Long non‐coding RNA and transfer RNA‐derived small fragments in exosomes are potential biomarkers for canine oral melanoma

Abstract

Novel small non-coding RNAs (sRNAs) represent an emerging line of research in both human and canine oncology, due to their diverse regulatory and functional roles. Novel sRNAs are regarded as distinct from microRNAs, although both are part of the exosomal cargo. Recently, we reported on exosomal miRNAs as biomarkers for canine melanoma; however, it is unknown if novel sRNAs hold similar potential. Accordingly, we aimed to identify and validate novel sRNAs as potential biomarkers of canine oral melanoma, as part of our larger project on sequencing small exosomal RNA for this disease. Next generation sequencing revealed several differentially expressed novel sRNAs in exosomes from two melanoma cell lines (KMeC and LMeC) when compared with reference exosomes (from tumour-free dogs). Among these novel sRNAs, long noncoding RNA fragments, tRNA-derived fragments, snoRNAs and snRNAs were abundantly expressed. We selected four novel sRNAs upregulated in each cell line, and validated their aberrant expression with qPCR. In analysis using plasma-derived exosomes from melanoma patients, six out of the eight selected novel sRNAs showed significantly elevated expression. Receiver operating curve (ROC) analysis showed that one long non-coding RNA-derived small fragment (ENSCAFT00000069599.1) and one transfer RNA-derived small fragment (tRNA-Ala-TGC-5-1) have more than 85% sensitivity and specificity for differentiating melanoma patients from tumour-free dogs.Therefore, we consider that novel sRNAs may serve as candidate biomarkers to facilitate more accurate diagnosis of canine oral melanoma in clinical settings.

Long Non-Coding RNA as a Potential Biomarker for Canine Tumors

“…The study identified 55 exosomal lncRNAs that were differentially expressed and lncRNAs ENSCAFT00000069599.1 and EN-SCAFT00000090032.1 verified significantly high expression levels in canine oral melanoma patients [35]. A particularly interesting finding is that lncRNA ENSCAFT00000069599.1 demonstrated the highest diagnostic efficacy, as determined by receiver operating characteristic (ROC) curve analysis of sensitivity and specificity [35]. This suggests that lncRNA ENSCAFT00000069599.1 has the potential to be a valuable diagnostic biomarker for canine oral melanoma.…”

“…In another study, the analysis focused on novel small non-coding RNAs found in exosomes of two melanoma cell lines (KMeC and LMeC). The study identified 55 exosomal lncRNAs that were differentially expressed and lncRNAs ENSCAFT00000069599.1 and EN-SCAFT00000090032.1 verified significantly high expression levels in canine oral melanoma patients [35]. A particularly interesting finding is that lncRNA ENSCAFT00000069599.1 demonstrated the highest diagnostic efficacy, as determined by receiver operating characteristic (ROC) curve analysis of sensitivity and specificity [35].…”

Exosomal non-coding RNAs: Blueprint in colorectal cancer metastasis and therapeutic targets

“…Small nuclear RNAs (snRNAs) [ 106 ], small nucleolar RNAs (snoRNAs) [ 107 ], and PIWI-interacting RNAs (piRNAs) [ 108 ], are additional ncRNAs that can be discovered in exosomes. In the RNA processing, modification, and genome stability processes, these ncRNA molecules play unique roles [ 107 , 108 ].…”

Novel Y RNA-Derived Fragments Can Differentiate Canine Hepatocellular Carcinoma from Hepatocellular Adenoma

“…Y RNA was selected based on a previously published NGS dataset (SRA: PRJNA716131) for canine mammary gland tumors [36]. The qRT-PCR protocol was described previously [45][46][47]. Briefly, 2 ng (for tissues and cell lines) or 1.25 µL (for plasma and plasma EVs) of total RNA were reverse transcribed to cDNA using the TaqMan MicroRNA Reverse Transcription Kit (Thermo Fisher Scientific) with a T100 thermal cycler, following the manufacturer's protocol.…”