Interferon gene therapy reprograms the leukemia microenvironment inducing protective immunity to multiple tumor antigens
ABSTRACT: Single-cell transcriptome profiling using a 3' droplet-based platform (Chromium,10x Genomics) of CD11b+ cells isolated from the spleen of control and tumor-bearing mice, treated or not with IFN gene therapy.
Project description:Single-cell transcriptome profiling using a 3' droplet-based platform (Chromium,10x Genomics) of human CD45+ leukocytes isolated from leukemic HuSGM3 mice infused with CD19.28z CAR-T cells, two days after cytokine release syndrome (CRS) onset and 5 days later.
Project description:We sought to evaluate in an unbiased way the heterogeneity of lung interstitial macrophages and their relationship with alveolar macrophages, lung Ly-6Chi classical monocytes and Ly-6Clo patrolling monocytes, by single cell RNA-Seq.
Project description:In dogs, a species for which markers of cell populations are often limiting, we sought to evaluate in an unbiased way the heterogeneity of cell subpopulations in the bronchoalveolar lavage fluid of healthy dogs, by single-cell RNA-sequencing.
Project description:We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.
Project description:Single-cell RNA-seq was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare single-cell gene expression patterns across tissues.
Project description:Mice intranasally exposed to a low dose of LPS (i.e., 100 ng) are prone to develop features of allergic asthma upon subsequent exposure to house dust mites (HDM) allergens, while mice exposed to vehicle or 100 µg LPS do not develop such features. In order to understand the mechanisms that promote allergic asthma, we sought to characterize the lung neutrophils, which are massively recruited after LPS exposure, by single cell RNA-Seq.
Project description:Renal endothelial cells (RECs) from glomerular cortical and medullary kidney compartments are exposed to different microenvironmental conditions. Upon dehydration medullary RECs (mRECs) are exposed to extreme hyperosmolarity. However the heterogeneous phenotypes of RECs remain in-completely inventoried and how mRECs respond to dehydration is unknown. By single cell RNA-sequencing of >40000 RECs we identified 24 (including 8 novel) REC phenotypes highlighting extensive heterogeneity of RECs between and within the cortex glomeruli and medulla. In response to dehydration mRECs upregulated primarily the expression of genes involved in the hypoxia response glycolysis and surprisingly oxidative phosphorylation (OXPHOS). In vitro mRECs increased oxygen consumption in response to hyperosmolarity presumably to sustain ATP production for Na+/K+ ATPase pump-mediated salt excretion and to generate metabolic water during OXPHOS in order to counteract mREC hyperosmolarity unveiling a previously underappreciated role of OXPHOS. Overall RECs exhibit extensive heterogeneity and plasticity to adapt their metabolic transcriptome to overcome dehydration.
Project description:Ischemic stroke is a serious medical condition that leads to the onset of neurological symptoms such as loss of motor and cognitive functions. Focal cerebral ischemia (FCI) occurs due to the interrupted blood supply to the site of injury, resulting in the demise of brain cells. The subventricular zone (SVZ) is a source of stem and progenitor cells (NS/PCs), which proliferate and differentiate in multiple cell types in order to substitute the injured tissue. We isolated cells from the SVZ and the adjacent striatum three days after middle cerebral artery occlusion (MCAO) in order to map cellular changes and NS/PCs plasticity in adult brain upon injury. Expression profiling of the isolated tissue at the single cell level enables the identification of cell population subtypes in the region and their characteristic gene expression.
Project description:The heterogeneity of endothelial cells (ECs), lining blood vessels, across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomic data from 11 tissues of the model organism Mus musculus. We propose a new classification of EC phenotypes based on transcriptome signatures and inferred putative biological features. We identified top-ranking markers for ECs from each tissue. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) resembled each other across tissues, but only arterial, venous and lymphatic (not capillary) ECs shared markers, illustrating a greater heterogeneity of capillary ECs. We identified high-endothelial-venule and lacteal-like ECs in the intestines, and angiogenic ECs in healthy tissues. Metabolic transcriptomes of ECs differed amongst spleen, lung, liver, brain and testis, while being similar for kidney, heart, muscle and intestines. Within tissues, metabolic gene expression was heterogeneous amongst ECs from different vascular beds, altogether highlighting large EC heterogeneity.
Project description:Single-cell RNA sequencing was performed on retinal tissue from 12-week-old wild-type and Akimba (Ins2AkitaxVEGF+/-) mice, which are known to replicate features of clinical diabetic retinopathy. The aim of this study was to provide deeper insight into the complex network of molecular and cellular changes that underlie diabetic retinopathy by measuring the transcriptional changes that occur in the different cellular compartments of the degenerating diabetic mouse retina. Retinas (n=4 for Akimba, n=2 for wild-type) were isolated in ice-cold Dulbecco’s Modified Eagle Medium. After rinsing with Dulbecco’s Phosphate-Buffered Saline containing 2% fetal bovine serum, each retina was incubated with 1mL digestion buffer (2mg/mL collagenase-P, 200U/mL DNAse-I (Sigma-Aldrich) in M199 medium (Life Technologies) at 37°C for 10min. Retinal tissue was further dissociated by trituration and the suspension was filtered through a 40µm cell strainer and centrifuged for 5min at 300xg (4°C). Pooled retinal single-cell suspensions from wild-type and Akimba were counted on a Luna-FL Cell Counter (Logos Biosystems) and libraries were prepared with the Chromium Single-cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics) aiming for 5000 cells per library. Barcoded libraries were sequenced on an Illumina HiSeq4000 in 25-8-98 paired-end configuration.