Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq analysis of subcutaneous patient-derived neuroblastoma xenografts (LU-NB-3R): Comparison of BAY390, A967079, and vehicle controls

ABSTRACT: Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, particularly in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide valuable insights into potential therapeutic strategies. This experiment assessed the in vivo response to treatment with BAY390 and A967079. A neuroblastoma in vivo model was established via subcutaneous injection of human high-risk, MYCN-amplified neuroblastoma organoids into female NSG mice (PDX, LU-NB-3R). Once tumors reached 150 mm³, mice were randomized into treatment groups: control (n=8), A967079 (n=6), and BAY390 (n=7). All drugs were administered via oral gavage at the following concentrations: A967079 (300 mg/kg, once daily) or BAY390 (90 mg/kg, once daily), with a vehicle control group. Treatment was administered for 21 days, after which mice were euthanized. Tumor samples were collected in RNA later and frozen at -80 °C until RNA extraction. RNA was extracted from tumor tissue, and RNA sequencing was performed.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Erick Andrés Muciño Olmos

PROVIDER: E-MTAB-15002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Underdeveloped lungs are the primary cause of death in premature infants, however, little is known about stem and progenitor cell maintenance during human lung development. In this study, we have identified that FGF7, Retinoic Acid and CHIR-99021, a small molecule that inhibits GSK3 to activate Wnt signaling, support in vitro maintenance of primary human fetal lung bud tip progenitor cells in a progenitor state. Furthermore, these factors are sufficient to derive a population of human bud tip-like progenitor cells in 3D organoid structures from human pluripotent stem cells (hPSC). Functional studies showed that hPSC-derived bud tip progenitor organoids do not contain any mesenchymal cell types, maintain multilineage potential in vitro and are able to engraft into the airways of injured mice and respond to systemic factors. We performed RNA-sequencing to assess the degree of similarity in global gene expression profiles between the full human fetal lung (59-127 days gestation), isolated human fetal bud tip progenitors, organoids grown from primary fetal bud tip progenitors, and hPSC-derived bud tip organoids. Results showed that hPSC-derived organoids have molecular profiles similar to organoids generated from primary human fetal lung tissue. Gene expression differences between hPSC-derived bud tip organoids and fetal progenitor organoids may be related to the presence of contaminating mesenchymal cells in primary cultures. hPSC-derived bud tip organoids are generated from a well-defined human cell sources, offering a distinct advantage over rare primary tissue as a means to study human specific lung development, homeostasis and disease. Sample Nomenclature - Description ------------------------------------------------------------------------- Peripheral fetal lung the distal/peripheral portion of the fetal lung (i.e., distal 0.5 cm) was excised from the rest of the lung using a scalpel. This includes all components of the lung (e.g., epithelial, mesenchymal, vascular). Isolated fetal bud tip the bud peripheral portion of the fetal lung was excised with a scalpel and subjected to enzymatic digestion and microdissection. The epithelium was dissected and separated from the mesenchyme, but a small amount of associated mesenchyme likely remained. Fetal progenitor organoid 3D organoid structures that arose from culturing isolated fetal epithelial bud tips. Foregut spheroid 3D foregut endoderm structure as described in Dye et al. (2015). Gives rise to patterned lung organoid (PLO) when grown in 3F medium. Patterned lung organoid (PLO) lung organoids that were generated by differentiating hPSCs, as described throughout the manuscript. Bud tip organoid organoids derived from PLOs, enriched for SOX2/SOX9 co-expressing cells, and grown/passaged in 3F medium.

Dataset Information

RNA-Seq analysis of subcutaneous patient-derived neuroblastoma xenografts (LU-NB-3R): Comparison of BAY390, A967079, and vehicle controls

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets