Background
Methods
Study sample
Serum 25(OH)D assessment
Methylation analysis
Candidate gene selection
Statistical analysis
25(OH)D and methylation of vitamin D-related genes in the subcohort
25(OH)D-methylation interaction and breast cancer risk in the case-cohort
Epigenome-wide association study of 25(OH)D in subcohort or cases
Results
25(OH)D and methylation of vitamin D-related genes in the subcohort
Rank | CpG | Gene / location type | Chromosome: position | Mean methylation level (SD) | Association with 25(OH)Da | |
---|---|---|---|---|---|---|
β | p value | |||||
1 | cg21201924 | RXRA / body | 9: 137251825 | 0.76 (0.042) | −0.020 | 0.0004 |
2 | cg02127980 | RXRA / body | 9: 137252116 | 0.40 (0.067) | −0.015 | 0.0004 |
3 | cg17559402b | NADSYN1 / body | 11: 71187890 | 0.97 (0.006) | −0.017 | 0.003 |
4 | cg02059519 | RXRA / body | 9: 137250935 | 0.83 (0.026) | −0.012 | 0.003 |
5 | cg09997530 | GC / body | 4: 72636217 | 0.91 (0.017) | 0.015 | 0.005 |
6 | cg04329455b | RXRA | 9: 137215364 | 0.96 (0.008) | 0.014 | 0.007 |
7 | cg00268518b | NADSYN1 / TSS200 | 11: 71164106 | 0.01 (0.001) | 0.011 | 0.008 |
8 | cg03146219 | NADSYN1 / body | 11: 71189514 | 0.47 (0.097) | −0.012 | 0.009 |
9 | cg13510651b | RXRA / body | 9: 137227772 | 0.94 (0.008) | −0.010 | 0.01 |
10 | cg03490288b | DHCR7 / body | 11: 71146658 | 0.97 (0.006) | 0.015 | 0.01 |
11 | cg05785753 | NADSYN1 / body | 11: 71189490 | 0.59 (0.074) | −0.010 | 0.01 |
12 | cg13687497 | RXRA / body | 9: 137249839 | 0.80 (0.023) | −0.010 | 0.01 |
13 | cg07793224b | NADSYN1 / body | 11: 71183180 | 0.97 (0.008) | 0.017 | 0.02 |
14 | cg26044621b | DHCR7 / 3´ UTR | 11: 71145665 | 0.94 (0.011) | 0.012 | 002 |
15 | cg04837494 | GC / 3´ UTR | 4: 72608149 | 0.85 (0.033) | 0.013 | 0.03 |
16 | cg14236758 | RXRA / body | 9: 137252129 | 0.48 (0.066) | −0.009 | 0.03 |
17 | cg04774822 | NADSYN1 / body | 11: 71165839 | 0.78 (0.033) | −0.009 | 0.03 |
18 | cg16151558b | DHCR7 / TSS1500 | 11: 71159853 | 0.02 (0.066) | 0.013 | 0.04 |
19 | cg20372759b | CYP27B1 / TSS1500 | 12: 58162287 | 0.97 (0.006) | −0.010 | 0.04 |
20 | cg24806812 | GC / body | 4: 72635202 | 0.93 (0.018) | 0.012 | 0.04 |
21 | cg14154547b | RXRA / body | 9: 137293309 | 0.92 (0.010) | −0.007 | 0.04 |
22 | cg07099121b | DHCR7 / 3´ UTR | 11: 71146096 | 0.98 (0.004) | −0.010 | 004 |
23 | cg16910670b | NADSYN1 | 11: 71215361 | 0.97 (0.005) | −0.011 | 0.05 |
25(OH)D-methylation interaction and breast cancer risk in the case-cohort
Rank | CpG site | Gene / location type | HR (95% CI) for methylation-breast cancer association | HR (95% CI) for methylation-breast cancer association, if 25(OH)D ≤ 38.0 ng/mL | HR (95% CI) for methylation-breast cancer association, if 25(OH)D > 38.0 ng/mL | Ratio of Hazard Ratios (95% CI)b | Interaction p value |
---|---|---|---|---|---|---|---|
1 | cg21201924 | RXRA / body | 1.00 (0.96–1.04) | 0.97 (0.93–1.01) | 1.18 (1.08–1.29) | 1.22 (1.10–1.34) | 7.0 × 10−5 |
2 | cg13786567 | RXRA / body | 1.01 (0.94–1.08) | 0.94 (0.87–1.02) | 1.34 (1.12–1.60) | 1.42 (1.17–1.73) | 4.0 × 10−4 |
3 | cg02127980 | RXRA / body | 1.00 (0.94–1.06) | 0.95 (0.88–1.01) | 1.22 (1.07–1.38) | 1.29 (1.11–1.49) | 7.0 × 10−4 |
4 | cg12978433 | CYP24A1 / 1st exon | 1.01 (0.98–1.04) | 1.04 (1.00–1.07) | 0.93 (0.88–0.98) | 0.90 (0.84–0.96) | 9.0 × 10−4 |
5 | cg14154547c | RXRA / body | 0.96 (0.90–1.03) | 0.91 (0.84–0.98) | 1.17 (1.01–1.36) | 1.29 (1.09–1.53) | 0.003 |
6 | cg18956481c | CYP24A1 / 5´ UTR | 0.99 (0.97–1.02) | 1.01 (0.99–1.04) | 0.93 (0.88–0.98) | 0.92 (0.86–0.98) | 0.006 |
7 | cg13510651c | RXRA / body | 0.99 (0.93–1.06) | 0.95 (0.88–1.02) | 1.18 (1.03–1.35) | 1.24 (1.06–1.45) | 0.007 |
8 | cg14236758 | RXRA / body | 1.00 (0.94–1.06) | 0.96 (0.90–1.03) | 1.19 (1.03–1.37) | 1.23 (1.05–1.44) | 0.01 |
9 | cg09253762 | CYP27B1 / TSS1500 | 0.99 (0.95–1.04) | 0.96 (0.91–1.01) | 1.12 (1.01–1.24) | 1.16 (1.04–1.31) | 0.01 |
10 | cg18482822c | DHCR7 / body | 1.02 (0.97–1.06) | 0.99 (0.93–1.04) | 1.13 (1.02–1.24) | 1.14 (1.02–1.27) | 0.02 |
11 | cg05072492c | NADSYN1 / TSS1500 | 1.01 (0.96–1.06) | 0.97 (0.92–1.03) | 1.11 (1.00–1.24) | 1.15 (1.01–1.29) | 0.03 |
12 | cg11035813c | DHCR7 / TSS1500 | 1.02 (0.98–1.07) | 1.00 (0.95–1.05) | 1.13 (1.02–1.24) | 1.13 (1.01–1.26) | 0.03 |
13 | cg14854850 | VDR / 3´ UTR | 0.99 (0.94–1.03) | 1.02 (0.97–1.07) | 0.90 (0.82–0.99) | 0.89 (0.79–0.99) | 0.03 |
14 | cg25588697c | DHCR7 / body | 1.01 (0.95–1.08) | 0.96 (0.89–1.05) | 1.14 (1.00–1.30) | 1.18 (1.01–1.38) | 0.04 |
15 | cg10592901 | VDR / body | 1.04 (1.01–1.07) | 1.06 (1.03–1.10) | 0.98 (0.92–1.05) | 0.92 (0.86–1.00) | 0.04 |
16 | cg12474705c | NADSYN1 / body | 0.96 (0.92–1.01) | 0.99 (0.94–1.05) | 0.88 (0.80–0.98) | 0.89 (0.79–1.00) | 0.04 |
17 | cg16984335c | CYP27B1 / body | 1.00 (0.96–1.04) | 1.02 (0.97–1.06) | 0.92 (0.83–1.00) | 0.90 (0.81–1.00) | 0.05 |
18 | cg13941235 | RXRA / body | 1.00 (0.97–1.02) | 0.98 (0.95–1.01) | 1.04 (0.99–1.10) | 1.06 (1.00–1.13) | 0.05 |
Epigenome-wide association study of 25(OH)D in subcohort or cases
CpG site | Location (Chr:position) | Location type | Gene | Effect estimatea (95% CI) | p value | q value |
---|---|---|---|---|---|---|
cg24350360 | 1:225997662b | TSS200 |
EPHX1
| −0.04 (−0.06 to −0.03) | 3.4 × 10−8 | 0.01 |
cg06177555 | 16:29678624 | 3′ UTR |
SPN
| −0.02 (−0.03 to −0.01) | 9.8 × 10−8 | 0.02 |
cg13243168 | 17:61915833 | Body |
SMARCD2
| −0.02 (−0.03 to −0.01) | 2.9 × 10−7 | 0.04 |
cg23761815 | 10:73083123 | Body |
SLC29A3
| −0.02 (−0.03 to −0.01) | 5.1 × 10−7 | 0.05 |
cg10401362 | 7:157185402 | Body |
DNAJB6
| −0.02 (−0.03 to −0.01) | 1.0 × 10−6 | 0.09 |
Rank | CpG | Gene/ Location | 25(OH)D-methylation association, subcohort | 25(OH)D-methylation association, cases | Fisher combined p value | HR (95% CI) for methylation-breast cancer association | RHRs (95% CI)c | Interaction p value | ||
---|---|---|---|---|---|---|---|---|---|---|
Cofficientb | p value | Cofficientb | p value | |||||||
1 | cg08092930 | PPFIA1 | −0.03 | 1.3 × 10−5 | 0.02 | 0.04 | 8.5 × 10−6* | 1.01 (0.98–1.05) | 1.15 (1.06–1.24) | 6.3 × 10−4 |
2 | cg23761815 | SLC29A3 | −0.02 | 5.1 × 10−7 | − 0.01 | 0.03 | 2.7 × 10−7 | 1.13 (1.07–1.18) | 1.22 (1.08–1.38) | 0.002 |
3 | cg13243168 | SMARCD2 | −0.02 | 2.9 × 10−7 | − 7 × 10−4 | 0.87 | 4.0 × 10−6 | 1.05 (0.98–0.91) | 1.29 (1.09–1.51) | 0.002 |
4 | cg15544721 | PPP1R9A | −0.01 | 0.09 | −0.03 | 6.4 × 10−6 | 8.8 × 10−6 | 0.98 (0.94–1.03) | 0.87 (0.79–0.96) | 0.008 |
5 | cg11568290 | 5p15.1 | −0.02 | 1.4 × 10−4 | −0.01 | 0.004 | 7.7 × 10−6 | 1.15 (1.08–1.22) | 1.23 (1.05–1.44) | 0.009 |
6 | cg19420720 | P4HB | −0.01 | 0.002 | 0.02 | 2.3 × 10−4 | 8.1 × 10−6* | 1.01 (0.94–1.08) | 1.27 (1.06–1.52) | 0.01 |
7 | cg23839180 | FAM49A | −0.02 | 0.05 | −0.05 | 3.0 × 10−6 | 2.3 × 10−6 | 0.97 (0.94–1.03) | 0.92 (0.86–0.98) | 0.01 |
8 | cg15320474d | UBD | 0.02 | 2.8 × 10−6 | − 0.01 | 0.16 | 7.0 × 10−6* | 0.98 (0.83–1.04) | 0.87 (0.77–0.99) | 0.03 |
9 | cg24350360d | EPHX1 | −0.04 | 3.4 × 10−8 | 0.01 | 0.48 | 3.1 × 10−7* | 1.02 (0.99–1.05) | 1.08 (1.01–1.16) | 0.04 |
10 | cg22488164 | PLBD1 | −0.03 | 1.5 × 10−4 | −0.03 | 5.0 × 10−4 | 1.3 × 10−6 | 1.06 (1.02–1.10) | 0.93 (0.85–1.01) | 0.07 |
11 | cg10401362 | DNAJB6 | −0.02 | 1.0 × 10−6 | −0.01 | 0.27 | 4.4 × 10−6 | 1.02 (0.97–1.07) | 1.10 (0.98–1.24) | 0.10 |
12 | cg06177555 | SPN | −0.02 | 9.8 × 10−8 | −0.003 | 0.54 | 9.3 × 10−7 | 0.97 (0.91–1.03) | 1.12 (0.98–1.28) | 0.10 |
13 | cg11277126 | TRPC4AP | −0.02 | 7.7 × 10−5 | −0.02 | 4.8 × 10−4 | 6.7 × 10−7 | 1.04 (0.98–1.11) | 1.07 (0.92–1.24) | 0.39 |
14 | cg21527411 | GLYAT | 0.02 | 2.1 × 10−6 | −0.01 | 0.30 | 9.6 × 10−6* | 1.02 (0.97–1.07) | 0.95 (0.83–1.08) | 0.40 |
15 | cg09914444 | DMBX1 | 0.02 | 5.4 × 10−6 | −0.01 | 0.08 | 6.9 × 10−6* | 1.05 (1.01–1.10) | 0.96 (0.87–1.06) | 0.44 |
16 | cg23999318 | HIPK2 | −0.02 | 2.8 × 10−4 | −0.02 | 3.5 × 10−4 | 1.7 × 10−6 | 1.00 (0.94–1.05) | 1.00 (0.88–1.14) | 1.00 |