Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.
Vivian LoboEvgeniia ShcherbininaJakub O WestholmIwona NowakHsiang-Chi HuangDavide AngelettiDimitrios G AnastasakisAishe A SarshadPublished in: Scientific data (2024)
In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.
Keyphrases
- genome wide analysis
- single cell
- gene expression
- rna seq
- cell therapy
- molecular dynamics
- mass spectrometry
- dna methylation
- electronic health record
- induced apoptosis
- mesenchymal stem cells
- high resolution
- oxidative stress
- big data
- transcription factor
- small molecule
- liquid chromatography
- deep learning
- cell proliferation
- protein protein
- signaling pathway
- amino acid
- simultaneous determination