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Rosenberger A, Crossland RE, Dressel R, Kube D, Wolff D, Wulf G, Bickeböller H, Dickinson A, Holler E. A genome-wide association study on hematopoietic stem cell transplantation reveals novel genomic loci associated with transplant outcomes. Front Immunol 2024; 15:1280876. [PMID: 38384455 PMCID: PMC10879589 DOI: 10.3389/fimmu.2024.1280876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Data on genomic susceptibility for adverse outcomes after hematopoietic stem cell transplantation (HSCT) for recipients are scarce. Methods We performed a genome wide association study (GWAS) to identify genes associated with survival/mortality, relapse, and severe graft-versus-host disease (sGvHD), fitting proportional hazard and subdistributional models to data of n=1,392 recipients of European ancestry from three centres. Results The single nucleotide polymorphism (SNP) rs17154454, intronic to the neuronal growth guidant semaphorin 3C gene (SEMA3C), was genome-wide significantly associated with event-free survival (p=7.0x10-8) and sGvHD (p=7.5x10-8). Further associations were detected for SNPs in the Paxillin gene (PXN) with death without prior relapse or sGvHD, as well as for SNPs of the Plasmacytoma Variant Translocation 1 gene (PVT1, a long non-coding RNA gene), the Melanocortin 5 Receptor (MC5R) gene and the WW Domain Containing Oxidoreductase gene (WWOX), all associated with the occurrence of sGvHD. Functional considerations support the observed associations. Discussion Thus, new genes were identified, potentially influencing the outcome of HSCT.
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Affiliation(s)
- Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Rachel E. Crossland
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Dieter Kube
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Gerald Wulf
- Hematology and Medical Oncology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Anne Dickinson
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ernst Holler
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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Mushtaq AH, Shafqat A, Salah HT, Hashmi SK, Muhsen IN. Machine learning applications and challenges in graft-versus-host disease: a scoping review. Curr Opin Oncol 2023; 35:594-600. [PMID: 37820094 DOI: 10.1097/cco.0000000000000996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
PURPOSE OF REVIEW This review delves into the potential of artificial intelligence (AI), particularly machine learning (ML), in enhancing graft-versus-host disease (GVHD) risk assessment, diagnosis, and personalized treatment. RECENT FINDINGS Recent studies have demonstrated the superiority of ML algorithms over traditional multivariate statistical models in donor selection for allogeneic hematopoietic stem cell transplantation. ML has recently enabled dynamic risk assessment by modeling time-series data, an upgrade from the static, "snapshot" assessment of patients that conventional statistical models and older ML algorithms offer. Regarding diagnosis, a deep learning model, a subset of ML, can accurately identify skin segments affected with chronic GVHD with satisfactory results. ML methods such as Q-learning and deep reinforcement learning have been utilized to develop adaptive treatment strategies (ATS) for the personalized prevention and treatment of acute and chronic GVHD. SUMMARY To capitalize on these promising advancements, there is a need for large-scale, multicenter collaborations to develop generalizable ML models. Furthermore, addressing pertinent issues such as the implementation of stringent ethical guidelines is crucial before the widespread introduction of AI into GVHD care.
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Affiliation(s)
- Ali Hassan Mushtaq
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Haneen T Salah
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Shahrukh K Hashmi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Medicine, Sheikh Shakbout Medical City
- Medical Affairs, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Ibrahim N Muhsen
- Section of Hematology and Oncology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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Mougeot JLC, Beckman MF, Hovan AJ, Hasséus B, Legert KG, Johansson JE, von Bültzingslöwen I, Brennan MT, Bahrani Mougeot F. Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation. Support Care Cancer 2023; 31:587. [PMID: 37731134 PMCID: PMC10511391 DOI: 10.1007/s00520-023-08044-3] [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: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( -) (N = 66) HCT patients. METHODS Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher's exact test. One cGVHD( -) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform's SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA's GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci. RESULTS Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher's exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1. CONCLUSIONS Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.
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Affiliation(s)
- Jean-Luc C Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
| | - Micaela F Beckman
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
| | - Allan J Hovan
- BC Cancer, Oral Oncology and Dentistry, Vancouver, BC, Canada
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jan-Erik Johansson
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Michael T Brennan
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Farah Bahrani Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
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Siemaszko J, Ussowicz M, Rybka B, Ryczan-Krawczyk R, Kałwak K, Bogunia-Kubik K. The impact of NKG2A and NKG2D receptors and HLA-E and MICA ligands polymorphisms on post-transplant complications after paediatric allogeneic HSCT: a single-centre experience. Front Genet 2023; 14:1186123. [PMID: 37351346 PMCID: PMC10282657 DOI: 10.3389/fgene.2023.1186123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction: Natural Killer cells are the first subpopulation of lymphocytes that reconstitute after allogeneic haematopoietic stem cell transplantation (HSCT). Their activity is regulated by various receptor-ligand interactions, including stimulation of the activating NKG2D receptor by the MICA molecule, and inhibitory NKG2A receptor interacting with the HLA-E. In this study the research effort focused on the effect of selected NKG2A and NKG2D receptors and their ligands (HLA-E and MICA molecules) polymorphisms that may affect the pathomechanisms of post-transplant complications after HSCT in children. Methods: One hundred donor-recipient pairs from a single paediatric transplantation centre were investigated. Altogether six single nucleotide substitutions (NKG2A rs7301582; NKG2D rs1049174, rs1154831; HLA-E rs1264457; MICA rs1051792, rs1063635) were genotyped, and the influence of polymorphisms was analysed on acute and chronic graft-versus-host disease (GvHD), cytomegalovirus (CMV) infection incidence, disease relapse and survival. Results: The distribution of the evaluated polymorphisms did not differ between patients and their donors. The results showed a significant influence of HLA-E rs1264457 polymorphism in patients' HLA-E*01:01 allele, which was associated with increased risk of CMV infection (p = 0.050), especially in children positive for CMV IgG before transplantation (p = 0.001). Furthermore, the effect of HLA-E*01:01 allele on CMV infections was more evident in children above the age of 7 years (p = 0.031). Strong tendencies (0.05 < p < 0.10) towards association with the risk of acute GvHD were also observed for the NKG2A or MICA polymorphisms of the recipients. In addition, NKG2D rs1154831 AA and MICA rs1063635 GG might play a protective role as they were not present in any recipient who died after transplantation. Conclusion: In summary, there is emerging evidence that genotyping results of NKG2 receptors and their ligands, may have prognostic value for the outcome of paediatric allogeneic HSCT, but more extensive studies performed on larger groups of donors and transplant recipients are required to confirm these observations.
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Affiliation(s)
- Jagoda Siemaszko
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Marek Ussowicz
- Department and Clinic of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Wroclaw, Poland
| | - Blanka Rybka
- Department and Clinic of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Wroclaw, Poland
| | - Renata Ryczan-Krawczyk
- Department and Clinic of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Wroclaw, Poland
| | - Krzysztof Kałwak
- Department and Clinic of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Heydemann A, Siemionow M. A Brief Review of Duchenne Muscular Dystrophy Treatment Options, with an Emphasis on Two Novel Strategies. Biomedicines 2023; 11:biomedicines11030830. [PMID: 36979809 PMCID: PMC10044847 DOI: 10.3390/biomedicines11030830] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Despite the full cloning of the Dystrophin cDNA 35 years ago, no effective treatment exists for the Duchenne Muscular Dystrophy (DMD) patients who have a mutation in this gene. Many treatment options have been considered, investigated preclinically and some clinically, but none have circumvented all barriers and effectively treated the disease without burdening the patients with severe side-effects. However, currently, many novel therapies are in the pipelines of research labs and pharmaceutical companies and many of these have progressed to clinical trials. A brief review of these promising therapies is presented, followed by a description of two novel technologies that when utilized together effectively treat the disease in the mdx mouse model. One novel technology is to generate chimeric cells from the patient’s own cells and a normal donor. The other technology is to systemically transplant these cells into the femur via the intraosseous route.
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Affiliation(s)
- Ahlke Heydemann
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL 60607, USA
- Correspondence:
| | - Maria Siemionow
- Department of Orthopaedics, University of Illinois at Chicago, Chicago, IL 60607, USA
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Milosevic E, Babic A, Iovino L, Markovic M, Grce M, Greinix H. Use of the NIH consensus criteria in cellular and soluble biomarker research in chronic graft-versus-host disease: A systematic review. Front Immunol 2022; 13:1033263. [DOI: 10.3389/fimmu.2022.1033263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesChronic graft-versus-host disease (cGvHD) is the most frequent cause of late non-relapse mortality after allogeneic haematopoietic stem cell transplantation (alloHCT). Nevertheless, established biomarkers of cGvHD are still missing. The National Institutes of Health (NIH) Consensus Development Project on Criteria for Clinical Trials in cGvHD provided recommendations for biomarker research. We evaluated to which extent studies on cellular and soluble biomarkers in cGvHD published in the last 10 years complied with these recommendations. Also, we highlight the most promising biomarker candidates, verified in independent cohorts and/or repeatedly identified by separate studies.MethodsWe searched Medline and EMBASE for “cGvHD”, “biomarkers”, “soluble” and “cells” as MeSH terms or emtree subject headings, and their variations on July 28th, 2021, limited to human subjects, English language and last ten years. Reviews, case reports, conference abstracts and single nucleotide polymorphism studies were excluded. Criteria based on the set of recommendations from the NIH group for biomarker research in cGvHD were used for scoring and ranking the references.ResultsA total of 91 references encompassing 15,089 participants were included, 54 prospective, 17 retrospective, 18 cross-sectional, and 2 studies included both prospective and retrospective cohorts. Thirty-five papers included time-matched controls without cGvHD and 20 studies did not have any control subjects. Only 9 studies were randomized, and 8 were multicentric. Test and verification cohorts were included in 11 studies. Predominantly, diagnostic biomarkers were explored (n=54). Assigned scores ranged from 5-34. None of the studies fulfilled all 24 criteria (48 points). Nevertheless, the scores improved during the last years. Three cell subsets (CXCR3+CD56bright NK cells, CD19+CD21low and BAFF/CD19+ B cells) and several soluble factors (BAFF, IL-15, CD163, DKK3, CXCL10 and the panel of ST2, CXCL9, MMP3 and OPN) had the highest potential as diagnostic and/or prognostic biomarkers in cGvHD.ConclusionDespite several limitations of this review (limited applicability for paediatric population, definition of verification, missing data on comorbidities), we identified promising candidate biomarkers for further evaluation in multicentre collaborative studies. This review confirms the importance of the NIH consensus group criteria for improving the quality and reproducibility of cGvHD biomarker research.
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Artificial Intelligence in Clinical Immunology. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Artificial Intelligence in Clinical Immunology. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_83-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Crossland RE, Perutelli F, Bogunia-Kubik K, Mooney N, Milutin Gašperov N, Pučić-Baković M, Greinix H, Weber D, Holler E, Pulanić D, Wolff D, Dickinson AM, Inngjerdingen M, Grce M. Potential Novel Biomarkers in Chronic Graft-Versus-Host Disease. Front Immunol 2020; 11:602547. [PMID: 33424849 PMCID: PMC7786047 DOI: 10.3389/fimmu.2020.602547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Prognostic, diagnostic or predictive biomarkers are urgently needed for assessment of chronic graft-versus-host disease (cGvHD), a major risk for patients undergoing allogeneic hematopoietic stem cell transplantation. The main goal of this review generated within the COST Action EUROGRAFT "Integrated European Network on Chronic Graft Versus Host Disease" was to identify potential novel biomarkers for cGvHD besides the widely accepted molecular and cellular biomarkers. Thus, the focus was on cellular biomarkers, alloantibodies, glycomics, endothelial derived particles, extracellular vesicles, microbiome, epigenetic and neurologic changes in cGvHD patients. Both host-reactive antibodies in general, and particularly alloantibodies have been associated with cGvHD and require further consideration. Glycans attached to IgG modulate its activity and represent a promising predictive and/or stratification biomarker for cGVHD. Furthermore, epigenetic changes such as microRNAs and DNA methylation represent potential biomarkers for monitoring cGvHD patients and novel targets for developing new treatment approaches. Finally, the microbiome likely affects the pathophysiology of cGvHD; bacterial strains as well as microbial metabolites could display potential biomarkers for dysbiosis and risk for the development of cGvHD. In summary, although there are no validated biomarkers currently available for clinical use to better inform on the diagnosis, prognosis or prediction of outcome for cGvHD, many novel sources of potential markers have shown promise and warrant further investigation using well characterized, multi-center patient cohorts.
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Affiliation(s)
- Rachel E. Crossland
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Francesca Perutelli
- Department of Molecular Biotechnology and Health Sciences, School of Medicine, University of Torino, Torino, Italy
| | - Katarzyna Bogunia-Kubik
- Department of Clinical Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Nuala Mooney
- INSERM U976, Human Immunology, Pathophysiology and Immunotherapies, Hôpital Saint Louis, Paris, France
| | | | | | - Hildegard Greinix
- Division of Hematology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Daniela Weber
- Department of Internal Medicine III, Faculty of Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Ernst Holler
- Department of Internal Medicine III, Faculty of Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Dražen Pulanić
- Division of Hematology, Department of Internal Medicine, University Hospital Centre Zagreb, Medical School, University of Zagreb, Zagreb, Croatia
| | - Daniel Wolff
- Department of Internal Medicine III, Faculty of Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Anne M. Dickinson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marit Inngjerdingen
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Magdalena Grce
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
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Bogunia-Kubik K, Łacina P. Non-KIR NK cell receptors: Role in transplantation of allogeneic haematopoietic stem cells. Int J Immunogenet 2020; 48:157-171. [PMID: 33352617 DOI: 10.1111/iji.12523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Natural killer (NK) cells are of major significance in patients after allogeneic haematopoietic stem cell transplantation (HSCT). They are the first subset of lymphocytes to appear in peripheral blood after transplantation and play an important role in the immune responses against cancer and viral infections. The function of NK cells is controlled by various surface receptors, of which type I integral proteins with immunoglobulin-like domains (killer-cell immunoglobulin-like receptors, KIRs) have been the most extensively studied. The present review focuses on less studied NK cell receptors, such as type II integral proteins with lectin-like domains (CD94/NKG2, NKG2D), natural cytotoxicity receptors (NCRs), immunoglobulin-like transcripts (ILTs) and their ligands. Their potential role in patients with haematological disorders subjected to HSC transplant procedure in the context of post-transplant complications such as viral reactivation and acute graft-versus-host disease (GvHD) will be presented and discussed.
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Affiliation(s)
- Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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