Epigenome-wide association scan identifies methylation sites associated with HIV infection

Chang Shu; Andrew E Jaffe; Sarven Sabunciyan; Hongkai Ji; Jacquie Astemborski; Jing Sun; Kelly M Bakulski; Shruti H Mehta; Gregory D Kirk; Brion S Maher

doi:10.2217/epi-2020-0123

Epigenome-wide association scan identifies methylation sites associated with HIV infection

Epigenomics. 2020 Nov;12(21):1917-1927. doi: 10.2217/epi-2020-0123. Epub 2020 Nov 24.

Authors

Chang Shu^{1

2}, Andrew E Jaffe^{1

3

4}, Sarven Sabunciyan⁵, Hongkai Ji⁴, Jacquie Astemborski⁶, Jing Sun⁶, Kelly M Bakulski⁷, Shruti H Mehta⁶, Gregory D Kirk⁶, Brion S Maher¹

Affiliations

¹ Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
² Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA.
³ Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.
⁴ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
⁵ Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁶ Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
⁷ Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.

Abstract

Aim: To investigate the role of epigenetics in HIV pathophysiology. Materials & methods: We conducted an epigenome-wide association scan on HIV infection status among people who inject drugs in the AIDS Linked to the IntraVenous Experience study with primary (n = 397) and validation samples (n = 390). DNA methylation from blood was measured by the Illumina EPIC BeadChip. We controlled for cell type heterogeneity by HIV status. Results: HIV infection status was associated (p < 10^-8) with DNA methylation at 49 CpG sites. Sites were enriched in response to virus, interferon signaling pathway, etc. Among these sites, discovery and validation t-statistics were highly correlated (r = 0.96). Conclusion: In a cohort of people who inject drugs, HIV status was associated with differential DNA methylation at biologically meaningful sites.

Keywords: DNA methylation; HIV; epigenetics; epigenome-wide association; people who inject drugs.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

CpG Islands
DNA Methylation*
Disease Susceptibility
Epigenesis, Genetic*
Epigenomics* / methods
Genome-Wide Association Study
HIV Infections / genetics*
HIV Infections / virology
High-Throughput Nucleotide Sequencing
Host-Pathogen Interactions / genetics*
Humans

Abstract

Publication types

MeSH terms

Grants and funding