Abstract 269: Small non-coding RNA profiling in stool and plasma samples to explore potential biomarkers for colorectal cancer diagnosis
Authors: Antonio Francavilla, Sonia Tarallo, Giulio Ferrero, Francesca Cordero, Gaetano Gallo, Veronika Vymetalkova, Ludmila Vodickova, Pavel Vodicka, Barbara Pardini, Alessio Naccarati
Journal: Cancer Research (2020)

Abstract Colorectal cancer (CRC) is one of the most frequent cancers worldwide. The available screening tests have reduced the incidence and mortality for this cancer; however, the research of new potential molecular biomarkers to use concomitantly could improve advanced adenomas/CRC early detection. Small non-coding RNAs (sncRNAs) are stable, easy detectable molecules that have been found dysregulated in several diseases including CRC. Besides the most studied microRNAs (miRNAs), sncRNAs include also P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), transfer RNAs (tRNAs) and other miscellaneous RNAs, all with key roles in post-transcriptional regulation. The aim of the present study was to identify by next-generation sequencing (NGS) signatures of sncRNAs other than miRNAs, in fecal and plasma extracellular vesicles (EVs) samples potentially able to detect patients with adenomas or CRC. We initially performed a small RNA-sequencing in samples from 221 subjects collected at colonoscopy. The group included: i) 80 healthy subjects with negative colonoscopy results; (ii) 43 adenoma patients; (iii) 41 individuals with inflammatory bowel disease and (iv) 57 newly diagnosed CRC patients. A computational pipeline for the identification of sncRNAs after miRNA mapping reads was previously implemented by our group. In stool samples, comparing the categories of interest mentioned above, we identified 395 differentially expressed sncRNAs (DEsncRNAs), mainly piRNAs (46.3%) and tRNAs (43.6%) (likelihood ratio test adjusting for sex and age, FDR adjusted p ≤ 0.05). Similarly, a group of 32 DEsncRNAs was detected in plasma EVs with piRNAs (41%) and tRNAs (44%) resulting among the most altered. Small RNA-sequencing has also been performed in a subset of 24 paired colorectal tumor and adjacent non-malignant tissues from the CRC patients for whom stool and plasma samples were analysed. Fifty-seven DEsncRNAs were found in tumor vs. non-malignant adjacent tissue with a similar distribution of dysregulated sncRNA biotypes. Some DEsncRNAs were shared between stool and tissues (n=35), plasma EVs and tissues (n=11) and, interestingly, among the profiles of the three different biospecimens (n=10). To validate our findings, we also sequenced stool samples from an independent cohort from the Czech Republic (at present 22 healthy subjects, 19 with inflammations, 21 with adenomas and 34 CRC patients). A total of 100 DEsncRNAs were detected in this validation cohort, among which 43 overlapped with those detected in the Italian cohort. In conclusions, we show that besides the most widely performed miRNA profiling, also the detection of sncRNAs in surrogate tissues by NGS may help to identify reliable and comparable results with those of primary tissues. To further investigate these molecules may provide new accurate markers for CRC diagnostic purposes. Citation Format: Antonio Francavilla, Sonia Tarallo, Giulio Ferrero, Francesca Cordero, Gaetano Gallo, Veronika Vymetalkova, Ludmila Vodickova, Pavel Vodicka, Barbara Pardini, Alessio Naccarati. Small non-coding RNA profiling in stool and plasma samples to explore potential biomarkers for colorectal cancer diagnosis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 269.