1. Identifying somatic changes in drug transporters using whole genome and transcriptome sequencing data of advanced tumors
- Author
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van de Geer, Wesley S., Mathijssen, Ron H.J., van Riet, Job, Steeghs, Neeltje, Labots, Mariette, van Herpen, Carla, Devriese, Lot A., Tjan-Heijnen, Vivianne C.G., Voest, Emile E., Sleijfer, Stefan, Martens, John W.M., Cuppen, Edwin, van de Werken, Harmen J.G., Bins, Sander, Internal medicine, AII - Cancer immunology, CCA - Cancer biology and immunology, CCA - Imaging and biomarkers, RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, Interne Geneeskunde, MUMC+: MA Medische Oncologie (9), Medical Oncology, and Immunology
- Subjects
Pharmacology ,Whole-genome sequencing ,CELL LUNG-CANCER ,Precision medicine ,RNA sequencing ,ANTHRACYCLINE-INDUCED CARDIOTOXICITY ,General Medicine ,All institutes and research themes of the Radboud University Medical Center ,SDG 3 - Good Health and Well-being ,Pharmacogenetics ,Drug transporters ,SLC28A3 ,Pharmacogenomics ,Metastatic cancer ,RESISTANCE ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] - Abstract
Drug resistance is a perpetual problem in cancer therapy with many underlying mechanisms. Alterations in drug transport over the cancer cell membrane can severely alter intratumoral drug exposure, contributing to resistance. Here, we present the somatic mutational landscape of 48 ATP-binding cassette and 416 solute carrier transporter genes in a cohort (CPCT-02; NCT01855477) of 3290 patients with different types of advanced and metastasized cancer through analysis of whole genome and transcriptome sequencing. In order to identify potential stressor mechanisms, we stratified patients based on previous systemic therapies and subsequently investigated the enrichment of mutations and copy-number alterations of transporter genes. In tumors from patients pretreated with protein kinase inhibitors (PKIs), genes encoding for specific copper (SLC31A1 and SLC31A2, χ2-test adjusted p-values: 6.9e-09 and 2.5e-09) and nucleoside transporters (SLC28A2 and SLC28A3, χ2-test adjusted p-values: 3.5e-06 and 6.8e-07) were deleted significantly more frequently than in patients pretreated with chemotherapy. Moreover, we detected 16 transporters that were differentially expressed at RNA level between these treatment groups. These findings contradict mechanisms of selective pressure, as they would be expected to originate during treatment with chemotherapy rather than with PKIs. Hence, they might constitute primary drug resistance mechanisms and, therefore, warrant further study.
- Published
- 2023