2442 - RNA expression profiles and splicing alterations in grade 1/2 neuroendocrine neoplasms from small intestine origin (siNENs). Final results of the GETNE-NETSEQ study

Background

Despite favorable clinical and pathological prognostic factors, some patients (pts) with siNENs have impaired survival. In this study, we aimed to identify distinct RNA expression and splicing profiles (EP and SP, respectively) to correlate with prognosis.

Methods

Paraffin-embedded tumor samples of 48 pts with metastatic grade 1/2 siNENs were analyzed for RNAseq. We generated on average 66 million paired-end reads for each sample on HiSeq2500 (Illumina). RNAseq reads were mapped against the human reference genome (hg19) with Tophat (v2.0.14) and quantified using Cufflinks tools suite for expression analysis. As for splicing, SUPPA2 software was used to detect and quantify the splicing isoforms. 41 samples had sufficient quality to be included in the analysis. We used multivariate Cox proportional models to study the association between clinical variables and EP, SP and overall survival (OS). Poor outcome was defined as death within the first 3 years from advanced stage diagnosis.

Results

9348 transcripts for unique genes were quantified and over 160000 splicing isoforms were examined. A gene signature of 329 transcripts was defined by a two-way statistical analysis between short- and long-term survivors. A pathway enrichment analysis showed a dysregulation in the poor prognosis group on the mTOR and the Toll-like pathways. The EP signature was shown to be an independent prognostic variable for OS (HR 0.05, 95% CI 0.005-0.51, p = 0.011 in multivariate analysis). The analysis of splicing revealed that 90 isoforms were differentially expressed, including those from ELOA and C14orf178 genes, which were associated with aggressiveness.

Conclusions

Different RNA-clusters, different deregulated pathways, and selective splicing alterations were identified for those pts with advanced siNENs with poor prognosis. To our knowledge, this is the first time that Toll-like pathway is involved in the pathogenesis of siNENs and that variants of ELOA and C14orf178 are linked to this pathology. These results may open the future option for a better management and new actionable pathways in this setting.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

GETNE (Spanish Taskforce for Neuroendocrine and Endocrine Tumors).

Funding

GETNE.

Disclosure

J. Capdevila: Advisory / Consultancy, Speaker Bureau / Expert testimony: Bayer, Sanofi, Eisai, Ipsen, Pfizer, Novartis, Advanced Accelerator Applications, Merck; Leadership role, Research grant / Funding (institution): Astrazeneca, Eisai; Travel / Accommodation / Expenses: Ipsen, Eisai. J. Hernando: Speaker Bureau / Expert testimony: Eisai, Ipsen, Angelini, Roche; Travel / Accommodation / Expenses: Adacap, Novartis, Ipsen, Roche, Astrazeneca, Eisai. All other authors have declared no conflicts of interest.