| Literature DB >> 28387357 |
Delphine Fradin1, Pierre-Yves Boëlle2, Marie-Pierre Belot1, Fanny Lachaux1, Jorg Tost3, Céline Besse4, Jean-François Deleuze4, Gianpaolo De Filippo5, Pierre Bougnères1,5.
Abstract
Obesity is a heterogeneous disease with many different subtypes. Epigenetics could contribute to these differences. The aim of this study was to investigate genome-wide DNA methylation searching for methylation marks associated with obesity in children and adolescents. We studied DNA methylation profiles in whole blood cells from 40 obese children and controls using Illumina Infinium HumanMethylation450 BeadChips. After correction for cell heterogeneity and multiple tests, we found that compared to lean controls, 31 CpGs are differentially methylated in obese patients. A greatest proportion of these CpGs is hypermethylated in obesity and located in CpG shores regions. We next focused on severely obese children and identified 151 differentially methylated CpGs among which 10 with a difference in methylation greater than 10%. The top pathways enriched among the identified CpGs included the "IRS1 target genes" and several pathways in cancer diseases. This study represents the first effort to search for differences in methylation in obesity and severe obesity, which may help understanding these different forms of obesity and their complications.Entities:
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Year: 2017 PMID: 28387357 PMCID: PMC5384222 DOI: 10.1038/srep46311
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Characteristic of obese and control children.
| ID | Sex | Age (years) | Weight (kg) | Height (m) | BMI (kg/m2) | BMI Z-score | Birth Weight (g) | Birth Height (cm) | Term (weeks) | Physical activity* | Physical activity (hr/wk)* | Dietary intake (kcal/day)** |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| M | 12.02 | 64.9 | 1.54 | 27.36 | 3.58 | 4400 | 54 | 41 | YES | 2.5 | 3230 | |
| M | 11.48 | 74 | 1.59 | 29.27 | 4.15 | 3570 | 52.5 | 40 | YES | 4 | 2800 | |
| M | 13.12 | 89 | 1.65 | 32.69 | 4.31 | 4310 | 52.5 | 39 | YES | 5 | 3000 | |
| F | 7.62 | 32 | 1.3 | 18.93 | 2.9 | 2450 | 44 | 34 | YES | 1 | 1910 | |
| F | 12.82 | 81.6 | 1.56 | 33.53 | 4.32 | 2900 | 48 | 40 | YES | 1.5 | — | |
| F | 13.11 | 66.6 | 1.61 | 25.69 | 2.58 | 3300 | 51 | 41 | YES | 6.5 | — | |
| M | 12.79 | 87.9 | 1.56 | 36.12 | 4.96 | 3700 | 50 | 40 | YES | 4 | 2900 | |
| F | 12.06 | 60 | 1.57 | 24.34 | 2.6 | 2790 | 46.5 | 36 | YES | 1 | 2815 | |
| F | 11.55 | 60.9 | 1.49 | 27.43 | 3.59 | 3610 | 51.5 | 41 | NO | — | 3130 | |
| F | 9.53 | 46.6 | 1.37 | 24.83 | 3.85 | 3250 | 50 | 41 | YES | 1 | 1660 | |
| M | 5.49 | 28 | 1.21 | 19.12 | 2.71 | 4315 | 52.5 | 41 | YES | 1 | 1800 | |
| M | 12.48 | 69 | 1.45 | 32.82 | 4.48 | 3100 | — | 36 | YES | 2 | — | |
| F | 8.34 | 36 | 1.29 | 21.63 | 3.4 | 4230 | 52.5 | 41 | YES | 1 | 2080 | |
| M | 8.58 | 58.5 | 1.53 | 24.99 | 4.34 | 3050 | 48 | 40 | YES | 6 | — | |
| M | 9.46 | 53.6 | 1.41 | 26.96 | 4.43 | 3950 | 51 | 40 | YES | 6.5 | 2200 | |
| M | 9.17 | 42 | 1.34 | 23.39 | 3.56 | 3300 | 49 | — | YES | 2 | 2400 | |
| F | 7.53 | 35.5 | 1.3 | 21.01 | 3.32 | 3310 | 50.5 | 39 | YES | 7 | 2550 | |
| F | 9.72 | 37.7 | 1.33 | 21.31 | 2.64 | 3430 | 49 | 39 | YES | 2 | 1954 | |
| M | 11.77 | 58.3 | 1.49 | 26.26 | 3.49 | 2760 | 46 | 36 | NO | — | 2400 | |
| F | 10.42 | 46.3 | 1.43 | 22.64 | 2.91 | 2660 | 47 | 38 | YES | 5 | 2200 | |
| M | 6.25 | 21 | 1.2 | 14.58 | −0.74 | 2790 | 49 | — | — | — | — | |
| F | 9.28 | 47 | 1.55 | 19.56 | 2.09 | 3650 | 52.5 | — | — | — | — | |
| F | 11.23 | 52 | 1.62 | 19.81 | 1.46 | 2960 | 47 | — | — | — | — | |
| M | 11.52 | 38 | 1.4 | 19.39 | 1.23 | 2800 | — | — | — | — | — | |
| F | 13.00 | 41 | 1.51 | 17.98 | −0.07 | 2700 | 47 | — | — | — | — | |
| F | 12.84 | 48 | 1.58 | 19.23 | 0.67 | — | — | — | — | — | — | |
| M | 7.45 | 23.5 | 1.23 | 15.53 | 0 | — | — | — | — | — | — | |
| F | 6.03 | 22 | 1.22 | 14.78 | −0.31 | 3560 | 49.5 | — | — | — | — | |
| M | 6.66 | 25.1 | 1.2 | 17.43 | 1.45 | 3550 | 50 | — | — | — | — | |
| M | 10.00 | 37 | 1.49 | 16.66 | 0.19 | 2900 | — | — | — | — | — | |
| F | 11.15 | 37 | 1.45 | 17.59 | 0.45 | — | — | — | — | — | — | |
| M | 7.59 | 28.2 | 1.32 | 16.18 | 0.41 | — | — | — | — | — | — | |
| F | 5.95 | 15 | 1.08 | 12.86 | −2.08 | 3040 | 49 | — | — | — | — | |
| M | 9.27 | 30 | 1.4 | 15.31 | −0.51 | 2630 | 52 | — | — | — | — | |
| M | 10.16 | 32 | 1.4 | 16.33 | −0.02 | 3200 | 52 | — | — | — | — | |
| M | 11.28 | 33 | 1.39 | 17.08 | 0.2 | — | — | — | — | — | — | |
| M | 2.90 | 12 | 0.92 | 14.18 | −1.91 | 3260 | 51 | — | — | — | — |
*Data obtained from a self-completed questionnaire; **A 24-hour dietary recall was conducted for all patients by a dietitian, based on individual interview with parents or caregivers.
Differentially methylated CpGs in obese children.
| Probes | CHR | UCSC RefGene Name | UCSC RefGene Group | Relation to UCSC CpG Island | Methylation percent in obese children | Methylation percent in control subjects | p.value | q.value |
|---|---|---|---|---|---|---|---|---|
| cg23314826 | 8 | 0.962 ± 0.003 | 0.965 ± 0.003 | 1.31e-08 | 0.003 | |||
| cg11324650 | 3 | Island | 0.449 0.056 | 0.521 0.034 | 4.59e-08 | 0.005 | ||
| cg08468401 | 3 | 0.390 0.070 | 0.501 0.087 | 7.09e-08 | 0.005 | |||
| cg04052934 | 6 | 0.752 0.050 | 0.796 0.052 | 2.29e-07 | 0.012 | |||
| cg06769708 | 20 | Body | S_Shore | 0.970 0.007 | 0.976 0.005 | 2.05e-07 | 0.012 | |
| cg19835478 | 21 | TSS1500 | Island | 0.039 0.007 | 0.029 0.006 | 2.78e-07 | 0.013 | |
| cg26645655 | 3 | 0.426 0.062 | 0.502 0.071 | 3.23e-07 | 0.013 | |||
| cg00562180 | 16 | N_Shelf | 0.891 0.021 | 0.793 0.110 | 5.87e-07 | 0.018 | ||
| cg07060864 | 16 | 0.604 0.024 | 0.558 0.038 | 6.01e-07 | 0.018 | |||
| cg13844049 | 1 | 0.131 0.018 | 0.166 0.045 | 6.36e-07 | 0.018 | |||
| cg26834418 | 11 | TSS1500 | S_Shore | 0.206 0.087 | 0.324 0.095 | 7.21e-07 | 0.019 | |
| cg16427670 | 13 | TSS1500 | 0.056 0.007 | 0.046 0.007 | 9.24e-07 | 0.021 | ||
| cg16705578 | 3 | Island | 0.019 0.004 | 0.025 0.005 | 9.19e-07 | 0.021 | ||
| cg26138821 | 11 | TSS200 | S_Shore | 0.054 0.031 | 0.093 0.031 | 9.61e-07 | 0.021 | |
| cg14720024 | 5 | S_Shore | 0.939 0.015 | 0.961 0.010 | 1.09e-06 | 0.023 | ||
| cg00103778 | 20 | N_Shore | 0.202 0.028 | 0.264 0.054 | 1.36e-06 | 0.027 | ||
| cg06686058 | 11 | 5′UTR;1stExon | N_Shore | 0.039 0.005 | 0.034 0.004 | 1.44e-06 | 0.027 | |
| cg08025415 | 19 | Body | N_Shelf | 0.981 0.002 | 0.982 0.002 | 1.48e-06 | 0.027 | |
| cg16906712 | 6 | TSS1500;3′UTR;1stExon | S_Shore | 0.019 0.004 | 0.024 0.003 | 1.53e-06 | 0.027 | |
| cg23043119 | 5 | TSS1500 | S_Shore | 0.039 0.006 | 0.033 0.005 | 1.61e-06 | 0.027 | |
| cg07607077 | 7 | Body | S_Shore | 0.941 0.009 | 0.950 0.005 | 1.71e-06 | 0.027 | |
| cg02399233 | 11 | Body | 0.977 0.004 | 0.979 0.003 | 2.23e-06 | 0.032 | ||
| cg08515072 | 8 | N_Shore | 0.967 0.005 | 0.971 0.005 | 2.16e-06 | 0.032 | ||
| cg12093371 | 10 | N_Shore | 0.073 0.009 | 0.058 0.010 | 2.16e-06 | 0.032 | ||
| cg06918474 | 5 | 3′UTR | 0.110 0.031 | 0.084 0.049 | 2.38e-06 | 0.034 | ||
| cg16331674 | 22 | Island | 0.843 0.048 | 0.785 0.063 | 2.56e-06 | 0.035 | ||
| cg15991546 | 1 | TSS200 | Island | 0.050 0.009 | 0.068 0.013 | 2.82e-06 | 0.036 | |
| cg17128312 | 19 | Body | N_Shore | 0.572 0.028 | 0.537 0.036 | 2.79e-06 | 0.036 | |
| cg16334849 | 8 | 0.970 0.004 | 0.973 0.005 | 3.19e-06 | 0.040 | |||
| cg03607644 | 8 | 0.929 0.018 | 0.950 0.014 | 3.88e-06 | 0.045 | |||
| cg24317742 | 1 | 0.958 0.007 | 0.967 0.008 | 4.32e-06 | 0.048 |
Table listing the differentially methylated CpG probes with corresponding UCSC RefGene Name, group and group related to CpG Island, methylation percent in obese and control children, p.values and q.values after cell type estimate adjustments.
Figure 1Correlation between DNA methylation and age in 20 obese children and 17 controls at the 31 associated CpGs.
*Significant correlation (p < 0.05), DNA methylation value in the y-axis and age in years in the x-axis.
Figure 2Association between DNA methylation and sex in 20 obese children and 17 controls at the 31 associated CpGs.
*Significant correlation (p < 0.05), DNA methylation value in the y-axis and sex (M = male, F = female) in the x-axis.
Figure 3Distribution of differentially methylated CpGs versus all CpGs sites on the Infinium HumanMethylation450 BeadChip in relation to (A) CpG island regions; (B) the nearest gene regions. Chi-square analysis was performed to test over- or under-representation of sequence features among the differentially methylated CpGs, *P.value < 0.05. (C) Venn diagram of the identified CpGs in obese or severely obese children, below the 13 common CpGs.
Gene set enrichment analysis of severe obese children associated CpGs.
| Gene Set Name | Genes in Gene Set | Description of the Set | Genes in Overlap (n) | Genes in Overlap (Name) | p.value | FDR q.value |
|---|---|---|---|---|---|---|
| TUMOR ZONE PERIPHERA VS CENTRAL DN | 634 | Down-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone | 8 | 6.22e-6 | 1.78e-2 | |
| ENDOCRINE THERAPY RESISTANCE 3 | 720 | The ‘group 3 set’ of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 | 8 | 1.56e-5 | 1.78e-2 | |
| ADULT TISSUE STEM MODULE | 721 | The ‘adult tissue stem’ module: genes coordinately up-regulated in a compendium of adult tissue stem cells | 8 | 1.57e-5 | 1.78e-2 | |
| IRS1 TARGETS UP | 113 | Up-regulated in brown preadipocytes with IRS1 knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation | 4 | 2.97e-5 | 2.34e-2 | |
| LIVER CANCER SUBCLASS S1 | 237 | Genes from ‘subtype S1′ signature of hepatocellular carcinoma (HCC): aberrant activation of the WNT signaling pathway | 5 | 3.45e-5 | 2.34e-2 | |
| COLON CANCER UP | 871 | Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples | 8 | 5.98e-5 | 3.39e-2 |
This table displays gene pathways overrepresented among the 151 differentially methylated CpGs (FDR q.value < 0.05).