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Fischer G, Bättig L, Stienen MN, Curt A, Fehlings MG, Hejrati N. Advancements in neuroregenerative and neuroprotective therapies for traumatic spinal cord injury. Front Neurosci 2024; 18:1372920. [PMID: 38812974 PMCID: PMC11133582 DOI: 10.3389/fnins.2024.1372920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/31/2024] Open
Abstract
Traumatic spinal cord injuries (SCIs) continue to be a major healthcare concern, with a rising prevalence worldwide. In response to this growing medical challenge, considerable scientific attention has been devoted to developing neuroprotective and neuroregenerative strategies aimed at improving the prognosis and quality of life for individuals with SCIs. This comprehensive review aims to provide an up-to-date and thorough overview of the latest neuroregenerative and neuroprotective therapies currently under investigation. These strategies encompass a multifaceted approach that include neuropharmacological interventions, cell-based therapies, and other promising strategies such as biomaterial scaffolds and neuro-modulation therapies. In addition, the review discusses the importance of acute clinical management, including the role of hemodynamic management as well as timing and technical aspects of surgery as key factors mitigating the secondary injury following SCI. In conclusion, this review underscores the ongoing scientific efforts to enhance patient outcomes and quality of life, focusing on upcoming strategies for the management of traumatic SCI. Each section provides a working knowledge of the fundamental preclinical and patient trials relevant to clinicians while underscoring the pathophysiologic rationale for the therapies.
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Affiliation(s)
- Gregor Fischer
- Department of Neurosurgery, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
- Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
| | - Linda Bättig
- Department of Neurosurgery, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
- Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
| | - Martin N. Stienen
- Department of Neurosurgery, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
- Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
| | - Armin Curt
- Spinal Cord Injury Center, University Hospital Balgrist, Zurich, Switzerland
| | - Michael G. Fehlings
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Nader Hejrati
- Department of Neurosurgery, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
- Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, Medical School of St.Gallen, St.Gallen, Switzerland
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2
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Madbouly A, Bolon YT. Race, ethnicity, ancestry, and aspects that impact HLA data and matching for transplant. Front Genet 2024; 15:1375352. [PMID: 38560292 PMCID: PMC10978785 DOI: 10.3389/fgene.2024.1375352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Race, ethnicity, and ancestry are terms that are often misinterpreted and/or used interchangeably. There is lack of consensus in the scientific literature on the definition of these terms and insufficient guidelines on the proper classification, collection, and application of this data in the scientific community. However, defining groups for human populations is crucial for multiple healthcare applications and clinical research. Some examples impacted by population classification include HLA matching for stem-cell or solid organ transplant, identifying disease associations and/or adverse drug reactions, defining social determinants of health, understanding diverse representation in research studies, and identifying potential biases. This article describes aspects of race, ethnicity and ancestry information that impact the stem-cell or solid organ transplantation field with particular focus on HLA data collected from donors and recipients by donor registries or transplant centers.
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Affiliation(s)
- Abeer Madbouly
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research (CIBMTR), Minneapolis, MN, United States
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3
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Cambridge CA, Turner TR, Georgiou X, Robinson J, Mayor NP, Marsh SGE. Fifty novel HLA-DPB1 alleles identified in a UK cohort of unrelated hematopoietic cell donors and recipients. HLA 2024; 103:e15261. [PMID: 37850248 DOI: 10.1111/tan.15261] [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: 07/17/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
HLA-DPB1 is the classical HLA class II genes with the least recorded variation on the IPD-IMGT/HLA Database, suggesting the full extent of its diversity is perhaps yet to be characterized. Here, a full-gene typing strategy was employed to genotype a UK cohort of 1470 HCT recipients (n = 744) and donors (n = 726). In total, 2940 full-length HLA-DPB1 sequences were generated, comprising 193 distinct alleles. Of these, 107 sequences contained novel variation, totaling 49 unique intronic HLA-DPB1 alleles, and one coding variant (HLA-DPB1*1188:01). Full-gene sequencing resulted in zygosity changes for 129 individuals by identifying two distinct intronic variants of the same coding allele. We verified the existence of nine unconfirmed alleles and extended the sequence of two existing alleles on the IPD-IMGT/HLA Database.
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Affiliation(s)
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
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4
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Hejrati N, Wong R, Khazaei M, Fehlings MG. How can clinical safety and efficacy concerns in stem cell therapy for spinal cord injury be overcome? Expert Opin Biol Ther 2023; 23:883-899. [PMID: 37545020 DOI: 10.1080/14712598.2023.2245321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
INTRODUCTION Spinal cord injury (SCI) can lead to severe neurological dysfunction. Despite scientific and medical advances, clinically effective regenerative therapies including stem cells are lacking for SCI. AREAS COVERED This paper discusses translational challenges related to the safe, effective use of stem cells for SCI, with a focus on mesenchymal stem cells (MSCs), neural stem cells (NSCs), Schwann cells (SCs), olfactory ensheathing cells (OECs), oligodendrocyte precursor cells (OPCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs). We discuss approaches to enhance the efficacy of cell-based strategies by i) addressing patient heterogeneity and enhancing patient selection; ii) selecting cell type, cell source, cell developmental stage, and delivery technique; iii) enhancing graft integration and mitigating immune-mediated graft rejection; and iv) ensuring availability of cells. Additionally, we review strategies to optimize outcomes including combinatorial use of rehabilitation and discuss ways to mitigate potential risks of tumor formation associated with stem cell-based strategies. EXPERT OPINION Basic science research will drive translational advances to develop stem cell-based therapies for SCI. Genetic, serological, and imaging biomarkers may enable individualization of cell-based treatments. Moreover, combinatorial strategies will be required to enhance graft survival, migration and functional integration, to enable precision-based intervention.
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Affiliation(s)
- Nader Hejrati
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Neurosurgery & Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
| | - Raymond Wong
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Mohamad Khazaei
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Michael G Fehlings
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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5
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Cheung SKF, Choi LCW, Chan YS, Ho JCY, Lee CK, Kwok JSY. Identification of 58 novel HLA alleles identified in Chinese individuals by next-generation sequencing. HLA 2023. [PMID: 37376846 DOI: 10.1111/tan.15127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023]
Abstract
HLA genes are the most polymorphic in the human genome. High resolution HLA typing from 13,870 bone marrow donors in Hong Kong was obtained using Next-generation sequencing (NGS) technology. Among the 67 novel alleles identified, official HLA allele names of 50 novel class I alleles (HLA-A, -B, -C) and 8 novel class II alleles (HLA-DRB1, -DQB1) were assigned by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System.
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Affiliation(s)
- Stephen K F Cheung
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - Leo C W Choi
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - Y S Chan
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - Jenny C Y Ho
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
| | - C K Lee
- Hong Kong Red Cross Blood Transfusion Services, Hong Kong SAR, China
| | - Janette S Y Kwok
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong SAR, China
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6
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
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7
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Anzar I, Sverchkova A, Samarakoon P, Ellingsen EB, Gaudernack G, Stratford R, Clancy T. Personalized
HLA
typing leads to the discovery of novel
HLA
alleles and tumor‐specific
HLA
variants. HLA 2022; 99:313-327. [PMID: 35073457 PMCID: PMC9546058 DOI: 10.1111/tan.14562] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/29/2022]
Abstract
Accurate and full‐length typing of the HLA region is important in many clinical and research settings. With the advent of next generation sequencing (NGS), several HLA typing algorithms have been developed, including many that are applicable to whole exome sequencing (WES). However, most of these solutions operate by providing the closest‐matched HLA allele among the known alleles in IPD‐IMGT/HLA Database. These database‐matching approaches have demonstrated very high performance when typing well characterized HLA alleles. However, as they rely on the completeness of the HLA database, they are not optimal for detecting novel or less well characterized alleles. Furthermore, the database‐matching approaches are also not adequate in the context of cancer, where a comprehensive characterization of somatic HLA variation and expression patterns of a tumor's HLA locus may guide therapy and clinical outcome, because of the pivotal role HLA alleles play in tumor antigen recognition and immune escape. Here, we describe a personalized HLA typing approach applied to WES data that leverages the strengths of database‐matching approaches while simultaneously allowing for the discovery of novel HLA alleles and tumor‐specific HLA variants, through the systematic integration of germline and somatic variant calling. We applied this approach on WES from 10 metastatic melanoma patients and validated the HLA typing results using HLA targeted NGS sequencing from patients where at least one HLA germline candidate was detected on Class I HLA. Targeted NGS sequencing confirmed 100% performance for the 1st and 2nd fields. In total, five out of the six detected HLA germline variants were because of Class I ambiguities at the third or fourth fields, and their detection recovered the correct HLA allele genotype. The sixth germline variant let to the formal discovery of a novel Class I allele. Finally, we demonstrated a substantially improved somatic variant detection accuracy in HLA alleles with a 91% of success rate in simulated experiments. The approach described here may allow the field to genotype more accurately using WES data, leading to the discovery of novel HLA alleles and help characterize the relationship between somatic variation in the HLA region and immunosurveillance.
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Affiliation(s)
- Irantzu Anzar
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Angelina Sverchkova
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Pubudu Samarakoon
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | | | - Gustav Gaudernack
- Ultimovacs ASA, Oslo Cancer Cluster, Ullernchausseen 64/66 Oslo Norway
| | - Richard Stratford
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Trevor Clancy
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
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8
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Mayor NP, Wang T, Lee SJ, Kuxhausen M, Vierra-Green C, Barker DJ, Auletta J, Bhatt VR, Gadalla SM, Gragert L, Inamoto Y, Morris GP, Paczesny S, Reshef R, Ringdén O, Shaw BE, Shaw P, Spellman SR, Marsh SGE. Impact of Previously Unrecognized HLA Mismatches Using Ultrahigh Resolution Typing in Unrelated Donor Hematopoietic Cell Transplantation. J Clin Oncol 2021; 39:2397-2409. [PMID: 33835855 PMCID: PMC8280068 DOI: 10.1200/jco.20.03643] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/08/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Ultrahigh resolution (UHR) HLA matching is reported to result in better outcomes following unrelated donor hematopoietic cell transplantation, improving survival and reducing post-transplant complications. However, most studies included relatively small numbers of patients. Here we report the findings from a large, multicenter validation study. METHODS UHR HLA typing was available on 5,140 conventionally 10 out of 10 HLA-matched patients with malignant disease transplanted between 2008 and 2017. RESULTS After UHR HLA typing, 82% of pairs remained 10 out of 10 UHR-matched; 12.3% of patients were 12 out of 12 UHR HLA-matched. Compared with 12 out of 12 UHR-matched patients, probabilities of grade 2-4 acute graft-versus-host disease (aGVHD) were significantly increased with UHR mismatches (overall P = .0019) and in those patients who were HLA-DPB1 T-cell epitope permissively mismatched or nonpermissively mismatched (overall P = .0011). In the T-cell-depleted subset, the degree of UHR HLA mismatch was only associated with increased transplant-related mortality (TRM) (overall P = .0068). In the T-cell-replete subset, UHR HLA matching was associated with a lower probability of aGVHD (overall P = .0020); 12 out of 12 UHR matching was associated with reduced TRM risk when compared with HLA-DPB1 T-cell epitope permissively mismatched patients, whereas nonpermissive mismatching resulted in a greater risk (overall P = .0003). CONCLUSION This study did not confirm that UHR 12 out of 12 HLA matching increases the probability of overall survival but does demonstrate that aGVHD risk, and in certain settings TRM, is lowest in UHR HLA-matched pairs and thus warrants consideration when multiple 10 out of 10 HLA-matched donors of equivalent age are available.
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Affiliation(s)
- Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Stephanie J. Lee
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | | | - Jeffrey Auletta
- Blood and Marrow Transplant Program and Host Defense Program, Nationwide Children's Hospital, Columbus, OH
| | - Vijaya R. Bhatt
- Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD
| | - Loren Gragert
- Tulane Cancer Center, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Yoshihiro Inamoto
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Gerald P. Morris
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Ran Reshef
- Division of Hematology/Oncology and Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY
| | - Olle Ringdén
- Department of Clinical Sciences, Intervention and Technology, Translational Cell Therapy Research Group, Karolinska Institute, Stockholm, Sweden
| | - Bronwen E. Shaw
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Peter Shaw
- Department of Child and Adolescent Health, Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London, London, UK
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9
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Hermsen J, Brown ME. Humanized Mouse Models for Evaluation of PSC Immunogenicity. ACTA ACUST UNITED AC 2021; 54:e113. [PMID: 32588980 DOI: 10.1002/cpsc.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
New human pluripotent stem cell (hPSC)-derived therapies are advancing to clinical trials at an increasingly rapid pace. In addition to ensuring that the therapies function properly, there is a critical need to investigate the human immune response to these cell products. A robust allogeneic (or autologous) immune response could swiftly eliminate an otherwise promising cell therapy, even in immunosuppressed patients. In coming years, researchers in the regenerative medicine field will need to utilize a number of in vitro and in vivo assays and models to evaluate and better understand hPSC immunogenicity. Humanized mouse models-mice engrafted with functional human immune cell types-are an important research tool for investigating the mechanisms of the adaptive immune response to hPSC therapies. This article provides an overview of humanized mouse models relevant to the study of hPSC immunogenicity and explores central considerations for investigators seeking to utilize these powerful models in their research. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- Jack Hermsen
- University of Wisconsin School of Medicine and Public Health Western Clinical Campus, Madison, Wisconsin
| | - Matthew E Brown
- University of Wisconsin School of Medicine and Public Health Western Clinical Campus, Madison, Wisconsin
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10
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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11
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Liu C, Yang X, Duffy BF, Hoisington-Lopez J, Crosby M, Porche-Sorbet R, Saito K, Berry R, Swamidass V, Mitra RD. High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells. Hum Immunol 2021; 82:288-295. [PMID: 33612390 DOI: 10.1016/j.humimm.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/12/2023]
Abstract
Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Xiao Yang
- GeneGenieDx, 160 E Tasman Dr Ste 109, San Jose, CA, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jessica Hoisington-Lopez
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - MariaLynn Crosby
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhonda Porche-Sorbet
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Rick Berry
- PlatformSTL, 4340 Duncan Ave. St. Louis, MO, USA
| | | | - Robi D Mitra
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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12
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Liu C, Duffy BF, Weimer ET, Montgomery MC, Jennemann JE, Hill R, Phelan D, Lay L, Parikh BA. Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing. PLoS One 2020; 15:e0232050. [PMID: 32324777 PMCID: PMC7179861 DOI: 10.1371/journal.pone.0232050] [Citation(s) in RCA: 11] [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: 12/16/2019] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplant-relevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. METHODS Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. RESULTS The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. CONCLUSION The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.
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Affiliation(s)
- Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian F. Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Eric T. Weimer
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Hospitals, Chapel Hill, North Carolina, United States of America
| | - Jo-Ellen Jennemann
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Rachel Hill
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Donna Phelan
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Lindsay Lay
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, United States of America
| | - Bijal A. Parikh
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
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13
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Schmidt AH, Sauter J, Baier DM, Daiss J, Keller A, Klussmeier A, Mengling T, Rall G, Riethmüller T, Schöfl G, Solloch UV, Torosian T, Means D, Kelly H, Jagannathan L, Paul P, Giani AS, Hildebrand S, Schumacher S, Markert J, Füssel M, Hofmann JA, Schäfer T, Pingel J, Lange V, Schetelig J. Immunogenetics in stem cell donor registry work: The DKMS example (Part 1). Int J Immunogenet 2020; 47:13-23. [PMID: 31903698 PMCID: PMC7003907 DOI: 10.1111/iji.12471] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023]
Abstract
Currently, stem cell donor registries include more than 35 million potential donors worldwide to provide HLA-matched stem cell products for patients in need of an unrelated donor transplant. DKMS is a leading stem cell donor registry with more than 9 million donors from Germany, Poland, the United States, the United Kingdom, India and Chile. DKMS donors have donated hematopoietic stem cells more than 80,000 times. Many aspects of donor registry work are closely related to topics from immunogenetics or population genetics. In this two-part review article, we describe, analyse and discuss these areas of donor registry work by using the example of DKMS. Part 1 of the review gives a general overview on DKMS and includes typical donor registry activities with special focus on the HLA system: high-throughput HLA typing of potential stem cell donors, HLA haplotype frequencies and resulting matching probabilities, and donor file optimization with regard to HLA diversity.
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Affiliation(s)
- Alexander H. Schmidt
- DKMSTübingenGermany
- DKMS Life Science LabDresdenGermany
- DKMSClinical Trials UnitDresdenGermany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Latha Jagannathan
- DKMS BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | | | | | | | | | - Johannes Schetelig
- DKMSClinical Trials UnitDresdenGermany
- University Hospital Carl Gustav CarusMedizinische Klinik IDresdenGermany
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14
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Cargou M, Ralazamahaleo M, Blouin L, Top I, Elsermans V, Andreani M, Guidicelli G, Visentin J. Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform. HLA 2019; 95:30-39. [DOI: 10.1111/tan.13708] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Marine Cargou
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
| | - Mamy Ralazamahaleo
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Laura Blouin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Isabelle Top
- CHRU de Lille, Institut d'Immunologie‐HLA Lille France
| | | | - Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti IRCCS Ospedale Pediatrico Bambino Gesù Roma Italy
| | - Gwendaline Guidicelli
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
| | - Jonathan Visentin
- CHU de Bordeaux, Laboratoire d'Immunologie et Immunogénétique Hôpital Pellegrin Bordeaux France
- Immuno ConcEpT Bordeaux France
- Université de Bordeaux Bordeaux France
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15
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Fürst D, Neuchel C, Tsamadou C, Schrezenmeier H, Mytilineos J. HLA Matching in Unrelated Stem Cell Transplantation up to Date. Transfus Med Hemother 2019; 46:326-336. [PMID: 31832058 DOI: 10.1159/000502263] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/13/2019] [Indexed: 12/27/2022] Open
Abstract
Unrelated hematopoietic stem cell transplantation (HSCT) has evolved from an experimental protocol to a potentially curative first-line treatment in certain disease instances. Factors enabling this transformation were the optimization of treatment protocols and supportive care as well as the availability of a large number of donors worldwide along with the higher quality and reliability of HLA typing. The main criterion for donor selection is HLA compatibility. In this review we discuss the current clinical evidence of HLA matching in unrelated HSCT. In this context, we address methodical aspects of transplantation immunobiology research and discuss the impact of locus and resolution of HLA differences. Furthermore, we address special constellations such as unidirectional mismatches or the presence of nonexpressed alleles as well as HLA alloimmunization and describe the perspective for HLA typing and matching strategies in the future, given the implementation of novel complete or near-complete gene typing approaches using next-generation sequencing short read technology, which are now entering the standard of clinical care.
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Affiliation(s)
- Daniel Fürst
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Christine Neuchel
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Chrysanthi Tsamadou
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Joannis Mytilineos
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen, and University Hospital Ulm, Ulm, Germany.,Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
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16
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Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, Marsh SGE. A reply to Hurley et al. regarding Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study. Biol Blood Marrow Transplant 2019; 25:e270-e271. [PMID: 31195138 DOI: 10.1016/j.bbmt.2019.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - James D Hayhurst
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Richard M Szydlo
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; Imperial College, London, United Kingdom
| | - Bronwen E Shaw
- Center for International Blood and Marrow Transplant Research, Froedtert and the Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Will P Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Jex-Ray Sayno
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom
| | - Franco Tavarozzi
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom
| | - Katy Latham
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom
| | - Chloe Anthias
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Henny Braund
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom
| | - Robert Danby
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Julia Perry
- British Society for Blood and Marrow Transplantation, Guy's Hospital, London, United Kingdom
| | - Marie C Wilson
- British Society for Blood and Marrow Transplantation, Guy's Hospital, London, United Kingdom
| | - Adrian J Bloor
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - David I Marks
- University Hospitals Bristol NHS Trust, Bristol, United Kingdom
| | | | | | | | | | | | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London, United Kingdom; University College London Cancer Institute, Royal Free Campus, London, United Kingdom.
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17
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Resolving MiSeq-Generated Ambiguities in HLA-DPB1 Typing by Using the Oxford Nanopore Technology. J Mol Diagn 2019; 21:852-861. [PMID: 31173929 DOI: 10.1016/j.jmoldx.2019.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 12/30/2022] Open
Abstract
The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, form the basis for the additional ambiguities encountered at an increasing rate in clinical practice. HLA-DPB1 characterization, particularly, generates a significant percentage of ambiguities (25.5%), posing a challenge for accurate and unambiguous HLA-DPB1 genotyping. Phasing of exonic heterozygous positions between exon 2 and all other downstream exons has been the major cause of ambiguities. In this study, the Oxford Nanopore MinION, a third-generation sequencing technology, was used to resolve the phasing. The accurate MiSeq sequencing data, combined with the long reads obtained from the MinION platform, allow for the resolution of the tested ambiguities.
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