Non-coding RNAs (ncRNAs) play a role in various hallmarks of cancer. Their expression pattern is often remarkably condition specific, suggesting that some may function as lineage survival oncogenes. As such, they can be exploited as targets for nucleic acid based therapy, avoiding on-target toxicity. We reprocessed small RNA and polyA+ RNA sequencing data of The Cancer Genome Atlas and Target database, resulting in the annotation and quantification of (iso)miRNAs, mRNAs and lncRNAs in almost 12,000 patient samples from 35 cancer types. Using specificity score analysis, a list of several hundreds ncRNAs with cancer-specific expression pattern was established. For further gene prioritization, expression data from healthy controls, matching DNA copy-number data and clinical data will be integrated. Top-ranked ncRNAs are likely to have both therapeutic relevance and diagnostic value.
Besides therapeutical importance, the cancer-type-specific RNAs have biomarker potential. In order to evaluate the potential of these cancer-type-specific ncRNAs as non-invasive biomarkers, we collected a cohort of plasma samples from metastatic cancer patients representing 34 cancer types. Our preliminary findings indicate that a subset of cancer-type specific RNAs are detectable in plasma and may be used as biomarkers for diagnosis or disease monitoring.
- I obtained a Master in Biochemistry and Biotechnology with a major in Bioinformatcis and System Biology (UGent, 2012), followed by a Teacher Education (UGent, 2013). Prior to being a full-time doctoral fellow (from 2015 onwards, FWO strategical basic research fellowship (former IWT)) at UGent, I was a lecturer at Ghent University College HoGent (2013-2015).
- I got the opportunity to talk about my doctoral research at OncoPoint 2016 (Ghent) (received presentation award), BIG N2N annual meeting (2016, Ghent), EMBL Big data in Biology and Health (2016, Heidelberg), Baylor College of Medicine (2017, Houston), MD Anderson (2017, Houston), Science Slam 200 years UGent (2nd place), OncoPoint 2018 (Ghent) (received a presentation award), Keystone Precision Medicine in Cancer (2018, Stockholm) and Pint of Science (2018, Ghent)
- Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope? Helsmoortel H., Everaert C., Lumen N., Ost P., Vandesompele J., Non-coding RNA Research 2018
- Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data. Everaert C, Luypaert M, Maag JLV , Xiu Cheng Q, Dinger M, Hellemans J & Mestdagh P, Scientific Reports 2017
- Zipper plot: visualizing transcriptional activity of genomic regions. Avila Cobos F, Anckaert J, Volders P, Everaert C, Rombaut D, Vandesompele J, De Preter K, & Mestdagh P, BMC Bioinformatics 2017
- The transcriptome of lung tumor-infiltrating dendritic cells reveals a tumor-supporting phenotype and a micro-RNA signature with negative impact on clinical outcome. Pyfferoen L, Brabants E, Everaert C, De Cabooter N, Heyns K, Deswarte K, Vanheerswynghels M, De Prijck S, Waegemans G, Dullaers M, Hammad H, De Wever O, Mestdagh P, Vandesompele J, Lambrecht BN & Vermaelen KY, Oncoimmunology 2017
- Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples. Van Goethem A, Yigit N, Everaert C, Moreno-Smith M, Liselot Mus M, Barbieri E, Speleman F, Mestdagh P, Shohet J, Van Maerken T & Vandesompele J, Scientific Reports 2016