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Mikaeeli S, Ben Djoudi Ouadda A, Evagelidis A, Essalmani R, Ramos OHP, Fruchart-Gaillard C, Seidah NG. Insights into PCSK9-LDLR Regulation and Trafficking via the Differential Functions of MHC-I Proteins HFE and HLA-C. Cells 2024; 13:857. [PMID: 38786080 PMCID: PMC11119474 DOI: 10.3390/cells13100857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
PCSK9 is implicated in familial hypercholesterolemia via targeting the cell surface PCSK9-LDLR complex toward lysosomal degradation. The M2 repeat in the PCSK9's C-terminal domain is essential for its extracellular function, potentially through its interaction with an unidentified "protein X". The M2 repeat was recently shown to bind an R-x-E motif in MHC-class-I proteins (implicated in the immune system), like HLA-C, and causing their lysosomal degradation. These findings suggested a new role of PCSK9 in the immune system and that HLA-like proteins could be "protein X" candidates. However, the participation of each member of the MHC-I protein family in this process and their regulation of PCSK9's function have yet to be determined. Herein, we compared the implication of MHC-I-like proteins such as HFE (involved in iron homeostasis) and HLA-C on the extracellular function of PCSK9. Our data revealed that the M2 domain regulates the intracellular sorting of the PCSK9-LDLR complex to lysosomes, and that HFE is a new target of PCSK9 that inhibits its activity on the LDLR, whereas HLA-C enhances its function. This work suggests the potential modulation of PCSK9's functions through interactions of HFE and HLA-C.
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Affiliation(s)
- Sepideh Mikaeeli
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, QC H2W 1R7, Canada; (S.M.); (A.B.D.O.); (A.E.); (R.E.)
| | - Ali Ben Djoudi Ouadda
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, QC H2W 1R7, Canada; (S.M.); (A.B.D.O.); (A.E.); (R.E.)
| | - Alexandra Evagelidis
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, QC H2W 1R7, Canada; (S.M.); (A.B.D.O.); (A.E.); (R.E.)
| | - Rachid Essalmani
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, QC H2W 1R7, Canada; (S.M.); (A.B.D.O.); (A.E.); (R.E.)
| | - Oscar Henrique Pereira Ramos
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SIMoS, 91191 Gif-sur-Yvette, France; (O.H.P.R.); (C.F.-G.)
| | - Carole Fruchart-Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SIMoS, 91191 Gif-sur-Yvette, France; (O.H.P.R.); (C.F.-G.)
| | - Nabil G. Seidah
- Laboratory of Biochemical Neuroendocrinology, Montreal Clinical Research Institute (IRCM), University of Montreal, Montreal, QC H2W 1R7, Canada; (S.M.); (A.B.D.O.); (A.E.); (R.E.)
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2
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Skaug B, Guo X, Li YJ, Charles J, Pham KT, Couturier J, Lewis DE, Bracaglia C, Caiello I, Mayes MD, Assassi S. Reduced digestion of circulating genomic DNA in systemic sclerosis patients with the DNASE1L3 R206C variant. Rheumatology (Oxford) 2023; 62:3197-3204. [PMID: 36708011 PMCID: PMC10473277 DOI: 10.1093/rheumatology/kead050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/01/2023] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES Polymorphism in a coding region of deoxyribonuclease I-like III (DNASE1L3), causing amino acid substitution of Arg-206 to Cys (R206C), is a robustly replicated heritable risk factor for SSc and other autoimmune diseases. DNASE1L3 is secreted into the circulation, where it can digest genomic DNA (gDNA) in apoptosis-derived membrane vesicles (AdMVs). We sought to determine the impact of DNASE1L3 R206C on digestion of circulating gDNA in SSc patients and healthy controls (HCs). METHODS The ability of DNASE1L3 to digest AdMV-associated gDNA was tested in vitro. The effect of R206C substitution on extracellular secretion of DNASE1L3 was determined using a transfected cell line and primary monocyte-derived dendritic cells from SSc patients. Plasma samples from SSc patients and HCs with DNASE1L3 R206C or R206 wild type were compared for their ability to digest AdMV-associated gDNA. The digestion status of endogenous gDNA in plasma samples from 123 SSc patients and 74 HCs was determined by measuring the proportion of relatively long to short gDNA fragments. RESULTS The unique ability of DNASE1L3 to digest AdMV-associated gDNA was confirmed. Extracellular secretion of DNASE1L3 R206C was impaired. Plasma from individuals with DNASE1L3 R206C had reduced ability to digest AdMV-associated gDNA. The ratio of long: short gDNA fragments was increased in plasma from SSc patients with DNASE1L3 R206C, and this ratio correlated inversely with DNase activity. CONCLUSION Our results confirm that circulating gDNA is a physiological DNASE1L3 substrate and show that its digestion is reduced in SSc patients with the DNASE1L3 R206C variant.
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Affiliation(s)
- Brian Skaug
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Xinjian Guo
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Yuanteng Jeff Li
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Julio Charles
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Kay T Pham
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jacob Couturier
- Division of Infectious Diseases, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Dorothy E Lewis
- Division of Infectious Diseases, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Claudia Bracaglia
- Division of Rheumatology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Ivan Caiello
- Division of Rheumatology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maureen D Mayes
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
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Oda T, Yanagisawa H, Shinmori H, Ogawa Y, Kawamura T. Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation. eLife 2022; 11:79990. [PMID: 35758632 PMCID: PMC9259017 DOI: 10.7554/elife.79990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 01/03/2023] Open
Abstract
Langerhans cells are specialized antigen-presenting cells localized within the epidermis and mucosal epithelium. Upon contact with Langerhans cells, pathogens are captured by the C-type lectin langerin and internalized into a structurally unique vesicle known as a Birbeck granule. Although the immunological role of Langerhans cells and Birbeck granules have been extensively studied, the mechanism by which the characteristic zippered membrane structure of Birbeck granules is formed remains elusive. In this study, we observed isolated Birbeck granules using cryo-electron tomography and reconstructed the 3D structure of the repeating unit of the honeycomb lattice of langerin at 6.4 Å resolution. We found that the interaction between the two langerin trimers was mediated by docking the flexible loop at residues 258–263 into the secondary carbohydrate-binding cleft. Mutations within the loop inhibited Birbeck granule formation and the internalization of HIV pseudovirus. These findings suggest a molecular mechanism for membrane zippering during Birbeck granule biogenesis and provide insight into the role of langerin in the defense against viral infection.
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Affiliation(s)
- Toshiyuki Oda
- Department of Anatomy and Structural Biology, University of Yamanashi, Yamanashi, Japan
| | - Haruaki Yanagisawa
- Department of Cell Biology and Anatomy, University of Tokyo, Tokyo, Japan
| | - Hideyuki Shinmori
- Faculty of Life and Environmental Science, University of Yamanashi, Yamanashi, Japan
| | - Youichi Ogawa
- Department of Dermatology, University of Yamanashi, Yamanashi, Japan
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Hovhannisyan A, Madelian V, Avagyan S, Nazaretyan M, Hyussyan A, Sirunyan A, Arakelyan R, Manukyan Z, Yepiskoposyan L, Mayilyan KR, Jordan F. HLA-C*04:01 Affects HLA Class I Heterozygosity and Predicted Affinity to SARS-CoV-2 Peptides, and in Combination With Age and Sex of Armenian Patients Contributes to COVID-19 Severity. Front Immunol 2022; 13:769900. [PMID: 35185875 PMCID: PMC8850920 DOI: 10.3389/fimmu.2022.769900] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
The novel SARS-CoV-2 coronavirus infection has become a global health concern, causing the COVID-19 pandemic. The disease symptoms and outcomes depend on the host immunity, in which the human leukocyte antigen (HLA) molecules play a distinct role. The HLA alleles have an inter-population variability, and understanding their link to the COVID-19 in an ethnically distinct population may contribute to personalized medicine. The present study aimed at detecting associations between common HLA alleles and COVID-19 susceptibility and severity in Armenians. In 299 COVID-19 patients (75 asymptomatic, 102 mild/moderate, 122 severe), the association between disease severity and classic HLA-I and II loci was examined. We found that the advanced age, male sex of patients, and sex and age interaction significantly contributed to the severity of the disease. We observed that an age-dependent effect of HLA-B*51:01 carriage [odds ratio (OR)=0.48 (0.28-0.80), Pbonf <0.036] is protective against severe COVID-19. Contrary, the HLA-C*04:01 allele, in a dose-dependent manner, was associated with a significant increase in the disease severity [OR (95% CI) =1.73 (1.20-2.49), Pbonf <0.021] and an advancing age (P<0.013). The link between HLA-C*04:01 and age was secondary to a stronger association between HLA-C*04:01 and disease severity. However, HLA-C*04:01 exerted a sex-dependent differential distribution between clinical subgroups [females: P<0.0012; males: P=0.48]. The comparison of HLA-C*04:01 frequency between subgroups and 2,781 Armenian controls revealed a significant incidence of HLA-C*04:01 deficiency in asymptomatic COVID-19. HLA-C*04:01 homozygous genotype in patients blueprinted a decrease in heterozygosity of HLA-B and HLA class-I loci. In HLA-C*04:01 carriers, these changes translated to the SARS-CoV-2 peptide presentation predicted inefficacy by HLA-C and HLA class-I molecules, simultaneously enhancing the appropriate HLA-B potency. In patients with clinical manifestation, due to the high prevalence of HLA-C*04:01, these effects provided a decrease of the HLA class-I heterozygosity and an ability to recognize SARS-CoV-2 peptides. Based on our observations, we developed a prediction model involving demographic variables and HLA-C*04:01 allele for the identification of potential cases with the risk of hospitalization (the area under the curve (AUC) = 86.2%) or severe COVID-19 (AUC =71%).
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Affiliation(s)
- Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
- Russian-Armenian University, Yerevan, Armenia
| | - Vergine Madelian
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Sevak Avagyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Mihran Nazaretyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Armine Hyussyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Alina Sirunyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | | | | | | | - Karine R. Mayilyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Frieda Jordan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
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5
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High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD). Sci Rep 2022; 12:106. [PMID: 34997058 PMCID: PMC8742014 DOI: 10.1038/s41598-021-04074-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/13/2021] [Indexed: 11/08/2022] Open
Abstract
Neuromyelitis optica spectrum disorder (NMOSD) is a relapsing autoimmune disease characterized by the presence of pathogenic autoantibodies, anti-aquaporin 4 (AQP4) antibodies. Recently, HLA-DQA1*05:03 was shown to be significantly associated with NMOSD in a Japanese patient cohort. However, the specific mechanism by which HLA-DQA1*05:03 is associated with the development of NMOSD has yet to be elucidated. In the current study, we revealed that HLA-DQA1*05:03 exhibited significantly higher cell surface expression levels compared to other various DQA1 alleles, and that its expression strongly depended on the amino acid sequence of the α1 domain, with a preference for leucine at position 75. Moreover, in silico analysis indicated that the HLA-DQ encoded by HLA-DQA1*05:03 preferentially presents immunodominant AQP4 peptides, and that the peptide major histocompatibility complexes (pMHCs) are more energetically stable in the presence of HLA-DQA1*05:03 than other HLA-DQA1 alleles. In silico 3D structural models were also applied to investigate the validity of the energetic stability of pMHCs. Taken together, our findings indicate that HLA-DQA1*05:03 possesses a distinct property to play a pathogenic role in the development of NMOSD.
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6
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Sakaguchi T, Okumura R, Ono C, Okuzaki D, Kawai T, Okochi Y, Tanimura N, Murakami M, Kayama H, Umemoto E, Kioka H, Ohtani T, Sakata Y, Miyake K, Okamura Y, Baba Y, Takeda K. TRPM5 Negatively Regulates Calcium-Dependent Responses in Lipopolysaccharide-Stimulated B Lymphocytes. Cell Rep 2021; 31:107755. [PMID: 32521253 DOI: 10.1016/j.celrep.2020.107755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/16/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
B cells produce high amounts of cytokines and immunoglobulins in response to lipopolysaccharide (LPS) stimulation. Calcium signaling cascades are critically involved in cytokine production of T cells, and the cytosolic calcium concentration is regulated by calcium-activated monovalent cation channels (CAMs). Calcium signaling is also implicated in B cell activation; however, its involvement in the cytokine production of LPS-stimulated B cells remains less well characterized. Here, we show that the transient receptor potential melastatin 5 channel (TRPM5), which is one of the CAMs, negatively modulates calcium signaling, thereby regulating LPS-induced proliferative and inflammatory responses by B cells. LPS-stimulated B cells of Trpm5-deficient mice exhibit an increased cytosolic calcium concentration, leading to enhanced proliferation and the production of the inflammatory cytokines interleukin-6 and CXCL10. Furthermore, Trpm5-deficient mice show an exacerbation of endotoxic shock with high mortality. Our findings demonstrate the importance of TRPM5-dependent regulatory mechanisms in LPS-induced calcium signaling of splenic B cells.
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Affiliation(s)
- Taiki Sakaguchi
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan; Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Ryu Okumura
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Chisato Ono
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Takafumi Kawai
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yoshifumi Okochi
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Natsuko Tanimura
- Department of Pharmacology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Mari Murakami
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Hisako Kayama
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan; Institute for Advanced Co-Creation Studies, Osaka University, Suita, Japan
| | - Eiji Umemoto
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Hidetaka Kioka
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tomohito Ohtani
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yoshihiro Baba
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
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7
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Jappe EC, Garde C, Ramarathinam SH, Passantino E, Illing PT, Mifsud NA, Trolle T, Kringelum JV, Croft NP, Purcell AW. Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design. Nat Commun 2020; 11:6305. [PMID: 33298915 PMCID: PMC7726561 DOI: 10.1038/s41467-020-20166-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The features of peptide antigens that contribute to their immunogenicity are not well understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a method that provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra-allelic and inter-allelic differences in pMHC stability and reveals profiles of stability that are broader than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improves the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.
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Affiliation(s)
- Emma C Jappe
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | | | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ethan Passantino
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thomas Trolle
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
| | | | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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Suzuki H, Joshita S, Hirayama A, Shinji A, Mukawa K, Sako M, Yoshimura N, Suga T, Umemura T, Ashihara N, Yamazaki T, Ota M. Polymorphism at rs9264942 is associated with HLA-C expression and inflammatory bowel disease in the Japanese. Sci Rep 2020; 10:12424. [PMID: 32709981 PMCID: PMC7381613 DOI: 10.1038/s41598-020-69370-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
An expression quantitative trait locus (eQTL) single-nucleotide polymorphism (SNP) at rs9264942 was earlier associated with human leukocyte antigen (HLA)-C expression in Europeans. HLA-C has also been related to inflammatory bowel disease (IBD) risk in the Japanese. This study examined whether an eQTL SNP at rs9264942 could regulate HLA-C expression and whether four SNP haplotypes, including the eQTL SNP at rs9264942 and three SNPs at rs2270191, rs3132550, and rs6915986 of IBD risk carried in the HLA-C*12:02~B*52:01~DRB1*15:02 allele, were associated with IBD in the Japanese. HLA-C expression on CD3e+CD8a+ lymphocytes was significantly higher for the CC or CT genotype than for the TT genotype of rs9264942. The TACC haplotype of the four SNPs was associated with a strong susceptibility to ulcerative colitis (UC) but protection against Crohn’s disease (CD) as well as with disease clinical outcome. While UC protectivity was significant but CD susceptibility was not for the CGTT haplotype, the significance of UC protectivity disappeared but CD susceptibility reached significance for the CGCT haplotype. In conclusion, our findings support that the eQTL SNP at rs9264942 regulates HLA-C expression in the Japanese and suggest that the four SNPs, which are in strong linkage disequilibrium, may be surrogate marker candidates of a particular HLA haplotype, HLA-C*12:02~B*52:01~DRB1*15:02, related to IBD susceptibility and disease outcome.
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Affiliation(s)
- Hiroshi Suzuki
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Satoru Joshita
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Atsuhiro Hirayama
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,Department of Inflammatory Bowel Disease, Yokohama City University Medical Center, Yokohama, Japan
| | - Akihiro Shinji
- Department of Medical Oncology, Japanese Red Cross Society Suwa Red Cross Hospital, Suwa, Japan
| | - Kenji Mukawa
- Department of Gastroenterology, Japanese Red Cross Society Suwa Red Cross Hospital, Suwa, Japan
| | - Minako Sako
- Center for Inflammatory Bowel Disease, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Naoki Yoshimura
- Center for Inflammatory Bowel Disease, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Tomoaki Suga
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Takeji Umemura
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,Department of Life Innovation, Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan
| | - Norihiro Ashihara
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Tomoo Yamazaki
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Masao Ota
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
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9
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Jiang T, Cheng R, Pan Y, Zhang H, He Y, Su C, Ren S, Zhou C. Heterogeneity of neoantigen landscape between primary lesions and their matched metastases in lung cancer. Transl Lung Cancer Res 2020; 9:246-256. [PMID: 32420064 PMCID: PMC7225166 DOI: 10.21037/tlcr.2020.03.03] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background Personalized cancer vaccines based on tumor-derived neoantigens have shown strong and long-lasting antitumor effect in patients with some solid tumors. However, whether neoantigens identified from primary lesions could represent their metastatic lesions, and consequently the effect of vaccine therapy remained unknown. Methods To investigate whether neoantigens identified from primary tumors are similar to their matched metastases in lung cancer, we identified 79 samples from 24 cases. All of samples were collected before any systemic therapy. Major criteria for neoantigen identification included: derived from tumor-specific mutations, fold change >10 comparing to germline expression level, high predicted human leukocyte antigen (HLA) binding affinity and peptide of 9–11 amino acids in length. Results We found a wide range of tumor neoantigen burden in both primaries and metastases. The counts, overall distribution pattern and predicted HLA binding affinity of neoantigens were similar between primaries and metastases. However, only 20% of shared neoantigens (presented in both primaries and metastases) was observed, which were mainly derived from single nucleotide variants (SNVs) and fusions. A variety of corresponding HLA alleles were observed and 50.0% of cases were HLA-C*06:02. Finally, we observed the neoantigen intrametastases homogeneity in patients with sole brain metastases. Conclusions Neoantigen landscape in terms of the number, type and predicted HLA binding affinity was similar between primaries and metastases, but the percentage of shared neoantigens is only modest, suggesting vaccine development based solely on primary tumor neoantigen may not offer optimal therapeutic outcome, and shared neoantigen needs to be seriously considered.
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Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Ruirui Cheng
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yuanwei Pan
- Department of Imaging and Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Henghui Zhang
- Beijing Genecast Biotechnology Co., Beijing 100000, China
| | - Ying He
- Shanghai Hengrui Pharmaceutical Co., LTD, Shanghai 200245, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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10
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Abstract
Major histocompatibility complex (MHC) class I molecules function to present pathogen derived peptides to cytotoxic T cells and act as ligands for Natural Killer cells, thus alerting the immune system to the presence of invading pathogens. However, some MHC class I molecules, most notably HLA-B27, can be strongly associated with autoimmune diseases. In addition, the MHC class I pathway is a target for numerous viral evasion strategies Understanding not only the antigen presenting functions, but also the biosynthesis and the degradation pathways of MHC class I molecules has therefore become important in determining their role in pathogen and autoimmune related diseases. Here, we describe how using epitope tagged MHC class I molecules can aid in the analysis of MHC class I molecule biosynthesis and degradation as well as complementary studies using conventional conformationally specific antibodies. Coupled together with pharmacological manipulation which can target both biosynthetic and degradative pathways, this offers a powerful tool in analyzing MHC class I molecules.
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11
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Chen H, Liu S, Padula S, Lesman D, Griswold K, Lin A, Zhao T, Marshall JL, Chen F. Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nat Biotechnol 2019; 38:165-168. [PMID: 31844291 DOI: 10.1038/s41587-019-0331-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 10/28/2019] [Indexed: 11/10/2022]
Abstract
Here we describe TRACE (T7 polymerase-driven continuous editing), a method that enables continuous, targeted mutagenesis in human cells using a cytidine deaminase fused to T7 RNA polymerase. TRACE induces high rates of mutagenesis over multiple cell generations in genes under the control of a T7 promoter integrated in the genome. We used TRACE in a MEK1 inhibitor-resistance screen, and identified functionally correlated mutations.
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Affiliation(s)
- Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sophia Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Biophysics Program, Harvard University, Boston, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samuel Padula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Lesman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kettner Griswold
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Charles Stark Draper Laboratory, Cambridge, MA, USA
| | - Allen Lin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tongtong Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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12
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Qiu Z, Guo J, Kala S, Zhu J, Xian Q, Qiu W, Li G, Zhu T, Meng L, Zhang R, Chan HC, Zheng H, Sun L. The Mechanosensitive Ion Channel Piezo1 Significantly Mediates In Vitro Ultrasonic Stimulation of Neurons. iScience 2019; 21:448-457. [PMID: 31707258 PMCID: PMC6849147 DOI: 10.1016/j.isci.2019.10.037] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 09/04/2019] [Accepted: 10/18/2019] [Indexed: 10/28/2022] Open
Abstract
Ultrasound brain stimulation is a promising modality for probing brain function and treating brain disease non-invasively and with high spatiotemporal resolution. However, the mechanism underlying its effects remains unclear. Here, we examine the role that the mouse piezo-type mechanosensitive ion channel component 1 (Piezo1) plays in mediating the in vitro effects of ultrasound in mouse primary cortical neurons and a neuronal cell line. We show that ultrasound alone could activate heterologous and endogenous Piezo1, initiating calcium influx and increased nuclear c-Fos expression in primary neurons but not when pre-treated with a Piezo1 inhibitor. We also found that ultrasound significantly increased the expression of the important proteins phospho-CaMKII, phospho-CREB, and c-Fos in a neuronal cell line, but Piezo1 knockdown significantly reduced this effect. Our findings demonstrate that the activity of mechanosensitive ion channels such as Piezo1 stimulated by ultrasound is an important contributor to its ability to stimulate cells in vitro.
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Affiliation(s)
- Zhihai Qiu
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Jinghui Guo
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China; Department of Physiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shashwati Kala
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Jiejun Zhu
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Quanxiang Xian
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Weibao Qiu
- Paul C. Lauterbur Research Center for Biomedical Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, P. R. China
| | - Guofeng Li
- Paul C. Lauterbur Research Center for Biomedical Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, P. R. China
| | - Ting Zhu
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Long Meng
- Paul C. Lauterbur Research Center for Biomedical Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, P. R. China
| | - Rui Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China
| | - Hsiao Chang Chan
- Department of Physiology, School of Medicine, Jinan University, Guangzhou, China
| | - Hairong Zheng
- Paul C. Lauterbur Research Center for Biomedical Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, P. R. China.
| | - Lei Sun
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong SAR 999077, P. R. China.
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13
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Shimizu C, Kim J, Eleftherohorinou H, Wright VJ, Hoang LT, Tremoulet AH, Franco A, Hibberd ML, Takahashi A, Kubo M, Ito K, Tanaka T, Onouchi Y, Coin LJM, Levin M, Burns JC, Shike H. HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease. Hum Immunol 2019; 80:731-738. [PMID: 31122742 PMCID: PMC10793643 DOI: 10.1016/j.humimm.2019.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 10/26/2022]
Abstract
Kawasaki disease (KD) is a pediatric vasculitis caused by an unknown trigger in genetically susceptible children. The incidence varies widely across genetically diverse populations. Several associations with HLA Class I alleles have been reported in single cohort studies. Using a genetic approach, from the nine single nucleotide variants (SNVs) associated with KD susceptibility in children of European descent, we identified SNVs near the HLA-C (rs6906846) and HLA-B genes (rs2254556) whose association was replicated in a Japanese descent cohort (rs6906846 p = 0.01, rs2254556 p = 0.005). The risk allele (A at rs6906846) was also associated with HLA-C*07:02 and HLA-C*04:01 in both US multi-ethnic and Japanese cohorts and HLA-C*12:02 only in the Japanese cohort. The risk A-allele was associated with eight non-conservative amino acid substitutions (amino acid positions); Asp or Ser (9), Arg (14), Ala (49), Ala (73), Ala (90), Arg (97), Phe or Ser (99), and Phe or Ser (116) in the HLA-C peptide binding groove that binds peptides for presentation to cytotoxic T cells (CTL). This raises the possibility of increased affinity to a "KD peptide" that contributes to the vasculitis of KD in genetically susceptible children.
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Affiliation(s)
- Chisato Shimizu
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA.
| | - Jihoon Kim
- Division of Biomedical Informatics, Department of Medicine, University California San Diego, La Jolla, CA, USA
| | - Hariklia Eleftherohorinou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Victoria J Wright
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | | | - Adriana H Tremoulet
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA; Department of Cardiology, Rady Childrens' Hospital San Diego, San Diego, CA, USA
| | - Alessandra Franco
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA
| | | | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Bunkyo-ku, Tokyo, Japan
| | - Yoshihiro Onouchi
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Michael Levin
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Jane C Burns
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA; Department of Cardiology, Rady Childrens' Hospital San Diego, San Diego, CA, USA
| | - Hiroko Shike
- Department of Pathology, HLA Laboratory, Penn State Hershey Medical Center, Hershey, PA, USA
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14
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Guy J, Alexander-Howden B, FitzPatrick L, DeSousa D, Koerner MV, Selfridge J, Bird A. A mutation-led search for novel functional domains in MeCP2. Hum Mol Genet 2019; 27:2531-2545. [PMID: 29718204 PMCID: PMC6030874 DOI: 10.1093/hmg/ddy159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/26/2018] [Indexed: 12/15/2022] Open
Abstract
Most missense mutations causing Rett syndrome (RTT) affect domains of MeCP2 that have been shown to either bind methylated DNA or interact with a transcriptional co-repressor complex. Several mutations, however, including the C-terminal truncations that account for ∼10% of cases, fall outside these characterized domains. We studied the molecular consequences of four of these ‘non-canonical’ mutations in cultured neurons and mice to see if they reveal additional essential domains without affecting known properties of MeCP2. The results show that the mutations partially or strongly deplete the protein and also in some cases interfere with co-repressor recruitment. These mutations therefore impact the activity of known functional domains and do not invoke new molecular causes of RTT. The finding that a stable C-terminal truncation does not compromise MeCP2 function raises the possibility that small molecules which stabilize these mutant proteins may be of therapeutic value.
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Affiliation(s)
- Jacky Guy
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Laura FitzPatrick
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dina DeSousa
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martha V Koerner
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Jim Selfridge
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Adrian Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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15
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Boegel S, Löwer M, Bukur T, Sorn P, Castle JC, Sahin U. HLA and proteasome expression body map. BMC Med Genomics 2018; 11:36. [PMID: 29587858 PMCID: PMC5872580 DOI: 10.1186/s12920-018-0354-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/19/2018] [Indexed: 12/21/2022] Open
Abstract
Background The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA genes and the complex composition of the proteasome make it difficult to map their expression profiles across tissues. Methods Here we applied a tailored gene quantification pipeline to 4323 publicly available RNA-Seq datasets representing 55 normal tissues and cell types to examine expression profiles of (classical and non-classical) HLA class I, class II and proteasomal genes. Results We generated the first comprehensive expression atlas of antigen presenting-related genes across 56 normal tissues and cell types, including immune cells, pancreatic islets, platelets and hematopoietic stem cells. We found a surprisingly heterogeneous HLA expression pattern with up to 100-fold difference in intra-tissue median HLA abundances. Cells of the immune system and lymphatic organs expressed the highest levels of classical HLA class I (HLA-A,-B,-C), class II (HLA-DQA1,-DQB1,-DPA1,-DPB1,-DRA,-DRB1) and non-classical HLA class I (HLA-E,-F) molecules, whereas retina, brain, muscle, megakaryocytes and erythroblasts showed the lowest abundance. In contrast, we identified a distinct and highly tissue-restricted expression pattern of the non-classical class I gene HLA-G in placenta, pancreatic islets, pituitary gland and testis. While the constitutive proteasome showed relatively constant expression across all tissues, we found the immunoproteasome to be enriched in lymphatic organs and almost absent in immune privileged tissues. Conclusions Here, we not only provide a reference catalog of tissue and cell type specific HLA expression, but also highlight extremely variable expression of the basic components of antigen processing and presentation in different cell types. Our findings indicate that low expression of classical HLA class I molecules together with lack of immunoproteasome components as well as upregulation of HLA-G may be of key relevance to maintain tolerance in immune privileged tissues. Electronic supplementary material The online version of this article (10.1186/s12920-018-0354-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Boegel
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany.
| | - Martin Löwer
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - Thomas Bukur
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - Patrick Sorn
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - John C Castle
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany.,Present address: Agenus Inc, Lexington MA, 02421, USA
| | - Ugur Sahin
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
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16
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Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, Solit D, Berger M, Zhou R, Rizvi NA, Chan TA. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 2018; 359:582-587. [PMID: 29217585 PMCID: PMC6057471 DOI: 10.1126/science.aao4572] [Citation(s) in RCA: 722] [Impact Index Per Article: 120.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CD8+ T cell-dependent killing of cancer cells requires efficient presentation of tumor antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to which patient-specific HLA-I genotype influences response to anti-programmed cell death protein 1 or anti-cytotoxic T lymphocyte-associated protein 4 is currently unknown. We determined the HLA-I genotype of 1535 advanced cancer patients treated with immune checkpoint blockade (ICB). Maximal heterozygosity at HLA-I loci ("A," "B," and "C") improved overall survival after ICB compared with patients who were homozygous for at least one HLA locus. In two independent melanoma cohorts, patients with the HLA-B44 supertype had extended survival, whereas the HLA-B62 supertype (including HLA-B*15:01) or somatic loss of heterozygosity at HLA-I was associated with poor outcome. Molecular dynamics simulations of HLA-B*15:01 revealed different elements that may impair CD8+ T cell recognition of neoantigens. Our results have important implications for predicting response to ICB and for the design of neoantigen-based therapeutic vaccines.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claud M Grigg
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA
| | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Robert M Samstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sviatoslav M Kendall
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Oncological Sciences, and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James Carroll
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - Edward Garon
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Naiyer A Rizvi
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
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17
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Villain G, Poissonnier L, Noueihed B, Bonfils G, Rivera JC, Chemtob S, Soncin F, Mattot V. miR-126-5p promotes retinal endothelial cell survival through SetD5 regulation in neurons. Development 2018; 145:dev.156232. [PMID: 29180574 DOI: 10.1242/dev.156232] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/20/2017] [Indexed: 12/17/2022]
Abstract
MicroRNAs are key regulators of angiogenesis, as illustrated by the vascular defects observed in miR-126-deficient animals. The miR-126 duplex gives rise to two mature microRNAs (miR-126-3p and -5p). The vascular defects in these mutant animals were attributed to the loss of miR-126-3p but the role of miR-126-5p during normal angiogenesis in vivo remains unknown. Here, we show that miR-126-5p is expressed in endothelial cells but also by retinal ganglion cells (RGCs) of the mouse postnatal retina and participates in protecting endothelial cells from apoptosis during the establishment of the retinal vasculature. miR-126-5p negatively controls class 3 semaphorin protein (Sema3A) in RGCs through the repression of SetD5, an uncharacterized member of the methyltransferase family of proteins. In vitro, SetD5 controls Sema3A expression independently of its SET domain and co-immunoprecipitates with BRD2, a bromodomain protein that recruits transcription regulators onto the chromatin. Both SetD5 and BRD2 bind to the transcription start site and to upstream promoter regions of the Sema3a locus and BRD2 is necessary for the regulation of Sema3A expression by SetD5. Thus, neuronally expressed miR-126-5p regulates angiogenesis by protecting endothelial cells of the developing retinal vasculature from apoptosis.
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Affiliation(s)
- Gaëlle Villain
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Loïc Poissonnier
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Baraa Noueihed
- Department of Pediatrics, Ophthalmology, and Pharmacology, CHU Sainte-Justine Research Center, Université de Montréal, Montréal, H1T 2M4 Québec, Canada
| | - Gaëlle Bonfils
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Jose Carlos Rivera
- Department of Pediatrics, Ophthalmology, and Pharmacology, CHU Sainte-Justine Research Center, Université de Montréal, Montréal, H1T 2M4 Québec, Canada
| | - Sylvain Chemtob
- Department of Pediatrics, Ophthalmology, and Pharmacology, CHU Sainte-Justine Research Center, Université de Montréal, Montréal, H1T 2M4 Québec, Canada
| | - Fabrice Soncin
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Virginie Mattot
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
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18
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Stability and Expression Levels of HLA-C on the Cell Membrane Modulate HIV-1 Infectivity. J Virol 2017; 92:JVI.01711-17. [PMID: 29070683 PMCID: PMC5730790 DOI: 10.1128/jvi.01711-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/16/2017] [Indexed: 12/17/2022] Open
Abstract
HLA-C expression is associated with a differential ability to control HIV-1 infection. Higher HLA-C levels may lead to better control of HIV-1 infection through both a higher efficiency of antigen presentation to cytotoxic T lymphocytes and the triggering of activating killer immunoglobulin-like receptors on NK cells, whereas lower levels may provide poor HIV-1 control and rapid progression to AIDS. We characterized the relative amounts of HLA-C heterotrimers (heavy chain/β2 microglobulin [β2m]/peptide) and HLA-C free heavy chains on peripheral blood mononuclear cells (PBMCs) from healthy blood donors harboring both alleles with stable or unstable binding to β2m/peptide. We analyzed the stability of HLA-C heterotrimers of different allotypes and the infectivity of HIV-1 virions produced by PBMCs with various allotypes. We observed significant differences in HLA-C heterotrimer stability and in expression levels. We found that R5 HIV-1 virions produced by PBMCs harboring unstable HLA-C alleles were more infectious than those produced by PBMCs carrying the stable variants. We propose that HIV-1 infectivity might depend both on the amounts of HLA-C molecules and on their stability as trimeric complex. According to this model, individuals with low-expression HLA-C alleles and unstable binding to β2m/peptide might have worse control of HIV-1 infection and an intrinsically higher capacity to support viral replication. IMPORTANCE Following HIV-1 infection, some people advance rapidly to AIDS while others have slow disease progression. HLA-C, a molecule involved in immunity, is a key determinant of HIV-1 control. Here we reveal how HLA-C variants contribute to the modulation of viral infectivity. HLA-C is present on the cell surface in two different conformations. The immunologically active conformation is part of a complex that includes β2 microglobulin/peptide; the other conformation is not bound to β2 microglobulin/peptide and can associate with HIV-1, increasing its infectivity. Individuals with HLA-C variants with a predominance of immunologically active conformations would display stronger immunity to HIV-1, reduced viral infectivity and effective control of HIV-1 infection, while subjects with HLA-C variants that easily dissociate from β2 microglobulin/peptide would have a reduced immunological response to HIV-1 and produce more infectious virions. This study provides new information that could be useful in the design of novel vaccine strategies and therapeutic approaches to HIV-1.
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19
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Di Marco M, Schuster H, Backert L, Ghosh M, Rammensee HG, Stevanović S. Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:2639-2651. [PMID: 28904123 DOI: 10.4049/jimmunol.1700938] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2023]
Abstract
The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides. To that end, the 15 most frequently expressed HLA-C alleles as well as HLA-E*01:01 and HLA-G*01:01 were transfected into lymphoblastoid C1R cells expressing low endogenous HLA. Identification of naturally presented peptides was performed by immunoprecipitation of HLA and subsequent analysis of HLA-bound peptides by liquid chromatographic tandem mass spectrometry. Peptide motifs of HLA-C unveil anchors in position 2 or 3 with high variances between allotypes, and a less variable anchor at the C-terminal end. The previously reported small ligand repertoire of HLA-E was confirmed within our analysis, and we could show that HLA-G combines a large ligand repertoire with distinct features anchoring peptides at positions 3 and 9, supported by an auxiliary anchor in position 1 and preferred residues in positions 2 and 7. The wealth of HLA ligands resulted in prediction matrices for octa-, nona-, and decamers. Matrices were validated in terms of their binding prediction and compared with the latest NetMHC prediction algorithm NetMHCpan-3.0, which demonstrated their predictive power.
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Affiliation(s)
- Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Immatics Biotechnologies GmbH, 72076 Tübingen, Germany; and
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany;
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20
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TGF-β induces phosphorylation of phosphatase and tensin homolog: implications for fibrosis of the trabecular meshwork tissue in glaucoma. Sci Rep 2017; 7:812. [PMID: 28400560 PMCID: PMC5429747 DOI: 10.1038/s41598-017-00845-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/16/2017] [Indexed: 01/06/2023] Open
Abstract
Fundamental cell signaling mechanisms that regulate dynamic remodeling of the extracellular matrix (ECM) in mechanically loaded tissues are not yet clearly understood. Trabecular meshwork (TM) tissue in the eye is under constant mechanical stress and continuous remodeling of ECM is crucial to maintain normal aqueous humor drainage and intraocular pressure (IOP). However, excessive ECM remodeling can cause fibrosis of the TM as in primary open-angle glaucoma (POAG) patients, and is characterized by increased resistance to aqueous humor drainage, elevated IOP, optic nerve degeneration and blindness. Increased levels of active transforming growth factor-β2 (TGF-β2) in the aqueous humor is the main cause of fibrosis of TM in POAG patients. Herein, we report a novel finding that, in TM cells, TGF-β-induced increase in collagen expression is associated with phosphorylation of phosphatase and tensin homolog (PTEN) at residues Ser380/Thr382/383. Exogenous overexpression of a mutated form of PTEN with enhanced phosphatase activity prevented the TGF-β-induced collagen expression by TM cells. We propose that rapid alteration of PTEN activity through changes in its phosphorylation status could uniquely regulate the continuous remodeling of ECM in the normal TM. Modulating PTEN activity may have high therapeutic potential to alleviating the fibrosis of TM in POAG patients.
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Prevosto C, Usmani MF, McDonald S, Gumienny AM, Key T, Goodman RS, Gaston JSH, Deery MJ, Busch R. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules. PLoS One 2016; 11:e0161011. [PMID: 27529174 PMCID: PMC4987023 DOI: 10.1371/journal.pone.0161011] [Citation(s) in RCA: 7] [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: 02/29/2016] [Accepted: 07/28/2016] [Indexed: 11/29/2022] Open
Abstract
Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles.
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Affiliation(s)
- Claudia Prevosto
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - M. Farooq Usmani
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah McDonald
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tim Key
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Reyna S. Goodman
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - J. S. Hill Gaston
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Life Sciences, University of Roehampton, London, United Kingdom
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22
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Frietze KK, Pappy AL, Melson JW, O'Driscoll EE, Tyler CM, Perlman DH, Boulanger LM. Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins. BMC Immunol 2016; 17:24. [PMID: 27435737 PMCID: PMC4950430 DOI: 10.1186/s12865-016-0154-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/27/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Major histocompatibility complex class I (MHCI) proteins present antigenic peptides for immune surveillance and play critical roles in nervous system development and plasticity. Most MHCI are transmembrane proteins. The extracellular domain of MHCI interacts with immunoreceptors, peptides, and co-receptors to mediate immune signaling. While the cytoplasmic domain also plays important roles in endocytic trafficking, cross-presentation of extracellularly derived antigens, and CTL priming, the molecular mediators of cytoplasmic signaling by MHCI remain largely unknown. RESULTS Here we show that the cytoplasmic domain of MHCI contains putative protein-protein interaction domains known as PDZ (PSD95/disc large/zonula occludens-1) ligands. PDZ ligands are motifs that bind to PDZ domains to organize and mediate signaling at cell-cell contacts. PDZ ligands are short, degenerate motifs, and are therefore difficult to identify via sequence homology alone, but several lines of evidence suggest that putative PDZ ligand motifs in MHCI are under positive selective pressure. Putative PDZ ligands are found in all of the 99 MHCI proteins examined from diverse species, and are enriched in the cytoplasmic domain, where PDZ interactions occur. Both the position of the PDZ ligand and the class of ligand motif are conserved across species, as well as among genes within a species. Non-synonymous substitutions, when they occur, frequently preserve the motif. Of the many specific possible PDZ ligand motifs, a handful are strikingly and selectively overrepresented in MHCI's cytoplasmic domain, but not elsewhere in the same proteins. Putative PDZ ligands in MHCI encompass conserved serine and tyrosine residues that are targets of phosphorylation, a post-translational modification that can regulate PDZ interactions. Finally, proof-of-principle in vitro interaction assays demonstrate that the cytoplasmic domains of particular MHCI proteins can bind directly and specifically to PDZ1 and PDZ4&5 of MAGI-1, and identify a conserved PDZ ligand motif in the classical MHCI H2-K that is required for this interaction. CONCLUSIONS These results identify cryptic protein interaction motifs in the cytoplasmic domain of MHCI. In so doing, they suggest that the cytoplasmic domain of MHCI could participate in previously unsuspected PDZ mediated protein-protein interactions at neuronal as well as immunological synapses.
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Affiliation(s)
- Karla K Frietze
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Adlai L Pappy
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jack W Melson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Emily E O'Driscoll
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Carolyn M Tyler
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA
| | - David H Perlman
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Lisa M Boulanger
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
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23
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Screening and identification of proteins interacting with IL-24 by the yeast two-hybrid screen, Co-IP, and FRET assays. Anticancer Drugs 2016; 27:318-27. [PMID: 26930462 DOI: 10.1097/cad.0000000000000343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Interleukin-24 (IL-24) is an ideal tumor-suppressor gene, but the mechanisms underlying its antitumor specificity remain to be elucidated. The best way to investigate these problems is to begin from the initiation of corresponding signaling cascades activated by IL-24 with screening and identifying those proteins that interacted with IL-24. With the aim of identifying these initial interactions, a yeast two-hybrid screening was performed by transforming AH109 cells containing PGBKT7-IL-24 with a liver cDNA plasmid library. These cells were then plated on synthetic nutrient medium (SD/-Trp/-Leu/-His) for the first screening and on quadruple dropout medium containing X-α-gal for the second screening. Positive colonies were further verified by repeating the MATE experiments, co-immunoprecipitation (Co-IP) analysis, and fluorescence resonance energy transfer (FRET) assays in vitro. Following the yeast two-hybrid screening, 15 genes were selected for sequencing, with two genes, HLA-C and NDUFA13, further verified using Co-IP assays and FRET assays. Both HLA-C and NDUFA13 were found to interact with IL-24. We found that HLA-C and NDUFA13 could interact with IL-24 and it may be involved in the signal induced by IL-24. Overall, this study contributes further insight into the cancer-specific apoptosis-inducing abilities of IL-24 to potentially enhance its therapeutic potential, and it also provides outlets for other biological functions of IL-24.
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24
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Abstract
HIV-1 Nef binds to the cytoplasmic region of HLA-A and HLA-B and downregulates these molecules from the surface of virus-infected cells, thus evading immune detection by CD8+ T cells. Polymorphic residues within the HLA cytoplasmic region may affect Nef’s downregulation activity. However, the effects of HLA polymorphisms on recognition by primary Nef isolates remain elusive, as do the specific Nef regions responsible for downregulation of HLA-A versus HLA-B. Here, we examined 46 Nef clones isolated from chronically HIV-1 subtype B-infected subjects for their ability to downregulate various HLA-A, HLA-B, and HLA-C molecules on the surface of virus-infected cells. Overall, HLA-B exhibited greater resistance to Nef-mediated downregulation than HLA-A, regardless of the cell type examined. As expected, no Nef clone downregulated HLA-C. Importantly, the differential abilities of patient-derived Nef clones to downregulate HLA-A and HLA-B correlated inversely with the sensitivities of HIV-infected target cells to recognition by effector cells expressing an HIV-1 Gag-specific T cell receptor. Nef codon function analysis implicated amino acid variation at position 202 (Nef-202) in differentially affecting the ability to downregulate HLA-A and HLA-B, an observation that was subsequently confirmed by experiments using Nef mutants constructed by site-directed mutagenesis. The in silico and mutagenesis analyses further suggested that Nef-202 may interact with the C-terminal Cys-Lys-Val residues of HLA-A, which are absent in HLA-B. Taken together, the results show that natural polymorphisms within Nef modulate its interaction with natural polymorphisms in the HLA cytoplasmic tails, thereby affecting the efficiency of HLA downregulation and consequent recognition by HIV-specific T cells. These results thus extend our understanding of this complex pathway of retroviral immune evasion. Recognition of genetically diverse pathogens by the adaptive immune system represents a primary strategy for host defense; however, pathogens such as HIV-1 can evade these responses to achieve persistent infection. The HIV-1 nef gene and the HLA class I locus rank among the most diverse genes of virus and host, respectively. The HIV-1 Nef protein interacts with the cytoplasmic region of HLA-A and HLA-B and downregulates these molecules to evade cellular immunity. By combining molecular, genetic, and in silico analyses, we demonstrate that patient-derived Nef clones downregulate HLA-A more effectively than HLA-B molecules. This in turn modulates the ability of HIV-specific T cells to recognize HIV-infected cells. We also identify a naturally polymorphic site at Nef codon 202 and HLA cytoplasmic motifs (GG314,315 and CKV339–341) that contribute to differential HLA downregulation by Nef. Our results highlight new interactions between HIV-1 and the human immune system that may contribute to pathogenesis.
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25
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Schellens IMM, Hoof I, Meiring HD, Spijkers SNM, Poelen MCM, van Gaans-van den Brink JAM, van der Poel K, Costa AI, van Els CACM, van Baarle D, Kesmir C. Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PLoS One 2015; 10:e0136417. [PMID: 26375851 PMCID: PMC4574158 DOI: 10.1371/journal.pone.0136417] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/04/2015] [Indexed: 01/23/2023] Open
Abstract
The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.
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Affiliation(s)
- Ingrid M. M. Schellens
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Hugo D. Meiring
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Sanne N. M. Spijkers
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Martien C. M. Poelen
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Kees van der Poel
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ana I. Costa
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cecile A. C. M. van Els
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debbie van Baarle
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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26
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Goyos A, Guethlein LA, Horowitz A, Hilton HG, Gleimer M, Brodsky FM, Parham P. A Distinctive Cytoplasmic Tail Contributes to Low Surface Expression and Intracellular Retention of the Patr-AL MHC Class I Molecule. THE JOURNAL OF IMMUNOLOGY 2015; 195:3725-36. [PMID: 26371256 DOI: 10.4049/jimmunol.1500397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/07/2015] [Indexed: 01/24/2023]
Abstract
Chimpanzees have orthologs of the six fixed, functional human MHC class I genes. But, in addition, the chimpanzee has a seventh functional gene, Patr-AL, which is not polymorphic but contributes substantially to population diversity by its presence on only 50% of MHC haplotypes. The ancestral AL gene emerged long before the separation of human and chimpanzee ancestors and then subsequently and specifically lost function during human evolution, but was maintained in chimpanzees. Patr-AL is an alloantigen that participates in negative and positive selection of the T cell repertoire. The three-dimensional structure and the peptide-binding repertoire of Patr-AL and HLA-A*02 are surprisingly similar. In contrast, the expression of these two molecules is very different, as shown using specific mAbs and polyclonal Abs made against Patr-AL. Peripheral blood cells and B cell lines express low levels of Patr-AL at the cell surface. Higher levels are seen for 221-cell transfectants expressing Patr-AL, but in these cells a large majority of Patr-AL molecules are retained in the early compartments of the secretory pathway: mainly the endoplasmic reticulum, but also cis-Golgi. Replacing the cytoplasmic tail of Patr-AL with that of HLA-A*02 increased the cell-surface expression of Patr-AL substantially. Four substitutions distinguish the Patr-AL and HLA-A*02 cytoplasmic tails. Systematic mutagenesis showed that each substitution contributes changes in cell-surface expression. The combination of residues present in Patr-AL appears unique, but each individual residue is present in other primate MHC class I molecules, notably MHC-E, the most ancient of the functional human MHC class I molecules.
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Affiliation(s)
- Ana Goyos
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Amir Horowitz
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael Gleimer
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Frances M Brodsky
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143; and Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Stanford Immunology, Stanford University School of Medicine, Stanford, CA 94305;
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27
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Thus KA, Te Boome L, Kuball J, Spierings E. Indirectly Recognized HLA-C Mismatches and Their Potential Role in Transplant Outcome. Front Immunol 2014; 5:210. [PMID: 24860572 PMCID: PMC4026718 DOI: 10.3389/fimmu.2014.00210] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/27/2014] [Indexed: 01/02/2023] Open
Abstract
HLA-C mismatches are clearly associated to alloreactivity after hematopoietic stem-cell transplantation; in a number of large cohorts, HLA-C mismatches are correlated to an increased risk of acute graft-versus-host disease (GVHD) or even impaired survival. While for HLA-A and -B, both antigenic as well as allelic mismatches are associated with an increased risk of acute GVHD, such an increased risk is only observed for antigenic HLA-C mismatches and not for allelic mismatches. These observations raise the question what sets HLA-C apart from HLA-A and -B. The difference may well be related to the reduced levels of cell-surface expression of HLA-C as compared to HLA-A and -B, possibly due to, among other factors, a limited peptide-binding capacity. This limited peptide-binding capacity may retain HLA-C in the ER and enhance degradation of the HLA-C protein. Once degraded, HLA-C-derived peptides can be presented to the immune system via other HLA alleles and are thus available for indirect recognition. Indeed, such HLA-C-derived peptides have previously been eluted from other HLA alleles. We have recently developed an approach to predict indirect recognition of HLA molecules, by establishing the numbers of predicted indirectly recognizable HLA epitopes (PIRCHES). The number of PIRCHES presented on HLA class I and II (PIRCHE-I and -II, respectively), are highly correlated to clinical measures of alloreactivity, such as acute GVHD. In the present “Hypothesis & Theory,” we reviewed the current knowledge on HLA-C mismatches and alloreactivity. Moreover, we speculate about the role of direct and indirect recognition of HLA-C and the consequences for donor selection in HLA-C mismatched stem-cell transplantation.
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Affiliation(s)
- Kirsten A Thus
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Liane Te Boome
- Department of Hematology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Jürgen Kuball
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands ; Department of Hematology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Eric Spierings
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
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28
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Kulkarni S, Qi Y, O’hUigin C, Pereyra F, Ramsuran V, McLaren P, Fellay J, Nelson G, Chen H, Liao W, Bass S, Apps R, Gao X, Yuki Y, Lied A, Ganesan A, Hunt PW, Deeks SG, Wolinsky S, Walker BD, Carrington M. Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease. Proc Natl Acad Sci U S A 2013; 110:20705-10. [PMID: 24248364 PMCID: PMC3870724 DOI: 10.1073/pnas.1312237110] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Variation in the 3' untranslated region (3'UTR) of the HLA-C locus determines binding of the microRNA Hsa-miR-148a, resulting in lower cell surface expression of alleles that bind miR-148a relative to those alleles that escape its binding. The HLA-C 3'UTR variant was shown to associate with HIV control, but like the vast majority of disease associations in a region dense with causal candidates, a direct effect of HLA-C expression level on HIV control was not proven. We demonstrate that a MIR148A insertion/deletion polymorphism associates with its own expression levels, affecting the extent to which HLA-C is down-regulated, the level of HIV control, and the risk of Crohn disease only among those carrying an intact miR-148a binding site in the HLA-C 3'UTR. These data illustrate a direct effect of HLA-C expression level on HIV control that cannot be attributed to other HLA loci in linkage disequilibrium with HLA-C and highlight the rich complexity of genetic interactions in human disease.
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Affiliation(s)
- Smita Kulkarni
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Colm O’hUigin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Veron Ramsuran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Paul McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne and Institute of Microbiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne and Institute of Microbiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - George Nelson
- Basic Research Program, Center for Cancer Research Genetics Core, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Haoyan Chen
- Department of Dermatology, University of California, San Francisco, CA 94115
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA 94115
| | - Sara Bass
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
| | - Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Alexandra Lied
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD 20817
| | - Peter W. Hunt
- San Francisco General Hospital AIDS Division, University of California, San Francisco, CA 94110; and
| | - Steven G. Deeks
- San Francisco General Hospital AIDS Division, University of California, San Francisco, CA 94110; and
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
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Marchesi M, Andersson E, Villabona L, Seliger B, Lundqvist A, Kiessling R, Masucci GV. HLA-dependent tumour development: a role for tumour associate macrophages? J Transl Med 2013; 11:247. [PMID: 24093459 PMCID: PMC3856519 DOI: 10.1186/1479-5876-11-247] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/01/2013] [Indexed: 02/06/2023] Open
Abstract
HLA abnormalities on tumour cells for immune escape have been widely described. In addition, cellular components of the tumour microenvironment, in particular myeloid derived suppressor cells (MDSC) and alternatively activated M2 tumour-associated macrophages (TAMs), are involved in tumour promotion, progression, angiogenesis and suppression of anti-tumour immunity. However, the role of HLA in these activities is poorly understood. This review details MHC class I characteristics and describes MHC class I receptors functions. This analysis established the basis for a reflection about the crosstalk among the tumour cells, the TAMs and the cells mediating an immune response.The tumour cells and TAMs exploit MHC class I molecules to modulate the surrounding immune cells. HLA A, B, C and G molecules down-regulate the macrophage myeloid activation through the interaction with the inhibitory LILRB receptors. HLA A, B, C are able to engage inhibitory KIR receptors negatively regulating the Natural Killer and cytotoxic T lymphocytes function while HLA-G induces the secretion of pro-angiogenic cytokines and chemokine thanks to an activator KIR receptor expressed by a minority of peripheral NK cells. The open conformer of classical MHC-I is able to interact with LILRA receptors described as being associated to the Th2-type cytokine response, triggering a condition for the M2 like TAM polarization. In addition, HLA-E antigens on the surface of the TAMs bind the inhibitory receptor CD94/NKG2A expressed by a subset of NK cells and activated cytotoxic T lymphocytes protecting from the cytolysis.Furthermore MHC class II expression by antigen presenting cells is finely regulated by factors provided with immunological capacities. Tumour-associated macrophages show an epigenetically controlled down-regulation of the MHC class II expression induced by the decoy receptor DcR3, a member of the TNFR, which further enhances the M2-like polarization. BAT3, a positive regulator of MHC class II expression in normal macrophages, seems to be secreted by TAMs, consequently lacking its intracellular function, it looks like acting as an immunosuppressive factor.In conclusion HLA could cover a considerable role in tumour-development orchestrated by tumour-associated macrophages.
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Affiliation(s)
- Maddalena Marchesi
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
- Roche Pharma, Basel, Switzerland
| | - Emilia Andersson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Lisa Villabona
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Andreas Lundqvist
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Rolf Kiessling
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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30
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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31
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Adaptor protein 1 promotes cross-presentation through the same tyrosine signal in major histocompatibility complex class I as that targeted by HIV-1. J Virol 2013; 87:8085-98. [PMID: 23678182 DOI: 10.1128/jvi.00701-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain antigen-presenting cells (APCs) process and present extracellular antigen with major histocompatibility complex class I (MHC-I) molecules to activate naive CD8(+) T cells in a process termed cross-presentation. We used insights gained from HIV immune evasion strategies to demonstrate that the clathrin adaptor protein adaptor protein 1 (AP-1) is necessary for cross-presentation by MHC-I molecules containing a cytoplasmic tail tyrosine signal (murine MHC-I molecules, human MHC-I HLA-A and HLA-B allotypes). In contrast, AP-1 activity was not needed for cross-presentation by MHC-I molecules containing a human MHC-I HLA-C cytoplasmic tail, which does not contain a tyrosine signal. AP-1 activity was also dispensable for presentation of endogenous antigens by MHC-I via the classical pathway. In APCs, we show that HIV Nef disrupts cross-presentation by MHC-I containing the tyrosine signal but does not affect cross-presentation by MHC-I containing the HLA-C cytoplasmic tail. Thus, we provide evidence for two separable cross-presentation pathways, only one of which is targeted by HIV.
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32
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Guiliano DB, Antoniou AN. Measuring synthesis and degradation of MHC class I molecules. Methods Mol Biol 2013; 960:93-108. [PMID: 23329481 DOI: 10.1007/978-1-62703-218-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Major histocompatibility complex (MHC) class I molecules function to present pathogen-derived peptides to cytotoxic T cells or act as ligands for Natural Killer cells, thus alerting the immune system to the presence of invading pathogens. Furthermore MHC class I molecules can be strongly associated with autoimmune diseases. Therefore understanding not only the biosynthesis and the degradation pathways of MHC class I molecules has become important in determining their role in pathogen and autoimmune-related diseases. Here we describe how using epitope-tagged MHC class I molecules can aid in the analysis of MHC class I molecule biosynthesis and degradation and also complement studies using conventional conformationally specific antibodies. Coupled together with pharmacological manipulation which can target both biosynthetic and degradative pathways, this offers a powerful tool in analyzing MHC class I molecules.
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Affiliation(s)
- David B Guiliano
- School of Health, Sport and Bioscience, University of East London, London, UK
| | - Antony N Antoniou
- Division of Infection and Immunity/Centre of Rheumatology, Department of Immunology and Molecular Pathology, London, UK.
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33
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HLA-B may be more protective against HIV-1 than HLA-A because it resists negative regulatory factor (Nef) mediated down-regulation. Proc Natl Acad Sci U S A 2012; 109:13353-8. [PMID: 22826228 DOI: 10.1073/pnas.1204199109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen HLA-B alleles have better protective activity against HIV-1 than HLA-A alleles, possibly due to differences in HLA-restricted HIV-1-specific CD8+ cytotoxic T lymphocyte (CTL) function, but the mechanism is unknown. HIV-1 negative regulatory factor (Nef) mediates down-regulation of surface expression of class I HLA (HLA-I) and may therefore impair immune recognition by CTL. Because of sequence differences in the cytoplasmic domains, HLA-A and -B are down-regulated by Nef but HLA-C and -E are not affected. However, the latter are expressed at low levels and are not of major importance in the CTL responses to HIV-1. Here, we compared the role of the cytoplasmic domains of HLA-A and -B in Nef-mediated escape from CTL. We found HLA-B cytoplasmic domains were more resistant to Nef-mediated down-regulation than HLA-A cytoplasmic domains and demonstrated that these differences affect CTL recognition of virus-infected cells in vitro. We propose that the relative resistance to Nef-mediated down-regulation by the cytoplasmic domains of HLA-B compared with HLA-A contributes to the better control of HIV-1 infection associated with HLA-B-restricted CTLs.
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34
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Zipeto D, Beretta A. HLA-C and HIV-1: friends or foes? Retrovirology 2012; 9:39. [PMID: 22571741 PMCID: PMC3386009 DOI: 10.1186/1742-4690-9-39] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/09/2012] [Indexed: 12/20/2022] Open
Abstract
The major histocompatibility complex class I protein HLA-C plays a crucial role as a molecule capable of sending inhibitory signals to both natural killer (NK) cells and cytotoxic T lymphocytes (CTL) via binding to killer cell Ig-like receptors (KIR). Recently HLA-C has been recognized as a key molecule in the immune control of HIV-1. Expression of HLA-C is modulated by a microRNA binding site. HLA-C alleles that bear substitutions in the microRNA binding site are more expressed at the cell surface and associated with the control of HIV-1 viral load, suggesting a role of HLA-C in the presentation of antigenic peptides to CTLs. This review highlights the role of HLA-C in association with HIV-1 viral load, but also addresses the contradiction of the association between high cell surface expression of an inhibitory molecule and strong cell-mediated immunity. To explore additional mechanisms of control of HIV-1 replication by HLA-C, we address specific features of the molecule, like its tendency to be expressed as open conformer upon cell activation, which endows it with a unique capacity to associate with other cell surface molecules as well as with HIV-1 proteins.
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Affiliation(s)
- Donato Zipeto
- Department of Life and Reproduction Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
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35
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Abstract
Host genetic variation is presently estimated to account for about one-fourth of the observed differences in control of HIV across infected individuals. Genome-wide association studies have confirmed that polymorphism within the HLA class I locus is the primary host genetic contributor to determining outcome after infection. Here we progress beyond the genetic associations alone to consider the functional explanations for these correlations. In this process, the complex and multidimensional effects of HLA molecules in viral disease become apparent.
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Affiliation(s)
- Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC–Frederick, Inc., NCI–Frederick, Frederick, Maryland 20882;
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114;
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114;
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36
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Abstract
Recently, genome-wide association studies have identified the major histocompatibility complex class I protein HLA-C as an important molecule that affects HIV disease progression. The association between HLA-C and HIV disease outcome was originally determined through a single nucleotide polymorphism (SNP) 35 kb upstream of the HLA-C locus. More recent work has focused on elucidating the functional significance of the -35 SNP, and several groups now have demonstrated HLA-C surface expression to be a key element in control of HIV viral load, with higher surface expression associating with slower disease progression. Most recently, control of HLA-C surface expression has been correlated with the presence of microRNA binding sites that affect HLA-C expression and control of HIV disease. This review highlights these results and explores the ways in which HLA-C surface expression could affect immune system function in the setting of HIV disease.
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Affiliation(s)
- Deanna A Kulpa
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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37
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Lee KW, Jung YA. Refined information on alleles belonging to the C*07:01/07:06/07:18 group in the Korean population. Hum Immunol 2011; 72:723-6. [DOI: 10.1016/j.humimm.2011.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 04/28/2011] [Accepted: 05/13/2011] [Indexed: 12/27/2022]
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Xu Y, Deng Z, O'hUigin C, Wang D, Gao S, Zeng J, Yang B, Jin S, Zou H. Characterization and polymorphic analysis of 4.5 kb genomic full-length HLA-C in the Chinese Han population. TISSUE ANTIGENS 2011; 78:102-14. [PMID: 21658009 PMCID: PMC7366323 DOI: 10.1111/j.1399-0039.2011.01710.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This study used long-range polymerase chain reaction to sequence 4.5 or 4.3 kb of genomic DNA covering human leukocyte antigen C (HLA-C) and its flanks in 45 Chinese Han subjects to better characterize variation in the gene in a single population. Sequences of 35 HLA-C alleles were obtained from the population, including major alleles of 13 lineages of HLA-C. Four novel alleles, C*03:04:01:02, C*04:01:01:03, C*08:22, and C*17:01:01:02, were identified, and complete full-length sequences of 18 HLA-C alleles were obtained for the first time. All sequences herein reported also represent extensions through the promoter region and the 3'-untranslated region. Fourteen 5'-nucleotide sequences and 14 3'-nucleotide sequences were detected outside the coding region. In total, 316 single-nucleotide polymorphisms unequally distributed in HLA-C subregions were observed. In addition to exons 2 and 3, nucleotide variability was found to be particularly high in exon 5, which encodes the transmembrane region. The differentiation of the C*07 and C*17 lineages in this region accounts for the high variability. The congruence of phylogeny across most regions of the gene suggests that gene conversion or recombination has not markedly influenced divergence between lineages in the evolution of HLA-C.
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Affiliation(s)
- Y Xu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, China
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39
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HIV-1 Nef disrupts intracellular trafficking of major histocompatibility complex class I, CD4, CD8, and CD28 by distinct pathways that share common elements. J Virol 2011; 85:6867-81. [PMID: 21543478 DOI: 10.1128/jvi.00229-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Nef protein is an important HIV virulence factor that promotes the degradation of host proteins to augment virus production and facilitate immune evasion. The best-characterized targets of Nef are major histocompatibility complex class I (MHC-I) and CD4, but Nef also has been reported to target several other proteins, including CD8β, CD28, CD80, CD86, and CD1d. To compare and contrast the effects of Nef on each protein, we constructed a panel of chimeric proteins in which the extracellular and transmembrane regions of the MHC-I allele HLA-A2 were fused to the cytoplasmic tails of CD4, CD28, CD8β, CD80, CD86, and CD1d. We found that Nef coprecipitated with and disrupted the expression of molecules with cytoplasmic tails from MHC-I HLA-A2, CD4, CD8β, and CD28, but Nef did not bind to or alter the expression of molecules with cytoplasmic tails from CD80, CD86, and CD1d. In addition, we used short interfering RNA (siRNA) knockdown and coprecipitation experiments to implicate AP-1 as a cellular cofactor for Nef in the downmodulation of both CD28 and CD8β. The interaction with AP-1 required for CD28 and CD8β differed from the AP-1 interaction required for MHC-I downmodulation in that it was mediated through the dileucine motif within Nef (LL(164,165)AA) and did not require the tyrosine binding pocket of the AP-1 μ subunit. In addition, we demonstrate a requirement for β-COP as a cellular cofactor for Nef that was necessary for the degradation of targeted molecules HLA-A2, CD4, and CD8. These studies provide important new information on the similarities and differences with which Nef affects intracellular trafficking and help focus future research on the best potential pharmaceutical targets.
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40
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Kulkarni S, Savan R, Qi Y, Gao X, Yuki Y, Bass SE, Martin MP, Hunt P, Deeks SG, Telenti A, Pereyra F, Goldstein D, Wolinsky S, Walker B, Young HA, Carrington M. Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature 2011; 472:495-8. [PMID: 21499264 PMCID: PMC3084326 DOI: 10.1038/nature09914] [Citation(s) in RCA: 269] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 02/10/2011] [Indexed: 12/28/2022]
Abstract
The HLA-C locus is distinct relative to the other classical HLA class I loci in that it has relatively limited polymorphism, lower expression on the cell surface, and more extensive ligand-receptor interactions with killer-cell immunoglobulin-like receptors. A single nucleotide polymorphism (SNP) 35 kb upstream of HLA-C (rs9264942; termed -35) associates with control of HIV, and with levels of HLA-C messenger RNA transcripts and cell-surface expression, but the mechanism underlying its varied expression is unknown. We proposed that the -35 SNP is not the causal variant for differential HLA-C expression, but rather is marking another polymorphism that directly affects levels of HLA-C. Here we show that variation within the 3' untranslated region (UTR) of HLA-C regulates binding of the microRNA hsa-miR-148 to its target site, resulting in relatively low surface expression of alleles that bind this microRNA and high expression of HLA-C alleles that escape post-transcriptional regulation. The 3' UTR variant associates strongly with control of HIV, potentially adding to the effects of genetic variation encoding the peptide-binding region of the HLA class I loci. Variation in HLA-C expression adds another layer of diversity to this highly polymorphic locus that must be considered when deciphering the function of these molecules in health and disease.
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Affiliation(s)
- Smita Kulkarni
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
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41
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Raposo RAS, Thomas B, Ridlova G, James W. Proteomic-based identification of CD4-interacting proteins in human primary macrophages. PLoS One 2011; 6:e18690. [PMID: 21533244 PMCID: PMC3076427 DOI: 10.1371/journal.pone.0018690] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 03/15/2011] [Indexed: 11/19/2022] Open
Abstract
Background Human macrophages (Mφ) express low levels of CD4 glycoprotein, which is
constitutively recycled, and 40–50% of its localization is
intracellular at steady-state. Although CD4-interacting proteins in lymphoid
cells are well characterised, little is known about the CD4 protein
interaction-network in human Mφ, which notably lack LCK, a Src family
protein tyrosine kinase believed to stabilise CD4 at the surface of T cells.
As CD4 is the main cellular receptor used by HIV-1, knowledge of its
molecular interactions is important for the understanding of viral infection
strategies. Methodology/Principal Findings We performed large-scale anti-CD4 immunoprecipitations in human primary
Mφ followed by high-resolution mass spectrometry analysis to elucidate
the protein interaction-network involved in induced CD4 internalization and
degradation. Proteomic analysis of CD4 co-immunoisolates in resting Mφ
showed CD4 association with a range of proteins found in the cellular
cortex, membrane rafts and components of clathrin-adaptor proteins, whereas
in induced internalization and degradation CD4 is associated with components
of specific signal transduction, transport and the proteasome. Conclusions/Significance This is the first time that the anti-CD4 co-immunoprecipitation sub-proteome
has been analysed in human primary Mφ. Our data have identified
important Mφ cell surface CD4-interacting proteins, as well as
regulatory proteins involved in internalization and degradation. The data
give valuable insights into the molecular pathways involved in the
regulation of CD4 expression in Mφ and provide candidates/targets for
further biochemical studies.
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42
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Jones DC, Kosmoliaptsis V, Apps R, Lapaque N, Smith I, Kono A, Chang C, Boyle LH, Taylor CJ, Trowsdale J, Allen RL. HLA class I allelic sequence and conformation regulate leukocyte Ig-like receptor binding. THE JOURNAL OF IMMUNOLOGY 2011; 186:2990-7. [PMID: 21270408 DOI: 10.4049/jimmunol.1003078] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Leukocyte Ig-like receptors (LILRs) are a family of innate immune receptors predominantly expressed by myeloid cells that can alter the Ag presentation properties of macrophages and dendritic cells. Several LILRs bind HLA class I. Altered LILR recognition due to HLA allelic variation could be a contributing factor in disease. We comprehensively assessed LILR binding to >90 HLA class I alleles. The inhibitory receptors LILRB1 and LILRB2 varied in their level of binding to different HLA alleles, correlating in some cases with specific amino acid motifs. LILRB2 displayed the weakest binding to HLA-B*2705, an allele genetically associated with several autoimmune conditions and delayed progression of HIV infection. We also assessed the effect of HLA class I conformation on LILR binding. LILRB1 exclusively bound folded β(2)-microglobulin-associated class I, whereas LILRB2 bound both folded and free H chain forms. In contrast, the activating receptor LILRA1 and the soluble LILRA3 protein displayed a preference for binding to HLA-C free H chain. To our knowledge, this is the first study to identify the ligand of LILRA3. These findings support the hypothesis that LILR-mediated detection of unfolded versus folded MHC modulates immune responses during infection or inflammation.
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Affiliation(s)
- Des C Jones
- Immunology Division, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.
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43
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Wonderlich ER, Leonard JA, Collins KL. HIV immune evasion disruption of antigen presentation by the HIV Nef protein. Adv Virus Res 2011; 80:103-27. [PMID: 21762823 PMCID: PMC3782996 DOI: 10.1016/b978-0-12-385987-7.00005-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Human Immunodeficiency Virus (HIV) Nef protein is necessary for high viral loads and for timely progression to AIDS. Nef plays a number of roles, but its effect on antigen presentation and immune evasion are among the best characterized. Cytotoxic T lymphocytes (CTLs) recognize and lyse virally infected cells by detecting viral antigens in complex with host major histocompatibility complex class I (MHC-I) molecules on the infected cell surface. The HIV Nef protein disrupts antigen presentation at the cell surface by interfering with the normal trafficking pathway of MHC-I and thus reduces CTL recognition and lysis of infected cells. The molecular mechanism by which Nef causes MHC-I downmodulation is becoming more clear, but some questions remain. A better understanding of how Nef disrupts antigen presentation may lead to the development of drugs that enhance the ability of the anti-HIV CTLs to control HIV disease.
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Affiliation(s)
- Elizabeth R Wonderlich
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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44
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Taner SB, Pando MJ, Roberts A, Schellekens J, Marsh SGE, Malmberg KJ, Parham P, Brodsky FM. Interactions of NK cell receptor KIR3DL1*004 with chaperones and conformation-specific antibody reveal a functional folded state as well as predominant intracellular retention. THE JOURNAL OF IMMUNOLOGY 2010; 186:62-72. [PMID: 21115737 DOI: 10.4049/jimmunol.0903657] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Variable interaction between the Bw4 epitope of HLA-B and the polymorphic KIR3DL1/S1 system of inhibitory and activating NK cell receptors diversifies the development, repertoire formation, and response of human NK cells. KIR3DL1*004, a common KIR3DL1 allotype, in combination with Bw4(+) HLA-B, slows progression of HIV infection to AIDS. Analysis in this study of KIR3DL1*004 membrane traffic in NK cells shows this allotype is largely misfolded but stably retained in the endoplasmic reticulum, where it binds to the chaperone calreticulin and does not induce the unfolded protein response. A small fraction of KIR3DL1*004 folds correctly and leaves the endoplasmic reticulum to be expressed on the surface of primary NK and transfected NKL cells, in a form that can be triggered to inhibit NK cell activation and secretion of IFN-γ. Consistent with this small proportion of correctly folded molecules, trace amounts of MHC class I coimmunoprecipitated with KIR3DL1*004. There was no indication of any extensive intracellular interaction between unfolded KIR3DL1*004 and cognate Bw4(+) HLA-B. A similarly limited interaction of Bw4 with KIR3DL1*002, when both were expressed by the same cell, was observed despite the efficient folding of KIR3DL1*002 and its abundance on the NK cell surface. Several positions of polymorphism modulate KIR3DL1 abundance at the cell surface, differences that do not necessarily correlate with the potency of allotype function. In this context, our results suggest the possibility that the effect of Bw4(+) HLA-B and KIR3DL1*004 in slowing progression to AIDS is mediated by interaction of Bw4(+) HLA-B with the small fraction of cell surface KIR3DL1*004.
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Affiliation(s)
- Sabrina B Taner
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
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