Soluble CD14-associated DNA methylation sites predict mortality among men with HIV infection

Abstract

Objectives: Elevated plasma levels of sCD14 predict all-cause mortality in people with HIV (PWH). Epigenetic regulation plays a key role in infection and inflammation. To reveal the epigenetic relationships between sCD14, immune function and disease progression among PWH, we conducted an epigenome-wide association study (EWAS) of sCD14 and investigated the relationship with mortality.

Design and methods: DNA methylation (DNAm) levels of peripheral blood samples from PWH in the Veterans Aging Cohort Study (VACS) were measured using the Illumina Infinium Methylation 450K (n = 549) and EPIC (850K) BeadChip (n = 526). Adjusted for covariates and multiple testing, we conducted an epigenome-wide discovery, replication, and meta-analysis to identify significant associations with sCD14. We then examined and replicated the relationship between the principal epigenetic sites and survival using Cox regression models.

Findings: We identified 118 DNAm sites significantly associated with sCD14 in the meta-analysis of 1075 PWH. The principal associated DNAm sites mapped to genes (e.g. STAT1, PARP9, IFITM1, MX1, and IFIT1) related to inflammation and antiviral response. Adjusting for multiple testing, 10 of 118 sCD14-associated DNAm sites significantly predicted survival time conditional on sCD14 levels.

Conclusion: The identification of DNAm sites independently predicting survival may improve our understanding of prognosis and potential therapeutic targets among PWH.

Figure 1.

Meta-analysis summary of the sCD14 EWAS. A: Quantile-quantile (Q-Q) plot of 366,197 CpG sites; X axis shows the expected −log10 (p-value) while Y axis shows the observed −log10 (p-value); Red line in the middle is a diagonal line; B: Manhattan plot showing observed −log10 (p-value) of each CpG site, organized by chromosomal positions including the X-chromosome; The horizontal red line represents the genome-wide significant threshold (Bonferroni corrected p-value of 0.05, nominal p-value of 1.40×10⁻⁷).

Figure 1.

Meta-analysis summary of the sCD14 EWAS. A: Quantile-quantile (Q-Q) plot of 366,197 CpG sites; X axis shows the expected −log10 (p-value) while Y axis shows the observed −log10 (p-value); Red line in the middle is a diagonal line; B: Manhattan plot showing observed −log10 (p-value) of each CpG site, organized by chromosomal positions including the X-chromosome; The horizontal red line represents the genome-wide significant threshold (Bonferroni corrected p-value of 0.05, nominal p-value of 1.40×10⁻⁷).

Figure 2.

Comparison of significant epigenetic associations from the EPIC vs 450K chip subsets. X axis shows estimated beta coefficients from the 450K chip subsets and Y axis shows estimated beta coefficients from EPIC chip subsets. Blue line in the middle is a diagonal line.

Figure 3:

HIV-infection, triggers innate immune responses which contribute to inflammation in people with HIV (PWH). Gut dysbiosis engendered by destruction and loss of gut immune cells during HIV-infection leads to translocation of gut microbiota and bacterial toxins which further stimulate a proinflammatory immune response (including type 1 interferons) by binding to toll-like receptors on innate immune cells. As part of this response, soluble CD14 (sCD14) is produced primarily by monocytes and macrophages and is an important marker of inflammation in HIV pathogenesis. This study demonstrates a strong association between sCD14 and DNA methylation changes with principal associated sites mapping to interferon stimulated genes. Determining whether a pro-inflammatory state in chronic HIV-infection via biomarkers such as sCD14 leads to differential DNAm or whether DNA methylation changes in the setting of HIV contribute to sustaining chronic inflammatory pathways and elevate levels of relevant biomarkers need to be verified and confirmed by experimental studies.