Whole genome transcriptome profiling is a valuable tool for the understanding of drug mode of action. Identifying drug targets and affected pathways upon perturbation or treatment and assigning functions to specific genes are, amongst other, questions that can be tackled through transcriptome analysis.
Biogazelle is a pioneer in the study of long non-coding RNAs. While more than 60,000 lncRNAs have been identified in the human genome, just a tiny fraction of them has been functionally characterized to date. With the aim of establishing a catalog of human lncRNA functions, we performed a systematic study where we analyzed the transcriptome of cancer cells upon treatment with 90 different chemical compounds or 90 siRNAs targeting transcription factors. In total, over 200 samples underwent total RNA sequencing, providing comprehensive information on both protein coding and lncRNA expression levels.
The generated data, and its integration with publicly available datasets such as The Cancer Genome Atlas (TCGA) has spurred the development of LNCarta, a proprietary catalog of human lncRNA functions. Further, perturbation and pathway specific lncRNAs were catalogued and used as one of the integrated information layers for therapeutic target selection in Biogazelle’s own drug development program: the development of antisense therapies against oncogenic lncRNAs in lung, liver and colon cancer.