Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation

Moufarrej, Mira N.; Wong, Ronald J.; Shaw, Gary M.; Stevenson, David K.; Quake, Stephen R.

doi:10.3389/fped.2020.605219

Cited by 28 publications

(24 citation statements)

References 51 publications

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“…Due to the high amount of starting material needed and the restricted availability of fetal tissues, this approach has rarely been applied to prenatal fetuses, even for research purposes, causing an evident lack of data on prenatal tissues in the major gene expression atlases developed. Recently, the introduction of single-cell RNA-Seq, with a low amount of RNA required, has boosted the development of less invasive procedures which could in future be implemented in the molecular prenatal diagnosis and pregnancy monitoring, such as the detection of cell-free RNA in amniotic fluid [344], umbilical cord blood, placenta and maternal plasma [345].…”

Section: Rna Sequencingmentioning

confidence: 99%

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges—Systematic Review of the Literature and Meta-Analysis

et al. 2022

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Fetal malformations occur in 2–3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. “Structural anomalies” include non-transient anatomic alterations. “Soft markers” are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as “dynamic”. This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

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Section: Rna Sequencingmentioning

confidence: 99%

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges—Systematic Review of the Literature and Meta-Analysis

et al. 2022

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“…For every sequenced sample, we estimated three quality parameters as previously described 62,63 . To estimate RNA degradation in each sample, we first counted the number of reads per exon and then annotated each exon with its corresponding gene ID and exon number using htseq-count.…”

Section: Methodsmentioning

confidence: 99%

“…Because cfRNA measurements can be noisy 31,72 , we have previously developed and reported on three quality metrics that can flag sequenced cfRNA samples with poor quality 62,63 . Specifically, these metrics aim to quantify unusually high levels of RNA degradation and/or DNA contamination by comparing a given sample’s value for any of these metrics with what we expect empirically.…”

Section: Supplementary Textmentioning

confidence: 99%

Early prediction of preeclampsia in pregnancy with circulating cell-free RNA

Moufarrej

Wong

Campos

et al. 2021

Preprint

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Liquid biopsies that measure circulating, cell-free RNA (cfRNA) offer an unprecedented opportunity to noninvasively study the development of pregnancy-related complications and to bridge gaps in clinical care. Here, we identify cfRNA transcriptomic changes across gestation and at post-partum that are associated with preeclampsia (PE), a multi-organ syndrome diagnosed after 20 weeks of gestation, using 118 samples from 42 pregnant mothers (18 normotensive (NT), 24 with PE). We find that changes in cfRNA gene expression between NT and PE mothers are most striking and stable early in gestation, suggesting that the identified cfRNA signals may correlate with PE pathogenesis. These changes also reflect our understanding of the known biology of PE, as supported by gene ontology analysis. Finally, we identify and independently validate (8 NT, 8 with PE/gestational hypertension) 11 genes, which when measured between 5-16 weeks of gestation can form a liquid biopsy test with clinically relevant specificity (88% [55-99%]) and sensitivity (100% [74-100%]) (All reported as value, [95% confidence interval]). Taken together, these results show that cfRNA measurements can form the basis of a test that would predict PE early in pregnancy, which has been an important and until now unrealized objective for obstetric care, and can help characterize the pathogenesis of PE in real time.

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“…For every sample for which raw sequencing data was available, we estimated three quality parameters as previously described 44,45 : RNA degradation, ribosomal read fraction, and DNA contamination. RNA degredation was estimated by calculating a 3' bias ratio.…”

Section: Sample Quality Filteringmentioning

confidence: 99%

“…To estimate DNA contamination, we used an intron to exon ratio and quantified the number of reads that mapped to intronic as compared to exonic regions of the genome. We applied the following thresholds as previously reported 44 :…”

Section: Sample Quality Filteringmentioning

confidence: 99%

Cell Types of Origin in the Cell Free Transcriptome in Human Health and Disease

2021

Preprint

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Liquid biopsies using cell-free RNA (cfRNA) can noninvasively measure dynamic physiological changes throughout the body. While there is much effort in the liquid biopsy field to determine disease tissue-of-origin, pathophysiology occurs at the cellular level. Here, we show that it is possible to determine cell type-of-origin from cfRNA by leveraging single cell transcriptomic atlases to perform computational deconvolution. We derived cell type gene signatures by combining the whole-body single cell atlas Tabula Sapiens, individual tissue single cell atlases, and bulk tissue atlases. Using deconvolution, we identified cell types-of-origin in the healthy human cell-free transcriptome, including contributions from multiple cell types in the brain, liver, lung, intestine, kidney, and pancreas in addition to hematopoietic cell types. We further showed that it is possible not only to detect cell types implicated in the pathology of chronic kidney disease (CKD) and Alzheimer’s disease (AD), but also to measure changes in these cell types as a function of disease state. Altogether, our results show that cfRNA measurements reflect cellular contributions in health and disease from diverse tissue-specific cell types. These findings underscore the resolution at which one can monitor pathophysiological changes and the broad potential prognostic utility afforded by non-invasive transcriptomic measurement.

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Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation

Cited by 28 publications

References 51 publications

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges—Systematic Review of the Literature and Meta-Analysis

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges—Systematic Review of the Literature and Meta-Analysis

Early prediction of preeclampsia in pregnancy with circulating cell-free RNA

Cell Types of Origin in the Cell Free Transcriptome in Human Health and Disease

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