1
|
Sullivan S, Fairchild PJ, Marsh SGE, Müller CR, Turner ML, Song J, Turner D. Haplobanking induced pluripotent stem cells for clinical use. Stem Cell Res 2020; 49:102035. [PMID: 33221677 DOI: 10.1016/j.scr.2020.102035] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/20/2020] [Accepted: 10/05/2020] [Indexed: 02/08/2023] Open
Abstract
The development of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka and colleagues in 2006 has led to a potential new paradigm in cellular therapeutics, including the possibility of producing patient-specific, disease-specific and immune matched allogeneic cell therapies. One can envisage two routes to immunologically compatible iPSC therapies: using genetic modification to generate a 'universal donor' with reduced expression of Human Leukocyte Antigens (HLA) and other immunological targets or developing a haplobank containing iPSC lines specifically selected to provide HLA matched products to large portions of the population. HLA matched lines can be stored in a designated physical or virtual global bank termed a 'haplobank'. The process of 'iPSC haplobanking' refers to the banking of iPSC cell lines, selected to be homozygous for different HLA haplotypes, from which therapeutic products can be derived and matched immunologically to patient populations. By matching iPSC and derived products to a patient's HLA class I and II molecules, one would hope to significantly reduce the risk of immune rejection and the use of immunosuppressive medication. Immunosuppressive drugs are used in several conditions (including autoimmune disease and in transplantation procedures) to reduce rejection of infused cells, or transplanted tissue and organs, due to major and minor histocompatibility differences between donor and recipient. Such regimens can lead to immune compromise and pathological consequences such as opportunistic infections or malignancies due to decreased cancer immune surveillance. In this article, we will discuss what is practically involved if one is developing and executing an iPSC haplobanking strategy.
Collapse
Affiliation(s)
- Stephen Sullivan
- Global Alliance for iPSC Therapies, Jack Copland Centre, Heriot-Watt Research Park, Edinburgh, UK.
| | - Paul J Fairchild
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Steven G E Marsh
- HLA Informatics Group, Anthony Nolan Research Institute, Royal Free Campus, London, UK; UCL Cancer Institute, University College London, London, UK
| | - Carlheinz R Müller
- Zentrales Knochenmarkspender-Register Deutschland (ZKRD), Helmholtzstraße, 1089081 Ulm, Germany
| | - Marc L Turner
- Global Alliance for iPSC Therapies, Jack Copland Centre, Heriot-Watt Research Park, Edinburgh, UK; Advanced Therapeutics, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Jihwan Song
- Global Alliance for iPSC Therapies, Jack Copland Centre, Heriot-Watt Research Park, Edinburgh, UK; Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - David Turner
- Global Alliance for iPSC Therapies, Jack Copland Centre, Heriot-Watt Research Park, Edinburgh, UK; Histocompatibility and Immunogenetics Laboratory, Royal Infirmary of Edinburgh, Edinburgh, UK
| |
Collapse
|
2
|
Hu X, Kueppers ST, Kooreman NG, Gravina A, Wang D, Tediashvili G, Schlickeiser S, Frentsch M, Nikolaou C, Thiel A, Marcus S, Fuchs S, Velden J, Reichenspurner H, Volk HD, Deuse T, Schrepfer S. The H-Y Antigen in Embryonic Stem Cells Causes Rejection in Syngeneic Female Recipients. Stem Cells Dev 2020; 29:1179-1189. [PMID: 32723003 DOI: 10.1089/scd.2019.0299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pluripotent stem cells are promising candidates for cell-based regenerative therapies. To avoid rejection of transplanted cells, several approaches are being pursued to reduce immunogenicity of the cells or modulate the recipient's immune response. These include gene editing to reduce the antigenicity of cell products, immunosuppression of the host, or using major histocompatibility complex-matched cells from cell banks. In this context, we have investigated the antigenicity of H-Y antigens, a class of minor histocompatibility antigens encoded by the Y chromosome, to assess whether the gender of the donor affects the cell's antigenicity. In a murine transplant model, we show that the H-Y antigen in undifferentiated embryonic stem cells (ESCs), as well as ESC-derived endothelial cells, provokes T- and B cell responses in female recipients.
Collapse
Affiliation(s)
- Xiaomeng Hu
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Simon T Kueppers
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Nigel G Kooreman
- Stanford Cardiovascular Institute, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA.,Department of Vascular Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Alessia Gravina
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany
| | - Dong Wang
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Grigol Tediashvili
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Stephan Schlickeiser
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, BIH, Berlin, Germany
| | - Marco Frentsch
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Christos Nikolaou
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Thiel
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Sivan Marcus
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA
| | - Sigrid Fuchs
- Institute of Human Genetics, University Medical Center Hamburg, Hamburg, Germany
| | - Joachim Velden
- Evotec AG, Histopathology and In Vivo Pharmacology, Hamburg, Germany
| | - Hermann Reichenspurner
- Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Hans-Dieter Volk
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, BIH, Berlin, Germany
| | - Tobias Deuse
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA
| | - Sonja Schrepfer
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| |
Collapse
|
3
|
Krieger E, Toor AA. Can Graft vs. Leukemia Effect Be Uncoupled From Graft vs. Host Disease? An Examination of Proportions. Front Immunol 2020; 11:777. [PMID: 32425947 PMCID: PMC7212371 DOI: 10.3389/fimmu.2020.00777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/06/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Elizabeth Krieger
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, United States
| | - Amir Ahmed Toor
- Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| |
Collapse
|
4
|
Fuchs KJ, Honders MW, van der Meijden ED, Adriaans AE, van der Lee DI, Pont MJ, Monajemi R, Kielbasa SM, 't Hoen PAC, van Bergen CAM, Falkenburg JHF, Griffioen M. Optimized Whole Genome Association Scanning for Discovery of HLA Class I-Restricted Minor Histocompatibility Antigens. Front Immunol 2020; 11:659. [PMID: 32362897 PMCID: PMC7180171 DOI: 10.3389/fimmu.2020.00659] [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: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
Patients undergoing allogeneic stem cell transplantation as treatment for hematological diseases face the risk of Graft-versus-Host Disease as well as relapse. Graft-versus-Host Disease and the favorable Graft-versus-Leukemia effect are mediated by donor T cells recognizing polymorphic peptides, which are presented on the cell surface by HLA molecules and result from single nucleotide polymorphism alleles that are disparate between patient and donor. Identification of polymorphic HLA-binding peptides, designated minor histocompatibility antigens, has been a laborious procedure, and the number and scope for broad clinical use of these antigens therefore remain limited. Here, we present an optimized whole genome association approach for discovery of HLA class I minor histocompatibility antigens. T cell clones isolated from patients who responded to donor lymphocyte infusions after HLA-matched allogeneic stem cell transplantation were tested against a panel of 191 EBV-transformed B cells, which have been sequenced by the 1000 Genomes Project and selected for expression of seven common HLA class I alleles (HLA-A∗01:01, A∗02:01, A∗03:01, B∗07:02, B∗08:01, C∗07:01, and C∗07:02). By including all polymorphisms with minor allele frequencies above 0.01, we demonstrated that the new approach allows direct discovery of minor histocompatibility antigens as exemplified by seven new antigens in eight different HLA class I alleles including one antigen in HLA-A∗24:02 and HLA-A∗23:01, for which the method has not been originally designed. Our new whole genome association strategy is expected to rapidly augment the repertoire of HLA class I-restricted minor histocompatibility antigens that will become available for donor selection and clinical use to predict, follow or manipulate Graft-versus-Leukemia effect and Graft-versus-Host Disease after allogeneic stem cell transplantation.
Collapse
Affiliation(s)
- Kyra J Fuchs
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - M Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Edith D van der Meijden
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.,Department of Internal Medicine, Hematology and Internal Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Alwin E Adriaans
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Margot J Pont
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ramin Monajemi
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Szymon M Kielbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
5
|
Zhen X, Wanxin A, Chunling J, Hui L. Exploring the Risks of Genetic Similarity Between Donor and Recipient in Human Leukocyte Antigen-Matched Transplantation. Transplant Proc 2020; 52:754-758. [PMID: 32248911 DOI: 10.1016/j.transproceed.2019.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/14/2019] [Accepted: 12/06/2019] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Successful allogeneic hematopoietic stem cell transplantation (HSCT) relies on human leukocyte antigen (HLA) matching. However, whether HLA-matching between donors and recipients increases recipients' risk of genetic disease remains unclear. METHODS We investigated whether HLA-matched donor cells used for HSCT have similar microsatellite DNA polymorphisms to HSCT recipients at 19 randomly selected loci including CSF1PO, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, PentaD, PentaE, TH01, TPOX, and VWA. We analyzed allele matching at each short tandem repeat (STR) loci in HLA-matched and mismatched (control) groups using binary outcomes and a quantitative numerical method. RESULTS The frequencies were similar between the HLA-matched group and the mismatched group for D6S1043. However, the allele matching rate was higher in the HLA-matched group than that in the mismatched group at 14 of the 19 STR loci. Overall, a significant increase in the rate of STR matching was observed in the HLA-matched group compared to the mismatched group (P = .004). CONCLUSION It would be interesting to know if the HLA matched pairs came more often in question than their mismatched counterparts as candidates for fully HLA-matched unrelated HSCT. The actual risk for HSCT donors developing these diseases needs further evaluation.
Collapse
Affiliation(s)
- Xi Zhen
- College of Medical Laboratory, Dalian Medical University, Dalian, China; Dalian Blood Center, Dalian, China
| | | | - Jiang Chunling
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian, China.
| |
Collapse
|
6
|
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-SCT) is the most established and commonly used cellular immunotherapy in cancer care. It is the most potent anti-leukemic therapy in patients with acute myeloid leukemia (AML) and is routinely used with curative intent in patients with intermediate and poor risk disease. Donor T cells, and possibly other immune cells, eliminate residual leukemia cells after prior (radio)chemotherapy. This immune-mediated response is known as graft-versus-leukemia (GvL). Donor alloimmune responses can also be directed against healthy tissues, which is known as graft-versus-host disease (GvHD). GvHD and GvL often co-occur and, therefore, a major barrier to exploiting the full immunotherapeutic benefit of donor immune cells against patient leukemia is the immunosuppression required to treat GvHD. However, curative responses to allo-SCT and GvHD do not always occur together, suggesting that these two immune responses could be de-coupled in some patients. To make further progress in successfully promoting GvL without GvHD, we must transform our limited understanding of the cellular and molecular basis of GvL and GvHD. Specifically, in most patients we do not understand the antigenic basis of immune responses in GvL and GvHD. Identification of antigens important for GvL but not GvHD, and vice versa, could impact on donor selection, allow us to track GvL immune responses and begin to specifically harness and strengthen anti-leukemic immune responses against patient AML cells, whilst minimizing the toxicity of GvHD.
Collapse
Affiliation(s)
- Connor Sweeney
- MRC Molecular Haematology Unit, Oxford Biomedical Research Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Oxford Biomedical Research Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| |
Collapse
|
7
|
Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant. Blood Adv 2019; 2:2419-2429. [PMID: 30262602 DOI: 10.1182/bloodadvances.2018019513] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HCT) is a curative option for blood cancers, but the coupled effects of graft-versus-tumor and graft-versus-host disease (GVHD) limit its broader application. Outcomes improve with matching at HLAs, but other factors are required to explain residual risk of GVHD. In an effort to identify genetic associations outside the major histocompatibility complex, we conducted a genome-wide clinical outcomes study on 205 acute myeloid leukemia patients and their fully HLA-A-, HLA-B-, HLA-C-, HLA-DRB1-, and HLA-DQB1-matched (10/10) unrelated donors. HLA-DPB1 T-cell epitope permissibility mismatches were observed in less than half (45%) of acute GVHD cases, motivating a broader search for genetic factors affecting clinical outcomes. A novel bioinformatics workflow adapted from neoantigen discovery found no associations between acute GVHD and known, HLA-restricted minor histocompatibility antigens (MiHAs). These results were confirmed with microarray data from an additional 988 samples. On the other hand, Y-chromosome-encoded single-nucleotide polymorphisms in 4 genes (PCDH11Y, USP9Y, UTY, and NLGN4Y) did associate with acute GVHD in male patients with female donors. Males in this category with acute GVHD had more Y-encoded variant peptides per patient with higher predicted HLA-binding affinity than males without GVHD who matched X-paralogous alleles in their female donors. Methods and results described here have an immediate impact for allo-HCT, warranting further development and larger genomic studies where MiHAs are clinically relevant, including cancer immunotherapy, solid organ transplant, and pregnancy.
Collapse
|
8
|
Ritari J, Hyvärinen K, Koskela S, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, Itälä-Remes M, Partanen J. Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT. Front Immunol 2019; 10:1625. [PMID: 31379830 PMCID: PMC6646417 DOI: 10.3389/fimmu.2019.01625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022] Open
Abstract
Genetic mismatches in protein coding genes between allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipient and donor can elicit an alloimmunity response via peptides presented by the recipient HLA receptors as minor histocompatibility antigens (mHAs). While the impact of individual mHAs on allo-HSCT outcome such as graft-vs.-host and graft-vs.-leukemia effects has been demonstrated, it is likely that established mHAs constitute only a small fraction of all immunogenic non-synonymous variants. In the present study, we have analyzed the genetic mismatching in 157 exome-sequenced sibling allo-HSCT pairs to evaluate the significance of polymorphic HLA class I associated peptides on clinical outcome. We applied computational mismatch estimation approaches based on experimentally verified HLA ligands available in public repositories, published mHAs, and predicted HLA-peptide affinites, and analyzed their associations with chronic graft-vs.-host disease (cGvHD) grades. We found that higher estimated recipient mismatching consistently increased the risk of severe cGvHD, suggesting that HLA-presented mismatching influences the likelihood of long-term complications in the patient. Furthermore, computational approaches focusing on estimation of HLA-presentation instead of all non-synonymous mismatches indiscriminately may be beneficial for analysis sensitivity and could help identify novel mHAs.
Collapse
Affiliation(s)
- Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Riitta Niittyvuopio
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Anne Nihtinen
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Urpu Salmenniemi
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Mervi Putkonen
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Liisa Volin
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy, Kansas City, MO, United States
| | - Maija Itälä-Remes
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | | |
Collapse
|
9
|
Meier JA, Haque M, Fawaz M, Abdeen H, Coffey D, Towlerton A, Abdeen A, Toor A, Warren E, Reed J, Kanakry CG, Keating A, Luznik L, Toor AA. T Cell Repertoire Evolution after Allogeneic Bone Marrow Transplantation: An Organizational Perspective. Biol Blood Marrow Transplant 2019; 25:868-882. [PMID: 30677510 DOI: 10.1016/j.bbmt.2019.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
Abstract
High-throughput sequencing (HTS) of human T cell receptors has revealed a high level of complexity in the T cell repertoire, which makes it difficult to correlate T cell reconstitution with clinical outcomes. The associations identified thus far are of a broadly statistical nature, precluding precise modeling of outcomes based on T cell repertoire development following bone marrow transplantation (BMT). Previous work has demonstrated an inherent, mathematically definable order observed in the T cells from a diverse group of donors, which is perturbed in recipients following BMT. In this study, T cell receptor (TCR)-β sequences from HLA-matched related donor and recipient pairs are analyzed to further develop this methodology. TCR-β sequencing from unsorted and sorted T cell subsets isolated from the peripheral blood samples of BMT donors and recipients show conservation and symmetry of VJ segment usage in the clonal frequencies, linked to the organization of the gene segments along the TCR locus. This TCR-β VJ segment translational symmetry is preserved post-transplantation and even in cases of acute graft-versus-host disease (aGVHD), suggesting that GVHD occurrence represents a polyclonal donor T cell response to recipient antigens. The complexity of the repertoire is significantly diminished after BMT, and the T cell clonal hierarchy is altered post-transplantation. Low-frequency donor clones tended to take on a higher rank in the recipients following BMT, especially in patients with aGVHD. Over time, the repertoire evolves to a more donor-like state in the recipients who did not develop GVHD as opposed to those who did. The results presented here support new methods of quantifying and characterizing post-transplantation T cell repertoire reconstitution.
Collapse
Affiliation(s)
- Jeremy A Meier
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Mahdee Haque
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Mohamed Fawaz
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Hamdi Abdeen
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - David Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ahmed Abdeen
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Abdullah Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Edus Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia
| | - Christopher G Kanakry
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Armand Keating
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amir A Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
| |
Collapse
|
10
|
Salman A, Koparde V, Hall CE, Jameson-Lee M, Roberts C, Serrano M, AbdulRazzaq B, Meier J, Kennedy C, Manjili MH, Spellman SR, Wijesinghe D, Hashmi S, Buck G, Qayyum R, Neale M, Reed J, Toor AA. Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation. Front Immunol 2018; 9:2284. [PMID: 30364159 PMCID: PMC6193078 DOI: 10.3389/fimmu.2018.02284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/14/2018] [Indexed: 11/25/2022] Open
Abstract
Alloreactivity compromising clinical outcomes in stem cell transplantation is observed despite HLA matching of donors and recipients. This has its origin in the variation between the exomes of the two, which provides the basis for minor histocompatibility antigens (mHA). The mHA presented on the HLA class I and II molecules and the ensuing T cell response to these antigens results in graft vs. host disease. In this paper, results of a whole exome sequencing study are presented, with resulting alloreactive polymorphic peptides and their HLA class I and HLA class II (DRB1) binding affinity quantified. Large libraries of potentially alloreactive recipient peptides binding both sets of molecules were identified, with HLA-DRB1 generally presenting a greater number of peptides. These results are used to develop a quantitative framework to understand the immunobiology of transplantation. A tensor-based approach is used to derive the equations needed to determine the alloreactive donor T cell response from the mHA-HLA binding affinity and protein expression data. This approach may be used in future studies to simulate the magnitude of expected donor T cell response and determine the risk for alloreactive complications in HLA matched or mismatched hematopoietic cell and solid organ transplantation.
Collapse
Affiliation(s)
- Ali Salman
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Vishal Koparde
- Virginia Commonwealth University Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
| | - Charles E. Hall
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Max Jameson-Lee
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Catherine Roberts
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Myrna Serrano
- Virginia Commonwealth University Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
| | - Badar AbdulRazzaq
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Jeremy Meier
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Caleb Kennedy
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Masoud H. Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, United States
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Dayanjan Wijesinghe
- School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Shahrukh Hashmi
- Mayo Clinic, Rochester Minnesota and King Faisal Research Hospital, Riyadh, Saudi Arabia
| | - Greg Buck
- Virginia Commonwealth University Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
| | - Rehan Qayyum
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Michael Neale
- Department of Psychiatry & Statistical Genomics, Virginia Commonwealth University, Richmond, VA, United States
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, VA, United States
| | - Amir A. Toor
- Bone Marrow Transplant, Virginia Commonwealth University Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| |
Collapse
|
11
|
Toor AA, Chesney A, Zweit J, Reed J, Hashmi SK. A dynamical systems perspective on chimeric antigen receptor T-cell dosing. Bone Marrow Transplant 2018; 54:485-489. [PMID: 30171224 DOI: 10.1038/s41409-018-0329-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/30/2018] [Accepted: 08/13/2018] [Indexed: 01/01/2023]
Abstract
Chimeric antigen receptor T cells (CAR T cells) are dosed similarly to donor lymphocyte infusions following hematopoietic cell transplantation. However, the mechanism driving proliferation in CAR T cells is distinct from conventional T cells. As such there are quantitative differences in the antigen response of these engineered cells when compared with conventional T cells. In this perspective paper the logistic equation of growth is used to develop a mathematical basis for understanding the difference between CAR T cell and conventional T cell response to antigen burden.
Collapse
Affiliation(s)
- Amir A Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
| | - Alden Chesney
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jamal Zweit
- Department of Radiology, Virginia Commonwealth University, Richmond, VA, USA
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, VA, USA
| | - Shahrukh K Hashmi
- Division of Hematology, Dept. of Medicine, Mayo Clinic, Rochester, MN, USA.,Dept. Of Stem Cell Transplant, Oncology Center, KFSHRC, Riyadh, Saudi Arabia
| |
Collapse
|
12
|
Bykova NA, Malko DB, Efimov GA. In Silico Analysis of the Minor Histocompatibility Antigen Landscape Based on the 1000 Genomes Project. Front Immunol 2018; 9:1819. [PMID: 30166983 PMCID: PMC6105694 DOI: 10.3389/fimmu.2018.01819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/24/2018] [Indexed: 12/30/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is routinely used to treat hematopoietic malignancies. The eradication of residual tumor cells during engraftment is mediated by donor cytotoxic T lymphocytes reactive to alloantigens. In a HLA-matched transplantation context, alloantigens are encoded by various polymorphic genes situated outside the HLA locus, also called minor histocompatibility antigens (MiHAs). Recently, MiHAs have been recognized as promising targets for post-transplantation T-cell immunotherapy as they have several appealing advantages over tumor-associated antigens (TAAs) and neoantigens, i.e., they are more abundant than TAAs, which potentially facilitates multiple targeting; and unlike neoantigens, they are encoded by germline polymorphisms, some of which are common and thus, suitable for off-the-shelf therapy. The genetic sources of MiHAs are nonsynonymous polymorphisms that cause differences between the recipient and donor proteomes and subsequently, the immunopeptidomes. Systematic description of the alloantigen landscape in HLA-matched transplantation is still lacking as previous studies focused only on a few immunogenic and common MiHAs. Here, we perform a thorough in silico analysis of the public genomic data to classify genetic polymorphisms that lead to MiHA formation and estimate the number of potentially available MiHA mismatches. Our findings suggest that a donor/recipient pair is expected to have at least several dozen mismatched strong MHC-binding SNP-associated peptides per HLA allele (116 ± 26 and 65 ± 15 for non-related pairs and siblings respectively in European populations as predicted by two independent algorithms). Over 70% of them are encoded by relatively frequent polymorphisms (minor allele frequency > 0.1) and thus, may be targetable by off-the-shelf therapeutics. We showed that the most appealing targets (probability of mismatch over 20%) reside in the asymmetric allele frequency region, which spans from 0.15 to 0.47 and corresponds to an order of several hundred (213 ± 47) possible targets per HLA allele that can be considered for immunogenicity validation. Overall, these findings demonstrate the significant potential of MiHAs as targets for T-cell immunotherapy and emphasize the need for the systematic discovery of novel MiHAs.
Collapse
Affiliation(s)
- Nadia A Bykova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Dmitry B Malko
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Grigory A Efimov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| |
Collapse
|
13
|
Koparde V, Abdul Razzaq B, Suntum T, Sabo R, Scalora A, Serrano M, Jameson-Lee M, Hall C, Kobulnicky D, Sheth N, Feltz J, Contaifer D, Wijesinghe D, Reed J, Roberts C, Qayyum R, Buck G, Neale M, Toor A. Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation. PLoS One 2017; 12:e0187771. [PMID: 29194460 PMCID: PMC5711034 DOI: 10.1371/journal.pone.0187771] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/25/2017] [Indexed: 12/01/2022] Open
Abstract
Quantitative relationship between the magnitude of variation in minor histocompatibility antigens (mHA) and graft versus host disease (GVHD) pathophysiology in stem cell transplant (SCT) donor-recipient pairs (DRP) is not established. In order to elucidate this relationship, whole exome sequencing (WES) was performed on 27 HLA matched related (MRD), & 50 unrelated donors (URD), to identify nonsynonymous single nucleotide polymorphisms (SNPs). An average 2,463 SNPs were identified in MRD, and 4,287 in URD DRP (p<0.01); resulting peptide antigens that may be presented on HLA class I molecules in each DRP were derived in silico (NetMHCpan ver2.0) and the tissue expression of proteins these were derived from determined (GTex). MRD DRP had an average 3,670 HLA-binding-alloreactive peptides, putative mHA (pmHA) with an IC50 of <500 nM, and URD, had 5,386 (p<0.01). To simulate an alloreactive donor cytotoxic T cell response, the array of pmHA in each patient was considered as an operator matrix modifying a hypothetical cytotoxic T cell clonal vector matrix; each responding T cell clone’s proliferation was determined by the logistic equation of growth, accounting for HLA binding affinity and tissue expression of each alloreactive peptide. The resulting simulated organ-specific alloreactive T cell clonal growth revealed marked variability, with the T cell count differences spanning orders of magnitude between different DRP. Despite an estimated, uniform set of constants used in the model for all DRP, and a heterogeneously treated group of patients, higher total and organ-specific T cell counts were associated with cumulative incidence of moderate to severe GVHD in recipients. In conclusion, exome wide sequence differences and the variable alloreactive peptide binding to HLA in each DRP yields a large range of possible alloreactive donor T cell responses. Our findings also help understand the apparent randomness observed in the development of alloimmune responses.
Collapse
Affiliation(s)
- Vishal Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Badar Abdul Razzaq
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Tara Suntum
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Roy Sabo
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Allison Scalora
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Myrna Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Max Jameson-Lee
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Charles Hall
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - David Kobulnicky
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nihar Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Juliana Feltz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel Contaifer
- School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dayanjan Wijesinghe
- School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine Roberts
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rehan Qayyum
- Section of Hospital Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael Neale
- Departments of Psychiatry and Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Amir Toor
- Bone Marrow Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| |
Collapse
|
14
|
Hall CE, Koparde VN, Jameson-Lee M, Elnasseh AG, Scalora AF, Kobulnicky DJ, Serrano MG, Roberts CH, Buck GA, Neale MC, Nixon DE, Toor AA. Sequence homology between HLA-bound cytomegalovirus and human peptides: A potential trigger for alloreactivity. PLoS One 2017; 12:e0178763. [PMID: 28800601 PMCID: PMC5553991 DOI: 10.1371/journal.pone.0178763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 05/18/2017] [Indexed: 11/18/2022] Open
Abstract
Human cytomegalovirus (hCMV) reactivation may often coincide with the development of graft-versus-host-disease (GVHD) in stem cell transplantation (SCT). Seventy seven SCT donor-recipient pairs (DRP) (HLA matched unrelated donor (MUD), n = 50; matched related donor (MRD), n = 27) underwent whole exome sequencing to identify single nucleotide polymorphisms (SNPs) generating alloreactive peptide libraries for each DRP (9-mer peptide-HLA complexes); Human CMV CROSS (Cross-Reactive Open Source Sequence) database was compiled from NCBI; HLA class I binding affinity for each DRPs HLA was calculated by NetMHCpan 2.8 and hCMV- derived 9-mers algorithmically compared to the alloreactive peptide-HLA complex libraries. Short consecutive (≥6) amino acid (AA) sequence homology matching hCMV to recipient peptides was considered for HLA-bound-peptide (IC50<500nM) cross reactivity. Of the 70,686 hCMV 9-mers contained within the hCMV CROSS database, an average of 29,658 matched the MRD DRP alloreactive peptides and 52,910 matched MUD DRP peptides (p<0.001). In silico analysis revealed multiple high affinity, immunogenic CMV-Human peptide matches (IC50<500 nM) expressed in GVHD-affected tissue-specific manner. hCMV+GVHD was found in 18 patients, 13 developing hCMV viremia before GVHD onset. Analysis of patients with GVHD identified potential cross reactive peptide expression within affected organs. We propose that hCMV peptide sequence homology with human alloreactive peptides may contribute to the pathophysiology of GVHD.
Collapse
Affiliation(s)
- Charles E. Hall
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Vishal N. Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Maximilian Jameson-Lee
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Abdelrhman G. Elnasseh
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Allison F. Scalora
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - David J. Kobulnicky
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Myrna G. Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine H. Roberts
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory A. Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael C. Neale
- Departments of Psychiatry and Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel E. Nixon
- Division of Infectious Diseases, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Amir A. Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| |
Collapse
|
15
|
Gam R, Shah P, Crossland RE, Norden J, Dickinson AM, Dressel R. Genetic Association of Hematopoietic Stem Cell Transplantation Outcome beyond Histocompatibility Genes. Front Immunol 2017; 8:380. [PMID: 28421078 PMCID: PMC5377073 DOI: 10.3389/fimmu.2017.00380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/16/2017] [Indexed: 12/18/2022] Open
Abstract
The outcome of hematopoietic stem cell transplantation (HSCT) is controlled by genetic factors among which the leukocyte antigen human leukocyte antigen (HLA) matching is most important. In addition, minor histocompatibility antigens and non-HLA gene polymorphisms in genes controlling immune responses are known to contribute to the risks associated with HSCT. Besides single-nucleotide polymorphisms (SNPs) in protein coding genes, SNPs in regulatory elements such as microRNAs (miRNAs) contribute to these genetic risks. However, genetic risks require for their realization the expression of the respective gene or miRNA. Thus, gene and miRNA expression studies may help to identify genes and SNPs that indeed affect the outcome of HSCT. In this review, we summarize gene expression profiling studies that were performed in recent years in both patients and animal models to identify genes regulated during HSCT. We discuss SNP–mRNA–miRNA regulatory networks and their contribution to the risks associated with HSCT in specific examples, including forkheadbox protein 3 and regulatory T cells, the role of the miR-155 and miR-146a regulatory network for graft-versus-host disease, and the function of MICA and its receptor NKG2D for the outcome of HSCT. These examples demonstrate how SNPs affect expression or function of proteins that modulate the alloimmune response and influence the outcome of HSCT. Specific miRNAs targeting these genes and directly affecting expression of mRNAs are identified. It might be valuable in the future to determine SNPs and to analyze miRNA and mRNA expression in parallel in cohorts of HSCT patients to further elucidate genetic risks of HSCT.
Collapse
Affiliation(s)
- Rihab Gam
- Hematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Pranali Shah
- Institute of Cellular and Molecular Immunology, University Medical Centre Göttingen, Göttingen, Germany
| | - Rachel E Crossland
- Hematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jean Norden
- Hematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Anne M Dickinson
- Hematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ralf Dressel
- Institute of Cellular and Molecular Immunology, University Medical Centre Göttingen, Göttingen, Germany
| |
Collapse
|
16
|
Matching for the MICA-129 polymorphism is beneficial in unrelated hematopoietic stem cell transplantation. Blood 2016; 128:3169-3176. [PMID: 27811019 DOI: 10.1182/blood-2016-05-716357] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/22/2016] [Indexed: 12/15/2022] Open
Abstract
Major histocompatibility complex class I polypeptide-related sequence A (MICA) is a highly polymorphic ligand of the activating NKG2D receptor on natural killer (NK) cells, γδ-T cells, and NKT cells. MICA incompatibilities have been associated with an increased graft-versus-host disease (GVHD) incidence, and the MICA-129 (met/val) dimorphism has been shown to influence NKG2D signaling in unrelated hematopoietic stem cell transplantation (uHSCT). We investigated the effect of MICA matching on survival after uHSCT. We sequenced 2172 patients and their respective donors for MICA. All patients and donors were high-resolution HLA-typed and matched for 10/10 (n = 1379), 9/10 (n = 636), or 8/10 (n = 157) HLA alleles. Within each HLA match group, cases matched and mismatched for MICA and MICA-129 were analyzed for the end points overall survival (OS), disease-free survival (DFS), nonrelapse mortality (NRM), relapse-incidence (RI), and GVHD. Mismatches at the MICA locus as well as MICA-129 increased with the number of HLA mismatches (MICA mismatched 10/10, 9.2% [n = 127]; 9/10, 22.3% [n = 142]; 8/10, 38.2% [n = 60]; MICA-129 mismatched 10/10, 3.9% [n = 54]; 9/10, 10.2% [n = 65]; 8/10, 17.2% [n = 27]). Adverse OS was observed in the 10/10 match group if MICA-129 was mismatched (10/10, hazard ratio [HR], 1.77; confidence interval [CI], 1.22-2.57; P = .003). MICA-129 mismatches correlated with a significantly worse outcome for DFS in the 10/10 HLA match group (HR, 1.77; CI, 1.26-2.50; P = .001). Higher rates of aGVHD were seen in MICA-129 mismatched cases. Our results indicate that MICA-129 matching is relevant in uHSCT. Prospective typing of patients and donors in unrelated donor search may identify mismatches for MICA-129, and compatible donor selection may improve outcome for this small but high-risk subgroup.
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Marieke Griffioen
- Department of Hematology, Leiden University Medical Center , Leiden , Netherlands
| | | | | |
Collapse
|
18
|
Abdul Razzaq B, Scalora A, Koparde VN, Meier J, Mahmood M, Salman S, Jameson-Lee M, Serrano MG, Sheth N, Voelkner M, Kobulnicky DJ, Roberts CH, Ferreira-Gonzalez A, Manjili MH, Buck GA, Neale MC, Toor AA. Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and -Mismatched Donor-Recipient Pairs. Biol Blood Marrow Transplant 2015; 22:850-61. [PMID: 26688192 DOI: 10.1016/j.bbmt.2015.11.1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/29/2015] [Indexed: 12/11/2022]
Abstract
Immune reconstitution kinetics and subsequent clinical outcomes in HLA-matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA-matched SCT donor-recipient pairs (DRPs) and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance with the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone's growth was calculated with the steady-state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire, including sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity, and alteration of clonal dominance when a different antigen array is encountered, such as in SCT. The simulated, alloreactive T cell repertoire was markedly different in HLA-matched DRPs. The patterns were differentiated by rate of growth and steady-state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRPs may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression after SCT.
Collapse
Affiliation(s)
- Badar Abdul Razzaq
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Allison Scalora
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Vishal N Koparde
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Jeremy Meier
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Musa Mahmood
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Salman Salman
- Virginia Commonwealth University School of Engineering, Virginia Commonwealth University, Richmond, VA 23298
| | - Max Jameson-Lee
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Myrna G Serrano
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Nihar Sheth
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Mark Voelkner
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298
| | - David J Kobulnicky
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | - Catherine H Roberts
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298
| | | | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298
| | - Gregory A Buck
- Center for Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298
| | - Michael C Neale
- Department of Psychiatry and Statistical Genomics, Virginia Commonwealth University, Richmond, VA 23298
| | - Amir A Toor
- Bone Marrow Transplant Program, Massey Cancer Center & Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Dynamical System Modeling of Immune Reconstitution after Allogeneic Stem Cell Transplantation Identifies Patients at Risk for Adverse Outcomes. Biol Blood Marrow Transplant 2015; 21:1237-45. [PMID: 25849208 DOI: 10.1016/j.bbmt.2015.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/14/2015] [Indexed: 11/24/2022]
Abstract
Systems that evolve over time and follow mathematical laws as they evolve are called dynamical systems. Lymphocyte recovery and clinical outcomes in 41 allograft recipients conditioned using antithymocyte globulin (ATG) and 4.5-Gy total body irradiation were studied to determine if immune reconstitution could be described as a dynamical system. Survival, relapse, and graft-versus-host disease (GVHD) were not significantly different in 2 cohorts of patients receiving different doses of ATG. However, donor-derived CD3(+) cell reconstitution was superior in the lower ATG dose cohort, and there were fewer instances of donor lymphocyte infusion (DLI). Lymphoid recovery was plotted in each individual over time and demonstrated 1 of 3 sigmoid growth patterns: Pattern A (n = 15) had rapid growth with high lymphocyte counts, pattern B (n = 14) had slower growth with intermediate recovery, and pattern C (n = 10) had poor lymphocyte reconstitution. There was a significant association between lymphocyte recovery patterns and both the rate of change of donor-derived CD3(+) at day 30 after stem cell transplantation (SCT) and clinical outcomes. GVHD was observed more frequently with pattern A, relapse and DLI more so with pattern C, with a consequent survival advantage in patients with patterns A and B. We conclude that evaluating immune reconstitution after SCT as a dynamical system may differentiate patients at risk of adverse outcomes and allow early intervention to modulate that risk.
Collapse
|
21
|
Toor AA, Kobulnicky JD, Salman S, Roberts CH, Jameson-Lee M, Meier J, Scalora A, Sheth N, Koparde V, Serrano M, Buck GA, Clark WB, McCarty JM, Chung HM, Manjili MH, Sabo RT, Neale MC. Stem cell transplantation as a dynamical system: are clinical outcomes deterministic? Front Immunol 2014; 5:613. [PMID: 25520720 PMCID: PMC4253954 DOI: 10.3389/fimmu.2014.00613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/14/2014] [Indexed: 12/22/2022] Open
Abstract
Outcomes in stem cell transplantation (SCT) are modeled using probability theory. However, the clinical course following SCT appears to demonstrate many characteristics of dynamical systems, especially when outcomes are considered in the context of immune reconstitution. Dynamical systems tend to evolve over time according to mathematically determined rules. Characteristically, the future states of the system are predicated on the states preceding them, and there is sensitivity to initial conditions. In SCT, the interaction between donor T cells and the recipient may be considered as such a system in which, graft source, conditioning, and early immunosuppression profoundly influence immune reconstitution over time. This eventually determines clinical outcomes, either the emergence of tolerance or the development of graft versus host disease. In this paper, parallels between SCT and dynamical systems are explored and a conceptual framework for developing mathematical models to understand disparate transplant outcomes is proposed.
Collapse
Affiliation(s)
- Amir A Toor
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Jared D Kobulnicky
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Salman Salman
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Catherine H Roberts
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Max Jameson-Lee
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Jeremy Meier
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Allison Scalora
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Nihar Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University , Richmond, VA , USA
| | - Vishal Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University , Richmond, VA , USA
| | - Myrna Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University , Richmond, VA , USA
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University , Richmond, VA , USA
| | - William B Clark
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - John M McCarty
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Harold M Chung
- Stem Cell Transplant Program, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University , Richmond, VA , USA
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University , Richmond, VA , USA
| | - Roy T Sabo
- Department of Biostatistics, Virginia Commonwealth University , Richmond, VA , USA
| | - Michael C Neale
- Department of Psychiatry and Statistical Genomics, Virginia Commonwealth University , Richmond, VA , USA
| |
Collapse
|