Proteomics of the amniotic fluid in assessment of the placenta. Relevance for preterm birth

Human placental proteomics and exon variant studies link AAT/SERPINA1 with spontaneous preterm birth

BACKGROUND

Preterm birth is defined as live birth before 37 completed weeks of pregnancy, and it is a major problem worldwide. The molecular mechanisms that lead to onset of spontaneous preterm birth are incompletely understood. Prediction and evaluation of the risk of preterm birth is challenging as there is a lack of accurate biomarkers. In this study, our aim was to identify placental proteins that associate with spontaneous preterm birth.

METHODS

We analyzed the proteomes from placentas to identify proteins that associate with both gestational age and spontaneous labor. Next, rare and potentially damaging gene variants of the identified protein candidates were sought for from our whole exome sequencing data. Further experiments we performed on placental samples and placenta-associated cells to explore the location and function of the spontaneous preterm labor-associated proteins in placentas.

RESULTS

Exome sequencing data revealed rare damaging variants in SERPINA1 in families with recurrent spontaneous preterm deliveries. Protein and mRNA levels of alpha-1 antitrypsin/SERPINA1 from the maternal side of the placenta were downregulated in spontaneous preterm births. Alpha-1 antitrypsin was expressed by villous trophoblasts in the placenta, and immunoelectron microscopy showed localization in decidual fibrinoid deposits in association with specific extracellular proteins. siRNA knockdown in trophoblast-derived HTR8/SVneo cells revealed that SERPINA1 had a marked effect on regulation of the actin cytoskeleton pathway, Slit-Robo signaling, and extracellular matrix organization.

CONCLUSIONS

Alpha-1 antitrypsin is a protease inhibitor. We propose that loss of the protease inhibition effects of alpha-1 antitrypsin renders structures critical to maintaining pregnancy susceptible to proteases and inflammatory activation. This may lead to spontaneous premature birth.

Lower concentrations of receptor for advanced glycation end products and epiregulin in amniotic fluid correlate to chemically induced cleft palate in mice

This study investigated the correlation between differentially expressed proteins in amniotic fluid (AF) and cleft palate induced by all-trans retinoic acid (atRA), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in mice. Seven proteins were differentially expressed at embryonic day (E) 16.5 in atRA and control groups as revealed by label-based mouse antibody array. Enzyme-linked immunosorbent assay was further used to detect the expression levels of these proteins in AF from E13.5 to E16.5 in atRA, TCDD, and control groups. The cleft palate groups showed lower concentrations of receptor for advanced glycation end products (RAGE) and epiregulin at E16.5. RAGE immunostaining obviously decreased in palatal tissue sections obtained from E14.5 to E16.5 in the cleft palate groups as revealed by immunohistochemistry. These findings indicate that reduced levels of RAGE and epiregulin in AF are correlated to chemically induced cleft palate in mice.

Use of amniotic fluid for determining pregnancies at risk of preterm birth and for studying diseases of potential environmental etiology

Amniotic fluid (AF) is a biological medium uniquely suited for the study of early exposure of the human fetus to environmental contaminants acquired by the mother before and during pregnancy. Traditional diagnostic applications of AF have focused almost exclusively on the diagnosis of genetic aberrations such as Trisomy-21 and on heritable diseases in high-risk pregnancies. Since more than 50 anthropogenic compounds have been detected in AF, there is considerable potential in utilizing fetal protein biomarkers as indicators of health effects related to prenatal toxic exposure. Here, we focus on preterm birth (PTB) to illustrate opportunities and limitations of using AF as a diagnostic matrix. Representing a pervasive public health challenge worldwide, PTB cannot be managed simply by improving hygiene and broadening access to healthcare. This is illustrated by 15-year increases of PTB in the U.S. from 1989 to 2004. AF is uniquely suited as a matrix for early detection of the association between fetal exposures and PTB due to its fetal origin and the fact that it is sampled from women who are at higher risk of PTB. This critical review shows the occurrence in AF of a number of xenobiotics, including endocrine-disrupting compounds (EDCs), which are known or may reasonably be expected to shorten fetal gestation. It is not yet known whether EDCs, including bisphenol A, phytoestrogens, and polychlorinated biphenyls (PCBs), can affect the expression of proteins considered viable or potential biomarkers for the onset of PTB. As such, the diagnostic value of AF is broad and has not yet been fully explored for prenatal diagnosis of pregnancies at risk from toxic, environmental exposures and for the elucidation of mechanisms underlying important public health challenges including PTB.

Global gene expression analysis of term amniotic fluid cell-free fetal RNA

OBJECTIVE

To identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants.

METHODS

This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid.

RESULTS

There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid.

CONCLUSIONS

Transcriptomic analysis of amniotic fluid cell-free fetal RNA detects fetal maturation processes activated in term pregnancy. These findings further develop the concept of amniotic fluid supernatant as a real-time gene expression "summary fluid" and support its potential for future studies of fetal development.

Dynamic proteome in enigmatic preeclampsia: an account of molecular mechanisms and biomarker discovery

The coevolution of genomics and proteomics has led to advancements in the field of diagnosis and molecular mechanisms of disease. Proteomics is now stepping into the field of obstetrics, where early diagnosis of pregnancy complication such as preeclampsia (PE) is imperative. PE is a multifactorial disease characterized by hypertension with proteinuria, which is a leading cause of maternal and neonatal morbidity and mortality occurring in 5-7% of pregnancies worldwide. This review discusses the probable molecular mechanisms that lead to PE and summarizes the proteomics research carried out in understanding the pathogenicity of PE, and for identifying the candidate biomarker for diagnosis of the disease.

Proteomics/diagnosis of chorioamnionitis and of relationships with the fetal exposome

Proteomics, a relatively young science, originally emerged as a complement to genomics research. By definition, the goal of proteomics is to provide a snapshot of all the proteins within an organism, tissue or biological sample at a given moment. Proteomics has the ability to single out one or more proteins (biomarkers) that change consistently in affected subjects as compared to those disease-free. From a proteomics perspective, chorioamnionitis poses both challenges and opportunities. Challenges relate to the dynamic course of the inflammatory process, and compartmentalization of the gestational sac in relation to the maternal compartment. An inability to evaluate the amniotic fluid non-invasively and repeatedly for meaningful changes in its proteome, and lack of a true gold standard for diagnosis of inflammation and/or infection, represent additional challenges. On the other hand, the unbiased and holistic nature of proteomics offers a real opportunity to improve the current diagnostic and prognostic algorithms for chorioamnionitis. Even at this current stage there are reasons to believe that proteomic biomarkers will improve the understanding of how chorioamnionitis programs or affects the fetus in utero, thus defining its exposome (sum of interactions between genetic make-up of the fetus and the intrauterine environment) of pregnancies affected by infection and/or inflammation. This review summarizes the results of proteomics studies that have aimed or reached these goals.

Using SELDI-TOF mass spectrometry on amniotic fluid and for clinical proteomics and theranostics in disorders of pregnancy

Clinical proteomics encompasses a multitude of experimental approaches, tools, and techniques based on proteomics technology which are directly aimed to accelerate and improve diagnosis and treatment of human diseases. Surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF) mass spectrometry is a variant of matrix-enhanced laser desorption ionization (MALDI) that makes use of chemically-modified surfaces to reduce the complexity of biological samples prior to separation in the mass analyzer. Compared to other proteomic techniques, SELDI has several important advantages such as ability to analyze complex biological samples with minimal pre-processing, ease of handling and high throughput. Importantly, once the biomarker or combination of biomarkers with potential clinical value has been established, validation analyses can be conducted in close proximity to clinical settings which is important for establishing the utility of new diagnostics in clinical decision making and perhaps future theranostic interventions. This chapter provides protocols for experimental design and methodology aimed at (1) discovering biologically relevant biomarkers in amniotic fluid using SELDI-TOF; (2) validating the clinical utility of the biomarkers as new diagnostics; (3) translating the biomarker findings into pathophysiological phenomena to provide further insight and extend the current understanding of the disease process. Many of the principles described herein for amniotic fluid could be generalized to studies involving other types of biological samples and other clinical questions.

Cell-free fetal nucleic acids in amniotic fluid

BACKGROUND

Research into cell-free fetal (cff) nucleic acids has primarily focused on maternal plasma; however, cff DNA and RNA are also detectable in other body fluids such as amniotic fluid (AF). In AF, cff DNA is present in much greater concentrations than in maternal plasma and represents a pure fetal sample uncontaminated by maternal- and trophoblast-derived nucleic acids. The aim of this review was to summarize the current knowledge on cff nucleic acids in AF and to outline future research directions.

METHODS

MEDLINE and PREMEDLINE were searched up to August 2010 for original investigations of cell-free RNA or DNA in AF. Sixteen studies were included in the review.

RESULTS

AF cff DNA represents a physiologically separate pool from cff DNA in maternal plasma. The placenta is not a major source of nucleic acids in AF. It is feasible to isolate cff nucleic acids from small volumes of discarded AF supernatant in sufficient quality and quantity to perform microarray studies and downstream applications such as pathway analysis. This 'discovery-driven approach' has resulted in new information on the pathogenesis of Down syndrome and polyhydramnios. There is otherwise a paucity of information relating to the basic biology and clinical applications of cff nucleic acids in AF.

CONCLUSIONS

AF supernatant is a valuable and widely available but under-utilized biological resource. Further studies of cff nucleic acids in AF may lead to new insights into human fetal development and ultimately new approaches to antenatal treatment of human disease.

The role of proteomics in the diagnosis of chorioamnionitis and early-onset neonatal sepsis

Intrauterine infection is a unique pathologic process that raises the risk for early-onset neonatal sepsis (EONS). By acting synergistically with prematurity, EONS increases the risk for adverse neonatal outcomes, including intraventricular hemorrhage and cerebral palsy. Although several pathways for the pathogenesis of fetal damage have been proposed, the basic molecular mechanisms that modulate these events remain incompletely understood. Discovery of clinically and biologically relevant biomarkers able to reveal key pathogenic pathways and predict pregnancies at risk for antenatal fetal damage is a priority. Proteomics provides a unique opportunity to fill this gap.

Geographic ancestry and markers of preterm birth

Several biomarkers associated with spontaneous preterm birth (PTB) have been discovered over the last decade. Many of these markers, such as cytokines, are associated with infection and inflammation. As such, these biomarkers represent biologically plausible candidates for assessing those at risk of PTB. However, in the early association studies of biomarker-pregnancy outcome, the geographic ancestry of subjects was not considered. Based on more recent data, it is becoming increasingly evident that these biomarkers, and a universal approach that uses a single biomarker, fail to provide adequate assessment of risk in all subjects. Rather, recent data support the conclusion that some markers associate in subjects of African descent and another nonoverlapping set associates in subjects of European descent. These data indicate that diagnostic or predictive tests will have to use different biomarkers for different sets of subjects. If this is true, it poses severe restrictions on how to predict outcome or perform tests of association, and may make it impossible to determine risk or provide proper intervention. An alternative is presented that, although not yet proven, may make it possible to use a common set of biomarkers and their relationships to assess risk.

Using proteomics in perinatal and neonatal sepsis: hopes and challenges for the future

PURPOSE OF REVIEW

Particularities of the fetal immune response to infection cause a heightened inflammatory state that acts synergistically with microbial insult to induce damage. Proteomics offers the opportunity for detecting fetuses at risk of sepsis and neurological injury.

RECENT FINDINGS

Molecular tools (16S-rRNA) demonstrate that the diversity of microbial agents of intra-amniotic infection exceeds what is suspected clinically or is documented by cultures. The resulting inflammatory process has the potential to damage the fetus in utero. Stepwise algorithms (mass restricted score) have been developed to extract proteomic profiles characteristic of amniotic fluid inflammation. The mass restricted score includes four proteomic biomarkers: defensin-2, defensin-1, S100A12, and S100A8 proteins. Other amniotic fluid biomarkers relevant for preterm birth are S100A9 and insulin-like growth factor-binding protein 1. S100A12 - ligand for the receptor of advanced glycation end products - has the strongest association with histological chorioamnionitis and funisitis. Presence of S100A12 and S100A8 in amniotic fluid is predictive of early-onset neonatal sepsis and poor neurodevelopmental outcome.

SUMMARY

Presence of amniotic fluid proteomic biomarkers of inflammation is associated with increased inflammatory status of the fetus at birth. Future challenges are to find biomarkers that provide insight into molecular mechanisms of chronic fetal and neonatal cellular damage and to identify candidates for early neuroprotection strategies.

Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia

OBJECTIVE

The cause of preeclampsia remains unknown and the diagnosis can be uncertain. We used proteomic-based analysis of urine to improve disease classification and extend the pathophysiologic understanding of preeclampsia.

STUDY DESIGN

Urine samples from 284 women were analyzed by surface-enhanced laser desorption/ionization. In the exploratory phase, 59 samples were used to extract the proteomic fingerprint characteristic of severe preeclampsia requiring mandated delivery and to develop a diagnostic algorithm. In the challenge phase, we sought to prospectively validate the algorithm in 225 women screened for a variety of high- and low-risk conditions, including preeclampsia. Of these, 19 women were followed longitudinally throughout pregnancy. The presence of biomarkers was interpreted relative to clinical classification, need for delivery, and other urine laboratory measures (ratios of protein to creatinine and soluble fms-like tyrosine kinase-1 to placental growth factor). In the translational phase, biomarker identification by tandem mass spectrometry and validation experiments in urine, serum, and placenta were used to identify, quantify, and localize the biomarkers or related proteins.

RESULTS

We report that women with preeclampsia appear to present a unique urine proteomic fingerprint that predicts preeclampsia in need of mandated delivery with highest accuracy. This characteristic proteomic profile also has the ability to distinguish preeclampsia from other hypertensive or proteinuric disorders in pregnancy. Pregnant women followed longitudinally who developed preeclampsia displayed abnormal urinary profiles more than 10 weeks before clinical manifestation. Tandem mass spectrometry and de novo sequencing identified the biomarkers as nonrandom cleavage products of SERPINA1 and albumin. Of these, the 21 amino acid C-terminus fragment of SERPINA1 was highly associated with severe forms of preeclampsia requiring early delivery. In preeclampsia, increased and aberrant SERPINA1 immunoreactivity was found in urine, serum, and placenta, in which it localized predominantly to placental villi and placental vascular spaces adherent to the endothelium. In addition, significant perivascular deposits of misfolded SERPINA1 aggregates were exclusively identified in preeclamptic placentae.

CONCLUSION

Proteomics-based characterization of urine in preeclampsia identified a proteomic fingerprint composed of SERPINA1 and albumin fragments, which can accurately diagnose preeclampsia and shows promise to discriminate it from other hypertensive proteinuric diseases. These findings provide insight into a novel pathophysiological mechanism of preeclampsia related to SERPINA1 misfolding, which may offer new therapeutic opportunities in the future.