Birthweight DNA methylation signatures in infant saliva

Abstract

Background Low birthweight has been repeatedly associated with long-term adverse health outcomes and many non-communicable diseases. Our aim was to look-up cord blood birthweight-associated CpG sites identified by the PACE Consortium in infant saliva, and to explore saliva-specific DNA methylation signatures of birthweight. Methods DNA methylation was assessed using Infinium HumanMethylation450K array in 135 saliva samples collected from children of the NINFEA birth cohort at an average age of 10.8 (range 7–17) months. The association analyses between birthweight and DNA methylation variations were carried out using robust linear regression models both in the exploratory EWAS analyses and in the look-up of the PACE findings in infant saliva. Results None of the cord blood birthweight-associated CpGs identified by the PACE Consortium was associated with birthweight when analysed in infant saliva. In saliva EWAS analyses, considering a false discovery rate p-values < 0.05, birthweight as continuous variable was associated with DNA methylation in 44 CpG sites; being born small for gestational age (SGA, lower 10th percentile of birthweight for gestational age according to WHO reference charts) was associated with DNA methylation in 44 CpGs, with only one overlapping CpG between the two analyses. Despite no overlap with PACE results at the CpG level, two of the top saliva birthweight CpGs mapped at genes associated with birthweight with the same direction of the effect also in the PACE Consortium (MACROD1 and RPTOR). Conclusion Our study provides an indication of the birthweight and SGA epigenetic salivary signatures in children around 10 months of age. DNA methylation signatures in cord blood may not be comparable with saliva DNA methylation signatures at about 10 months of age, suggesting that the birthweight epigenetic marks are likely time and tissue specific.

Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood

“…Birthweight has been reported to have significant associations with neonatal DNA methylation [ 7 , 14 , 15 ]. However, previous reports did not take into consideration possible effects from genetics.…”

Promising applications of human-derived saliva biomarker testing in clinical diagnostics

“… 33 Rounge et al concluded an association between the saliva methylome and body-mass index (BMI) in adolescence. 34 Moccia et al showed that DNA methylation patterns differed in cord blood and infant saliva, 35 leading to distinct birthweight signatures. Another study reported that three obesity-related outcomes were negatively associated with LEP gene methylation in obese boys only.…”

“…MALDI-TOF mass spectrometer 27 CpG sites in the promoter (MT2 region) 25 2. Infinium HumanMethylation450K array 485 000 probes 26 , 35 , 37 , 41 , 42 , 44 , 46 , 47 , 51 , 301 3. ddPCR (1) cg05575921 and DMR16( 27 , 29 , 30 2) cg14361627, cg14361627, cg08928145 and cg07547549 302 4. Illumina MethylationEPIC BeadChip 795,694 probes 33 , 54 5. methylation specific polymerase chain reaction and agarose gel electrophoresis (1) p16INK4a and p14ARF 28 (2) SOCS1 40 (3) p16, DAP- K, MGMT, and GSTP1 38 (4) ZNF282 and HPCAL1 52 6. targeted bisulfite sequencing (TBS) protocol 3.1 million CpG sites 34 7. pyrosequencing (1) LEP, ICAM-1, CRH, and LINE-1 genes 36 (2) BDNF 45 (3) NMUR2 and UBE2U 50 (4) ZC3H12D, BCAS4 and cg06379435 53 (5) FADS1 and FADS2 43 8. real-time methylation-specific polymerase chain reaction (1) P16 39 …”