Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas.

Christophe Hitte,Céline Le Béguec,Benoît Hédan,Edouard Cadieu,Anaïs Prouteau,Nadine Botherel,Kerstin Lindblad-Toh,Thomas Derrien,Aline Primot,Catherine André,Valentin Wucher

doi:10.3390/genes10060477

Abstract

Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression, and more particularly, in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort (n = 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers, and golden retrievers), and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog–human conserved DE lncRNAs, including SOX21-AS, ZEB2-AS, and CASC15 lncRNAs. Using unsupervised co-expression network analysis with coding genes, we inferred the potential functions of the DE lncRNAs, suggesting associations with cancer-related genes, cell cycle, and carbohydrate metabolism Gene Ontology (GO) terms. Finally, we exploited our multi-breed design to identify DE lncRNAs within breeds. This study provides a unique transcriptomic resource for studying oral melanoma in dogs, and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.

Highlights

Mucosal melanomas (MM) are the most frequent form of melanomas in dogs, and they display more aggressive behavior in comparison to cutaneous melanomas
We sampled 39 oral melanomas from three breeds (16 golden retrievers, 13 Labrador retrievers and 10 poodles) that were classified with respect to their oral melanoma locations, which included the tongue for 26% of the annotated cases, followed by the maxilla (18%)
Amongst the long non-coding RNAs (lncRNAs) genes, we focused on long intergenic ncRNAs and antisense lncRNAs, removing sense intronic lncRNAs which may correspond to the misannotation of coding alternative isoforms, and observed that 59.0% and 58.5% respectively could be considered as being expressed, using a soft filter of 10 reads in total per gene

Summary

Introduction

Mucosal melanomas (MM) are the most frequent form of melanomas in dogs, and they display more aggressive behavior in comparison to cutaneous melanomas. Dog breeds with high melanoma risk have been proposed as relevant natural models for the comparative oncology of melanomas, especially for deciphering their non-UV-dependent pathways, and for developing clinical trials that are based on homologous melanoma subtypes [1,2]. A consequence of cumulative genetic and epigenetic alterations in coding and non-coding genes is reflected by the study of gene expression, which has not yet been investigated in detail in canine model cancers. Despite the recent identification of thousands of canine long non-coding RNAs (lncRNA) [5,6], little is known about their impact in dog cancers, they constitute an extensive component of dog genomes [7,8,9]. LncRNA expression is recurrently altered in many types of cancers [10,11,12], including melanomas [13]. Because lncRNAs are expressed in a tissue-specific manner in both humans [8,16] and dogs [6], they represent a vast and still unexplored repertoire of potential targets and/or biomarkers for comparative oncology approaches

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Conclusion