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Background  Systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are systemic autoimmune connective tissue diseases that share overlapping clinico-pathological features. It is highly probable that there is an overlap in epigenetic landscapes of both diseases. This study aimed to identify similarities in DNA methylation changes in genes involved in SLE and SSc. Global DNA methylation and twelve genes selected on the basis of their involvement in inflammation, autoimmunity and/or fibrosis were analyzed using PCR arrays in three groups, each of 30 Black South Africans with SLE and SSc, plus 40 healthy control subjects.    Results  Global methylation in both diseases was significantly lower (<25 %) than in healthy subjects (>30 %, p = 0.1). In comparison to healthy controls, a similar gene-specific methylation pattern was observed in both SLE and SSc. Three genes, namely;  PRF1 ,  ITGAL and FOXP3  were consistently hypermethylated while CDKN2A and CD70 were hypomethylated in both diseases. The other genes ( SOCS1, CTGF, THY1, CXCR4, MT1-G, FLI1,  and  DNMT1 ) were generally hypomethylated in SLE whereas they were neither hyper- nor hypo-methylated in SSc.    Conclusions  SSc and SLE patients have a higher global hypomethylation than healthy subjects with specific genes being hypomethylated and others hypermethylated. The majority of genes studied were hypomethylated in SLE compared to SSc. In addition to the commonly known hypomethylated genes in SLE and SSc, there are other hypomethylated genes (such as  MT-1G and THY-1 ) that have not previously been investigated in SLE and SSc though are known to be hypermethylated in cancer.

DNA methylation similarities in genes of black South Africans with systemic lupus erythematosus and systemic sclerosis