title: Relative Resistance of HLA-B to Downregulation by Naturally Occurring HIV-1 Nef Sequences.
abstract: HIV-1 Nef binds to the cytoplasmic region of HLA-A and HLA-B and downregulates these molecules from the surface of virus-infected cells, thus evading immune detection by CD8(+) T cells. Polymorphic residues within the HLA cytoplasmic region may affect Nef's downregulation activity. However, the effects of HLA polymorphisms on recognition by primary Nef isolates remain elusive, as do the specific Nef regions responsible for downregulation of HLA-A versus HLA-B. Here, we examined 46 Nef clones isolated from chronically HIV-1 subtype B-infected subjects for their ability to downregulate various HLA-A, HLA-B, and HLA-C molecules on the surface of virus-infected cells. Overall, HLA-B exhibited greater resistance to Nef-mediated downregulation than HLA-A, regardless of the cell type examined. As expected, no Nef clone downregulated HLA-C. Importantly, the differential abilities of patient-derived Nef clones to downregulate HLA-A and HLA-B correlated inversely with the sensitivities of HIV-infected target cells to recognition by effector cells expressing an HIV-1 Gag-specific T cell receptor. Nef codon function analysis implicated amino acid variation at position 202 (Nef-202) in differentially affecting the ability to downregulate HLA-A and HLA-B, an observation that was subsequently confirmed by experiments using Nef mutants constructed by site-directed mutagenesis. The in silico and mutagenesis analyses further suggested that Nef-202 may interact with the C-terminal Cys-Lys-Val residues of HLA-A, which are absent in HLA-B. Taken together, the results show that natural polymorphisms within Nef modulate its interaction with natural polymorphisms in the HLA cytoplasmic tails, thereby affecting the efficiency of HLA downregulation and consequent recognition by HIV-specific T cells. These results thus extend our understanding of this complex pathway of retroviral immune evasion.
  
  
  OBJECTIVE
  Recognition of genetically diverse pathogens by the adaptive immune system represents a primary strategy for host defense; however, pathogens such as HIV-1 can evade these responses to achieve persistent infection. The HIV-1 nef gene and the HLA class I locus rank among the most diverse genes of virus and host, respectively. The HIV-1 Nef protein interacts with the cytoplasmic region of HLA-A and HLA-B and downregulates these molecules to evade cellular immunity. By combining molecular, genetic, and in silico analyses, we demonstrate that patient-derived Nef clones downregulate HLA-A more effectively than HLA-B molecules. This in turn modulates the ability of HIV-specific T cells to recognize HIV-infected cells. We also identify a naturally polymorphic site at Nef codon 202 and HLA cytoplasmic motifs (GG314,315 and CKV339-341) that contribute to differential HLA downregulation by Nef. Our results highlight new interactions between HIV-1 and the human immune system that may contribute to pathogenesis.
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Japan International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
authors.forename: Macdonald
authors.initials: M
authors.lastname: Mahiti
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Japan.
authors.forename: Mako
authors.initials: M
authors.lastname: Toyoda
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Jia
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Xiaomei T
authors.initials: XT
authors.lastname: Kuang
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Japan.
authors.forename: Francis
authors.initials: F
authors.lastname: Mwimanzi
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Japan Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Philip
authors.initials: P
authors.lastname: Mwimanzi
authors.affiliation: Ragon Institute of MGH, MIT and Harvard University, Boston, Massachusetts, USA Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Walker
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xiong
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.
authors.forename: Zabrina L
authors.initials: ZL
authors.lastname: Brumme
authors.affiliation: Simon Fraser University, Burnaby, British Columbia, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Brockman
authors.affiliation: Center for AIDS Research, Kumamoto University, Kumamoto, Japan International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan uenotaka@kumamoto-u.ac.jp.
authors.forename: Takamasa
authors.identifier: http://orcid.org/0000-0003-4852-4236
authors.initials: T
authors.lastname: Ueno
mesh_terms: D002460:Cell Line; D015536:Down-Regulation; D014644:Genetic Variation; D015497:HIV-1 / Q000502:physiology*; D015234:HLA-A Antigens / Q000378:metabolism; D015235:HLA-B Antigens / Q000378:metabolism*; D015236:HLA-C Antigens / Q000378:metabolism; D054884:Host-Pathogen Interactions; D006801:Humans; D016297:Mutagenesis, Site-Directed; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000235:genetics / Q000378:metabolism*
chemical_list: D015234:HLA-A Antigens; D015235:HLA-B Antigens; D015236:HLA-C Antigens; D054311:nef Gene Products, Human Immunodeficiency Virus; C514837:nef protein, Human immunodeficiency virus 1