Hypermethylated ERG as a cell-free fetal DNA biomarker for non-invasive prenatal testing of Down syndrome

Precision of Fetal DNA Fraction Estimation by Quantitative Polymerase Chain Reaction Quantification of a Differently Methylated Target in Noninvasive Prenatal Testing

BACKGROUND

The performance of noninvasive prenatal testing (NIPT) assays is critically determined by the proportion of fetal DNA or fetal fraction (FF). Fetomaternal differential methylation of certain genomic regions has been proposed as a universal marker of fetal origin, and previous reports have suggested the use of methylation-sensitive restriction enzyme (MSRE) assays to estimate FF.

METHODS

We analyzed the performance of FF estimation using an MSRE assay with duplex quantitative polymerase chain reaction (qPCR). Mixtures of genomic DNA from placental cells and from adult women were digested with 2 MSRE and FF estimates obtained, for a total of 221 pairwise treatment/control comparisons.

RESULTS

The coefficient of variance (CV) of the MSRE assays was high, ranging from 24% to 60%. An alternative in silico FF estimation algorithm, SeqFF, displayed slightly lower variability, with a CV of 22%.

CONCLUSION

These results cast doubts on the usefulness of the MSRE-based assay of differentially methylated markers for FF estimation. The lack of a universal method capable of precisely estimating FF remains an incompletely solved issue.

The Length and Distribution of Plasma Cell-Free DNA Fragments in Stroke Patients

A number of studies have shown that plasma cell-free DNA is closely related to the risk of stroke, but the fragmentation status of plasma cell-free DNA and its clinical application value in ischemic stroke are still unclear. In this study, 48 patients with new ischemic stroke and 20 healthy subjects were enrolled. The second-generation high-throughput sequencing technique was used to study the plasma cell-free fragment length and regional distribution of the subjects. As noted in our results, the ratio of plasma cell-free DNA fragments in the disease group was significantly greater than that of the healthy group in the 300–400 bp range; conversely for fragments at the 75–250 bp range, the ratio of plasma cell-free DNA fragments in the patient group was apparently lower than that of the healthy group. In-depth analysis of the proportion of fragments distributed on each component of the genome was carried out. Our results recorded that the plasma cell-free DNA fragments in the disease group were inclined to the EXON, CpG islands, and ALU regions in contrast to that of the healthy group. In particular, fragments within the 300–400 bp range of the disease group were enrichment in the regions of EXON, INTRON, INTERGENIC, LINE, Fragile, ALU, and CpG islands. In summary, our findings suggested that the intracellular DNA degradation profiles could be applied to distinguish the stroke group and the healthy group, which provided a theoretical basis for the clinical diagnosis and prognosis of stroke by profiling the characteristic of plasma cell-free DNA fragments.

DNA Methylation as a Future Therapeutic and Diagnostic Target in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a long-term autoimmune disease of unknown etiology that leads to progressive joint destruction and ultimately to disability. RA affects as much as 1% of the population worldwide. To date, RA is not a curable disease, and the mechanisms responsible for RA development have not yet been well understood. The development of more effective treatments and improvements in the early diagnosis of RA is direly needed to increase patients' functional capacity and their quality of life. As opposed to genetic mutation, epigenetic changes, such as DNA methylation, are reversible, making them good therapeutic candidates, modulating the immune response or aggressive synovial fibroblasts (FLS-fibroblast-like synoviocytes) activity when it is necessary. It has been suggested that DNA methylation might contribute to RA development, however, with insufficient and conflicting results. Besides, recent studies have shown that circulating cell-free methylated DNA (ccfDNA) in blood offers a very convenient, non-invasive, and repeatable "liquid biopsy", thus providing a reliable template for assessing molecular markers of various diseases, including RA. Thus, epigenetic therapies controlling autoimmunity and systemic inflammation may find wider implications for the diagnosis and management of RA. In this review, we highlight current challenges associated with the treatment of RA and other autoimmune diseases and discuss how targeting DNA methylation may improve diagnostic, prognostic, and therapeutic approaches.

Noninvasive Prenatal Diagnosis Significance of ERG Methylation as a Biomarker in Down's Syndrome

Background

Down’s syndrome (DS) is a genetic disease with chromosome abnormality due to the increasing chromosome 21. This study focused on the clinical application value of ERG methylation level in blood of pregnant women as a biomarker in Down’s syndrome.

Material/Methods

The sham group consisted of 210 nonpregnant women, the positive control group consisted of 33 women with a delivery history of DS fetus, and the negative control group consisted of 60 women with eutocia history. A combination of restriction enzyme digestion experiment and PCR was performed to examine ERG methylation levels, methylation sites, and distribution in blood of pregnant women and in chorion tissues from abortion samples. Gene sequencing was performed to determine the ERG sequence in chromosome 21. Homology between normal tissues and chorion tissues from abortion samples was analyzed with bioinformatics technology.

Results

ERG methylation in chorion tissues from 210 abortion samples at 8, 9, and 10 weeks gestational age were determined; however, no ERG methylation was determined in blood of pregnant women. Gene sequencing indicated that normal ERG sequence in chromosome 21 was in fetus chorion tissues, and these ERG sequences were aberrantly methylated. Bioinformatics result showed that homology and DNA methylation level was discrepancy in normal tissues and chorion tissues from abortion samples.

Conclusions

It was worthwhile to use ERG methylation as biomarker in noninvasive prenatal diagnosis, and ERG methylation should be applied with consent of pregnancy and her relatives.