ABSTRACT: Patient-matched normal kidney organoid (103H) and MRT tumoroid (103T2) models were treated for 24h with either DMSO (ctrl), 400nM MTX, or 50nM BAY to investigate the direct effects of drug treatment on the expression of key metabolic enzymes in the nucleotide biosynthesis pathways.
Project description:This experiment sought to explore the niche factors that intestinal smooth muscle tissue provide to intestinal epithelium, and how this can affect epithelial growth. We first generated a conditioned medium from dissected duodenal smooth muscle explants, then used this conditioned medium to treat 3 intestinal organoid lines from WT C57Bl6 mice and 3 intestinal tumoroid lines from ApcMin mice (C57Bl6 background) 2 days after seeding. To see initial gene expression changes and how these develop over time, we collected samples for bulk RNASeq at 0min (untreated control), 20min, 2h, and 24h after treatment with conditioned medium.
Project description:Our goal and objective of this study is to identify genetic alterations using RNA-seq in a lung cancer organoid (tumoroid) line that we generated in our hospital.
Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome after treatment of organoids with 5ng/mL TNFalpha for 24h and 48h compared with vehicle control (VC). Incubation of organoids (day 25 of differentiation) with TNFalpha led to an activation of NFkappaB signaling, and, interestingly, secretion of cytokines and complement components, alongside with extracellular matrix components. Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement; and production of extracellular matrix. Thus, we provide a repository of kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases. Organoids were grown according to the Freedman protocol (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. We started TNFa stimulation at day 25, with the 24h stimulation ending on day 26 and the 48h stimulation ending on day 27. We chose day 25 because it lies centrally in the day 21 to day 29 window, where we observe reproducible spheroids with limited off-target differentiation of organoids, which becomes an issue after day 29.
Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome after treatment of organoids with 5ng/mL TNFalpha for 24h and 48h compared with vehicle control (VC). Incubation of organoids (day 25 of differentiation) with TNFalpha led to an activation of NFkappaB signaling, and, interestingly, secretion of cytokines and complement components, alongside with extracellular matrix components. Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement; and production of extracellular matrix. Thus, we provide a repository of kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases. Organoids were grown according to the Freedman protocol (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. We started TNFa stimulation at day 25, with the 24h stimulation ending on day 26 and the 48h stimulation ending on day 27. We chose day 25 because it lies centrally in the day 21 to day 29 window, where we observe reproducible spheroids with limited off-target differentiation of organoids, which becomes an issue after day 29.
Project description:To determine the effects of chemotherapy on cell state dyanmics, VAKPS tumroids were treated with FOLFIRI or DMSO for 72hrs before analyzing their transcriptome. We then performed gene expression profiling analysis using data obtained from mRNA-seq of the indicated tumoroid lines.
Project description:Transcriptional profiling of Curcumin treated S. mansoni adult worms (15uM of Curcumin in DMSO during 24h) vs. Non-treated S.mansoni adult worms (DMSO during 24h)
Project description:Background: Though it is acknowledged that ischemia reperfusion injury is the primary pathology of cold storage associated kidney transplantation, its underlying mechanism is not well elucidated. Method: To extend the understanding of molecular event and mine hub genes post-transplantation, we performed bulk RNA-sequencing at different time points (24h, day7 and 14) on a murine kidney transplantation model with prolonged cold storage (10h). Result: In the present study, we showed that genes related to regulation of apoptotic process, DNA damage response, cell cycle/proliferation and inflammatory response were steadily elevated at 24h and day7. The upregulated gene profiling delicately transformed to extracellular matrix organization and fibrosis at day 14. It is prominent that metabolic associated genes persistently took the first place among downregulated genes. The gene ontology terms of particular note to enrich are fatty acid oxidation and mitochondria energy metabolism. Correspondingly, the key enzymes of the above processes were the products of hub genes as recognized. Moreover, we highlighted the proximal tubular cell specific increased genes at 24h by combining the data with public RNA-seq performed on proximal tubules. We also focused on ferroptosis related genes and fatty acid oxidation genes to show profound gene dysregulation in kidney transplantation. Conclusion: The comprehensive characterization of transcriptomic analysis may help provide diagnostic biomarkers and therapeutic targets in kidney transplantation.
Project description:Use of single-cell transcriptomics to test early HD selective vulnerability by comparing CTRL and HD telencephalic organoids at day 45 and 120 of differentiation. To test the influence and the interactions between healthy and HD cells, chimeric organoids composed of CTRL and HD cells juxtaposed within the same organoid were grown and analyzed by scRNAseq at day 120.
Project description:AU-15330 treatment RNA-seq dataset: Fastq transcriptomic sequencing files from Z138 mantle cell lymphoma (MCL) cell line treated with the SMARCA4 degrader AU-15530. Cells were treated for 8 or 24 hours with 0.5 μM AU-15530 or control (DMSO). The dataset includes 3 biological replicates per condition (AU-15530 8h, AU-15530 24h, DMSO 8h, DMSO 24h).
