Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn.

BACKGROUND: Analysis of lymphocyte cell lines revealed substantial differences in the expression of mRNA and microRNA (miRNA) among human populations. The extent of such population-associated differences in actual human tissues remains largely unexplored. The placenta is one of the few solid human tissues that can be collected in substantial numbers in a controlled manner, enabling quantitative analysis of transient biomolecules such as RNA transcripts. Here, we analyzed microRNA (miRNA) expression in human placental samples derived from 36 individuals representing four genetically distinct human populations: African Americans, European Americans, South Asians, and East Asians. All samples were collected at the same hospital following a unified protocol, thus minimizing potential biases that might influence the results. RESULTS: Sequence analysis of the miRNA fraction yielded 938 annotated and 70 novel miRNA transcripts expressed in the placenta. Of them, 82 (9%) of annotated and 11 (16%) of novel miRNAs displayed quantitative expression differences among populations, generally reflecting reported genetic and mRNA-expression-based distances. Several co-expressed miRNA clusters stood out from the rest of the population-associated differences in terms of miRNA evolutionary age, tissue-specificity, and disease-association characteristics. Among three non-environmental influenced demographic parameters, the second largest contributor to miRNA expression variation after population was the sex of the newborn, with 32 miRNAs (3% of detected) exhibiting significant expression differences depending on whether the newborn was male or female. Male-associated miRNAs were evolutionarily younger and correlated inversely with the expression of target mRNA involved in neuron-related functions. In contrast, both male and female-associated miRNAs appeared to mediate different types of hormonal responses. Demographic factors further affected reported imprinted expression of 66 placental miRNAs: the imprinting strength correlated with the mother's weight, but not height. CONCLUSIONS: Our results showed that among 12 assessed demographic variables, population affiliation and fetal sex had a substantial influence on miRNA expression variation among human placental samples. The effect of newborn-sex-associated miRNA differences further led to expression inhibition of the target genes clustering in specific functional pathways. By contrast, population-driven miRNA differences might mainly represent neutral changes with minimal functional impacts.

Clinical experience of noninvasive prenatal testing with cell-free DNA for fetal trisomies 21, 18, and 13, in a general screening population.

OBJECTIVE: Evaluate noninvasive prenatal testing (NIPT) with cell-free DNA as a screening method for trisomies 21, 18, and 13 in an obstetrical clinical practice setting. METHODS: Observational study of pregnant women who underwent prenatal screening for fetal trisomy from 30 July 2012 to 1 December 2012. NIPT was offered to all patients in addition to first trimester combined screening (FTS). RESULTS: The cohort included 289 women with mean age of 32.3 years (range: 17.8-42.0) who underwent testing at 13.0 gestational age weeks (range: 10.1-20.7). NIPT results were provided for 98.6% of patients at a mean reporting time of 9.3 calendar days. With NIPT, all patients had a risk less than 1:10 000 for trisomy 21, 18, or 13. With FTS, 4.5% of patients had screening results indicating an increased risk for trisomy 21. One patient who had an elevated trisomy 21 risk with FTS elected to have an amniocentesis, which revealed a euploid fetus. CONCLUSIONS: NIPT has the potential to be a highly effective screening method as a standard test for risk assessment of fetal trisomies 21, 18, and 13 in general pregnant populations.

Non-invasive prenatal testing with cell-free DNA: US physician attitudes toward implementation in clinical practice.

OBJECTIVE: The aim of this study was to assess awareness, potential adoption, and current utilization of non-invasive prenatal testing (NIPT) analysis for common fetal aneuploidies among obstetricians. METHODS: A 36-item web-based survey was designed to assess the current practice of fetal aneuploidy screening and knowledge and utilization of NIPT for fetal trisomy. Practicing obstetricians in the United States were invited via email to participate in the survey. RESULTS: Of the 101 obstetricians that completed the survey (27% academic-based, 73% private practice), 97% offer screening to high-risk patients and 91% offer screening to average-risk patients. With regard to current screening tests, the top three advantages were as follows: recommendation by professional societies, no risk to the pregnancy, and long history/experience with the test, whereas the top three limitations were as follows: patient anxiety, risks of follow-up invasive testing, and high false positives. NIPT had been used by 32% of respondents and 22% were familiar with NIPT and the associated clinical data. The majority of physicians predicted that they would offer NIPT to high-risk women (86.1%) and average-risk women (76.2%) within 12 months. CONCLUSION: Obstetricians plan to increase their utilization of NIPT and expect that the majority of both high-risk and average-risk patients will be offered NIPT as an option.

Prenatal screening for fetal aneuploidies with cell-free DNA in the general pregnancy population: a cost-effectiveness analysis.

OBJECTIVE: To estimate the cost-effectiveness of fetal aneuploidy screening in the general pregnancy population using non-invasive prenatal testing (NIPT) as compared to first trimester combined screening (FTS) with serum markers and NT ultrasound. METHODS: Using a decision-analytic model, we estimated the number of fetal T21, T18, and T13 cases identified prenatally, the number of invasive procedures performed, corresponding normal fetus losses, and costs of screening using FTS or NIPT with cell-free DNA (cfDNA). Modeling was based on a 4 million pregnant women cohort, which represents annual births in the U.S. RESULTS: For the general pregnancy population, NIPT identified 15% more trisomy cases, reduced invasive procedures by 88%, and reduced iatrogenic fetal loss by 94% as compared to FTS. The cost per trisomy case identified with FTS was $497,909. At a NIPT unit, cost of $453 and below, there were cost savings as compared to FTS. Accounting for additional trisomy cases identified by NIPT, a NIPT unit cost of $665 provided the same per trisomy cost as that of FTS. CONCLUSIONS: NIPT in the general pregnancy population leads to more prenatal identification of fetal trisomy cases as compared to FTS and is more economical at a NIPT unit cost of $453.

Evaluating intra- and inter-individual variation in the human placental transcriptome.

BACKGROUND: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. RESULTS: We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection. CONCLUSIONS: We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

NMR and X-ray crystallographic studies of the conformation of a 3,4,6-triphenyl-delta-lactone.

1-Oxa-3S,4S,6R-triphenyl-2-cyclohexanone and its enantiomer were synthesized, and the structure was determined by NMR and X-ray crystallography. The X-ray crystal structure showed that the delta-lactone adopts a boat conformation in the solid. The X-ray data showed a shortened C-O bond between the carbonyl carbon and the ether oxygen, consistent with delocalization involving the ester group. (1)H and (13)C NMR measurements in acetone-d(6) showed that the lactone is biased in favor of a boat conformation. In the less polar solvent chloroform-d(1), changes in the (1)H NMR coupling constants indicate a shift in the equilibrium in favor of a less rigid twist-boat conformation. The IR absorption of the lactone carbonyl at 1740 cm(-)(1) would suggest a half-chair conformation inconsistent with the dominance of the boat forms shown by NMR and X-ray.