1
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Fuchs KJ, van de Meent M, Honders MW, Khatri I, Kester MGD, Koster EAS, Koutsoumpli G, de Ru AH, van Bergen CAM, van Veelen PA, ’t Hoen PAC, van Balen P, van den Akker EB, Veelken JH, Halkes CJM, Falkenburg JHF, Griffioen M. Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens. Blood 2024; 143:1856-1872. [PMID: 38427583 PMCID: PMC11076866 DOI: 10.1182/blood.2023022343] [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: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
ABSTRACT Allogeneic stem cell transplantation (alloSCT) is a curative treatment for hematological malignancies. After HLA-matched alloSCT, antitumor immunity is caused by donor T cells recognizing polymorphic peptides, designated minor histocompatibility antigens (MiHAs), that are presented by HLA on malignant patient cells. However, T cells often target MiHAs on healthy nonhematopoietic tissues of patients, thereby inducing side effects known as graft-versus-host disease. Here, we aimed to identify the dominant repertoire of HLA-I-restricted MiHAs to enable strategies to predict, monitor or modulate immune responses after alloSCT. To systematically identify novel MiHAs by genome-wide association screening, T-cell clones were isolated from 39 transplanted patients and tested for reactivity against 191 Epstein-Barr virus transformed B cell lines of the 1000 Genomes Project. By discovering 81 new MiHAs, we more than doubled the antigen repertoire to 159 MiHAs and demonstrated that, despite many genetic differences between patients and donors, often the same MiHAs are targeted in multiple patients. Furthermore, we showed that one quarter of the antigens are cryptic, that is translated from unconventional open reading frames, for example long noncoding RNAs, showing that these antigen types are relevant targets in natural immune responses. Finally, using single cell RNA-seq data, we analyzed tissue expression of MiHA-encoding genes to explore their potential role in clinical outcome, and characterized 11 new hematopoietic-restricted MiHAs as potential targets for immunotherapy. In conclusion, we expanded the repertoire of HLA-I-restricted MiHAs and identified recurrent, cryptic and hematopoietic-restricted antigens, which are fundamental to predict, follow or manipulate immune responses to improve clinical outcome after alloSCT.
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Affiliation(s)
- Kyra J. Fuchs
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva A. S. Koster
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Georgia Koutsoumpli
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. C. ’t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B. van den Akker
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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2
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Jadi O, Tang H, Olsen K, Vensko S, Zhu Q, Wang Y, Haiman CA, Pooler L, Sheng X, Brock G, Webb A, Pasquini MC, McCarthy PL, Spellman SR, Hahn T, Vincent B, Armistead P, Sucheston-Campbell LE. Associations of minor histocompatibility antigens with outcomes following allogeneic hematopoietic cell transplantation. Am J Hematol 2023; 98:940-950. [PMID: 37052167 PMCID: PMC10368187 DOI: 10.1002/ajh.26925] [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: 01/14/2023] [Revised: 03/09/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023]
Abstract
The role of minor histocompatibility antigens (mHAs) in mediating graft versus leukemia and graft versus host disease (GvHD) following allogeneic hematopoietic cell transplantation (alloHCT) is recognized but not well-characterized. By implementing improved methods for mHA prediction in two large patient cohorts, this study aimed to comprehensively explore the role of mHAs in alloHCT by analyzing whether (1) the number of predicted mHAs, or (2) individual mHAs are associated with clinical outcomes. The study population consisted of 2249 donor-recipient pairs treated for acute myeloid leukemia and myelodysplastic syndrome with alloHCT. A Cox proportional hazard model showed that patients with a class I mHA count greater than the population median had an increased hazard of GvHD mortality (hazard ratio [HR] = 1.39, 95% confidence interval [CI] = 1.01, 1.77, p = .046). Competing risk analyses identified the class I mHAs DLRCKYISL (GSTP), WEHGPTSLL (CRISPLD2), and STSPTTNVL (SERPINF2) were associated with increased GVHD mortality (HR = 2.84, 95% CI = 1.52, 5.31, p = .01), decreased leukemia-free survival (LFS) (HR = 1.94, 95% CI = 1.27, 2.95, p = .044), and increased disease-related mortality (DRM) (HR = 2.32, 95% CI = 1.5, 3.6, p = .008), respectively. One class II mHA YQEIAAIPSAGRERQ (TACC2) was associated with increased risk of treatment-related mortality (TRM) (HR = 3.05, 95% CI = 1.75, 5.31, p = .02). WEHGPTSLL and STSPTTNVL were both present within HLA haplotype B*40:01-C*03:04 and showed a positive dose-response relationship with increased all-cause mortality and DRM and decreased LFS, indicating these two mHAs contribute to the risk of mortality in an additive manner. Our study reports the first large-scale investigation of the associations of predicted mHA peptides with clinical outcomes following alloHCT.
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Affiliation(s)
- Othmane Jadi
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Hancong Tang
- College of Pharmacy, The Ohio State University, Columbus, OH
| | - Kelly Olsen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Yiwen Wang
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Loreall Pooler
- The Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Guy Brock
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Marcelo C. Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Philip L McCarthy
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Theresa Hahn
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Benjamin Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC
| | - Paul Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH
- College of Veterinary Medicine, The Ohio State University, Columbus, OH
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3
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Du X, Yan X, Zhang W, Zhu Z, Qin W, Dong X, Zhang X. A SNP in Cathepsin L is associated with carapace length trait in giant freshwater prawn Macrobrachium rosenbergii. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Li Z, Liu X, Li Y, Wang W, Wang N, Xiao F, Gao H, Guo H, Li H, Wang S. Chicken C/EBPζ gene: Expression profiles, association analysis, and identification of functional variants for abdominal fat. Domest Anim Endocrinol 2021; 76:106631. [PMID: 33979717 DOI: 10.1016/j.domaniend.2021.106631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
CCAAT enhancer binding protein ζ (C/EBPζ) plays an important role in adipose proliferation and differentiation in humans. However, very little is known about the effect of C/EBPζ on the growth and development of adipose tissues in domesticated animals. The present study attempted to investigate the mRNA expression profiles of chicken C/EBPζ in a variety of tissues; analyze the association of its variants with abdominal fat; and identify the functional variants for abdominal fat. The tissue expression profiles revealed that C/EBPζ was highly expressed in 19 tissues obtained from broilers. The expression level of C/EBPζ in fat broilers was significantly lower than that in lean broilers in the duodenum, ileum, cecum, kidney, pectoral muscle, and liver (P < 0.05). Among 170 polymorphic loci of C/EBPζ, 9 single nucleotide polymorphisms (SNPs) demonstrated a significant association with chicken abdominal fat traits (P < 0.05) as well as significant discrepancies in their allelic frequencies between fat and lean birds. Particularly, only C/EBPζ g.7085A>C exhibited significant correlation with abdominal fat traits (P < 0.00015) using the Bonferroni method. The results revealed that, in preadipocyte immortalized cells (ICPI), the luciferase activity of the A allele of g.7085A>C locus was remarkably stronger than that of the C allele (P < 0.05). In silico analysis showed that g.7085A>C locus was located in the binding region of the transcription factor SOX5, which possesses the ability to transform C/EBPζ transcription efficiency through binding with SOX5. In summary, the data obtained from this study suggested that C/EBPζ is a potential candidate gene responsible for abdominal fat deposition in chicken and that g.7085A>C is a functional SNP that can be promisingly leveraged for marker assisted selection (MAS) in future chicken breeding programs.
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Affiliation(s)
- Z Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - X Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Y Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - W Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - N Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - F Xiao
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Gao
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Guo
- Fujian Sunnzer Biotechnology Development Co., Ltd, 354100, Guangze, Fujian Province, China
| | - H Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - S Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
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5
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Miralaei N, Hoghoughi N, Azadeh M, Alborzian K, Ghaedi K. rs12287003 modifies the susceptibility to breast cancer by altering the interactions between KDM2A and miRNAs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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6
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Mutis T, Xagara A, Spaapen RM. The Connection Between Minor H Antigens and Neoantigens and the Missing Link in Their Prediction. Front Immunol 2020; 11:1162. [PMID: 32670277 PMCID: PMC7326952 DOI: 10.3389/fimmu.2020.01162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
For hundreds of thousands of years, the human genome has extensively evolved, resulting in genetic variations in almost every gene. Immunological reflections of these genetic variations become clearly visible after an allogeneic stem cell transplantation (allo-SCT) as minor Histocompatibility (H) antigens. Minor H antigens are peptides cleaved from genetically encoded variable protein regions after which they are presented at the cell surface by HLA molecules. After allo-SCT with minor H antigen mismatches between donor and recipient, donor T cells recognize the minor H antigens of the recipient as foreign, evoking strong alloreactive immune responses. Studies in the late eighties have discovered that a subset of minor H antigens are encoded by hematopoietic system-specific genes. After allo-SCT, this subset is strictly expressed on the hematopoietic malignant cells and was therefore the first well-defined highly immunogenic group of tumor-specific antigens. In the last decade, neoantigens derived from genetic mutations in tumors have been identified as another group of immunogenic tumor-specific antigens. Therefore, hematopoietic minor H antigens and neoantigens are therapeutic equivalents. This review will connect our current knowledge about the immune biology and identification of minor H antigens and neoantigens leading to novel conclusions on their prediction.
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Affiliation(s)
- Tuna Mutis
- Department of Hematology, Amsterdam UMC, VU Medical Center, Amsterdam, Netherlands
| | - Anastasia Xagara
- Department of Immunopathology, Sanquin Research, Amsterdam, Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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7
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Penter L, Wu CJ. Personal tumor antigens in blood malignancies: genomics-directed identification and targeting. J Clin Invest 2020; 130:1595-1607. [PMID: 31985488 PMCID: PMC7108890 DOI: 10.1172/jci129209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hematological malignancies have long been at the forefront of the development of novel immune-based treatment strategies. The earliest successful efforts originated from the extensive body of work in the field of allogeneic hematopoietic stem cell transplantation. These efforts laid the foundation for the recent exciting era of cancer immunotherapy, which includes immune checkpoint blockade, personal neoantigen vaccines, and adoptive T cell transfer. At the heart of the specificity of these novel strategies is the recognition of target antigens presented by malignant cells to T cells. Here, we review the advances in systematic identification of minor histocompatibility antigens and neoantigens arising from personal somatic alterations or recurrent driver mutations. These exciting efforts pave the path for the implementation of personalized combinatorial cancer therapy.
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Affiliation(s)
- Livius Penter
- Department of Hematology, Oncology, and Tumor Immunology, Charité – Universitätsmedizin Berlin (CVK), Berlin, Germany
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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8
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Kremer AN, Bausenwein J, Lurvink E, Kremer AE, Rutten CE, van Bergen CAM, Kretschmann S, van der Meijden E, Honders MW, Mazzeo D, Watts C, Mackensen A, Falkenburg JHF, Griffioen M. Discovery and Differential Processing of HLA Class II-Restricted Minor Histocompatibility Antigen LB-PIP4K2A-1S and Its Allelic Variant by Asparagine Endopeptidase. Front Immunol 2020; 11:381. [PMID: 32218783 PMCID: PMC7078166 DOI: 10.3389/fimmu.2020.00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/17/2020] [Indexed: 12/03/2022] Open
Abstract
Minor histocompatibility antigens are the main targets of donor-derived T-cells after allogeneic stem cell transplantation. Identification of these antigens and understanding their biology are a key requisite for more insight into how graft vs. leukemia effect and graft vs. host disease could be separated. We here identified four new HLA class II-restricted minor histocompatibility antigens using whole genome association scanning. For one of the new antigens, i.e., LB-PIP4K2A-1S, we measured strong T-cell recognition of the donor variant PIP4K2A-1N when pulsed as exogenous peptide, while the endogenously expressed variant in donor EBV-B cells was not recognized. We showed that lack of T-cell recognition was caused by intracellular cleavage by a protease named asparagine endopeptidase (AEP). Furthermore, microarray gene expression analysis showed that PIP4K2A and AEP are both ubiquitously expressed in a wide variety of healthy tissues, but that expression levels of AEP were lower in primary acute myeloid leukemia (AML). In line with that, we confirmed low activity of AEP in AML cells and demonstrated that HLA-DRB1*03:01 positive primary AML expressing LB-PIP4K2A-1S or its donor variant PIP4K2A-1N were both recognized by specific T-cells. In conclusion, LB-PIP4K2A-1S not only represents a novel minor histocompatibility antigen but also provides evidence that donor T-cells after allogeneic stem cell transplantation can target the autologous allelic variant as leukemia-associated antigen. Furthermore, it demonstrates that endopeptidases can play a role in cell type-specific intracellular processing and presentation of HLA class II-restricted antigens, which may be explored in future immunotherapy of AML.
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Affiliation(s)
- Anita N Kremer
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Judith Bausenwein
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Ellie Lurvink
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Andreas E Kremer
- Department of Internal Medicine 1, Gastroenterology, Pneumology and Endocrinology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Caroline E Rutten
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Sascha Kretschmann
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Edith van der Meijden
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Maria W Honders
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Daniela Mazzeo
- Division of Cell Signaling & Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Colin Watts
- Division of Cell Signaling & Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andreas Mackensen
- Department of Internal Medicine 5, Hematology/Oncology, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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9
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Akatsuka Y. TCR-Like CAR-T Cells Targeting MHC-Bound Minor Histocompatibility Antigens. Front Immunol 2020; 11:257. [PMID: 32184779 PMCID: PMC7058980 DOI: 10.3389/fimmu.2020.00257] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/30/2020] [Indexed: 11/20/2022] Open
Abstract
Minor histocompatibility antigens (mHAgs) in allogeneic hematopoietic stem cell transplantation are highly immunogenic as they are foreign antigens and cause polymorphism between donors and recipients. Adoptive cell therapy with mHAg-specific T cells may be an effective option for therapy against recurring hematological malignancies following transplantation. Genetically modified T cells with T cell receptors (TCRs) specific to mHAgs have been developed, but formation of mispaired chimeric TCRs between endogenous and exogenous TCR chains may compromise their function. An alternative approach is the development of chimeric antigen receptor (CAR)-T cells with TCR-like specificity whose CAR transmembrane and intracellular domains do not compete with endogenous TCR for CD3 complexes and transmit their own activation signals. However, it has been shown that the recognition of low-density antigens by high-affinity CAR-T cells has poor sensitivity and specificity. This mini review focuses on the potential for and limitations of TCR-like CAR-T cells in targeting human leukocyte antigen-bound peptide antigens, based on their recognition mechanisms and their application in targeting mHAgs.
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Affiliation(s)
- Yoshiki Akatsuka
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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10
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Xue LL, Wang F, Xiong LL, Du RL, Zhou HL, Zou Y, Wu MX, Yang MA, Dai J, He MX, Wang TH. A single-nucleotide polymorphism induced alternative splicing in Tacr3 involves in hypoxic-ischemic brain damage. Brain Res Bull 2020; 154:106-115. [PMID: 31722250 DOI: 10.1016/j.brainresbull.2019.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/28/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023]
Abstract
Single-nucleotide polymorphism (SNP) and Alternative splicing (AS) were found to be implicated in certain diseases, nevertheless, the contributions of mRNA SNPs and AS to pathogenesis in developing rat brains with hypoxic-ischemic encephalopathy (HIE) remained largely vague. Additionally, the disease associated with Tacr3 was normosmic congenital hypogonadotropic hypogonadism, while the relationship between HIE and Tacr3 remained largely elusive. The current study was designed to investigate the differentially expressed mRNAs and related SNPs as well as AS in neonatal rats subjected to HIE to identify if the exhibition of AS was associated with SNPs under pathological condition. Firstly, we used postnatal day 7 Sprague-Dawley rats to construct neonatal HIE model, and analyzed the expression profiles of SNP mRNA in hypoxic-ischemic (HI) and sham brains by using RNA sequencing. Then four genes, including Mdfic, Lpp, Bag3 and Tacr3, connecting with HIE and exhibiting SNPs and AS were identified by bioinformatics analysis. Moreover, combined with exonic splicing enhancer (ESE) and alternative splice site predictor (ASSP) analysis, we found that Tacr3 is associated specifically with HIE through 258547789 G > A SNP in inside the Alt First Exon and 258548573 G > A SNP in outside the Alt First Exon. Taken together, our study provides new evidence to understand the role of Tacr3 in HIE and it is possibly a potential target for the treatment of HIE in future clinic trial.
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MESH Headings
- Animals
- Humans
- Male
- Rats
- Alternative Splicing/genetics
- Animals, Newborn
- Brain/metabolism
- Disease Models, Animal
- Hypoxia-Ischemia, Brain/genetics
- Hypoxia-Ischemia, Brain/metabolism
- Neurons/metabolism
- Polymorphism, Single Nucleotide/genetics
- Rats, Sprague-Dawley
- Receptors, Neurokinin-3/genetics
- Receptors, Neurokinin-3/metabolism
- Receptors, Tachykinin/genetics
- Receptors, Tachykinin/metabolism
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Affiliation(s)
- Lu-Lu Xue
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China
| | - Fang Wang
- Department of Science and Technology, Kunming Medical University, Kunming 650031, China
| | - Liu-Lin Xiong
- Department of Anesthesiology, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P. R. 563000, China
| | - Ruo-Lan Du
- Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China
| | - Hao-Li Zhou
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Zou
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Ma-Xiu Wu
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Ming-An Yang
- Division of Biostatistics and Epidemiology, School of Public Health, San Diego State University, USA
| | - Jing Dai
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Man-Xi He
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.
| | - Ting-Hua Wang
- Institute of Neurological Disease, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Neuroscience, Animal Zoology Department, Kunming Medical University, Kunming 650031, China.
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11
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Summers C, Sheth VS, Bleakley M. Minor Histocompatibility Antigen-Specific T Cells. Front Pediatr 2020; 8:284. [PMID: 32582592 PMCID: PMC7283489 DOI: 10.3389/fped.2020.00284] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 01/05/2023] Open
Abstract
Minor Histocompatibility (H) antigens are major histocompatibility complex (MHC)/Human Leukocyte Antigen (HLA)-bound peptides that differ between allogeneic hematopoietic stem cell transplantation (HCT) recipients and their donors as a result of genetic polymorphisms. Some minor H antigens can be used as therapeutic T cell targets to augment the graft-vs.-leukemia (GVL) effect in order to prevent or manage leukemia relapse after HCT. Graft engineering and post-HCT immunotherapies are being developed to optimize delivery of T cells specific for selected minor H antigens. These strategies have the potential to reduce relapse risk and thereby permit implementation of HCT approaches that are associated with less toxicity and fewer late effects, which is particularly important in the growing and developing pediatric patient. Most minor H antigens are expressed ubiquitously, including on epithelial tissues, and can be recognized by donor T cells following HCT, leading to graft-vs.-host disease (GVHD) as well as GVL. However, those minor H antigens that are expressed predominantly on hematopoietic cells can be targeted for selective GVL. Once full donor hematopoietic chimerism is achieved after HCT, hematopoietic-restricted minor H antigens are present only on residual recipient malignant hematopoietic cells, and these minor H antigens serve as tumor-specific antigens for donor T cells. Minor H antigen-specific T cells that are delivered as part of the donor hematopoietic stem cell graft at the time of HCT contribute to relapse prevention. However, in some cases the minor H antigen-specific T cells delivered with the graft may be quantitatively insufficient or become functionally impaired over time, leading to leukemia relapse. Following HCT, adoptive T cell immunotherapy can be used to treat or prevent relapse by delivering large numbers of donor T cells targeting hematopoietic-restricted minor H antigens. In this review, we discuss minor H antigens as T cell targets for augmenting the GVL effect in engineered HCT grafts and for post-HCT immunotherapy. We will highlight the importance of these developments for pediatric HCT.
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Affiliation(s)
- Corinne Summers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Vipul S Sheth
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
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12
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Zhu Q, Wang J, Zhang L, Bian W, Lin M, Xu X, Zhou X. LCK rs10914542-G allele associates with type 1 diabetes in children via T cell hyporesponsiveness. Pediatr Res 2019; 86:311-315. [PMID: 31112992 DOI: 10.1038/s41390-019-0436-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Abnormal lymphocyte-specific protein tyrosine kinase (LCK)-related T cell hyporesponsiveness was discovered in type 1 diabetes (T1D). This study aims to investigate the potential associations between LCK single-nucleotide polymorphisms (SNPs) and the susceptibility of T1D. METHODS DNAs were extracted from blood samples of 589 T1D patients and 596 healthy controls to genotype seven SNPs of the LCK gene using PCR and Sanger sequencing. Associations of these SNPs with the susceptibility of T1D were determined by χ2 test. LCKs were knocked out in peripheral blood mononuclear cells (PBMCs) using CRISPR-Cas9 to investigate the role of LCK SNP in T-lymphocyte activation in T1D. RESULTS SNP rs10914542 but not the other six SNPs of the LCK gene was significantly associated with (C vs. G, odds ratio (OR) = 0.581, 95% confidence interval (CI) = 0.470-0.718, P value = 4.13E - 7) the susceptibility of T1D. Peripheral T-lymphocyte activation in response to T cell receptor (TCR)/CD3 stimulation is significantly lower in the rs10914542-G-allele group than in the C-allele group. In vitro experiments revealed that rs10914542 G allele impaired the TCR/CD3-mediated T-cell activation in PBMCs. CONCLUSIONS This study reveals that the G allele of SNP rs10914542 of LCK impairs the TCR/CD3-mediated T-cell activation and increases the risk of T1D.
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Affiliation(s)
- Qingwen Zhu
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Jing Wang
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Lingli Zhang
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Wenjun Bian
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Mengsi Lin
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Xiaoning Xu
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China
| | - Xiang Zhou
- Prenatal Screening and Diagnosis Center, Nantong Municipal Maternal and Child Health Hospital, 226010, Nantong, China.
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13
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Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS. Alternative tumour-specific antigens. Nat Rev Cancer 2019; 19:465-478. [PMID: 31278396 PMCID: PMC6874891 DOI: 10.1038/s41568-019-0162-4] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
The study of tumour-specific antigens (TSAs) as targets for antitumour therapies has accelerated within the past decade. The most commonly studied class of TSAs are those derived from non-synonymous single-nucleotide variants (SNVs), or SNV neoantigens. However, to increase the repertoire of available therapeutic TSA targets, 'alternative TSAs', defined here as high-specificity tumour antigens arising from non-SNV genomic sources, have recently been evaluated. Among these alternative TSAs are antigens derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other processes. Unlike the patient-specific nature of SNV neoantigens, some alternative TSAs may have the advantage of being widely shared by multiple tumours, allowing for universal, off-the-shelf therapies. In this Opinion article, we will outline the biology, available computational tools, preclinical and/or clinical studies and relevant cancers for each alternative TSA class, as well as discuss both current challenges preventing the therapeutic application of alternative TSAs and potential solutions to aid in their clinical translation.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Bioinformatics Core, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, Chapel Hill, NC, USA
| | - Shengjie Chai
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Ma GW, Chu YK, Zhang WJ, Qin FY, Xu SS, Yang H, Rong EG, Du ZQ, Wang SZ, Li H, Wang N. Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep. PLoS One 2017; 12:e0174868. [PMID: 28384189 PMCID: PMC5383234 DOI: 10.1371/journal.pone.0174868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/16/2017] [Indexed: 11/19/2022] Open
Abstract
Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep. Immunostaining showed that FST was localized in inner root sheath (IRS) and matrix of hair follicle (HF) in both SF and Suffolk sheep. Sequencing analysis identified a total of seven SNPs (termed SNPs 1-7) in the FST gene in Chinese Merino sheep (Junken Type). Association analysis showed that SNP2 (Chr 16. 25,633,662 G>A) was significantly associated with average wool fiber diameter, wool fineness SD, and wool crimp (P < 0.05). SNP4 (Chr 16. 25,633,569 C>T) was significantly associated with wool fineness SD and CV of fiber diameter (P < 0.05). Similarly, the haplotypes derived from these seven identified SNPs were also significantly associated with average wool fiber diameter, wool fineness SD, CV of fiber diameter, and wool crimp (P < 0.05). Our results suggest that FST influences wool quality traits and its SNPs 2 and 4 might be useful markers for marker-assisted selection and sheep breeding.
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Affiliation(s)
- Guang-Wei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Yan-Kai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Wen-Jian Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Fei-Yue Qin
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Song-Song Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, P. R. China
| | - En-Guang Rong
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Shou-Zhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
- * E-mail:
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15
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Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. eLife 2016; 5. [PMID: 27232982 PMCID: PMC4940163 DOI: 10.7554/elife.13328] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 05/26/2016] [Indexed: 01/19/2023] Open
Abstract
Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans. DOI:http://dx.doi.org/10.7554/eLife.13328.001
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Affiliation(s)
- Anil Raj
- Department of Genetics, Stanford University, Stanford, United States
| | - Sidney H Wang
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Heejung Shim
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Arbel Harpak
- Department of Biology, Stanford University, Stanford, United States
| | - Yang I Li
- Department of Genetics, Stanford University, Stanford, United States
| | - Brett Engelmann
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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16
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Martin SD, Brown SD, Wick DA, Nielsen JS, Kroeger DR, Twumasi-Boateng K, Holt RA, Nelson BH. Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines. PLoS One 2016; 11:e0155189. [PMID: 27192170 PMCID: PMC4871527 DOI: 10.1371/journal.pone.0155189] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/25/2016] [Indexed: 01/07/2023] Open
Abstract
Due to advances in sequencing technology, somatically mutated cancer antigens, or neoantigens, are now readily identifiable and have become compelling targets for immunotherapy. In particular, neoantigen-targeted vaccines have shown promise in several pre-clinical and clinical studies. However, to date, neoantigen-targeted vaccine studies have involved tumors with exceptionally high mutation burdens. It remains unclear whether neoantigen-targeted vaccines will be broadly applicable to cancers with intermediate to low mutation burdens, such as ovarian cancer. To address this, we assessed whether a derivative of the murine ovarian tumor model ID8 could be targeted with neoantigen vaccines. We performed whole exome and transcriptome sequencing on ID8-G7 cells. We identified 92 somatic mutations, 39 of which were transcribed, missense mutations. For the 17 top predicted MHC class I binding mutations, we immunized mice subcutaneously with synthetic long peptide vaccines encoding the relevant mutation. Seven of 17 vaccines induced robust mutation-specific CD4 and/or CD8 T cell responses. However, none of the vaccines prolonged survival of tumor-bearing mice in either the prophylactic or therapeutic setting. Moreover, none of the neoantigen-specific T cell lines recognized ID8-G7 tumor cells in vitro, indicating that the corresponding mutations did not give rise to bonafide MHC-presented epitopes. Additionally, bioinformatic analysis of The Cancer Genome Atlas data revealed that only 12% (26/220) of HGSC cases had a ≥90% likelihood of harboring at least one authentic, naturally processed and presented neoantigen versus 51% (80/158) of lung cancers. Our findings highlight the limitations of applying neoantigen-targeted vaccines to tumor types with intermediate/low mutation burdens.
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Affiliation(s)
- Spencer D. Martin
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Scott D. Brown
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Darin A. Wick
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Julie S. Nielsen
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - David R. Kroeger
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Kwame Twumasi-Boateng
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Robert A. Holt
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Brad H. Nelson
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Biochemistry, University of Victoria, Victoria, Canada
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17
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Griffioen M, van Bergen CAM, Falkenburg JHF. Autosomal Minor Histocompatibility Antigens: How Genetic Variants Create Diversity in Immune Targets. Front Immunol 2016; 7:100. [PMID: 27014279 PMCID: PMC4791598 DOI: 10.3389/fimmu.2016.00100] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/01/2016] [Indexed: 11/13/2022] Open
Abstract
Allogeneic stem cell transplantation (alloSCT) can be a curative treatment for hematological malignancies. Unfortunately, the desired anti-tumor or graft-versus-leukemia (GvL) effect is often accompanied with undesired side effects against healthy tissues known as graft-versus-host disease (GvHD). After HLA-matched alloSCT, GvL and GvHD are both mediated by donor-derived T-cells recognizing polymorphic peptides presented by HLA surface molecules on patient cells. These polymorphic peptides or minor histocompatibility antigens (MiHA) are produced by genetic differences between patient and donor. Since polymorphic peptides may be useful targets to manipulate the balance between GvL and GvHD, the dominant repertoire of MiHA needs to be discovered. In this review, the diversity of autosomal MiHA characterized thus far as well as the various molecular mechanisms by which genetic variants create immune targets and the role of cryptic transcripts and proteins as antigen sources are described. The tissue distribution of MiHA as important factor in GvL and GvHD is considered as well as possibilities how hematopoietic MiHA can be used for immunotherapy to augment GvL after alloSCT. Although more MiHA are still needed for comprehensive understanding of the biology of GvL and GvHD and manipulation by immunotherapy, this review shows insight into the composition and kinetics of in vivo immune responses with respect to specificity, diversity, and frequency of specific T-cells and surface expression of HLA-peptide complexes and other (accessory) molecules on the target cell. A complex interplay between these factors and their environment ultimately determines the spectrum of clinical manifestations caused by immune responses after alloSCT.
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Affiliation(s)
- Marieke Griffioen
- Department of Hematology, Leiden University Medical Center , Leiden , Netherlands
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18
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Pont MJ, van der Lee DI, van der Meijden ED, van Bergen CAM, Kester MGD, Honders MW, Vermaat M, Eefting M, Marijt EWA, Kielbasa SM, Hoen PAC', Falkenburg JHF, Griffioen M. Integrated Whole Genome and Transcriptome Analysis Identified a Therapeutic Minor Histocompatibility Antigen in a Splice Variant of ITGB2. Clin Cancer Res 2016; 22:4185-96. [PMID: 26964570 DOI: 10.1158/1078-0432.ccr-15-2307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/29/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE In HLA-matched allogeneic hematopoietic stem cell transplantation (alloSCT), donor T cells recognizing minor histocompatibility antigens (MiHAs) can mediate desired antitumor immunity as well as undesired side effects. MiHAs with hematopoiesis-restricted expression are relevant targets to augment antitumor immunity after alloSCT without side effects. To identify therapeutic MiHAs, we analyzed the in vivo immune response in a patient with strong antitumor immunity after alloSCT. EXPERIMENTAL DESIGN T-cell clones recognizing patient, but not donor, hematopoietic cells were selected for MiHA discovery by whole genome association scanning. RNA-sequence data from the GEUVADIS project were analyzed to investigate alternative transcripts, and expression patterns were determined by microarray analysis and qPCR. T-cell reactivity was measured by cytokine release and cytotoxicity. RESULTS T-cell clones were isolated for two HLA-B*15:01-restricted MiHA. LB-GLE1-1V is encoded by a nonsynonymous SNP in exon 6 of GLE1 For the other MiHAs, an associating SNP in intron 3 of ITGB2 was found, but no SNP disparity was present in the normal gene transcript between patient and donor. RNA-sequence analysis identified an alternative ITGB2 transcript containing part of intron 3. qPCR demonstrated that this transcript is restricted to hematopoietic cells and SNP-positive individuals. In silico translation revealed LB-ITGB2-1 as HLA-B*15:01-binding peptide, which was validated as hematopoietic MiHA by T-cell experiments. CONCLUSIONS Whole genome and transcriptome analysis identified LB-ITGB2-1 as MiHAs encoded by an alternative transcript. Our data support the therapeutic relevance of LB-ITGB2-1 and illustrate the value of RNA-sequence analysis for discovery of immune targets encoded by alternative transcripts. Clin Cancer Res; 22(16); 4185-96. ©2016 AACR.
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Affiliation(s)
- Margot J Pont
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | | | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maria W Honders
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthias Eefting
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik W A Marijt
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Szymon M Kielbasa
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
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19
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Wu X, Hurst LD. Determinants of the Usage of Splice-Associated cis-Motifs Predict the Distribution of Human Pathogenic SNPs. Mol Biol Evol 2015; 33:518-29. [PMID: 26545919 PMCID: PMC4866546 DOI: 10.1093/molbev/msv251] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 10/25/2015] [Indexed: 12/11/2022] Open
Abstract
Where in genes do pathogenic mutations tend to occur and does this provide clues as to the possible underlying mechanisms by which single nucleotide polymorphisms (SNPs) cause disease? As splice-disrupting mutations tend to occur predominantly at exon ends, known also to be hot spots of cis-exonic splice control elements, we examine the relationship between the relative density of such exonic cis-motifs and pathogenic SNPs. In particular, we focus on the intragene distribution of exonic splicing enhancers (ESE) and the covariance between them and disease-associated SNPs. In addition to showing that disease-causing genes tend to be genes with a high intron density, consistent with missplicing, five factors established as trends in ESE usage, are considered: relative position in exons, relative position in genes, flanking intron size, splice sites usage, and phase. We find that more than 76% of pathogenic SNPs are within 3–69 bp of exon ends where ESEs generally reside, this being 13% more than expected. Overall from enrichment of pathogenic SNPs at exon ends, we estimate that approximately 20–45% of SNPs affect splicing. Importantly, we find that within genes pathogenic SNPs tend to occur in splicing-relevant regions with low ESE density: they are found to occur preferentially in the terminal half of genes, in exons flanked by short introns and at the ends of phase (0,0) exons with 3′ non-“AGgt” splice site. We suggest the concept of the “fragile” exon, one home to pathogenic SNPs owing to its vulnerability to splice disruption owing to low ESE density.
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Affiliation(s)
- XianMing Wu
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
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20
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Oostvogels R, Lokhorst HM, Mutis T. Minor histocompatibility Ags: identification strategies, clinical results and translational perspectives. Bone Marrow Transplant 2015; 51:163-71. [PMID: 26501766 DOI: 10.1038/bmt.2015.256] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/11/2015] [Accepted: 08/15/2015] [Indexed: 12/14/2022]
Abstract
Allogeneic stem cell transplantation (allo-SCT) and donor lymphocyte infusion are effective treatment modalities for various hematological malignancies. Their therapeutic effect, the graft-versus-tumor (GvT) effect, is based mainly on an alloimmune response of donor T cells directed at tumor cells, in which differences in the expression of minor histocompatibility Ags (mHags) on the cells of the patient and donor have a crucial role. However, these differences are also responsible for induction of sometimes detrimental GvHD. As relapse and development of GvHD pose major threats for a large proportion of allotransplanted patients, additional therapeutic strategies are required. To augment the GvT response without increasing the risk of GvHD, specific mHag-directed immunotherapeutic strategies have been developed. Over the past years, much effort has been put into the identification of therapeutically relevant mHags to enable these strategies for a substantial proportion of patients. Currently, the concept of mHag-directed immunotherapy is tested in clinical trials on feasibility, safety and efficacy. In this review, we will summarize the recent developments in mHag identification and the clinical data on mHag-specific immune responses and mHag-directed therapies in patients with hematological malignancies. Finally, we will outline the current challenges and future prospectives in the field.
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Affiliation(s)
- R Oostvogels
- Department of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - H M Lokhorst
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - T Mutis
- Department of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
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21
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Yu J, Liu RL, Luo XP, Shi HM, Ma D, Pan JJ, Ni HC. Tissue Factor Pathway Inhibitor-2 Gene Polymorphisms Associate With Coronary Atherosclerosis in Chinese Population. Medicine (Baltimore) 2015; 94:e1675. [PMID: 26496276 PMCID: PMC4620828 DOI: 10.1097/md.0000000000001675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tissue factor pathway inhibitor-2 (TFPI-2) may play critical roles in the pathogenesis of atherosclerosis. In this study, we aimed to investigate the association between TFPI-2 gene polymorphisms and coronary atherosclerosis.Four hundred and seven patients with coronary atherosclerosis and 306 individuals with normal coronary artery were enrolled in the present study. Nine single-nucleotide polymorphisms (SNPs) (rs3763473, rs59805398, rs60215632, rs59999573, rs59740167, rs34489123, rs4517, rs4264, and rs4271) were detected with polymerase chain reaction-direct sequencing method. Severity of coronary atherosclerosis was assessed by Gensini score. After the baseline investigation, patients with coronary atherosclerosis were followed up for incidence of cardiovascular events (CVEs).Eight SNPs were in accordance with the Hardy-Weinberg equilibrium, and 8 haplotypes were constructed based on rs59999573, rs59740167, and rs34489123 after linkage disequilibrium and haplotype analysis. Two SNPs (rs59805398 and rs34489123) and 5 haplotypes correlated with coronary atherosclerosis even after adjustment by Gensini score. At follow-up (median 53 months, range 1-60 months), 85 patients experienced CVE. However, there was no strong association between the gene polymorphisms and the occurrence of CVE.Tissue factor pathway inhibitor-2 gene polymorphisms were associated with coronary atherosclerosis in the Chinese population, suggesting that the information about TFPI-2 gene polymorphisms was useful for assessing the risk of developing coronary atherosclerosis, but there was not enough evidence showing it could predict occurrence of CVE.
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Affiliation(s)
- Jia Yu
- From the Department of Cardiology, Huashan Hospital, Fudan University, Shanghai, 200040, China (JY, R-IL, X-PL, H-MS, J-JP, H-CN); and Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai, 200032, China (DM)
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22
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Spierings E. Minor histocompatibility antigens: past, present, and future. ACTA ACUST UNITED AC 2015; 84:374-60. [PMID: 25262921 DOI: 10.1111/tan.12445] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Indexed: 01/02/2023]
Abstract
Minor histocompatibility (H) antigens are key molecules driving allo-immune responses in both graft-versus-host-disease (GvHD) and in graft-versus-leukemia (GvL) reactivity in human leukocyte antigen (HLA)-matched hematopoietic stem-cell transplantation (HSCT). Dissection of the dual function of minor H antigens became evident through their different modes of tissue and cell expression, i.e. hematopoietic system-restricted or broad. Broadly expressed minor H antigens can cause both GvHD and GvL effects, while hematopoietic system-restricted minor H antigens are more prone to induce GvL responses. This phenomenon renders the latter group of minor H antigens as curative tools for HSCT-based immunotherapy of hematological malignancies and disorders, in which minor H antigen-specific responses are enhanced in order to eradicate the malignant cells. This article describes the immunogenetics of minor H antigens and methods that have been developed to identify them. Moreover, it summarizes the clinical relevance of minor H antigens in transplantation, with special regards to allogeneic HSCT and solid-organ transplantation.
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Affiliation(s)
- Eric Spierings
- Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
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23
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Kang B, Gu Q, Tian P, Xiao L, Cao H, Yang W. A chimeric transcript containing Psy1 and a potential mRNA is associated with yellow flesh color in tomato accession PI 114490. PLANTA 2014; 240:1011-21. [PMID: 24663441 DOI: 10.1007/s00425-014-2052-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 03/04/2014] [Indexed: 05/19/2023]
Abstract
Carotenoid content is the primary determinant of fruit color that affects nutritional value and appearance in tomato. Phytoene synthase (PSY) is the key regulatory enzyme in the carotenoid biosynthesis pathway. Absent function of PSY1 in tomato fruit results in yellow flesh phenotype. We, here, report that two different transcripts, a wild-type (Psy1) and a chimeric mRNA (Psy1/Unknown), exist in a yellow-fruited tomato accession PI 114490. Psy1/Unknown is generated by joining exons from two different genes, Psy1 and an unknown gene, transcribed using both complementary DNA strands. The Psy1 shows low expression in the fruit of PI 114490, while the expression of Psy1/Unknown in the fruit of PI 114490 shows the same pattern as Psy1 in red fruit. The PSY1/Unknown has a lower function than PSY1 in a bacterial expression system. Coincidence of one single-nucleotide polymorphism (SNP) in the fourth intron and one simple sequence repeat (SSR) with 19 AT repeats in the downstream sequence of Psy1 gene with Psy1/Unknown in a set of yellow-fruited tomato lines indicates that Psy1/Unknown might be caused by the SNP and/or SSR. One possible explanation of these observations is trans-splicing. Severely reduced Psy1 transcript caused by Psy1/Unknown results in low accumulation of carotenoid and yellow flesh in PI 114490.
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Affiliation(s)
- Baoshan Kang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
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24
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Greger L, Su J, Rung J, Ferreira PG, Lappalainen T, Dermitzakis ET, Brazma A. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PLoS One 2014; 9:e104567. [PMID: 25133550 PMCID: PMC4136775 DOI: 10.1371/journal.pone.0104567] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/14/2014] [Indexed: 01/18/2023] Open
Abstract
Chimeric RNAs originating from two or more different genes are known to exist not only in cancer, but also in normal tissues, where they can play a role in human evolution. However, the exact mechanism of their formation is unknown. Here, we use RNA sequencing data from 462 healthy individuals representing 5 human populations to systematically identify and in depth characterize 81 RNA tandem chimeric transcripts, 13 of which are novel. We observe that 6 out of these 81 chimeras have been regarded as cancer-specific. Moreover, we show that a prevalence of long introns at the fusion breakpoint is associated with the chimeric transcripts formation. We also find that tandem RNA chimeras have lower abundances as compared to their partner genes. Finally, by combining our results with genomic data from the same individuals we uncover intronic genetic variants associated with the chimeric RNA formation. Taken together our findings provide an important insight into the chimeric transcripts formation and open new avenues of research into the role of intronic genetic variants in post-transcriptional processing events.
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Affiliation(s)
- Liliana Greger
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
- * E-mail:
| | - Jing Su
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Johan Rung
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Pedro G. Ferreira
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Alvis Brazma
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
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25
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Chen JH, Chen YC, Mao CL, Chiou JM, Tsao CK, Tsai KS. Association between secreted phosphoprotein-1 (SPP1) polymorphisms and low bone mineral density in women. PLoS One 2014; 9:e97428. [PMID: 24831687 PMCID: PMC4022728 DOI: 10.1371/journal.pone.0097428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/21/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A recent meta-analysis found that secreted phosphoprotein-1 (SPP1) can predict the risk of both osteoporosis and fracture. No study has explored the association of SPP1 haplotype-tagging single nucleotide polymorphisms (htSNPs) and haplotypes with bone mineral density (BMD). METHODS This is a cross-sectional study. A total of 1,313 healthy Taiwanese women aged 40 to 55 years were recruited from MJ Health Management Institute from 2009 to 2010. BMD was dichotomized into high and low BMD groups. Three common (allele frequency ≥5%) htSNPs were selected to examine the association between sequence variants of SPP1 and BMD. RESULTS Homozygosity for the T allele of rs4754 were protective from low BMD [TT vs. CC: adjusted OR (AOR) = 0.58, 95% confidence interval (CI) = 0.83-0.89]. A protective effect was also found for women carrying 2 copies of Hap3 TCT (AOR = 0.57, 95% CI = 0.34-0.95). Menopausal status marginally interacted with SPP1 rs6839524 on BMD (p = 0.049). Postmenopausal women carrying variant rs6839524 (GG+GC vs. CC: AOR = 2.35, 95% CI = 1.06-5.20) or Hap1 TGC (AOR = 2.36, 95% CI = 1.06-5.24) were associated with 2.4-fold risk of low BMD. For women with low BMI (<18.5 kg/m2), variant rs6839524 (AOR = 7.64) and Hap1 (AOR = 6.42) were associated with increased risk of low BMD. These findings did not reach statistical significance after correction for multiple tests. CONCLUSIONS SPP1 htSNP protected against low BMD in middle-aged women. SPP1 genetic markers may be important for the prediction of osteoporosis at an early age.
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Affiliation(s)
- Jen-Hau Chen
- Department of Geriatrics and Gerontology, National Taiwan University Hospital, No. 1, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yen-Ching Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chien-Lin Mao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Jeng-Min Chiou
- Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chwen Keng Tsao
- MJ Health Management Institution, 12F., No. 413, Section 4, Taipei, Taiwan
| | - Keh-Sung Tsai
- Department of Geriatrics and Gerontology, National Taiwan University Hospital, No. 1, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, No. 7, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, No. 7, Taipei, Taiwan,
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Ex vivo detection of CD8 T cells specific for H-Y minor histocompatibility antigens in allogeneic hematopoietic stem cell transplant recipients. Transpl Immunol 2014; 30:128-35. [DOI: 10.1016/j.trim.2014.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 11/18/2022]
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Fritsch EF, Rajasagi M, Ott PA, Brusic V, Hacohen N, Wu CJ. HLA-binding properties of tumor neoepitopes in humans. Cancer Immunol Res 2014; 2:522-9. [PMID: 24894089 DOI: 10.1158/2326-6066.cir-13-0227] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer genome sequencing has enabled the rapid identification of the complete repertoire of coding sequence mutations within a patient's tumor and facilitated their use as personalized immunogens. Although a variety of techniques are available to assist in the selection of mutation-defined epitopes to be included within the tumor vaccine, the ability of the peptide to bind to patient MHC is a key gateway to peptide presentation. With advances in the accuracy of predictive algorithms for MHC class I binding, choosing epitopes on the basis of predicted affinity provides a rapid and unbiased approach to epitope prioritization. We show herein the retrospective application of a prediction algorithm to a large set of bona fide T cell-defined mutated human tumor antigens that induced immune responses, most of which were associated with tumor regression or long-term disease stability. The results support the application of this approach for epitope selection and reveal informative features of these naturally occurring epitopes to aid in epitope prioritization for use in tumor vaccines.
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Affiliation(s)
- Edward F Fritsch
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mohini Rajasagi
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Patrick A Ott
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vladimir Brusic
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nir Hacohen
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Catherine J Wu
- Authors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, MassachusettsAuthors' Affiliations: Cancer Vaccine Center; Department of Medical Oncology, Dana-Farber Cancer Institute; The Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Massachusetts General Hospital; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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28
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Mateos MV. Role of bortezomib for the treatment of previously untreated multiple myeloma. Expert Rev Hematol 2014; 1:17-28. [DOI: 10.1586/17474086.1.1.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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29
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Chen X, Chang CH, Goldenberg DM. Novel strategies for improved cancer vaccines. Expert Rev Vaccines 2014; 8:567-76. [DOI: 10.1586/erv.09.11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Abstract
Minor histocompatibility (H) antigen mismatching leads to clinically relevant alloimmune reactivity. Depending on the tissue expression pattern of the involved minor H antigens, the immune response may either cause graft-versus-host disease and a graft-versus-tumor effect or lead to only a graft-versus-leukemia effect. Thus, identification of recipient-donor pairs with minor H antigen mismatches has clinical importance. This chapter describes molecular typing methods for molecular typing of minor H antigens.
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Affiliation(s)
- Eric Spierings
- Laboratory for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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31
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Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet 2013; 29:593-9. [PMID: 23972387 DOI: 10.1016/j.tig.2013.07.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/05/2013] [Accepted: 07/24/2013] [Indexed: 01/04/2023]
Abstract
Exome sequencing is one of the most cost-efficient sequencing approaches for conducting genome research on coding regions. However, significant portions of the reads obtained in exome sequencing come from outside of the designed target regions. These additional reads are generally ignored, potentially wasting an important source of genomic data. There are three major types of unintentionally sequenced read that can be found in exome sequencing data: reads in introns and intergenic regions, reads in the mitochondrial genome, and reads originating in viral genomes. All of these can be used for reliable data mining, extending the utility of exome sequencing. Large-scale exome sequencing data repositories, such as The Cancer Genome Atlas (TCGA), the 1000 Genomes Project, National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project, and The Sequence Reads Archive, provide researchers with excellent secondary data-mining opportunities to study genomic data beyond the intended target regions.
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Affiliation(s)
- David C Samuels
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37232, USA
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32
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Linscheid C, Petroff MG. Minor histocompatibility antigens and the maternal immune response to the fetus during pregnancy. Am J Reprod Immunol 2013; 69:304-14. [PMID: 23398025 PMCID: PMC4048750 DOI: 10.1111/aji.12075] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 12/20/2012] [Indexed: 12/21/2022] Open
Abstract
The tolerance of the semiallogeneic fetus by the maternal immune system is an important area of research for understanding how the maternal and fetal systems interact during pregnancy to ensure a successful outcome. Several lines of research reveal that the maternal immune system can recognize and respond to fetal minor histocompatibility antigens during pregnancy. Reactions to these antigens arise because of allelic differences between the mother and fetus and have been shown more broadly to play an important role in mediating transplantation outcomes. This review outlines the discovery of minor histocompatibility antigens and their importance in solid organ and hematopoietic stem cell transplantations, maternal T-cell responses to minor histocompatibility antigens during pregnancy, expression of minor histocompatibility antigens in the human placenta, and the potential involvement of minor histocompatibility antigens in the development and manifestation of pregnancy complications.
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Affiliation(s)
- Caitlin Linscheid
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS
| | - Margaret G. Petroff
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS
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Pei Q, Huang Q, Yang GP, Zhao YC, Yin JY, Song M, Zheng Y, Mo ZH, Zhou HH, Liu ZQ. PPAR-γ2 and PTPRD gene polymorphisms influence type 2 diabetes patients' response to pioglitazone in China. Acta Pharmacol Sin 2013; 34:255-61. [PMID: 23147557 DOI: 10.1038/aps.2012.144] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
AIM To investigate the influence of peroxisome proliferator-activated receptor γ2 (PPAR-γ2) gene polymorphism rs1801282 and protein tyrosine phosphatase receptor type D (PTPRD) gene polymorphism rs17584499 on the occurrence of type 2 diabetes and pioglitazone efficacy in a Chinese Han population. METHODS One hundred ninety seven type 2 diabetes patients and 212 healthy controls were enrolled. Among them, 67 type 2 diabetes patients were administered pioglitazone (30 mg/d, po) for 3 months. All the subjects were genotyped for genetic variants in PPAR-γ2 and PTPRD using MALDI-TOF mass spectrometry. Fasting plasma glucose, postprandial plasma glucose, glycated hemoglobin, serum triglyceride, total cholesterol, low-density and high-density lipoprotein-cholesterol were determined. RESULTS The PPAR-γ2 gene rs1801282 polymorphism was significantly associated with type 2 diabetes susceptibility (OR=0.515, 95% CI 0.268-0.990) and the PTPRD gene rs17584499 polymorphism was also significantly associated with type 2 diabetes (OR=1.984, 95% CI 1.135-3.469) in a dominant model adjusted for age, gender and BMI. After pioglitazone treatment for 3 months, the type 2 diabetes patients with PPAR-γ2 rs1801282 CG genotypes significantly showed higher differential values of postprandial plasma glucose and serum triglyceride compared with those with rs1801282 CC genotype. The patients with PTPRD rs17584499 CT+TT genotypes showed significantly lower differential value of postprandial plasma glucose compared to those with rs17584499 CC genotype. CONCLUSION Diabetes risk alleles in PPAR-γ2 (rs1801282) and PTPRD (rs17584499) are associated with pioglitazone therapeutic efficacy.
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Spierings E, Goulmy E. Minor histocompatibility antigen typing by DNA sequencing for clinical practice in hematopoietic stem-cell transplantation. Methods Mol Biol 2012; 882:509-30. [PMID: 22665253 DOI: 10.1007/978-1-61779-842-9_29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In HLA-matched stem-cell transplantation (SCT), minor H antigens are key molecules driving allo-immune responses in both graft-versus-host disease (GvHD) and in graft-versus-leukemia (GvL) reactivity. Dissection of the dual function of minor H antigens became evident through their different modes of tissue and cell expression, i.e., hematopoietic system restricted or broad. Broadly expressed minor H antigens are the targets of immune responses in both arms of graft-versus-host (GvH) responses, i.e., both GvHD and GvL, whereas the immune responses against the hematopoietic system-specific minor H antigens are restricted to the GvL arm of SCT. Evidently, it is this latter group of minor H antigens that can function as curative tools for stem-cell (SC)-based immunotherapy of hematological malignancies and disorders. The HLA-matched patient/donor combinations, incompatible for one of the hematopoietic-specific minor H antigens, are suitable for minor H antigen immunotherapy (Goulmy, Immunol Rev 157:125-140, 1997). Information on the minor H antigen phenotype is therefore needed. Hereto, genomic typing for minor H antigens has been implemented in many HLA laboratories. Here, we firstly summarize the relevance of minor H antigens particularly in hematopoietic SCT. Secondly, we describe a method for typing the various polymorphic minor H antigens molecularly identified to date by DNA sequencing.
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Affiliation(s)
- Eric Spierings
- Department of Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
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Mortensen BK, Rasmussen AH, Larsen ME, Larsen MV, Lund O, Braendstrup P, Harndahl M, Rasmussen M, Buus S, Stryhn A, Vindeløv L. Identification of a novel UTY-encoded minor histocompatibility antigen. Scand J Immunol 2012; 76:141-50. [PMID: 22536994 DOI: 10.1111/j.1365-3083.2012.02708.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Minor histocompatibility antigens (mHags) encoded by the Y-chromosome (H-Y-mHags) are known to play a pivotal role in allogeneic haematopoietic cell transplantation (HCT) involving female donors and male recipients. We present a new H-Y-mHag, YYNAFHWAI (UTY(139-147)), encoded by the UTY gene and presented by HLA-A*24:02. Briefly, short peptide stretches encompassing multiple putative H-Y-mHags were designed using a bioinformatics predictor of peptide-HLA binding, NetMHCpan. These peptides were used to screen for peptide-specific HLA-restricted T cell responses in peripheral blood mononuclear cells obtained post-HCT from male recipients of female donor grafts. In one of these recipients, a CD8+ T cell response was observed against a peptide stretch encoded by the UTY gene. Another bioinformatics tool, HLArestrictor, was used to identify the optimal peptide and HLA-restriction element. Using peptide/HLA tetramers, the specificity of the CD8+ T cell response was successfully validated as being HLA-A*24:02-restricted and directed against the male UTY(139-147) peptide. Functional analysis of these T cells demonstrated male UTY(139-147) peptide-specific cytokine secretion (IFNγ, TNFα and MIP-1β) and cytotoxic degranulation (CD107a). In contrast, no responses were seen when the T cells were stimulated with patient tumour cells alone. CD8+ T cells specific for this new H-Y-mHag were found in three of five HLA-A*24:02-positive male recipients of female donor HCT grafts available for this study.
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Affiliation(s)
- B K Mortensen
- Allogeneic Hematopoietic Cell Transplantation Laboratory, Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
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Jakubauskiene E, Janaviciute V, Peciuliene I, Söderkvist P, Kanopka A. G/A polymorphism in intronic sequence affects the processing of MAO-B gene in patients with Parkinson disease. FEBS Lett 2012; 586:3698-704. [PMID: 22974659 DOI: 10.1016/j.febslet.2012.08.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/16/2012] [Accepted: 08/21/2012] [Indexed: 11/27/2022]
Abstract
Monoamine oxidase B (MAO-B) plays an important role in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. Increased levels of MAO-B mRNA and enzymatic activity have been reported in platelets from patients with Parkinson's and Alzheimer's diseases, however the triggers of enhanced mRNA levels are unknown. Our results demonstrate for the first time that G/A dimorphism in intron 13 sequence creates splicing enhancer thus stimulating intron 13 removal efficiency. The increased MAO-B protein levels might serve as a surrogate marker for - Parkinson disease.
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Affiliation(s)
- Egle Jakubauskiene
- Department of Immunology and Cell Biology, Vilnius University, Institute of Biotechnology, LT-02241 Vilnius, Lithuania
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Effect of MHC and non-MHC donor/recipient genetic disparity on the outcome of allogeneic HCT. Blood 2012; 120:2796-806. [PMID: 22859606 DOI: 10.1182/blood-2012-04-347286] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The outcome of allogeneic hematopoietic cell transplantation is influenced by donor/recipient genetic disparity at loci both inside and outside the MHC on chromosome 6p. Although disparity at loci within the MHC is the most important risk factor for the development of severe GVHD, disparity at loci outside the MHC that encode minor histocompatibility (H) antigens can elicit GVHD and GVL activity in donor/recipient pairs who are otherwise genetically identical across the MHC. Minor H antigens are created by sequence and structural variations within the genome. The enormous variation that characterizes the human genome suggests that the total number of minor H loci is probably large and ensures that all donor/recipient pairs, despite selection for identity at the MHC, will be mismatched for many minor H antigens. In addition to mismatch at minor H loci, unrelated donor/recipient pairs exhibit genetic disparity at numerous loci within the MHC, particularly HLA-DP, despite selection for identity at HLA-A, -B, -C, and -DRB1. Disparity at HLA-DP exists in 80% of unrelated pairs and clearly influences the outcome of unrelated hematopoietic cell transplantation; the magnitude of this effect probably exceeds that associated with disparity at any locus outside the MHC.
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Bleakley M, Turtle CJ, Riddell SR. Augmentation of anti-tumor immunity by adoptive T-cell transfer after allogeneic hematopoietic stem cell transplantation. Expert Rev Hematol 2012; 5:409-25. [PMID: 22992235 PMCID: PMC3590108 DOI: 10.1586/ehm.12.28] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation (HCT) is currently the standard of care for most patients with high-risk acute leukemias and some other hematologic malignancies. Although HCT can be curative, many patients who undergo allogeneic HCT will later relapse. There is, therefore, a critical need for the development of novel post-HCT therapies for patients who are at high risk for disease recurrence following HCT. One potentially efficacious approach is adoptive T-cell immunotherapy, which is currently undergoing a renaissance that has been inspired by scientific insight into the key issues that impeded its previous clinical application. Translation of the next generation of adoptive T-cell therapies to the allogeneic HCT setting, using donor T cells of defined specificity and function, presents a unique set of challenges and opportunities. The challenges, progress and future of adoptive T-cell therapy following allogeneic HCT are discussed in this review.
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Affiliation(s)
- Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Yamamura T, Hikita J, Bleakley M, Hirosawa T, Sato-Otsubo A, Torikai H, Hamajima T, Nannya Y, Demachi-Okamura A, Maruya E, Saji H, Yamamoto Y, Takahashi T, Emi N, Morishima Y, Kodera Y, Kuzushima K, Riddell SR, Ogawa S, Akatsuka Y. HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype. ACTA ACUST UNITED AC 2012; 80:119-25. [PMID: 22568758 DOI: 10.1111/j.1399-0039.2012.01883.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Minor histocompatibility (H) antigens are targets of graft-vs-host disease and graft-vs-tumor responses after human leukocyte antigen matched allogeneic hematopoietic stem cell transplantation. Recently, we reported a strategy for genetic mapping of linkage disequilibrium blocks that encoded novel minor H antigens using the large dataset from the International HapMap Project combined with conventional immunologic assays to assess recognition of HapMap B-lymphoid cell line by minor H antigen-specific T cells. In this study, we have constructed and provide an online interactive program and demonstrate its utility for searching for single-nucleotide polymorphisms (SNPs) responsible for minor H antigen generation. The website is available as 'HapMap SNP Scanner', and can incorporate T-cell recognition and other data with genotyping datasets from CEU, JPT, CHB, and YRI to provide a list of candidate SNPs that correlate with observed phenotypes. This method should substantially facilitate discovery of novel SNPs responsible for minor H antigens and be applicable for assaying of other specific cell phenotypes (e.g. drug sensitivity) to identify individuals who may benefit from SNP-based customized therapies.
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Affiliation(s)
- T Yamamura
- Division of Immunology, Aichi Cancer Center Research Center, Nagoya, Aichi, Japan
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40
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Lu ZX, Jiang P, Xing Y. Genetic variation of pre-mRNA alternative splicing in human populations. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:581-92. [PMID: 22095823 DOI: 10.1002/wrna.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The precise splicing outcome of a transcribed gene is controlled by complex interactions between cis regulatory splicing signals and trans-acting regulators. In higher eukaryotes, alternative splicing is a prevalent mechanism for generating transcriptome and proteome diversity. Alternative splicing can modulate gene function, affect organismal phenotype and cause disease. Common genetic variation that affects splicing regulation can lead to differences in alternative splicing between human individuals and consequently impact expression level or protein function. In several well-documented examples, such natural variation of alternative splicing has indeed been shown to influence disease susceptibility and drug response. With new microarray and sequencing-based genomic technologies that can analyze eukaryotic transcriptomes at the exon or nucleotide level, it has become possible to globally compare the alternative splicing profiles across human individuals in any tissue or cell type of interest. Recent large-scale transcriptome studies using high-density splicing-sensitive microarray and deep RNA sequencing (RNA-Seq) have revealed widespread genetic variation of alternative splicing in humans. In the future, an extensive catalog of alternative splicing variation in human populations will help elucidate the molecular underpinnings of complex traits and human diseases, and shed light on the mechanisms of splicing regulation in human cells.
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Affiliation(s)
- Zhi-Xiang Lu
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
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41
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Heo KN, Kim NK, Lee SH, Kim NY, Jeon JT, Park EW, Oh SJ, Kim TH, Seong HH, Yoon DH. Association between the Polymorphism of the Fatty acid binding protein 5 (FABP5) Gene within the BTA 14 QTL Region and Carcass/Meat Quality Traits in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5187/jast.2011.53.4.311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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A polymorphism in the splice donor site of ZNF419 results in the novel renal cell carcinoma-associated minor histocompatibility antigen ZAPHIR. PLoS One 2011; 6:e21699. [PMID: 21738768 PMCID: PMC3125305 DOI: 10.1371/journal.pone.0021699] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/05/2011] [Indexed: 01/12/2023] Open
Abstract
Nonmyeloablative allogeneic stem cell transplantation (SCT) can induce remission in patients with renal cell carcinoma (RCC), but this graft-versus-tumor (GVT) effect is often accompanied by graft-versus-host disease (GVHD). Here, we evaluated minor histocompatibility antigen (MiHA)-specific T cell responses in two patients with metastatic RCC who were treated with reduced-intensity conditioning SCT followed by donor lymphocyte infusion (DLI). One patient had stable disease and emergence of SMCY.A2-specific CD8+ T cells was observed after DLI with the potential of targeting SMCY-expressing RCC tumor cells. The second patient experienced partial regression of lung metastases from whom we isolated a MiHA-specific CTL clone with the capability of targeting RCC cell lines. Whole genome association scanning revealed that this CTL recognizes a novel HLA-B7-restricted MiHA, designated ZAPHIR, resulting from a polymorphism in the splice donor site of the ZNF419 gene. Tetramer analysis showed that emergence of ZAPHIR-specific CD8+ T cells in peripheral blood occurred in the absence of GVHD. Furthermore, the expression of ZAPHIR in solid tumor cell lines indicates the involvement of ZAPHIR-specific CD8+ T cell responses in selective GVT immunity. These findings illustrate that the ZNF419-encoded MiHA ZAPHIR is an attractive target for specific immunotherapy after allogeneic SCT.
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Hirosawa T, Torikai H, Yanagisawa M, Kamei M, Imahashi N, Demachi-Okamura A, Tanimoto M, Shiraishi K, Ito M, Miyamura K, Shibata K, Kikkawa F, Morishima Y, Takahashi T, Emi N, Kuzushima K, Akatsuka Y. Mismatched human leukocyte antigen class II-restricted CD8⁺ cytotoxic T cells may mediate selective graft-versus-leukemia effects following allogeneic hematopoietic cell transplantation. Cancer Sci 2011; 102:1281-6. [PMID: 21466613 DOI: 10.1111/j.1349-7006.2011.01949.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Partial human leukocyte antigen (HLA)-mismatched hematopoietic stem cell transplantation (HSCT) is often performed when an HLA-matched donor is not available. In these cases, CD8(+) or CD4(+) T cell responses are induced depending on the mismatched HLA class I or II allele(s). Herein, we report on an HLA-DRB1*08:03-restricted CD8(+) CTL clone, named CTL-1H8, isolated from a patient following an HLA-DR-mismatched HSCT from his brother. Lysis of a patient Epstein-Barr virus-transformed B cell line (B-LCL) by CTL-1H8 was inhibited after the addition of blocking antibodies against HLA-DR and CD8, whereas antibodies against pan-HLA class I or CD4 had no effect. The 1H8-CTL clone did not lyse the recipient dermal fibroblasts whose HLA-DRB1*08:03 expression was upregulated after 1 week cytokine treatment. Engraftment of HLA-DRB1*08:03-positive primary leukemic stem cells in non-obese diabetic/severe combined immunodeficient/γc-null (NOG) mice was completely inhibited by the in vitro preincubation of cells with CTL-1H8, suggesting that HLA-DRB1*08:03 is expressed on leukemic stem cells. Finally, analysis of the precursor frequency of CD8(+) CTL specific for recipient antigens in post-HSCT peripheral blood T cells revealed a significant fraction of the total donor CTL responses towards the individual mismatched HLA-DR antigen in two patients. These findings underscore unexpectedly significant CD8 T cell responses in the context of HLA class II.
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Affiliation(s)
- Tomoya Hirosawa
- Division of Immunology, Aichi Cancer Center Research Institute, Nagoya, Japan
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Bleakley M, Riddell SR. Exploiting T cells specific for human minor histocompatibility antigens for therapy of leukemia. Immunol Cell Biol 2011; 89:396-407. [PMID: 21301477 PMCID: PMC3061548 DOI: 10.1038/icb.2010.124] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Minor histocompatibility (H) antigens are major targets of a graft-versus-leukemia (GVL) effect mediated by donor CD8(+) and CD4(+) T cells following allogeneic hematopoietic cell transplantation (HCT) between human leukocyte antigen identical individuals. In the 15 years since the first molecular characterization of human minor H antigens, significant strides in minor H antigen discovery have been made as a consequence of advances in cellular, genetic and molecular techniques. Much has been learned about the mechanisms of minor H antigen immunogenicity, their expression on normal and malignant cells, and their role in GVL responses. T cells specific for minor H antigens expressed on leukemic cells, including leukemic stem cells, can be isolated and expanded in vitro and infused into allogeneic HCT recipients to augment the GVL effect to prevent and treat relapse. The first report of the adoptive transfer of minor H antigen-specific T-cell clones to patients with leukemic relapse in 2010 illustrates the potential for the manipulation of alloreactivity for therapeutic benefit. This review describes the recent developments in T-cell recognition of human minor H antigens, and efforts to translate these discoveries to reduce leukemia relapse after allogeneic HCT.
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Affiliation(s)
- Marie Bleakley
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-981024, USA.
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45
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Bleakley M, Riddell SR. Exploiting T cells specific for human minor histocompatibility antigens for therapy of leukemia. Immunol Cell Biol 2011. [PMID: 21301477 DOI: 10.1038/icb.2010.124.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Minor histocompatibility (H) antigens are major targets of a graft-versus-leukemia (GVL) effect mediated by donor CD8(+) and CD4(+) T cells following allogeneic hematopoietic cell transplantation (HCT) between human leukocyte antigen identical individuals. In the 15 years since the first molecular characterization of human minor H antigens, significant strides in minor H antigen discovery have been made as a consequence of advances in cellular, genetic and molecular techniques. Much has been learned about the mechanisms of minor H antigen immunogenicity, their expression on normal and malignant cells, and their role in GVL responses. T cells specific for minor H antigens expressed on leukemic cells, including leukemic stem cells, can be isolated and expanded in vitro and infused into allogeneic HCT recipients to augment the GVL effect to prevent and treat relapse. The first report of the adoptive transfer of minor H antigen-specific T-cell clones to patients with leukemic relapse in 2010 illustrates the potential for the manipulation of alloreactivity for therapeutic benefit. This review describes the recent developments in T-cell recognition of human minor H antigens, and efforts to translate these discoveries to reduce leukemia relapse after allogeneic HCT.
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Affiliation(s)
- Marie Bleakley
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-981024, USA.
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46
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Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet 2010; 20:1084-96. [PMID: 21224255 DOI: 10.1093/hmg/ddq553] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
There has been growing evidence for extensive diversity of alternative splicing in human populations. Genetic variants within the 5' splice site can cause splicing differences among human individuals and constitute an important class of human disease mutations. In this study, we explored whether natural variations of splicing could reveal important signals of 5' splice site recognition. In seven lymphoblastoid cell lines of Asian, European and African ancestry, we identified 1174 single nucleotide polymorphisms (SNPs) within the consensus 5' splice site. We selected 129 SNPs predicted to significantly alter the splice site activity, and quantitatively examined their splicing impact in the seven individuals. Surprisingly, outside of the essential GT dinucleotide position, only ∼14% of the tested SNPs altered splicing. Bioinformatic and minigene analyses identified signals that could modify the impact of 5' splice site polymorphisms, most notably a strong 3' splice site and the presence of intronic motifs downstream of the 5' splice site. Strikingly, we found that the poly-G run, a known intronic splicing enhancer, was the most significantly enriched motif downstream of exons unaffected by 5' splice site SNPs. In TRIM62, the upstream 3' splice site and downstream intronic poly-G runs functioned redundantly to protect an exon from its 5' splice site polymorphism. Collectively, our study reveals widespread context-dependent robustness to 5' splice site polymorphisms in human transcriptomes. Consequently, certain exons are more susceptible to 5' splice site mutations. Additionally, our work demonstrates that genetic diversity of alternative splicing can provide significant insights into the splicing code of mammalian cells.
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Affiliation(s)
- Zhi-xiang Lu
- Department of Internal Medicine, University of Iowa, 3294 CBRB, 285 Newton Rd, Iowa City, IA 52242, USA
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47
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Van Bergen CA, Rutten CE, Van Der Meijden ED, Van Luxemburg-Heijs SA, Lurvink EG, Houwing-Duistermaat JJ, Kester MG, Mulder A, Willemze R, Falkenburg JF, Griffioen M. High-Throughput Characterization of 10 New Minor Histocompatibility Antigens by Whole Genome Association Scanning. Cancer Res 2010; 70:9073-83. [DOI: 10.1158/0008-5472.can-10-1832] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Minor histocompatibility antigens: presentation principles, recognition logic and the potential for a healing hand. Curr Opin Organ Transplant 2010; 15:512-25. [PMID: 20616723 DOI: 10.1097/mot.0b013e32833c1552] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW There is ample evidence indicating a pathologic role for minor histocompatibility antigens in inciting graft-versus-host disease in major histocompatibility complex (MHC)-matched bone marrow transplantation and rejection of solid organ allografts. Here we review the current knowledge of the genetic and biochemical bases for the cause of minor histoincompatibility and the structural basis for the recognition of the resulting alloantigens by the T-cell receptor. RECENT FINDINGS Recent evidence indicates that we as independently conceived individuals are genetically unique, thus, offering a mechanism for minor histoincompatibility between MHC-identical donor-recipient pairs. Furthermore, advances in delineating the mechanisms underlying antigen cross-presentation by MHC class I molecules and a critical role for autophagy in presenting cytoplasmic antigens by MHC class II molecules have been made. These new insights coupled with the X-ray crystallographic solution of several peptide/MHC-T-cell receptor structures have revealed mechanisms of histoincompatibility. SUMMARY On the basis of these new insights, ways to test for allograft compatibility and concoction of immunotherapies are discussed.
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Larsen ME, Kornblit B, Larsen MV, Masmas TN, Nielsen M, Thiim M, Garred P, Stryhn A, Lund O, Buus S, Vindelov L. Degree of Predicted Minor Histocompatibility Antigen Mismatch Correlates with Poorer Clinical Outcomes in Nonmyeloablative Allogeneic Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2010; 16:1370-81. [DOI: 10.1016/j.bbmt.2010.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/23/2010] [Indexed: 11/12/2022]
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50
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Shumay E, Fowler JS, Volkow ND. Genomic features of the human dopamine transporter gene and its potential epigenetic States: implications for phenotypic diversity. PLoS One 2010; 5:e11067. [PMID: 20548783 PMCID: PMC2883569 DOI: 10.1371/journal.pone.0011067] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 05/18/2010] [Indexed: 02/06/2023] Open
Abstract
Human dopamine transporter gene (DAT1 or SLC6A3) has been associated with various brain-related diseases and behavioral traits and, as such, has been investigated intensely in experimental- and clinical-settings. However, the abundance of research data has not clarified the biological mechanism of DAT regulation; similarly, studies of DAT genotype-phenotype associations yielded inconsistent results. Hence, our understanding of the control of the DAT protein product is incomplete; having this knowledge is critical, since DAT plays the major role in the brain's dopaminergic circuitry. Accordingly, we reevaluated the genomic attributes of the SLC6A3 gene that might confer sensitivity to regulation, hypothesizing that its unique genomic characteristics might facilitate highly dynamic, region-specific DAT expression, so enabling multiple regulatory modes. Our comprehensive bioinformatic analyzes revealed very distinctive genomic characteristics of the SLC6A3, including high inter-individual variability of its sequence (897 SNPs, about 90 repeats and several CNVs spell out all abbreviations in abstract) and pronounced sensitivity to regulation by epigenetic mechanisms, as evident from the GC-bias composition (0.55) of the SLC6A3, and numerous intragenic CpG islands (27 CGIs). We propose that this unique combination of the genomic features and the regulatory attributes enables the differential expression of the DAT1 gene and fulfills seemingly contradictory demands to its regulation; that is, robustness of region-specific expression and functional dynamics.
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Affiliation(s)
- Elena Shumay
- Brookhaven National Laboratory, Medical Department, Upton, New York, United States of America
- * E-mail: (ES); (JSF); (NDV)
| | - Joanna S. Fowler
- Brookhaven National Laboratory, Medical Department, Upton, New York, United States of America
- * E-mail: (ES); (JSF); (NDV)
| | - Nora D. Volkow
- National Institute on Drug Abuse, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (ES); (JSF); (NDV)
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