Epigenetic control of CD4 expression in African green monkeys

Sanjana Shah

Mentor: Dr. Jason Brenchley, National Institute of Allergy and Infectious Diseases, National Institutes of Health

Date/Time: August 27, 2019 at 2pm

Location: Room 1300, Harris Building

African green monkeys (genus Chlorocebus) are a natural host of simian immunodeficiency virus (SIVagm). Since they do not develop simian AIDS, there is great interest in understanding how this species has evolved to avoid immunodeficiency. Adult African green monkeys naturally have low numbers of CD4 T cells and a large population of MHC Class II-restricted CD8α^dim T cells that are generated through CD4 downregulation in CD4⁺ T cells. Mechanisms that drive this process of CD4 downregulation are unknown. The CD4 downregulation induced by SIV infection is not limited to SIV-specific T cells, and vaccination of an adult AGM who had a negligible number of CD4 T cells demonstrated that CD4 downregulation can occur without antigenic exposure. CD4 expression is lost by CD4 T cells as they experience immunological pressure both in vivo and in vitro.

To understand the mechanisms underlying CD4 down regulation, CD4 down regulation was induced by CD4 T cells from AGM in vitro and flow cytometrically isolated CD4 T cells in the process of CD4 down regulation. Transcriptional analysis by RNAseq was then performed. Our preliminary analysis suggests that differential expression of DNA methylation enzymes underlies CD4 down regulation.

We used next generation sequencing to understand the degree to which cytosine base pairs within the CD4 gene are methylated in African green monkeys. In order to assess CpG methylation of the CD4 locus, we developed a bioinformatics pipeline which used the Bismark mapping program in the command line to align DNA sequences to the AGM genome and to assess CpG methylation of the CD4 locus AGM. The R package “Bsseq” was then used to analyze and visualize CpG methylation of the CD4 locus. In this study, we found methylation profiles within capture region of CD4⁺ T cells are distinct from AGM CD4^– populations. The degree to which CpGs were methylated were greater in the CD4^– CD8aa⁺ T cells comparted to the CD4⁺ T cells, starting in transcription start site and extending into the gene body. The CD4⁺ T cells were relatively unmethylated in the gene body. Data from this study could lead to novel therapeutic interventions to cause CD4 down regulation in HIV+ individuals, thus creating an avenue that could lead to a cure for HIV as the virus would ultimately run out of target cells while maintaining immunological competence for the host.