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Updated: Jul 5, 2025
Assessing Cell Cycle Progression of Neural Stem and Progenitor Cells in the Mouse Developing Brain after Genotoxic Stress
Published on: May 7, 2014
Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer
Jonatan L Gabre1,2,3, Peter Merseburger1,2,3, Arne Claeys1,2
1Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent, Belgium.
Abstract:
Neuroblastoma (NB) is the most common cancer in infancy with an urgent need for more efficient targeted therapies. The development of novel (combinatorial) treatment strategies relies on extensive explorations of signaling perturbations in neuroblastoma cell lines, using RNA-Seq or other high throughput technologies (e.g. phosphoproteomics). This typically requires dedicated bioinformatics support, which is not always available. Additionally, while data from published studies are highly valuable and raw data (e.g. fastq files) are nowadays released in public repositories, data processing is time-consuming and again difficult without bioinformatics support. To facilitate NB research, more user-friendly and immediately accessible platforms are needed to explore newly generated as well as existing high throughput data. To make this possible, we developed an interactive data centralization and visualization web application, called CLEAN (the Cell Line Explorer web Application of Neuroblastoma data; https://ccgg.ugent.be/shiny/clean/). By focusing on the regulation of the DNA damage response, a therapeutic target of major interest in neuroblastoma, we demonstrate how CLEAN can be used to gain novel mechanistic insights and identify putative drug targets in neuroblastoma.
Insights
Neuroblastoma (NB) research is advanced by CLEAN, a web tool for exploring high-throughput data. This platform aids in identifying new therapeutic targets by analyzing signaling in neuroblastoma cell lines.
Area of Science:
- Oncology
- Bioinformatics
- Genomics
Background:
- Neuroblastoma (NB) is a prevalent infant cancer requiring improved targeted therapies.
- Developing novel treatments necessitates analyzing signaling perturbations using high-throughput data like RNA-Seq.
- Bioinformatics support is often limited, hindering data exploration and analysis.
Purpose of the Study:
- To develop a user-friendly platform for exploring high-throughput data in neuroblastoma research.
- To facilitate access to and analysis of both new and existing neuroblastoma datasets.
- To aid in identifying novel therapeutic targets by focusing on DNA damage response pathways.
Main Methods:
- Development of an interactive web application named CLEAN (Cell Line Explorer web Application of Neuroblastoma data).
- Centralization and visualization of high-throughput data from neuroblastoma cell lines.
- Focus on the DNA damage response pathway as a key therapeutic area.
Main Results:
- CLEAN provides accessible exploration of neuroblastoma data.
- The platform enables novel mechanistic insights into NB signaling.
- Potential drug targets within the DNA damage response pathway were identified.
Conclusions:
- CLEAN facilitates neuroblastoma research by simplifying data exploration and analysis.
- The application aids in discovering new therapeutic strategies for neuroblastoma.
- CLEAN supports the identification of actionable drug targets for neuroblastoma treatment.
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