Surveying lncRNA-lncRNA cooperations reveals dominant effect on tumor immunity cross cancers

Long non-coding RNAs (lncRNAs) can crosstalk with each other by post-transcriptionally co-regulating genes involved in the same or similar functions; however, the regulatory principles and biological insights in tumor-immune are still unclear. Here, we show a multiple-step model to identify lncRNA-lncRNA immune cooperation based on co-regulating functional modules by integrating multi-omics data across 20 cancer types. Moreover, lncRNA immune cooperative networks (LICNs) are constructed, which are likely to modulate tumor-immune microenvironment by regulating immune-related functions. We highlight conserved and rewired network hubs which can regulate interactions between immune cells and tumor cells by targeting ligands and activating or inhibitory receptors such as PDCD1, CTLA4 and CD86. Immune cooperative lncRNAs (IC-lncRNAs) playing central roles in many cancers also tend to target known anticancer drug targets. In addition, these IC-lncRNAs tend to be highly expressed in immune cell populations and are significantly correlated with immune cell infiltration. The similar immune mechanisms cross cancers are revealed by the LICNs. Finally, we identify two subtypes of skin cutaneous melanoma with different immune context and prognosis based on IC-lncRNAs. In summary, this study contributes to a comprehensive understanding of the cooperative behaviours of lncRNAs and accelerating discovery of lncRNA-based biomarkers in cancer.