ScRNA-seq of stromal cells in WT and LRRC15 DTR mice
Ontology highlight
ABSTRACT: KPR tumors were subcutaneously implanted in Lrrc15DTRGFPwt/wt (DTR–) or Lrrc15DTRGFPwt/ki (DTR+) mice and DT treatment was initiated in both DTR– and DTR+ mice when tumors reached a mean volume of 100-200mm3. scRNAseq of CD24-CD45- stromal cells from a total of 40 tumor-bearing animals across both DTR– and DTR+ genotypes was carried out at four different time points including 10 days post tumor implantation and immediately prior to initiation of DT treatment (IOT) (referred to as day 0) and on days 7, 14, and 21 post IOT.
Project description:Single-cell RNA-seq in mice with subcutaneous tumors was used to determine if TGFβR2 signaling in DPT+ universal fibroblasts drives LRRC15+ myofibroblast differentiation using DptIresCreERT2Tgfbr2fl/fl and WT control mice.
Project description:In an effort to define transcriptional heterogeneity in the stromal cell compartment of lymph nodes scRNA-seq analysis of CD45- cells from skin-draining LNs (SLN) was performed. Flow sorted CD45 depleted single cell suspension from SLN of ten mice were profiled by 10x 3’ single-cell RNA-sequencing in two runs, each containing cells from five mice.
Project description:Single cell RNA-seq was performed on healthy mouse skin fibroblasts. This data along with single cell transcriptomics datasets of fibroblasts from other healthy tissues was used to construct a steady state mouse fibroblast atlas.
Project description:The aims of the experiment were to profile the cardiac interstitial (non-myocyte) cell types in the adult mouse from injured and uninjured hearts and how they respond to modulation of platelet-derived growth factor receptor alpha (PDGFRa) signaling. Adult, male, C57BL/BJ mice were subject to either a myocardial infarction or sham injury, and given either PDGF-AB or PBS treatment via mini-pump, with single-cell RNA-seq profiles obtained from interstitial cells isolated from cardiac ventricles 3 or 7 days following surgery.
Project description:The aims of the experiment were to profile the cell types in the adult mouse cardiac interstitium (non-myocyte cells) and how they respond to myocardial infarction injury. Adult, male, Pdgfra +/GFP mice were subject to either a myocardial infarction or sham injury, with cells isolated from cardiac ventricles 3 or 7 days following surgery. We obtained scRNA-seq profiles of two cell fractions: total interstitial (non-myocyte) cell population (TIP) and FACS-sorted GFP+/Cd31- cells (GFP).
Project description:In this project we explore the role of the master hypoxia regulator, Hypoxia inducible factor-1alpha (Hif-1a), in governing cardiac fibroblast (CF) function in homeostasis and following an acute ischaemic injury - myocardial infarction (MI). CF-specific Hif-1a conditional knockout (cKO) mice were generated by breeding Pdgfra-merCremer (PdgfraMCM/+) Cre recombinase driver mice with Hif-1a-floxed mice (Hif-1aflox/). In Hif-1afl/-; PdgfraMCM/+ progeny, Hif-1a could be conditionally deleted in adult CFs by tamoxifen (tam) administration. We also introduced a Cre-dependent R26tdTomato reporter allele allowing marking of Pdgfra+ CFs and their progeny. In this experiment, we first performed single-cell RNA sequencing (scRNA-seq) on tdTomato+ cells from the hearts of healthy cKO or heterozygous (HET) adult, male mice using the 10x Genomics Chromium system. We also performed scRNA-seq on tdTomato+/CD31-/CD45- cells from the hearts of cKO or HET mice at day-3 post-sham or -MI surgery.
Project description:With the advent of cancer immunotherapy, intense investigation has been focused on tumor-infiltrating immune cells. With only a fraction of patients responding to these new therapies, a better understanding of all elements of the tumor microenvironment (TME) that may influence therapeutic outcome is needed. Stromal elements of the TME, chiefly fibroblasts, have emerged as potential contributors to tumor progression and most recently resistance to immunotherapy, but their precise composition and clinical relevance remain incompletely understood. Here we use single-cell transcriptomics to chart the fibroblastic landscape during pancreatic ductal adenocarcinoma (PDAC) progression in animal models, identifying two healthy tissue fibroblast subsets that co-evolve along individual trajectories into four subsets of carcinoma-associated fibroblasts (CAFs).
Project description:To identify heterogeneity of stromal cells in human lymph nodes, we performed single-cell RNA-seq of stromal cells (CD45-, CD31- PDPN+) from 3 donors. Additionally, dendritic cells (DCs, CD45+, CD11C+) were isolated from the LNs of the same donors to predict potential interactions between these two types of cells. As potentially human identifiable data, he raw sequencing data files for this experiment will be deposited in the controlled-access EGA archive.
Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.