Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer.
Dorothee Pflueger, Christiane Mittmann, Silvia Dehler, Mark A Rubin, Holger Moch, Peter Schraml
Author Information
Dorothee Pflueger: Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland. dorothee.pflueger@usz.ch.
Christiane Mittmann: Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland. christiane.mittmann@usz.ch.
Silvia Dehler: Cancer Registry Zurich and Zug, University Hospital Zurich, Zurich, Switzerland. silvia.dehler@usz.ch.
Mark A Rubin: Institute of Precision Medicine of Weill Cornell Medical College and New York-Presbyterian Hospital, New York, USA. rubinma@med.cornell.edu.
Holger Moch: Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland. holger.moch@usz.ch.
Peter Schraml: Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland. peter.schraml@usz.ch.
BACKGROUND: Chimeric read-through RNAs are transcripts originating from two directly adjacent genes (<10 kb) on the same DNA strand. Although they are found in next-generation whole transcriptome sequencing (RNA-Seq) data on a regular basis, investigating them further has usually been refrained from. Therefore, their expression patterns or functions in general, and in oncogenesis in particular, are poorly understood. RESULTS: We used paired-end RNA-Seq and a specifically designed computational data analysis pipeline (FusionSeq) to nominate read-through events in a small discovery set of renal cell carcinomas (RCC) and confirmed them in a larger validation cohort. 324 read-through events were called overall; 22/27 (81%) selected nominees passed validation with conventional PCR and were sequenced at the junction region. We frequently identified various isoforms of a given read-through event. 2/22 read-throughs were up-regulated: BC039389-GATM was higher expressed in RCC compared to benign adjacent kidney; KLK4-KRSP1 was expressed in 46/169 (27%) RCCs, but rarely in normal tissue. KLK4-KRSP1 expression was associated with worse clinical outcome in the patient cohort. In cell lines, both read-throughs influenced molecular mechanisms (i.e. target gene expression or migration/invasion) in a way that counteracted the effect of the respective parent transcript GATM or KLK4. CONCLUSIONS: Our data suggests that the up-regulation of read-through RNA chimeras in tumors is not random but causes regulatory effects on cellular mechanisms and may impact patient survival.
