Top DMCs and the corresponding differential gene expression in CD19+ B cells in patients with primary Sjögren's syndrome (pSS) and healthy controls
| CpG site | Gene symbol | Gene name | Interferon-induced | CpG island information | Gene property | Enhancer* | Promoter† | Methylation Δβ‡ | Methylation p value§ | Expression log2 (FC)¶ | Expression p value** |
|---|---|---|---|---|---|---|---|---|---|---|---|
| cg21549285 | MX1 | MX dynamin-like GTPase 1 | Yes | Shore | 5′UTR | No | Yes | −0.34 | 2.3×10−11 | 1.97 | <5×10−5 |
| cg05696877 | IFI44L | Interferon-induced protein 44-like | Yes | Open sea | 5′UTR | No | No | −0.33 | 3.8×10−20 | 3.79 | <5×10−5 |
| cg03607951 | IFI44L | Interferon-induced protein 44-like | Yes | Open sea | TSS1500 | Yes | Yes | −0.30 | 2.6×10−18 | 3.79 | <5×10−5 |
| cg23570810 | IFITM1 | Interferon-induced transmembrane protein 1 | Yes | Shore | Gene body | Yes | No | −0.26 | 1.3×10−10 | 1.63 | <5×10−5 |
| cg05552874 | IFIT1 | Interferon-induced protein with tetratricopeptide repeats 1 | Yes | Open sea | Gene body | Yes | Yes | −0.26 | 2.1×10−16 | 4.44 | <5×10−5 |
| cg06981309 | PLSCR1 | Phospholipid scramblase 1 | Yes | Shore | 5′UTR | No | Yes | −0.25 | 2.3×10−12 | 1.64 | <5×10−5 |
| cg14293575 | USP18 | Ubiquitin-specific peptidase 18 | Yes | Shelf | 5′UTR | No | No | −0.25 | 9.7×10−14 | 3.27 | <5×10−5 |
| cg03038262 | IFITM1 | Interferon-induced transmembrane protein 1 | Yes | Shore | 3′UTR | Yes | No | −0.25 | 2.9×10−10 | 1.63 | <5×10−5 |
| cg22930808 | PARP9 | Poly (ADP-ribose) polymerase family, member 9 | Yes | Shore | 5′UTR | Yes | No | −0.24 | 2.4×10−10 | 1.89 | <5×10−5 |
| cg00959259 | PARP9 | Poly (ADP-ribose) polymerase family, member 9 | Yes | Shore | 5′UTR | Yes | No | −0.24 | 1.3×10−13 | 1.89 | <5×10−5 |
| cg22862003 | MX1 | MX dynamin-like GTPase 1 | Yes | Shore | TSS1500 | Yes | Yes | −0.22 | 5.8×10−12 | 1.97 | <5×10−5 |
| cg10549986 | RSAD2 | Radical S-adenosyl methionine domain containing 2 | Yes | Open sea | First exon | Yes | Yes | −0.21 | 1.4×10−17 | 3.19 | <5×10−5 |
| cg16810031 | ZPBP2 | Zona pellucida binding protein 2 | No | CpG island | TSS1500 | Yes | No | 0.21 | 7.4×10−8 | n.a. | n.a. |
| cg25330422 | STAT3 | Signal transducer and activator of transcription 3 | Yes | Shelf | 3′UTR | Yes | Yes | 0.22 | 3.2×10−13 | -0.09 | n.s. |
*Genomic location of differentially methylated CpG site (DMC) overlapping H3K4me1 (poised enhancer mark) and/or H3K27ac (active enhancer mark) peak in reference CD19+ B cells.
†Genomic location of DMC overlapping H3K4me3 (active promoter mark) peak in reference CD19+ B cells.
‡Methylation Δβ refers to the difference in mean methylation β (β-values) between patients with pSS and healthy controls. A negative Δβ represents hypomethylation in the patients.
§p Value of the association between CpG methylation and pSS (significance threshold p<1.3×10−7; Bonferroni corrected).
¶Differential gene expression as log2(FC) between patients with pSS and healthy controls.
**p Value of differential gene expression between patients with pSS and healthy controls.
FC, fold change; n.a., not available; n.s., not significant; TSS, transcription start site.