1
|
Pons-Fuster E, Bernal E, Guillamón CF, Gimeno L, Martínez-Sánchez MV, Ruiz-Lorente I, Campillo JA, Ceballos D, Torres A, Tomás C, Muñoz Á, Alcaraz A, Selma P, Ruiz-Nicolas C, Muro M, Minguela A. HLA-C*07 is associated with symptomatic HIV-1-associated neurocognitive disorders (HAND) and immune dysregulation. Infect Dis (Lond) 2024:1-12. [PMID: 38743055 DOI: 10.1080/23744235.2024.2351047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND HIV-1-associated neurocognitive disorders (HAND) in stable patients undergoing antiretroviral therapy (ART) may result from ongoing immune dysregulation and chronic inflammation. A contributing factor may result from the unstable HLA class I allele, HLA-C*07. OBJECTIVE To assess the genetic profile of killer-cell immunoglobulin-like receptors (KIR), human leukocyte antigens (HLA), and immune activation or senescence markers and their association with HAND in stable HIV-1 patients receiving ART. METHODS An observational cross-sectional study was carried out with 96 patients with asymptomatic or symptomatic HAND. HLA and KIR as well as immune activation/senescence biomarkers in peripheral blood cells were assessed by SSO-Luminex typing and flow cytometry, respectively. RESULTS HLA-C*07 is associated with symptomatic HAND. The frequency of two copies of HLA-C*07 was higher in patients with symptomatic than with asymptomatic HAND (12.0 vs. 2.2%, ρ < 0.001). The percentage of senescent CD8+CD28- T-cells was higher in patients with two copies of HLA-C*07 (ρ < 0.05). In patients with symptomatic HAND, the percentages of non-senescent CD8+CD28+ T cells were inversely proportional to the number of copies of the HLA-C*07 (ρ < 0.05). CONCLUSION Patients with symptomatic HAND showed a higher frequency of the homozygotic unstable HLA-C*07 allotype, which could be associated with neurocognitive complications. Two copies of HLA-C*07 were associated with immune senescent T lymphocyte profiles characterized by the loss of CD28 expression.
Collapse
Affiliation(s)
- Eduardo Pons-Fuster
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Enrique Bernal
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Concepción F Guillamón
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Lourdes Gimeno
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - María V Martínez-Sánchez
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Inmaculada Ruiz-Lorente
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - José A Campillo
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Diana Ceballos
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Ana Torres
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Cristina Tomás
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Ángeles Muñoz
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Antonia Alcaraz
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Pedro Selma
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Carlos Ruiz-Nicolas
- Infectious Disease Unit, University Hospital Reina Sofía and Murcia University and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Manuel Muro
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| | - Alfredo Minguela
- Immunologyservice, Clinic University Hospital Virgen de la Arrixaca and Biomedical Research Institute of Murcia Pascual Parrilla (IMIB), Murcia, Spain
| |
Collapse
|
2
|
Apoorva E, Jacob R, Rao DN, Kumar S. Helicobacter pylori enhances HLA-C expression in the human gastric adenocarcinoma cells AGS and can protect them from the cytotoxicity of natural killer cells. Helicobacter 2024; 29:e13069. [PMID: 38516860 DOI: 10.1111/hel.13069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Helicobacter pylori (H. pylori) seems to play causative roles in gastric cancers. H. pylori has also been detected in established gastric cancers. How the presence of H. pylori modulates immune response to the cancer is unclear. The cytotoxicity of natural killer (NK) cells, toward infected or malignant cells, is controlled by the repertoire of activating and inhibitory receptors expressed on their surface. Here, we studied H. pylori-induced changes in the expression of ligands, of activating and inhibitory receptors of NK cells, in the gastric adenocarcinoma AGS cells, and their impacts on NK cell responses. AGS cells lacked or had low surface expression of the class I major histocompatibility complex (MHC-I) molecules HLA-E and HLA-C-ligands of the major NK cell inhibitory receptors NKG2A and killer-cell Ig-like receptor (KIR), respectively. However, AGS cells had high surface expression of ligands of activating receptors DNAM-1 and CD2, and of the adhesion molecules LFA-1. Consistently, AGS cells were sensitive to killing by NK cells despite the expression of inhibitory KIR on NK cells. Furthermore, H. pylori enhanced HLA-C surface expression on AGS cells. H. pylori infection enhanced HLA-C protein synthesis, which could explain H. pylori-induced HLA-C surface expression. H. pylori infection enhanced HLA-C surface expression also in the hepatoma Huh7 and HepG2 cells. Furthermore, H. pylori-induced HLA-C surface expression on AGS cells promoted inhibition of NK cells by KIR, and thereby protected AGS cells from NK cell cytotoxicity. These results suggest that H. pylori enhances HLA-C expression in host cells and protects them from the cytotoxic attack of NK cells expressing HLA-C-specific inhibitory receptors.
Collapse
Affiliation(s)
- Etikala Apoorva
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rini Jacob
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Santosh Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
3
|
Chikata T, Gatanaga H, Nguyen HT, Mizushima D, Zhang Y, Kuse N, Oka S, Takiguchi M. HIV-1 protective epitope-specific CD8 + T cells in HIV-1-exposed seronegative individuals. iScience 2023; 26:108089. [PMID: 37867946 PMCID: PMC10589889 DOI: 10.1016/j.isci.2023.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/08/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Although previous studies have reported HIV-1-specific T cell responses in HIV-1-exposed seronegative (HESN) individuals, there has been no detailed analysis of these T cells against HIV-1 infection. We investigated HIV-1-specific CD8+ T cell responses in 200 Japanese HESN men who have sex with men (MSM). T cell responses to 143 well-characterized HIV-1 epitope peptides were analyzed by intracellular cytokine staining assay consisting of 3-week cultures of PBMCs stimulated with peptides. HLA-B∗51:01-restricted Pol TI8-specific and HLA-A∗02:06-restricted Pol SV9-specific CD8+ T cells were identified in two and one individuals, respectively, whereas CD8+ T cells specific for other HLA-A∗02:06-restricted or HLA-B∗51:01 epitopes were not present in these individuals. These epitope-specific T cells recognized HIV-1-infected cells. Because these two epitopes were previously reported to be protective in HIV-1-infected individuals, these protective epitope-specific T cells might suppress HIV-1 replication in HESN-MSM individuals. The present study suggests the contribution of protective epitope-specific T cells to protection against HIV-1 infection.
Collapse
Affiliation(s)
- Takayuki Chikata
- Tokyo Laboratory and Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 162-0052, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
| | - Hung The Nguyen
- Tokyo Laboratory and Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 162-0052, Japan
| | - Daisuke Mizushima
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
| | - Yu Zhang
- Tokyo Laboratory and Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 162-0052, Japan
| | - Nozomi Kuse
- Tokyo Laboratory and Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 162-0052, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
| | - Masafumi Takiguchi
- Tokyo Laboratory and Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 162-0052, Japan
| |
Collapse
|
4
|
Tay GK, Alnaqbi H, Chehadeh S, Peramo B, Mustafa F, Rizvi TA, Mahboub BH, Uddin M, Alkaabi N, Alefishat E, Jelinek HF, Alsafar H. HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates. PLoS One 2023; 18:e0285712. [PMID: 37708194 PMCID: PMC10501655 DOI: 10.1371/journal.pone.0285712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/29/2023] [Indexed: 09/16/2023] Open
Abstract
SARS-CoV-2 appears to induce diverse innate and adaptive immune responses, resulting in different clinical manifestations of COVID-19. Due to their function in presenting viral peptides and initiating the adaptive immune response, certain Human Leucocyte Antigen (HLA) alleles may influence the susceptibility to severe SARS-CoV-2 infection. In this study, 92 COVID-19 patients from 15 different nationalities, with mild (n = 30), moderate (n = 35), and severe (n = 27) SARS-CoV-2 infection, living in the United Arab Emirates (UAE) were genotyped for the Class I HLA -A, -C, and -B alleles using next-generation sequencing (NGS) between the period of May 2020 to June 2020. Alleles and inferred haplotype frequencies in the hospitalized patient group (those with moderate to severe disease, n = 62) were compared to non-hospitalized patients (mild or asymptomatic, n = 30). An interesting trend was noted between the severity of COVID-19 and the HLA-C*04 (P = 0.0077) as well as HLA-B*35 (P = 0.0051) alleles. The class I haplotype HLA-C*04-B*35 was also significantly associated (P = 0.0049). The involvement of inflammation, HLA-C*04, and HLA-B*35 in COVID-19 severity highlights the potential roles of both the adaptive and innate immune responses against SARS-CoV-2. Both alleles have been linked to several respiratory diseases, including pulmonary arterial hypertension along with infections caused by the coronavirus and influenza. This study, therefore, supports the potential use of HLA testing in prioritizing public healthcare interventions for patients at risk of COVID-19 infection and disease progression, in addition to providing personalized immunotherapeutic targets.
Collapse
Affiliation(s)
- Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Psychiatry, UWA Medical School, The University of Western Australia, Perth, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Sarah Chehadeh
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | | | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Tahir A. Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam H. Mahboub
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Pulmonary Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
| | - Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | | |
Collapse
|
5
|
Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
Collapse
Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
| |
Collapse
|
6
|
Israr M, Lam F, DeVoti J, Mace EM, Papayannakos C, Abramson A, Steinberg BM, Bonagura VR. PGE 2 expression by HPV6/11-induced respiratory papillomas blocks NK cell activation in patients with recurrent respiratory papillomatosis. Eur J Immunol 2023; 53:e2250036. [PMID: 36608264 DOI: 10.1002/eji.202250036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/12/2022] [Accepted: 01/05/2023] [Indexed: 01/07/2023]
Abstract
Recurrent respiratory papillomatosis (RRP), a rare chronic disease caused primarily by human papillomavirus types 6 and 11, consists of repeated growth of premalignant papillomas in the airway. RRP is characterized by multiple abnormalities in innate and adaptive immunity. Natural killer (NK) cells play important roles in immune surveillance and are part of the innate immune responses that help prevent tumor growth. We identified that papillomas lack classical class I MHC and retain nonclassical class I MHC expression. Moreover, in this study, we have identified and characterized the mechanism that blocks NK cell targeting of papilloma cells. Here, we show for the first time that the PGE2 secreted by papilloma cells directly inhibits NK cells activation/degranulation principally through the PGE2 receptor EP2, and to a lesser extent through EP4 signaling. Thus, papilloma cells have a potent mechanism to block NK cell function that likely supports papilloma cell growth.
Collapse
Affiliation(s)
- Mohd Israr
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Fung Lam
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - James DeVoti
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia Medical Center, NY, USA
| | | | - Allan Abramson
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Bettie M Steinberg
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Vincent R Bonagura
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| |
Collapse
|
7
|
Srivastava A, Hollenbach JA. The immunogenetics of COVID-19. Immunogenetics 2022; 75:309-320. [PMID: 36534127 PMCID: PMC9762652 DOI: 10.1007/s00251-022-01284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
Collapse
Affiliation(s)
- Anshika Srivastava
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| | - Jill A. Hollenbach
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| |
Collapse
|
8
|
Increased Prevalence of Unstable HLA-C Variants in HIV-1 Rapid-Progressor Patients. Int J Mol Sci 2022; 23:ijms232314852. [PMID: 36499177 PMCID: PMC9741376 DOI: 10.3390/ijms232314852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
HIV-1 infection in the absence of treatment results in progression toward AIDS. Host genetic factors play a role in HIV-1 pathogenesis, but complete knowledge is not yet available. Since less-expressed HLA-C variants are associated with poor HIV-1 control and unstable HLA-C variants are associated with higher HIV-1 infectivity, we investigated whether there was a correlation between the different stages of HIV-1 progression and the presence of specific HLA-C allotypes. HLA-C genotyping was performed using allele-specific PCR by analyzing a treatment-naïve cohort of 96 HIV-1-infected patients from multicentric cohorts in the USA, Canada, and Brazil. HIV-1-positive subjects were classified according to their different disease progression status as progressors (Ps, n = 48), long-term non-progressors (LTNPs, n = 37), and elite controllers (ECs, n = 11). HLA-C variants were classified as stable or unstable according to their binding stability to β2-microglobulin/peptide complex. Our results showed a significant correlation between rapid progression to AIDS and the presence of two or one unstable HLA-C variants (p-value: 0.0078, p-value: 0.0143, respectively). These findings strongly suggest a link between unstable HLA-C variants both at genotype and at allele levels and rapid progression to AIDS. This work provides further insights into the impact of host genetic factors on AIDS progression.
Collapse
|
9
|
Sharif-zak M, Abbasi-Jorjandi M, Asadikaram G, Ghoreshi ZAS, Rezazadeh-Jabalbarzi M, Rashidinejad H. Influence of Disease Severity and Gender on HLA-C Methylation in COVID-19 Patients. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022; 46:1309-1316. [PMID: 35912367 PMCID: PMC9325662 DOI: 10.1007/s40995-022-01334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/01/2022] [Indexed: 12/03/2022]
Abstract
In the pathophysiology of COVID-19, immunomodulatory factors play a vital role. Viruses have epigenetic effects on various genes, particularly methylation. Explaining the changes in immunological factor methylation levels during viral infections requires substantial consideration. HLA-C is a crucial determinant of immune function and NK cell activity and is primarily implicated in viral infections. This research focused on studying HLA-C methylation in COVID-19 patients with different severity. Peripheral blood samples were collected from 470 patients (235 men and 235 women) with RT-qPCR-confirmed COVID-19 test and classified into moderate, severe, and critical groups based on WHO criteria. Also, one hundred (50 men and 50 women) healthy subjects were selected as the control group. Peripheral blood mononuclear cells were used for DNA extraction, and the methylation-specific PCR (MSP) method and gel electrophoresis were used to determine the methylation status of the HLA-C. Significant statistical differences in HLA-C methylation were observed among cases and controls and various stages of the disease. HLA-C methylation in men and women has decreased in all stages (p < 0.05). In comparison with control, HLA-C methylation in both genders were as follows: moderate (women: 41.0%, men: 52.33%), severe (women: 43.42%, men: 64.86%), critical (women: 42.33%, men: 60.07%), and total patients (women: 45.52%, men: 56.97%). Furthermore, the methylation levels in men were higher than in women in all groups (p < 0.05). Significantly, among all groups, the severe group of men participants showed the highest methylation percentage (p < 0.05). No significant differences were detected for different disease severity in the women group (p > 0.1). This study found that HLA-C methylation was significantly lower in COVID-19 patients with different disease severity. There were also significant differences in HLA-C methylation between men and women patients with different severity. Therefore, during managing viral infections, particularly COVID-19, it is critical to consider patient gender and disease severity.
Collapse
|
10
|
Natural Immunity against HIV-1: Progression of Understanding after Association Studies. Viruses 2022; 14:v14061243. [PMID: 35746714 PMCID: PMC9227919 DOI: 10.3390/v14061243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Natural immunity against HIV has been observed in many individuals in the world. Among them, a group of female sex workers enrolled in the Pumwani sex worker cohort remained HIV uninfected for more than 30 years despite high-risk sex work. Many studies have been carried out to understand this natural immunity to HIV in the hope to develop effective vaccines and preventions. This review focuses on two such examples. These studies started from identifying immunogenetic or genetic associations with resistance to HIV acquisition, and followed up with an in-depth investigation to understand the biological relevance of the correlations of protection, and to develop and test novel vaccines and preventions.
Collapse
|
11
|
Bernard NF, Kant S, Kiani Z, Tremblay C, Dupuy FP. Natural Killer Cells in Antibody Independent and Antibody Dependent HIV Control. Front Immunol 2022; 13:879124. [PMID: 35720328 PMCID: PMC9205404 DOI: 10.3389/fimmu.2022.879124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Infection with the human immunodeficiency virus (HIV), when left untreated, typically leads to disease progression towards acquired immunodeficiency syndrome. Some people living with HIV (PLWH) control their virus to levels below the limit of detection of standard viral load assays, without treatment. As such, they represent examples of a functional HIV cure. These individuals, called Elite Controllers (ECs), are rare, making up <1% of PLWH. Genome wide association studies mapped genes in the major histocompatibility complex (MHC) class I region as important in HIV control. ECs have potent virus specific CD8+ T cell responses often restricted by protective MHC class I antigens. Natural Killer (NK) cells are innate immune cells whose activation state depends on the integration of activating and inhibitory signals arising from cell surface receptors interacting with their ligands on neighboring cells. Inhibitory NK cell receptors also use a subset of MHC class I antigens as ligands. This interaction educates NK cells, priming them to respond to HIV infected cell with reduced MHC class I antigen expression levels. NK cells can also be activated through the crosslinking of the activating NK cell receptor, CD16, which binds the fragment crystallizable portion of immunoglobulin G. This mode of activation confers NK cells with specificity to HIV infected cells when the antigen binding portion of CD16 bound immunoglobulin G recognizes HIV Envelope on infected cells. Here, we review the role of NK cells in antibody independent and antibody dependent HIV control.
Collapse
Affiliation(s)
- Nicole F. Bernard
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Clinical Immunology, McGill University Health Centre, Montreal, QC, Canada
- *Correspondence: Nicole F. Bernard,
| | - Sanket Kant
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Zahra Kiani
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Microbiology Infectiology and Immunology, University of Montreal, Montreal, QC, Canada
| | - Franck P. Dupuy
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| |
Collapse
|
12
|
Slatkin M. Joint estimation of selection intensity and mutation rate under balancing selection with applications to HLA. Genetics 2022; 221:6569836. [PMID: 35435218 PMCID: PMC9157114 DOI: 10.1093/genetics/iyac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
A composite likelihood method is introduced for jointly estimating the intensity of selection and the rate of mutation, both scaled by the effective population size, when there is balancing selection at a single multi-allelic locus in an isolated population at demographic equilibrium. The performance of the method is tested using simulated data. Average estimated mutation rates and selection intensities are close to the true values but there is considerable variation about the averages. Allowing for both population growth and population subdivision does not result in qualitative differences but the estimated mutation rates and selection intensities do not in general reflect the current effective population size. The method is applied to three class I (HLA-A, HLA-B and HLA-C) and two class II loci (HLA-DRB1 and HLA-DQA1) in the 1000 Genomes populations. Allowing for asymmetric balancing selection has only a slight effect on the results from the symmetric model. Mutations that restore symmetry of the selection model are preferentially retained because of the tendency of natural selection to maximize average fitness. However, slight differences in selective effects result in much longer persistence time of some alleles. Trans-species polymorphism (TSP), which is characteristic of major-histocompatibility loci in vertebrates, is more likely when there are small differences in allelic fitness than when complete symmetry is assumed. Therefore, variation in allelic fitness expands the range of parameter values consistent with observations of TSP.
Collapse
Affiliation(s)
- Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| |
Collapse
|
13
|
Factors Influencing Immune Restoration in People Living with HIV/AIDS. J Clin Med 2022; 11:jcm11071887. [PMID: 35407496 PMCID: PMC9000185 DOI: 10.3390/jcm11071887] [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: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Introduction: Immune restoration is a key clinical aspect that is pursued in the care of human immunodeficiency virus (HIV)-infected patients. Despite effective antiretroviral treatment and undetectable viremia, immune recovery is often incomplete. Materials and methods: Data from 311 Caucasian patients were collected. SNP in CCR2(rs1799864), CX3CR1(rs3732378), HLAC-35(rs9264942), and CCR5(promoter, rs1799988); a 32bp deletion(Δ32) in CCR5; and HLA-B*5701 genotypes were correlated with clinical data and selected endpoints. Kaplan−Meier and Cox proportional hazards models were used to analyze the effects of genetic factors over time. Results: For HLA-B*5701, the effect on the CD4+/CD8+ >0.8 cell ratio was lost within 48 months (HR = 2.04, 95% CI: 1.04−4.03), and the effect on the CD4+ cell count >500 cells/µL was lost within 12 months (HR = 2.12, CI: 1.11−4.04). The effect of CCR2 GG on the CD4+/CD8+ >0.8 cell ratio was lost within 36 months (HR = 1.7, CI: 1.05−2.75). For CCR5 wt/Δ32, the effect on the CD4+/CD8+ >1.0 cell ratio was lost within 24 months (HR = 2.0, CI: 1.08−3.69), and the effect on the CD4+ >800 cells/µL cell count was lost within 18 months (HR = 1.98, CI: 1.14−4.73). Conclusions: Selected genetic polymorphisms, namely CCR2 GG and CCR5 Δ32, and the presence of the HLA-B*5701 allele positively influenced immune restoration in cART-treated patients with HIV/AIDS.
Collapse
|
14
|
Zhang Z, Trypsteen W, Blaauw M, Chu X, Rutsaert S, Vandekerckhove L, van der Heijden W, Dos Santos JC, Xu CJ, Swertz MA, van der Ven A, Li Y. IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis. BMC Med 2021; 19:282. [PMID: 34781942 PMCID: PMC8594146 DOI: 10.1186/s12916-021-02156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combination antiretroviral treatment (cART) cannot eradicate HIV-1 from the body due to the establishment of persisting viral reservoirs which are not affected by therapy and reinitiate new rounds of HIV-1 replication after treatment interruption. These HIV-1 reservoirs mainly comprise long-lived resting memory CD4+ T cells and are established early after infection. There is a high variation in the size of these viral reservoirs among virally suppressed individuals. Identification of host factors that contribute to or can explain this observed variation could open avenues for new HIV-1 treatment strategies. METHODS In this study, we conducted a genome-wide quantitative trait locus (QTL) analysis to probe functionally relevant genetic variants linked to levels of cell-associated (CA) HIV-1 DNA, CA HIV-1 RNA, and RNA:DNA ratio in CD4+ T cells isolated from blood from a cohort of 207 (Caucasian) people living with HIV-1 (PLHIV) on long-term suppressive antiretroviral treatment (median = 6.6 years). CA HIV-1 DNA and CA HIV-1 RNA levels were measured with corresponding droplet digital PCR (ddPCR) assays, and genotype information of 522,455 single-nucleotide variants was retrieved via the Infinium Global Screening array platform. RESULTS The analysis resulted in one significant association with CA HIV-1 DNA (rs2613996, P < 5 × 10-8) and two suggestive associations with RNA:DNA ratio (rs7113204 and rs7817589, P < 5 × 10-7). Then, we prioritized PTDSS2, IRF7, RNH1, and DEAF1 as potential HIV-1 reservoir modifiers and validated that higher expressions of IRF7 and RNH1 were accompanied by rs7113204-G. Moreover, RNA:DNA ratio, indicating relative HIV-1 transcription activity, was lower in PLHIV carrying this variant. CONCLUSIONS The presented data suggests that the amount of CA HIV-1 DNA and RNA:DNA ratio can be influenced through PTDSS2, RNH1, and IRF7 that were anchored by our genome-wide association analysis. Further, these observations reveal potential host genetic factors affecting the size and transcriptional activity of HIV-1 reservoirs and could indicate new targets for HIV-1 therapeutic strategies.
Collapse
Affiliation(s)
- Zhenhua Zhang
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Marc Blaauw
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, and Pediatrics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands.,Genomics Coordination Center, University Medical Center Groningen, 9700RB, Groningen, the Netherlands
| | - Andre van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands.
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525HP, Nijmegen, the Netherlands. .,Department of Genetics, University Medical Center Groningen, 9700RB, Groningen, the Netherlands. .,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany. .,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
| |
Collapse
|
15
|
Celerino da Silva R, Segat L, Kuhn L, Chies JAB, Crovella S. Association of SNPs in HLA-C and ZNRD1 Genes With HIV-1 Mother-to-Child Transmission in Zambia Population. J Acquir Immune Defic Syndr 2021; 86:509-515. [PMID: 33252547 DOI: 10.1097/qai.0000000000002584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human leukocyte antigen C (HLA-C) and Zinc ribbon domain containing 1 (ZNRD1) are considered HIV-1 restriction factors and are expressed in the placenta. Variations in HLA-C and ZNRD1 genes are known to influence HIV-1 infection, including viral replication and progression to AIDS. Little is known about the role of variants in these genes in HIV-1 mother-to-child transmission. METHODS We evaluated the distribution of HLA-C (rs10484554, rs9264942) and ZNRD1 (rs8321, rs3869068) variants in a Zambian population composed of 333 children born to HIV-1+ mothers (248 HIV-1 noninfected/85 HIV-1 infected) and 97 HIV-1+ mothers. RESULTS Genotypic distribution of HLA-C and ZNRD1 were in Hardy-Weinberg equilibrium, except for HLA-C rs10484554 in both groups. In mothers, no significant differences were observed in their allele and genotypic distributions for both genes. The T and TT variants (rs10484554-HLA-C) were significantly more frequent among HIV-1+ children, specifically those who acquired the infection in utero (IU) and intrapartum (IP). For ZNRD1, the T allele (rs3869068) was more frequent in HIV-1- children, showing significant differences in relation to those infected via IP and postpartum (PP). The CT and TT genotypes were significantly more frequent in HIV-1- children. CONCLUSIONS Variations in HLA-C (T and TT-rs10484554) and ZNRD1 (T and CT/TT-rs3869068) can increase and decrease the susceptibility to HIV-1 infection via mother-to-child transmission, respectively. Further studies are encouraged focusing on a greater number of variants and sample size, with functional validation and in other populations.
Collapse
Affiliation(s)
- Ronaldo Celerino da Silva
- Department of Genetics, Federal University of Pernambuco (UFPE), Recife, Brazil
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE) Recife, Brazil
| | - Ludovica Segat
- Department of Surgical and Health Medical Sciences, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), UCO Hygiene and Public Health, University of Trieste, Trieste, Italy
| | - Louise Kuhn
- Gertrude H. Sergievsky Center and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY; and
| | - José Artur Bogo Chies
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Sergio Crovella
- Department of Genetics, Federal University of Pernambuco (UFPE), Recife, Brazil
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE) Recife, Brazil
| |
Collapse
|
16
|
Lobov AA, Yudintceva NM, Mittenberg AG, Shabelnikov SV, Mikhailova NA, Malashicheva AB, Khotin MG. Proteomic Profiling of the Human Fetal Multipotent Mesenchymal Stromal Cells Secretome. Molecules 2020; 25:E5283. [PMID: 33198321 PMCID: PMC7716221 DOI: 10.3390/molecules25225283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 01/08/2023] Open
Abstract
Secretome of multipotent mesenchymal stromal cells (MSCs) is actively used in biomedical applications such as alveolar bone regeneration, treatment of cardiovascular disease, and neurodegenerative disorders. Nevertheless, hMSCs have low proliferative potential and production of the industrial quantity of their secretome might be challenging. Human fetal multipotent mesenchymal stromal cells (FetMSCs) isolated from early human embryo bone marrow are easy to expand and might be a potential source for pharmaceutical substances production based on their secretome. However, the secretome of FetMSCs was not previously analyzed. Here, we describe the secretome of FetMSCs using LC-MALDI shotgun proteomics. We identified 236 proteins. Functional annotation of the identified proteins revealed their involvement in angiogenesis, ossification, regulation of apoptosis, and immune response processes, which made it promising for biomedical applications. The proteins identified in the FetMSCs secretome are involved in the same biological processes as proteins from previously described adult hMSCs secretomes. Nevertheless, many of the common hMSCs secretome components (such as VEGF, FGF, Wnt and TGF-β) have not been identified in the FetMSCs secretome.
Collapse
Affiliation(s)
| | | | | | | | | | - Anna B. Malashicheva
- Institute of Cytology of the Russian Academy of Science, 194064 St. Petersburg, Russia; (A.A.L.); (N.M.Y.); (A.G.M.); (S.V.S.); (N.A.M.); (M.G.K.)
| | | |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Targeted ultra-deep sequencing of a South African Bantu-speaking cohort to comprehensively map and characterize common and novel variants in 65 pharmacologically-related genes. Pharmacogenet Genomics 2020; 29:167-178. [PMID: 31162291 PMCID: PMC6675649 DOI: 10.1097/fpc.0000000000000380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Supplemental Digital Content is available in the text. Background African populations are characterised by high genetic diversity, which provides opportunities for discovering and elucidating novel variants of clinical importance, especially those affecting therapeutic outcome. Significantly more knowledge is however needed before such populations can take full advantage of the advances in precision medicine. Coupled with the need to concisely map and better understand the pharmacological implications of genetic diversity in populations of sub-Sharan African ancestry, the aim of this study was to identify and characterize known and novel variants present within 65 important absorption, distribution, metabolism and excretion genes. Patients and methods Targeted ultra-deep next-generation sequencing was used to screen a cohort of 40 South African individuals of Bantu ancestry. Results We identified a total of 1662 variants of which 129 are novel. Moreover, out of the 1662 variants 22 represent potential loss-of-function variants. A high level of allele frequency differentiation was observed for variants identified in this study when compared with other populations. Notably, on the basis of prior studies, many appear to be pharmacologically important in the pharmacokinetics of a broad range of drugs, including antiretrovirals, chemotherapeutic drugs, antiepileptics, antidepressants, and anticoagulants. An in-depth analysis was undertaken to interrogate the pharmacogenetic implications of this genetic diversity. Conclusion Despite the new insights gained from this study, the work illustrates that a more comprehensive understanding of population-specific differences is needed to facilitate the development of pharmacogenetic-based interventions for optimal drug therapy in patients of African ancestry.
Collapse
|
19
|
Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
Collapse
Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
| |
Collapse
|
20
|
Abstract
Major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA) in humans, is one of the most genetically diverse regions in the genome of various species. The human MHC contains about 400 genes in a ∼7.6-Mb span located on the short arm of the chromosomal region 6p21.3. According to the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/) in HLA region, more than 500 associations have been identified for about 200 traits or phenotypes, including primary immune deficiencies, autoimmune diseases, susceptibility to infections, malignancies, and psychiatric conditions (Welter et al., 2014). For example, multiple sclerosis is associated with HLA-DRB1∗1501 (Handunnetthi et al., 2010); the control of HIV viral load is associated with variants near HLA-C (Kulpa and Collins, 2011). Some acute drug reactions are associated with specific HLA alleles. Carbamazepine-induced Stevens-Johnson syndrome and toxic epidermal necrolysis have been strongly associated with HLA-B*1502 in Han Chinese population and HLA-A*3101 in European populations (Chung et al., 2004; McCormack et al., 2011). The HLA-B*13:01 is associated with the development of the dapsone hypersensitivity syndrome among patients with leprosy (Zhang et al., 2013).
Collapse
Affiliation(s)
- Fusheng Zhou
- The Institute of Dermatology and Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, China
| | - Xuejun Zhang
- The Institute of Dermatology and Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, China.
| |
Collapse
|
21
|
Li L, Liu Y, Gorny MK. Association of Diverse Genotypes and Phenotypes of Immune Cells and Immunoglobulins With the Course of HIV-1 Infection. Front Immunol 2018; 9:2735. [PMID: 30534128 PMCID: PMC6275200 DOI: 10.3389/fimmu.2018.02735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Disease progression among HIV-1-infected individuals varies widely, but the mechanisms underlying this variability remains unknown. Distinct disease outcomes are the consequences of many factors working in concert, including innate and adaptive immune responses, cell-mediated and humoral immunity, and both genetic and phenotypic factors. Current data suggest that these multifaceted aspects in infected individuals should be considered as a whole, rather than as separate unique elements, and that analyses must be performed in greater detail in order to meet the requirements of personalized medicine and guide optimal vaccine design. However, the wide adoption of antiretroviral therapy (ART) influences the implementation of systematic analyses of the HIV-1-infected population. Consequently, fewer data will be available for acquisition in the future, preventing the comprehensive investigations required to elucidate the underpinnings of variability in disease outcome. This review seeks to recapitulate the distinct genotypic and phenotypic features of the immune system, focusing in particular on comparing the surface proteins of immune cells among individuals with different HIV infection outcomes.
Collapse
Affiliation(s)
- Liuzhe Li
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Yan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hengyang, China
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Sundaramurthi JC, Ashokkumar M, Swaminathan S, Hanna LE. HLA based selection of epitopes offers a potential window of opportunity for vaccine design against HIV. Vaccine 2017; 35:5568-5575. [PMID: 28888341 DOI: 10.1016/j.vaccine.2017.08.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
The pace of progression to AIDS after HIV infection varies from individual to individual. While some individuals develop AIDS quickly, others are protected from the onset of disease for more than a decade (elite controllers and long term non-progressors). The mechanisms of protection are not yet clearly understood, though various factors including host genetics, immune components and virus attenuation have been elucidated partly. The influence of HLA alleles on HIV-1 infection and disease outcome has been studied extensively. Several HLA alleles are known to be associated with resistance to infection or delayed progression to AIDS after infection. Similarly, certain HLA alleles are reported to be associated with rapid progression to disease. Since HLA alleles influence the outcome of HIV infection differentially, selection of epitopes specifically recognized by protective alleles could serve asa rational means for HIV vaccine design. In this review article, we discuss existing knowledge on HLA alleles and their association with resistance/susceptibility to HIV and its relevance to vaccine design.
Collapse
Affiliation(s)
- Jagadish Chandrabose Sundaramurthi
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Manickam Ashokkumar
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India.
| |
Collapse
|
24
|
Zulfiqar HF, Javed A, Sumbal, Afroze B, Ali Q, Akbar K, Nadeem T, Rana MA, Nazar ZA, Nasir IA, Husnain T. HIV Diagnosis and Treatment through Advanced Technologies. Front Public Health 2017; 5:32. [PMID: 28326304 PMCID: PMC5339269 DOI: 10.3389/fpubh.2017.00032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) is the chief contributor to global burden of disease. In 2010, HIV was the fifth leading cause of disability-adjusted life years in people of all ages and leading cause for people aged 30-44 years. It is classified as a member of the family Retroviridae and genus Lentivirus based on the biological, morphological, and genetic properties. It infects different cells of the immune system, such as CD4+ T cells (T-helper cells), dendritic cells, and macrophages. HIV has two subtypes: HIV-1 and HIV-2. Among these strains, HIV-1 is the most virulent and pathogenic. Advanced diagnostic methods are exploring new ways of treatment and contributing in the reduction of HIV cases. The diagnostic techniques like PCR, rapid test, EIA, p24 antigen, and western blot have markedly upgraded the diagnosis of HIV. Antiretroviral therapy and vaccines are promising candidates in providing therapeutic and preventive regimes, respectively. Invention of CRISPR/Cas9 is a breakthrough in the field of HIV disease management.
Collapse
Affiliation(s)
| | - Aneeqa Javed
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Sumbal
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Bakht Afroze
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Khadija Akbar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tariq Nadeem
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | | | - Zaheer Ahmad Nazar
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| |
Collapse
|
25
|
Malnati MS, Ugolotti E, Monti MC, Battista DD, Vanni I, Bordo D, Sironi F, Larghero P, Marco ED, Biswas P, Poli G, Vicenzi E, Riva A, Tarkowski M, Tambussi G, Nozza S, Tripodi G, Marras F, Maria AD, Pistorio A, Biassoni R. Activating Killer Immunoglobulin Receptors and HLA-C: a successful combination providing HIV-1 control. Sci Rep 2017; 7:42470. [PMID: 28211903 PMCID: PMC5304173 DOI: 10.1038/srep42470] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 01/11/2017] [Indexed: 11/29/2022] Open
Abstract
Several studies demonstrated a relevant role of polymorphisms located within the HLA-B and -C loci and the Killer Immunoglobulin Receptors (KIRs) 3DL1 and 3DS1 in controlling HIV-1 replication. KIRs are regulatory receptors expressed at the surface of NK and CD8+ T-cells that specifically bind HLA-A and -B alleles belonging to the Bw4 supratype and all the -C alleles expressing the C1 or C2 supratype. We here disclose a novel signature associated with the Elite Controller but not with the long-term nonprogressor status concerning 2DS activating KIRs and HLA-C2 alleles insensitive to miRNA148a regulation. Overall, our findings support a crucial role of NK cells in the control of HIV-1 viremia.
Collapse
Affiliation(s)
- Mauro S. Malnati
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Maria Cristina Monti
- Department of Public Health Unit of biostatistics and clinical epidemiology University of Pavia, Pavia Italy
| | - Davide De Battista
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Francesca Sironi
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Priscilla Biswas
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | - Guido Poli
- Vita-Salute San Raffaele University, School of Medicine, Milan, Italy
| | - Elisa Vicenzi
- Unit of Viral Pathogens and Biosafety, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Agostino Riva
- Department of Clinical Sciences Chair of Infectious Diseases and Tropical Medicine University of Milan,“L. Sacco” Hospital, Milan, Italy
| | - Maciej Tarkowski
- Department of Clinical Sciences Chair of Infectious Diseases and Tropical Medicine University of Milan,“L. Sacco” Hospital, Milan, Italy
| | - Giuseppe Tambussi
- Department of Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Silvia Nozza
- Department of Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Andrea De Maria
- IRCCS AOU San Martino-IST, Genoa, Italy
- Department of Health Science, DISSAL and Center for excellence in Biomedical Research CEBR University of Genoa, Genoa, Italy
| | | | | |
Collapse
|
26
|
Bardeskar NS, Mania-Pramanik J. HIV and host immunogenetics: unraveling the role of HLA-C. HLA 2016; 88:221-231. [PMID: 27620973 DOI: 10.1111/tan.12882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 01/09/2023]
Abstract
Host genetic factors play a major role in determining the outcome of many infections including human immunodeficiency virus (HIV). Multiple host factors have been studied till date showing their varied role in susceptibility or resistance to HIV infection. HLA-C, however, has been recently started gaining interest in researchers mind revealing its polymorphisms to have an important effect on viral load set-points, disease progression as well as transmission. In this review report, we have compiled these significant findings of HLA-C in HIV infection, in an attempt to highlight the need for further research in the area in different ethnic population to establish its role in the infection.
Collapse
Affiliation(s)
- N S Bardeskar
- Infectious Diseases Biology Department, National Institute for Research in Reproductive Health, Mumbai, 400012, India
| | - J Mania-Pramanik
- Infectious Diseases Biology Department, National Institute for Research in Reproductive Health, Mumbai, 400012, India.
| |
Collapse
|
27
|
Cell Surface Downregulation of NK Cell Ligands by Patient-Derived HIV-1 Vpu and Nef Alleles. J Acquir Immune Defic Syndr 2016; 72:1-10. [PMID: 26656785 DOI: 10.1097/qai.0000000000000917] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE HIV-1 Vpu and Nef proteins downregulate cell surface levels of natural killer (NK) cell ligands but functional consequences of individual downregulation events are unclear. We tested how well-conserved NK cell ligand downregulation is among Vpu and Nef variants isolated from chronic HIV patients. METHODS Proviral vpu and nef sequences were amplified from 27 chronic HIV patients, subcloned, and tested for their ability to downregulate cell surface receptors. RESULTS Cell surface downregulation of CD4, CD317/tetherin, and major histocompatibility complex class 1 that exert biological functions other than NK cell activation were well conserved among patient-derived Vpu and Nef variants. Among NK cell ligands, NK-T-B-antigen, poliovirus receptor, and UL16-binding protein were identified as main targets for Vpu and Nef, the downregulation of which by at least 1 viral protein was highly conserved. NK cell ligands displayed specific sensitivity to Vpu (NK-T-B-antigen) or Nef (poliovirus receptor), and downregulation of cell surface UL16-binding protein was identified as a novel and highly conserved activity of HIV-1 Vpu but not Nef. CONCLUSIONS The conservation of downregulation of major NK cell ligands by either HIV-1 Vpu or Nef suggests an important pathophysiological role of this activity, which may impact the acute but not the chronic phase of HIV infection.
Collapse
|
28
|
Thørner LW, Erikstrup C, Harritshøj LH, Larsen MH, Kronborg G, Pedersen C, Larsen CS, Pedersen G, Gerstoft J, Obel N, Ullum H. Impact of polymorphisms in the HCP5 and HLA-C, and ZNRD1 genes on HIV viral load. INFECTION GENETICS AND EVOLUTION 2016; 41:185-190. [PMID: 27083073 DOI: 10.1016/j.meegid.2016.03.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/11/2016] [Accepted: 03/30/2016] [Indexed: 01/16/2023]
Abstract
AIMS Single nucleotide polymorphisms (SNPs) in the human leucocyte antigen (HLA) complex P5 (HCP5), HLA-C, and near the zinc ribbon domain containing 1 (ZNRD1) have been shown to influence viral load (VL) set point in HIV-infected individuals with a known seroconversion onset. We aimed to determine the influence of HCP5 rs2395029, HLA-C rs9264942, and ZNRD1 rs3869068 on VL in antiretroviral-naïve individuals and on time to the first VL<51 copies/ml and on CD4(+) T-cell recovery after initiation of combination antiretroviral therapy (cART). MATERIAL AND METHODS We genotyped the rs2395029 (A>C), rs9264942 (T>C), and rs3869068 (C>T) SNPs in 1897 Caucasians from The Danish HIV Cohort Study - a prospective, nationwide, population-based study of HIV-infected individuals in Denmark. General linear models evaluated the effect of SNPs on VL in antiretroviral-naïve individuals 0-18months after diagnosis and on CD4(+) T-cell recovery during cART. Cox proportional hazard regression analysis assessed the association with time to first VL<51 copies/ml. All models were assuming additive genetic effects. RESULTS The rs2395029, rs9264942, and rs3869068 minor alleles were associated with lower VL in antiretroviral-naïve individuals (rs2395029: [mean VL (copies/ml)], A/A: 70,795 [61,660-79,433], A/C: 33,884 [19,498-58,884], P=0.002; rs9264942: TT: 81,283 [67,608-97,724], T/C: 63,096 [54,954-75,858], CC: 38,905 [25,119-58,884], P<0.0001; rs3869068, CC: 72,444 [63,096-83,176], C/T: 45,709 [33,113-64,565], TT: 58,884 [20,417-169,824], P=0.01). Moreover, the C-alleles of rs2395029 and rs9264942 were associated with shorter time to VL<51 copies/ml: (HR [95% confidence interval], 1.67 [1.09-1.72], P=0.008; 1.16 [1.06-1.28], P=0.002; 1.30 [1.08-1.53], P=0.005, respectively, adjusted for last VL before cART). None of the SNPs predicted CD4(+) T-cell recovery during cART. CONCLUSIONS The minor alleles of rs2395029, rs9264942, and rs3689068 associate with lower VL among antiretroviral-naïve individuals and with shorter time to first VL<51copies/ml during cART even after adjustment for VL before cART.
Collapse
Affiliation(s)
- Lise Wegner Thørner
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Christian Erikstrup
- Dept. of Clinical Immunology, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Lene Holm Harritshøj
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gitte Kronborg
- Dept. of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Court Pedersen
- Dept. of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | - Gitte Pedersen
- Dept. of Infectious Diseases, Aarhus University Hospital, Aalborg, Denmark
| | - Jan Gerstoft
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Obel
- Dept. of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Ullum
- Dept. of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| |
Collapse
|
29
|
Ma Y, Li X, Kuang E. Viral Evasion of Natural Killer Cell Activation. Viruses 2016; 8:95. [PMID: 27077876 PMCID: PMC4848590 DOI: 10.3390/v8040095] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022] Open
Abstract
Natural killer (NK) cells play a key role in antiviral innate defenses because of their abilities to kill infected cells and secrete regulatory cytokines. Additionally, NK cells exhibit adaptive memory-like antigen-specific responses, which represent a novel antiviral NK cell defense mechanism. Viruses have evolved various strategies to evade the recognition and destruction by NK cells through the downregulation of the NK cell activating receptors. Here, we review the recent findings on viral evasion of NK cells via the impairment of NK cell-activating receptors and ligands, which provide new insights on the relationship between NK cells and viral actions during persistent viral infections.
Collapse
Affiliation(s)
- Yi Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74, Zhongshan 2nd Road, Guangzhou 510080, China.
| | - Xiaojuan Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74, Zhongshan 2nd Road, Guangzhou 510080, China.
| | - Ersheng Kuang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, No. 74, Zhongshan 2nd Road, Guangzhou 510080, China.
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China.
| |
Collapse
|
30
|
Marwoto, Lismana UHV, Prasetyo AA, Suradi, Reviono, Harsini. Correlation of Single Nucleotide Polymorphism 35-Kb Upstream of HLA-C and Clinical Profile of Multidrug-Resistant Tuberculosis. J Clin Diagn Res 2015; 9:DC10-3. [PMID: 26500904 DOI: 10.7860/jcdr/2015/14439.6451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
INTRODUCTION The SNP HLA-C-35 kb (rs9264942) may contribute to the host immune defense mechanism by affecting the cell surface expression pattern of HLA-C and antigen presentation to CD8+ cytotoxic cells. Thus, this SNP may contribute to intracellular multidrug-resistant (MDR)-tuberculosis (TB) infection. AIM To examine the association between the SNP HLA-C-35 kb (rs9264942) and the clinical profile of MDR-TB infection. SETTINGS AND DESIGN MDR-TB-positive patients were followed from May 2012 to December 2013 to observe the progression of MDR-TB infection. Non-TB individuals and non-MDR-TB individuals were also recruited as controls. MATERIALS AND METHODS The patients' HLA-C-35 kb (rs9264942) status was determined by PCR. RESULTS The C allele was slightly more frequent in the MDR-TB patients than in the non-MDR TB patients (OR= 1.28; 95% CI: 0.701 - 2.328). The C allele was found to be more frequent in the MDR-TB patients exhibiting pulmonary fibrosis (OR= 2.13; 95% CI: 0.606 - 7.480) or pulmonary infiltrates (OR= 3.17; 95% CI: 0.690 - 14.598) and among the MDR-TB patients who were classified as underweight (OR= 8.00; 95% CI: 1.261 - 50.770). The CC genotype was associated with the treatment after failure of category II group (OR= 4.17; 95% CI: 1.301 - 13.346). CONCLUSION The C allele SNP HLA-C-35 kb (rs9264942) may contribute to the clinical profile in MDR-TB infection.
Collapse
Affiliation(s)
- Marwoto
- A-Infection Genomic Immunology Cancer (A-IGIC) Research Group, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia; Department of Microbiology Faculty of Medicine, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Umi Hani' Vismayanti Lismana
- A-Infection Genomic Immunology Cancer (A-IGIC) Research Group, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Afiono Agung Prasetyo
- A-Infection Genomic Immunology Cancer (A-IGIC) Research Group, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia; Department of Microbiology Faculty of Medicine, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia; Center of Biotechnology and Biodiversity Research and Development, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Suradi
- Department of Pulmonology Faculty of Medicine, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Reviono
- A-Infection Genomic Immunology Cancer (A-IGIC) Research Group, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia; Department of Pulmonology Faculty of Medicine, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Harsini
- A-Infection Genomic Immunology Cancer (A-IGIC) Research Group, Sebelas Maret University , Jl. Ir. Sutami 36A, Surakarta, Indonesia; Department of Pulmonology, Dr. Moewardi General Hospital, Jl. Kolonel Sutarto 132, Surakarta, Indonesia; Doctoral Program of Medical Sciences Faculty of Medicine, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| |
Collapse
|
31
|
René C, Lozano C, Villalba M, Eliaou JF. 5' and 3' untranslated regions contribute to the differential expression of specific HLA-A alleles. Eur J Immunol 2015; 45:3454-63. [PMID: 26399450 DOI: 10.1002/eji.201545927] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/19/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
In hematopoietic stem cell transplantation (HSCT), when no HLA full-matched donor is available, alternative donors could include one HLA-mismatched donor. Recently, the low expressed HLA-C alleles have been identified as permissive mismatches for the best donor choice. Concerning HLA-A, the degree of variability of expression is poorly understood. Here, we evaluated HLA-A expression in healthy individuals carrying HLA-A*02 allele in different genotypes using flow cytometry and allele-specific quantitative RT-PCR. While an interindividual variability of HLA-A*02 cell surface expression, not due to the allele associated, was observed, no difference of the mRNA expression level was shown, suggesting the involvement of the posttranscriptional regulation. The results of qRT-PCR analyses exhibit a differential expression of HLA-A alleles with HLA-A*02 as the strongest expressed allele independently of the second allele. The associated non-HLA-A*02 alleles were differentially expressed, particularly the HLA-A*31 and HLA-A*33 alleles (strong expression) and the HLA-A*29 (low expression). The presence of specific polymorphisms in the 5' and 3' untranslated regions of the HLA-A*31 and HLA-A*33 alleles could contribute to this high level of expression. As previously described for HLA-C, low-expressed HLA-A alleles, such as HLA-A*29, could be considered as a permissive mismatch, although this needs to be confirmed by clinical studies.
Collapse
Affiliation(s)
- Céline René
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1183, Université de Montpellier, UFR Médecine, Montpellier, France
| | - Claire Lozano
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France
| | - Martin Villalba
- INSERM U1183, Université de Montpellier, UFR Médecine, Montpellier, France.,Institute for Regenerative Medicine and Biotherapy (IRMB), CHRU Montpellier, Montpellier, France
| | - Jean-François Eliaou
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1194, IRCM University of Montpellier, Montpellier, France
| |
Collapse
|
32
|
Protective Effect of HLA-B*5701 and HLA-C -35 Genetic Variants in HIV-Positive Caucasians from Northern Poland. PLoS One 2015; 10:e0127867. [PMID: 26068923 PMCID: PMC4465896 DOI: 10.1371/journal.pone.0127867] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/21/2015] [Indexed: 11/24/2022] Open
Abstract
Aim of the Study Association of two HLA class I variants with HIV-1 pretreatment viremia, CD4+ T cell count at the care-entry and CD4+ T cell nadir. Methods 414 HIV-positive Caucasians (30% women) aged 19-73 years were genotyped for HLA-C -35 (rs9264942) and HLA-B*5701 variants. HIV-1 viral load, as well as CD4+ T cell count at care-entry and nadir, were compared across alleles, genotypes and haplotypes. Results HLA-C -35 C/C genotype was found in 17.6% patients, C/T genotype in 48.1%, and T/T genotype in 34.3% patients. HLA-B*5701 variant was present in 5.8% of studied population. HIV plasma viremia in the group with C allele was significantly lower (p=0.0002) compared to T/T group [mean:4.66 log (SD:1.03) vs. 5.07 (SD:0.85) log HIV-RNA copies/ml, respectively], while CD4+ T cell count at baseline was notably higher among C allele carriers compared to T/T homozygotes [median: 318 (IQR:127-537) cells/μl vs. median: 203 (IQR:55-410) cells/μl, respectively] (p=0.0007). Moreover, CD4+ T cell nadir among patients with C allele [median: 205 (IQR:83.5-390) cells/μl] was significantly higher compared to T/T group [median: 133 (IQR:46-328) cells/μl] (p=0.006). Among cases with HLA-B*5701 allele, significantly lower pretreatment viremia and higher baseline CD4+ T cell count were found (mean: 4.08 [SD: 1.2] vs. mean: 4.84 [SD:0.97] log HIV-RNA copies/ml, p=0.003 and 431 vs. 270 cells/μl, p=0.04, respectively) compared to HLA-B*5701 negative individuals. The lowest viremia (mean: 3.85 log [SD:1.3]) HIV-RNA copies/ml and the highest baseline and nadir CD4+ T cell [median: 476 (IQR:304-682) vs. median: 361 (IQR: 205-574) cells/μl, respectively) were found in individuals with HLA-B*5701(+)/HLA-C –35 C/C haplotype. Conclusions HLA-C -35 C and HLA-B*5701 allele exert a favorable effect on the immunological (higher baseline and nadir CD4+ T cell count) and virologic (lower pretreatment HIV viral load) variables. This protective effect is additive for the compound HLA-B*5701(+)/HLA-C -35 C/C haplotype.
Collapse
|
33
|
Kilpeläinen A, Axelsson Robertson R, Leitner T, Sandström E, Maeurer M, Wahren B. Short communication: HIV-1 Nef protein carries multiple epitopes suitable for induction of cellular immunity for an HIV vaccine in Africa. AIDS Res Hum Retroviruses 2014; 30:1065-71. [PMID: 24866397 DOI: 10.1089/aid.2013.0299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using the early protein HIV Nef, new HLA class I binding epitopes of importance for immune responses to HIV were predicted for common African alleles. In total we identified 45 epitopes previously not described for the HLA alleles A*30:01, A*30:02, B*58:01, and C*07:01 and compared them to reported epitopes, primarily from HLA-A*02:01, from the Los Alamos database and our own vaccine studies. Related to its small size, the Nef gene/protein appears to be able to contribute effectively to confer both stronger and broader cellular immunogenicity to an HIV-1 vaccine. We also propose feasible mutations of such an additional vaccine antigen to preserve its immunogenicity, modified not to confer HLA or CD4(+) down-regulating activities. This article includes data on a valuable HIV immunogenic component for a vaccine in Africa.
Collapse
Affiliation(s)
- Athina Kilpeläinen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Rebecca Axelsson Robertson
- Therapeutic Immunology (TIM), Department of Laboratory Medicine, Karolinska Institutet and CAST, Karolinska Hospital, Stockholm, Sweden
| | | | - Eric Sandström
- Department of Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Markus Maeurer
- Therapeutic Immunology (TIM), Department of Laboratory Medicine, Karolinska Institutet and CAST, Karolinska Hospital, Stockholm, Sweden
| | - Britta Wahren
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
34
|
Israeli M, Roelen DL, Carrington M, Petersdorf EW, Claas FHJ, Haasnoot GW, Oudshoorn M. Association between CTL Precursor Frequency to HLA-C Mismatches and HLA-C Antigen Cell Surface Expression. Front Immunol 2014; 5:547. [PMID: 25386183 PMCID: PMC4209872 DOI: 10.3389/fimmu.2014.00547] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/14/2014] [Indexed: 01/05/2023] Open
Abstract
Previous studies showed the relevance of the cytotoxic T-cell precursor (CTLp) frequency assay for prediction of the outcome of HLA mismatched hematopoietic cell transplantation (HCT). Recently, it has been shown that HLA-C cell surface expression is correlated with virus specific cytotoxic T-cell responses and viremia control in HIV patients. The aim of the current study was to investigate the association between HLA-C antigen expression and the CTLp frequency to the mismatched HLA-C antigen. In total 115 recipient-donor pairs, for whom a successful CTLp assay was performed, were evaluated for this pilot study. All donor-recipient pairs were matched at 9/10 alleles with a single mismatch at the HLA-C locus. Antigen expression level of the mismatched HLA-C allele for each recipient and donor was based on the mean fluorescence intensity (MFI) values as described by Apps et al. (1). The cell surface expression of recipient's mismatched HLA-C antigen was significantly lower among CTLp negative (n = 59) compared to CTLp positive (n = 56) pairs (154 and 193 MFI units, respectively, p = 0.0031). This difference was more pronounced in donor-recipient pairs that were mismatched for amino-acid residue-116 located in the groove of the HLA-C antigen, suggesting that the importance of peptide binding in the allo-recognition. Furthermore, in the particular case of low expression of the recipient mismatched HLA-C antigen (MFI < 115), CTLp reactivity depended on HLA-C expression level in the donor, the median MFI of donor's mismatched HLA-C antigen was 114 in CTLp negative cases (n = 26), while in CTLp positive cases (n = 15) the median MFI of donor's HLA-C antigen was 193 (p = 0.0093). We conclude that the expression level of the donor and recipient mismatched HLA-C antigens affect CTLp outcome. HLA-C antigen expression levels in combination with the CTLp assay may prove useful for the prediction of the clinical outcome of HLA-C mismatched HCT.
Collapse
Affiliation(s)
- Moshe Israeli
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands ; Tissue Typing Laboratory, Rabin Medical Center , Petach Tikva , Israel
| | - Dave L Roelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. , Frederick, MD , USA ; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University , Boston, MA , USA
| | - Effie Wang Petersdorf
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, WA , USA
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands
| | - Geert W Haasnoot
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands
| | - Machteld Oudshoorn
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands ; Europdonor Foundation , Leiden , Netherlands
| |
Collapse
|
35
|
Rasmussen M, Harndahl M, Stryhn A, Boucherma R, Nielsen LL, Lemonnier FA, Nielsen M, Buus S. Uncovering the peptide-binding specificities of HLA-C: a general strategy to determine the specificity of any MHC class I molecule. THE JOURNAL OF IMMUNOLOGY 2014; 193:4790-802. [PMID: 25311805 DOI: 10.4049/jimmunol.1401689] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I molecules (HLA-I in humans) present peptides derived from endogenous proteins to CTLs. Whereas the peptide-binding specificities of HLA-A and -B molecules have been studied extensively, little is known about HLA-C specificities. Combining a positional scanning combinatorial peptide library approach with a peptide-HLA-I dissociation assay, in this study we present a general strategy to determine the peptide-binding specificity of any MHC class I molecule. We applied this novel strategy to 17 of the most common HLA-C molecules, and for 16 of these we successfully generated matrices representing their peptide-binding motifs. The motifs prominently shared a conserved C-terminal primary anchor with hydrophobic amino acid residues, as well as one or more diverse primary and auxiliary anchors at P1, P2, P3, and/or P7. Matrices were used to generate a large panel of HLA-C-specific peptide-binding data and update our pan-specific NetMHCpan predictor, whose predictive performance was considerably improved with respect to peptide binding to HLA-C. The updated predictor was used to assess the specificities of HLA-C molecules, which were found to cover a more limited sequence space than HLA-A and -B molecules. Assessing the functional significance of these new tools, HLA-C*07:01 transgenic mice were immunized with stable HLA-C*07:01 binders; six of six tested stable peptide binders were immunogenic. Finally, we generated HLA-C tetramers and labeled human CD8(+) T cells and NK cells. These new resources should support future research on the biology of HLA-C molecules. The data are deposited at the Immune Epitope Database, and the updated NetMHCpan predictor is available at the Center for Biological Sequence Analysis and the Immune Epitope Database.
Collapse
Affiliation(s)
- Michael Rasmussen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Mikkel Harndahl
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anette Stryhn
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rachid Boucherma
- INSERM, Unité 1016, Institut Cochin, Equipe Immunologie du Diabète, Groupe Hospitalier Cochin-Port-Royal, 75014 Paris, France
| | - Lise Lotte Nielsen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - François A Lemonnier
- INSERM, Unité 1016, Institut Cochin, Equipe Immunologie du Diabète, Groupe Hospitalier Cochin-Port-Royal, 75014 Paris, France
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark; and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires, Argentina
| | - Søren Buus
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark;
| |
Collapse
|
36
|
Vineretsky KA, Karagas MR, Kuriger-Laber JK, Waterboer T, Pawlita M, Nelson HH. HLA-C -35kb expression SNP is associated with differential control of β-HPV infection in squamous cell carcinoma cases and controls. PLoS One 2014; 9:e103710. [PMID: 25083782 PMCID: PMC4118903 DOI: 10.1371/journal.pone.0103710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 07/04/2014] [Indexed: 12/23/2022] Open
Abstract
A single nucleotide polymorphism (SNP) 35 kb upstream of the HLA-C gene is associated with HLA-C expression, and the high expressing genotype (CC) has been associated with HIV-I control. HLA-C is unique among the classical MHC class I molecules for its role in the control of viral infections and recognition of abnormal or missing self. This immunosurveillance is central to the pathogenesis of non-melanoma skin cancer (NMSC), and of squamous cell carcinoma (SCC) in particular. While sun exposure is a major risk factor for these cancers, cutaneous infections with genus β-HPV have been implicated in the development of SCC. We hypothesized that the high expression HLA-C genotype is associated with β-HPV infections. Therefore, we investigated the association between β-HPV serology and the -35 kb SNP (rs9264942) in a population-based case-control study of 510 SCC cases and 608 controls. Among controls, the high expression -35 kb SNP genotype (CC) reduced the likelihood of positive serology for multiple (≥2) β-HPV infections (OR = 0.49, 95% CI: 0.25-0.97), and β-HPV species 2 infection (OR = 0.43, 95% CI: 0.23-0.79). However, no association with β-HPV status was observed among SCC cases. Our findings suggest that underlying immunogenotype plays an important role in differential control of β-HPV in SCC cases and controls.
Collapse
Affiliation(s)
- Karin A. Vineretsky
- Department of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret R. Karagas
- Department of Community and Family Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jacquelyn K. Kuriger-Laber
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Tim Waterboer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Heather H. Nelson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
37
|
Al-Mawsawi LQ, Wu NC, De La Cruz J, Shi VC, Wu TT, Daar ES, Lewis MJ, Yang OO, Sun R. Short communication: HIV-1 gag genetic variation in a single acutely infected participant defined by high-resolution deep sequencing. AIDS Res Hum Retroviruses 2014; 30:806-11. [PMID: 24914638 DOI: 10.1089/aid.2014.0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Acute HIV-1 infection is characterized by the rapid generation of highly diverse genetic variants to adapt to the new host environment. Understanding the dynamics of viral genetic variation at this stage of infection is critical for vaccine design efforts and early drug treatment. Here, using a high-resolution deep sequencing approach targeting the HIV-1 gag region, we reveal very early immune pressure with dramatic subpopulation shifts in a single acutely infected participant providing further insight into the genetic dynamics of acute HIV-1 infection.
Collapse
Affiliation(s)
- Laith Q Al-Mawsawi
- 1 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California , Los Angeles, Los Angeles, California
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Kaposi's sarcoma-associated herpesvirus K3 and K5 ubiquitin E3 ligases have stage-specific immune evasion roles during lytic replication. J Virol 2014; 88:9335-49. [PMID: 24899205 DOI: 10.1128/jvi.00873-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED The downregulation of immune synapse components such as major histocompatibility complex class I (MHC-I) and ICAM-1 is a common viral immune evasion strategy that protects infected cells from targeted elimination by cytolytic effector functions of the immune system. Kaposi's sarcoma-associated herpesvirus (KSHV) encodes two membrane-bound ubiquitin E3 ligases, called K3 and K5, which share the ability to induce internalization and degradation of MHC-I molecules. Although individual functions of K3 and K5 outside the viral genome are well characterized, their roles during the KSHV life cycle are still unclear. In this study, we individually introduced the amino acid-coding sequences of K3 or K5 into a ΔK3 ΔK5 recombinant virus, at either original or interchanged genomic positions. Recombinants harboring coding sequences within the K5 locus showed higher K3 and K5 protein expression levels and more rapid surface receptor downregulation than cognate recombinants in which coding sequences were introduced into the K3 locus. To identify infected cells undergoing K3-mediated downregulation of MHC-I, we employed a novel reporter virus, called red-green-blue-BAC16 (RGB-BAC16), which was engineered to harbor three fluorescent protein expression cassettes: EF1α-monomeric red fluorescent protein 1 (mRFP1), polyadenylated nuclear RNA promoter (pPAN)-enhanced green fluorescent protein (EGFP), and pK8.1-monomeric blue fluorescent protein (tagBFP), marking latent, immediate early, and late viral gene expression, respectively. Analysis of RGB-derived K3 and K5 deletion mutants showed that while the K5-mediated downregulation of MHC-I was concomitant with pPAN induction, the reduction of MHC-I surface expression by K3 was evident in cells that were enriched for pPAN-driven EGFP(high) and pK8.1-driven blue fluorescent protein-positive (BFP(+)) populations. These data support the notion that immunoreceptor downregulation occurs by a sequential process wherein K5 is critical during the immediately early phase and K3 plays a significant role during later stages. IMPORTANCE Although the roles of K3 and K5 outside the viral genome are well characterized, the function of these proteins in the context of the KSHV life cycle has remained unclear, particularly in the case of K3. This study examined the relative contributions of K3 and K5 to the downregulation of MHC-I during the lytic replication of KSHV. We show that while K5 acts immediately upon entry into the lytic phase, K3-mediated downregulation of MHC-I was evident during later stages of lytic replication. The identification of distinctly timed K3 and K5 activities significantly advances our understanding of KSHV-mediated immune evasion. Crucial to this study was the development of a novel recombinant KSHV, called RGB-BAC16, which facilitated the delineation of stage-specific phenotypes.
Collapse
|
39
|
Comparison of IFN-β inducible gene expression in primary-progressive and relapsing-remitting multiple sclerosis. J Neuroimmunol 2013; 265:68-74. [DOI: 10.1016/j.jneuroim.2013.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 11/18/2022]
|
40
|
Kaur G, Sharma G, Kumar N, Kaul MH, Bansal RA, Vajpayee M, Wig N, Sharma SK, Mehra NK. Genomic architecture of HIV-1 infection: current status & challenges. Indian J Med Res 2013; 138:663-81. [PMID: 24434320 PMCID: PMC3928698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Indexed: 11/02/2022] Open
Abstract
Studies on host genomics have revealed the existence of identifiable HIV-1 specific protective factors among infected individuals who remain naturally resistant viraemia controllers with little or no evidence of virus replication. These factors are broadly grouped into those that are immune associated (MHC, chemokines, cytokines, CTLs and others), linked to viral entry (chemokine co-receptors and ligands), act as post-entry restriction elements (TRIM5a, APOBEC3) and those associated with viral replication (cytokines and others). These features have been identified through multiple experimental approaches ranging from candidate gene approaches, genome wide association studies (GWAS), expression analysis in conjunction with functional assays in humans to primate based models. Several studies have highlighted the individual and population level gross differences both in the viral clade sequences as well as host determined genetic associations. This review collates current information on studies involving major histocompatibility complex (MHC) as well as non MHC genes in the context of HIV-1 infection and AIDS involving varied ethnic groups. Special focus of the review is on the genetic studies carried out on the Indian population. Further challenges with regard to therapeutic interventions based on current knowledge have been discussed along with discussion on documented cases of stem cell therapy and very early highly active antiretroviral therapy (HAART) interventions.
Collapse
Affiliation(s)
- Gurvinder Kaur
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Sharma
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Neeraj Kumar
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Mrinali H. Kaul
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Rhea A. Bansal
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhu Vajpayee
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Surender K. Sharma
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Narinder K. Mehra
- Department of Transplant Immunology & Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
41
|
Abstract
Over several decades, various forms of genomic analysis of the human major histocompatibility complex (MHC) have been extremely successful in picking up many disease associations. This is to be expected, as the MHC region is one of the most gene-dense and polymorphic stretches of human DNA. It also encodes proteins critical to immunity, including several controlling antigen processing and presentation. Single-nucleotide polymorphism genotyping and human leukocyte antigen (HLA) imputation now permit the screening of large sample sets, a technique further facilitated by high-throughput sequencing. These methods promise to yield more precise contributions of MHC variants to disease. However, interpretation of MHC-disease associations in terms of the functions of variants has been problematic. Most studies confirm the paramount importance of class I and class II molecules, which are key to resistance to infection. Infection is likely driving the extreme variation of these genes across the human population, but this has been difficult to demonstrate. In contrast, many associations with autoimmune conditions have been shown to be specific to certain class I and class II alleles. Interestingly, conditions other than infections and autoimmunity are also associated with the MHC, including some cancers and neuropathies. These associations could be indirect, owing, for example, to the infectious history of a particular individual and selective pressures operating at the population level.
Collapse
Affiliation(s)
- John Trowsdale
- Department of Pathology and Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
| | | |
Collapse
|
42
|
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.
Collapse
|
43
|
Elboim M, Grodzovski I, Djian E, Wolf DG, Mandelboim O. HSV-2 specifically down regulates HLA-C expression to render HSV-2-infected DCs susceptible to NK cell killing. PLoS Pathog 2013; 9:e1003226. [PMID: 23555244 PMCID: PMC3610627 DOI: 10.1371/journal.ppat.1003226] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/18/2013] [Indexed: 12/03/2022] Open
Abstract
Both NK cells and CTLs kill virus-infected and tumor cells. However, the ways by which these killer cells recognize the infected or the tumorigenic cells are different, in fact almost opposite. CTLs are activated through the interaction of the TCR with MHC class I proteins. In contrast, NK cells are inhibited by MHC class I molecules. The inhibitory NK receptors recognize mainly MHC class I proteins and in this regard practically all of the HLA-C proteins are recognized by inhibitory NK cell receptors, while only certain HLA-A and HLA-B proteins interact with these receptors. Sophisticated viruses developed mechanisms to avoid the attack of both NK cells and CTLs through, for example, down regulation of HLA-A and HLA-B molecules to avoid CTL recognition, leaving HLA-C proteins on the cell surface to inhibit NK cell response. Here we provide the first example of a virus that through specific down regulation of HLA-C, harness the NK cells for its own benefit. We initially demonstrated that none of the tested HSV-2 derived microRNAs affect NK cell activity. Then we show that surprisingly upon HSV-2 infection, HLA-C proteins are specifically down regulated, rendering the infected cells susceptible to NK cell attack. We identified a motif in the tail of HLA-C that is responsible for the HSV-2-meduiated HLA-C down regulation and we show that the HLA-C down regulation is mediated by the viral protein ICP47. Finally we show that HLA-C proteins are down regulated from the surface of HSV-2 infected dendritic cells (DCs) and that this leads to the killing of DC by NK cells. Thus, we propose that HSV-2 had developed this unique and surprising NK cell-mediated killing strategy of infected DC to prevent the activation of the adaptive immunity. Approximately 20% of all humans are latently and asymptomatically infected with HSV-2. This suggests that the virus developed mechanisms to avoid immune cell detection; many of which are still unknown. Infected cells are killed mainly by two lymphocyte populations; NK cells and CTLs that belong to the innate and the adaptive immunity, respectively. While the killing machinery of these two cell types is similar, almost identical, the ways by which they discriminate between infected and uninfected cells is different. CTLs are activated, primarily by DCs, to become effector cells. They then recognize virus-derived peptides in the groove of MHC class I molecules and eliminate the virally infected cells. In contrast, NK cells recognize infected cells through several NK cell activating receptors, while the recognition of MHC class I proteins by NK cells leads to inhibition of NK cell killing. Viruses, such as HIV, developed mechanisms to interfere with the function of both NK cells and CTLs via targeting of specific MHC class I proteins. Here we show that HSV-2 developed a MHC class I-dependent mechanism in which the virus, through specific targeting of HLA-C by the viral protein ICP47, harness the NK cells for its own benefit, probably to avoid the activation of adaptive immune response.
Collapse
Affiliation(s)
- Moran Elboim
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Inna Grodzovski
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Esther Djian
- Virology Unit, Hadassah Hospital, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Dana G. Wolf
- Virology Unit, Hadassah Hospital, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel-Canada of the Faculty of Medicine, The Hebrew University Hadassah Medical School, Jerusalem, Israel
- * E-mail:
| |
Collapse
|
44
|
Peterson TA, Kimani J, Wachihi C, Bielawny T, Mendoza L, Thavaneswaran S, Narayansingh MJ, Kariri T, Liang B, Ball TB, Ngugi EN, Plummer FA, Luo M. HLA class I associations with rates of HIV-1 seroconversion and disease progression in the Pumwani Sex Worker Cohort. ACTA ACUST UNITED AC 2013; 81:93-107. [DOI: 10.1111/tan.12051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/20/2012] [Accepted: 12/16/2012] [Indexed: 12/01/2022]
Affiliation(s)
- T. A. Peterson
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | | | - C. Wachihi
- Department of Medical Microbiology; University of Nairobi; Nairobi; Kenya
| | - T. Bielawny
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | - L. Mendoza
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | - S. Thavaneswaran
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | - M. J. Narayansingh
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | - T. Kariri
- Department of Medical Microbiology; University of Nairobi; Nairobi; Kenya
| | - B. Liang
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | | | - E. N. Ngugi
- Department of Community Health; University of Nairobi; Nairobi; Kenya
| | | | | |
Collapse
|
45
|
Shea PR, Shianna KV, Carrington M, Goldstein DB. Host genetics of HIV acquisition and viral control. Annu Rev Med 2012; 64:203-17. [PMID: 23020875 DOI: 10.1146/annurev-med-052511-135400] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Since the discovery of HIV as the cause of AIDS, numerous insights have been gained from studies of its natural history and epidemiology. It has become clear that there are substantial interindividual differences in the risk of HIV acquisition and course of disease. Meanwhile, the field of human genetics has undergone a series of rapid transitions that have fundamentally altered the approach to studying HIV host genetics. We aim to describe the field as it has transitioned from the era of candidate-gene studies and the era of genome-wide association studies (GWAS) to its current state in the infancy of comprehensive sequencing. In some ways the field has come full circle, having evolved from being driven almost exclusively by our knowledge of immunology, to a bias-free GWAS approach, to a point where our ability to catalogue human variation far outstrips our ability to biologically interpret it.
Collapse
Affiliation(s)
- Patrick R Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina 27708, USA.
| | | | | | | |
Collapse
|
46
|
Tan Gana NH, Onuki T, Victoriano AFB, Okamoto T. MicroRNAs in HIV-1 infection: an integration of viral and cellular interaction at the genomic level. Front Microbiol 2012; 3:306. [PMID: 22936931 PMCID: PMC3426883 DOI: 10.3389/fmicb.2012.00306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/01/2012] [Indexed: 12/15/2022] Open
Abstract
The microRNA pathways govern complex interactions of the host and virus at the transcripts level that regulate cellular responses, viral replication and viral pathogenesis. As a group of single-stranded short non-coding ribonucleotides (ncRNAs), the microRNAs complement their messenger RNA (mRNA) targets to effect post-transcriptional or translational gene silencing. Previous studies showed the ability of human immunodeficiency virus 1 (HIV-1) to encode microRNAs which modify cellular defence mechanisms thus creating an environment favorable for viral invasion and replication. In corollary, cellular microRNAs were linked to the alteration of HIV-1 infection at different stages of replication and latency. As evidences further establish the regulatory involvement of both cellular and viral microRNA in HIV-1-host interactions, there is a necessity to organize this information. This paper would present current and emerging knowledge on these multi-dimensional interactions that may facilitate the design of microRNAs as effective antiretroviral reagents.
Collapse
Affiliation(s)
- Neil H Tan Gana
- Department of Molecular and Cell Biology, Nagoya City University Graduate School of Medical Sciences Nagoya, Japan
| | | | | | | |
Collapse
|
47
|
Lank SM, Golbach BA, Creager HM, Wiseman RW, Keskin DB, Reinherz EL, Brusic V, O'Connor DH. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics 2012; 13:378. [PMID: 22866951 PMCID: PMC3575390 DOI: 10.1186/1471-2164-13-378] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 07/07/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. RESULTS We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. CONCLUSIONS The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.
Collapse
Affiliation(s)
- Simon M Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Zhuang YL, Ren GJ, Tian KL, Li XY, Zhu YB, Liu JL, Si GL, Li P, Zhang Y, Wang L, Zhang WJ, Wang DJ, Zhu CF. Human leukocyte antigen-C and killer cell immunoglobulin-like receptor gene polymorphisms among patients with syphilis in a Chinese Han population. APMIS 2012; 120:828-35. [PMID: 22958291 DOI: 10.1111/j.1600-0463.2012.02911.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/02/2012] [Indexed: 12/18/2022]
Abstract
Syphilis is a sexually transmitted infection caused by the Treponema pallidum subspecies pallidum spirochete bacterium. The killer cell immunoglobulin-like receptors (KIR), interacting with human leukocyte antigens (HLA), regulate the activations of natural killer (NK) cells and certain T-cell subsets in response to microbe infection. The objective of this study was to explore whether KIR and HLA-C gene polymorphisms were associated with syphilis in a Chinese Han population. Polymerase chain reaction with sequence-specific primers (PCR-SSP) method was used to genotype KIR and HLA-C genes in 231 syphilis patients and 247 healthy controls. Framework genes KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 were present in all individuals. The frequencies of KIR2DS3 and KIR3DS1 were higher in syphilis patients than in healthy controls (p = 0.030 and p = 0.038, respectively), while the frequency of KIR2DS5 was higher in healthy controls than in syphilis patients (p = 0.015; OR = 0.575). The homozygote for HLA-C1 allele (HLA-C1C1) was more common in controls compared with syphilis patients (p = 0.030; OR = 0.667). The frequency of individuals with HLA-C1C1 and KIR2DL3 genotype was higher in control group relative to syphilis patient group (p = 0.018; OR = 0.647). These data indicated that KIR2DS3 and KIR3DS1 were more prevalent in syphilis patients than in controls, and that KIR2DS5, HLA-C1C1 and HLA-C1C1-KIR2DL3 were more prevalent in controls than in syphilis patients, respectively. These will require further investigation using functional studies.
Collapse
|
49
|
Blais ME, Zhang Y, Rostron T, Griffin H, Taylor S, Xu K, Yan H, Wu H, James I, John M, Dong T, Rowland-Jones SL. High frequency of HIV mutations associated with HLA-C suggests enhanced HLA-C-restricted CTL selective pressure associated with an AIDS-protective polymorphism. THE JOURNAL OF IMMUNOLOGY 2012; 188:4663-70. [PMID: 22474021 DOI: 10.4049/jimmunol.1103472] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Delayed HIV-1 disease progression is associated with a single nucleotide polymorphism upstream of the HLA-C gene that correlates with differential expression of the HLA-C Ag. This polymorphism was recently shown to be a marker for a protective variant in the 3'UTR of HLA-C that disrupts a microRNA binding site, resulting in enhanced HLA-C expression at the cell surface. Whether individuals with "high" HLA-C expression show a stronger HLA-C-restricted immune response exerting better viral control than that of their counterparts has not been established. We hypothesized that the magnitude of the HLA-C-restricted immune pressure on HIV would be greater in subjects with highly expressed HLA-C alleles. Using a cohort derived from a unique narrow source epidemic in China, we identified mutations in HIV proviral DNA exclusively associated with HLA-C, which were used as markers for the intensity of the immune pressure exerted on the virus. We found an increased frequency of mutations in individuals with highly expressed HLA-C alleles, which also correlated with IFN-γ production by HLA-C-restricted CD8(+) T cells. These findings show that immune pressure on HIV is stronger in subjects with the protective genotype and highlight the potential role of HLA-C-restricted responses in HIV control. This is, to our knowledge, the first in vivo evidence supporting the protective role of HLA-C-restricted responses in nonwhites during HIV infection.
Collapse
Affiliation(s)
- Marie-Eve Blais
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Immunodominance: a pivotal principle in host response to viral infections. Clin Immunol 2012; 143:99-115. [PMID: 22391152 DOI: 10.1016/j.clim.2012.01.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 11/24/2022]
Abstract
We encounter pathogens on a daily basis and our immune system has evolved to mount an immune response following an infection. An interesting phenomenon that has evolved in response to clearing bacterial and viral infections is called immunodominance. Immunodominance refers to the phenomenon that, despite co-expression of multiple major histocompatibility complex class I alleles by host cells and the potential generation of hundreds of distinct antigenic peptides for recognition following an infection, a large portion of the anti-viral cytotoxic T lymphocyte population targets only some peptide/MHC class I complexes. Here we review the main factors contributing to immunodominance in relation to influenza A and HIV infection. Of special interest are the factors contributing to immunodominance in humans and rodents following influenza A infection. By critically reviewing these findings, we hope to improve understanding of the challenges facing the discovery of new factors enabling better anti-viral vaccine strategies in the future.
Collapse
|