Epigenetics of cell-free plasma DNA for non-invasive prenatal diagnosis of fetal aneuploidies

Since the discovery of cell-free fetal DNA in the circulation of pregnant women fetal-specific DNA biomarkers for non-invasive prenatal diagnosis of fetal aneuploidy have been sought. A model system assessing the DNA methylation of placental DNA and adult peripheral leukocyte DNA has been developed previously to represent fetal and maternal plasma DNA. To use DNA methylation to detect specific DNA molecules it is desirable that cellfree plasma DNA maintains the methylation profile of its tissue source. Using the imprinted gene GNAS1, a test has been developed to assess, for the first time the relative abundance of methylated and unmethylated DNA circulating in plasma. Methylated and unmethylated DNA sequences were found in equal abundance. If this finding is applicable to all plasma DNA sequences, we conclude that the steadystate concentration of DNA in methylated and unmethylated form is a reliable indicator of its input into the circulation. We have also investigated whether the abundances of different single copy gene sequences in cell-free plasma DNA are equal. Using real-time PCR, the relative abundances of six unique genomic DNA sequences in plasma were assessed. We find that plasma DNA from different sequences is not present in equal abundance in normal healthy individuals. The relative abundance of sequences tested differed by as much as 12.3 fold. We present a panel of novel candidate epigenetic biomarkers which have been identified using the model system. Of 366 DNA regions tested 3% were found to be differential. Further characterisation of these candidate epigenetic biomarkers has revealed limitations of the model system. In view of these results, future epigenetic biomarker development should be achieved by a direct assessment of first trimester plasma DNA

Epigenetics of cell-free plasma DNA for non-invasive prenatal diagnosis of fetal aneuploidies

Since the discovery of cell-free fetal DNA in the circulation of pregnant women fetal-specific DNA biomarkers for non-invasive prenatal diagnosis of fetal aneuploidy have been sought. A model system assessing the DNA methylation of placental DNA and adult peripheral leukocyte DNA has been developed previously to represent fetal and maternal plasma DNA. To use DNA methylation to detect specific DNA molecules it is desirable that cellfree plasma DNA maintains the methylation profile of its tissue source. Using the imprinted gene GNAS1, a test has been developed to assess, for the first time the relative abundance of methylated and unmethylated DNA circulating in plasma. Methylated and unmethylated DNA sequences were found in equal abundance. If this finding is applicable to all plasma DNA sequences, we conclude that the steadystate concentration of DNA in methylated and unmethylated form is a reliable indicator of its input into the circulation. We have also investigated whether the abundances of different single copy gene sequences in cell-free plasma DNA are equal. Using real-time PCR, the relative abundances of six unique genomic DNA sequences in plasma were assessed. We find that plasma DNA from different sequences is not present in equal abundance in normal healthy individuals. The relative abundance of sequences tested differed by as much as 12.3 fold. We present a panel of novel candidate epigenetic biomarkers which have been identified using the model system. Of 366 DNA regions tested 3% were found to be differential. Further characterisation of these candidate epigenetic biomarkers has revealed limitations of the model system. In view of these results, future epigenetic biomarker development should be achieved by a direct assessment of first trimester plasma DNA.EThOS - Electronic Theses Online ServiceSAFE Network of Excellence (LSHB-CT-2004–503243)GBUnited Kingdo

Epigenetics of cell-free plasma DNA for non-invasive prenatal diagnosis of fetal aneuploidies

Since the discovery of cell-free fetal DNA in the circulation of pregnant women fetal-specific DNA biomarkers for non-invasive prenatal diagnosis of fetal aneuploidy have been sought. A model system assessing the DNA methylation of placental DNA and adult peripheral leukocyte DNA has been developed previously to represent fetal and maternal plasma DNA. To use DNA methylation to detect specific DNA molecules it is desirable that cellfree plasma DNA maintains the methylation profile of its tissue source. Using the imprinted gene GNAS1, a test has been developed to assess, for the first time the relative abundance of methylated and unmethylated DNA circulating in plasma. Methylated and unmethylated DNA sequences were found in equal abundance. If this finding is applicable to all plasma DNA sequences, we conclude that the steadystate concentration of DNA in methylated and unmethylated form is a reliable indicator of its input into the circulation. We have also investigated whether the abundances of different single copy gene sequences in cell-free plasma DNA are equal. Using real-time PCR, the relative abundances of six unique genomic DNA sequences in plasma were assessed. We find that plasma DNA from different sequences is not present in equal abundance in normal healthy individuals. The relative abundance of sequences tested differed by as much as 12.3 fold. We present a panel of novel candidate epigenetic biomarkers which have been identified using the model system. Of 366 DNA regions tested 3% were found to be differential. Further characterisation of these candidate epigenetic biomarkers has revealed limitations of the model system. In view of these results, future epigenetic biomarker development should be achieved by a direct assessment of first trimester plasma DNA.EThOS - Electronic Theses Online ServiceSAFE Network of Excellence (LSHB-CT-2004–503243)GBUnited Kingdo

Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart

Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human

Unequal representation of different unique genomic DNA sequences in the cell-free plasma DNA of individual donors

Objectives: To assess whether different genomic cell-free DNAs are equally abundant in the plasma of individual donors, and any relationship between DNA methylation and representation in plasma. Design and methods: The concentrations of DNA in plasma were determined by real-time PCR. Results: Different DNA sequences were not equally represented. The relative abundances were similar in different donors. Conclusions: Different DNA sequences are not equally abundant in plasma, with no relationship between DNA methylation and abundance. (C) 2008 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved

Candidate epigenetic biomarkers for non-invasive prenatal diagnosis of Down syndrome

This report describes the first identification and characterization of three chromosome-21-specific DNA sequences (and reference sequences from other chromosomes) that are differentially methylated between peripheral blood and placental tissue, with the aim of providing epigenetic biomarkers for quantifying cell-free fetal DNA in maternal plasma. To select sequences to be screened for differential methylation, three strategies were adopted: (i) investigating promoters of highly differentially expressed genes; (ii) choosing 'random' promoter regions; and (iii) choosing 'random' non-promoter regions. Over 200 pre-selected DNA sequences were screened using a methylation-specific restriction enzyme assay. Differentially methylated sequences located at 21 q22.3 (AIRE, SIM2 and ERG genes), 1q32.1 (CD48 gene and FAIM3 gene), 2p14 (ARHGAP25 gene) and 12q24 (SELPLG gene) were identified. Bisulphite conversion confirmed that CpG sites within the AIRE promoter region are highly differentially methylated, and optimized methylation-specific primers for this region that are highly specific for placental DNA were devised. Next, it was shown that the methylation status of chorionic villus sample DNA from first trimester pregnancies matched the hypermethylated state of term placenta. Thus there is no indication of a difference in methylation status between early and term pregnancy for the sequences tested. The identified sequences constitute candidate biomarkers for non-invasive prenatal diagnosis of Down syndrome