Ontology highlight
ABSTRACT:
PROVIDER: PRJNA701628 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13699971_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699971_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699972_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699972_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699973_1.fastq.gz | Fastqsanger.gz |
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Project description:It is poorly understood how maternal covid-19 results in severe placental disorders. Single nuclei sequencing (sci-rna-seq3) was used to profle transcriptomic changes in the human placenta in response to maternal COVID-19.
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Project description:Pregnant women appear to be at increased risk for severe outcomes associated with COVID-19, but the pathophysiology underlying this increased morbidity and its potential impact on the developing fetus is not well understood. In this study of pregnant women with and without COVID-19, we assessed viral and immune dynamics at the placenta during maternal SARS-CoV-2 infection. Amongst uninfected women, ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term. Term placentas from women infected with SARS-CoV-2, however, displayed a significant increase in ACE2 levels. Using immortalized cell lines and primary isolated placental cells, we determined the vulnerability of various placental cell types to direct infection by SARS-CoV-2 in vitro. Yet, despite the susceptibility of placental cells to SARS-CoV-2 infection, viral RNA was detected in the placentas of only a subset (∼13%) of women in this cohort. Through single cell transcriptomic analyses, we found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited markers associated with pregnancy complications, such as preeclampsia, and robust immune responses, including increased activation of placental NK and T cells and increased expression of interferon-related genes. Overall, this study suggests that SARS-CoV-2 is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. While this likely represents a protective mechanism shielding the placenta from infection, inflammatory changes in the placenta may also contribute to poor pregnancy outcomes and thus warrant further investigation.
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Project description:SARS-CoV-2 infection during pregnancy leads to an increased risk of adverse pregnancy outcomes. To determine the host response of the human placenta to SARS-CoV-2 infection, we performed RNA-Seq on placentas from COVID-19+ and COVID-19- mothers, as well as placentas that presented with non-COVID related inflammatory pathologies. We found that placentas infected by SARS-CoV-2 at term show an induction of inflammatory genes, including a robust increase in chemokine and cytokine signaling. Furthermore, when SARS-CoV-2 is detected in the placenta, placenta cell marker identity genes are lost with a concomitant increase in macrophage gene expression. Furthermore, when infected ex vivo, a strong inflammatory response and cellular de-identification is similarly observed, along with an acute increase in cell death in response to viral infection. Our data describes the inflammatory responses that occur in the placenta after SARS-CoV-2 infection both acutely and long-term, and provides a comparison with other placental inflammatory pathologies.
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Project description:Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 72 samples In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.
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Project description:Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces. RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta. Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data. 48 samples In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.
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