Cellular noncoding RNA (ncRNA) transcription and regulation has only recently been systematically investigated. Extended transcriptomic analysis from recent studies has demonstrated abundant transcription of a set of ncRNAs preferentially within tumors, as opposed to normal tissue. Many of those ncRNA are associated with repeated regions of the genomes that in steady state are prone to regulation by epigenetic silencing. The contribution of the abnormal expression of this component of the dark matter genome to the oncogenic or antitumoral process remains unknown. In some cases, these tumor-associated ncRNAs have been associated with specific inflammatory transcriptomic regulation such as type I-IFN signatures, suggesting that the cell can sense these ncRNA and that they have potential immunostimulatory qualities. Derived from Eukaryotic cells possess a large panel of innate immune nucleic acid sensors, allowing the recognition of exogenous nucleic acids associated with microbial infections, but also of endogenous nucleic acids. Nucleic acid recognition is strongly associated with the antiviral innate immune response, autoimmune diseases development such as SLE and RA, but also inflammatory cancer development and anti-cancer immunity priming. The goal of this project was to identify novel endogenous immune modulators derived from tumor-associated ncRNAs that have immune stimulatory properties.

Using mathematical methods adapted from physics statistics we previously analyzed the viral genome versus their host genomes and identified abnormal nucleotide motifs patterns. Using this novel approach to quantify transcriptome-wide motif usage in human and murine ncRNAs, we observed that, whereas most of the ncRNA are similar to the coding genome, an outlier subset of tumor-associated ncRNAs, typically of recent evolutionary origin, has motif usage more associated with pathogen derived RNA. Previous extended analysis of viral genomes highlighted that such motif patterns are strongly associated with immunogenic properties and absence of host-pathogen adaptation.

We have now demonstrated that those ncRNA function directly as immunostimulatory “self-agonists” and can be classified as danger associated molecular patterns (DAMPS). A key subset of these ncRNA directly activate cells of the mononuclear phagocytic system (MPS), inducing pro-inflammatory cytokines in a MYD88 and UNC93b-dependent and possibly TLR8-dependant manner. Some of these ncRNA are also upregulated in specific tumor cell lines when they proliferate in spheroids. We have shown that the high level of ncRNA expression also correlates with immunogenic properties related to the RNA extracted from those tumor spheroids versus their 2D counterparts.

We therefore propose that a part of the innate response in tumors could initiate from direct, likely extrinsic, interaction of immunogenic ncRNAs expressed in cancer cells, with innate pattern recognition receptors on APC. We are extensively characterizing the innate immune pathways involved in their sensing using forward genetic strategies, biochemistry and cellular biology techniques. We are also characterizing their intrinsic functions at the cellular level and to understand their function in the tumor microenvironment. The pattern of expression in different cancer models is under evaluation to establish their relevancy as prognostic and therapeutic strategies, or as biomarkers in addition to characterizing their relevancy as new immunotherapeutic adjuvants.

In conclusion, we are characterizing an epigenome guardian function related to the newly discovered immunogenic properties of those non-coding RNA. Deeper analysis and refinement of our computational analysis will allow us to associate specific RNA features to their immunogenic properties in cancer.

Citation Format: Antoine Tanne, Luciana Muniz, David Ting, Arnold Levine, Nina Bhardwaj, Benjamin Greenbaum. Unraveling predicted immunomodulatory effects of novel cancer-associated noncoding RNAs. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A077.