Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21583700_1.fastq.gz | Fastqsanger.gz | |||
| SRR21583700_2.fastq.gz | Fastqsanger.gz | |||
| SRR21583701_1.fastq.gz | Fastqsanger.gz | |||
| SRR21583701_2.fastq.gz | Fastqsanger.gz | |||
| SRR21583702_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Treatment of head and neck squamous cell carcinoma (HNSCC) remains challenging and the survival rates of affected patients remain poor. A three-dimensional organotypic co-culture (3D-OTC) model where patient derived tumor tissue is cultured on human-derived fibroblasts (dermal equivalent, DE) was evaluated regarding its comparability to primary tumor tissue and the identification of potential individualized therapeutic targets. Methods: 3D-OTC models were cultured from n=10 HNSCC patients for up to 21 days. The growth pattern at the DE was compared to tumor budding of corresponding resection specimens. Furthermore, we immunohistochemically determined the immune cell infiltrate of primary tumor tissue and corresponding 3D-OTC models. Spatially resolved gene expression analysis (“Xenium in situ”) was performed for separate regions of interest within the 3D-OTC specimens and within primary tumor tissue. Up-regulated and down-regulated genes of the 3D-OTC samples were included in gene set enrichment analysis and up-regulated genes between invasive (invading the DE) and non-invasive tumor cells within the 3D-OTC samples were included in drug sensitivity analyses using publicly available cell line data. Results: The growth pattern observed at the DE was associated with tumor budding in primary tumor tissue. The density of CD3-/CD20-/CD56-positive cells was lower in 3D-OTC samples compared to primary tumor tissue. No such changes were observed for CD68-positive cells and no significant changes in the density of the immune cell infiltrate were detected during the cultivation period. The centroids and dispersion of the gene expression of the 3D-OTC samples did not differ from the corresponding primary tumor tissue. The regions of interest within the 3D-OTC samples showed distinct functional states in gene set enrichment analysis. The comparison of genes up-regulated in invasive tumor parts of the 3D-OTC samples with cell line data revealed potential therapeutic targets. Conclusion: The 3D-OTC model morphologically and transcriptomically resembles primary tumor tissue and its biology while preserving the tumor microenvironment. Furthermore, the 3D-OTC model allows the standardized evaluation of tumor tissue by the definition of transcriptomically separate regions of interest and thus, could help to evaluate the impact of personalized therapeutic interventions on the tumor and its microenvironment in vitro.
2026-05-11 | GSE324934 | GEO
Project description:Urea cycle dysbiosis—a severe metabolic liver disease caused by ornithine transcarbamylase (OTC) deficiency—is associated with hyperammonemia. Its only curative treatment is liver transplantation; however, severe shortage of organ donors poses a major challenge. Here, we report the generation of clinical-grade liver organoids from human induced pluripotent stem cells (hiPSC), which exhibit in vitro and in vivo ammonia metabolic functions. Quantitative metabolic flux analysis shows that the organoids have sufficient OTC enzyme activity and urea-producing function, implying their ammonia-metabolizing efficacy. The organoids show clear ameliorative effects on hyperammonemia when transplanted into mice with mild/severe OTC deficiency. Isotope-labeled ammonia-loading tests in post-transplant recipients confirm the graft’s efficiency in in vivo urea conversion. Moreover, organoid transplantation improves activity and survival rates in severe OTC-deficient mice. Overall, we demonstrate the therapeutic effects of clinically applicable hiPSC-derived organoids, which highlights their potential application in regenerative therapy.
2026-04-01 | GSE263559 | GEO
Project description:Antibiotic resistance (AMR) in aquatic bacteria affecting aquaculture has been a growing concern given the potential for mixing of bacterial populations in the aquatic environment and exposure to different pharmaceuticals from drugs used in aquaculture, as well as wastewater effluent and agricultural run-off. To better understand the mechanism for AMR in a common aquatic fish pathogen exposed to low dose antibiotics we monitored the genetic changes, as well as gene expression, in Aeromonas hydrophila as the bacteria was exposed to incremental doses of oxytetracycline (OTC), a commonly used drug in aquaculture. We were able to render all three isolates of our original A. hydrophila resistant to therapeutic levels of OTC (i.e. ≥100ppm). The relatively quick phenotypic adaptation (often less than 3 days) to different OTC concentrations was very similar across our replicates. Our whole genome sequencing data and transcriptome results suggested several genes underwent point mutations across all replicates. Further differential gene expression was observed and likely impacted several pathways which may explain the progressive resistance to OTC associated with incremental exposure to the drug. The specific mutations consistently identified in isolates exposed to OTC were on AHA_ 2785 (associated with an outer membrane protein), AHA_2910 (involved in the efflux pump mechanism), and AHA_0308 (associated with the small ribosomal subunit protein S10). The pathways involved in the differential gene expression included efflux- pump mechanisms, outer membrane proteins, and ribosomal protein OTC target. Our findings support the notion that AMR can occur via genetic regulation of several intrinsic mechanisms within a bacterial population. This finding could have implications in aquaculture where bacteria such as A. hydrophila can be exposed to varying levels of antibiotics during in-feed treatments.
2025-10-01 | GSE290492 | GEO
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2023-05-16 | GSE232318 | GEO
Project description:Ammonia production via glutamate dehydrogenase is inhibited by SIRT4, a sirtuin that displays both amidase and non-amidase activities. The processes underlying the regulation of ammonia removal by amino acids remain unclear. Here, we report that SIRT4 acts as a decarbamylase that responds to amino acid sufficiency and regulates ammonia removal. Amino acids promote lysine 307 carbamylation (OTCCP-K307) of ornithine transcarbamylase (OTC), which activates OTC and the urea cycle. Proteomic and interactome screening identified OTC as a substrate of SIRT4. SIRT4 decarbamylates OTCCP-K307 and inactivates OTC in a NAD+-dependent manner. SIRT4 expression was transcriptionally upregulated by the amino acid insufficiency-activated GCN2–eIF2a–ATF4 axis. SIRT4 knockout in cultured cells caused higher OTCCP-K307 levels, activated OTC, elevated urea cycle intermediates, and urea production via amino acid catabolism. Sirt4 ablation decreased mouse blood ammonia levels and ameliorated CCl4-induced hepatic encephalopathy phenotypes. We reveal that SIRT4 safeguards cellular ammonia toxicity during amino acid catabolism.
2023-03-29 | PXD037101 | Pride
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2024-01-26 | PXD042182 | Pride