Negative binomial mixed models for analyzing longitudinal CD4 count data
SCIENTIFIC REPORTS
Authors: Yirga, Ashenafi A.; Melesse, Sileshi F.; Mwambi, Henry G.; Ayele, Dawit G.
Abstract
It is of great interest for a biomedical analyst or an investigator to correctly model the CD4 cell count or disease biomarkers of a patient in the presence of covariates or factors determining the disease progression over time. The Poisson mixed-effects models (PMM) can be an appropriate choice for repeated count data. However, this model is not realistic because of the restriction that the mean and variance are equal. Therefore, the PMM is replaced by the negative binomial mixed-effects model (NBMM). The later model effectively manages the over-dispersion of the longitudinal data. We evaluate and compare the proposed models and their application to the number of CD4 cells of HIV-Infected patients recruited in the CAPRISA 002 Acute Infection Study. The results display that the NBMM has appropriate properties and outperforms the PMM in terms of handling over-dispersion of the data. Multiple imputation techniques are also used to handle missing values in the dataset to get valid inferences for parameter estimates. In addition, the results imply that the effect of baseline BMI, HAART initiation, baseline viral load, and the number of sexual partners were significantly associated with the patient's CD4 count in both fitted models. Comparison, discussion, and conclusion of the results of the fitted models complete the study.
Preclinical Evaluation of a Novel TALEN Targeting CCR5 Confirms Efficacy and Safety in Conferring Resistance to HIV-1 Infection
BIOTECHNOLOGY JOURNAL
Authors: Romito, Marianna; Juillerat, Alexandre; Kok, Yik Lim; Hildenbeutel, Markus; Rhiel, Manuel; Andrieux, Geoffroy; Geiger, Johannes; Rudolph, Carsten; Mussolino, Claudio; Duclert, Aymeric; Metzner, Karin J.; Duchateau, Philippe; Cathomen, Toni; Cornu, Tatjana I.
Abstract
Therapies to treat patients infected with human immunodeficiency virus (HIV) aim at preventing viral replication but fail to eliminate the virus. Although transplantation of allogeneic CCR5 Delta 32 homozygous stem cell grafts provided a cure for a few patients, this approach is not considered a general therapeutic strategy because of potential side effects. Conversely, gene editing to disrupt the C-C chemokine receptor type 5 (CCR5) locus, which encodes the major HIV coreceptor, has shown to confer resistance to CCR5-tropic HIV strains. Here, an engineered transcription activator-like effector nuclease (TALEN) that enables efficient CCR5 editing in hematopoietic cells is presented. After transferring TALEN-encoding mRNA into primary CD4+ T cells, up to 89% of CCR5 alleles are disrupted. Genotyping confirms the genetic stability of the CCR5-edited cells, and genome-wide off-target analyses established the absence of relevant mutagenic events. When challenging the edited T cells with CCR5-tropic HIV, protection in a dose-dependent manner is observed. Functional assessments reveal no significant differences between edited and control cells in terms of proliferation and their ability to secrete cytokines upon exogenous stimuli. In conclusion, a highly active and specific TALEN to disrupt CCR5 is successfully engineered, paving the way for its clinical application in hematopoietic stem cell grafts.