Recent advances in non-invasive prenatal DNA diagnosis through analysis of maternal blood

Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility

Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.

Comparison between paramagnetic and CD71 magnetic activated cell sorting of fetal nucleated red blood cells from the maternal blood

Background

Fetal nucleated red blood cells (NRBC) from maternal circulation are rare events but can be enriched and used to evaluate the genetics of the fetus. We compared two simplified selection methods of the fetal cells from the maternal blood.

Methods

We isolated fetal cells from maternal blood through double‐density gradient centrifugation followed either by magnetic cell selection, based on the paramagnetic proprieties of the NRBC hemoglobin, converted to methemoglobin, or by a positive magnetic‐activated cell sorting (MACS) enrichment, using anti‐CD71 monoclonal antibodies. Finally, the cells were identified through fluorescence in situ hybridization (FISH) with specific chromosome X and Y probes.

Results

We processed 10 mL of peripheral blood samples from 27 pregnant women with singleton normal male fetuses. Hemoglobin‐based enrichment isolated significantly more NRBCs: 29.7 × 10⁴ cells than anti‐CD71 MACS: 10.1 × 10⁴ cells (P < .001). The FISH analysis found at least one XY cell in 81.5% and 61.5% of cases, respectively, for paramagnetic and anti‐CD71 selection. Also, the average number of XY cells identified through paramagnetic selection was 5.09 ± 2.5, significantly higher than those observed through CD71 sorting: 3.38 ± 1.7 cells (average ± SE) (P = .03).

Conclusion

The combination of density gradient centrifugation with paramagnetic selection has the advantage of simplicity and achieves a minimal manipulation and treatment of cells. It yields an increased number of NRBCs and FISH confirmed fetal cells, compared to the anti‐CD71 sorting.

Evaluation of fetal hypermethylated RASSF1A in pre-eclampsia and its relationship with placental protein-13, pregnancy associated plasma protein-A and urine protein

OBJECTIVES

Cell free fetal DNA (cffDNA) and its hypermethylated RASSF1A gene signify a recent advancement in non-invasive prenatal diagnosis of feto-placental anomalies like pre-eclampsia. The study uses hypermethylated RASSF1A gene to quantify cffDNA and to assess its relationship with placental and urine proteins in pre-eclampsia cases.

DESIGN AND METHODS

DNA was isolated from plasma samples of clinically diagnosed cases of pre-eclampsia (n=103) and normal pregnancy (n=616) from 21weeks of gestation. Through methylation sensitive enzyme (BstUI) digestion; followed by real time-polymerase chain reaction (RT-PCR), quantification of hypermethylated RASSF1A was done. Immunoassays determined: placental protein-13 (pp-13) and pregnancy associated plasma protein A (PAPP-A) and pyrogallol red molybdate assay for 24h urine protein.

RESULTS

Highly significant differences between control and pre-eclampsia cases for hypermethylated RASSF1A concentrations were found; Group I: 33±7.35 vs 74.46±16.71, Group II: 53.75±16.65 vs 244.22±35.68, Group III: 93.25±19.08 vs 412.31±80.18, Group IV: 144.30±18.13 vs 1056.89±153.78, Group V: 307.55±40.76 vs 2763.76±259.76copies/ml. Multivariate Pearson's correlation analysis of hypermethylated RASSF1A with pp-13, PAPP-A and urine proteins showed positive and very highly significant (P<0.001) associations.

CONCLUSIONS

Diagnostic potential of fetal specific, hypermethylated RASSF1A was evaluated. Its positive relationship with placental and urine proteins submit the case for considering it as a reliable marker for pre-eclampsia.

Fetal-specific hypermethylated RASSF1A quantification in pregnancy

OBJECTIVE

To quantify cell free fetal DNA (cffDNA) with fetal specific epigenetic marker, hypermethylated RASSF1A, in maternal plasma of normal pregnant women from 20 weeks of gestation and to assess its relationship with maternal age, height, pre-pregnancy weight and body mass index (BMI).

METHODS

Hundred normal pregnant women within the gestational age of 21-40 weeks were randomly selected and grouped into five (n = 20). Group 1: 21-24, Group 2: 25-28, Group 3: 29-32, Group 4: 33-36 and Group 5: 37-40 weeks. Maternal plasma DNA was extracted, digested with methylation-sensitive restriction enzyme, BstUI and the fetal specific DNA (cffDNA) was quantified by Real-time polymerase chain reaction (qRT-PCR).

RESULTS

The mean hypermethylated RASSF1A concentrations in different gestational groups were Group 1: 30.1 ± 14.9, Group 2: 52.6 ± 22.18, Group 3: 93.2 ± 19.08, Group 4: 172.8 ± 26.81 and Group 5: 337.8 ± 52.9 copies/ml. Pearson's correlation analysis showed highly significant positive correlation between cffDNA and gestational age (r = 0.899, p < 0.001). BMI was also found to be positively related to cffDNA (r = 0.217, p < 0.05). However, it did not show any correlation with maternal age, height and pre-pregnancy weight.

CONCLUSIONS

The gestational age-dependent increase of hypermethylated RASSF1A; the fetal specific epigenetic marker in maternal plasma was demonstrated, in an Indian study group of normal pregnant women. Findings would form the basis of future studies involving pregnancy complications that would aid in the early diagnosis of placental pathologies with hypermethylated RASSF1A.

Embryonic-maternal cross-talk via exosomes: potential implications

A myriad of locally produced factors into the microenvironment of the reproductive tract is regulated, not one-way but rather, through embryonic-maternal cross-talk. In this mini-review, we focused on the exosomes, which are cell-derived vesicles of 30-100 nm in diameter, as a communicating language facilitating this dialog. These nanovesicles are secreted from pre-implantation embryos, oviduct epithelium, and endometrium as well as from the placenta, and contain proteins, messenger RNA (mRNA), microRNA, and DNA cargoes, and have pleiotropic effects on both embryonic and maternal environments. A better understanding of the molecular mechanisms mediating this cross-talk will lead to the development of new regulating agents, with novel diagnostic, biological, and therapeutic potential for either supporting or hindering the normal reproductive functions.

Alteration of Delta-like ligand 1 and Notch 1 receptor in various placental disorders with special reference to early onset preeclampsia

Notch signaling pathway has been shown to be dysregulated in placentas with preeclampsia, but there has been a lack of studies on methylation of Notch family genes in this disorder. We therefore executed methylation-specific polymerase chain reaction and immunostaining for Notch 1 receptor and the activating ligand, Delta-like (DLL) 1, with placental tissues from cases of preeclampsia (early onset, n = 18; late-onset, n = 19) and other placental disorders, including maternal complications such as diabetes mellitus and collagen disease (n = 10), fetal growth restriction (n = 17), fetal anomaly (n = 23), preterm birth (n = 15), miscarriage (n = 25), and hydatidiform moles (n = 9) as well as term births (n = 12). The frequency of DLL1 methylation was higher in early onset preeclamptic placentas (61%) than the other subjects (0%-36%; P ≤ .016). Appreciable samples (36%) of miscarriage also represented DLL1 methylation. None of the samples studied showed Notch 1 methylation. On gestational period-matched analysis, the rate of DLL1 methylation was higher in early onset preeclampsia (83.3%) than preterm birth (13.3%; P < .001), with no significant differences in clinical backgrounds between the two. In this analysis, increase of syncytial knots and accelerated villous maturation were most prominent in DLL1-methylated placentas with early onset preeclampsia. Notch 1 and DLL1 expressions in villous trophoblasts and endothelial cells were significantly lower in early onset preeclamptic placentas as compared with preterm birth controls. In conclusion, altered Notch signaling via methylation of DLL1 is likely involved in possible disease-related mechanisms of early onset preeclampsia. Alternatively, DLL1 methylation in early onset preeclampsia could be a manifestation of a lack of placental maturation, similar to miscarriage.

Tay-Sachs disease: current perspectives from Australia

Tay-Sachs disease (TSD) is a fatal, recessively inherited neurodegenerative condition of infancy and early childhood. Although rare in most other populations, the carrier frequency is one in 25 in Ashkenazi Jews. Australian high-school-based TSD preconception genetic screening programs aim to screen, educate, and optimize reproductive choice for participants. These programs have demonstrated high uptake, low psychological morbidity, and have been shown to result in fewer than expected Jewish TSD-affected births over 18 years of operation. The majority of Jewish individuals of reproductive age outside of the high school screening program setting in Australia have not accessed screening. Recent recommendations advocate supplementing the community high school screening programs with general practitioner- and obstetrician-led genetic screening of Ashkenazi Jewish individuals for TSD and other severe recessive diseases for which this group is at risk. Massively parallel DNA sequencing is expected to become the testing modality of choice over the coming years.

Efficiency of manual scanning in recovering rare cellular events identified by fluorescence in situ hybridization: simulation of the detection of fetal cells in maternal blood

Fluorescence in situ hybridization (FISH) and manual scanning is a widely used strategy for retrieving rare cellular events such as fetal cells in maternal blood. In order to determine the efficiency of these techniques in detection of rare cells, slides of XX cells with predefined numbers (1–10) of XY cells were prepared. Following FISH hybridization, the slides were scanned blindly for the presence of XY cells by different observers. The average detection efficiency was 84% (125/148). Evaluation of probe hybridization in the missed events showed that 9% (2/23) were not hybridized, 17% (4/23) were poorly hybridized, while the hybridization was adequate for the remaining 74% (17/23). In conclusion, manual scanning is a relatively efficient method to recover rare cellular events, but about 16% of the events are missed; therefore, the number of fetal cells per unit volume of maternal blood has probably been underestimated when using manual scanning.

Micronuclei and their association with sperm abnormalities, infertility, pregnancy loss, pre-eclampsia and intra-uterine growth restriction in humans

The micronucleus (MN) assay is increasingly being used to study the association between DNA damage and infertility or pregnancy complications in humans. This review provides a brief overview of the studies published to date. The results of these studies appear to support the plausibility of the following hypotheses: (i) MN in spermatids in semen may be indicative of infertility risk, (ii) MN in peripheral blood lymphocytes in males correlate positively with DNA damage in sperm, (iii) infertile couples exhibit higher frequencies of MN than fertile couples and (iv) an abnormally high frequency of MN in peripheral blood lymphocytes is associated with pregnancy complications including miscarriage, intra-uterine growth restriction and pre-eclampsia. The studies published to date consistently indicate an association of MN in peripheral blood lymphocytes with impaired reproductive capacity. However, the conclusions of these studies, although statistically significant, are limited by small sample sizes and the need for verification in other independent cohorts. In conclusion, more attention should be given to the possibility of using MN assays in peripheral blood lymphocytes and reproductive tissues as a biomarker of risk for infertility and pregnancy complications in humans.

Prenatal diagnosis: update on invasive versus noninvasive fetal diagnostic testing from maternal blood

The modern obstetrics care includes noninvasive prenatal diagnosis testing such as first trimester screening performed between 11 and 14 weeks' gestation and second trimester screening performed between 15 and 20 weeks. In these screening tests, biochemical markers are measured in the maternal blood with or without ultrasound for fetal nuchal translucency with reported accuracy of up to 90%. Invasive procedures, including amniocentesis or chorionic villi sampling, are used to achieve over 99% accuracy. During these procedures direct fetal material is examined and, therefore, these tests are highly accurate with the caveat of a small risk for pregnancy loss. Much research now focuses on other noninvasive highly accurate and risk-free tests that will identify fetal material in the maternal blood. Fetal cells and fetal DNA/RNA provide fetal information but are hard to find in an overwhelming background of maternal cells and in the absence of specific fetal cell markers. The most experience has been accumulated with fetal rhesus and fetal sex determination from maternal blood, with an accuracy of up to 100% by using gene sequences that are absent from maternal blood. Although not clinically applicable yet, fetal cells, fetal DNA/RNA and fetal proteomics in combination with cutting edge technology are described to prenatally diagnose aneuploidies and single-gene disorders.