Table 2.
EWAS of IR and IR-related diseases.
| Disease/trait1 | Tissue | Cohort size | Differential methylation | Loci reported2 | Study |
|---|---|---|---|---|---|
| HOMA-IR | Blood | 332 participants | 798 CpGs | CLCA4, LECT1, CXCR1, HDAC4, IGFR1, LEPR, ABCG1, SH3RF3, MAN2C1 | (63) |
| T2D | Liver | 60 controls, 35 cases |
251 genes |
GRB10, PPP1R1A, IGFBP2, ABCC3, MOGAT1, PRDM16 |
(64) |
| 11 controls, 13 obese non-diabetic, 11 obese T2D |
5,682 CpGs (3,058 genes) | PRKCE, PDGFA | (65) | ||
| 96 controls, 96 cases |
381 DMRs3 | PDGFA | (66) | ||
| 23 controls, 23 cases |
185 CpGs | SYT7, LTBR, CATSPER2, LPAL2, NCALD, ZDHHC11, LGTN, OXT, PRSS21 | (67) | ||
| Blood | 10 controls, 10 obese T2D |
74 DMRs | SLC19A1, EFNA2 | (68) | |
| 4,808 (discovery), 11,750 (replication) |
28 CpGs | LETM1, RBM20, IRS2, MAN2A2, 1q25.3, FCRL6, SLAMF1, APOBEC3H, 15q26.1 | (69) | ||
| 1,590 controls, 1,074 cases |
5 genes | ABCG1, PHOSPHO1, SOCS3, SREBF1, TXNIP | (70) | ||
| 129 controls, 129 cases |
2 genes | ABCG1, PHOSPHO1 | (71) | ||
| 5,387 (discovery), 4,874 (replication) |
278 CpGs | ABCG1, PHOSPHO1, SREBF, NFATC2IP, KLHL18, FTH1P20 | (72) | ||
| 701 controls, 563 cases |
18 CpGs |
ABCG1, SREBF1, TXNIP, PROC, SLC43A1, PHGDH, MAN2A2 |
(73) | ||
| 42 monozygotic twin pairs | 4 CpGs | Alu repeats methylation | (74) | ||
| NAFLD | Liver | 18 controls, 45 cases |
467 CpGs (292 genes) |
IGFBP2, IGF1, PRKCE, PGC1A, SREBF2, FOXA1, FOXA2, ZNF274 | (78) |
| 33 mild, 23 advanced |
69,247 CpGs (2,503 genes) |
FGFR2, MAT1A, CASP1, COL1A1, COL1A2, COL4A1, COL4A2, LAMA4, LAMB1, CTGF, PDGFA, CCR7, CCL5, STAT1, TNFAIP8 | (75) | ||
| 34 controls, 35 simple steatosis, 26 NASH |
1,292 CpGs (677 genes) |
PPARGC1A, DNMT1, HDAC9, ALKBH5, LDHB, COL4A1, ARL4C, SEMA3E, ITGB4 | (76) | ||
| 35 controls, 34 simple steatosis, 26 NASH |
20,396 CpGs (594 genes) |
E2F1, TFAP2A NFKB1, HNF4A, HNF1A, SREBF1, TCF4, ETS1 | (77) | ||
| 35 mild, 25 advanced |
610 DMRs3 | FGFR2, IGF1, MTHFD2, PTGFRN, ZBTB38, MGMT, FBLIM1, CYR61, NQO1 | (78) | ||
| Blood | 1496 (discovery), 1904 (replication) | 22 replicated CpGs | SLC7A11, SLC1A5, SLC43A1, PHGDH, PSORS1C1, SREBF1, ABCG1 | (79) | |
| 731 (discovery), 719 (replication) |
6 replicated CpGs | SLC7A11, SLC43A1, SLC1A5, PHGDH, PSORS1C1, SREBF1, ANKS3 | (80) |
1The primary outcomes reported in the study are shown.
2Note this is not an exhaustive list of all differentially methylated loci, but key genes of interest which are discussed in each paper.
3DMRs, differentially methylated regions. DMRs are discrete genomic sequences that contain a distinct methylation signature across a number of CpGs, enabling researchers to segregate one phenotypical group from another. Different computational methods can be used to identify DMRs, but in general terms, the number of CpGs used to define a DMR depends both on the type of method used to profile DNA methylation and on the distribution of CpGs at specific loci.