Mark Oette

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for protease and reverse transcriptase, the molecular targets of current antiretroviral therapy. Genotypic resistance testing depends on the ability to interpret such sequence data, whereas phenotypic resistance testing directly measures relative in vitro susceptibility to a drug. From a set of 650 matched genotype-phenotype pairs we construct regression models for the prediction of phenotypic drug resistance from genotypes. Since the range of resistance factors varies considerably between different drugs, two scoring functions are derived from different sets of predicted phenotypes. Firstly, we compare predicted values to those of samples derived from 178 treatment-naive patients and report the relative deviance. Secondly, estimation of the probability density of 2000 predicted phenotypes gives rise to an intrinsic definition of a susceptible and a resistant subpopulation. Thus, for a predicted phenotype, we calculate the probability of membership in the resistant subpopulation. Both scores provide standardized measures of resistance that can be calculated from the genotype and are comparable between drugs. The geno2pheno system makes these genotype interpretations available via the Internet (http://www.genafor.org/).

Computational methods for the design of effective therapies against drug resistant HIV strains

The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted by the human immune system and by combination drug therapy. We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data.

Lipodystrophy Syndrome and Self-Assessment of Well-Being and Physical Appearance in HIV-Positive Patients

The lipodystrophy syndrome (LDS) is a growing problem in human immunodeficiency virus (HIV)-positive patients treated with highly active antiretroviral therapy (HAART). It is characterized by alterations of body composition and metabolic abnormalities. The goal of the study was to investigate attitudes toward health condition, well-being, and individual appearance in relation to LDS. Outpatients between July and October 2000 in an HIV-specialized unit at the University Hospital of Düsseldorf, Germany, underwent clinical evaluation and received a standardized written questionnaire. Of 389 patients eligible for analysis, 313 patients returned completed questionnaires (response rate, 80.5%). LDS was observed in 37.7%; the predominant manifestation was lipoatrophy of the face (32.9%). Individuals with and without LDS did not differ significantly in their attitude to the quality of their health condition and the amount of disturbance of their well-being by HIV infection. Participants with LDS felt recognizable as HIV-positive by physical appearance in 30.1%, compared to 18.3% in patients without LDS (p = 0.027). This difference became more pronounced after adjustment for gender, age, stage of disease, CD4 cell count, and duration of HAART (odds ratio, 2.04, 95%-confidence interval [CI] 1.09-3.84). In conclusion, LDS does not seem to disturb the general attitude toward health condition and well-being. However, patients presenting with lipodystrophy are about twice as likely to feel recognizable as HIV-positive by their physical appearance. LDS may thus be perceived as a characteristic mark of being HIV-positive by affected persons. A stigmatizing effect and social disadvantages may be the consequences.

Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure

BACKGROUND AND OBJECTIVES Minority HIV-1 populations with resistance mutations might result in therapy failure. The prevalence of transmitted minorities in therapy-naïve patients and their influence on the virological outcome of the first-line-therapy need clarification. STUDY DESIGN The HIV reverse transcriptase (RT) of 159 therapy-naïve patients from the RESINA-cohort was genotyped. The relative amount of RT-K103N was measured by primer specific PCR. The response to first-line non-nucleoside reverse transcriptase inhibitor (NNRTI)-therapy was evaluated. RESULTS Bulk-sequencing detected 1 NNRTI mutation (no K103N) in six patients (1.26%). K103N minorities were found in 20.1% of the samples, more frequently in HIV-1 non-B subtypes (40.6%) than in subtype B (15.0%) (p=0.0025). NNRTI treatment failed after 12 weeks in 24% of 17 patients with minority, but only in 15% of 67 patients without minority. CONCLUSIONS K103N minorities were found in 20.1% of the patients, whereas the prevalence of major K103N populations was 3% in the total RESINA-cohort. K103N minorities were more frequent in non-B subtypes. There is some evidence for a higher risk of NNRTI-treatment failure in patients with K103N minorities; however, the majority of patients with minority underwent a successful first-line-treatment.

AIDS-related B-cell lymphoma (ARL): correlation of prognosis with differentiation profiles assessed by immunophenotyping.

This study was undertaken to analyze the differentiation profiles assessed by immunophenotyping in AIDS-related B-cell lymphoma (ARL) and their relation to the clinical course. Paraffin-embedded sections of 89 ARL cases during 1989 to 2004 were stained immunohistochemically with antibodies to CD3, CD10, CD20, CD38, CD138/Syndecan-1 (Syn-1), multiple myeloma-1/interferon regulatory factor-4 (MUM1/IRF4), B-cell lymphoma protein-2 (BCL-2), BCL-6, latent membrane protein-1 (LMP-1), and Ki-67. Expression of CD10 and CD20 were associated with better overall survival (OS; P = .009 and P = .04, respectively). Expression of CD20 was associated with longer disease-free survival (DFS; P = .03), whereas expression of CD138/Syn-1 was associated with shorter DFS (P = .03). OS and DFS were worse in patients with immunophenotypic profiles related to post-germinal center (GC) differentiation (BCL-6 and CD10 negative, MUM1/IRF4 and/or CD138/Syn-1 positive) when compared with GC differentiation (P = .01). When controlled for age-adjusted International Prognostic Index (IPI), prior AIDS-defining illness (ADI), and year of ARL diagnosis, a post-GC differentiation remained significantly associated with poor OS and DFS. Expression of CD10 was associated with a preserved immunocompetence, whereas CD20 was less frequent in patients developing ARL while on highly active antiretroviral therapy (P = .04). In summary, lack of CD20 or CD10 expression and a post-germinal center signature are associated with a worse prognosis in ARL.

Efficacy and safety of twice daily first-line ritonavir/indinavir plus double nucleoside combination therapy in HIV-infected individuals.

ObjectiveTo evaluate the virological efficacy and safety of quadruple therapy with two nucleoside analogues and ritonavir (400 mg twice daily) plus indinavir (400 mg twice daily) combination in antiretroviral therapy-naive patients. Design and methodsAn open-label, uncontrolled multicentre trial. Antiretroviral therapy-naive patients (n = 90) with high median baseline HIV RNA levels of 220 000 copies/ml (range, 36 000–2 943 000 copies/ml) and median CD4 cell count of 189 × 106/l (range, 4–656 × 106/l) were started on a twice daily regimen of either zidovudine/lamivudine (49%), stavudine/lamivudine (38%) or stavudine/didanosine (13%) plus ritonavir 400 mg twice daily and indinavir 400 mg twice daily combination therapy. CD4 cell counts and HIV RNA were determined at weeks 0, 4, 8, 12, 16, 20, and 24. Statistical analysis was performed on treatment as well as intent-to-treat, where missing values were accounted for as failure. ResultsIn the intent-to-treat analysis at week 24, the proportion of patients with HIV RNA of < 500 copies/ml, and < 80 copies/ml was 86.7% and 71.1%, respectively. In the on-treatment analysis at week 24, 80.0% of patients had undetectable viral load in the ultrasensitive assay (< 80 copies/ml; n = 80). The quadruple therapy was well tolerated except for mild diarrhoea, initial nausea and increased triglyceride levels. Treatment was stopped in seven (7.7%) patients because of adverse events and three (3.3%) were lost to follow-up. ConclusionsOur preliminary data suggest that the protease inhibitor combination ritonavir/indinavir plus double nucleoside therapy appears to be effective and safe in short-term treatment (up to 24 weeks).

Characterization of novel HIV drug resistance mutations using clustering, multidimensional scaling and SVM-Based feature ranking

We present a case study on the discovery of clinically relevant domain knowledge in the field of HIV drug resistance. Novel mutations in the HIV genome associated with treatment failure were identified by mining a relational clinical database. Hierarchical cluster analysis suggests that two of these mutations form a novel mutational complex, while all others are involved in known resistance-conferring evolutionary pathways. The clustering is shown to be highly stable in a bootstrap procedure. Multidimensional scaling in mutation space indicates that certain mutations can occur within multiple pathways. Feature ranking based on support vector machines and matched genotype-phenotype pairs comprehensively reproduces current domain knowledge. Moreover, it indicates a prominent role of novel mutations in determining phenotypic resistance and in resensitization effects. These effects may be exploited deliberately to reopen lost treatment options. Together, these findings provide valuable insight into the interpretation of genotypic resistance tests.

German-Austrian guidelines on anal dysplasia and anal cancer in HIV-positive individuals: prevention, diagnosis, and treatment.

(1) University Hospital Essen, HPSTD Outpatient Clinic, Department of Dermatology and Venereology, Essen, Germany (2) HELIOS St. Elisabeth Hospital Oberhausen, Department of Dermatology, Venereology, and Allergology, Oberhausen, Germany (3) Augustinerinnen Hospital, Department of General Medicine, Gastroenterology; and Infectious Diseases, Cologne, Germany (4) Ludwig-Maximilians-University, University Hospital Munich, Department of Gynecology, Munich, Germany (5) Medical Specialist Practice for Hematology, Oncology, and Infectious Diseases, Karlsruhe, Germany (6) City Hospital Karlsruhe, Department of Radiooncology and Radiation Therapy, Karlsruhe, Germany (7) Medical Specialist Practice for Proctology, Kiel, Germany (8) Ruhr-University, St. Josef Hospital, Department of Dermatology, Venereology, and Allergology, Center for Sexual Health und Medicine, Bochum, Germany (9) Cytologic Institute, Bensberg, Germany (10) Cytologic Institute, Bonn Bad Godesberg, Germany (11) Prinzmed Medical Practice, Munich, Germany (12) University Hospital Hamburg-Eppendorf, Outpatient Clinic Center for Infectious Diseases, Hamburg, Germany (13) Medical Practice Center of General Medicine, Vienna, Austria (14) Medical Group Practice, Berlin, Germany (15) Medical Practice for Internal Medicine and Infectious Diseases, Aachen, Germany (16) Medical Group Practice for Internal Medicine and Rheumatology, Freiburg, Germany (17) ICH, Hamburg, Germany (18) Deutsche AIDS Hilfe, Berlin, Germany (19) University Köln, Institute of Virology, National Reference Center for Papilloma and Polyomavirus, Cologne, Germany AWMF-Register-No.: 055/007

Maraviroc in treatment-experienced patients with HIV-1 infection - experience from routine clinical practice.

ObjectiveFew data are available about the efficacy of maraviroc (MVC) during routine use. We characterized indications for MVC use and the efficacy of MVC in clinical practice.MethodsThirty-two patients treated with MVC at our institution between 2006 and 2009 were included. Genotypic (n = 31) and phenotypic (n = 13) tropism analysis was performed. We determined indications for MVC use, characteristics of antiretroviral combination partners and treatment outcome.ResultsComplete suppression of viral replication was achieved in 78% after 6 months. A median increase of 124 CD4+ cells/μl after 6 months was observed. Concordance between phenotypic and genotypic tropism was found in 75%. Indications for MVC treatment included treatment failure (n = 15), intolerance to previous antiretrovirals (n = 6) and add-on MVC for intensification without changing the current regimen (n = 11). The add-on strategy was used in patients with a relatively low viremia in order to achieve complete viral load suppression or in situations with suppressed viral load but judged as unstable due to an extensive resistance pattern. Salvage drugs most frequently combined with MVC were darunavir (n = 14) and raltegravir (n = 14).The genotypic assay had predicted CXCR4 tropism in 5 patients, using a false positive rate (FPR) of 20%. Lowering the FPR to 5% predicted CCR5 tropism in 4 cases, still resulting in sustained complete viral response under MVC use.ConclusionsMVC containing salvage regimens achieve relevant CD4 cell increases and high viral response rates. In patients with few remaining treatment options it may be justified to lower the FPR-cutoff to 5% when predicting the coreceptor usage. Hereby, MVC could still be applied in selected patients with otherwise limited treatment options.

Long-term efficacy and safety of ritonavir/indinavir at 400/400 mg twice a day in combination with two nucleoside reverse transcriptase inhibitors as first line antiretroviral therapy

Objective To determine the long‐term antiretroviral efficacy and tolerability of dual protease inhibitor (PI) therapy with indinavir (IDV)/ritonavir (RTV) at 400/400 mg twice a day (BID) in combination with two nucleoside reverse trancriptase inhibitors (NRTIs).