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Geo JA, Ameen R, Al Shemmari S, Thomas J. Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine. Med Princ Pract 2024; 33:215-231. [PMID: 38442703 PMCID: PMC11175610 DOI: 10.1159/000538176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
HLA typing serves as a standard practice in hematopoietic stem cell transplantation to ensure compatibility between donors and recipients, preventing the occurrence of allograft rejection and graft-versus-host disease. Conventional laboratory methods that have been widely employed in the past few years, including sequence-specific primer PCR and sequencing-based typing (SBT), currently face the risk of becoming obsolete. This risk stems not only from the extensive diversity within HLA genes but also from the rapid advancement of next-generation sequencing and third-generation sequencing technologies. Third-generation sequencing systems like single-molecule real-time (SMRT) sequencing and Oxford Nanopore (ONT) sequencing have the capability to analyze long-read sequences that span entire intronic-exonic regions of HLA genes, effectively addressing challenges related to HLA ambiguity and the phasing of multiple short-read fragments. The growing dominance of these advanced sequencers in HLA typing is expected to solidify further through ongoing refinements, cost reduction, and error rate minimization. This review focuses on hematopoietic stem cell transplantation (HSCT) and explores prospective advancements and application of HLA DNA typing techniques. It explores how the adoption of third-generation sequencing technologies can revolutionize the field by offering improved accuracy, reduced ambiguity, and enhanced assessment of compatibility in HSCT. Embracing these cutting-edge technologies is essential to advancing the success rates and outcomes of hematopoietic stem cell transplantation. This review underscores the importance of staying at the forefront of HLA typing techniques to ensure the best possible outcomes for patients undergoing HSCT.
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Affiliation(s)
- Jeethu Anu Geo
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Reem Ameen
- Medical Laboratory Sciences Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Salem Al Shemmari
- Department of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Jibu Thomas
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, India
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2
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Arroyo-Sánchez D, Gil-Etayo FJ, Niño Ramírez JE, Jiménez-Hernaz I, Tejeda Velarde A. Detection of two HLA-B*35 variants: HLA-B*35:01:01:39 and -B*35:03:01:32. HLA 2024; 103:e15416. [PMID: 38494835 DOI: 10.1111/tan.15416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 03/19/2024]
Abstract
Two nucleotide substitutions in intronic regions give rise to the novel alleles: HLA-B*35:01:01:39 and -B*35:03:01:32.
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Affiliation(s)
- Daniel Arroyo-Sánchez
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Francisco Javier Gil-Etayo
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Jairo Eduardo Niño Ramírez
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Universidad de Salamanca (USAL), Salamanca, Spain
| | - Isabel Jiménez-Hernaz
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Amalia Tejeda Velarde
- Laboratorio de HLA-Biología Molecular, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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3
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Pagkrati I, Duke JL, Mbunwe E, Mosbruger TL, Ferriola D, Wasserman J, Dinou A, Tairis N, Damianos G, Kotsopoulou I, Papaioannou J, Giannopoulos D, Beggs W, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi AK, Fokunang C, Woldemeskel D, Belay G, Maiers M, Tishkoff SA, Monos DS. Genomic characterization of HLA class I and class II genes in ethnically diverse sub-Saharan African populations: A report on novel HLA alleles. HLA 2023; 102:192-205. [PMID: 36999238 PMCID: PMC10524506 DOI: 10.1111/tan.15035] [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: 09/14/2022] [Revised: 03/11/2023] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
HLA allelic variation has been well studied and documented in many parts of the world. However, African populations have been relatively under-represented in studies of HLA variation. We have characterized HLA variation from 489 individuals belonging to 13 ethnically diverse populations from rural communities from the African countries of Botswana, Cameroon, Ethiopia, and Tanzania, known to practice traditional subsistence lifestyles using next generation sequencing (Illumina) and long-reads from Oxford Nanopore Technologies. We identified 342 distinct alleles among the 11 HLA targeted genes: HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1, with 140 of those alleles containing novel sequences that were submitted to the IPD-IMGT/HLA database. Sixteen of the 140 alleles contained novel content within the exonic regions of the genes, while 110 alleles contained novel intronic variants. Four alleles were found to be recombinants of already described HLA alleles and 10 alleles extended the sequence content of already described alleles. All 140 alleles include complete allelic sequence from the 5' UTR to the 3' UTR that are inclusive of all exons and introns. This report characterizes the HLA allelic variation from these individuals and describes the novel allelic variation present within these specific African populations.
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Affiliation(s)
- Ioanna Pagkrati
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jamie L. Duke
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Eric Mbunwe
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy L. Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Jenna Wasserman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Amalia Dinou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Nikolaos Tairis
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Georgios Damianos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Ioanna Kotsopoulou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Joanna Papaioannou
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - Diamantoula Giannopoulos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
| | - William Beggs
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania (KIUT), Dar es Salaam, Tanzania
| | - Sununguko W. Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Gaonyadiwe G. Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Alfred K. Njamnshi
- Department of Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Department of Neurology & Neuroscience, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Dawit Woldemeskel
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Martin Maiers
- National Marrow Donor Program/Be The Match, Minneapolis, Minnesota, USA
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dimitri S. Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia,Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Digby B, Finn SP, Ó Broin P. nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs. BMC Bioinformatics 2023; 24:27. [PMID: 36694127 PMCID: PMC9875403 DOI: 10.1186/s12859-022-05125-8] [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: 07/08/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due to their stability, tissue-specific expression and role as transcriptional modulators via sequestration of miRNAs. Currently, multiple quantification tools capable of detecting circRNAs exist, yet none delineate circRNA-miRNA interactions, and only one employs differential expression analysis. Efforts have been made to bridge this gap by way of circRNA workflows, however these workflows are limited by both the types of analyses available and computational skills required to run them. RESULTS We present nf-core/circrna, a multi-functional, automated high-throughput pipeline implemented in nextflow that allows users to characterise the role of circRNAs in RNA Sequencing datasets via three analysis modules: (1) circRNA quantification, robust filtering and annotation (2) miRNA target prediction of the mature spliced sequence and (3) differential expression analysis. nf-core/circrna has been developed within the nf-core framework, ensuring robust portability across computing environments via containerisation, parallel deployment on cluster/cloud-based infrastructures, comprehensive documentation and maintenance support. CONCLUSION nf-core/circrna reduces the barrier to entry for researchers by providing an easy-to-use, platform-independent and scalable workflow for circRNA analyses. Source code, documentation and installation instructions are freely available at https://nf-co.re/circrna and https://github.com/nf-core/circrna .
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Affiliation(s)
- Barry Digby
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Dublin, Ireland
| | - Pilib Ó Broin
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
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5
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Tait BD. The importance of establishing genetic phase in clinical medicine. Int J Immunogenet 2021; 49:1-7. [PMID: 34958529 DOI: 10.1111/iji.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/27/2022]
Abstract
Haplotyping or determination of genetic phase has always played a pivotal role in MHC (HLA studies) both in helping to understand inheritance patterns in diseases such as type 1 diabetes (T1D) and in ensuring better matching in transplantation scenarios such as haematopoietic stem cell transplantation (HSCT), using donors genetically related to the patient. In recent years the need to establish genetic phase in a number of clinical scenarios has become apparent. These include: Genetic phasing for hematopoietic stem cell transplants using unrelated donors, where the HLA haplotypes are not known but where haplotype-matched recipients fare better clinically than allele matched, but haplotype mismatched patients. The use of checkpoint inhibitors is one of the most innovative and exciting developments in cancer treatment in years. An example is the use of the monoclonal ipilimumab to block the CTLA-4 receptor which is known to contain polymorphic sites. Until the phase of these polymorphisms is known it will not be possible to determine how effectively this monoclonal will perform in individual patients. The role of miRNA single strand molecules and their effect on gene expression. Thousands of non-coding genes have been identified and have been shown to be polymorphic, as have their target genes. Genetic phasing of polymorphism both in the miRNA source genes and their targets is clearly a fertile area of research In areas such a drug metabolism where the polymorphic family of CYP genes is responsible for the metabolism of the majority of prescription drugs, determining phase of SNPs is critical to understanding drug metabolism and efficacy. In multigenic disease studies combinations of single nucleotide polymorphisms (SNPs) in participating genes require accurate phasing in order to fully appreciate their role in the disease process. In addition, the level of expression of genes (point 3) is also important in understanding disease processes at the functional level. This review outlines the techniques that are currently available for approximating phase and discusses the clinical relevance of establishing genetic phase in areas of clinical medicine outlined in points 1-3.
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Affiliation(s)
- Brian D Tait
- Haplomic Technologies, Melbourne, Australia.,Department of Medicine, University of Melbourne, Royal Melbourne Hospital, Australia
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6
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Wu C, Wu Z, Wang L, Chen Y, Huang X, Wang Z, Tian B. The Modulating Mechanisms of miRNA-196 in Malignancies and Its Prognostic Value: A Systematic Review and Meta-Analysis. Nutr Cancer 2021; 74:423-436. [PMID: 34435522 DOI: 10.1080/01635581.2021.1922718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accumulating studies have revealed that up- or downregulated miRNA-196 expression correlates with the prognostic value in various malignancies; however, existing single studies lack robust evidence to elucidate the role of miRNA-196 in malignancy. The pooled results showed that the upregulation of miRNA-196 expression was significantly correlated with unfavorable OS [HR 2.14; 95% confidence interval (CI), 1.78-2.57; p < 0.001)] and worse PFS (HR 2.84; 95% CI, 1.29-6.23, P = 0.01) in various malignancies. According to the regulatory mechanisms, studies shown that multiple tumors associated with transcription processes could be modulated by the miRNA-196 family; correspondingly, the miRNA-196 family exerted biological functions that could be regulated by various molecules. The upregulation of miRNA-196a, miRNA-196b and miRNA-196 expression is correlated with significantly unfavorable OS in multiple malignancies; similarly, miRNA-196 overexpression predicts poor PFS in multiple malignancies. Taken together, these findings indicate that miRNA-196a and miRNA-196b may serve as oncogenic molecules and may be potential prognostic biomarkers in multiple malignancies.
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Affiliation(s)
- Chao Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zuowei Wu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Chen
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xing Huang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zihe Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
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7
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Padariya M, Kalathiya U, Mikac S, Dziubek K, Tovar Fernandez MC, Sroka E, Fahraeus R, Sznarkowska A. Viruses, cancer and non-self recognition. Open Biol 2021; 11:200348. [PMID: 33784856 PMCID: PMC8061760 DOI: 10.1098/rsob.200348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Virus-host interactions form an essential part of every aspect of life, and this review is aimed at looking at the balance between the host and persistent viruses with a focus on the immune system. The virus-host interaction is like a cat-and-mouse game and viruses have developed ingenious mechanisms to manipulate cellular pathways, most notably the major histocompatibility (MHC) class I pathway, to reside within infected cell while evading detection and destruction by the immune system. However, some of the signals sensing and responding to viral infection are derived from viruses and the fact that certain viruses can prevent the infection of others, highlights a more complex coexistence between the host and the viral microbiota. Viral immune evasion strategies also illustrate that processes whereby cells detect and present non-self genetic material to the immune system are interlinked with other cellular pathways. Immune evasion is a target also for cancer cells and a more detailed look at the interfaces between viral factors and components of the MHC class I peptide-loading complex indicates that these interfaces are also targets for cancer mutations. In terms of the immune checkpoint, however, viral and cancer strategies appear different.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Maria C. Tovar Fernandez
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Ewa Sroka
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
- Department of Medical Biosciences, Umeå University, Building 6M, 901 85 Umeå, Sweden
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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8
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Chitnis NS, Shieh M, Monos D. Regulatory noncoding RNAs and the major histocompatibility complex. Hum Immunol 2020; 82:532-540. [PMID: 32636038 DOI: 10.1016/j.humimm.2020.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/21/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022]
Abstract
The Major Histocompatibility Complex (MHC) is a 4 Mbp genomic region located on the short arm of chromosome 6. The MHC region contains many key immune-related genes such as Human Leukocyte Antigens (HLAs). There has been a growing realization that, apart from MHC encoded proteins, RNAs derived from noncoding regions of the MHC-specifically microRNAs (miRNAs) and long noncoding RNAs (lncRNAs)-play a significant role in cellular regulation. Furthermore, regulatory noncoding RNAs (ncRNAs) derived from other parts of the genome fine-tune the expression of many immune-related MHC proteins. Although the field of ncRNAs of the MHC is a research area that is still in its infancy, ncRNA regulation of MHC genes has already been shown to be vital for immune function, healthy pregnancy and cellular homeostasis. Dysregulation of this intricate network of ncRNAs can lead to serious perturbations in homeostasis and subsequent disease.
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Affiliation(s)
- Nilesh Sunil Chitnis
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mengkai Shieh
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Sznarkowska A, Mikac S, Pilch M. MHC Class I Regulation: The Origin Perspective. Cancers (Basel) 2020; 12:cancers12051155. [PMID: 32375397 PMCID: PMC7281430 DOI: 10.3390/cancers12051155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.
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10
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Matern BM, Olieslagers TI, Voorter CEM, Groeneweg M, Tilanus MGJ. Insights into the polymorphism in HLA-DRA and its evolutionary relationship with HLA haplotypes. HLA 2019; 95:117-127. [PMID: 31617688 DOI: 10.1111/tan.13730] [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: 07/31/2019] [Revised: 10/07/2019] [Accepted: 10/12/2019] [Indexed: 01/05/2023]
Abstract
HLA-DRA encodes the alpha chain of the HLA-DR protein, one of the classical HLA class II molecules. Reported polymorphism within HLA-DRA is currently limited compared with other HLA genes, as only a single polymorphism encodes an amino acid difference in the translated protein. Since this SNP (rs7192, HLA00662.1:g.4276G>T p.Val217Leu) lies within exon 4, in the region encoding the cytoplasmic tail, the resulting protein is effectively monomorphic. For this reason, in-depth studies on HLA-DRA and its function have been limited. However, analysis of sequences from the 1000 Genomes Project and preliminary data from our lab reveals unrepresented polymorphism within HLA-DRA, suggesting a more complex role within the MHC than previously assumed. This study focuses on elucidating the extent of HLA-DRA polymorphism, and extending our understanding of the gene's role in HLA-DR~HLA-DQ haplotypes. Ninety-eight samples were sequenced for full-length HLA-DRA, and from this analysis, we identified 20 novel SNP positions in the intronic sequences within the 5711 bp region represented in IPD-IMGT/HLA. This polymorphism gives rise to at least 22 novel HLA-DRA alleles, and the patterns of intronic and 3' UTR polymorphism correspond to HLA-DRA~HLA-DRB345~HLA-DRB1~HLA-DQB1 haplotypes. The current understanding of the organization of the genes within the HLA-DR region assumes a single lineage for the HLA-DRA gene, as opposed to multiple gene lineages, such as in HLA-DRB. This study suggests that the intron and 3' UTR polymorphism of HLA-DRA indicates different lineages, and represents the HLA-DRA~HLA-DRB345~HLA-DRB1~HLA-DQB1 haplotypes.
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Affiliation(s)
- Ben M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Timo I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
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11
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Genomic Diversity of the Major Histocompatibility Complex in Health and Disease. Cells 2019; 8:cells8101270. [PMID: 31627481 PMCID: PMC6830316 DOI: 10.3390/cells8101270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
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12
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Bennett D, Bargagli E, Refini RM, Rottoli P. New concepts in the pathogenesis of sarcoidosis. Expert Rev Respir Med 2019; 13:981-991. [DOI: 10.1080/17476348.2019.1655401] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David Bennett
- Respiratory Diseases and Lung Transplantation Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elena Bargagli
- Respiratory Diseases and Lung Transplantation Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
- Department of Medical and Surgical Sciences & Neurosciences, University of Siena, Siena, Italy
| | - Rosa Metella Refini
- Respiratory Diseases and Lung Transplantation Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
- Department of Medical and Surgical Sciences & Neurosciences, University of Siena, Siena, Italy
| | - Paola Rottoli
- Department of Medical and Surgical Sciences & Neurosciences, University of Siena, Siena, Italy
- Regional Coordinator for Rare Respiratory Diseases for Tuscany, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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13
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Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
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14
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Brennan S, Keon M, Liu B, Su Z, Saksena NK. Panoramic Visualization of Circulating MicroRNAs Across Neurodegenerative Diseases in Humans. Mol Neurobiol 2019; 56:7380-7407. [PMID: 31037649 PMCID: PMC6815273 DOI: 10.1007/s12035-019-1615-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases (NDs) such as Alzheimer’s disease (AD), Parkinson’s disease (PD), multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), and dementia pose one of the greatest health challenges this century. Although these NDs have been looked at as single entities, the underlying molecular mechanisms have never been collectively visualized to date. With the advent of high-throughput genomic and proteomic technologies, we now have the opportunity to visualize these diseases in a whole new perspective, which will provide a clear understanding of the primary and secondary events vital in achieving the final resolution of these diseases guiding us to new treatment strategies to possibly treat these diseases together. We created a knowledge base of all microRNAs known to be differentially expressed in various body fluids of ND patients. We then used several bioinformatic methods to understand the functional intersections and differences between AD, PD, ALS, and MS. These results provide a unique panoramic view of possible functional intersections between AD, PD, MS, and ALS at the level of microRNA and their cognate genes and pathways, along with the entities that unify and separate them. While the microRNA signatures were apparent for each ND, the unique observation in our study was that hsa-miR-30b-5p overlapped between all four NDS, and has significant functional roles described across NDs. Furthermore, our results also show the evidence of functional convergence of miRNAs which was associated with the regulation of their cognate genes represented in pathways that included fatty acid synthesis and metabolism, ECM receptor interactions, prion diseases, and several signaling pathways critical to neuron differentiation and survival, underpinning their relevance in NDs. Envisioning this group of NDs together has allowed us to propose new ways of utilizing circulating miRNAs as biomarkers and in visualizing diverse NDs more holistically . The critical molecular insights gained through the discovery of ND-associated miRNAs, overlapping miRNAs, and the functional convergence of microRNAs on vital pathways strongly implicated in neurodegenerative processes can prove immensely valuable in the identifying new generation of biomarkers, along with the development of miRNAs into therapeutics.
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Affiliation(s)
- Samuel Brennan
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Matthew Keon
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Bing Liu
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Zheng Su
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Nitin K. Saksena
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
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15
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Ferreira SN, Leite MDM, Silveira MSLD, Santos EFD, Silva ALSD, Santos EJMD. MicroRNA layer of MHC in infectious diseases. Hum Immunol 2019; 80:243-247. [PMID: 30769034 DOI: 10.1016/j.humimm.2019.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/17/2019] [Accepted: 02/11/2019] [Indexed: 01/02/2023]
Abstract
The Major Histocompatibility Complex (MHC) harbors key genes of the immune response that are likely useful as biomarkers for infectious diseases. However, little is known about their microRNAs and what role they play in infections. The present study aimed to describe the miRNA genes in the MHC (MHC-miRNA), their variability and associations with infectious diseases. Additionally, MHC-miRNA host and target genes were also evaluated in associations with infectious diseases. Surveys in several databases and literature reviews identified 48 MHC-miRNA genes, with high SNP and CNV variability able to disrupt MHC-miRNA expression and putatively under selective pressure. Eight MHC-miRNAs were found inside or close regions of classical MHC rearrangements (RCCX and DRB genome organization). The proportion of MHC-miRNAs associated with infections (23%) was higher than the proportion found for the 1917 hsa-miRNA (4%). Additionally, 35 MHC-miRNAs (57%) have at least one of their target genes associated with infectious diseases, while all nine MHC-miRNA whose host genes were associated with infections have also their target genes associated with infections, being host and target genes of five MHC-miRNAs reported to be associated with the same diseases. This finding may reflect a concerted miRNA-mediated immune response mechanism triggered by infection.
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Affiliation(s)
- Sâmila Natiane Ferreira
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil
| | - Mauro de Meira Leite
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil
| | | | | | | | - Eduardo José Melo Dos Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Brazil; Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Brazil.
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16
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Shieh M, Chitnis N, Clark P, Johnson FB, Kamoun M, Monos D. Computational assessment of miRNA binding to low and high expression HLA-DPB1 allelic sequences. Hum Immunol 2019; 80:53-61. [DOI: 10.1016/j.humimm.2018.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/27/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022]
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17
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Petersdorf EW, O'hUigin C. The MHC in the era of next-generation sequencing: Implications for bridging structure with function. Hum Immunol 2019; 80:67-78. [PMID: 30321633 PMCID: PMC6542361 DOI: 10.1016/j.humimm.2018.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022]
Abstract
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms. These relationships are critical for understanding the qualitative and quantitative implications of HLA gene diversity. This article summarizes current understanding of non-coding region variation of HLA loci, the consequences of regulatory variation on HLA expression, the role for evolution in shaping lineage-specific expression, and the impact of HLA expression on disease susceptibility and transplantation outcomes. A role for phased sequencing methods for the MHC, and perspectives for future directions in basic and applied immunogenetic studies of the MHC are presented.
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Affiliation(s)
- Effie W Petersdorf
- University of Washington, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-115, Seattle, WA 98109, United States.
| | - Colm O'hUigin
- Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Microbiome and Genetics Core, Building 37, Room 4140B, Bethesda, MD 20852, United States.
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19
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Kishore A, Petrek M. Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis. Front Genet 2018; 9:503. [PMID: 30410504 PMCID: PMC6210504 DOI: 10.3389/fgene.2018.00503] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/05/2018] [Indexed: 12/31/2022] Open
Abstract
Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA loci. A lack of in phase sequence information, a relative deficiency of high resolution genotyping including non-coding regions and ambiguous haplotype assignment make it difficult to compare findings across association studies and to attribute a causal role to specific HLA alleles/haplotypes in disease susceptibility and modification of disease phenotypes. Earlier, historical antibody and DNA-based methods of HLA typing, primarily of low resolution at antigen/alellic group levels, yielded "indicative" findings which were partially improved by high-resolution DNA-based typing. Only recently, next-generation sequencing (NGS) approaches based on deep-sequencing of the complete HLA genes combined with bioinformatics tools began to provide the access to complete information at an allelic level. Analyzing HLA with NGS approaches, therefore, promises to provide further insight in the etiopathogenesis of several immune disorders in which HLA associations have been implicated. These range from coeliac disease and rheumatological conditions to even more complex disorders, such as type-1 diabetes, systemic lupus erythematosus and sarcoidosis. A systemic disease of unknown etiology, sarcoidosis has previously been associated with numerous HLA variants and also other gene polymorphisms, often in linkage with the HLA region. To date, the biological significance of these associations has only partially been defined. Therefore, more precise assignments of HLA alleles/haplotypes using NGS approaches could help to elucidate the exact role of HLA variation in the multifaceted etiopathogenesis of sarcoidosis, including epigenetic mechanisms. NGS-based HLA analyses may be also relevant for defining variable clinical phenotypes and for predicting the disease course or the response to current/plausible novel therapies.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
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20
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A sarcoidosis clinician's perspective of MHC functional elements outside the antigen binding site. Hum Immunol 2018; 80:85-89. [PMID: 29859205 DOI: 10.1016/j.humimm.2018.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023]
Abstract
Sarcoidosis is a multisystem granulomatous disease of unknown cause. Evidence supports an integral role for interactions at the MHC binding site in the development of sarcoidosis. However, despite this evidence, there are clinical data that suggest that additional mechanisms are involved in the immunopathogenesis of this disease. This manuscript provides a brief clinical description of sarcoidosis, and a clinician's perspective of the immunopathogenesis of sarcoidosis in terms of the MHC binding site, MHC functional elements beyond the binding site, and other possible alternative mechanisms. Input from clinicians will be essential in establishing the immunologic cause of sarcoidosis as a detailed phenotypic characterization of disease will be required.
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