Comprehensive proteomics analyses identify PIM kinases as key regulators of IL-15 driven activation of intestinal intraepithelial lymphocytes

Abstract

Intestinal intraepithelial lymphocytes (IEL) are an abundant population of tissue-resident T cells that protect the gut from pathogens and maintain intestinal homeostasis. The cytokine IL-15 is transpresented by epithelial cells to IEL in complex with the IL-15 receptor α chain (IL-15Rα). It plays essential roles both in maintaining IEL homeostasis, and in inducing IEL activation in response to epithelial stress. IL-15 overexpression also drives the gluten-induced enteropathy Coeliac disease, through cytotoxic activation of IEL. In order to better understand how IL-15 directly regulates both homeostatic and inflammatory functions of IEL, we set up quantitative proteomics of IL-15/Rα stimulated IEL. We reveal that high IL-15/Rα stimulation licenses cell cycle activation, upregulates the biosynthetic machinery in IEL, increases mitochondrial respiratory capacity and induces expression of cell surface immune receptors and adhesion proteins that potentially drive IEL activation. We find that high IL-15/Rα selectively upregulated the Ser/Thr kinases PIM1 and PIM2 and demonstrate that PIM1/2 are essential for IEL to proliferate, grow, and upregulate Granzyme B in response to high IL-15. Significantly, IEL from Coeliac disease patients express high levels of PIM kinases. These unexpected findings reveal PIM kinases to be key determinants of IEL responses to elevated levels of IL-15.3

Tissue environment, not ontogeny, defines intestinal intraepithelial T lymphocytes

“…This substantial commitment to Granzyme expression is consistent with the expression of the whole cytotoxic machinery, including perforin and key molecules involved in degranulation (Suppl. Table 1, (James et al , 2020)), all of which are either barely detectable, or altogether absent, in the naïve T cells. Thus, these data support the hypothesis that all T-IEL in the gut are geared towards cytotoxic activity.…”

“…It is also interesting to note that amino acid transporters were expressed at very low levels in T-IEL, thus limiting amino acid availability for protein translation. In this context, we recently showed that activation of T-IEL with IL-15 involves both upregulation of ribosome biogenesis and upregulation of amino acid transporters (James et al , 2020). The low rates of protein translation also support our analyses of the proteomes of T-IEL as there may be a significant disconnect between protein and mRNA expression in T-IEL.…”

“…T-IEL were isolated for sorting from C57/Bl6 mice and as described in (James et al , 2020). Briefly, small intestines were extracted and flushed.…”