CD4 and MHC class 1 down-modulation activities of nef alleles from brain- and lymphoid tissue-derived primary HIV-1 isolates

Abstract

HIV-1 nef undergoes adaptive evolution in the CNS, reflecting altered requirements for HIV-1 replication in macrophages/microglia and brain-specific immune selection pressures. The role of Nef in HIV-1 neurotropism and the pathogenesis of HIV-associated dementia (HAD) is unclear. In this study, we characterized 82 nef alleles cloned from brain, CSF, spinal cord and blood/lymphoid tissue-derived HIV-1 isolates from 7 subjects with HAD. CNS isolate-derived nef alleles were genetically compartmentalized and had reduced sequence diversity compared to those from lymphoid tissue isolates. Defective nef alleles predominated in a brain-derived isolate from one of the 7 subjects (MACS2-br). The ability of Nef to down-modulate CD4 and MHC class 1 (MHC-1) was generally conserved among nef alleles from both CNS and lymphoid tissues. However, the potency of CD4 and MHC-1 down-modulation was variable, which was associated with sequence alterations known to influence these Nef functions. These results suggest that CD4 and MHC-1 down-modulation are highly conserved functions among nef alleles from CNS- and lymphoid tissue-derived HIV-1 isolates that may contribute to viral replication and escape from immune surveillance in the CNS.

Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

“…The macaque with SIVE was also the one with the strongest selective pressure and highest evolutionary rate in nef, encoding a viral protein known to induce proinflammatory gene expression in astrocytes (65) and to downmodulate CD4 and MHC class I activities (66).…”

HIV-1-Related Central Nervous System Disease: Current Issues in Pathogenesis, Diagnosis, and Treatment

“…It is likely that different scenarios take place depending on the host, the route of infection, and possibly the individual isolates. Nevertheless, although the details may vary, long-term HIV infection leads to genetically isolated populations in the CNS, as evidenced by studies using pol, env, nef, and other genes (Thomas et al 2007;Brown et al 2011;Cowley et al 2011;Gray et al 2011). The most recent studies (Brown et al 2011) have used single genome analysis (SGA) to overcome potential PCR artifacts and confirmed the conclusions derived with bulk amplification before the development of SGA.…”

Reduced Basal Transcriptional Activity of Central Nervous System-Derived HIV Type 1 Long Terminal Repeats

“…[21][22][23] Blast searching, detailed quasispecies analyses, and viral sequence comparisons to sequences derived directly from the autopsy tissues without culture indicate that the brain/CNS-derived primary isolates and cloned viral genes are not laboratory contaminants or derived from contaminating patient blood. 21,22,[24][25][26] The clinical characteristics of the subjects and the LTR clones generated are summarized in Table 1. A 0.6-kb fragment spanning the KpnI to HindIII restriction sites in the HIV-1 LTR (corresponding to nucleotides 9015 to 9621 in the HXB2 strain) was amplified from viral cDNA by polymerase chain reaction (PCR) and cloned into the pGL3-Basic luciferase reporter vector (Promega, USA).…”

“…For these The clinical and neuropathological details of the study subjects and the derivation and characterization of the primary tissue-derived HIV-1 isolates have been published previously 21,23,26 and are summarized again here to assist in the interpretation of the data derived from the cloned long terminal repeats (LTRs). LTRs were amplified from primary virus isolates by PCR and cloned into the pGL3-Basic vector to act as a promoter for the luciferase gene.…”