Background
Methods
Study group
Assessment of childhood trauma
DNA methylation array
DNA methylation data analysis
Gene enrichment analysis
Results
Child laborer | Control |
p-value | |
---|---|---|---|
N for analysis |
N = 30 |
N = 15 | |
Age (years; mean ± SD) | 75.9 ± 5.8 | 72.8 ± 5.8 | 0.103 |
Gender (F/M) | 14 F/16 M | 8 F/7 M | 0.673 |
CTQ - total (mean ± SD) | 82.2 ± 16.2 | 34.4 ± 7.89 | <0.001 |
CTQ physical abuse | 17.3 ± 6 | 5.7 ± 1.2 | |
CTQ emotional abuse | 17.4 ± 5.2 | 6.3 ± 1.4 | |
CTQ sexual abuse | 9.5 ± 7 | 5.4 ± 1.3 | |
Age at indenture (years; mean ± SD) | 4.8 ± 4.6 | none | |
Duration of indenture (years; mean ± SD) | 11.6 ± 5 | none |
Differential methylation between former indentured child laborers and controls
CpG number | Chromosome | Gene symbol |
p-value | FDR | CpG site location within the gene |
---|---|---|---|---|---|
cg09426383 | 7 |
SKAP2
| 1.32 × 10−7
| 0.035 | Body |
cg21852117 | 7 | 3.57 × 10−7
| 0.035 | Intergenic | |
cg09303678 | 16 |
C16orf11
| 4.05 × 10−7
| 0.035 | TSS1500 |
cg20436912 | 22 |
SEC14L4
| 4.32 × 10−7
| 0.035 | TSS1500 |
cg24377150 | 1 |
SKI
| 4.51 × 10−7
| 0.035 | Body |
cg22718696 | 1 |
MTOR
| 4.63 × 10−7
| 0.035 | Body |
cg02500267 | 20 |
DTD1
| 7.45 × 10−7
| 0.045 | TSS200 |
cg19216792 | 7 |
SKAP2
| 8.55 × 10−7
| 0.045 | Body |
cg17256234 | 11 | 9.01 × 10−7
| 0.045 | Intergenic | |
cg00325149 | 1 |
COL11A1
| 1.11 × 10−6
| 0.047 | TSS200 |
cg12140851 | 7 |
SKAP2
| 1.34 × 10−6
| 0.047 | Body |
cg09997372 | 17 |
CSHL1
| 1.65 × 10−6
| 0.047 | TSS1500 |
cg03126199 | 19 |
ZNF486
| 1.66 × 10−6
| 0.047 | TSS1500 |
cg26437522 | 7 | 1.87 × 10−6
| 0.047 | Intergenic | |
cg14954143 | 3 | 1.91 × 10−6
| 0.047 | Intergenic | |
cg12252069 | 7 |
SKAP2
| 1.96 × 10−6
| 0.047 | Body |
cg22519265 | 17 |
ATP2A3
| 2.06 × 10−6
| 0.047 | 5’UTR |
cg22324029 | 6 |
HLA-DMB
| 2.22 × 10−6
| 0.047 | Body |
cg14895646 | 19 |
MED25
| 2.26 × 10−6
| 0.047 | TSS200 |
cg25121513 | 7 | 2.28 × 10−6
| 0.047 | Intergenic | |
cg10993074 | 6 |
C6orf47
| 2.37 × 10−6
| 0.047 | 1st Exon |
cg19313023 | 4 | 2.44 × 10−6
| 0.047 | Intergenic | |
cg19395289 | 6 | 2.53 × 10−6
| 0.047 | Intergenic | |
cg23595621 | 14 |
RNASE6
| 2.64 × 10−6
| 0.047 | Body |
cg18423591 | 15 |
SHF
| 2.72 × 10−6
| 0.047 | TSS1500 |
cg10313047 | 3 |
DNAH1
| 2.76 × 10−6
| 0.047 | 5’UTR |
cg12074024 | 1 | 2.79 × 10−6
| 0.047 | Intergenic | |
cg16669619 | 18 | 3.33 × 10−6
| 0.047 | Intergenic | |
cg11923320 | 1 | 3.46 × 10−6
| 0.047 | Intergenic | |
cg06793062 | 16 |
CNTNAP4
| 3.53 × 10−6
| 0.047 | Body |
cg11068049 | 4 | 3.58 × 10−6
| 0.047 | Intergenic | |
cg07424912 | 16 |
SLC38A7
| 3.68 × 10−6
| 0.047 | TSS1500 |
cg00150025 | 15 |
PLA2G4F
| 3.74 × 10−6
| 0.047 | Body |
cg00292312 | 1 |
CAMTA1
| 3.79 × 10−6
| 0.047 | Body |
cg01909551 | 3 | 3.88 × 10−6
| 0.047 | Intergenic | |
cg18708013 | 6 |
ZC3H12D
| 3.89 × 10−6
| 0.047 | 5’UTR |
cg15641398 | 7 | 3.95 × 10−6
| 0.047 | Intergenic | |
cg04910277 | 8 |
DLGAP2
| 4.05 × 10−6
| 0.047 | Body |
cg06226516 | 7 | 4.07 × 10−6
| 0.047 | Intergenic | |
cg18431765 | 2 | 4.25 × 10−6
| 0.047 | Intergenic | |
cg09168222 | 4 |
HERC6
| 4.25 × 10−6
| 0.047 | TSS200 |
cg05941631 | 2 | 4.55 × 10−6
| 0.048 | Intergenic | |
cg14889079 | 19 |
NDUFA3
| 4.65 × 10−6
| 0.048 | TSS200 |
cg23196756 | 10 |
EIF4EBP2
| 4.96 × 10−6
| 0.048 | Body |
cg21054842 | 4 | 5.09 × 10−6
| 0.048 | Intergenic | |
cg00884805 | 1 |
GNG12
| 5.13 × 10−6
| 0.048 | 5’UTR |
cg01833485 | 1 |
ESRRG
| 5.14 × 10−6
| 0.048 | 5’UTR |
cg01409163 | 8 |
ERICH1
| 5.35 × 10−6
| 0.048 | Body |
cg08101977 | 16 |
CACNA1H
| 5.44 × 10−6
| 0.048 | Body |
cg22026150 | 8 | 5.47 × 10−6
| 0.048 | Intergenic | |
cg23385732 | 14 | 5.69 × 10−6
| 0.048 | Intergenic | |
cg11891395 | 7 |
DLX5
| 5.72 × 10−6
| 0.048 | Body |
cg24954668 | 7 | 5.72 × 10−6
| 0.048 | Intergenic | |
cg22727965 | 7 | 5.77 × 10−6
| 0.048 | Intergenic | |
cg24378250 | 11 |
TAF10
| 5.88 × 10−6
| 0.049 | Body |
cg14740251 | 19 | 6.32 × 10−6
| 0.049 | Intergenic | |
cg05717473 | 6 | 6.52 × 10−6
| 0.049 | Intergenic | |
cg23012579 | 5 |
ERGIC1
| 6.65 × 10−6
| 0.049 | Body |
cg02388718 | 9 |
NCRNA00032
| 6.7 × 10−6
| 0.049 | Body |
cg07936950 | 2 |
DLX1
| 6.72 × 10−6
| 0.049 | 3’UTR |
cg00169412 | 6 | 6.78 × 10−6
| 0.049 | Intergenic | |
cg03730533 | 7 |
SKAP2
| 6.9 × 10−6
| 0.049 | Body |
cg13432339 | 4 | 7.05 × 10−6
| 0.049 | Intergenic | |
cg11782208 | 1 |
C1orf170
| 7.15 × 10−6
| 0.049 | TSS1500 |
cg11014810 | 10 |
SH3PXD2A
| 7.25 × 10−6
| 0.049 | Body |
cg11673092 | 10 |
ARMC3
| 7.31 × 10−6
| 0.049 | TSS1500 |
cg01573140 | 7 |
OGDH
| 7.32 × 10−6
| 0.049 | Body |
cg02013146 | 16 |
ANKRD11
| 7.33 × 10−6
| 0.049 | 5’UTR |
cg19975800 | 2 |
UGT1A10
| 7.48 × 10−6
| 0.049 | TSS200 |
cg16270079 | 3 |
PLXNB1
| 7.75 × 10−6
| 0.049 | Body |
cg18703601 | 3 |
ROBO1
| 7.82 × 10−6
| 0.049 | TSS1500 |
Enrichment analysis of differentially methylated genes between the former indentured child labor and control groups
Annotation Cluster 1 (Enrichment Score 1.74) | ||
---|---|---|
Term | Genes |
p-value |
Positive regulation of cell projection organization |
MTOR; PLXNB1; ROBO1
| 0.0052 |
Regulation of cell projection organization |
MTOR; PLXNB1; ROBO1
| 0.018 |
Annotation Cluster 2 (Enrichment Score 1.65) | ||
Cell projection |
SH3PXD2A; CACNA1H; DLGAP2; DNAH1; MTOR; ROBO1
| 0.01 |
Neuron projection |
CACNA1H; DLGAP2; MTOR; ROBO1
| 0.028 |
Dendrite |
CACNA1H; DLGAP2; MTOR
| 0.04 |
Effect of psychiatric and somatic comorbidities, education duration and proportion of buccal epithelial cells on differentially methylated genes between the groups
CpG number | Chr | Gene symbol |
p-value before additional correction |
p-value |
---|---|---|---|---|
cg09426383 | 7 |
SKAP2
| 1.32 × 10−7
| 2.61 × 10−5
|
cg21852117 | 7 | 3.57 × 10−7
| 6.4 × 10−5
| |
cg09303678 | 16 |
C16orf11
| 4.05 × 10−7
| 9.47 × 10−6
|
cg20436912 | 22 |
SEC14L4
| 4.32 × 10−7
| 1.59 × 10−4
|
CpG number | Chr | Gene symbol |
p-value before additional correction |
p-value |
---|---|---|---|---|
cg11891395 | 7 |
DLX5
| 5.72 × 10−6
| 0.00159 |
cg07936950 | 2 |
DLX1
| 6.72 × 10−6
| 0.00148 |
cg01833485 | 1 |
ESRRG
| 5.14 × 10−6
| 0.000132 |
cg18703601 | 3 |
ROBO1
| 7.82 × 10−6
| 3.55 × 10−5
|
cg01573140 | 7 |
OGDH
| 7.32 × 10−6
| 0.00193 |
cg08101977 | 16 |
CACNA1H
| 5.44 × 10−6
| 0.00139 |
cg04910277 | 8 |
DLGAP2
| 4.05 × 10−6
| 0.000393 |
cg06793062 | 16 |
CNTNAP4
| 3.53 × 10−6
| 0.000423 |
cg22718696 | 1 |
MTOR
| 4.63 × 10−7
| 0.000378 |
cg16270079 | 3 |
PLXNB1
| 7.75 × 10−6
| 0.000549 |