Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Jaclyn K. Mann, Helen Byakwaga, Xiaomei T. Kuang, Anh Q. Le, Chanson J. Brumme, Philip Mwimanzi, Saleha Omarjee, Eric Martin, Guinevere Q. Lee, Bemuluyigza Baraki, Ryan Danroth, Rosemary McCloskey, Conrad Muzoora, David Bangsberg, Peter W. Hunt, Philip J R Goulder, Bruce D. Walker, P. R. Harrigan, Jeff N. Martin, Thumbi Ndung'u & 2 others Mark A. Brockman, Zabrina L. Brumme

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Background: The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.Results: Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.Conclusions: Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.

Original languageEnglish (US)
Article number100
JournalRetrovirology
Volume10
Issue number1
DOIs
StatePublished - Sep 16 2013
Externally publishedYes

Fingerprint

HIV-1
Down-Regulation
Clone Cells
Virulence
North America
Transfection
Sequence Analysis
Linear Models
Flow Cytometry
Western Blotting
RNA
T-Lymphocytes
Cell Line

Keywords

  • CD4
  • HIV/AIDS
  • HLA class I
  • Nef
  • Pathogenesis
  • Viral diversity

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Mann, J. K., Byakwaga, H., Kuang, X. T., Le, A. Q., Brumme, C. J., Mwimanzi, P., ... Brumme, Z. L. (2013). Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology, 10(1), [100]. https://doi.org/10.1186/1742-4690-10-100

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. / Mann, Jaclyn K.; Byakwaga, Helen; Kuang, Xiaomei T.; Le, Anh Q.; Brumme, Chanson J.; Mwimanzi, Philip; Omarjee, Saleha; Martin, Eric; Lee, Guinevere Q.; Baraki, Bemuluyigza; Danroth, Ryan; McCloskey, Rosemary; Muzoora, Conrad; Bangsberg, David; Hunt, Peter W.; Goulder, Philip J R; Walker, Bruce D.; Harrigan, P. R.; Martin, Jeff N.; Ndung'u, Thumbi; Brockman, Mark A.; Brumme, Zabrina L.

In: Retrovirology, Vol. 10, No. 1, 100, 16.09.2013.

Research output: Contribution to journalArticle

Mann, JK, Byakwaga, H, Kuang, XT, Le, AQ, Brumme, CJ, Mwimanzi, P, Omarjee, S, Martin, E, Lee, GQ, Baraki, B, Danroth, R, McCloskey, R, Muzoora, C, Bangsberg, D, Hunt, PW, Goulder, PJR, Walker, BD, Harrigan, PR, Martin, JN, Ndung'u, T, Brockman, MA & Brumme, ZL 2013, 'Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes', Retrovirology, vol. 10, no. 1, 100. https://doi.org/10.1186/1742-4690-10-100
Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P et al. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology. 2013 Sep 16;10(1). 100. https://doi.org/10.1186/1742-4690-10-100
Mann, Jaclyn K. ; Byakwaga, Helen ; Kuang, Xiaomei T. ; Le, Anh Q. ; Brumme, Chanson J. ; Mwimanzi, Philip ; Omarjee, Saleha ; Martin, Eric ; Lee, Guinevere Q. ; Baraki, Bemuluyigza ; Danroth, Ryan ; McCloskey, Rosemary ; Muzoora, Conrad ; Bangsberg, David ; Hunt, Peter W. ; Goulder, Philip J R ; Walker, Bruce D. ; Harrigan, P. R. ; Martin, Jeff N. ; Ndung'u, Thumbi ; Brockman, Mark A. ; Brumme, Zabrina L. / Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. In: Retrovirology. 2013 ; Vol. 10, No. 1.
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abstract = "Background: The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.Results: Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-na{\"i}ve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25{\%} of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.Conclusions: Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.",
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T1 - Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

AU - Mann, Jaclyn K.

AU - Byakwaga, Helen

AU - Kuang, Xiaomei T.

AU - Le, Anh Q.

AU - Brumme, Chanson J.

AU - Mwimanzi, Philip

AU - Omarjee, Saleha

AU - Martin, Eric

AU - Lee, Guinevere Q.

AU - Baraki, Bemuluyigza

AU - Danroth, Ryan

AU - McCloskey, Rosemary

AU - Muzoora, Conrad

AU - Bangsberg, David

AU - Hunt, Peter W.

AU - Goulder, Philip J R

AU - Walker, Bruce D.

AU - Harrigan, P. R.

AU - Martin, Jeff N.

AU - Ndung'u, Thumbi

AU - Brockman, Mark A.

AU - Brumme, Zabrina L.

PY - 2013/9/16

Y1 - 2013/9/16

N2 - Background: The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.Results: Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.Conclusions: Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.

AB - Background: The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D.Results: Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function.Conclusions: Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.

KW - CD4

KW - HIV/AIDS

KW - HLA class I

KW - Nef

KW - Pathogenesis

KW - Viral diversity

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DO - 10.1186/1742-4690-10-100

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JO - Retrovirology

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