood transplantation (sCBT), the clinical significance of the HLA supertype in sCBT remains unknown. Therefore, we retrospectively analyzed clinical data of 1603 patients who received sCBT in eight institutes in Japan between 2000 and 2017. Each HLA allele was categorized into 19 supertypes, and the prognostic effect of disparities was then assessed. An HLA-B supertype mismatch was identified as a poor prognostic factor (PFS: hazard ratio [HR] = 1.23, p = 0.00044) and was associated with a higher cumulative incidence (CI) of relapse (HR = 1.24, p = 0.013). However, an HLA-B supertype mismatch was not associated with the CI of acute and chronic graft-versus-host-disease. The multivariate analysis for relapse and PFS showed the significance of an HLA-B supertype mismatch independent of allelic mismatches, and other previously reported prognostic factors. HLA-B supertype-matched grafts should be selected in sCBT.
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Affiliation(s)
- Takeshi Sugio
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuju Ohno
- Department of Hematology, Kitakyushu Municipal Medical Center, Fukuoka, Japan
| | - Tetsuya Eto
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Yasuo Mori
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Goichi Yoshimoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yoshikane Kikushige
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yuya Kunisaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinichi Mizuno
- Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Nagafuji
- Department of Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Hiromi Iwasaki
- Department of Hematology, National Hospital Organization Kyushu Medical Center, Fukuoka, Japan
| | | | - Ryosuke Ogawa
- Department of Hematology, JCHO Kyushu Hospital, Fukuoka, Japan
| | - Toshihiro Miyamoto
- Department of Hematology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
- Department of Hematology, Hamanomachi Hospital, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
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2
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Stokidis S, Baxevanis CN, Fortis SP. The Prognostic Significance of Selected HLA Alleles on Prostate Cancer Outcome. Int J Mol Sci 2023; 24:14454. [PMID: 37833904 PMCID: PMC10572221 DOI: 10.3390/ijms241914454] [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: 06/29/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Recently, we have shown that HLA-A*02:01 and HLA-A*24:02 in de novo metastatic prostate cancer (MPCa) have an important role in disease progression. Since de novo MPCa represents a small group among patients diagnosed with prostate cancer (PCa), it was obvious to try to extend the validity of our results to larger cohorts of PCa patients. Herein, we analyzed patients irrespective of their disease status at diagnosis to include, besides patients with MPCa, those with localized PCa (LPCa). Our goal was to specify the prognostic value of HLA-A*02:01 and HLA-A*24:02 for overall survival (OS) prospectively and for early biochemical recurrence (BCR) and castrate resistance (CR) as additional clinical endpoints in a prospective/retrospective manner, to improve clinical decisions for patients covering all stages of PCa. On univariate analysis, HLA-A alleles were significantly associated as prognostic biomarkers with early BCR (p = 0.028; HR = 1.822), OS (p = 0.013; HR = 1.547) and showed a trend for CR (p = 0.150; HR = 1.239). On multivariate analysis, HLA-A alleles proved to be independent prognosticators for early BCR (p = 0.017; HR = 2.008), CR (p = 0.005; HR = 1.615), and OS (p = 0.002; HR = 2.063). Kaplan-Meier analyses revealed that patients belonging to the HLA-A*02:01+HLA-A*24:02- group progressed much faster to BCR and CR and had also shorter OS compared to HLA-A*24:02+ patients. Patients being HLA-A*02:01-HLA-A*24:02- exhibited varying clinical outcomes, pointing to the presence of additional HLA-A alleles with potential prognostic value. Our data underline the HLA-A alleles as valuable prognostic biomarkers for PCa that may assist with the appropriate treatment and follow-up schedule based on the risk for disease progression to avoid over-diagnosis and over-treatment.
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Affiliation(s)
| | | | - Sotirios P. Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522 Athens, Greece; (S.S.); (C.N.B.)
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3
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Foix A, López D, Díez-Fuertes F, McConnell MJ, Martín-Galiano AJ. Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1009726. [PMID: 35143484 PMCID: PMC8830725 DOI: 10.1371/journal.pcbi.1009726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
The massive assessment of immune evasion due to viral mutations that increase COVID-19 susceptibility can be computationally facilitated. The adaptive cytotoxic T response is critical during primary infection and the generation of long-term protection. Here, potential HLA class I epitopes in the SARS-CoV-2 proteome were predicted for 2,915 human alleles of 71 families using the netMHCIpan EL algorithm. Allele families showed extreme epitopic differences, underscoring genetic variability of protective capacity between humans. Up to 1,222 epitopes were associated with any of the twelve supertypes, that is, allele clusters covering 90% population. Next, from all mutations identified in ~118,000 viral NCBI isolates, those causing significant epitope score reduction were considered epitope escape mutations. These mutations mainly involved non-conservative substitutions at the second and C-terminal position of the ligand core, or total ligand removal by large recurrent deletions. Escape mutations affected 47% of supertype epitopes, which in 21% of cases concerned isolates from two or more sub-continental areas. Some of these changes were coupled, but never surpassed 15% of evaded epitopes for the same supertype in the same isolate, except for B27. In contrast to most supertypes, eight allele families mostly contained alleles with few SARS-CoV-2 ligands. Isolates harboring cytotoxic escape mutations for these families co-existed geographically within sub-Saharan and Asian populations enriched in these alleles according to the Allele Frequency Net Database. Collectively, our findings indicate that escape mutation events have already occurred for half of HLA class I supertype epitopes. However, it is presently unlikely that, overall, it poses a threat to the global population. In contrast, single and double mutations for susceptible alleles may be associated with viral selective pressure and alarming local outbreaks. The integration of genomic, geographical and immunoinformatic information eases the surveillance of variants potentially affecting the global population, as well as minority subpopulations.
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Affiliation(s)
- Anna Foix
- European Bioinformatic Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Daniel López
- Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Michael J. McConnell
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital Infections Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
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4
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The pockets guide to HLA class I molecules. Biochem Soc Trans 2021; 49:2319-2331. [PMID: 34581761 PMCID: PMC8589423 DOI: 10.1042/bst20210410] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 01/11/2023]
Abstract
Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells. These peptides are bound within the peptide binding cleft of HLA, and together as a complex, are recognised by T cells using their specialised T cell receptors. Within the cleft, the peptide residue side chains bind into distinct pockets. These pockets ultimately determine the specificity of peptide binding. As HLAs are the most polymorphic molecules in humans, amino acid variants in each binding pocket influences the peptide repertoire that can be presented on the cell surface. Here, we review each of the 6 HLA binding pockets of HLA class I (HLA-I) molecules. The binding specificity of pockets B and F are strong determinants of peptide binding and have been used to classify HLA into supertypes, a useful tool to predict peptide binding to a given HLA. Over the years, peptide binding prediction has also become more reliable by using binding affinity and mass spectrometry data. Crystal structures of peptide-bound HLA molecules provide a means to interrogate the interactions between binding pockets and peptide residue side chains. We find that most of the bound peptides from these structures conform to binding motifs determined from prediction software and examine outliers to learn how these HLAs are stabilised from a structural perspective.
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5
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Sun H, Lu Z, Xuan G, Liu N, Wang T, Liu Y, Lan M, Xu J, Feng Y, Xu S, Lu Y, Sun B, Zhang J, Zhang X, Sun Y, Yang S, Zhang Y, Zhang Y, Cheng L, Jiang D, Yang K. Integrative Analysis of HTNV Glycoprotein Derived MHC II Epitopes by In Silico Prediction and Experimental Validation. Front Cell Infect Microbiol 2021; 11:671694. [PMID: 34350130 PMCID: PMC8326763 DOI: 10.3389/fcimb.2021.671694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/21/2021] [Indexed: 12/02/2022] Open
Abstract
Hantaan virus (HTNV), the causative pathogen of hemorrhagic fever with renal syndrome (HFRS), is a negative RNA virus belonging to the Orthohantaviridae family. HTNV envelope glycoprotein (GP), encoded by the genomic medium segment, is immunogenic and is therefore a promising vaccine candidate. Major histocompatibility complex class I (MHC-I) epitopes derived from HTNV has been extensively studied, but little is known of MHC-II epitopes. In silico predictions based on four databases indicated that the full-length HTNV GP has 1121 15-mer epitopes, of which 289 had a high score for binding to the human and murine MHC-II superfamily. It found that epitope ILTVLKFIANIFHTS could potentially bind most MHC-II molecules covering human and murine haplotypes. Dominant epitopes were validated by enzyme-linked immunospot assay of splenocytes from immunized mice; 6 of 10 epitopes supported the predictions including TATYSIVGPANAKVP, TKTLVIGQCIYTITS, FSLLPGVAHSIAVEL, CETYKELKAHGVSCP, CGLYLDRLKPVGSAY, and NLGENPCKIGLQTSS. Conservation analysis of dominant epitopes revealed host–virus interactions without geographic stratification, thus meeting the requirements of candidate vaccines for large-population prophylaxis. These findings provide insight into hantavirus antigenicity and suggest that vaccines targeting MHC-II could provide immune protection in large population to complement symptomatic therapies for the treatment of HFRS.
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Affiliation(s)
- Hao Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Zhenhua Lu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China.,Department of Epidemiology, Public Health School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Guoyun Xuan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Ning Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Tianhu Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yang Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Mingfu Lan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Jiahao Xu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yuancai Feng
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Shuang Xu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yuchen Lu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Jinpeng Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China.,Department of Surgery, Jinling Hospital, Nanjing, China
| | - Xiyang Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yuanjie Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Shuya Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yun Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Yusi Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (The Fourth Military Medical University), Xi'an, China
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6
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Li F, Deng L, Jackson KR, Talukder AH, Katailiha AS, Bradley SD, Zou Q, Chen C, Huo C, Chiu Y, Stair M, Feng W, Bagaev A, Kotlov N, Svekolkin V, Ataullakhanov R, Miheecheva N, Frenkel F, Wang Y, Zhang M, Hawke D, Han L, Zhou S, Zhang Y, Wang Z, Decker WK, Sonnemann HM, Roszik J, Forget MA, Davies MA, Bernatchez C, Yee C, Bassett R, Hwu P, Du X, Lizee G. Neoantigen vaccination induces clinical and immunologic responses in non-small cell lung cancer patients harboring EGFR mutations. J Immunother Cancer 2021; 9:jitc-2021-002531. [PMID: 34244308 PMCID: PMC8268925 DOI: 10.1136/jitc-2021-002531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Background Neoantigen (NeoAg) peptides displayed at the tumor cell surface by human leukocyte antigen molecules show exquisite tumor specificity and can elicit T cell mediated tumor rejection. However, few NeoAgs are predicted to be shared between patients, and none to date have demonstrated therapeutic value in the context of vaccination. Methods We report here a phase I trial of personalized NeoAg peptide vaccination (PPV) of 24 stage III/IV non-small cell lung cancer (NSCLC) patients who had previously progressed following multiple conventional therapies, including surgery, radiation, chemotherapy, and tyrosine kinase inhibitors (TKIs). Primary endpoints of the trial evaluated feasibility, tolerability, and safety of the personalized vaccination approach, and secondary trial endpoints assessed tumor-specific immune reactivity and clinical responses. Of the 16 patients with epidermal growth factor receptor (EGFR) mutations, nine continued TKI therapy concurrent with PPV and seven patients received PPV alone. Results Out of 29 patients enrolled in the trial, 24 were immunized with personalized NeoAg peptides. Aside from transient rash, fatigue and/or fever observed in three patients, no other treatment-related adverse events were observed. Median progression-free survival and overall survival of the 24 vaccinated patients were 6.0 and 8.9 months, respectively. Within 3–4 months following initiation of PPV, seven RECIST-based objective clinical responses including one complete response were observed. Notably, all seven clinical responders had EGFR-mutated tumors, including four patients that had continued TKI therapy concurrently with PPV. Immune monitoring showed that five of the seven responding patients demonstrated vaccine-induced T cell responses against EGFR NeoAg peptides. Furthermore, two highly shared EGFR mutations (L858R and T790M) were shown to be immunogenic in four of the responding patients, all of whom demonstrated increases in peripheral blood neoantigen-specific CD8+ T cell frequencies during the course of PPV. Conclusions These results show that personalized NeoAg vaccination is feasible and safe for advanced-stage NSCLC patients. The clinical and immune responses observed following PPV suggest that EGFR mutations constitute shared, immunogenic neoantigens with promising immunotherapeutic potential for large subsets of NSCLC patients. Furthermore, PPV with concurrent EGFR inhibitor therapy was well tolerated and may have contributed to the induction of PPV-induced T cell responses.
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Affiliation(s)
- Fenge Li
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ligang Deng
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Kyle R Jackson
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amjad H Talukder
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arjun S Katailiha
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sherille D Bradley
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qingwei Zou
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Caixia Chen
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Chong Huo
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Yulun Chiu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew Stair
- Mary Bird Perkins Cancer Center, Baton Rouge, Louisiana, USA
| | - Weihong Feng
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | | | | | | | | | | | | | - Yaling Wang
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Minying Zhang
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ling Han
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Shuo Zhou
- Provincial Clinical College, Fujian Medical University, Fujian, China
| | - Yan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhenglu Wang
- Biological Sample Resource Sharing Center, Tianjin First Central Hospital, Tianjin, China
| | - William K Decker
- Department of Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Heather M Sonnemann
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Roszik
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andree Forget
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roland Bassett
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xueming Du
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Gregory Lizee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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7
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Chiou SH, Tseng D, Reuben A, Mallajosyula V, Molina IS, Conley S, Wilhelmy J, McSween AM, Yang X, Nishimiya D, Sinha R, Nabet BY, Wang C, Shrager JB, Berry MF, Backhus L, Lui NS, Wakelee HA, Neal JW, Padda SK, Berry GJ, Delaidelli A, Sorensen PH, Sotillo E, Tran P, Benson JA, Richards R, Labanieh L, Klysz DD, Louis DM, Feldman SA, Diehn M, Weissman IL, Zhang J, Wistuba II, Futreal PA, Heymach JV, Garcia KC, Mackall CL, Davis MM. Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity 2021; 54:586-602.e8. [PMID: 33691136 PMCID: PMC7960510 DOI: 10.1016/j.immuni.2021.02.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.
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Affiliation(s)
- Shin-Heng Chiou
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Diane Tseng
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Irene S Molina
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephanie Conley
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Julie Wilhelmy
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Alana M McSween
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Xinbo Yang
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Daisuke Nishimiya
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Mark F Berry
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Leah Backhus
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Natalie S Lui
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Heather A Wakelee
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Joel W Neal
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Sukhmani K Padda
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Patrick Tran
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Jalen A Benson
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Richards
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Louis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Jianjun Zhang
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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8
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Pharmacogenetic and Association Studies on the Influence of HLA Alleles and Rivastigmine on the Iranian Patients with Late-Onset Alzheimer's Disease. Mol Neurobiol 2021; 58:2792-2802. [PMID: 33502736 DOI: 10.1007/s12035-021-02295-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder affecting cognitive function. A number of allelic genes from HLA complex have shown variable associations with AD in different populations. In this study, we investigated the association of DQB1*06:00/x, DRB1*04:00/x, DRB1*15:00/x, and B*07:00/x genotypes with AD and their relevance to the efficacy of rivastigmine treatment in the Iranian population. Our findings suggest that DQB1*06:00/x genotype offers strong protection against AD (P = 0.0074), while B*07:00/x genotype imposes a significant susceptibility for sporadic Alzheimer's disease (SAD) (P = 0.009). Interestingly, B*07:00/x genotype does not show any apparent associations with familial Alzheimer's disease (FAD). Our studies also suggest a pharmacogenetic relationship between drug treatment and presence of a particular genotype in the Iranian LOAD patient population. The Clinical Dementia Rating analysis showed that LOAD patients carrying DRB1*04:00/x genotype tend to display a downward trend in the disease severity and symptoms after 2-year follow-up with rivastigmine treatment. Moreover, in our total patient population, the carriers of DQB1*06:00/x and B*07:00/x alleles have better and worse responses to rivastigmine respectively. We also measured the clinical relevance of the testing for these genotypes employing prevalence-corrected positive predictive value (PcPPV) formula. The PcPPV of testing for DQB1*06:00/x in the Iranian LOAD patients was 1.17% which means that people carrying this genotype have half of the probability of the absolute risk for developing LOAD, whereas the PcPPV of testing for B*07:00/x was 4.45% for SAD, which can be interpreted as a doubling chance for developing LOAD among the Iranian population carrying this genotype. These results also suggest that DQβ1 peptide containing positively charged AAs histidine30 and arginine55 and HLA class I β chain containing negatively charges aspartic acid114 and glutamic acid45,152 in their binding groove plays important roles in protection against and susceptibility for LOAD respectively.
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9
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Serçinoğlu O, Ozbek P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PLoS One 2020; 15:e0232849. [PMID: 32421728 PMCID: PMC7233585 DOI: 10.1371/journal.pone.0232849] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Faculty of Engineering, Fener, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Faculty of Engineering, Goztepe, Istanbul, Turkey
- * E-mail:
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10
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Balas A, Ramírez E, Trigo E, Cabañas R, Fiandor A, Arsuaga M, Lerma V, Sanz B, LuisVicario J, Herranz P, de Abajo F, Bellón T. HLA-A∗68, -A∗11:01, and -A∗29:02 alleles are strongly associated with benznidazole-induced maculopapular exanthema (MPE)/DRESS. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2020; 8:3198-3200.e3. [PMID: 32417447 DOI: 10.1016/j.jaip.2020.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio Balas
- Histocompatibility, Centro de Transfusión de Madrid, Madrid, Spain
| | - Elena Ramírez
- Clinical Pharmacology Department, Hospital Universitario La Paz-Carlos III-Cantoblanco, IdiPAZ, School of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Elena Trigo
- Tropical Medicine and Travel Health Unit, Department of Internal Medicine, Hospital Universitario La Paz-Carlos III-Cantoblanco, Madrid, Spain
| | - Rosario Cabañas
- Allergy Department, Hospital Universitario La Paz-Carlos III-Cantoblanco, Madrid, Spain
| | - Ana Fiandor
- Allergy Department, Hospital Universitario La Paz-Carlos III-Cantoblanco, Madrid, Spain
| | - Marta Arsuaga
- Tropical Medicine and Travel Health Unit, Department of Internal Medicine, Hospital Universitario La Paz-Carlos III-Cantoblanco, Madrid, Spain
| | - Victoria Lerma
- Clinical Pharmacology Unit, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, Spain
| | - Beatriz Sanz
- Drug Hypersensitivity Laboratory, Institute for Health Research Hospital Universitario La Paz (IdiPaz), Madrid, Spain
| | - José LuisVicario
- Histocompatibility, Centro de Transfusión de Madrid, Madrid, Spain
| | - Pedro Herranz
- Dermatology Department, Hospital Universitario La Paz-Carlos III-Cantoblanco, Madrid, Spain
| | - Francisco de Abajo
- Clinical Pharmacology Unit, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, Spain; Department of Biomedical Sciences, University of Alcalá (IRYCIS), Alcalá de Henares, Madrid, Spain
| | - Teresa Bellón
- Drug Hypersensitivity Laboratory, Institute for Health Research Hospital Universitario La Paz (IdiPaz), Madrid, Spain.
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11
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Mumtaz S, Nabney IT, Flower DR. Scrutinizing human MHC polymorphism: Supertype analysis using Poisson-Boltzmann electrostatics and clustering. J Mol Graph Model 2017; 77:130-136. [PMID: 28850895 DOI: 10.1016/j.jmgm.2017.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/25/2017] [Indexed: 11/26/2022]
Abstract
Peptide-binding MHC proteins are thought the most variable across the human population; the extreme MHC polymorphism observed is functionally important and results from constrained divergent evolution. MHCs have vital functions in immunology and homeostasis: cell surface MHC class I molecules report cell status to CD8+ T cells, NKT cells and NK cells, thus playing key roles in pathogen defence, as well as mediating smell recognition, mate choice, Adverse Drug Reactions, and transplantation rejection. MHC peptide specificity falls into several supertypes exhibiting commonality of binding. It seems likely that other supertypes exist relevant to other functions. Since comprehensive experimental characterization is intractable, structure-based bioinformatics is the only viable solution. We modelled functional MHC proteins by homology and used calculated Poisson-Boltzmann electrostatics projected from the top surface of the MHC as multi-dimensional descriptors, analysing them using state-of-the-art dimensionality reduction techniques and clustering algorithms. We were able to recover the 3 MHC loci as separate clusters and identify clear sub-groups within them, vindicating unequivocally our choice of both data representation and clustering strategy. We expect this approach to make a profound contribution to the study of MHC polymorphism and its functional consequences, and, by extension, other burgeoning structural systems, such as GPCRs.
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Affiliation(s)
- Shahzad Mumtaz
- School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom; Department of Computer Science, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Ian T Nabney
- School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom
| | - Darren R Flower
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom.
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12
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How an alloreactive T-cell receptor achieves peptide and MHC specificity. Proc Natl Acad Sci U S A 2017; 114:E4792-E4801. [PMID: 28572406 DOI: 10.1073/pnas.1700459114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
T-cell receptor (TCR) allorecognition is often presumed to be relatively nonspecific, attributable to either a TCR focus on exposed major histocompatibility complex (MHC) polymorphisms or the degenerate recognition of allopeptides. However, paradoxically, alloreactivity can proceed with high peptide and MHC specificity. Although the underlying mechanisms remain unclear, the existence of highly specific alloreactive TCRs has led to their use as immunotherapeutics that can circumvent central tolerance and limit graft-versus-host disease. Here, we show how an alloreactive TCR achieves peptide and MHC specificity. The HCV1406 TCR was cloned from T cells that expanded when a hepatitis C virus (HCV)-infected HLA-A2- individual received an HLA-A2+ liver allograft. HCV1406 was subsequently shown to recognize the HCV nonstructural protein 3 (NS3):1406-1415 epitope with high specificity when presented by HLA-A2. We show that NS3/HLA-A2 recognition by the HCV1406 TCR is critically dependent on features unique to both the allo-MHC and the NS3 epitope. We also find cooperativity between structural mimicry and a crucial peptide "hot spot" and demonstrate its role, along with the MHC, in directing the specificity of allorecognition. Our results help explain the paradox of specificity in alloreactive TCRs and have implications for their use in immunotherapy and related efforts to manipulate TCR recognition, as well as alloreactivity in general.
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13
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Lazaryan A, Wang T, Spellman SR, Wang HL, Pidala J, Nishihori T, Askar M, Olsson R, Oudshoorn M, Abdel-Azim H, Yong A, Gandhi M, Dandoy C, Savani B, Hale G, Page K, Bitan M, Reshef R, Drobyski W, Marsh SG, Schultz K, Müller CR, Fernandez-Viña MA, Verneris MR, Horowitz MM, Arora M, Weisdorf DJ, Lee SJ. Human leukocyte antigen supertype matching after myeloablative hematopoietic cell transplantation with 7/8 matched unrelated donor allografts: a report from the Center for International Blood and Marrow Transplant Research. Haematologica 2016; 101:1267-1274. [PMID: 27247320 DOI: 10.3324/haematol.2016.143271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
The diversity of the human leukocyte antigen (HLA) class I and II alleles can be simplified by consolidating them into fewer supertypes based on functional or predicted structural similarities in epitope-binding grooves of HLA molecules. We studied the impact of matched and mismatched HLA-A (265 versus 429), -B (230 versus 92), -C (365 versus 349), and -DRB1 (153 versus 51) supertypes on clinical outcomes of 1934 patients with acute leukemias or myelodysplasia/myeloproliferative disorders. All patients were reported to the Center for International Blood and Marrow Transplant Research following single-allele mismatched unrelated donor myeloablative conditioning hematopoietic cell transplantation. Single mismatched alleles were categorized into six HLA-A (A01, A01A03, A01A24, A02, A03, A24), six HLA-B (B07, B08, B27, B44, B58, B62), two HLA-C (C1, C2), and five HLA-DRB1 (DR1, DR3, DR4, DR5, DR9) supertypes. Supertype B mismatch was associated with increased risk of grade II-IV acute graft-versus-host disease (hazard ratio =1.78, P=0.0025) compared to supertype B match. Supertype B07-B44 mismatch was associated with a higher incidence of both grade II-IV (hazard ratio=3.11, P=0.002) and III-IV (hazard ratio=3.15, P=0.01) acute graft-versus-host disease. No significant associations were detected between supertype-matched versus -mismatched groups at other HLA loci. These data suggest that avoiding HLA-B supertype mismatches can mitigate the risk of grade II-IV acute graft-versus-host disease in 7/8-mismatched unrelated donor hematopoietic cell transplantation when multiple HLA-B supertype-matched donors are available. Future studies are needed to define the mechanisms by which supertype mismatching affects outcomes after alternative donor hematopoietic cell transplantation.
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Affiliation(s)
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Hai-Lin Wang
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Joseph Pidala
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Taiga Nishihori
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | - Richard Olsson
- Karolinska University Hospital, Centre for Allogeneic Stem Cell Transplantation, Stockholm, Sweden
| | | | | | - Agnes Yong
- Royal Adelaide Hospital/SA Pathology, Australia
| | | | | | - Bipin Savani
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gregory Hale
- All Children's Hospital, St. Petersburg, FL, USA
| | - Kristin Page
- Duke University Medical Center, Pediatric Blood and Marrow Transplant, Durham, NC, USA
| | | | - Ran Reshef
- Columbia University Medical Center, New York, NY, USA
| | | | - Steven Ge Marsh
- Anthony Nolan Research Institute & University College London Cancer Institute, Royal Free Campus, UK
| | - Kirk Schultz
- British Columbia's Children's Hospital, Vancouver, British Columbia, Canada
| | | | | | | | - Mary M Horowitz
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI, USA
| | - Mukta Arora
- University of Minnesota Medical Center, Fairview, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- University of Minnesota Medical Center, Fairview, Minneapolis, MN, USA
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14
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Szender JB, Eng KH, Matsuzaki J, Miliotto A, Gnjatic S, Tsuji T, Odunsi K. HLA superfamily assignment is a predictor of immune response to cancer testis antigens and survival in ovarian cancer. Gynecol Oncol 2016; 142:158-162. [PMID: 27103177 DOI: 10.1016/j.ygyno.2016.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/15/2016] [Accepted: 04/16/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To characterize the association between major histocompatibility complex (MHC) types and spontaneous antibody development to the cancer testis (CT) antigen NY-ESO-1. METHODS Tumor expression of NY-ESO-1 and serum antibodies to NY-ESO-1 were characterized in addition to human leukocyte antigen (HLA) type for patients with epithelial ovarian cancer. HLA types were assigned to structure-based superfamilies and statistical associations were examined. HLA types were compared to existing reference libraries of HLA frequencies in a European-Caucasian American population. RESULTS Out of 126 patients identified, 81% were expression positive and 48% had spontaneous antibody responses to NY-ESO-1. There was an association between HLA-B superfamily and seropositivity among patients with tumors expressing NY-ESO-1 (p<0.001). The differences in HLA-B superfamily assignment were driven by HLA-B44. Among all patients, the B27 superfamily was over-represented compared with the general population (p<0.001). CONCLUSIONS HLA type appears to be associated with spontaneous anti-CT antigen antibodies, as well as with the overall risk of ovarian cancer.
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Affiliation(s)
- J Brian Szender
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263, United States; Department of Epidemiology and Environmental Health, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Kevin H Eng
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263, United States
| | - Junko Matsuzaki
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY 14263, United States
| | - Anthony Miliotto
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY 14263, United States
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Takemasa Tsuji
- Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY 14263, United States
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263, United States; Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY 14263, United States.
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15
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Cole DK. The ultimate mix and match: making sense of HLA alleles and peptide repertoires. Immunol Cell Biol 2015; 93:515-6. [PMID: 25823993 DOI: 10.1038/icb.2015.40] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David K Cole
- The Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
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16
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Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping. Immunol Cell Biol 2015; 93:522-32. [PMID: 25708537 DOI: 10.1038/icb.2015.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/20/2014] [Accepted: 12/22/2014] [Indexed: 11/08/2022]
Abstract
T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.
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