RNA-seq of tumor organoids from patient-derived xenograft (PDX, LU-NB-2) of high-risk, MYCN-amplified neuroblastoma treated with prochlorperazine (PCZ), pitavastatin (PIT), the combination of both drugs, and untreated controls
Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, especially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of the experiment was to evaluate the effects of treatment of pitavastatin (PIT), prochloperazine (PCZ) and combination (PIT + PCZ) on LU-NB-2 PDX derived organoid model. In our experiments we observed synergistic effects on cell viability and cell death of those two compounds and further RNA-seq was intended to decipher effects of the combination on the neuroblastoma cells. Experimental Workflow:  Sample Preparation: Tumor organoids were generated from PDX models of high-risk neuroblastoma patients with MYCN amplification.   Treatment: LU-NB-2 PDX organoids were dissociated to single cells aseeded in T25 flasks, allowed to grow for 24 h, and treated for 48 h with the combination of PCZ +PIT (1.6 µM and 6.7 µM, n = 8), PCZ only (1.6 µM, n = 8), PIT only (6.7 µM, n = 8), or DMSO (n = 8). The treatment resulted in a ~15% decrease in NB cell viability in the combination group.  RNA Extraction: Total RNA was extracted from the treated and control organoids.  Library Preparation and Sequencing: RNA-seq libraries were prepared and sequenced to generate high-throughput sequencing data.  Data Analysis: Differential gene expression analysis was performed to compare the treated samples against the untreated controls, aiming to elucidate the molecular effects of each treatment.