ArticleMolecular oncology2024
Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer.
Article in Molecular oncology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Functional Depth Biomarkers Distinguish Lung Squamous Cell Carcinoma from Lung Adenocarcinoma.Research square · 2026Article
- Targeting of CDK1 and PRMT5 as a potential therapeutic combination for non-small cell lung cancer.Histology and histopathology · 2026Article
- Neural cues differentially modulate colorectal cancer cell behavior depending on patients' genomic background.iScience · 2026Article
- Common gene mutations in 103 authenticated colorectal cancer cell lines.Oncogenesis · 2026Article
- Fusion-Negative NTRK Overexpression Exhibit Biological Relevance in Colorectal Cancer: Implications for Prediction of Responses to Kinase Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Early host-parasite interaction models reveal a key role for fibrinolysis in Fasciola hepatica intestinal migration.Parasites & vectors · 2025Article
- Clinicopathological characterisation ofJournal of clinical pathology · 2025Article
- Exploring viral mimicry combined with epigenetics and tumor immunity: new perspectives in cancer therapy.International journal of biological sciences · 2025Review
- DNA demethylation triggers cell free DNA release in colorectal cancer cells.Genome medicine · 2024Article
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Authors and funding
19 authors.
Funding
Abstract
Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.
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