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Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. CCAAT Promoter element regulates transgenerational expression of the MHC class I gene. Chromosoma 2024:10.1007/s00412-024-00820-2. [PMID: 38922437 DOI: 10.1007/s00412-024-00820-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Transgenerational gene expression depends on both underlying DNA sequences and epigenetic modifications. The latter, which can result in transmission of variegated gene expression patterns across multiple generations without DNA alterations, has been termed epigenetic inheritance and has been documented in plants, worms, flies and mammals. Whereas transcription factors binding to cognate DNA sequence elements regulate gene expression, the molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. Here we report that mutation of the CCAAT box promoter element abrogates NF-Y binding and disrupts the stable transgenerational expression of an MHC class I transgene. Transgenic mice with a mutated CCAAT box in the MHC class I transgene display variegated expression of the transgene among littermates and progeny in multiple independently derived transgenic lines. After 4 generations, CCAAT mutant transgenic lines derived from a single founder stably displayed distinct patterns of expression. Histone modifications and RNA polymerase II binding correlate with expression of CCAAT mutant transgenic lines, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box also results in changes to CTCF binding and DNA looping patterns across the transgene that correlate with expression status. These studies identify the CCAAT promoter element as a regulator of stable transgenerational gene expression such that mutation of the CCAAT box results in variegated transgenerational inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study provides insights into how fidelity of gene expression patterns is maintained through multiple generations.
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Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Aparna Kotekar
- NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI), National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | | | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA.
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Hobson BD, Stanley AT, De Los Santos MB, Culbertson B, Mosharov EV, Sims PA, Sulzer D. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain Behav Immun 2023; 111:277-291. [PMID: 37100211 PMCID: PMC10460506 DOI: 10.1016/j.bbi.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023] Open
Abstract
Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it has been unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We found that IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were similar in neurons and glia, but with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, which were the only cells to undergo cellular proliferation and express MHC classII (MHC-II) and associated genes. To determine if neurons respond directly via cell-autonomous IFN-γ receptor (IFNGR) signaling, we produced mutant mice with a deletion of the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, which resulted in a complete loss of dopaminergic neuronal responses to IFN-γ. Our results demonstrate that IFN-γ induces neuronal IFNGR signaling and upregulation of MHC-I and related genes in vivo, although the expression level is low compared to oligodendrocytes, astrocytes, and microglia.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Adrien T Stanley
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Mark B De Los Santos
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Bruce Culbertson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, United States; Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
| | - David Sulzer
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, United States; Department of Pharmacology, Columbia University Irving Medical Center, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States.
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Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. Transgenerational Epigenetic Inheritance of MHC Class I Gene Expression is Regulated by the CCAAT Promoter Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536772. [PMID: 37333336 PMCID: PMC10274869 DOI: 10.1101/2023.04.13.536772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Transgenerational epigenetic inheritance is defined as the transmission of traits or gene expression patterns across multiple generations that do not derive from DNA alterations. The effect of multiple stress factors or metabolic changes resulting in such inheritance have been documented in plants, worms and flies and mammals. The molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. In this study, we show that mutation of a promoter element, the CCAAT box, disrupts stable expression of an MHC Class I transgene, resulting in variegated expression among progeny for at least 4 generations in multiple independently derived transgenic lines. Histone modifications and RNA polII binding correlate with expression, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box abrogates NF-Y binding and results in changes to CTCF binding and DNA looping patterns across the gene that correlate with expression status from one generation to the next. These studies identify the CCAAT promoter element as a regulator of stable transgenerational epigenetic inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study could provide important insights into how fidelity of gene expression patterns is maintained through multiple generations.
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Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Aparna Kotekar
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Zohar Barbash
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
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Sonon P, Collares CVA, Ferreira MLB, Almeida RS, Sadissou I, Cordeiro MT, de Fátima Militão de Albuquerque M, Castelli EC, Lucena-Silva N, Donadi EA. Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians. INFECTION GENETICS AND EVOLUTION 2021; 92:104855. [PMID: 33839310 DOI: 10.1016/j.meegid.2021.104855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections. METHODS We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complications in the Brazilian State of Pernambuco. In parallel, healthy blood donors from the same area were also studied. Plink and R software were used for genetic association study. To limit the false-positive results and enhance the reliability of the results, we adopted P-values <0.01 as significant levels. RESULTS Compared to controls, the HLA-F alleles: -1610 C (rs17875375), +1383 G (rs17178385), and +3537 A (rs17875384), all in complete linkage disequilibrium with each other (r2 = 1), were overrepresented in patients presenting peripheral spectrum disorders (PSD). The HLA-F*Distal-D haplotype that harbored the -1610 C allele exhibited a trend increase in PSD group. No associations were found for HLA-E. CONCLUSIONS Our findings showed that the HLA-F genetic background seems to be more important than HLA-E on the susceptibility to PSD complications.
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Affiliation(s)
- Paulin Sonon
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil; Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Cristhianna V A Collares
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Maria Lúcia Brito Ferreira
- Hospital da Restauração Gov. Paulo Guerra, Av. Gov. Agamenon Magalhães, s/n, Derby, 52171011 Recife, PE, Brazil
| | - Renata Santos Almeida
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Ibrahim Sadissou
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Marli Tenório Cordeiro
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Maria de Fátima Militão de Albuquerque
- Public Health Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Erick C Castelli
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Prof. Dr. Walter Maurício Correa, s/n Unesp, Campus de Botucatu, Botucatu CEP 18618681, SP, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, Brazil
| | - Norma Lucena-Silva
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Eduardo A Donadi
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil.
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Sonon P, Tokplonou L, Sadissou I, M'po KKG, Glitho SSC, Agniwo P, Ibikounlé M, Souza AS, Massaro JD, Gonzalez D, Tchégninougbo T, Ayitchédji A, Massougbodji A, Moreau P, Garcia A, Milet J, Sabbagh A, Mendes-Junior CT, Moutairou KA, Castelli EC, Courtin D, Donadi EA. Human leukocyte antigen (HLA)-F and -G gene polymorphisms and haplotypes are associated with malaria susceptibility in the Beninese Toffin children. INFECTION GENETICS AND EVOLUTION 2021; 92:104828. [PMID: 33781967 DOI: 10.1016/j.meegid.2021.104828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Little attention has been devoted to the role of the immunoregulatory HLA-E/-F/-G genes in malaria. We evaluated the entire HLA-E/-F/-G variability in Beninese children highly exposed to Plasmodium falciparum (P.f.) malaria. METHODS 154 unrelated children were followed-up for six months and evaluated for the presence and number of malaria episodes. HLA-E/-F/-G genes were genotyped using massively parallel sequencing. Anti P.f. antibodies were evaluated using ELISA. RESULTS Children carrying the G allele at HLA-F (-1499,rs183540921) showed increased P.f. asymptomatic/symptomatic ratio, suggesting that these children experienced more asymptomatic P.f. episodes than symptomatic one. Children carrying HLA-G-UTR-03 haplotype exhibited increased risk for symptomatic P.f. episodes and showed lower IgG2 response against P.f. GLURP-R2 when compared to the non-carriers. No associations were observed for the HLA-E gene. CONCLUSION HLA-F associations may be related to the differential expression profiles of the encoded immunomodulatory molecules, and the regulatory sites at the HLA-G 3'UTR may be associated to posttranscriptional regulation of HLA-G and to host humoral response against P.f.
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Affiliation(s)
- Paulin Sonon
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil; Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Léonidas Tokplonou
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Ibrahim Sadissou
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil; Intertryp, IRD, Cirad, University of Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Kuumaaté K G M'po
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sonya S C Glitho
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Privat Agniwo
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Andréia S Souza
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Av. Prof. Dr. Walter Maurício Correa, s/n, 1861868, Botucatu, SP, Brazil
| | - Juliana Doblas Massaro
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil
| | - Daniel Gonzalez
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | | | | | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin
| | - Philippe Moreau
- CEA, DRF-Institut François Jacob, Service de Recherches en Hémato-Immunologie, Hopital Saint-Louis, 75010 Paris, France; Université de Paris, CEA, U976 HIPI Unit (Human Immunology, Physiopathology, Immunotherapy), Institut de Recherche Saint-Louis, 75010 Paris, France
| | - André Garcia
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | | | - Audrey Sabbagh
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, AV Bandeirantes, 3900, 14040901 Ribeirão Preto, SP, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Erick C Castelli
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Av. Prof. Dr. Walter Maurício Correa, s/n, 1861868, Botucatu, SP, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, SP, Brazil
| | - David Courtin
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Eduardo A Donadi
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil.
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Buttura RV, Ramalho J, Lima TH, Donadi EA, Veiga-Castelli LC, Mendes-Junior CT, Castelli EC. HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels. Hum Immunol 2019; 80:112-119. [DOI: 10.1016/j.humimm.2018.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/10/2018] [Accepted: 10/26/2018] [Indexed: 12/30/2022]
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Human leukocyte antigen (HLA-F) polymorphism is associated with chronic HBV infection. 3 Biotech 2018; 8:49. [PMID: 29354360 DOI: 10.1007/s13205-017-1079-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 12/28/2017] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA)-F has been involved in immune regulation of infectious diseases. However, the role of HLA-F polymorphisms in hepatitis B infection outcomes remains unclear. Here, we aimed to determine HLA-F polymorphism implication in chronic HBV. Genotype analysis was performed for three single nucleotide polymorphisms (SNPs) of HLA-F and one SNP of HLA-E using PCR-SSP, in 252 Tunisian patients with chronic HBV infection stratified according to their HBV DNA levels (140 patients with low HBV DNA levels < 2000 IU/mL and 112 patients with high HBV DNA levels ≥ 2000 IU/mL) and 240 healthy controls (CTRL). The three HLA-F SNPs (HLA-F*01:02, -F*01:03 and -F*01:04) have the same allelic and genotypic frequencies in patients and in CTRL. We reported a low HLA-F*01:02 and F*01:04 allelic frequencies in the Tunisian population; however, high HLA-F*01:03 allele frequencies were observed (17%). A significant association was found between the HLA-F*01:03 allele and decreased level of HBV DNA (P = 0.02 OR 0.56, 95% CI 0.35-0.92). No significant differences were observed in haplotype distribution between patients and CTRL. A significant association of HLA-F*01:03 with the level of HBV DNA suggests an important role of HLA-F in HBV replication control.
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Ramalho J, Veiga-Castelli LC, Donadi EA, Mendes-Junior CT, Castelli EC. HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample. Mol Immunol 2017; 91:173-184. [PMID: 28946074 DOI: 10.1016/j.molimm.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 12/30/2022]
Abstract
The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by far the most variable segment. Further analyses involving the binding of transcription factors and non-coding RNAs, as well as the HLA-E expression in different tissues, are necessary to evaluate whether these variable sites at regulatory segments (or even at the coding sequence) may influence the gene expression profile.
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Affiliation(s)
- Jaqueline Ramalho
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, State of São Paulo, Brazil
| | - Eduardo A Donadi
- School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, State of São Paulo, Brazil
| | - Celso T Mendes-Junior
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Erick C Castelli
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil.
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Chelbi S, Dang A, Guarda G. Emerging Major Histocompatibility Complex Class I-Related Functions of NLRC5. Adv Immunol 2017; 133:89-119. [DOI: 10.1016/bs.ai.2016.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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10
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Abstract
CD40 ligand (CD40L, also known as CD154 or gp39) is a member of the tumor necrosis superfamily of transmembrane proteins. The interaction of CD40L on activated T cells with its receptor, CD40 on B cells, is necessary for normal immune function, including B cell differentiation, germinal center formation, and antibody isotype switching. Abnormal expressionof CD40L in patients with systemic lupus erythematosus (SLE) may contribute to autoantibody production and disease pathogenesis. Although murine models of monoclonal antibodies directed against CD40L initially showed promise, human trials either have failed to demonstrate efficacy or have been associated with adverse events. This review will summarize in vitro and murine model data and human clinical trials involving anti-CD40L monoclonal antibody.
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Affiliation(s)
- J Yazdany
- Division of Rheumatology, University of California San Francisco, San Francisco, USA
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Lv D, Shen Y, Peng Y, Liu J, Miao F, Zhang J. Neuronal MHC Class I Expression Is Regulated by Activity Driven Calcium Signaling. PLoS One 2015; 10:e0135223. [PMID: 26263390 PMCID: PMC4532511 DOI: 10.1371/journal.pone.0135223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/20/2015] [Indexed: 01/25/2023] Open
Abstract
MHC class I (MHC-I) molecules are important components of the immune system. Recently MHC-I have been reported to also play important roles in brain development and synaptic plasticity. In this study, we examine the molecular mechanism(s) underlying activity-dependent MHC-I expression using hippocampal neurons. Here we report that neuronal expression level of MHC-I is dynamically regulated during hippocampal development after birth in vivo. Kainic acid (KA) treatment significantly increases the expression of MHC-I in cultured hippocampal neurons in vitro, suggesting that MHC-I expression is regulated by neuronal activity. In addition, KA stimulation decreased the expression of pre- and post-synaptic proteins. This down-regulation is prevented by addition of an MHC-I antibody to KA treated neurons. Further studies demonstrate that calcium-dependent protein kinase C (PKC) is important in relaying KA simulation activation signals to up-regulated MHC-I expression. This signaling cascade relies on activation of the MAPK pathway, which leads to increased phosphorylation of CREB and NF-κB p65 while also enhancing the expression of IRF-1. Together, these results suggest that expression of MHC-I in hippocampal neurons is driven by Ca2+ regulated activation of the MAPK signaling transduction cascade.
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Affiliation(s)
- Dan Lv
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
| | - Yuqing Shen
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
| | - Yaqin Peng
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
| | - Jiane Liu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
| | - Fengqin Miao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, Jiangsu Province, China
- * E-mail:
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12
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Chen L, Reyes-Vargas E, Dai H, Escobar H, Rudd B, Fairbanks J, Ho A, Cusick MF, Kumánovics A, Delgado J, He X, Jensen PE. Expression of the mouse MHC class Ib H2-T11 gene product, a paralog of H2-T23 (Qa-1) with shared peptide-binding specificity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:1427-39. [PMID: 24958902 PMCID: PMC4211609 DOI: 10.4049/jimmunol.1302048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mouse MHC class Ib gene H2-T11 is 95% identical at the DNA level to H2-T23, which encodes Qa-1, one of the most studied MHC class Ib molecules. H2-T11 mRNA was observed to be expressed widely in tissues of C57BL/6 mice, with the highest levels in thymus. To circumvent the availability of a specific mAb, cells were transduced with cDNA encoding T11 with a substituted α3 domain. Hybrid T11D3 protein was expressed at high levels similar to control T23D3 molecules on the surface of both TAP(+) and TAP(-) cells. Soluble T11D3 was generated by folding in vitro with Qa-1 determinant modifier, the dominant peptide presented by Qa-1. The circular dichroism spectrum of this protein was similar to that of other MHC class I molecules, and it was observed to bind labeled Qa-1 determinant modifier peptide with rapid kinetics. By contrast to the Qa-1 control, T11 tetramers did not react with cells expressing CD94/NKG2A, supporting the conclusion that T11 cannot replace Qa-1 as a ligand for NK cell inhibitory receptors. T11 also failed to substitute for Qa-1 in the presentation of insulin to a Qa-1-restricted T cell hybridoma. Despite divergent function, T11 was observed to share peptide-loading specificity with Qa-1. Direct analysis by tandem mass spectrometry of peptides eluted from T11D3 and T23D3 isolated from Hela cells demonstrated a diversity of peptides with a clear motif that was shared between the two molecules. Thus, T11 is a paralog of T23 encoding an MHC class Ib molecule that shares peptide-binding specificity with Qa-1 but differs in function.
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Affiliation(s)
- Lili Chen
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | | | - Hu Dai
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | | | - Brant Rudd
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Jared Fairbanks
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Alexander Ho
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Mathew F Cusick
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Attila Kumánovics
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
| | - Julio Delgado
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
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13
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Tuncel J, Haag S, Yau ACY, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R. Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat. PLoS Genet 2014; 10:e1004151. [PMID: 24586191 PMCID: PMC3930506 DOI: 10.1371/journal.pgen.1004151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in the major histocompatibility complex (MHC) affects CD4∶CD8 lineage commitment and MHC expression. However, the contribution of specific genes in this gene-dense region has not yet been resolved. Nor has it been established whether the same genes regulate MHC expression and T cell selection. Here, we assessed the impact of natural genetic variation on MHC expression and CD4∶CD8 lineage commitment using two genetic models in the rat. First, we mapped Quantitative Trait Loci (QTLs) associated with variation in MHC class I and II protein expression and the CD4∶CD8 T cell ratio in outbred Heterogeneous Stock rats. We identified 10 QTLs across the genome and found that QTLs for the individual traits colocalized within a region spanning the MHC. To identify the genes underlying these overlapping QTLs, we generated a large panel of MHC-recombinant congenic strains, and refined the QTLs to two adjacent intervals of ∼0.25 Mb in the MHC-I and II regions, respectively. An interaction between these intervals affected MHC class I expression as well as negative selection and lineage commitment of CD8 single-positive (SP) thymocytes. We mapped this effect to the transporter associated with antigen processing 2 (Tap2) in the MHC-II region and the classical MHC class I gene(s) (RT1-A) in the MHC-I region. This interaction was revealed by a recombination between RT1-A and Tap2, which occurred in 0.2% of the rats. Variants of Tap2 have previously been shown to influence the antigenicity of MHC class I molecules by altering the MHC class I ligandome. Our results show that a restricted peptide repertoire on MHC class I molecules leads to reduced negative selection of CD8SP cells. To our knowledge, this is the first study showing how a recombination between natural alleles of genes in the MHC influences lineage commitment of T cells. Peptides from degraded cytoplasmic proteins are transported via TAP into the endoplasmic reticulum for loading onto MHC class I molecules. TAP is encoded by Tap1 and Tap2, which in rodents are located close to the MHC class I genes. In the rat, genetic variation in Tap2 gives rise to two different transporters: a promiscuous A variant (TAP-A) and a more restrictive B variant (TAP-B). It has been proposed that the class I molecule in the DA rat (RT1-Aa) has co-evolved with TAP-A and it has been shown that RT1-Aa antigenicity is changed when co-expressed with TAP-B. To study the contribution of different allelic combinations of RT1-A and Tap2 to the variation in MHC expression and T cell selection, we generated DA rats with either congenic or background alleles in the RT1-A and Tap2 loci. We found increased numbers of mature CD8SP cells in the thymus of rats which co-expressed RT1-Aa and TAP-B. This increase of CD8 cells could be explained by reduced negative selection, but did not correlate with RT1-Aa expression levels on thymic antigen presenting cells. Thus, our results identify a crucial role of the TAP and the quality of the MHC class I repertoire in regulating T cell selection.
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Affiliation(s)
- Jonatan Tuncel
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
| | - Sabrina Haag
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anthony C. Y. Yau
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika Norin
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Amelie Baud
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Erik Lönnblom
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Klio Maratou
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - A. Jimmy Ytterberg
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Diana Ekman
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Soley Thordardottir
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martina Johannesson
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alan Gillett
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Pernilla Stridh
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Neuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Alberto Fernández-Teruel
- Medical Psychology Unit, Department of Psychiatry & Forensic Medicine, Institute of Neurosciences, School of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Roman A. Zubarev
- Medical Proteomics, Department of Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Timothy J. Aitman
- Physiological Genomics and Medicine Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (JT); (RH)
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Mu J, Tai X, Iyer SS, Weissman JD, Singer A, Singer DS. Regulation of MHC class I expression by Foxp3 and its effect on regulatory T cell function. THE JOURNAL OF IMMUNOLOGY 2014; 192:2892-903. [PMID: 24523508 DOI: 10.4049/jimmunol.1302847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Expression of MHC class I molecules, which provide immune surveillance against intracellular pathogens, is higher on lymphoid cells than on any other cell types. In T cells, this is a result of activation of class I transcription by the T cell enhanceosome consisting of Runx1, CBFβ, and LEF1. We now report that MHC class I transcription in T cells also is enhanced by Foxp3, resulting in higher levels of class I in CD4(+)CD25(+) T regulatory cells than in conventional CD4(+)CD25(-) T cells. Interestingly, the effect of Foxp3 regulation of MHC class I transcription is cell type specific: Foxp3 increases MHC class I expression in T cells but represses it in epithelial tumor cells. In both cell types, Foxp3 targets the upstream IFN response element and downstream core promoter of the class I gene. Importantly, expression of MHC class I contributes to the function of CD4(+)CD25(+) T regulatory cells by enhancing immune suppression, both in in vitro and in vivo. These findings identify MHC class I genes as direct targets of Foxp3 whose expression augments regulatory T cell function.
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Affiliation(s)
- Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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15
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Major histocompatibility complex class I core promoter elements are not essential for transcription in vivo. Mol Cell Biol 2013; 33:4395-407. [PMID: 24019072 DOI: 10.1128/mcb.00553-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of core promoter elements in regulating transcription initiation is largely unknown for genes subject to complex regulation. Major histocompatibility complex class I genes are ubiquitously expressed and governed by tissue-specific and hormonal signals. Transcription initiates at multiple sites within the core promoter, which contains elements homologous to the canonical elements CCAAT, TATAA, Sp1 binding site (Sp1BS), and Initiator (Inr). To determine their functions, expression of class I transgenes with individually mutated elements was assessed. Surprisingly, all mutant promoters supported transcription. However, each mutated core promoter element had a distinct effect on expression: CAAT box mutations modulated constitutive expression in nonlymphoid tissues, whereas TATAA-like element mutations dysregulated transcription in lymphoid tissues. Inr mutations aberrantly elevated expression. Sp1BS element mutations resulted in variegated transgene expression. RNA polymerase II binding and histone H3K4me3 patterns correlated with transgene expression; H3K9me3 marks partially correlated. Whereas the wild-type, TATAA-like, and CAAT mutant promoters were activated by gamma interferon, the Sp1 and Inr mutants were repressed, implicating these elements in regulation of hormonal responses. These results lead to the surprising conclusion that no single element is required for promoter activity. Rather, each plays a distinct role in promoter activity, chromatin structure, tissue-specific expression, and extracellular signaling.
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16
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Chen L, Jay DC, Fairbanks JD, He X, Jensen PE. An MHC class Ib-restricted CD8+ T cell response to lymphocytic choriomeningitis virus. THE JOURNAL OF IMMUNOLOGY 2011; 187:6463-72. [PMID: 22084437 DOI: 10.4049/jimmunol.1101171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Conventional MHC class Ia-restricted CD8(+) T cells play a dominant role in the host response to virus infections, but recent studies indicate that T cells with specificity for nonclassical MHC class Ib molecules may also participate in host defense. To investigate the potential role of class Ib molecules in anti-viral immune responses, K(b-/-)D(b-/-)CIITA(-/-) mice lacking expression of MHC class Ia and class II molecules were infected with lymphocytic choriomeningitis virus (LCMV). These animals have a large class Ib-selected CD8(+) T cell population and they were observed to mediate partial (but incomplete) virus clearance during acute LCMV infection as compared with K(b-/-)D(b-/-)β(2)-microglobulin(-/-) mice that lack expression of both MHC class Ia and class Ib molecules. Infection was associated with expansion of splenic CD8(+) T cells and induction of granzyme B and IFN-γ effector molecules in CD8(+) T cells. Partial virus clearance was dependent on CD8(+) cells. In vitro T cell restimulation assays demonstrated induction of a population of β(2)-microglobulin-dependent, MHC class Ib-restricted CD8(+) T cells with specificity for viral Ags and yet to be defined nonclassical MHC molecules. MHC class Ib-restricted CD8(+) T cell responses were also observed after infection of K(b-/-)D(b-/-)mice despite the low number of CD8(+) T cells in these animals. Long-term infection studies demonstrated chronic infection and gradual depletion of CD8(+) T cells in K(b-/-)D(b-/-)CIITA(-/-) mice, demonstrating that class Ia molecules are required for viral clearance. These findings demonstrate that class Ib-restricted CD8(+) T cells have the potential to participate in the host immune response to LCMV.
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Affiliation(s)
- Lili Chen
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
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17
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Natural killer cells recognize friend retrovirus-infected erythroid progenitor cells through NKG2D-RAE-1 interactions In Vivo. J Virol 2011; 85:5423-35. [PMID: 21411527 DOI: 10.1128/jvi.02146-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural killer (NK) cells function as early effector cells in the innate immune defense against viral infections and also participate in the regulation of normal and malignant hematopoiesis. NK cell activities have been associated with early clearance of viremia in experimental simian immunodeficiency virus and clinical human immunodeficiency virus type 1 (HIV-1) infections. We have previously shown that NK cells function as major cytotoxic effector cells in vaccine-induced immune protection against Friend virus (FV)-induced leukemia, and NK cell depletion totally abrogates the above protective immunity. However, how NK cells recognize retrovirus-infected cells remains largely unclear. The present study demonstrates a correlation between the expression of the products of retinoic acid early transcript-1 (RAE-1) genes in target cells and their susceptibility to killing by NK cells isolated from FV-infected animals. This killing was abrogated by antibodies blocking the NKG2D receptor in vitro. Further, the expression of RAE-1 proteins on erythroblast surfaces increased early after FV inoculation, and administration of an RAE-1-blocking antibody resulted in increased spleen infectious centers and exaggerated pathology, indicating that FV-infected erythroid cells are recognized by NK cells mainly through the NKG2D-RAE-1 interactions in vivo. Enhanced retroviral replication due to host gene-targeting resulted in markedly increased RAE-1 expression in the absence of massive erythroid cell proliferation, indicating a direct role of retroviral replication in RAE-1 upregulation.
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Lee N, Iyer SS, Mu J, Weissman JD, Ohali A, Howcroft TK, Lewis BA, Singer DS. Three novel downstream promoter elements regulate MHC class I promoter activity in mammalian cells. PLoS One 2010; 5:e15278. [PMID: 21179443 PMCID: PMC3001478 DOI: 10.1371/journal.pone.0015278] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 11/09/2010] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MHC CLASS I TRANSCRIPTION IS REGULATED BY TWO DISTINCT TYPES OF REGULATORY PATHWAYS: 1) tissue-specific pathways that establish constitutive levels of expression within a given tissue and 2) dynamically modulated pathways that increase or decrease expression within that tissue in response to hormonal or cytokine mediated stimuli. These sets of pathways target distinct upstream regulatory elements, have distinct basal transcription factor requirements, and utilize discrete sets of transcription start sites within an extended core promoter. METHODOLOGY/PRINCIPAL FINDINGS We studied regulatory elements within the MHC class I promoter by cellular transfection and in vitro transcription assays in HeLa, HeLa/CIITA, and tsBN462 of various promoter constructs. We have identified three novel MHC class I regulatory elements (GLE, DPE-L1 and DPE-L2), located downstream of the major transcription start sites, that contribute to the regulation of both constitutive and activated MHC class I expression. These elements located at the 3' end of the core promoter preferentially regulate the multiple transcription start sites clustered at the 5' end of the core promoter. CONCLUSIONS/SIGNIFICANCE Three novel downstream elements (GLE, DPE-L1, DPE-L2), located between +1 and +32 bp, regulate both constitutive and activated MHC class I gene expression by selectively increasing usage of transcription start sites clustered at the 5' end of the core promoter upstream of +1 bp. Results indicate that the downstream elements preferentially regulate TAF1-dependent, relative to TAF1-independent, transcription.
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Affiliation(s)
- Namhoon Lee
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Cellular, Molecular, Developmental Biology and Biophysics, NIH-Johns Hopkins University, Bethesda, Maryland, United States of America
| | - Shankar S. Iyer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jie Mu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jocelyn D. Weissman
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anat Ohali
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - T. Kevin Howcroft
- Division of Cancer Biology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Brian A. Lewis
- Metabolism Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Dinah S. Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Metabolism Branch, National Cancer Institute, Bethesda, Maryland, United States of America
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Goyos A, Sowa J, Ohta Y, Robert J. Remarkable conservation of distinct nonclassical MHC class I lineages in divergent amphibian species. THE JOURNAL OF IMMUNOLOGY 2010; 186:372-81. [PMID: 21115732 DOI: 10.4049/jimmunol.1001467] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nonclassical MHC class Ib (class Ib) genes are heterogeneous genes encoding molecules that are structurally similar to classical MHC class Ia molecules but with limited tissue distribution and polymorphism. Mammalian class Ib genes have diverse and often uncharacterized functions, and because of their rapid rate of evolution, class Ib phylogeny is difficult to establish. We have conducted an extensive genomic, molecular, and phylogenetic characterization of class Ib genes in two Xenopodinae amphibian species of different genera that diverged from a common ancestor as long ago as primates and rodents (∼65 million years). In contrast with the unsteadiness of mammalian class Ib genes, our results reveal an unusual degree of conservation of most Xenopodinae class Ib gene lineages, including a novel monogenic lineage represented by the divergent Xenopus laevis XNC10 gene and its unequivocal Silurana (Xenopus) tropicalis orthologue, SNC10. The preferential expression of this gene lineage by thymocytes themselves from the onset of thymic organogenesis is consistent with a specialized role of class Ib in early T cell development and suggests such a function is conserved in all tetrapods.
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Affiliation(s)
- Ana Goyos
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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20
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Cho H, Choi HJ, Xu H, Felio K, Wang CR. Nonconventional CD8+ T cell responses to Listeria infection in mice lacking MHC class Ia and H2-M3. THE JOURNAL OF IMMUNOLOGY 2010; 186:489-98. [PMID: 21098224 DOI: 10.4049/jimmunol.1002639] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CD8(+) T cells restricted to MHC class Ib molecules other than H2-M3 have been shown to recognize bacterial Ags. However, the contribution of these T cells to immune responses against bacterial infection is not well defined. To investigate the immune potential of MHC class Ib-restricted CD8(+) T cells, we have generated mice that lack both MHC class Ia and H2-M3 molecules (K(b-/-)D (b-/-)M3(-/-)). The CD8(+) T cells present in K(b-/-)D (b-/-)M3(-/-) mice display an activated surface phenotype and are able to secrete IFN-γ rapidly upon anti-CD3 and anti-CD28 stimulation. Although the CD8(+) T cell population is reduced in K(b-/-)D (b-/-)M3(-/-) mice compared with that in K(b-/-)D (b-/-) mice, this population retains the capacity to expand significantly in response to primary infection with the bacteria Listeria monocytogenes. However, K(b-/-)D (b-/-)M3(-/-) CD8(+) T cells do not expand upon secondary infection, similar to what has been observed for H2-M3-restricted T cells. CD8(+) T cells isolated from Listeria-infected K(b-/-)D (b-/-)M3(-/-) mice exhibit cytotoxicity and secrete proinflammatory cytokines in response to Listeria-infected APCs. These T cells are protective against primary Listeria infection, as Listeria-infected K(b-/-)D (b-/-)M3(-/-) mice exhibit reduced bacterial burden compared with that of infected β(2)-microglobulin-deficient mice that lack MHC class Ib-restricted CD8(+) T cells altogether. In addition, adoptive transfer of Listeria-experienced K(b-/-)D (b-/-)M3(-/-) splenocytes protects recipient mice against subsequent Listeria infection in a CD8(+) T cell-dependent manner. These data demonstrate that other MHC class Ib-restricted CD8(+) T cells, in addition to H2-M3-restricted T cells, contribute to antilisterial immunity and may contribute to immune responses against other intracellular bacteria.
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Affiliation(s)
- Hoonsik Cho
- Department of Microbiology and Immunology, Northwestern University, Chicago, IL 60611, USA
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21
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Cohen H, Parekh P, Sercan Z, Kotekar A, Weissman JD, Singer DS. In vivo expression of MHC class I genes depends on the presence of a downstream barrier element. PLoS One 2009; 4:e6748. [PMID: 19707598 PMCID: PMC2727697 DOI: 10.1371/journal.pone.0006748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Accepted: 06/25/2009] [Indexed: 11/18/2022] Open
Abstract
Regulation of MHC class I gene expression is critical to achieve proper immune surveillance. In this work, we identify elements downstream of the MHC class I promoter that are necessary for appropriate in vivo regulation: a novel barrier element that protects the MHC class I gene from silencing and elements within the first two introns that contribute to tissue specific transcription. The barrier element is located in intergenic sequences 3' to the polyA addition site. It is necessary for stable expression in vivo, but has no effect in transient transfection assays. Accordingly, in both transgenic mice and stably transfected cell lines, truncation of the barrier resulted in transcriptional gene silencing, increased nucleosomal density and decreased histone H3K9/K14 acetylation and H3K4 di-methylation across the gene. Significantly, distinct sequences within the barrier element govern anti-silencing and chromatin modifications. Thus, this novel barrier element functions to maintain transcriptionally permissive chromatin organization and prevent transcriptional silencing of the MHC class I gene, ensuring it is poised to respond to immune signaling.
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Affiliation(s)
- Helit Cohen
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Palak Parekh
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Zeynep Sercan
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Aparna Kotekar
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Jocelyn D. Weissman
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Dinah S. Singer
- Experimental Immunology Branch, Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
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Poláková K, Bandžuchová E, Kuba D, Russ G. Demethylating agent 5-aza-2′-deoxycytidine activates HLA-G expression in human leukemia cell lines. Leuk Res 2009; 33:518-24. [DOI: 10.1016/j.leukres.2008.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 08/01/2008] [Accepted: 08/02/2008] [Indexed: 11/17/2022]
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French JD, Roark CL, Born WK, O'Brien RL. Gammadelta T lymphocyte homeostasis is negatively regulated by beta2-microglobulin. THE JOURNAL OF IMMUNOLOGY 2009; 182:1892-900. [PMID: 19201842 DOI: 10.4049/jimmunol.0803165] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Successful application of gammadelta T cells in adoptive cell therapies depends upon our ability to maintain these cells in vivo. Using an adoptive transfer model to study lymphopenia-induced homeostatic expansion, we show that CD8(+) and NK1.1(+) gammadelta T cell subsets are differentially regulated. While CD8(+) gammadelta T cells have an early and sustained advantage following transfer into TCRbeta(-/-)/delta(-/-) mice, NK1.1(+) gammadelta T cells proliferate slowly and are maintained at low numbers. The advantage of the CD8(+) subset could not be explained by increased bcl-2 or cytokine receptor expression but did correlate with Vgamma4(+) and Vdelta5(+) expression. Despite the role of CD8 in MHC class I recognition by alphabeta T cells, beta(2)-microglobulin (beta(2)m)-associated MHC class I molecules were not required for CD8(+) gammadelta T cell homeostatic expansion. Surprisingly, all gammadelta T cells, including the CD8(+) subset, exhibited enhanced proliferation following adoptive transfer into Rag1(-/-)/beta(2)m(-/-) compared with Rag1(-/-) recipients. This effect was most notable for the NK1.1(+) subset, which expresses high levels of NKG2A/CD94 and Ly49. Although expression of these inhibitory receptors correlated with poor homeostatic expansion in the presence of beta(2)m, gammadelta T cell homeostatic proliferation in TCRbeta(-/-)/delta(-/-) mice was not altered in the presence of Ly49C/I- and NKG2-blocking Abs. While the mechanism by which beta(2)m negatively regulates gammadelta T cell homeostasis remains to be determined, this observation is unique to gammadelta T cells and confirms that multiple mechanisms are in place to maintain strict regulation of both the size and the composition of the gammadelta T cell pool.
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Affiliation(s)
- Jena D French
- National Jewish Health, Integrated Department of Immunology, Denver, CO 80206, USA
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Malone KE, Stohlman SA, Ramakrishna C, Macklin W, Bergmann CC. Induction of class I antigen processing components in oligodendroglia and microglia during viral encephalomyelitis. Glia 2008; 56:426-35. [PMID: 18205173 PMCID: PMC7165990 DOI: 10.1002/glia.20625] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glia exhibit differential susceptibility to CD8 T cell mediated effector mechanisms during neurotropic coronavirus infection. In contrast to microglia, oligodendroglia are resistant to CD8 T cell perforin‐mediated viral control in the absence of IFNγ. Kinetic induction of MHC Class I expression by microglia and oligodendroglia in vivo was thus analyzed to assess responses to distinct inflammatory signals. Flow cytometry demonstrated delayed Class I surface expression by oligodendroglia compared with microglia. Distinct kinetics of Class I protein upregulation correlated with cell type specific transcription patterns of genes encoding Class I heavy chains and antigen processing components. Microglia isolated from naïve mice expressed high levels of these mRNAs, whereas they were near detection limits in oligodendroglia; nevertheless, Class I protein was undetectable on both cell types. Infection induced modest mRNA increases in microglia, but dramatic transcriptional upregulation in oligodendroglia coincident with IFNα or IFNγ mRNA increases in infected tissue. Ultimately mRNAs reached similar levels in both cell types at their respective time points of maximal Class I expression. Expression of Class I on microglia, but not oligodendroglia, in infected IFNγ deficient mice supported distinct IFN requirements for Class I presentation. These data suggest an innate immune preparedness of microglia to present antigen and engage CD8 T cells early following infection. The delayed, yet robust, IFNγ dependent capacity of oligodendroglia to express Class I suggests strict control of immune interactions to avoid CD8 T cell recognition and potential presentation of autoantigen to preserve myelin maintenance. © 2008 Wiley‐Liss, Inc.
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Affiliation(s)
- Karen E Malone
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
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Tennant LM, Renard C, Chardon P, Powell PP. Regulation of porcine classical and nonclassical MHC class I expression. Immunogenetics 2007; 59:377-89. [PMID: 17351769 DOI: 10.1007/s00251-007-0206-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 02/22/2007] [Indexed: 11/28/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules comprise a family of polymorphic cell surface receptors consisting of classical 1 a molecules that present antigenic peptides and nonclassical 1 b molecules. Gene expression for human classical and nonclassical MHC class I molecules has been shown to be differentially regulated by interferon, with variation in the nucleotide sequence of promoter regions, resulting in differences in interferon inducibility and basal levels of gene transcription. In this study on porcine classical and nonclassical swine leukocyte Ag (SLA) class I molecules, we show alignments of putative regulatory elements in the promoters of the three functional classical class I genes, SLA-1, SLA-2, and SLA-3; two nonclassical 1 b genes, SLA-6 and SLA-7; and a MIC-2 gene. Promoter elements were cloned upstream from a luciferase reporter gene, and the basal and inducible activities of each were characterized by expression in Max cells, an immortalized pig cell line that responds to interferon and tumor necrosis factor alpha (TNF-alpha). All three classical class I but not nonclassical promoters responded to interferon. This was confirmed by the transactivation of SLA-1, but not SLA-7, after the co expression with interferon regulatory factors (IRFs), IRF-1, IRF-2, IRF-3, IRF-7, and IRF-9. Classical class I genes were activated by cotransfection with nuclear factor kappa B (NF-kappaB) p65 and by treatment of cells with TNF-alpha, although, unlike human promoter there was no synergistic effect with interferon. The greatest effect on classical class I promoters was coexpression with the class II transactivator (CIITA), important for constitutive transactivation. These results determine the differential regulation of porcine classical and nonclassical MHC class I and reflects their importance in antigen presentation during infection.
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Affiliation(s)
- Laura M Tennant
- Department of Immunology, Institute for Animal Health, Ash Road, Pirbright, Surrey, GU24 0NF, UK
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Lee MP, Howcroft K, Kotekar A, Yang HH, Buetow KH, Singer DS. ATG deserts define a novel core promoter subclass. Genome Res 2005; 15:1189-97. [PMID: 16109972 PMCID: PMC1199533 DOI: 10.1101/gr.3873705] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro. Here, we define a novel core promoter feature that supports regulated transcription through selective transcription start site (TSS) usage. We demonstrate that TSS selection is actively regulated and context dependent. Basal and activated transcriptions initiate from largely nonoverlapping TSS regions. Transcripts derived from multiple TSS encode a single protein, due to the absence of any ATG triplets within approximately 430 bp upstream of the major transcription start site. Thus, the PD1 core promoter is embedded within an "ATG desert". Remarkably, extending this analysis genome-wide, we find that ATG deserts define a novel promoter subclass. They occur nonrandomly, are significantly associated with non-TATAA promoters that use multiple TSS, independent of the presence of CpG islands (CGI). We speculate that ATG deserts may provide a core promoter platform upon which complex upstream regulatory signals can be integrated, targeting multiple TSS whose products encode a single protein.
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Affiliation(s)
- Maxwell P Lee
- Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Howcroft TK, Weissman JD, Gegonne A, Singer DS. A T lymphocyte-specific transcription complex containing RUNX1 activates MHC class I expression. THE JOURNAL OF IMMUNOLOGY 2005; 174:2106-15. [PMID: 15699141 DOI: 10.4049/jimmunol.174.4.2106] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I expression is subject to both tissue-specific and hormonal regulatory mechanisms. Consequently, levels of expression vary widely among tissues, with the highest levels of class I occurring in the lymphoid compartment, in T cells and B cells. Although the high class I expression in B cells is known to involve the B cell enhanceosome, the molecular basis for high constitutive class I expression in T cells has not been explored. T cell-specific genes, such as TCR genes, are regulated by a T cell enhanceosome consisting of RUNX1, CBFbeta, LEF1, and Aly. In this report, we demonstrate that MHC class I gene expression is enhanced by the T cell enhanceosome and results from a direct interaction of the RUNX1-containing complex with the class I gene in vivo. T cell enhanceosome activation of class I transcription is synergistic with CIITA-mediated activation and targets response elements distinct from those targeted by CIITA. These findings provide a molecular basis for the high levels of MHC class I in T cells.
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Affiliation(s)
- T Kevin Howcroft
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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