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Epigenome-wide and transcriptome-wide analyses reveal gestational diabetes is associated with alterations in the human leukocyte antigen complex.

Binder AM, LaRocca J, Lesseur C, Marsit CJ, Michels KB - Clin Epigenetics (2015)

Bottom Line: Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study.Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region.Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into how GDM shapes the intrauterine environment, which may have implications for fetal (re)programming.

View Article: PubMed Central - PubMed

Affiliation: Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115 USA.

ABSTRACT

Background: Gestational diabetes mellitus (GDM) affects approximately 10 % of pregnancies in the United States and increases the risk of adverse health outcomes in the offspring. These adult disease propensities may be set by anatomical and molecular alterations in the placenta associated with GDM.

Results: To assess the mechanistic aspects of fetal programming, we measured genome-wide methylation (Infinium HumanMethylation450 BeadChips) and expression (Affymetrix transcriptome microarrays) in placental tissue of 41 GDM cases and 41 matched pregnancies without maternal complications from the Harvard Epigenetic Birth Cohort. Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study. Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region. This differential methylation and expression may be capturing shifts in cellular composition, reflecting physiological changes in the placenta associated with GDM.

Conclusions: Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into how GDM shapes the intrauterine environment, which may have implications for fetal (re)programming.

No MeSH data available.


Related in: MedlinePlus

Regions selected for pyrovalidation based on observed association between GDM and methylation level on the microarray. Purple ovals highlight the CpG site driving the selection of each candidate region, with purple boxes indicating regional changes detected via bump hunting. Plots include site-specific methylation of GDM cases (blue) and matched controls (pink), and genomic context, including proximal CpG islands (green), HUGO genes (teal; smaller width corresponding to UTR), and SNPs colored according to heterozygosity (increasing from yellow to red). Regions include the following: a one within an enhancer and 5′UTR of CCDC181, b one 285-bp upstream of the transcription start site of HLA-DOA, c one associated with the promoter of SNRPN/SNURF, and d one within the introns of HLA-H and HLA-J
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Fig1: Regions selected for pyrovalidation based on observed association between GDM and methylation level on the microarray. Purple ovals highlight the CpG site driving the selection of each candidate region, with purple boxes indicating regional changes detected via bump hunting. Plots include site-specific methylation of GDM cases (blue) and matched controls (pink), and genomic context, including proximal CpG islands (green), HUGO genes (teal; smaller width corresponding to UTR), and SNPs colored according to heterozygosity (increasing from yellow to red). Regions include the following: a one within an enhancer and 5′UTR of CCDC181, b one 285-bp upstream of the transcription start site of HLA-DOA, c one associated with the promoter of SNRPN/SNURF, and d one within the introns of HLA-H and HLA-J

Mentions: Based on this approach, we identified four candidate regions for verification in our samples and validation in an independent cohort (Fig. 1 and Table 1). These included one locus within an enhancer and 5′UTR of CCDC181, which was associated with a 0.137 (95 % CI: 0.068, 0.207) increase in placental methylation among GDM mothers in our adjusted model (cg25464921). A second locus, within the introns of HLA-H and HLA-J, also exhibited significantly higher methylation with GDM (cg23681866; 0.108 (95 % CI: 0.049, 0.168)). These two sites were additionally within the two largest differentially methylated regions associated with GDM (Additional file 1: Table S3). The remaining two loci chosen showed lower average methylation among the placentas of GDM mothers in our adjusted models. For the locus 285-bp upstream of the TSS of HLA-DOA, the average difference was 0.117 (cg08147094; 95 % CI: −0.177, −0.058), with a smaller difference of 0.089 (cg18506672; 95 % CI: −0.133, −0.044) at a locus associated with the promoter of SNRPN/SNURF. Validation of these associations was performed by pyrosequencing of placenta samples from GDM mothers and matched normal pregnancies selected from the Rhode Island Child Health Study (RICHS), consisting of mothers recruited following delivery at the Women and Infants Hospital of Rhode Island (Additional file 1: Table S4). Besides a regional change trending towards significance upstream of HLA-DOA, none of the associations estimated on the array replicated in the independent cohort (Table 1). In contrast, pyrosequencing of these regions in the HEBC identified significant differential methylation of similar magnitude to the changes estimated on the methylation array proximal to our four candidates and among surrounding loci (with a trend towards significance for the locus within HLA-H/HLA-J), thus verifying the array findings. A failure to validate may reflect a difference in the distribution of effect modifiers between the two study populations. Compared to the mothers from the HEBC, the RICHS mothers were younger, with a higher pre-pregnancy BMI, and a greater proportion self-reporting white ethnicity (Additional file 2: Figure S1). Accordingly, we investigated modification of the association between methylation and GDM by maternal age and BMI, dichotomized by the median of each in HEBC, as well as self-reported ethnicity (Additional file 1: Table S5). Among the RICHS placenta samples, we identified significant effect modification of the association between GDM and methylation in the 5′UTR of CCDC181 by maternal age (p value for interaction p = 0.0122). Similar to the change observed in the HEBC cohort, GDM was associated with a trend towards higher methylation in older mothers, but among the younger mothers in RICHS, placentas had significantly lower average methylation at this context (−5.807 % (95 % CI: −10.890 and −0.724)), respectively. Within the region upstream of HLA-DOA, the impact of GDM differed by maternal pre-pregnancy BMI category in the validation cohort (p value for interaction p = 0.0387); in the higher BMI category, GDM was associated with lower methylation (−5.123 % (95 % CI: −8.825, −1.421)), as observed in HEBC. Significantly lower methylation of this HLA-DOA-associated region was also identified in the maternal blood of the HEBC samples among the women with a higher pre-pregnancy BMI (p value for interaction p = 0.0342; −6.039 % (95 % CI: −11.721, −0.357), Additional file 1: Tables S6–S7).Fig. 1


Epigenome-wide and transcriptome-wide analyses reveal gestational diabetes is associated with alterations in the human leukocyte antigen complex.

Binder AM, LaRocca J, Lesseur C, Marsit CJ, Michels KB - Clin Epigenetics (2015)

Regions selected for pyrovalidation based on observed association between GDM and methylation level on the microarray. Purple ovals highlight the CpG site driving the selection of each candidate region, with purple boxes indicating regional changes detected via bump hunting. Plots include site-specific methylation of GDM cases (blue) and matched controls (pink), and genomic context, including proximal CpG islands (green), HUGO genes (teal; smaller width corresponding to UTR), and SNPs colored according to heterozygosity (increasing from yellow to red). Regions include the following: a one within an enhancer and 5′UTR of CCDC181, b one 285-bp upstream of the transcription start site of HLA-DOA, c one associated with the promoter of SNRPN/SNURF, and d one within the introns of HLA-H and HLA-J
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4524439&req=5

Fig1: Regions selected for pyrovalidation based on observed association between GDM and methylation level on the microarray. Purple ovals highlight the CpG site driving the selection of each candidate region, with purple boxes indicating regional changes detected via bump hunting. Plots include site-specific methylation of GDM cases (blue) and matched controls (pink), and genomic context, including proximal CpG islands (green), HUGO genes (teal; smaller width corresponding to UTR), and SNPs colored according to heterozygosity (increasing from yellow to red). Regions include the following: a one within an enhancer and 5′UTR of CCDC181, b one 285-bp upstream of the transcription start site of HLA-DOA, c one associated with the promoter of SNRPN/SNURF, and d one within the introns of HLA-H and HLA-J
Mentions: Based on this approach, we identified four candidate regions for verification in our samples and validation in an independent cohort (Fig. 1 and Table 1). These included one locus within an enhancer and 5′UTR of CCDC181, which was associated with a 0.137 (95 % CI: 0.068, 0.207) increase in placental methylation among GDM mothers in our adjusted model (cg25464921). A second locus, within the introns of HLA-H and HLA-J, also exhibited significantly higher methylation with GDM (cg23681866; 0.108 (95 % CI: 0.049, 0.168)). These two sites were additionally within the two largest differentially methylated regions associated with GDM (Additional file 1: Table S3). The remaining two loci chosen showed lower average methylation among the placentas of GDM mothers in our adjusted models. For the locus 285-bp upstream of the TSS of HLA-DOA, the average difference was 0.117 (cg08147094; 95 % CI: −0.177, −0.058), with a smaller difference of 0.089 (cg18506672; 95 % CI: −0.133, −0.044) at a locus associated with the promoter of SNRPN/SNURF. Validation of these associations was performed by pyrosequencing of placenta samples from GDM mothers and matched normal pregnancies selected from the Rhode Island Child Health Study (RICHS), consisting of mothers recruited following delivery at the Women and Infants Hospital of Rhode Island (Additional file 1: Table S4). Besides a regional change trending towards significance upstream of HLA-DOA, none of the associations estimated on the array replicated in the independent cohort (Table 1). In contrast, pyrosequencing of these regions in the HEBC identified significant differential methylation of similar magnitude to the changes estimated on the methylation array proximal to our four candidates and among surrounding loci (with a trend towards significance for the locus within HLA-H/HLA-J), thus verifying the array findings. A failure to validate may reflect a difference in the distribution of effect modifiers between the two study populations. Compared to the mothers from the HEBC, the RICHS mothers were younger, with a higher pre-pregnancy BMI, and a greater proportion self-reporting white ethnicity (Additional file 2: Figure S1). Accordingly, we investigated modification of the association between methylation and GDM by maternal age and BMI, dichotomized by the median of each in HEBC, as well as self-reported ethnicity (Additional file 1: Table S5). Among the RICHS placenta samples, we identified significant effect modification of the association between GDM and methylation in the 5′UTR of CCDC181 by maternal age (p value for interaction p = 0.0122). Similar to the change observed in the HEBC cohort, GDM was associated with a trend towards higher methylation in older mothers, but among the younger mothers in RICHS, placentas had significantly lower average methylation at this context (−5.807 % (95 % CI: −10.890 and −0.724)), respectively. Within the region upstream of HLA-DOA, the impact of GDM differed by maternal pre-pregnancy BMI category in the validation cohort (p value for interaction p = 0.0387); in the higher BMI category, GDM was associated with lower methylation (−5.123 % (95 % CI: −8.825, −1.421)), as observed in HEBC. Significantly lower methylation of this HLA-DOA-associated region was also identified in the maternal blood of the HEBC samples among the women with a higher pre-pregnancy BMI (p value for interaction p = 0.0342; −6.039 % (95 % CI: −11.721, −0.357), Additional file 1: Tables S6–S7).Fig. 1

Bottom Line: Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study.Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region.Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into how GDM shapes the intrauterine environment, which may have implications for fetal (re)programming.

View Article: PubMed Central - PubMed

Affiliation: Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115 USA.

ABSTRACT

Background: Gestational diabetes mellitus (GDM) affects approximately 10 % of pregnancies in the United States and increases the risk of adverse health outcomes in the offspring. These adult disease propensities may be set by anatomical and molecular alterations in the placenta associated with GDM.

Results: To assess the mechanistic aspects of fetal programming, we measured genome-wide methylation (Infinium HumanMethylation450 BeadChips) and expression (Affymetrix transcriptome microarrays) in placental tissue of 41 GDM cases and 41 matched pregnancies without maternal complications from the Harvard Epigenetic Birth Cohort. Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study. Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region. This differential methylation and expression may be capturing shifts in cellular composition, reflecting physiological changes in the placenta associated with GDM.

Conclusions: Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into how GDM shapes the intrauterine environment, which may have implications for fetal (re)programming.

No MeSH data available.


Related in: MedlinePlus