Table 2.
Genes showing concomitant evidence for differential DNA methylation and gene expression in blood from SSc patients
| DNA methylation | Reported gene expression | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Location | This study | Other reports | Expression | Refs | |||||||||||
| CpG | Gene location | CpG island location | All | lcSSc | dcSSc | SLE | SSc | |||||||||
| Naïve T cells [17, 23] | T cells [15] | B cells [15] | Mono- cytes [15] | Neutro- phils [45, 8] | WBC [47] | skin fibrob [34] | ||||||||||
| RPS6KA1 | 1p36.11 | cg24585377 | Body | S_Shore | down- | down- | up- | [53] | ||||||||
| IFI44L | 1p31.1 | cg03607951 | TSS1500 | - | down- | down- | down- | down- | down- | down- | down- | down- | up- | [49, 50, 52, 29, 27] | ||
| RSAD2 | 2p25.2 | cg15346781 | TSS1500 | - | down- | down- | down- | down- | down- | up- | up- | [49, 52, 27] | ||||
| LPIN1 | 2p25.1 | cg02069619 | TSS1500 | N_Shore | down- | down- | [49] | |||||||||
| LPP | 3q27.3 | cg05685023 | TSS1500 | N_Shore | down- | down- | [53] | |||||||||
| RPL37 | 5p13.1 | cg08754067 | Body | N_Shelf | up- | down- | [49] | |||||||||
| HMGCR | 5q13.3 | cg26399773 | 5'UTR | Island | up- | up- | [50] | |||||||||
| TNXB | 6p21.33 | cg06580770 | Body | N_Shore | up- | down- | down- | [53] | ||||||||
| cg02673305 | 5'UTR | S_Shore | down- | down- | down- | [53] | ||||||||||
| KCNQ1 | 11p15.5 | cg07824422 | Body | Island | down- | up- | [53] | |||||||||
| CD248 | 11q13.2 | cg00350296 | TSS1500 | S_Shore | down- | up- | [48] | |||||||||
| CACNA2D4 | 12p13.33 | cg19069360 | Body | - | down- | up- | [50] | |||||||||
| TNFRSF1A | 12p13.31 | cg26254667 | TSS1500 | - | up- | up- | up- | [50, 53, 24] | ||||||||
| WDFY2 | 13q14.3 | cg08029014 | Body | - | up- | up- | [50] | |||||||||
| ITPK1 | 14q32.12 | cg25095171 | Body | N_Shelf | down- | up- | [53] | |||||||||
| CRIP2 | 14q32.33 | cg15532667 | TSS1500 | N_Shore | down- | down- | [49] | |||||||||
| CYFIP1 | 15q11.2 | cg22432269* | 1stExon | Island | down- | up- | [50] | |||||||||
| SQRDL | 15q21.1 | cg01626885 | 5'UTR | - | down- | up- | [50] | |||||||||
| TLE3 | 15q23 | cg01666796 | Body | - | up- | up- | [48] | |||||||||
| cg12349571 | Body | - | up- | up- | [48] | |||||||||||
| ALOX15 | 17p13.2 | cg06222638 | Body | Island | down- | down- | [53] | |||||||||
| STAT3 | 17q21.2 | cg24312520 | Body | - | up- | up- | up- | up- | [48, 50, 26] | |||||||
| CBX4 | 17q25.3 | cg00483030 | Body | N_Shore | down- | up- | [52] | |||||||||
| PTPRS | 19p13.3 | cg08857677 | TSS1500 | S_Shore | down- | up- | [53] | |||||||||
| TYROBP | 19q13.12 | cg17925829 | TSS200 | - | down- | up- | [52, 53, 27] | |||||||||
| RASGRP4 | 19q13.2 | cg24376214 | TSS1500 | - | up- | up- | [50] | |||||||||
| RIN2 | 20p11.23 | cg12049875 | Body | Island | down- | up- | [50] | |||||||||
| PRIC285 | 20q13.33 | cg01458054 | Body | N_Shore | up- | up- | up- or down- | up- or down- | down- | up- | up- | [49] | ||||
| CERK | 22q13.31 | cg05602642 | 3'UTR | N_Shore | down- | down- | [49] | |||||||||
Up- and down- refer to hypo- or hypermethylation, or over- or underexpression, respectively. Italics denotes methylation of different CpG sites in the gene. TSS1500 (TSS200), within 1500 bps (200 bps) from transcription start site; 5′UTR (3'UTR), 5′ (3') untranslated region. WBC: white blood cells. Skin fibrob: skin fibroblasts. Refs: references. *Age-associated CpG [42].