Similar Datasets
Project description:The ability of a virus to infect a cell type is partly determined by host factors required for the viral life cycle. However, not every cell of a given type is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the susceptible subsets of cells could reveal additional host factors, but viral infection dramatically alters the state of the cell, obscuring the state of these cells prior to infection. We used single-cell clone tracing to retrospectively identify cells that were highly susceptible to infection with SARS-CoV-2. Our approach revealed candidate factors playing roles in viral entry and regulation of the infectable cell state itself. Patient samples revealed heterogeneous expression of these factors in vivo, with heightened expression in particular inflammatory pathologies. Thus, variable expression of intrinsic cell states is a major determinant of whether individual cells can be infected by SARS-CoV-2.
2023-07-12 | GSE236941 | GEO
Project description:The ability of a virus to infect a cell type is partly determined by host factors required for the viral life cycle. However, not every cell of a given type is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the susceptible subsets of cells could reveal additional host factors, but viral infection dramatically alters the state of the cell, obscuring the state of these cells prior to infection. We used single-cell clone tracing to retrospectively identify cells that were highly susceptible to infection with SARS-CoV-2. Our approach revealed candidate factors playing roles in viral entry and regulation of the infectable cell state itself. Patient samples revealed heterogeneous expression of these factors in vivo, with heightened expression in particular inflammatory pathologies. Thus, variable expression of intrinsic cell states is a major determinant of whether individual cells can be infected by SARS-CoV-2.
2023-07-12 | GSE236939 | GEO
Project description:Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states
| PRJNA993158 | ENA
Project description:Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states [scRNA-Seq]
| PRJNA993165 | ENA
Project description:Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states [bulkRNA-Seq]
| PRJNA993151 | ENA
Project description:Gastrointestinal effects associated with Coronavirus Disease 2019 (COVID-19) are highly variable for reasons that are not understood. In this study, we used intestinal organoid-derived cultures differentiated from primary human specimens as a model to examine interindividual variability. Infection of intestinal organoids derived from different donors with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in orders of magnitude differences in virus replication in small intestinal and colonic organoid-derived monolayers. Susceptibility to infection correlated with angiotensin I converting enzyme 2 (ACE2) expression level and was independent of donor demographic or clinical features. ACE2 transcript levels in cell culture matched the amount of ACE2 in primary tissue, indicating that this feature of the intestinal epithelium is retained in the organoids. Longitudinal transcriptomics of organoid-derived monolayers identified a delayed yet robust interferon signature, the magnitude of which corresponded to the degree of SARS-CoV-2 infection. Interestingly, virus with the Omicron variant spike (S) protein infected the organoids with the highest infectivity, suggesting increased tropism of the virus for intestinal tissue. These results suggest that heterogeneity in SARS-CoV-2 replication in intestinal tissues results from differences in ACE2 levels, which may underlie variable patient outcomes.
| S-EPMC9004766 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-09-28 | GSE234487 | GEO
Project description:Gaining a better understanding of the immune cell subsets and molecular factors associated with protective or pathological immunity against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 could aid the development of vaccines and therapeutics for coronavirus disease 2019 (COVID-19). Single-cell technologies, such as flow cytometry, mass cytometry, single-cell transcriptomics and single-cell multi-omic profiling, offer considerable promise in dissecting the heterogeneity of immune responses among individual cells and uncovering the molecular mechanisms of COVID-19 pathogenesis. Single-cell immune-profiling studies reported to date have identified innate and adaptive immune cell subsets that correlate with COVID-19 disease severity, as well as immunological factors and pathways of potential relevance to the development of vaccines and treatments for COVID-19. For facilitation of integrative studies and meta-analyses into the immunology of SARS-CoV-2 infection, we provide standardized, download-ready versions of 21 published single-cell sequencing datasets (over 3.2 million cells in total) as well as an interactive visualization portal for data exploration.
| S-EPMC9414121 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2013-07-30 | GSE47963 | GEO
Project description:Modelling cell infection in-a-dish can represent a useful tool to understand the susceptibility of different cell types towards severe acute respiratory coronavirus-2 (SARS-CoV-2) and to decipher its neurotropism. In this perspective, retinoic acid (RA)-differentiated neuroblastoma cell lines, SH-SY5Y and SK-N-BE(2) and glioblastoma cell lines, U-87 MG and U-373 MG, were infected with a SARS-CoV-2 strain, at various multiplicity-of-infection (MOI). We first demonstrated that the common entry genes - needed for invading epithelial cells - were expressed. RA-differentiation induced an upregulation of ace2 and tmprss2 gene expression while inducing downregulation of ctsb and ctsl. Using in situ hybridization and confocal analysis, SARS-CoV-2 gene S RNA was detected intracellularly at MOI 5.0, and localized in both soma and neuritic-like or glial-like processes. The infection was confirmed by quantification of viral gene E RNA and showed a dose-dependency, with few infected cells at MOI 0.1. After 24 h of infection, no cytopathic effect was observed in SH-SY5Y abilities to maintain neuritic processes or in U-373 MG for the uptake of glutamate. Unlike the permissive Vero E6 cells, no significant apoptosis death was detected following SARS-CoV-2 infection of neuroblastoma or glioblastoma cells. This study demonstrates the susceptibility of neuronal- and glial-like cell lines towards SARS-CoV-2 infection at high MOIs. Once inside the cells, the virus does not seem to rapidly replicate nor exert major cytopathic effect. Overall, our results strengthen the idea that SARS-CoV-2 has a tropism for nervous cells that express commonly described entry genes.
| S-EPMC7863753 | biostudies-literature