Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

Abstract

22Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases 23 such as cancer, although the functions of most remain poorly understood. To address this, here we apply 24 a novel strategy to integrate gene expression profiles across 32 cancer types, and cluster human lncRNAs 25 based on their pan-cancer protein-coding gene associations. By doing so, we derive 16 lncRNA modules 26 whose unique properties allow simultaneous inference of function, disease specificity and regulation for 27 over 800 lncRNAs. Remarkably, modules could be grouped into just four functional themes: 28 transcription regulation, immunological, extracellular, and neurological, with module generation 29 frequently driven by lncRNA tissue specificity. Notably, three modules associated with the extracellular 30 matrix represented potential networks of lncRNAs regulating key events in tumour progression. These 31 included a tumour-specific signature of 33 lncRNAs that may play a role in inducing epithelial-32 mesenchymal transition through modulation of TGFβ signalling, and two stromal-specific modules 33 comprising 26 lncRNAs linked to a tumour suppressive microenvironment, and 12 lncRNAs related to 34 cancer-associated fibroblasts. At least one member of the 12-lncRNA signature was experimentally 35 supported by siRNA knockdown, which resulted in attenuated differentiation of quiescent fibroblasts to a 36 cancer-associated phenotype. Overall, the study provides a unique pan-cancer perspective on the lncRNA 37 functional landscape, acting as a global source of novel hypotheses on lncRNA contribution to tumour 38 progression. 39 Author Summary 40The established view of protein production is that genomic DNA is transcribed into RNA, which is then 41 translated into protein. Proteins play a critical role in shaping the function of each individual cell in the 42human body yet they represent less than 2% of human genomic sequence whilst up to 90% of the genome 43 is transcribed. To explain this disparity, the existence of thousands of long non-coding RNAs (lncRNAs) 44 has emerged that do not encode proteins but perform function as an RNA molecule. Most lncRNAs have 45 yet to be assigned a specific biological role, so to address this we apply a novel computational approach 46 to characterise the function of >800 lncRNAs through consistent association with protein coding genes 47 across multiple cancer types. By doing so, we discover 16 "modules" of closely related lncRNAs that 48