DNA Methylation Regulates the Differential Expression of CX3CR1 on Human IL-7Rαlow and IL-7Rαhigh Effector Memory CD8+ T Cells with Distinct Migratory Capacities to the Fractalkine

Abstract

DNA methylation is an epigenetic mechanism that modulates gene expression in mammalian cells including T cells. Memory T cells are heterogeneous populations. Human effector memory (EM) CD8+ T cells in peripheral blood contain two cell subsets with distinct traits that express low and high levels of the IL-7 receptor alpha chain (IL-7Rα). However, epigenetic mechanisms involved in defining such cellular traits are largely unknown. Here we employ genome-wide DNA methylation and individual gene expression to show the possible role of DNA methylation in conferring distinct traits of chemotaxis and inflammatory responses in human IL-7Rαlow and high EM CD8+ T cells. In particular, IL-7Rαlow EM CD8+ T cells had increased expression of CX3C receptor 1 (CX3CR1) along with decreased DNA methylation in the CX3CR1 gene promoter compared to IL-7Rαhigh EM CD8+ T cells. Altering the DNA methylation status of the CX3CR1 gene promoter changed its activity and gene expression. IL-7Rαlow EM CD8+ T cells had an increased migratory capacity to the CX3CR1 ligand fractalkine compared to IL-7Rαhigh EM CD8+ T cells, suggesting an important biological outcome of the differential expression of CX3CR1. Moreover, IL-7Rαlow EM CD8+ T cells induced fractalkine expression on endothelial cells by producing IFN-γ and TNF-α, forming an autocrine amplification loop. Overall, our study shows the role of DNA methylation in generating unique cellular traits in human IL-7Rαlow and high EM CD8+ T cells, including differential expression of CX3CR1, as well as potential biological implications of this differential expression.

Transcriptomic analysis of human IL‐7 receptor alpha low and high effector memory CD8+ T cells reveals an age‐associated signature linked to influenza vaccine response in older adults

“…Among the 231 age‐associated signature genes of IL‐7Rα low EM CD8 + T cells, the genes encoding the cytotoxic molecules GZMH, GZMB, FGFBP2, and the chemokine receptor CX3CR1 were the ones with the highest levels of age‐associated z scores and fold changes of the gene expression between IL‐7Rα low and high EM CD8 + T cells (Table ). This finding is consistent with our previous studies showing increased gene and/or protein expression of GZMB and CX3CR1 by IL‐7Rα low EM CD8 + T cells compared to IL‐7Rα high EM CD8 + T cells (Shin et al, ). Similarly, we also noted higher levels of FGFBP2 and GZMH gene and protein expression in IL‐7Rα low EM CD8 + T cells than in IL‐7Rα high EM CD8 + T cells in mixed‐age adult donors (Figure a,b).…”

“…In humans, the proportions of peripheral IL‐7Rα low and high EM CD8 + T cells with distinct cellular phenotypes and functions alter with age (Kim et al, , ; Shin et al, ). However, their global gene expression profiles had not previously been defined.…”

“…Previously, we measured the expression of IL‐7 receptor alpha chain (IL‐7Rα or CD127) on human CD8 + T cells in young and older adults, considering the possible role of this cytokine receptor in expanding memory CD8 + T cells with age given its capacity to promote memory T‐cell survival. We found that human effector memory (EM) CD8 + T cells, which expand with age, comprise two different subsets of cells expressing IL‐7Rα low and high with distinct characteristics including the expression of effector molecules, transcription factors, and DNA methylation profiles (Kim, Hong, Dan, & Kang, ; Kim, Hwang, Kim, & Kang, ; Shin et al, ). Having high levels of perforin, granzyme B, IFN‐γ, and TNF‐α, IL‐7Rα low EM CD8 + T cells are a highly cytotoxic and pro‐inflammatory subset (Kim et al, , ; Shin et al, ).…”

“…We found that human effector memory (EM) CD8 + T cells, which expand with age, comprise two different subsets of cells expressing IL‐7Rα low and high with distinct characteristics including the expression of effector molecules, transcription factors, and DNA methylation profiles (Kim, Hong, Dan, & Kang, ; Kim, Hwang, Kim, & Kang, ; Shin et al, ). Having high levels of perforin, granzyme B, IFN‐γ, and TNF‐α, IL‐7Rα low EM CD8 + T cells are a highly cytotoxic and pro‐inflammatory subset (Kim et al, , ; Shin et al, ). However, IL‐7Rα low EM CD8 + T cells appear to be replication senescent cells with impaired T‐cell receptor‐mediated proliferation and increased expression levels of senescence markers like CD57 (Kim et al, , ).…”

Inflammatory Function of CX3CR1+CD8+T Cells in Treated HIV Infection Is Modulated by Platelet Interactions

“…CD8 + T cells can home and adhere to vascular endothelial and smooth-muscle cells through engagement of the fractalkine receptor, CX3CR1, to its ligand CX3CL1 that is expressed on activated endothelium [8][9][10]. Localization of immune cells to the vascular endothelium is likely an important step in atherogenesis, as polymorphisms in CX3CR1 have been shown to be associated with differential risk for atherosclerosis [11,12].…”