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Abstract 1538: Association of ceRNA dysregulation with clinical Response to Immunotherapy in cutaneous melanoma (CM)


 Cutaneous melanoma (CM) is an aggressive malignant tumor of epidermal melanocytes for which treatment options and survival chances decrease dramatically when metastatic. To date, immunotherapy is becoming a new standard treatment for CM although less than 30% of the patients´ response positively. Therefore, there is a strong interest to identify response predictors and molecular pathways that might lead to therapy failure. Two novel biomarker sources are LncRNA and CircRNA which can function as natural sponges of miRNA as competitive endogenous RNAs (ceRNA) or can associate to RNA-Binding Proteins (RBP) to regulate gene expression. Moreover, several studies have revealed that ceRNA networks are implicated in tumorigenic processes. Considering this, we set to interrogate the role of the ceRNA in the prediction of response to CM immunotherapy. In this pilot study, differential expression was quantified by RNA-seq in 16 FFPE pre-treatment metastatic samples from CM patients treated with Nivolumab. Total RNA isolation was performed from 10 µm slides (4) with RNAeasy FFPE kit. Total RNAseq was done with Truseq Stranded RNA gold kit, and libraries were sequenced on Illumina Nextseq 550. LncRNA were obtained by STARs alignment and explored on LncATLAS. To assess the presence of high confident cirRNA we used 5 different pipelines with a minimum filtering cut-off of 2 junction reads in at least 2 samples and with at least 3 software. Deseq2 pipeline of total mapped reads was used to perform differential expression. We identified 23 circRNA and 74 lncRNA differentially expressed (DE) with a fold change of 1.5 and a p value < 0,01. Ingenuity pathway analysis was carried out to generate DE ceRNA-mRNA networks and associated RBP networks. Interestingly, in the DE ceRNA-mRNA networks, most of the 47 significant canonical pathways comprised immunological pathways such the antigen presentation pathway, Th1 and Th2 activation pathways and PD1-PDL1 cancer immunotherapy pathways. Regarding the DE ceRNA associated RBP networks, HOTAIR regulatory pathway and senescence as well as G1/S cell cycle checkpoint regulator pathways were enriched. Furthermore, we were able to predict the interaction of the DE ceRNA with the activation of key promoters of the immune response such as IL27 (Interleukin 27), EIB3 (Epstein-Barr Virus Induced 3), IL2 (Interleukin 2) and IFNA2 (Interferon Alpha2), as well as the inhibition of negative immune regulators such as SAFB2 (Distal-Less Homeobox 2) and FOXD1 (Forkhead Box D1). In conclusion, we have evidenced for the first time the potential utility of ceRNA as immunotherapy predictors. We have generated a response signature of ceRNA expression and used network analysis to associate them with specific key modulators of the immune response. This study opens a new venue for the investigation of the role of these regulatory ncRNA in the resistance to immunotherapy in cancer.
 Citation Format: Javier Oliver, Juan Luis Onieva, Maria Garrido-Barros, Alicia Garrido-Aranda, Vanessa De Luque, Martina Alvarez, Alfonso Sanchez, Elisabeth Perez, Patricia Chaves, Maria Jose Lozano, Miguel Berciano, Manolo Cobo, Emilio Alba, Antonio Rueda, Isabel Barragan. Association of ceRNA dysregulation with clinical Response to Immunotherapy in cutaneous melanoma (CM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1538.