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R5X4 HIV-1 coreceptor use in primary target cells: implications for coreceptor entry blocking strategies.

Loftin LM, Kienzle M, Yi Y, Collman RG - J Transl Med (2011)

Bottom Line: However, these algorithms were developed to predict coreceptor use in cell lines and not primary cells and, furthermore, are not highly accurate for some classes of viruses.This article focuses on R5X4 HIV-1, the earliest CXCR4-using variants, reviewing the pattern of coreceptor use on primary CD4+ lymphocytes and macrophages, the relationship between primary cell coreceptor use and the two principal approaches to coreceptor analysis (genetic prediction and indicator cell phenotyping), and the implications of primary cell coreceptor use by these strains for treatment with a new class of small molecule antagonists that inhibit CCR5-mediated entry.These are important questions to consider given the development of new CCR5 blocking therapies and the prognosis associated with CXCR4 use.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 36th & Hamilton Walk, Philadelphia, PA 19104-6060, USA.

ABSTRACT
Entry coreceptor use by HIV-1 plays a pivotal role in viral transmission, pathogenesis and disease progression. In many HIV-1 infected individuals, there is an expansion in coreceptor use from CCR5 to include CXCR4, which is associated with accelerated disease progression. While targeting HIV-1 envelope interactions with coreceptor during viral entry is an appealing approach to combat the virus, the methods of determining coreceptor use and the changes in coreceptor use that can occur during disease progression are important factors that may complicate the use of therapies targeting this stage of HIV-1 replication. Indicator cells are typically used to determine coreceptor use by HIV-1 in vitro, but the coreceptors used on these cells can differ from those used on primary cell targets. V3 based genetic sequence algorithms are another method used to predict coreceptor use by HIV-1 strains. However, these algorithms were developed to predict coreceptor use in cell lines and not primary cells and, furthermore, are not highly accurate for some classes of viruses. This article focuses on R5X4 HIV-1, the earliest CXCR4-using variants, reviewing the pattern of coreceptor use on primary CD4+ lymphocytes and macrophages, the relationship between primary cell coreceptor use and the two principal approaches to coreceptor analysis (genetic prediction and indicator cell phenotyping), and the implications of primary cell coreceptor use by these strains for treatment with a new class of small molecule antagonists that inhibit CCR5-mediated entry. These are important questions to consider given the development of new CCR5 blocking therapies and the prognosis associated with CXCR4 use.

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R5X4 HIV-1 CCR5 use on CD4+ lymphocytes is associated with the predicted viral phenotype. (A) Predicted NSI/SI phenotype of the R5X4 HIV-1 viruses.  V3 sequences from each virus were analyzed using the NSI/SI PSSM algorithm.  The table shows the SI or NSI prediction and coreceptor use on cell lines and primary lymphocytes for each R5X4 virus from Figures 1 and 2, respectively. The strains shown in the table are found in the following references: [63-68] (B) Mean CCR5 use on CD4+ lymphocytes by R5X4 HIV-1 grouped by predicted viral phenotype.  R5X4 viruses were grouped by SI or NSI phenotype from (A) with CCR5 use for each virus represented by black circles.  The mean lymphocyte CCR5 use for each group was calculated, and the means were compared using a two-tailed, unpaired t-test in GraphPad Prism 4 software (***p<0.0001).
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Figure 4: R5X4 HIV-1 CCR5 use on CD4+ lymphocytes is associated with the predicted viral phenotype. (A) Predicted NSI/SI phenotype of the R5X4 HIV-1 viruses. V3 sequences from each virus were analyzed using the NSI/SI PSSM algorithm. The table shows the SI or NSI prediction and coreceptor use on cell lines and primary lymphocytes for each R5X4 virus from Figures 1 and 2, respectively. The strains shown in the table are found in the following references: [63-68] (B) Mean CCR5 use on CD4+ lymphocytes by R5X4 HIV-1 grouped by predicted viral phenotype. R5X4 viruses were grouped by SI or NSI phenotype from (A) with CCR5 use for each virus represented by black circles. The mean lymphocyte CCR5 use for each group was calculated, and the means were compared using a two-tailed, unpaired t-test in GraphPad Prism 4 software (***p<0.0001).

Mentions: A second consideration regarding sequence algorithms is that they have traditionally been used to predict coreceptor use by viral strains on indicator cell lines, but the success of these algorithms in predicting coreceptor use on primary cells is of central importance if they are to be used in clinical settings. To this end, we determined the viral phenotypes predicted by a widely used position-specific scoring matrix (PSSM) algorithm [46] for a panel of R5X4 viruses for which coreceptor used had been determined on CD4+ lymphocytes (Fig 4). This analysis showed that those R5X4 variants with significantly more efficient CCR5 use on primary CD4+ lymphocytes were likely to be incorrectly labeled as NSI, and thus erroneously presumed to be CCR5-restricted, by V3 sequence-based PSSM prediction. In contrast, R5X4 strains that were restricted in their ability to use lymphocyte CCR5 were typically categorized as syncytium inducing (SI) by PSSM (Fig 4 A and 4 B). Thus, using sequence algorithms, a number of R5X4 strains would be classified as R5 viruses, and this failure to detect CXCR4 could have important implications for entry blocking therapy as discussed below.


R5X4 HIV-1 coreceptor use in primary target cells: implications for coreceptor entry blocking strategies.

Loftin LM, Kienzle M, Yi Y, Collman RG - J Transl Med (2011)

R5X4 HIV-1 CCR5 use on CD4+ lymphocytes is associated with the predicted viral phenotype. (A) Predicted NSI/SI phenotype of the R5X4 HIV-1 viruses.  V3 sequences from each virus were analyzed using the NSI/SI PSSM algorithm.  The table shows the SI or NSI prediction and coreceptor use on cell lines and primary lymphocytes for each R5X4 virus from Figures 1 and 2, respectively. The strains shown in the table are found in the following references: [63-68] (B) Mean CCR5 use on CD4+ lymphocytes by R5X4 HIV-1 grouped by predicted viral phenotype.  R5X4 viruses were grouped by SI or NSI phenotype from (A) with CCR5 use for each virus represented by black circles.  The mean lymphocyte CCR5 use for each group was calculated, and the means were compared using a two-tailed, unpaired t-test in GraphPad Prism 4 software (***p<0.0001).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 4: R5X4 HIV-1 CCR5 use on CD4+ lymphocytes is associated with the predicted viral phenotype. (A) Predicted NSI/SI phenotype of the R5X4 HIV-1 viruses. V3 sequences from each virus were analyzed using the NSI/SI PSSM algorithm. The table shows the SI or NSI prediction and coreceptor use on cell lines and primary lymphocytes for each R5X4 virus from Figures 1 and 2, respectively. The strains shown in the table are found in the following references: [63-68] (B) Mean CCR5 use on CD4+ lymphocytes by R5X4 HIV-1 grouped by predicted viral phenotype. R5X4 viruses were grouped by SI or NSI phenotype from (A) with CCR5 use for each virus represented by black circles. The mean lymphocyte CCR5 use for each group was calculated, and the means were compared using a two-tailed, unpaired t-test in GraphPad Prism 4 software (***p<0.0001).
Mentions: A second consideration regarding sequence algorithms is that they have traditionally been used to predict coreceptor use by viral strains on indicator cell lines, but the success of these algorithms in predicting coreceptor use on primary cells is of central importance if they are to be used in clinical settings. To this end, we determined the viral phenotypes predicted by a widely used position-specific scoring matrix (PSSM) algorithm [46] for a panel of R5X4 viruses for which coreceptor used had been determined on CD4+ lymphocytes (Fig 4). This analysis showed that those R5X4 variants with significantly more efficient CCR5 use on primary CD4+ lymphocytes were likely to be incorrectly labeled as NSI, and thus erroneously presumed to be CCR5-restricted, by V3 sequence-based PSSM prediction. In contrast, R5X4 strains that were restricted in their ability to use lymphocyte CCR5 were typically categorized as syncytium inducing (SI) by PSSM (Fig 4 A and 4 B). Thus, using sequence algorithms, a number of R5X4 strains would be classified as R5 viruses, and this failure to detect CXCR4 could have important implications for entry blocking therapy as discussed below.

Bottom Line: However, these algorithms were developed to predict coreceptor use in cell lines and not primary cells and, furthermore, are not highly accurate for some classes of viruses.This article focuses on R5X4 HIV-1, the earliest CXCR4-using variants, reviewing the pattern of coreceptor use on primary CD4+ lymphocytes and macrophages, the relationship between primary cell coreceptor use and the two principal approaches to coreceptor analysis (genetic prediction and indicator cell phenotyping), and the implications of primary cell coreceptor use by these strains for treatment with a new class of small molecule antagonists that inhibit CCR5-mediated entry.These are important questions to consider given the development of new CCR5 blocking therapies and the prognosis associated with CXCR4 use.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 36th & Hamilton Walk, Philadelphia, PA 19104-6060, USA.

ABSTRACT
Entry coreceptor use by HIV-1 plays a pivotal role in viral transmission, pathogenesis and disease progression. In many HIV-1 infected individuals, there is an expansion in coreceptor use from CCR5 to include CXCR4, which is associated with accelerated disease progression. While targeting HIV-1 envelope interactions with coreceptor during viral entry is an appealing approach to combat the virus, the methods of determining coreceptor use and the changes in coreceptor use that can occur during disease progression are important factors that may complicate the use of therapies targeting this stage of HIV-1 replication. Indicator cells are typically used to determine coreceptor use by HIV-1 in vitro, but the coreceptors used on these cells can differ from those used on primary cell targets. V3 based genetic sequence algorithms are another method used to predict coreceptor use by HIV-1 strains. However, these algorithms were developed to predict coreceptor use in cell lines and not primary cells and, furthermore, are not highly accurate for some classes of viruses. This article focuses on R5X4 HIV-1, the earliest CXCR4-using variants, reviewing the pattern of coreceptor use on primary CD4+ lymphocytes and macrophages, the relationship between primary cell coreceptor use and the two principal approaches to coreceptor analysis (genetic prediction and indicator cell phenotyping), and the implications of primary cell coreceptor use by these strains for treatment with a new class of small molecule antagonists that inhibit CCR5-mediated entry. These are important questions to consider given the development of new CCR5 blocking therapies and the prognosis associated with CXCR4 use.

Show MeSH
Related in: MedlinePlus