Genome-wide DNA methylation in HIV infected drug users

Yale University, New Haven CT

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Abstract

? DESCRIPTION (provided by applicant): Intravenous drug use (IDU) is common among HIV-infected individuals and has been associated with HIV exposure, transmission, and progression. Preclinical studies have demonstrated that IDU compromises immune function and alters the inflammatory process. However, little is known about the molecular mechanisms of interplay between IDU and HIV infection. DNA methylation modulates gene expression without changing DNA sequence and is regulated by environmental (e.g. IDU, nicotine/alcohol use, and antiviral exposure) and genetic factors. We hypothesize that IDU may change host genome vulnerability for HIV infection by modifying DNA methylation. Methylation changes resulting from IDU can be regulated by genetic variants called methylation quantitative trait loci (mQTL). In this project, w aim 1) to identify genome-wide methylation marks for HIV-positive IDU in blood samples from 768 HIV-positive African American (AA) males with and without IDU. We will profile 480,000 methylation sites using the Illlumina Human Methylation 450K Beadchip (450K array); 2) to identify cis-mQTL for HIV-positive IDU versus non-IDU. Taking advantage of available genotypes for 980,000 single nucleotide polymorphisms (SNPs), we will conduct cis-mQTL (SNP near to its target CpG site) analysis. To prove feasibility, we have conducted a pilot study with 384 samples from AA male HIV- positive subjects using the 450K array. We found that CD4 count was lower in IDUs than non- IDUs. Methylation on the HLA-DQB2 was inversely correlated with CD4 count. Methylation on HLA-DMA gene was significantly higher in IDU than non-IDU. Based on these encouraging preliminary results, we expect to identify global methylation marks for comorbid of HIV and IDU with an increase of the sample size to 768. The project would be the largest evaluation if DNA methylation changes among HIV-positive IDU in AAs. The findings could open a new avenue for development of treatments for HIV-positive IDU because of the reversible nature of DNA methylation. The results from this project shall lead a R01 application to further understand the interaction of drug abuse and HIV infection using the integrated functional genomic approach for a new investigator. Long-term objective: We aim to integrate genome and methylome information to better understand the interaction between drug abuse and HIV infection.