Bulk RNA seq data from radiotherapy-treated glioma-bearing mice
Ontology highlight
ABSTRACT: The experiment goal was to unveil any modulation of the tumor micro-environment in GL261 and SB28 bearing mice following radiation treatment.
Project description:Total RNA-seq of blasts derived 100 adult T-ALL cases, 211 AML cases and 13 mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, CD34+ HSPCs derived from 9 healthy donors are used as a control. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011054, EGAD00001007646, EGAD00001007581 (datasets).
Project description:In this experiment we define the transcriptome of the adult mouse skeleton by performing total-RNA transcriptome-sequencing on osteocytes, the critical regulatory cells in bone. Osteocytes from 16 week-old male mice (n=8) were isolated for 4 bone types across the skeleton: the tibia, femur, humerus, and calvaria. All other soft tissues including marrow were removed from samples before sequencing.
Project description:We employed single-cell RNA sequencing to understand stromal changes in murine melanomas and draining lymph nodes at single cell resolution at different points of tumour development.
Project description:Tumor targeted therapies have been largely inefficient due to lack of concomitant effects on the tumor microenvironment (TME). We investigated the MAtrix REgulating MOtif (MAREMO) mimicking peptide MP5, that inhibits the pro-tumorigenic extracellular matrix (ECM) molecule tenascin-C, using immunocompetent autologous breast cancer bearing mice. MP5 treatment led to tumor regression and reduced tumor cell dissemination. Several cancer hallmarks were abolished such as tumor cell promoting growth suppression and inhibition of plasticity enhancing responsiveness to death inducers. MP5 acts on other TME players leading to blood vessel normalization and depletion of fibroblasts diminishing the ECM as an orchestrator of immune suppression, causing immune cell infiltration and reactivation of anti-tumor immunity involving IFNgamma. Thus, targeting the tumor matrix using MAREMO in tenascin-C represents a powerful novel anti-cancer strategy.
Project description:Sequenced samples are cultured posterior parts of the first mouse molar tooth primordia. RNA sequencing was performed based on explants after 0, 16 or 24 hours of in vitro culture respectively, with aim to define candidate genes playing a role in the tooth germ development.
Project description:Despite abundant evidence demonstrating that platelets foster metastasis, anti- platelet agents have low therapeutic potential due to the risk of hemorrhages. In addition, whether platelets can regulate metastasis at the late stages of the disease remains unknown. In this study, we subjected syngeneic models of metastasis to various thrombocytopenic regimes to show that platelets provide a biphasic contribution to metastasis. While potent intravascular binding of platelets to tumor cells efficiently promotes metastasis, platelets further support the outgrowth of established metastases via immune suppression. Genetic depletion and pharmacological targeting of the platelet-specific receptor GPVI in humanized mouse models efficiently reduced the growth of established metastases, independently of active platelet binding to tumor cells in the bloodstream. Our study is the first to demonstrate therapeutic efficacy when targeting animals bearing growing metastases. It further identifies GPVI as the first molecular target whose inhibition can impair metastasis without inducing collateral hemostatic perturbations.
Project description:The Notch signaling pathway is a cell-cell communication system with fundamental roles in embryonic development and the nervous system, including neural stem cell proliferation and differentiation. To investigate the multivalency effect of ligands on the activation of the Notch receptor, we treated iPSc-derived neuroepithelial stem-like (lt-NES) cells with different Jag1 nanopatterns on DNA origami nanostructures.
Project description:Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the transcriptional changes. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cluster 4 Mutation (ZFC4mut) and Sall4 Zinc Finger Cluster 4 Deletion (ZFC4Δ) respectively that we have considered for our study.
Project description:TRAIL cytotoxicity is exploited as anti-cancer therapy since many years, however incomplete knowledge is generating many obstacles. Here, we address whether the highly abundant extracellular matrix molecule tenascin-C (TNC) orchestrating an immune suppressive tumor microenvironment and binding TRAIL impacts TRAIL cytotoxicity. We used an immune competent autologous NT193 breast cancer model with a knockdown (KD) of Tnfsf10 (encoding TRAIL) and observed accelerated tumor growth marked by less apoptosis, more proliferation and less myeloid cell infiltration as seen by flow cytometry. Grafting the same Tnfsf10 KD cells into a TNC knockout host showed repressed tumor growth suggesting that TNC is involved in regulating TRAIL functions.
Project description:We investigated the features of cells eliminated during early mouse embryogenesis by means of Single Cell RNA-Sequencing (RNA-Seq). To enrich for apoptotic cells, we treated a number of embryos with caspase inhibitor, and then collected and sequenced single-cells isolated from them.