The transcriptome plasticity of genomic amplification in cancer

Genomic amplification, in the form of homogeneously staining regions, double minutes, and ring/giant rod-shaped markers, is a pivotal event in many tumors. It was recently shown that amplifications as extra-chromosomal DNA are present in nearly half of all tumors, representing a driving force towards their accelerated evolution. To achieve a better understanding of the implications of genomic amplifications we focused on their structure and impact upon transcription. Amplified cancer-associated genes are often overexpressed as a direct consequence of the copy number gain. We analyzed the whole genome (WGS) and transcriptome (RNA-seq) sequencing data of nine small lung carcinoma (SCLC), seven neuroblastoma (NB) and three well- differentiated liposarcoma (WDLPS) cell lines, all carrying genomic amplifications. A widespread heterogeneity was detected in the amplicon arrangement of many cell lines, disclosing the progressive evolution of their structure through cell division. By integrating the WGS (structural variation calling) and RNA-seq (chimeras detection) data we detected a burst of chimeric transcripts partially derived from post- transcriptional events (i.e cis- or trans-splicing) in most of the analyzed cell lines. Notably, we found PVT1 and RLF as hotspots for cis- or trans-splicing events in SCLC and NB cell lines with MYC and MYCL1 amplifications, respectively. In WDLPS cell lines we found fusion genes originated by extremely complex genomic rearrangements, such as those involving three partner genes or assembled by multiple interposed non-contiguous, non-collinear genomic fragments (spliced out in the mature transcript). Our results strongly indicate that the “amplification/overexpression” paradigm does not cover all aspects of the genomic amplification impact upon transcription. The extraordinary transcriptome plasticity herein described, enriching the genetic repertoire of cancer cells with genomic amplifications, likely provides a selective advantage and might have a crucial role in cancer establishment and progression.