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Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA.
Moore E, Grifoni A, Weiskopf D, Schulten V, Arlehamn CSL, Angelo M, Pham J, Leary S, Sidney J, Broide D, Frazier A, Phillips E, Mallal S, Mack SJ, Sette A
(2018) Hum Immunol 79: 821-822
MeSH Terms: Adolescent, Adult, Alleles, California, Female, Gene Frequency, Genotype, Genotyping Techniques, HLA-A Antigens, HLA-B Antigens, HLA-C Antigens, HLA-DP Antigens, HLA-DQ Antigens, HLA-DR Antigens, Histocompatibility Testing, Humans, Linkage Disequilibrium, Male, Middle Aged, Sequence Analysis, DNA, T-Lymphocytes, Young Adult
Show Abstract · Added March 30, 2020
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 496 healthy adult donors from San Diego, California, to characterize allele frequencies in support of studies of T cell responses to common allergens. Deviations from Hardy Weinberg proportions were detected at each locus except A and C. Several alleles were found in more than 15% of individuals, including the class II alleles DPB1∗02:01, DPB1∗04:01, DQA1∗01:02, DQA1∗05:01, DQB1∗03:01, and the class I allele A∗02:01. Genotype data will be available in the Allele Frequencies Net Database (AFND 3562).
Copyright © 2018. Published by Elsevier Inc.
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Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 159 individuals from the Worcester region of the Western Cape province of South Africa.
Grifoni A, Sidney J, Carpenter C, Phillips E, Mallal S, Scriba TJ, Sette A, Lindestam Arlehamn CS
(2018) Hum Immunol 79: 143-144
MeSH Terms: Databases, Genetic, Gene Frequency, Genotype, HLA-A Antigens, HLA-B Antigens, HLA-C Antigens, HLA-DQ Antigens, HLA-DR Antigens, Humans, Lymphocyte Activation, Mycobacterium tuberculosis, Sequence Analysis, DNA, South Africa, T-Lymphocytes, Tuberculosis
Show Abstract · Added March 30, 2020
DNA sequence-based typing at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, and -DRB3/4/5 loci was performed on samples provided by 159 individuals from the Worcester region of the Western Cape province of South Africa. The purpose of the study was to characterize allele frequencies in the local population, to support studies of T cell immunity against pathogens, including Mycobacterium tuberculosis. There are no detectable deviations from Hardy Weinberg proportions for the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, and -DRB1 loci. A minor deviation was detected at the HLA-DQB1 locus due to an excess of homozygotes. The genotype data are available in the Allele Frequencies Net Database under identifier 3425.
Copyright © 2018. Published by Elsevier Inc.
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Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka.
Grifoni A, Weiskopf D, Lindestam Arlehamn CS, Angelo M, Leary S, Sidney J, Frazier A, Phillips E, Mallal S, Mack SJ, Tippalagama R, Goonewardana S, Premawansa S, Premawansa G, Wijewickrama A, De Silva AD, Sette A
(2018) Hum Immunol 79: 87-88
MeSH Terms: Adult, Animals, Ethnic Groups, Female, Gene Frequency, Genotype, HLA-A Antigens, HLA-B Antigens, HLA-C Antigens, HLA-DP Antigens, HLA-DQ Antigens, HLA-DR Antigens, Healthy Volunteers, Histocompatibility Testing, Humans, Male, Mice, Sequence Analysis, DNA, Sri Lanka, T-Lymphocytes
Show Abstract · Added March 30, 2020
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies on T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were not detected at any locus. Several alleles were found in >30% of individuals, including the class II alleles DPB1 * 04:01, DPB1 * 02:01, DQB1 * 06:01 and DRB1 * 07:01, and the class I alleles A * 33:03 and A * 24:02. Genotype data will be available in the Allele Frequencies Net Database.
Copyright © 2018 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
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Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua.
Weiskopf D, Grifoni A, Arlehamn CSL, Angelo M, Leary S, Sidney J, Frazier A, Mack SJ, Phillips E, Mallal S, Cerpas C, Balmaseda A, Harris E, Sette A
(2018) Hum Immunol 79: 1-2
MeSH Terms: Adult, Databases, Genetic, Dengue, Gene Frequency, Genetics, Population, Genotype, HLA-A Antigens, HLA-B Antigens, HLA-C Antigens, HLA-DP Antigens, HLA-DQ Antigens, HLA-DR Antigens, Histocompatibility Testing, Humans, Linkage Disequilibrium, Nicaragua, Sequence Analysis, DNA, T-Lymphocytes
Show Abstract · Added March 30, 2020
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on anonymized samples provided by 339 healthy adult blood bank donors in Managua, Nicaragua. The purpose of the study was to characterize allele frequencies in the local population to support studies of T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were detected for all class II loci (HLA-DPB1, -DQA1, -DQB1 and -DRB1), and at the class I C locus, but not at the class I A and B loci. The genotype data will be available in the Allele Frequencies Net Database.
Copyright © 2017 American Society for Histocompatibility and Immunogenetics. All rights reserved.
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Mass Cytometry of Follicular Lymphoma Tumors Reveals Intrinsic Heterogeneity in Proteins Including HLA-DR and a Deficit in Nonmalignant Plasmablast and Germinal Center B-Cell Populations.
Wogsland CE, Greenplate AR, Kolstad A, Myklebust JH, Irish JM, Huse K
(2017) Cytometry B Clin Cytom 92: 79-87
MeSH Terms: B-Lymphocytes, Flow Cytometry, Germinal Center, HLA-DR Antigens, Humans, Immunophenotyping, Lymphoma, B-Cell, Lymphoma, Follicular, Plasma Cells, T-Lymphocyte Subsets
Show Abstract · Added December 10, 2016
BACKGROUND - Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma that has a risk of transformation to more aggressive lymphoma. Relatively little is known about the nonmalignant B-cell and T-cell subset composition within the tumor microenvironment and whether altered phenotypes are associated with patterns of lymphoma B-cell heterogeneity.
METHODS - Two mass cytometry (CyTOF) panels were designed to immunophenotype B and T cells in FL tumors. Populations of malignant B cells, nonmalignant B cells, and T cells from each FL tumor were identified and their phenotypes compared to B and T cells from healthy human tonsillar tissue.
RESULTS - Diversity in cellular phenotype between tumors was greater for the malignant B cells than for nonmalignant B or T cells. The malignant B-cell population bore little phenotypic similarity to any healthy B-cell subset, and unexpectedly clustered closer to naïve B-cell populations than GC B-cell populations. Among the nonmalignant B cells within FL tumors, a significant lack of GC and plasmablast B cells was observed relative to tonsil controls. In contrast, nonmalignant T cells in FL tumors were present at levels similar to their cognate tonsillar T-cell subsets.
CONCLUSION - Mass cytometry revealed that diverse HLA-DR expression on FL cells within individual tumors contributed greatly to tumor heterogeneity. Both malignant and nonmalignant B cells in the tumor bore little phenotypic resemblance to healthy GC B cells despite the presence of T follicular helper cells in the tumor. These findings suggest that ongoing signaling interactions between malignant B cells and intra-tumor T cells shape the tumor microenvironment. © 2016 International Clinical Cytometry Society.
© 2016 International Clinical Cytometry Society.
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10 MeSH Terms
Single cell analysis of human tissues and solid tumors with mass cytometry.
Leelatian N, Doxie DB, Greenplate AR, Mobley BC, Lehman JM, Sinnaeve J, Kauffmann RM, Werkhaven JA, Mistry AM, Weaver KD, Thompson RC, Massion PP, Hooks MA, Kelley MC, Chambless LB, Ihrie RA, Irish JM
(2017) Cytometry B Clin Cytom 92: 68-78
MeSH Terms: Antigens, CD, Flow Cytometry, HLA-DR Antigens, Humans, Jurkat Cells, Leukocyte Common Antigens, Neoplasms, Single-Cell Analysis
Show Abstract · Added September 7, 2016
BACKGROUND - Mass cytometry measures 36 or more markers per cell and is an appealing platform for comprehensive phenotyping of cells in human tissue and tumor biopsies. While tissue disaggregation and fluorescence cytometry protocols were pioneered decades ago, it is not known whether established protocols will be effective for mass cytometry and maintain cancer and stromal cell diversity.
METHODS - Tissue preparation techniques were systematically compared for gliomas and melanomas, patient derived xenografts of small cell lung cancer, and tonsil tissue as a control. Enzymes assessed included DNase, HyQTase, TrypLE, collagenase (Col) II, Col IV, Col V, and Col XI. Fluorescence and mass cytometry were used to track cell subset abundance following different enzyme combinations and treatment times.
RESULTS - Mechanical disaggregation paired with enzymatic dissociation by Col II, Col IV, Col V, or Col XI plus DNase for 1 h produced the highest yield of viable cells per gram of tissue. Longer dissociation times led to increasing cell death and disproportionate loss of cell subsets. Key markers for establishing cell identity included CD45, CD3, CD4, CD8, CD19, CD64, HLA-DR, CD11c, CD56, CD44, GFAP, S100B, SOX2, nestin, vimentin, cytokeratin, and CD31. Mass and fluorescence cytometry identified comparable frequencies of cancer cell subsets, leukocytes, and endothelial cells in glioma (R = 0.97), and tonsil (R = 0.98).
CONCLUSIONS - This investigation establishes standard procedures for preparing viable single cell suspensions that preserve the cellular diversity of human tissue microenvironments. © 2016 International Clinical Cytometry Society.
© 2016 International Clinical Cytometry Society.
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Homozygosity of the polymorphism MICA5.1 identifies extreme risk of progression to overt adrenal insufficiency among 21-hydroxylase antibody-positive patients with type 1 diabetes.
Triolo TM, Baschal EE, Armstrong TK, Toews CS, Fain PR, Rewers MJ, Yu L, Miao D, Eisenbarth GS, Gottlieb PA, Barker JM
(2009) J Clin Endocrinol Metab 94: 4517-23
MeSH Terms: Addison Disease, Alleles, Autoantibodies, Cross-Sectional Studies, Diabetes Mellitus, Type 1, Disease Progression, Genotype, Graves Disease, HLA-DQ Antigens, HLA-DQ beta-Chains, HLA-DR Antigens, HLA-DRB1 Chains, Histocompatibility Antigens Class I, Homozygote, Humans, Interferon-alpha, Microsatellite Repeats, Polymerase Chain Reaction, Polymorphism, Genetic, Risk Factors, Steroid 21-Hydroxylase
Show Abstract · Added March 29, 2019
CONTEXT - Autoimmunity associated with Addison's disease (AD) can be detected by measuring 21-hydroxylase (21OH) autoantibodies. Subjects with type 1 diabetes (T1D) are at increased risk for AD. Genetic factors including HLA-DRB1*0404 and MICA have been associated with AD in populations with and without T1D.
OBJECTIVE - The objective of the study was to examine the effect of the MICA5.1 allele in subjects with 21OH autoantibodies on progression to AD.
DESIGN - Two components were used: 1) a cross-sectional study with subjects with AD identified and enrolled from September 1993 to November 2008 and 2) a cohort study prospectively following up patients with T1D who screened positive for 21OH autoantibodies.
SETTING - Subjects were identified from the Barbara Davis Center and through the National Adrenal Diseases Foundation.
PATIENTS - Sixty-three subjects with AD were referred through the National Adrenal Diseases Foundation (AD referrals). Sixty-three subjects with positive 21OH antibodies from the Barbara Davis Center were followed up for progression to AD, and 11 were diagnosed with AD (progressors).
RESULTS - Seventy-three percent of progressors (eight of 11) and 57% of AD referrals (36 of 63) were MICA5.1 homozygous (P = ns). Overall, 59% of patients with AD (44 of 74) were MICA5.1/5.1 compared with 17% of nonprogressors (nine of 52) (P < 0.0001) and 19% of normal DR3/4-DQB1*0302 controls (64 of 336) (P < 0.0001).
CONCLUSIONS - Identifying extreme risk should facilitate monitoring of progression from 21OH antibody positivity to overt AD. The HLA-DR3/0404 genotype defines high-risk subjects for adrenal autoimmunity. MICA5.1/5.1 may define those at highest risk for progression to overt AD, a feature unique to AD and distinct from T1D.
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Mycobacterial ESAT-6 and katG are recognized by sarcoidosis CD4+ T cells when presented by the American sarcoidosis susceptibility allele, DRB1*1101.
Oswald-Richter K, Sato H, Hajizadeh R, Shepherd BE, Sidney J, Sette A, Newman LS, Drake WP
(2010) J Clin Immunol 30: 157-66
MeSH Terms: Alleles, Amino Acid Sequence, Antigens, Bacterial, Bacterial Proteins, CD4-Positive T-Lymphocytes, Catalase, Cell Separation, Cells, Cultured, Flow Cytometry, Genetic Association Studies, Genetic Predisposition to Disease, HLA-DR Antigens, HLA-DRB1 Chains, Histocompatibility Testing, Host-Pathogen Interactions, Humans, Interferon-gamma, Latent Tuberculosis, Lymphocyte Activation, Molecular Sequence Data, Mycobacterium, Sarcoidosis, Pulmonary, United States
Show Abstract · Added May 27, 2014
INTRODUCTION - Genetic associations of American sarcoidosis susceptibility implicate MHC class II allele, DRB1*1101. We previously reported immune recognition of Mycobacterium peptides from peripheral cells of 26 sarcoidosis subjects, 24 PPD- healthy volunteers, and eight with latent tuberculosis infection.
MATERIALS AND METHODS - In order to further link these genetic and immunologic pillars of sarcoidosis pathogenesis, we performed flow cytometry on these same subjects to identify the cells responsible for immune responses to ESAT-6 and katG peptides, followed by HLA typing to determine allelic associations with recognition.
DISCUSSION AND CONCLUSION - Sarcoidosis CD4+ T cells were primarily responsible for the systemic responses. Recognition was inhibited by monoclonal antibody against HLA-DR and HLA-DQ, but not HLA-DP. Immune recognition of ESAT-6 peptide NNALQNLARTISEAG was associated with possession of DRB1*1101. ESAT-6 and katG presented by antigen-presenting cells expressing DRB1*1101-induced Th-1 responses from sarcoidosis T cells, thus providing a mechanistic insight for the association of HLA DRB1*1101 with sarcoidosis, and sarcoidosis T cell interaction with microbial antigens.
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23 MeSH Terms
Two single nucleotide polymorphisms identify the highest-risk diabetes HLA genotype: potential for rapid screening.
Barker JM, Triolo TM, Aly TA, Baschal EE, Babu SR, Kretowski A, Rewers MJ, Eisenbarth GS
(2008) Diabetes 57: 3152-5
MeSH Terms: Diabetes Mellitus, Type 1, Gene Frequency, Genotype, HLA-D Antigens, HLA-DQ Antigens, HLA-DR Antigens, Humans, Polymorphism, Single Nucleotide, Risk Factors
Show Abstract · Added March 29, 2019
OBJECTIVE - People with the HLA genotype DRB1*0301-DQA1*0501-DQB1*0201/DRB1*04-DQA1*0301-DQB1*0302 (DR3/4-DQ8) are at the highest risk of developing type 1 diabetes. We sought to find an inexpensive, rapid test to identify DR3/4-DQ8 subjects using two single nucleotide polymorphisms (SNPs).
RESEARCH DESIGN AND METHODS - SNPs rs2040410 and rs7454108 were associated with DR3-DQB1*0201 and DR4-DQB1*0302. We correlated these SNPs with HLA genotypes and with publicly available data on 5,019 subjects from the Type 1 Diabetes Genetic Consortium (T1DGC). Additionally, we analyzed these SNPs in samples from 143 HLA-typed children who participated in the Diabetes Autoimmunity Study of the Young (DAISY) using Taqman probes (rs7454108) and restriction digest analysis (rs2040410).
RESULTS - With a simple combinatorial rule, the SNPs of interest identified the presence or absence of the DR3/4-DQ8 genotype. A wide variety of genotypes were tested for both SNPs. In T1DGC samples, the two SNPs were 98.5% (1,173 of 1,191) sensitive and 99.7% (3,815 of 3,828) specific for DR3/4-DQ8. In the DAISY population, the test was 100% (69 of 69) sensitive and 100% (74 of 74) specific. Overall, the sensitivity and specificity for the test were 98.57 and 99.67%, respectively.
CONCLUSIONS - A two-SNP screening test can identify the highest risk heterozygous genotype for type 1 diabetes in a time- and cost-effective manner.
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Coordinated changes of histone modifications and HDAC mobilization regulate the induction of MHC class II genes by Trichostatin A.
Gialitakis M, Kretsovali A, Spilianakis C, Kravariti L, Mages J, Hoffmann R, Hatzopoulos AK, Papamatheakis J
(2006) Nucleic Acids Res 34: 765-72
MeSH Terms: Acetylation, Antineoplastic Agents, Cell Line, Tumor, Chromatin Immunoprecipitation, DNA-Binding Proteins, Enhancer Elements, Genetic, Enzyme Inhibitors, Gene Expression Profiling, Genes, MHC Class II, HLA-DR Antigens, HLA-DR alpha-Chains, HeLa Cells, Histone Deacetylase Inhibitors, Histones, Humans, Hydroxamic Acids, Regulatory Factor X Transcription Factors, Transcription Factors, Transcriptional Activation
Show Abstract · Added November 18, 2010
The deacetylase inhibitor Trichostatin A (TSA) induces the transcription of the Major Histocompatibility Class II (MHC II) DRA gene in a way independent of the master coactivator CIITA. To analyze the molecular mechanisms by which this epigenetic regulator stimulates MHC II expression, we used chromatin immunoprecipitation (ChIP) assays to monitor the alterations in histone modifications that correlate with DRA transcription after TSA treatment. We found that a dramatic increase in promoter linked histone acetylation is followed by an increase in Histone H3 lysine 4 methylation and a decrease of lysine 9 methylation. Fluorescence recovery after photobleaching (FRAP) experiments showed that TSA increases the mobility of HDAC while decreasing the mobility of the class II enhanceosome factor RFX5. These data, in combination with ChIP experiments, indicate that the TSA-mediated induction of DRA transcription involves HDAC relocation and enhanceosome stabilization. In order to gain a genome-wide view of the genes responding to inhibition of deacetylases, we compared the transcriptome of B cells before and after TSA treatment using Affymetrix microarrays. This analysis showed that in addition to the DRA gene, the entire MHC II family and the adjacent histone cluster that are located in chromosome 6p21-22 locus are strongly induced by TSA. A complex pattern of gene reprogramming by TSA involves immune recognition, antiviral, apoptotic and inflammatory pathways and extends the rationale for using Histone Deacetylase Inhibitors (HDACi) to modulate the immune response.
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19 MeSH Terms