Abstract 2465: Long non-coding RNA ZNF-366-6 predicts lack of response to neoadjuvant chemoradiotherapy in locally advanced rectal adenocarcinoma and presents meaningful biological associations with potential coding cancer driver transcripts related to gastrointestinal cancer pathways
Authors: Ferrando Lorenzo , Cirmena Gabriella , Garuti A , Scabini Stefano , Grillo Federica , Mastracci Luca , Isnaldi Edoardo , Marrone Ciro , Murialdo Roberto , Brown David Norman , Fiocca Roberto , Romairone Emanuele , Ballestrero Alberto , Zoppoli Gabriele 
Published: August 2018

Abstract
Standard treatment for clinical stage II/III rectal adenocarcinoma (READ) includes a combination of chemotherapy with pyrimidine analogues, such as capecitabine, and radiation therapy, followed by surgery after 6 to 12 weeks. Currently no predictors of benefit from neoadjuvant chemoradiotherapy (NACT) exist, and transcriptomic studies, prevalently focused on coding transcripts or miRNAs have so far failed to find clinically useful gene signatures. In the present analysis we assessed the expression levels of 8,127 long non-coding RNAs (lncRNAs), poorly studied in the context of READ, to infer whether they could stratify pre-treatment READ samples according to patients' pathological complete response (pCR).
Methods: We collected and analysed with Agilent SurePrint G3 Human v2 8x60K microarrays, a consecutive series of 49 specimens from READ patients undergoing NACT with a combination of capecitabine (825 mg/m2) and radiation (50.4 Gy) cycles for 6 weeks. We performed a regularized variable selection regression (“glmnet” R package) to identify potential lncRNAs predicting pCR. We then analysed, with a bivariate correlation, the top lncRNAs predictors with the expression of 20,560 coding transcripts represented in the microarrays we used, and performed pathway enrichment analysis using Ingenuity® Pathway Analysis (Qiagen, Inc.).
Results: Out of 49 patients for whom we could obtain snap-frozen biopsies with complete clinical and pathological data, we analysed 30 patients, 12 with minor or absent pathological response and 18 with major or complete response to NACT. We identified a signature of 11 lncRNAs able to successfully stratify responder vs. non-responder patients. By investigating the correlation of these 11 lncRNAs with coding transcripts, we identified one of them, lnc-ZNF-366-6, presenting an unusually high correlation with more then 1136 coding genes (FDR &lt; 0.01). By gene enrichment analysis we found an enrichment in cancer-related pathways, especially alterations in solid and colon adenocarcinoma pathways (p &lt; 0.01), as well as mitochondrial dysfunction, oxidative phosphorylation and sirtuin signalling pathways (p &lt; 0.00001), defined by the positively and negatively correlated variables with lnc-ZNF-366-6. Moreover, we identified potential drivers of disease or therapeutic targets, either correlated or anti-correlated with lnc-ZNF-366-6.
Conclusions: LncRNAs have the potential to classify responder versus non-responder READ patients undergoing NACT. Lnc-ZNF-366-6 deserves further experimental validation and functional analyses to clarify its exact contribution to resistance to DNA damaging agents, such as radiation, and to inhibitors of DNA/RNA synthesis, such as capecitabine.
Citation Format: Lorenzo Ferrando, Gabriella Cirmena, A Garuti, Stefano Scabini, Federica Grillo, Luca Mastracci, Edoardo Isnaldi, Ciro Marrone, Roberto Murialdo, David Norman Brown, Roberto Fiocca, Emanuele Romairone, Alberto Ballestrero, Gabriele Zoppoli. Long non-coding RNA ZNF-366-6 predicts lack of response to neoadjuvant chemoradiotherapy in locally advanced rectal adenocarcinoma and presents meaningful biological associations with potential coding cancer driver transcripts related to gastrointestinal cancer pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2465.