Cell-Free Foetal DNA as a Useful Marker for Preeclampsia Prediction

Unique motif Sequences for early diagnosis of preeclampsia

Preeclampsia (PE) is a disease that significantly impacts both maternal and infant health with its prevalence varying across different ethnicities. Current diagnostic methods for PE typically identify the condition after 20 weeks of gestation, often when the disease has already manifested and reached an advanced stage. The situation underscores the urgent need for early biomarkers capable of effective screening and diagnosis. Our review addresses this challenge by utilizing bioinformatics approaches as an alternative method prior to preclinical and clinical studies. Specifically, we focus on FRAGmentomics-based Methylation Analysis (FRAGMA), targeting the CGCGCGG sequence motif for methylation studies in cell-free DNA (cfDNA). Since cfDNA is largely derived from the placenta, the FRAGMA approach is particularly promising, given that the primary pathophysiology of PE originates in the placenta, and methylation patterns are unique to specific tissues. In the previous research, we identified 66 genes containing this sequence motif that are implicated in the pathophysiology of PE, and only six genes - FN1, ITGA2, ITGA5, ITGB1, ITGB3, and VWF - show potential as early detection biomarkers for PE. These genes still require further investigation to confirm their utility as biomarkers for PE in the future studies.

The role of sex differences in cardiovascular, metabolic, and immune functions in health and disease: a review for "Sex Differences in Health Awareness Day"

Sexual dimorphism is a fundamental characteristic of the anatomy and physiology of animals and humans, yet biomedical research has largely ignored these phenomena in the study of health and disease, despite early studies in the eighteenth and nineteenth centuries that demonstrated the importance of sex differences. With the explosive growth of biomedical research following World War II, especially in the 1970s through the 1990s, preclinical and clinical studies led to a greater recognition of sex differences in physiological function, particularly the significant disparities in the incidence of and mortality from cardiovascular diseases, which generally occur more frequently in men than in premenopausal women. There is a growing awareness that metabolic and immune dysfunction are intimately tied to the development of cardiovascular diseases. Thus, this review article focuses on sexual dimorphism in cardiovascular, metabolic, and immune function in health and disease, and was prepared for the journal Biology of Sex Differences as part of its recognition of "Sex Differences in Health Awareness Day." This article clearly reveals the striking importance of sex differences in cardiovascular, metabolic, and immune system functions in health and in the pathogenesis of disease processes, which likely involve a combination of effects of the sex chromosomes as well as the gonadal steroid hormones. In the developing fetus, fetal sex clearly influences the pathogenesis of the hypertensive diseases of pregnancy, and sex differences in the effects of the fetus continue beyond pregnancy and appear to influence the future risk of maternal cardiometabolic diseases. Similarly, there is strong evidence of many clinically-relevant sexually dimorphic characteristics of obesity and type 2 diabetes mellitus which appear to involve both chromosomal and humoral effects, although the underlying pathophysiological mechanisms are poorly understood. The gonadal steroid hormones (both androgens and estrogens) are known to exert important effects on the regulation of intermediary metabolism; however, recent studies reveal the emerging importance of these hormones in the regulation of inflammation. For example, menopausal declines in estrogen are associated with increases in inflammatory markers and the development of heart failure in women. Similar effects on inflammatory function may also occur in men with progressive age-dependent declines in testosterone. Declines in androgen levels in men are also associated with detrimental effects on cardiovascular and metabolic function, especially the development of metabolic syndrome and type 2 diabetes, important risk factors for cardiovascular disease. Interestingly, pathophysiological increases in the normally lower testosterone levels in women are associated with the same detrimental effects on cardiovascular and metabolic function, revealing striking bi-directional sex differences in the effects of the androgens. Finally, it is increasingly apparent that the kidney plays an important role in the regulation of sex steroid hormone levels, and the declines in both estrogen and testosterone that occur with chronic kidney disease appear to play an important role in the linkage between chronic kidney disease and the development of cardiovascular disease. In conclusion. It is clear that sex differences in cardiovascular, metabolic, and immune function play important roles in health and in the pathogenesis of disease. Elucidation of the chromosomal and humoral mechanisms underlying sexual dimorphism in physiological functions will play important roles in the future development of age- and sex-specific prevention and pharmacotherapy of disease processes.

Maternal cell-free DNA in early pregnancy for preeclampsia screening: a systematic review

PURPOSE

To quantify the separation between maternal blood cell-free (cf)DNA markers in preeclampsia and unaffected pregnancies and compare with existing markers. This approach has not been used in previous studies.

METHODS

Comprehensive systematic literature search of PubMed to identify studies measuring total cfDNA, fetal cf(f)DNA or the fetal fraction (FF) in pregnant women. Included-studies of asymptomatic pregnancies with subsequent preeclampsia (cases) and unaffected pregnancies (controls) tested in the first or second trimester and before the clinical onset of preeclampsia. Excluded-studies not reporting the median or mean, standard deviation, inter-quartile range or range in cases and controls. Information from 26 eligible studies was entered into a meta-analysis to estimate, for each marker, the Mahalanobis distance, a measure of separation between the overlapping distributions in preeclampsia and unaffected pregnancies. This was compared with estimates for mean arterial pressure (MAP), uterine artery Doppler pulsatility index (UtA-PI), pregnancy associated plasma protein (PAPP)-A and placental growth factor (PlGF).

RESULTS

The mean Mahalanobis distance for total cfDNA was 0.44 (95% CI 0.12-0.76), which fell between UtA-PI (0.53) and the absolute value of PAPP-A (- 0.36). For cffDNA the distance was 1.03 (0.37-1.69), which is superior to MAP (0.74), UtA-PI, PlGF (- 0.57) and PAPP-A. The distance for FF was - 0.34 (- 0.56 to - 0.12), similar to PAPP-A.

CONCLUSION

All three markers have a potential preeclampsia screening role, particularly cffDNA. However, to estimate the screening performance in combination with existing markers further large studies are needed. The current analysis will help in the power calculation for such studies.

Trophoblast proliferation is higher in female than in male preeclamptic placentas

INTRODUCTION

Preeclampsia (PE) is a pregnancy-specific hypertensive disorder with inflammatory complications. There are no known placental histopathological features, which are unique to PE. It is often pooled with the fetal growth restriction (FGR) under a single umbrella pathophysiology, the maternal vascular malperfusion (MVM). The aim of this study is to assess the villous trophoblast and the villous tree quantitatively in PE placentas and to identify morpholgical correlates unique to PE.

METHODS

20 PE placentas (10 female and 10 male) and 20 Control placentas (10 female and 10 male) were included in the study. The villous trophoblast and the villous tree were assessed quantitatively by Stereology and 3D Microscopy. For Stereology measurements, the villous tree was classified in contractile and non-contractile parts based on immunohistochemical detection of perivascular myofibroblasts.

RESULTS

The density of proliferative trophoblast nuclei is increased, whereas the density of non-proliferative trophoblast nuclei is decreased in female PE placentas. The male PE placentas do not show this effect. Though no significant difference in the diffusion distance was observed, the non-contractile villi and the fetal vessels inside show a significantly reduced volume in PE placentas. The branching index of the villous tree is lower in PE placentas in general. However, in female PE placentas the deviation is accentuated.

CONCLUSION

In PE, the villous trophoblast shows a sexually dimorphic alteration in the density of proliferative and non-proliferative nuclei, which is inherently different from FGR.

Plasma cell-free DNA as a monitoring tool for high-risk pregnancies associated with antiphospholipid syndrome

INTRODUCTION

Despite thromboprophylaxis, women with antiphospholipid syndrome (APS) face high-risk pregnancies due to proinflammatory and prothrombotic states. This highlights the need for new monitoring and prognostic tools. Recent insights into the pathophysiological role of neutrophil activation and extracellular trap (NET) formation in this syndrome led to the exploration of plasma cell-free DNA (cfDNA), a derivative of NETosis, as a promising biomarker.

MATERIALS AND METHODS

cfDNA was isolated and quantified from plasma samples of healthy pregnant women (control group, HC) and women with APS (APS group). We assessed the physiological variability of cfDNA across the three trimesters in HC. Levels of cfDNA were compared between APS and HC by gestational trimester. ROC curve analysis was performed to evaluate the efficacy of cfDNA levels for classifying APS patients. Furthermore, cfDNA levels in pregnant women with APS with obstetric complications were compared to those from uncomplicated pregnancies.

RESULTS

Among HC, cfDNA significantly increased in the third trimester compared to the first and second. Elevated cfDNA levels in APS compared to HC were observed in the first and second trimesters. First-trimester cfDNA levels demonstrated the highest classification ability to discriminate between APS and HC patients (AUC: 0.906). Among APS, those with complicated pregnancies (fetal growth restriction, preeclampsia, placenta accreta) exhibited significantly elevated cfDNA levels in the second trimester.

CONCLUSIONS

Elevated levels of cfDNA in pregnant women with APS, particularly among those with obstetric complications, supports further investigation into the potential of cfDNA as a valuable tool in the obstetric management of women with APS.

The signature of cancer methylation markers in maternal plasma: Factors influencing the development and application of cancer liquid biopsy assay

BACKGROUND

DNA methylation is highly correlated with cancer and embryo development, and plasma-based methylation markers have been widely used for cancer early detection. However, whether the commonly used cancer methylation markers cause "false positives" in the plasma of pregnant women has not been comprehensively evaluated.

METHODS

We conducted a case-control study from February 2021 to March 2023, which included 138 pregnant women and 44 control women. Plasma cell-free DNA (cfDNA) was isolated and bisulfite-converted, and then the methylation levels of eight methylated markers related to gastrointestinal cancer (SEPT9, SDC2, C9orf50, KCNQ5, CLIP4, TFPI2, ELMO1 and ZNF582) and three markers related to lung cancer (SHOX2, RASSF1A and PTGER4) were analyzed.

RESULTS

When comparing the plasma of pregnant women to that of control women, SEPT9, CLIP4, ZNF582, SHOX2, RASSF1A and PTGER showed significantly higher levels of methylation (p < 0.05). These positive signals originate from the placenta/fetus rather than the mother. We found no discernible difference in DNA methylation levels between fetal cfDNA fractions of < 10 % and ≥ 10 % in pregnant women (p > 0.05), while CLIP4 and PTGER4 showed high methylation levels in the assisted fertilization group compared to the natural fertilization group (p < 0.05).

CONCLUSION

Our study shows that cancer and fetus/placenta exhibit similar DNA methylation patterns, and some gastrointestinal cancer and lung cancer-related methylation markers also show positives in maternal plasma. This is an important consideration in the design and application of plasma-based cancer liquid biopsy assays.

A Reliable Method for Quantifying Plasma Cell-Free DNA Using an Internal Standard Strategy: Evaluation in a Cohort of Non-Pregnant and Pregnant Women

The use of plasma cell-free DNA (cfDNA) as a useful biomarker in obstetric clinical practice has been delayed due to the lack of reliable quantification protocols. We developed a protocol to quantify plasma cfDNA using an internal standard strategy to overcome difficulties posed by low levels and high fragmentation of cfDNA. cfDNA was isolated from plasma samples of non-pregnant (NP, n = 26) and pregnant (P, n = 26) women using a commercial kit and several elution volumes were evaluated. qPCR parameters were optimized for cfDNA quantification, and several quantities of a recombinant standard were evaluated as internal standard. Absolute quantification was performed using a standard curve and the quality of the complete method was evaluated. cfDNA was eluted in a 50-μl volume, actin-β (ACTB) was selected as the target gene, and qPCR parameters were optimized. The ACTB standard was constructed and 1000 copies were selected as internal standard. The standard curve showed R2 = 0.993 and E = 109.7%, and the linear dynamic range was defined between 102 and 106 ACTB copies/tube. Repeatability and reproducibility in terms of CV were 19% and up to 49.5% for ACTB copies per milliliter of plasma, respectively. The range of cfDNA levels was 428-18,851 copies/mL in NP women and 4031-2,019,363 copies/mL in P women, showing significant differences between the groups. We recommend the application of internal standard strategy for a reliable plasma cfDNA quantification. This methodology holds great potential for a future application in the obstetric field.

Deciphering the immunological interactions: targeting preeclampsia with Hydroxychloroquine's biological mechanisms

Preeclampsia (PE) is a complex pregnancy-related disorder characterized by hypertension, followed by organ dysfunction and uteroplacental abnormalities. It remains a major cause of maternal and neonatal morbidity and mortality worldwide. Although the pathophysiology of PE has not been fully elucidated, a two-stage model has been proposed. In this model, a poorly perfused placenta releases various factors into the maternal circulation during the first stage, including pro-inflammatory cytokines, anti-angiogenic factors, and damage-associated molecular patterns into the maternal circulation. In the second stage, these factors lead to a systemic vascular dysfunction with consecutive clinical maternal and/or fetal manifestations. Despite advances in feto-maternal management, effective prophylactic and therapeutic options for PE are still lacking. Since termination of pregnancy is the only curative therapy, regardless of gestational age, new treatment/prophylactic options are urgently needed. Hydroxychloroquine (HCQ) is mainly used to treat malaria as well as certain autoimmune conditions such as systemic lupus and rheumatoid arthritis. The exact mechanism of action of HCQ is not fully understood, but several mechanisms of action have been proposed based on its pharmacological properties. Interestingly, many of them might counteract the proposed processes involved in the development of PE. Therefore, based on a literature review, we aimed to investigate the interrelated biological processes of HCQ and PE and to identify potential molecular targets in these processes.

Cell-free fetal DNA impairs trophoblast migration in a TLR9-dependent manner and can be reversed by hydroxychloroquine

Growing evidence suggests a relationship between elevated circulating placental-derived cell-free fetal DNA (cffDNA) and preeclampsia. Hypomethylation of CpG motifs, a hallmark of cffDNA, allows it to activate Toll-like receptor 9 (TLR9). Using an in vitro human first trimester extravillous trophoblast cell model, we sought to determine if trophoblast-derived cffDNA and ODN 2216, a synthetic unmethylated CpG oligodeoxynucleotide, directly impacted spontaneous trophoblast migration. The role of the DNA sensors TLR9, AIM2, and cGAS was assessed using the inhibitor A151. To test whether any effects could be reversed by therapeutic agents, trophoblasts were treated with or without cffDNA or ODN 2216 with or without aspirin (ASA; a known cGAS inhibitor), aspirin-triggered lipoxin (ATL), or hydroxychloroquine (HCQ; a known TLR9 inhibitor). Trophoblast-derived cffDNA and ODN 2216 reduced trophoblast migration without affecting cell viability. Reduced trophoblast migration in response to cffDNA or ODN 2216 was reversed by A151. cffDNA inhibition of trophoblast migration was reversed by HCQ, while ASA or ATL had no effect. In contrast ODN 2216 inhibition of trophoblast migration was reversed by ASA, ATL and HCQ. Our findings suggest that cffDNA can exert a local effect on placental function by impairing trophoblast migration through activation of innate immune DNA sensors. HCQ, a known TLR9 inhibitor, reversed the effects of cffDNA on trophoblast migration. Greater insights into the molecular underpinnings of how cffDNA impacts placentation can aid in our understanding of the pathogenesis of preeclampsia, and in the development of novel therapeutic approaches for preeclampsia therapy.

Toward a new taxonomy of obstetrical disease: improved performance of maternal blood biomarkers for the great obstetrical syndromes when classified according to placental pathology

BACKGROUND

The major challenge for obstetrics is the prediction and prevention of the great obstetrical syndromes. We propose that defining obstetrical diseases by the combination of clinical presentation and disease mechanisms as inferred by placental pathology will aid in the discovery of biomarkers and add specificity to those already known.

OBJECTIVE

To describe the longitudinal profile of placental growth factor (PlGF), soluble fms-like tyrosine kinase-1 (sFlt-1), and the PlGF/sFlt-1 ratio throughout gestation, and to determine whether the association between abnormal biomarker profiles and obstetrical syndromes is strengthened by information derived from placental examination, eg, the presence or absence of placental lesions of maternal vascular malperfusion.

STUDY DESIGN

This retrospective case cohort study was based on a parent cohort of 4006 pregnant women enrolled prospectively. The case cohort of 1499 pregnant women included 1000 randomly selected patients from the parent cohort and all additional patients with obstetrical syndromes from the parent cohort. Pregnant women were classified into six groups: 1) term delivery without pregnancy complications (n=540; control); 2) preterm labor and delivery (n=203); 3) preterm premature rupture of the membranes (n=112); 4) preeclampsia (n=230); 5) small-for-gestational-age neonate (n=334); and 6) other pregnancy complications (n=182). Maternal plasma concentrations of PlGF and sFlt-1 were determined by enzyme-linked immunosorbent assays in 7560 longitudinal samples. Placental pathologists, masked to clinical outcomes, diagnosed the presence or absence of placental lesions of maternal vascular malperfusion. Comparisons between mean biomarker concentrations in cases and controls were performed by utilizing longitudinal generalized additive models. Comparisons were made between controls and each obstetrical syndrome with and without subclassifying cases according to the presence or absence of placental lesions of maternal vascular malperfusion.

RESULTS

1) When obstetrical syndromes are classified based on the presence or absence of placental lesions of maternal vascular malperfusion, significant differences in the mean plasma concentrations of PlGF, sFlt-1, and the PlGF/sFlt-1 ratio between cases and controls emerge earlier in gestation; 2) the strength of association between an abnormal PlGF/sFlt-1 ratio and the occurrence of obstetrical syndromes increases when placental lesions of maternal vascular malperfusion are present (adjusted odds ratio [aOR], 13.6 vs 6.7 for preeclampsia; aOR, 8.1 vs 4.4 for small-for-gestational-age neonates; aOR, 5.5 vs 2.1 for preterm premature rupture of the membranes; and aOR, 3.3 vs 2.1 for preterm labor (all P<0.05); and 3) the PlGF/sFlt-1 ratio at 28 to 32 weeks of gestation is abnormal in patients who subsequently delivered due to preterm labor with intact membranes and in those with preterm premature rupture of the membranes if both groups have placental lesions of maternal vascular malperfusion. Such association is not significant in patients with these obstetrical syndromes who do not have placental lesions.

CONCLUSION

Classification of obstetrical syndromes according to the presence or absence of placental lesions of maternal vascular malperfusion allows biomarkers to be informative earlier in gestation and enhances the strength of association between biomarkers and clinical outcomes. We propose that a new taxonomy of obstetrical disorders informed by placental pathology will facilitate the discovery and implementation of biomarkers as well as the prediction and prevention of such disorders.

Diagnostic biomolecules and combination therapy for pre-eclampsia

Pre-eclampsia (PE), associated with placental malperfusion, is the primary reason for maternal and perinatal mortality and morbidity that can cause vascular endothelial injury and multi-organ injury. Despite considerable research efforts, no pharmaceutical has been shown to stop disease progression. If women precisely diagnosed with PE can achieve treatment at early gestation, the maternal and fetal outcomes can be maximally optimized by expectant management. Current diagnostic approaches applying maternal characteristics or biophysical markers, including blood test, urine analysis and biophysical profile, possess limitations in the precise diagnosis of PE. Biochemical factor research associated with PE development has generated ambitious diagnostic targets based on PE pathogenesis and dissecting molecular phenotypes. This review focuses on current developments in biochemical prediction of PE and the corresponding interventions to ameliorate disease progression, aiming to provide references for clinical diagnoses and treatments.

Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

Noninvasive sampling of an individual's body fluids is an easy means to capture circulating cell-free DNA (cfDNA). These small fragments of DNA carry information on the contributing cell's genome, epigenome, and nuclease content. Analysis of cfDNA for the assessment of genetic risk has already revolutionized clinical practice, and a compendium of increasingly higher-resolution approaches based on epigenetic and fragmentomic cfDNA signatures continues to expand. Profiling cfDNA has unlocked a wealth of molecular information that can be translated to the clinic. This review covers the biological characteristics of cfDNA, recent advances in liquid biopsy and the clinical utility of cfDNA.

Cell-free fetal DNA coming in all sizes and shapes

Cell‐free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non‐invasively from maternal blood. Through the years, evidence has accumulated to show that cell‐free fetal DNA molecules are derived from placental tissues, are mainly of short DNA fragments and have rapid post‐delivery clearance profiles. But questions regarding how they come to being short molecules from placental cells and in which physical forms do they exist remained largely unanswered until recently. We now know that the distributions of ending sites of cell‐free DNA molecules are non‐random across the genome and bear correlations with the chromatin structures of cells from which they have originated. Such an insight offers ways to deduce the tissue‐of‐origin of these molecules. Besides, the physical nature and sequence characteristics of the ends of each cell‐free DNA molecule provide tell‐tale signs of how the DNA fragmentation processes are orchestrated by nuclease enzymes. These realizations offered opportunities to develop methods for enriching cell‐free fetal DNA to facilitate non‐invasive prenatal diagnostics. Here we aimed to collate what is known about the biological and physical characteristics of cell‐free fetal DNA into one article and explain the implications of these observations.

What’s already known about this topic?

Cell‐free fetal DNA originates from placental tissues and circulates in maternal plasma as a minor population in the form of short fragments which disappears from maternal circulation rapidly after delivery.

What does this study add?

Cell‐free DNA studies at the per molecule per nucleotide level documented the detailed genomic distributions, fragment end characteristics and physical forms of cell‐free DNA unveiling the fine feature differences between maternal and fetal DNA as well as their intricate relationships with the chromatin structure of the cells‐of‐origin. These studies have substantially bridged the knowledge gaps in the biology of cell‐free fetal DNA and may provide insights on how to enhance prenatal tests based on their analyses.