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Hypomethylation of miR-17-92 cluster in lupus T cells and no significant role of genetic factors in the lupus-associated DNA methylation signature

Comment on: Coit, et al., Ann Rheum Dis 16 June 2022. doi:10.1136/annrheumdis-2022-222656

Comment by: Marta E. Alarcón-Riquelme

Epigenetics, and particular the study of the methylation of the CpG nucleotides in DNA has shown that lupus CD4+ T cells have aberrant methylation patterns1 and are poised towards activation of interferon-regulated genes2. DNA methylation is an important process of the regulation of gene expression through the addition of a methyl group to the cytosine bases of the genome. The more methylated cytosines are, the lower gene expression of particular genes in a given region of the genome where the CpG islands are located and targeted by the methylation machinery. This can be in gene promoters or intergenic regions. Thus, several of the changes in methylation observed in SLE are the hypomethyation of CpGs, which lead to overexpression of important genes. Some of the changes observed in the methylation, hypermethylation or hypomethylation of CpGs can be genetically controlled where the modification of a base pair may lead to changes in the methylation pattern.
In the presented work, the authors used the Illumina 450k array to determine methylation across 450 thousand CpG sites and performed genotyping of the DNA with the Global Screening Array. They also performed a MicroRNA analysis on the CD4+ naïve T cells in a subset of SLE patients. So firstly, the investigators performed an epigenome-side association study (EWAS) comparing methylated sites in T cells vs healthy controls. As previously, important hypomethylation of interferon-regulated genes was observed with important differences in the average of promoter methylation. Enrichment of a microRNA in cancer pathway was then identified and studied further. This pathway included genes encoding five microRNAs. Based on this, the authors examined the expression levels of the microRNAs, but no difference was observed in patients compared to controls. However, the median expression levels of two of the microRNAs had a significant positive correlation with SLEDAI scores. The authors went further to examine publicly available data to find evidence for the two microRNAs (has-miR-18a-5p and has-miR-19b1-5p), finding overexpression in CD4 T cells for miR-18a in SLE as compared to controls. Several targets (15 of 74) of this microRNA were downregulated in SLE as compared to controls, as for example TNFAIP3, a lupus susceptibility gene and a negative regulator of NFkB3.
Among their results, the authors also had hypomethylation of miR-17-92 cluster and looked for expression of the host gene called MIR17HG in single-cell RNA sequencing data from the AMP project. The MIR17HG gene was expressed in multiple immune cells infiltrating the kidney, mostly in T cell subsets. The authors then went to investigate the presence of methylation quantitative trait loci (meQTLs) which would be loci where allelic variants affect the methylation at the CpG sites due to a SNP. The authors find several meQTLs coinciding with reported SLE risk loci, including IRF5 and IRF7 and a few others were associated with risk loci because of linkage disequilibrium. However, few meQTLs were in differentially methylated CpGs between patients and controls. Finally, exploration of other meQTLs, particular the one in IRF7 did not show differences in methylation levels based on the genotypes.
This paper analyzes with a large coverage of CpG sites, the methylation patterns of CD4+ T cells. The main findings and the most interesting ones are those related on the miRNA 17 and the expression of the MIR17HG gene, and the importance of the mIR-17-92 cluster genes have in the differentiation of T cells. In fact, it has been described that overexpression of the micro-RNA cluster 17-92 promotes autoimmunity in mice and supports T helper, Th17 and follicular T helper cell differentiation. Also, of interest are the meQTLs that may modify risk loci of SLE, however, genetics does not have a major contribution in the lupus-associated methylation profiles, but the matter was discussed extensively in the paper and added, I believe, unnecessarily in the long title.

  1. Hughes, T., Webb, R., Fei, Y., Wren, J.D. & Sawalha, A.H. DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks. Genes and immunity 11, 554-60 (2010).
  2. Coit, P. et al. Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naive CD4+ T cells from lupus patients. Journal of Autoimmunity 43, 78-84 (2013).
  3. Adrianto, I. et al. Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus. Nature Genetics 43, 253-8 (2011).