Patterns of evolution of host proteins involved in retroviral pathogenesis

BACKGROUND: Evolutionary analysis may serve as a useful approach to identify and characterize host defense and viral proteins involved in genetic conflicts. We analyzed patterns of coding sequence evolution of genes with known (TRIM5α and APOBEC3G) or suspected (TRIM19/PML) roles in virus restriction, or in viral pathogenesis (PPIA, encoding Cyclophilin A), in the same set of human and non-human primate species. RESULTS AND CONCLUSION: This analysis revealed previously unidentified clusters of positively selected sites in APOBEC3G and TRIM5α that may delineate new virus-interaction domains. In contrast, our evolutionary analyses suggest that PPIA is not under diversifying selection in primates, consistent with the interaction of Cyclophilin A being limited to the HIV-1M/SIVcpz lineage. The strong sequence conservation of the TRIM19/PML sequences among primates suggests that this gene does not play a role in antiretroviral defense

Cellular Viral Rebound after Cessation of Potent Antiretroviral Therapy Predicted by Levels of Multiply Spliced HIV-1 RNA Encoding nef

To characterize newly arising replication of human immunodeficiency virus (HIV) type 1 in vivo at the cellular level, distinct viral RNA species in peripheral blood mononuclear cells (PBMCs) from HIV-1-infected patients were monitored during 2 weeks of structured treatment interruption (STI). HIV-1 RNA encoding tat/rev and PBMC-associated virions were almost completely depleted during antiretroviral therapy and emerged simultaneously after 2 weeks of STI, thus specifically reflecting productive viral infection at the cellular level. The magnitude of these correlates of reappearing cellular viral replication was predicted by during-therapy levels of nef transcripts in PBMCs. Significant rebound of plasma viremia, representing the progeny of a broader range of anatomical compartments, preceded and predicted productive infection in PBMCs. Thus, cellular viral rebound in PBMCs likely was primed before STI by the expression of nef in HIV-1-infected PBMCs that lacked virion production and was subsequently triggered by the plasma viremia that preceded the recurrence of productively infected PBMC

MDR1 Genetic Polymorphism Does Not Modify either Cell Permissiveness to HIV-1 or Disease Progression before Treatment

Nonphysiological overexpression of the ABC transporter Pglycoprotein (P-gp), which is encoded by MDR1, has been associated with reduced susceptibility to human immunodeficiency virus (HIV) type 1 infection in vitro. We analyzed (1) the expression and genotype of MDR1 and their relationship to HIV-1 permissiveness of CD4+ T cells from 128 healthy blood donors and (2) the role that alleles of MDR1 exons 21 and 26 play in modifying disease progression in 411 HIV-1-infected individuals. Differences in physiological levels of MDR1 expression did not modify HIV-1 infection in vitro, nor did MDR1 alleles and haplotypes significantly influence either permissiveness to infection in vitro or disease progression in vivo before the initiation of treatmen

Pharmacokinetics of midazolam in CYP3A4- and CYP3A5-genotyped subjects

Objective: We investigated whether differences in pharmacokinetics of midazolam, a CYP3A probe, could be demonstrated between subjects with different CYP3A4 and CYP3A5 genotypes. Methods: Plasma concentrations of midazolam, and of total (conjugated + unconjugated) 1′OH-midazolam, and 4′OH-midazolam were measured after the oral administration of 7.5mg or of 75µg of midazolam in 21 healthy subjects. Results: CYP3A5*7, CYP3A4*1E, CYP3A4*2, CYP3A4*4, CYP3A4*5, CYP3A4*6, CYP3A4*8, CYP3A4*11, CYP3A4*12, CYP3A4*13, CYP3A4*17 and CYP3A4*18 alleles were not identified in the 21 subjects. CYP3A5*3, CYP3A5*6, CYP3A4*1B and CYP3A4*1F alleles were identified in 20, 1, 4 and 2 subjects, respectively. No statistically significant differences were observed for the AUCinf values between the different genotypes after the 75-µg or the 7.5-mg dose. Conclusion: Presently, CYP3A4 and CYP3A5 genotyping methods do not sufficiently reflect the inter-individual variability of CYP3A activit

Gilbert Syndrome and the Development of Antiretroviral Therapy-Associated Hyperbilirubinemia

BackgroundUnconjugated hyperbilirubinemia results from Gilbert syndrome and from antiretroviral therapy (ART) containing protease inhibitors. An understanding of the interaction between genetic predisposition and ART may help to identify individuals at highest risk for developing jaundice MethodsWe quantified the contribution of UGT1A1*28 and ART to hyperbilirubinemia by longitudinally modeling 1386 total bilirubin levels in 96 human immunodeficiency virus (HIV)-infected individuals during a median of 6 years ResultsThe estimated average bilirubin level was 8.8 μmol/L (0.51 mg/dL). Atazanavir increased bilirubin levels by 15 μmol/L (0.87 mg/dL), and indinavir increased bilirubin levels by 8 μmol/L (0.46 mg/dL). Ritonavir, lopinavir, saquinavir, and nelfinavir had no or minimal effect on bilirubin levels. Homozygous UGT1A1*28 increased bilirubin levels by 5.2 μmol/L (0.3 mg/dL). As a consequence, 67% of individuals homozygous for UGT1A1*28 and receiving atazanavir or indinavir had ⩾2 episodes of hyperbilirubinemia in the jaundice range (>43 μmol/L [>2.5 mg/dL]), versus 7% of those with the common allele and not receiving either of those protease inhibitors (P<.001). Efavirenz resulted in decreased bilirubin levels, which is consistent with the induction of UDP-glucuronosyltransferase 1A1 ConclusionsGenotyping for UGT1A1*28 before initiation of ART would identify HIV-infected individuals at risk for hyperbilirubinemia and decrease episodes of jaundic

Oral administration of a low dose of midazolam (75μg) as an in vivo probe for CYP3A activity

Objective: We investigated whether the oral administration of a low dose (75µg) of midazolam, a CYP3A probe, can be used to measure the in vivo CYP3A activity. Methods: Plasma concentrations of midazolam, 1′OH-midazolam and 4′OH-midazolam were measured after the oral administration of 7.5mg and 75µg midazolam in 13 healthy subjects without medication, in four subjects pretreated for 2days with ketoconazole (200mg b.i.d.), a CYP3A inhibitor, and in four subjects pretreated for 4days with rifampicin (450mg q.d.), a CYP3A inducer. Results: After oral administration of 75µg midazolam, the 30-min total (unconjugated + conjugated) 1′OH-midazolam/midazolam ratios measured in the groups without co-medication, with ketoconazole and with rifampicin were (mean±SD): 6.23±2.61, 0.79±0.39 and 56.1±12.4, respectively. No side effects were reported by the subjects taking this low dose of midazolam. Good correlations were observed between the 30-min total 1′OH-midazolam/midazolam ratio and midazolam clearance in the group without co-medication (r2=0.64, P<0.001) and in the three groups taken together (r2=0.91, P<0.0001). Good correlations were also observed between midazolam plasma levels and midazolam clearance, measured between 1.5h and 4h. Conclusion: A low oral dose of midazolam can be used to phenotype CYP3A, either by the determination of total 1′OH-midazolam/midazolam ratios at 30min or by the determination of midazolam plasma levels between 1.5h and 4h after its administratio

Modeling the Influence of APOC3, APOE and TNF Polymorphisms on the Risk of Antiretroviral Therapy-Associated Lipid Disorders

BackgroundSingle-nucleotide polymorphisms in genes involved in lipoprotein and adipocyte metabolism may explain why dyslipidemia and lipoatrophy occur in some but not all antiretroviral therapy (ART)-treated individuals MethodsWe evaluated the contribution of APOC3 −482C→T, −455T→C, and 3238C→G; ɛ2 and ɛ4 alleles of APOE; and TNF −238G→A to dyslipidemia and lipoatrophy by longitudinally modeling >2600 lipid determinations and 2328 lipoatrophy assessments in 329 ART-treated patients during a median follow-up period of 3.4 years ResultsIn human immunodeficiency virus (HIV)-infected individuals, the effects of variant alleles of APOE on plasma cholesterol and triglyceride levels and of APOC3 on plasma triglyceride levels were comparable to those reported in the general population. However, when treated with ritonavir, individuals with unfavorable genotypes of APOC3 or APOE were at risk of extreme hypertriglyceridemia. They had median plasma triglyceride levels of 7.33 mmol/L, compared with 3.08 mmol/L in the absence of ART. The net effect of the APOE*APOC3*ritonavir interaction was an increase in plasma triglyceride levels of 2.23 mmol/L. No association between TNF −238G→A and lipoatrophy was observed ConclusionsVariant alleles of APOE and APOC3 contribute to an unfavorable lipid profile in patients with HIV. Interactions between genotypes and ART can lead to severe hyperlipidemia. Genetic analysis may identify patients at high risk for severe ritonavir-associated hypertriglyceridemi