The trilineage coexistence observed during the differentiation of porcine extended pluripotent stem cells in LCDM medium
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE315039 | GEO | 2026/06/03
REPOSITORIES: GEO
Similar Datasets
Project description:The trilineage coexistence observed during the differentiation of porcine extended pluripotent stem cells in LCDM medium
| PRJNA1394902 | ENA
Project description: Not available
| S-EPMC7083851 | biostudies-literature
Project description:Kilian2024 - Immune cell dynamics in Cue-Induced Extended Human Colitis Model
Single-cell technologies such as scRNA-seq and flow cytometry provide critical insights into immune cell behavior in inflammatory bowel disease (IBD). However, integrating these datasets into computational models for dynamic analysis remains challenging. Here, Kilian et al., (2024) developed a deterministic ODE-based model that incorporates these technologies to study immune cell population changes in murine colitis. The model parameters were optimized to fit experimental data, ensuring an accurate representation of immune cell behavior over time. It was then validated by comparing simulations with experimental data using Pearson’s correlation and further tested on independent datasets to confirm its robustness. Additionally, the model was applied to clinical bulk RNA-seq data from human IBD patients, providing valuable insights into immune system dynamics and potential therapeutic strategies.
Figure 4c, obtained from the simulation of human colitis model is highlighted here.
This model is described in the article:
Kilian, C., Ulrich, H., Zouboulis, V.A. et al. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. npj Syst Biol Appl 10, 69 (2024). https://doi.org/10.1038/s41540-024-00395-9
Abstract:
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
This model was curated during the Hackathon hosted by BioMed X GmbH in 2024.
2025-03-07 | MODEL2502180001 | BioModels
Project description:We performed 10× Genomics single-cell RNA sequencing on a mixed population of CD3+ PBMCs isolated from three healthy Large White pigs. Considering that cell resolution of scRNA-seq analysis can be improved based on large datasets, we also downloaded 7 pbulic PBMC scRNA-seq datasets using the same technique (10× Genomics). After rigorous quality control and the removal of batch effects, a total of 14,595 transcriptomes were obtained from 34,220 cells in 8 PBMC samples for subsequent analyses. Using the graph-based uniform manifold approximation and projection (UMAP) clustering algorithm in Seurat package, we identified 14 major cell types (32 clusters) from peripheral blood circulating cells of pigs, and observed remarkable heterogeneity among CD8 T cell types. Upon re-clustering of CD8+ T cells, we defined 4 CD8 T cell subtypes and revealed their potential differentiation trajectories and transcriptomic differences among them. Through single-cell regulatory network inference, we identified key regulatory factors during CD8 T cell differentiation. Moreover, cell-cell communication analysis underscored extensive intercellular interactions among different cell types. Lastly, our cross-species analysis highlighted both similarities and potential differences between species.
2024-03-07 | GSE247126 | GEO
Project description: Not available
| S-EPMC9598231 | biostudies-literature
Project description: Not available
| S-EPMC5854624 | biostudies-literature
Project description:To further understand the biological characteristics of porcine pluripotent stem cells (pLCDM) established under LCDM system, transcriptome analyses were performed. The data showed that the biological events related to placental development were found in pLCDMs, while pLCDMs expressed more biological events related to embryo development and organ development of each layer than TE. Transcriptomic analysis demonstrated that pLCDMs expressed higher levels of trophoblast lineage genes than pPSCs (KOFL). Furthermore, we successfully induced trophoblastic-like cells and pLCDM_TSCs with high expression of trophoblast lineage marker genes in vitro using a pure chemical medium. To comprehensively analyze the difference between pLCDM_TSCs and pLCDMs, low input RNA-seq was performed on the cell lines. A total of 3,594 DEGs were found, and 1,606 genes were significantly upregulated in pLCDM_TSCs, including BMP signaling pathway related genes BMPR1A, ID1, and trophoblast lineage marker genes ITGA1, ITGA6, FZD5, etc. It was worth noting that we found 509 highly expressed genes in hTSCs among the genes that were highly expressed in pLCDM_TSCs. Together, these results demonstrated the unique cellular potency of pLCDMs for trophoblast lineage.
2022-05-20 | GSE197451 | GEO
Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.
2023-09-12 | GSE157875 | GEO
Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.
2023-09-12 | GSE157874 | GEO
Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.
2023-09-12 | GSE157873 | GEO