Table 2.
Difference in DNA methylation change from baseline flare to follow-up visit comparing remitters to non-remitters (visit x remission interaction) for 25 CpGs genome-wide significant from Model 1 with largest interaction coefficient
| Model 1 | ||||||||
|---|---|---|---|---|---|---|---|---|
| Names | chr | pos | Gene | Group | Gene’s relevance to immune function, SLE, or autoimmunity | Coef | 95% CI | P-value |
| cg22873177 | chr1 | 229,761,584 | URB2; TAF5L | TSS1500; 5’UTR | Expression associated with cell cycle and TGF beta, ERBB, RIG I-like receptor, and P53 signaling pathways. PMID: 37033651 | − 0.23 | − 0.29, − 0.17 | 4.04E-12 |
| cg14543959 | chr3 | 113,557,658 | GRAMD1C | TSS200 | Expression associated with IL-6 levels. PMID: 25311648 | − 0.22 | − 0.28, − 0.17 | 3.94E-14 |
| cg03278573 | chr5 | 10,741,861 | DAP | Body | Multiple eQTLs downregulate its transcription in immune cells; expression associated with higher autoantibody titers. PMID: 33213505 | 0.22 | 0.16, 0.28 | 1.46E-11 |
| cg04038932 | chr9 | 135,286,214 | C9orf171 | Body | − 0.20 | − 0.26, − 0.15 | 1.14E-11 | |
| cg00102561 | chr9 | 138,799,260 | CAMSAP1 | TSS1500 | Expression associated with cell cycle and TGF beta, ERBB, and T-cell receptor signaling pathways. PMID: 36212130 | − 0.20 | − 0.26, − 0.14 | 3.00E-10 |
| cg23945273 | chr4 | 120,987,944 | MAD2L1 | 5’UTR; 1stExon | − 0.19 | − 0.24, − 0.13 | 1.11E-11 | |
| cg17988535 | chr13 | 114,808,856 | RASA3 | Body | T-cell homeostasis; promotes pathogenic T helper 17 cell generation. PMID: 37545505, 30446383 | − 0.19 | − 0.24, − 0.13 | 7.14E-11 |
| cg08323960 | chr10 | 45,684,508 | 0.19 | 0.13, 0.24 | 1.27E-10 | |||
| cg24566341 | chr7 | 98,909,383 | − 0.18 | − 0.22, − 0.13 | 4.22E-11 | |||
| cg22615071 | chr3 | 156,432,778 | 0.18 | 0.12, 0.23 | 1.59E-09 | |||
| cg10369197 | chr17 | 70,815,226 | SLC39A1 | Body | Expression associated with cell cycle and TGF beta, NOD-like receptor, and MAPK signaling pathways. PMID: 35211427 | 0.18 | 0.12, 0.24 | 7.18E-09 |
| cg09241617 | chr16 | 7,473,688 | RBFOX1 | Body | Implicated in SLE GWAS. PMID: 28246883 | − 0.17 | − 0.21, − 0.13 | 1.44E-12 |
| cg26118675 | chr2 | 96,256,841 | TRIM43 | TSS1500 | Antiviral defense mechanisms. PMID: 30420784 | 0.17 | 0.13, 0.21 | 2.49E-12 |
| cg08399134 | chr6 | 126,344,877 | TRMT11 | Body | T-cell proliferation; associated with lupus nephritis. PMID: 36168063, 34923866 | − 0.17 | − 0.21, − 0.12 | 4.12E-12 |
| cg17264064 | chr18 | 47,322,166 | ACAA2 | Body | Downregulated in T-cells of lupus-prone mice. PMID: 37216123 | 0.17 | 0.12, 0.22 | 1.08E-09 |
| cg11986223 | chr7 | 26,824,073 | SKAP2 | Body | myeloid cell activation and migration. PMID: 34172489 | − 0.17 | − 0.22, − 0.12 | 1.49E-09 |
| cg12615557 | chr1 | 109,046,245 | 0.17 | 0.12, 0.22 | 7.06E-09 | |||
| cg24600355 | chr20 | 34,329,943 | RBM39 | 5’UTR; 1stExon; Body | Splicing factor highly expressed in immune cells such as CD4+ and CD8+ T cells. PMID: 34389703 | − 0.17 | − 0.23, − 0.12 | 8.96E-09 |
| cg06089892 | chr2 | 128,101,198 | MAP3K2 | TSS1500 | Kinase dysregulated in SLE. PMID: 36309313 | − 0.17 | − 0.22, − 0.11 | 6.86E-08 |
| cg00470768 | chr15 | 41,285,147 | INO80 | Body | Chromatin remodeling; cell fate. PMID: 34139016 | 0.16 | 0.12, 0.21 | 6.13E-11 |
| cg00350932 | chr2 | 86,335,912 | PTCD3 | Body | − 0.16 | − 0.21, − 0.12 | 1.46E-10 | |
| cg06176124 | chr3 | 105,588,009 | CBLB | TSS200 | May contribute to the deregulated activation of T lymphocytes observed in SLE. PMID: 21558139 | 0.16 | 0.12, 0.20 | 1.51E-10 |
| cg05062679 | chr10 | 94,000,186 | CPEB3 | 5'UTR | Associated with immune biomarkers and infiltrating immune cell types. PMID: 38476610 | 0.16 | 0.12, 0.20 | 2.20E-10 |
| cg12981595 | chr17 | 39,254,427 | KRTAP4-8 | TSS200 | 0.16 | 0.11, 0.21 | 1.15E-08 | |
| cg13529755 | chr1 | 149,138,398 | − 0.16 | − 0.22, − 0.10 | 5.09E-08 | |||
chr, chromosome; CI, confidence interval; coef, interaction coefficient; pos, hg37 position; UTR, untranslated region; SLE, systemic lupus erythematosus; TSS, transcription start site
Bolded genes are interferon regulated genes