Biology subjects

Geretz, A.

Publications and source records attributed to Geretz, A..

3 recordsLinked to original sources

bioRxiv2025

Full-length next-generation sequencing of 11 HLA loci of more than 1000 individuals from clinical cohorts in East and West Africa

Human Leukocyte Antigen (HLA) loci have been implicated in several diseases from different world populations, including HIV-1. It is necessary to characterize HLA allele variation at the population level prior to investigating associations linked to human diseases. In global databases, limited high-resolution HLA allele types generated by next-generation sequencing (NGS) have been described for populations from African countries. We sought to expand our HLA NGS database to include a total of 1023 participants from multiple HIV clinical studies using full-length HLA genotyping by NGS. Collectively we describe HLA genotypes of individuals from Kenya (n=375), Uganda (n=338), Nigeria (n=139), Tanzania (n=89), and Mozambique (n=82). Overall, we identified 371 unique HLA alleles across 11 loci with the most frequent at each locus being A*02:01:01, B*53:01:01, C*04:01:01, C*06:02:01, DPA1*01:03:01, DPB1*01:01:01, DQA1*01:02:01, DQB1*06:02:01, DRB1*15:03:01, DRB3*02:02:01, DRB4*01:03:01, and DRB5*01:01:01. A total of 25 novel alleles were identified, including 4 with non-synonymous changes affecting the peptide binding groove of HLA molecules. This expansion of NGS based HLA data at the African population level will improve our understanding of human genetic variation and provide insights for vaccine development and targeted personalized therapies.

genetics↗

bioRxiv2024

Single-cell analyses reveal that monocyte gene expression profiles influence HIV-1 reservoir size in acutely treated cohorts

Elimination of latent HIV-1 is a major goal of AIDS research but the host factors determining the size of these reservoirs are poorly understood. Here, we investigated whether differences in host gene expression modulate the size of the HIV-1 reservoir during suppressive ART. Peripheral blood mononuclear cells (PBMC) from fourteen individuals initiating ART during acute infection who demonstrated effective viral suppression but varying magnitude of total HIV-1 DNA were characterized by single-cell RNA sequencing (scRNA-seq). Differentially expressed genes and enriched pathways demonstrated increased monocyte activity in participants with undetectable HIV-1 reservoirs. IL1B expression in CD14+ monocytes showed the greatest fold difference. The inverse association of IL1B with reservoir size was validated in an independent cohort comprised of 38 participants with different genetic backgrounds and HIV-1 subtype infections, and further confirmed with intact proviral DNA assay (IPDA(R)) measurements of intact HIV-1 proviruses in a subset of the samples. Modeling interactions with cell population frequencies showed that monocyte IL1B expression associated inversely with reservoir size in the context of higher frequencies of central memory CD4+ T cells, implicating an indirect effect of IL1B via the cell type well established to be a reservoir for persistent HIV-1. Signatures consisting of co-expressed genes including IL1B were highly enriched in the "TNF signaling via NF-{kappa}B" geneset. Functional analyses in cell culture revealed that IL1B activates NF-{kappa}B, thereby promoting productive HIV-1 infection while simultaneously suppressing viral spread, suggesting a natural latency reversing activity to deplete the reservoir in ART treated individuals. Altogether, unbiased high throughput scRNA-seq analyses revealed that monocyte IL1B variation could decrease HIV-1 proviral reservoirs in individuals initiating ART during acute infection.

immunology↗

bioRxiv2021

Monocyte-derived transcriptome signature indicates antibody-dependent cellular 1 phagocytosis as the primary mechanism of vaccine-induced protection against HIV-1

A gene signature previously correlated with mosaic adenovirus 26 vaccine protection in simian immunodeficiency virus (SIV) and SHIV challenge models in non-human primates (NHP). In this report we investigated presence of this signature as a correlate of reduced risk in human clinical trials and potential mechanism for protection. The absence of this gene signature in the DNA/rAd5 human vaccine trial which did not show efficacy, strengthens our hypothesis that this signature is only enriched in studies that demonstrated protection. This gene signature was enriched in the partially effective RV144 human trial that administered the ALVAC/protein vaccine, and we find that the signature associates with both decreased risk of HIV-1 acquisition and increased vaccine efficacy. Total RNA-seq in a clinical trial that used the same vaccine regimen as the RV144 HIV vaccine implicated antibody-dependent cellular phagocytosis (ADCP) as a potential mechanism of vaccine protection. CITE-seq profiling of 53 surface markers and transcriptomes of 53,777 single cells from the same trial, showed that genes in this signature were primarily expressed in cells belonging to the myeloid lineage including monocytes, which are major effector cells for ADCP. The consistent association of this transcriptome signature with vaccine efficacy represents a tool both to identify potential mechanisms, as with ADCP here, and to screen novel approaches to accelerate development of new vaccine candidates.

systems biology↗