Table 2. . Genes with increased DNA methylation in systemic lupus erythematosus (in alphabetical order).

Gene (protein)	(Mainly) expressed by	Physiological function	Proposed effects in SLE	Ref.
CD8A, CD8B (Cluster of differentiation genes 8A and 8B, encoding for CD8A, CD8B)	CD8+ T cells	Co-receptor to the CD3/T cell receptor complex	Generation of effector CD3+CD4-CD8- DN T cells	[28,78]
IL2 (IL-2 gene, encoding for IL-2)	T cells	Proliferation and activation of T cells	Impaired generation of regulatory T cells, reduced activation-induced cell death and longer survival of autoreactive T cells, impaired function of cytotoxic CD8+ T cells, effector CD4+ T-cell differentiation and cytokine expression	[25,30,41,74]
Foxp3 (Forkhead-Box-Protein P3)	Regulatory T cells	Transcription factor, controlling regulatory T-cell functions	Reduced number and altered function of regulatory T cells	[33,75]
NOTCH1 (Notch-1 trans-membrane receptor)	T cells	Role during T-cell lineage determination, e.g., polarization of T helper cells	T-cell activation, increased IL-17A expression	[76]
NR3C1 (nuclear receptor subfamily 3 group C member 1, encoding for glucocorticoid receptor)	Multiple cells and tissues	Regulates development, metabolisms, immune responses, etc. Exerts pleiotropic effects in different cells and tissues	Unknown, potentially increased immune activation	[77]

SLE: Systemic lupus erythematosus.