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Cornaby C, Montgomery MC, Liu C, Weimer ET. Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing. Front Genet 2022; 13:901377. [PMID: 35879986 PMCID: PMC9308011 DOI: 10.3389/fgene.2022.901377] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/05/2022] [Indexed: 01/03/2023] Open
Abstract
HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression of patient HLA transcripts can provide additional benefits for many of these same patient groups. Our study cohort was evaluated using a long-read RNA sequencing methodology to provide rapid HLA genotyping results and normalized HLA transcript expression. Our assay used NGSEngine to determine the HLA genotyping result and normalized mRNA transcript expression using Athlon2. The assay demonstrated an excellent concordance rate of 99.7%. Similar to previous studies, for the class I loci, patients demonstrated significantly lower expression of HLA-C than HLA-A and -B (Mann-Whitney U, p value = 0.0065 and p value = 0.0154, respectively). In general, the expression of class II transcripts was lower than that of class I transcripts. This study demonstrates a rapid high-resolution HLA typing assay using RNA-Seq that can provide accurate HLA genotyping and HLA allele-specific transcript expression in 7-8 h, a timeline short enough to perform the assay for deceased donors.
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Affiliation(s)
- Caleb Cornaby
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Maureen C Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Eric T Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States.,Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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2
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Park JM, Jun MS, Kim JA, Mali NM, Hsi TC, Cho A, Kim JC, Kim JY, Seo I, Kim J, Kim M, Oh JW. Restoration of Immune Privilege in Human Dermal Papillae Controlling Epithelial-Mesenchymal Interactions in Hair Formation. Tissue Eng Regen Med 2021; 19:105-116. [PMID: 34626334 DOI: 10.1007/s13770-021-00392-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/02/2021] [Accepted: 08/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hair follicles are among a handful of organs that exhibit immune privilege. Dysfunction of the hair follicle immune system underlies the development of inflammatory diseases, such as alopecia areata. METHODS Quantitative reverse transcription PCR and immunostaining was used to confirm the expression of major histocompatibility complex class I in human dermal papilla cells. Through transcriptomic analyses of human keratinocyte stem cells, major histocompatibility complex class I was identified as differentially expressed genes. Organ culture and patch assay were performed to assess the ability of WNT3a conditioned media to rescue immune privilege. Lastly, CD8+ T cells were detected near the hair bulb in alopecia areata patients through immunohistochemistry. RESULTS Inflammatory factors such as tumor necrosis factor alpha and interferon gamma were verified to induce the expression of major histocompatibility complex class I proteins in dermal papilla cells. Additionally, loss of immune privilege of hair follicles was rescued following treatment with conditioned media from outer root sheath cells. Transcriptomic analyses found 58 up-regulated genes and 183 down-regulated genes related in MHC class I+ cells. Using newborn hair patch assay, we demonstrated that WNT3a conditioned media with epidermal growth factor can restore hair growth. In alopecia areata patients, CD8+ T cells were increased during the transition from mid-anagen to late catagen. CONCLUSION Identification of mechanisms governing epithelial and mesenchymal interactions of the hair follicle facilitates an improved understanding of the regulation of hair follicle immune privilege.
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Affiliation(s)
- Jung Min Park
- Department of Anatomy, Kyungpook National University School of Medicine, Daegu, Korea.,Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Korea.,Department of Microbiology, Kyungpook National University School of Medicine, Daegu, Korea.,Immune Square Inc., Daegu, Korea
| | - Mee Sook Jun
- Department of Anatomy, Kyungpook National University School of Medicine, Daegu, Korea.,Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Korea
| | - Jung-A Kim
- Department of Immunology, Kyungpook National University School of Medicine, Daegu, Korea.,Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea
| | - Nanda Maya Mali
- Department of Anatomy, Kyungpook National University School of Medicine, Daegu, Korea.,Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Korea
| | - Tsai-Ching Hsi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Areum Cho
- Department of Anatomy, Kyungpook National University School of Medicine, Daegu, Korea
| | - Jung Chul Kim
- Department of Immunology, Kyungpook National University School of Medicine, Daegu, Korea.,Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea
| | - Jun Young Kim
- Department of Dermatology, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Incheol Seo
- Department of Microbiology, Dongguk University College of Medicine, Gyeongju, Korea
| | - Jungmin Kim
- Department of Microbiology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Moonkyu Kim
- Department of Immunology, Kyungpook National University School of Medicine, Daegu, Korea. .,Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea.
| | - Ji Won Oh
- Department of Anatomy, Kyungpook National University School of Medicine, Daegu, Korea. .,Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Korea. .,Immune Square Inc., Daegu, Korea. .,Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Korea.
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3
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Gerritsen KEH, Olieslagers TI, Groeneweg M, Voorter CEM, Tilanus MGJ. An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences. ACTA ACUST UNITED AC 2014; 84:450-8. [DOI: 10.1111/tan.12436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 11/27/2022]
Affiliation(s)
- K. E. H. Gerritsen
- Department of Transplantation Immunology; Tissue Typing Laboratory, Maastricht University Medical Centre; Maastricht The Netherlands
| | - T. I. Olieslagers
- Department of Transplantation Immunology; Tissue Typing Laboratory, Maastricht University Medical Centre; Maastricht The Netherlands
| | - M. Groeneweg
- Department of Transplantation Immunology; Tissue Typing Laboratory, Maastricht University Medical Centre; Maastricht The Netherlands
| | - C. E. M. Voorter
- Department of Transplantation Immunology; Tissue Typing Laboratory, Maastricht University Medical Centre; Maastricht The Netherlands
| | - M. G. J. Tilanus
- Department of Transplantation Immunology; Tissue Typing Laboratory, Maastricht University Medical Centre; Maastricht The Netherlands
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4
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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5
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Unbiased identification of target antigens of CD8+ T cells with combinatorial libraries coding for short peptides. Nat Med 2012; 18:824-8. [PMID: 22484809 DOI: 10.1038/nm.2720] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/03/2011] [Indexed: 12/13/2022]
Abstract
Cytotoxic CD8(+) T cells recognize the antigenic peptides presented by class I major histocompatibility complex (MHC) molecules. These T cells have key roles in infectious diseases, autoimmunity and tumor immunology, but there is currently no unbiased method for the reliable identification of their target antigens. This is because of the low affinities of antigen-specific T cell receptors (TCR) to their target MHC-peptide complexes, the polyspecificity of these TCRs and the requirement that these TCRs recognize protein antigens that have been processed by antigen-presenting cells (APCs). Here we describe a technology for the unbiased identification of the antigenic peptides presented by MHC class I molecules. The technology uses plasmid-encoded combinatorial peptide libraries and a single-cell detection system. We validated this approach using a well-characterized influenza-virus–specific TCR, MHC and peptide combination. Single APCs carrying antigenic peptides can be detected among several million APCs that carry irrelevant peptides. The identified peptide sequences showed a converging pattern of mimotopes that revealed the parent influenza antigen. This technique should be generally applicable to the identification of disease-relevant T cell antigens.
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6
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Alcaide M, Rodríguez A, Negro JJ. Sampling strategies for accurate computational inferences of gametic phase across highly polymorphic major histocompatibility complex loci. BMC Res Notes 2011; 4:151. [PMID: 21615903 PMCID: PMC3126723 DOI: 10.1186/1756-0500-4-151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 05/26/2011] [Indexed: 11/22/2022] Open
Abstract
Background Genes of the Major Histocompatibility Complex (MHC) are very popular genetic markers among evolutionary biologists because of their potential role in pathogen confrontation and sexual selection. However, MHC genotyping still remains challenging and time-consuming in spite of substantial methodological advances. Although computational haplotype inference has brought into focus interesting alternatives, high heterozygosity, extensive genetic variation and population admixture are known to cause inaccuracies. We have investigated the role of sample size, genetic polymorphism and genetic structuring on the performance of the popular Bayesian PHASE algorithm. To cover this aim, we took advantage of a large database of known genotypes (using traditional laboratory-based techniques) at single MHC class I (N = 56 individuals and 50 alleles) and MHC class II B (N = 103 individuals and 62 alleles) loci in the lesser kestrel Falco naumanni. Findings Analyses carried out over real MHC genotypes showed that the accuracy of gametic phase reconstruction improved with sample size as a result of the reduction in the allele to individual ratio. We then simulated different data sets introducing variations in this parameter to define an optimal ratio. Conclusions Our results demonstrate a critical influence of the allele to individual ratio on PHASE performance. We found that a minimum allele to individual ratio (1:2) yielded 100% accuracy for both MHC loci. Sampling effort is therefore a crucial step to obtain reliable MHC haplotype reconstructions and must be accomplished accordingly to the degree of MHC polymorphism. We expect our findings provide a foothold into the design of straightforward and cost-effective genotyping strategies of those MHC loci from which locus-specific primers are available.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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7
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Canal D, Alcaide M, Anmarkrud JA, Potti J. Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca. BMC Res Notes 2010; 3:236. [PMID: 20815923 PMCID: PMC2944132 DOI: 10.1186/1756-0500-3-236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/05/2010] [Indexed: 11/13/2022] Open
Abstract
Background Major Histocompatibility Complex (MHC) has drawn the attention of evolutionary biologists due to its importance in crucial biological processes, such as sexual selection and immune response in jawed vertebrates. However, the characterization of classical MHC genes subjected to the effects of natural selection still remains elusive in many vertebrate groups. Here, we have tested the suitability of flanking intron sequences to guide the selective exploration of classical MHC genes driving the co-evolutionary dynamics between pathogens and their passerine (Aves, Order Passeriformes) hosts. Findings Intronic sequences flanking the usually polymorphic exon 2 were isolated from different species using primers sitting on conserved coding regions of MHC class II genes (β chain). Taking the pied flycatcher Ficedula hypoleuca as an example, we demonstrate that careful primer design can evade non-classical MHC gene and pseudogene amplification. At least four polymorphic and expressed loci were co-replicated using a single pair of primers in five non-related individuals (N = 28 alleles). The cross-amplification and preliminary inspection of similar MHC fragments in eight unrelated songbird taxa suggests that similar approaches can also be applied to other species. Conclusions Intron sequences flanking the usually polymorphic exon 2 may assist the specific investigation of classical MHC class II B genes in species characterized by extensive gene duplication and pseudogenization. Importantly, the evasion of non-classical MHC genes with a more specific function and non-functional pseudogenes may accelerate data collection and diminish lab costs. Comprehensive knowledge of gene structure, polymorphism and expression profiles may be useful not only for the selective examination of evolutionarily relevant genes but also to restrict chimera formation by minimizing the number of co-amplifying loci.
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Affiliation(s)
- David Canal
- Estación Biológica de Doñana - CSIC, Department of Evolutionary Ecology, Av, Américo Vespucio s/n, 41092 Seville, Spain.
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8
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Niens M, Jarrett RF, Hepkema B, Nolte IM, Diepstra A, Platteel M, Kouprie N, Delury CP, Gallagher A, Visser L, Poppema S, te Meerman GJ, van den Berg A. HLA-A*02 is associated with a reduced risk and HLA-A*01 with an increased risk of developing EBV+ Hodgkin lymphoma. Blood 2007; 110:3310-5. [PMID: 17630352 DOI: 10.1182/blood-2007-05-086934] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies showed that the HLA class I region is associated with Epstein-Barr virus (EBV)-positive Hodgkin lymphoma (HL) and that HLA-A is the most likely candidate gene in this region. This suggests that antigenic presentation of EBV-derived peptides in the context of HLA-A is involved in the pathogenesis of EBV+ HL by precluding efficient immune responses. We genotyped exons 2 and 3, encoding the peptide-binding groove of HLA-A, for 32 single nucleotide polymorphisms in 70 patients with EBV+ HL, 31 patients with EBV- HL, and 59 control participants. HLA-A*01 was significantly overrepresented and HLA-A*02 was significantly underrepresented in patients with EBV+ HL versus controls and patients with EBV- HL. In addition, HLA-A*02 status was determined by immunohistochemistry or HLA-A*02-specific polymerase chain reaction (PCR) on 152 patients with EBV+ HL and 322 patients with EBV- HL. The percentage of HLA-A*02+ patients in the EBV+ HL group (35.5%) was significantly lower than in 6107 general control participants (53.0%) and the EBV- HL group (50.9%). Our results indicate that individuals carrying the HLA-A*02 allele have a reduced risk of developing EBV+ HL, while individuals carrying the HLA-A*01 allele have an increased risk. It is known that HLA-A*02 can present EBV-derived peptides and can evoke an effective immune response, which may explain the protective phenotype.
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Affiliation(s)
- Marijke Niens
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
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9
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Wahl A, Weidanz J, Hildebrand W. Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells. Expert Rev Proteomics 2007; 3:641-52. [PMID: 17181478 DOI: 10.1586/14789450.3.6.641] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Class I human leukocyte antigen molecules are nature's proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.
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Affiliation(s)
- Angela Wahl
- University of Oklahoma, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 NE, 10 Street, BRC Room 317, Oklahoma City, OK 73104, USA.
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10
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Huang J, Khong HT, Dudley ME, El-Gamil M, Li YF, Rosenberg SA, Robbins PF. Survival, persistence, and progressive differentiation of adoptively transferred tumor-reactive T cells associated with tumor regression. J Immunother 2005; 28:258-67. [PMID: 15838383 PMCID: PMC2174599 DOI: 10.1097/01.cji.0000158855.92792.7a] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objective clinical responses have been observed in approximately 50% of patients who received non-myeloablative chemotherapy prior to the adoptive transfer of autologous melanoma-reactive tumor-infiltrating lymphocytes (TILs). Recent studies carried out through the use of antibodies directed against T-cell-receptor beta chain variable region (TRBV) products, as well as by direct sequencing of the expressed TRBV gene products, indicated that clinical responses in this trial were associated with the level of persistence of adoptively transferred T cells. In an attempt to further characterize T cells that persist in vivo following adoptive transfer, five dominant T-cell clonotypes were identified in TIL 2035, an adoptively transferred TIL that was associated with the complete regression of multiple metastases. The most highly persistent clonotype, which expressed the BV1 TR gene product, recognized the MAGE-6 cancer/testis antigen in the context of HLA-A23. This clonotype was detected in peripheral blood for over 16 months following adoptive transfer, expressed relatively higher levels of the co-stimulatory markers CD28 and CD27, and possessed telomeres that were long relative to other clonotypes present in TIL 2035 that showed only short-term persistence. The long-term persistent BV1 clonotype appeared to differentiate more slowly toward an end-stage effector in vivo than short-term persistent clonotypes, as manifested by the downregulation of CD28, CD27, and CD45RO and upregulation of CD57 and CD45RA expression on these T cells. These results indicated that the differentiation stage and replicative history of individual TIL clonotypes might be associated with their ability to survive and to persist in vivo, and progressive differentiation of the persistent clonotypes occurred following adoptive transfer.
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MESH Headings
- Adult
- Antigens, CD/analysis
- Antigens, CD/genetics
- Antigens, Neoplasm
- Cell Differentiation
- Humans
- Immunotherapy, Adoptive
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/transplantation
- Male
- Melanoma/immunology
- Melanoma/therapy
- Neoplasm Proteins/immunology
- Phenotype
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
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Affiliation(s)
- Jianping Huang
- Surgery Branch, National Cancer Institute, National Institute of Health, Bethesda, Maryland 20892, USA
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Reinders J, Rozemuller EH, Otten HG, Houben AJS, Dormoy A, Mulder A, van den Tweel JG, Petersen EJ, Tilanus MGJ. Identification of HLA-A*0111N: a synonymous substitution, introducing an alternative splice site in exon 3, silenced the expression of an HLA-A allele. Hum Immunol 2005; 66:912-20. [PMID: 16216676 DOI: 10.1016/j.humimm.2005.06.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Indexed: 10/25/2022]
Abstract
A new variant of the HLA-A*010101 allele designated as HLA-A*0111N, previously known as HLA-A*010101var, was identified in a patient requiring a stem-cell transplantation. The patient was typed by serologic methods as HLA-A2 homozygous and by sequence-based typing (SBT) as A*010101,020601. Flow-cytometric (FCM) analysis with 11 human monoclonal antibodies (mAbs) for the A1 molecule confirmed lack of any cell membrane expression of the A*0111N allele. One-dimensional isoelectric focusing (1D-IEF) of total cell lysate from the patient's cells revealed no cell surface and cytoplasmic A1 protein expression, whereas the HLA-A2 molecule was identified by both FCM analysis and 1D-IEF. DNA sequence analysis showed the presence of a synonymous substitution from G to T at position 597 in codon 175. RNA SBT revealed a deletion of 24 bp in exon 3, position 596 through 619, encoding codons 175 through 182 of the HLA-A*0111N allele. The synonymous substitution introduced a new splice site, resulting in an efficient splicing, because no classical A1 protein could be detected in the patient. This alternative splicing prevented the translation into a correct and stable class I molecule expression on the cell surface.
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Affiliation(s)
- Judith Reinders
- Department of Pathology, University Medical Centre Utrecht (UMC-U), Utrecht, The Netherlands
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12
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Huang J, El-Gamil M, Dudley ME, Li YF, Rosenberg SA, Robbins PF. T cells associated with tumor regression recognize frameshifted products of the CDKN2A tumor suppressor gene locus and a mutated HLA class I gene product. THE JOURNAL OF IMMUNOLOGY 2004; 172:6057-64. [PMID: 15128789 PMCID: PMC2305724 DOI: 10.4049/jimmunol.172.10.6057] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dramatic tumor regression observed following adoptive T cell transfer in some patients has led to attempts to identify novel Ags to understand the nature of these responses. Nearly complete regression of multiple metastatic melanoma lesions was observed in patient 1913 following adoptive transfer of autologous tumor-infiltrating lymphocytes. The autologous 1913 melanoma cell line expressed a mutated HLA-A11 class I gene product that was recognized by the bulk tumor-infiltrating lymphocytes as well as a dominant T cell clone derived from this line. A second dominant T cell clone, T1D1, did not recognize the mutated HLA-A11 product, but recognized an allogeneic melanoma cell line that shared expression of HLA-A11 with the parental tumor cell line. Screening of an autologous melanoma cDNA library with clone T1D1 T cells in a cell line expressing the mutated HLA-A11 gene product resulted in the isolation of a p14ARF transcript containing a 2-bp deletion in exon 2. The T cell epitope recognized by T1D1, which was encoded within the frameshifted region of the deleted p14ARF transcript, was also generated from frameshifted p14ARF or p16INK4a transcripts that were isolated from two additional melanoma cell lines. The results of monitoring studies indicated that T cell clones reactive with the mutated HLA-A11 gene product and the mutated p14ARF product were highly represented in the peripheral blood of patient 1913 1 wk following adoptive transfer, indicating that they may have played a role in the nearly complete tumor regression that was observed following this treatment.
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MESH Headings
- Adult
- Amino Acid Sequence
- Base Sequence
- Cell Line, Tumor
- Clone Cells
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Cyclin-Dependent Kinase Inhibitor p16/immunology
- Cyclin-Dependent Kinase Inhibitor p16/metabolism
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/isolation & purification
- Female
- Frameshift Mutation/immunology
- Genetic Markers
- HLA-A Antigens/genetics
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- HLA-A11 Antigen
- Humans
- Immunotherapy, Adoptive
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/transplantation
- Melanoma, Experimental/immunology
- Melanoma, Experimental/secondary
- Melanoma, Experimental/therapy
- Molecular Sequence Data
- Open Reading Frames/immunology
- Remission Induction
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/transplantation
- Tumor Suppressor Protein p14ARF/genetics
- Tumor Suppressor Protein p14ARF/isolation & purification
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Affiliation(s)
| | | | | | | | | | - Paul F. Robbins
- Address correspondence and reprint requests to Dr. Paul F. Robbins, Surgery Branch, National Cancer Institute, National Institutes of Health, Building 10, Room 2B42, Bethesda, MD 20892-1502. E-mail address:
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