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Identifying network control elements in breast cancer oncogenic transformation via whole transcriptome analysis

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Transcriptome analysis in cancer

Understanding tumour development is a prerequisite to a rational design for cancer therapies. Modern molecular biology allows researchers to view the whole process of change during cancer development at high resolution using next generation sequencing (NGS) technology.

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The transcriptome is the set of all RNA molecules, including coding and non-coding RNA, produced in single cell or a population of cells. Development of new tools in transcriptome quantification helps to decipher the process of oncogenic transformation. An EU-funded Marie Curie project, CONTROLNETONCTRANS, has tested the hypothesis that the molecular pathway in transformation, as a network of defined interactions, can be quantified and used to build a picture for phenotype description. The goal of the project was to follow an in vitro oncogenic transformation using transcriptome modifications, and to identify specific interactions within the pathway as the basis for further study. Researchers established new protocols, collected biological materials, and analysed them using NGS. Analysis of the data from in vitro oncogenic transformations studies led to the conclusion that the transcription factor GATA-3 is of special importance in breast cancer. Additional experiments with this transcription factor have identified the role of specific mutations that are critical for progression and clinical manifestation of breast cancer. Identifying a unique role for micro RNA miR-190b in ER negative breast cancer phenotype added to novel methods to quantify the joint expressions of micro RNAs and genes. These molecular partnerships can be used to stratify patients into clinical phenotypes. CONTROLNETONCTRANS research has validated the whole-transcriptome approach to study the mechanisms of tumourigenesis. Such findings may improve our understanding of the transformation in cancer and produce novel targets for therapeutic intervention.

Keywords

Tumourigenesis, transcriptome, RNA, next generation sequencing, micro RNA, miR-190b

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