RNA-seq of mouse Lgr5 expressing intestinal stem cells (ISCs) and transit amplifying (TA) cells
Ontology highlight
ABSTRACT: The experiment shows the expression changes between Lgr5Hi and Lgr5Lo cells in young and old mice. These expression changes are related to the stem cell niche signalling in intestinal epithelium.
Project description:The experiment shows the aging related expression changes in Paneth and Lgr5Hi cells between young and old mice. These expression changes are related to the role of stem cell niche in aging and regeneration of intestinal epithelium.
Project description:We hypothesized that the immune microenvironment of the bone marrow influences the progression of myeloma outgrowth in the 5TGM1 transfer model of multiple myeloma. Therefore we sorted bone marrow T, NK, and non-hematopoietic stromal cells from control and tumor-bearing C57Bl/6 mice.
Project description:Neutrophils are the most abundant nucleated cell type in the bone marrow. A pro-tumor bias in this cell type may have implications for bone-marrow residing malignancies, such as multiple myeloma. Here, we generated single cell transcriptomic overviews of the entire myeloid compartment, including the entire neutrophilic lineage, of the bone marrow of 6 newly diagnosed myeloma patients, 5 treated myeloma patients and 4 non-cancer controls. We find dat mature neutrophils in myeloma patients, both newly diagnosed and treated, have an activated and pro-inflammatory phenotype, accompanied by increased transcription of pro-inflammatory cytokines, such as IL-1β, and myeloma cell survival factors, such as BCMA-ligand BAFF/TNFSF13B. Moreover, inflammatory stromal cells can activate naive neutrophils to acquire an inflammatory phenotype as is seen in patients. Previously, we have shown that inflammatory stromal cells characterized the bone marrow of newly diagnosed myeloma patients. Here, we generate single cell RNA sequencing dataset of non-hematopoietic bone marrow cells of patients after induction treatment, high-dose melphalan, stem cell transplantation and consolidation treatment. We show that this intensive treatment reduced, but did not normalize, stromal inflammation.
Project description:Innate lymphoid cells (ILCs) are part of the innate immune cell family. Three different subsets of ILCs, ILC1s, ILC2s and ILCPs can be identified in human peripheral blood. Based on their expression of transcription factors and cytokines, they are considered as being the innate counterparts of CD4 T helper subsets, namely Th1s, Th2s and Th17s. However, ILCs and Th cells have different roles in immunity. Therefore, we compared the transcriptomes of sorted ILC1s, ILC2s, ILCPs, Th1s, Th2s and Th17s from the peripheral blood of three different donors. RNA sequencing of ILC and Th subsets revealed differences in the expression of tens to hundreds of genes. These genes are involved in cell trafficking, innate activation and inhibitory functions. ILC and Th cell subsets also differ in their expressions of long-non coding RNAs.
Project description:By generating a paired single cell RNA-sequencing database of the tumor niche from 10 newly diagnosed MM patients, we created a unique dataset allowing the in-depth analyses of stromal-immune interactions within the tumor microenvironment. Using this database, we identified the presence of inflammatory stromal fibroblasts in the bone marrow of Myeloma patients.The stromal inflammation was associated with NF-κB signaling, and sources of IL-1β or TNFα were specific immune subsets previously shown to be altered in MM, suggesting the presence of an immune cell-mediated feed-forward loop of bone marrow inflammation in MM. By tracking inflammatory signatures over time in individual patients undergoing first-line treatment using bulk RNA sequencing, we show that bone marrow inflammation is not reverted by successful anti-tumor therapy (see related accession number), suggesting a role for stromal fibroblasts and bone marrow inflammation in disease persistence or relapse.
Project description:By generating a paired single cell RNA-sequencing database of the tumor niche from 10 newly diagnosed MM patients, we created a unique dataset allowing the in-depth analyses of stromal-immune interactions within the tumor microenvironment (see related accession number). Using this database, we identified the presence of inflammatory stromal fibroblasts in the bone marrow of Myeloma patients.The stromal inflammation was associated with NF-κB signaling, and sources of IL-1β or TNFα were specific immune subsets previously shown to be altered in MM, suggesting the presence of an immune cell-mediated feed-forward loop of bone marrow inflammation in MM. By tracking inflammatory signatures over time in individual patients undergoing first-line treatment using bulk RNA sequencing, we show that bone marrow inflammation is not reverted by successful anti-tumor therapy (this dataset), suggesting a role for stromal fibroblasts and bone marrow inflammation in disease persistence or relapse. Raw sequencing data files will be deposited to EGA.
Project description:RNA-seq was performed on FACS-isolated stem cells from the mouse intestinal epithelium. The purpose of the experiment was to compare the transcriptomes of stem cells enriched for recently generated (young) mitochondria and stem cells enriched with old mitochondria. The dataset also includes samples of stem cells with young mitochondria deliberately contaminated with a small amount of Paneth cells, to control for accidental Paneth cell contamination in the sorting scheme.
Project description:We performed lineage tracing experiments using VE-Cadherin-Cre;LoxP-tdTomato mice. In these mice, endothelial cells (ECs) and their progeny are permanently marked by tdTomato fluorescence. We found that a substantial subset of stromal cells is derived from ECs, as indicated by their tdTomato expression. These findings support the notion that endothelial to mesenchymal transition (EndoMT) contributes to hematopoietic bone marrow niche formation in mice. Here we sought to determine the transcriptomic differences between endothelial-derived (tdTomato-positive) and non-endothelial-derived (tdTomato-negative) bone marrow stromal cells (BMSCs) and osteo/chondrolineage progenitor cells (OLCs). Murine niche populations were obtained from collagenased bone fraction of VE-Cadherin-Cre;LoxP-tdTomato mice at 3 weeks (n=2) or 11 weeks (n=2) of age. BMSCs (CD45-TER119-CD31-CD144-SCA-1+ CD51+ cells) and OLCs (CD45-TER119-CD31-CD144-Sca1-CD51+ cells) were FACS-purified and sequenced.
Project description:Rare dormant hematopoietic stem cells (dHSCs) reside at the top of the blood hierarchy harboring the highest long-term reconstitution capacity. However, no markers exist to prospectively identify dHSCs and their molecular identity, as well as the mechanism leading to their activation remains poorly understood. Here, we present the global transcriptome of ex vivo isolated mouse multipotent hematopoietic stem cells (HSCs) and dHSCs at the single cell level.
Project description:Comparing transcriptomes of CD8 T cells derived from a fatal H7N9 influenza infection with those derived from a patient that survived the infection. Specifically, CD38+ HLA-DR+ cells were sorted by flow cytometry at different sampling time-points, and the transcriptome was analysed using Smart-seq2.