Abstract P4-04-09: Extensive novel hybrid isoforms revealed by RNA sequencing of 120 primary breast cancer samples
Authors: Kim J , Lee H-S , In Y-H , Moon H-G , Lee M , Lee JW , Kim MK , Kim J , You T , Lee E , Park J , Noh D-Y , Kim S , Han W 
Published: August 2014

Introduction

Recent studies of next generation sequencing (NGS) have highlighted the extensive transcriptional heterogeneity of cancer cells. Alternative splicing is one of the evolutionary process by which cells and tissues achieve their specificity within central dogma. Also it is highly assumed to contribute to oncogenesis and thought to be a critical mechanism how cancer cells gain resistance to therapeutic agents and adapt to various circumstances. Relevance of differential splicing in breast cancer biology is mostly unknown. We performed whole transcriptome sequencing (RNA-Seq) to reveal novel splicing alterations among 120 primary breast cancer samples.

Materials and Method

Total RNA was prepared using the Illumina TrueSeq™ RNA sample Preparation Kit and TrueSeq mRNA library was constructed. Clustering and sequencing was done using Illumina HiSeq 2000. RNA-Seq reads were aligned to human reference genome(hg19) using TopHat software and expression was measured using cufflinks software. We used tissues extracted from previously collected 120 fresh-frozen primary breast cancer samples obtained after surgical resection whose clinicopathological data are available. Patients undergone neoadjuvant systemic therapies or stage lV disease at diagnosis were excluded. Thirty-six(30%) cases occurred distant metastasis during follow up. Hormone receptor(HR) was positive in 61(50.8%) samples, 20(16.7%) had HER2 oncogene overexpression and 36(30%) were triple negative breast cancer.

Results and discussion

Total 11345 novel isoforms were detected among 120 tumors. Isoforms of pseudo-genes and exon skipping of the ‘non-coding exon’ were excluded. Splice variants detected in normal reference were sorted out as well. 4045 were in-frame exon skipping and 4960 were off-frame exon skipping which may lead to protein truncation. 5036 were private exon skipping and 3969 isoforms were detected recurrently in more than 2 samples. To minimize false positivity we confined ‘exon skipping’ analysis to those with the expression level (Fragments per kilo-base of exon per million fragments mapped, FPKM) of the skipped exon below 0.1 compared to the adjacent exons. Mean number of exon skipping events per sample was 196.8 (range 75-299, SD 35.9). There were no differences in numbers of exon skipping event among breast cancer subtypes nor distant metastasis. We have identified novel exon skipping in ESR1, CHEK2, EIF3E, FGFR, MAP2K, PIK3R2, TERT, VAV3 genes which is strongly suspected to be novel driver isoforms and is under validation process.

Conclusion We performed whole-transcriptome sequencing with a large set of primary breast cancer samples and revealed extensive transcriptional heterogeneity by isoform profiling. As distinguishing the natural transcriptomic dynamics from oncogenic ‘driver’ isoform is a major challenge, validation and functional studies are ongoing.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-09.