SARS-CoV-2 Niches in Human Placenta Revealed by Spatial Transcriptomics
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA924338 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23094132.fastq.gz | Fastqsanger.gz | |||
| SRR23094133.fastq.gz | Fastqsanger.gz | |||
| SRR23094134.fastq.gz | Fastqsanger.gz | |||
| SRR23094135.fastq.gz | Fastqsanger.gz | |||
| SRR23094136.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:Diverse placental functions are compartmentalized to separate maternal-fetal antigens and restrict vertical transmission of pathogens. We hypothesized a high-resolution map, with single-cell and spatial resolution, would identify previously undetectable microbe immune microenvironments. To test this hypothesis, we utilized Visium Spatial Transcriptomics paired with H&E staining to generate 17,927 spatial transcriptomes and integrated these data with 273,944 published placenta single-cell and single-nuclei transcriptomes to generate a term placenta atlas of the maternal decidua, fetal chorionic villi, and chorioamniotic membranes. Comparisons of healthy control placentae (n=4), SARS-CoV-2 asymptomatic (n=4; no COVID-19 symptoms), and symptomatic (n=5; pneumonia, respiratory failure) placentae identified distinct thresholds of SARS-CoV-2 detection including (i) no detectable virus, (ii) sparse virus (limit of detection determined to be 1/7,000 cells), and (iii) highly positive SARS-CoV-2 in syncytiotrophoblasts, rigorously cross-validated by RT-qPCR, RNAscope, and immunohistochemistry. High levels of SARS-CoV-2 in placentae were associated with histiocytic intervillositis and perivillous fibrin deposition. Spatial transcriptomics revealed that this led to a significant shift from anti-inflammatory M2 macrophage populations toward intermediate pro-inflammatory M1 macrophages. In conclusion, we identified immune microenvironments representing host-pathogen battlegrounds where SARS-CoV-2 detection in the placenta was not dependent on maternal symptoms. Additional studies utilizing this approach are warranted, especially in the placenta.
2023-07-05 | GSE222987 | GEO
Project description: Not available
| S-EPMC10527005 | biostudies-literature
Project description:Like hematopoiesis, erythropoiesis requires erythroid niches nurturing and support. We performed spatial transcriptomics to reveal the erythroid niches in human. Our results identified novel erythroid niches in human during development and stress.
2026-05-18 | GSE271150 | GEO
Project description:Like hematopoiesis, erythropoiesis requires erythroid niches nurturing and support. We performed subcellular spatial transcriptomics to reveal the erythroid niches in human. Our results identified novel erythroid niches in human during development and stress.
2026-05-18 | GSE271824 | GEO
Project description:The tsunami of new multiplexed spatial profiling technologies has opened a range of computational challenges focused on leveraging these powerful data for biological discovery. A key challenge underlying computation is a suitable representation for features of cellular niches. Here, we develop the covariance environment (COVET), a representation that can capture the rich, continuous multivariate nature of cellular niches by capturing the gene-gene covariate structure across cells in the niche, which can reflect the cell-cell communication between them. We define a principled optimal transport-based distance metric between COVET niches and develop a computationally efficient approximation to this metric that can scale to millions of cells. Using COVET to encode spatial context, we develop environmental variational inference (ENVI), a conditional variational autoencoder that jointly embeds spatial and single-cell RNA-seq data into a latent space. Two distinct decoders either impute gene expression across spatial modality, or project spatial information onto dissociated single-cell data. We show that ENVI is not only superior in the imputation of gene expression but is also able to infer spatial context to disassociated single-cell genomics data.
2024-03-08 | GSE246395 | GEO
Project description:Like hematopoiesis, erythropoiesis requires erythroid niches nurturing and support. We performed spatial transcriptomics to reveal the erythroid niches in mice. Our results identified novel erythroblastic island macrophage marker in mouse during development and stress.
2026-05-18 | GSE271077 | GEO
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.
2022-04-11 | GSE181238 | GEO
Project description:Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)
| PRJNA793008 | ENA
Project description:Like hematopoiesis, erythropoiesis requires erythroid niches nurturing and support. We performed subcellular spatial transcriptomics to reveal the erythroid niches in mice. Our results identified novel erythroblastic island macrophage marker in mouse during development and stress.
2026-05-18 | GSE271693 | GEO
Project description:Placenta is the vital reproductive organ of mouse, which is required for sustainable growth, protection, and nourishment of the fetus during gestation. It performs many crucial functions which include removal of waste products from the fetus, facilitation of the oxygen supply and nutrients to the fetus etc. Advances in the next generation sequencing technology, especially single cell transcriptional profiling, have provided the opportunity to explore the cell heterogeneity in mouse placenta. However spatial organization of these cell types and their functional mechanism, genes co-expression and regulations remain elusive yet. Visium Spatial 10x is a modern technology to study gene expression, where whole transcriptome analysis has been performed while taking account of their morphological context. This helps to gain a complete view of disease complexity, discover new biomarkers, identify novel cell types and developmental states. Along with it is used to identify spatiotemporal gene expression patterns and create map of the spatial organization of cell atlas. Placental tissue comprised of different cell types and are well organized display signature of developmental stages, along with their gene's expression. In this regard, exploring the new cell types and tracking their developmental trajectory is important to get insight into their role in spatial organizational context. Cellular functions and extensive interactions among cell types are unexplored taking consideration of spatial context in mouse placenta. It is required to explore the cell types, cell-to-cell communication which is essential for deciphering the regulation of placental development and functions. In this study, we have applied spatial transcriptomes for two developmental stages of mouse placenta E10.5 and E12.5 to explore the cell heterogeneity of the developing placenta. This work shows their significance by providing insight of tissue level identification cell types of clusters, identification of cell types of markers to get the significantly expressed genes in particular clusters. The arrangement of different cell types on tissue images are more informative to study the arrangement and cell differentiation in developmental stages. In conclusion, this study provides new insight into the development and functions of placenta.
2025-09-23 | GSE214004 | GEO