Abstract 2392: Transcriptome analysis from a linear melanoma progression model reveals lncRNAs involved with malignancy, EMT and metastasis

In the human genome, it is estimated that more than 90% of all transcripts are transcribed into non-coding RNAs (ncRNA), classified as small (such as miRNAs) and long (lncRNA). It has been demonstrated that ncRNAs have an important role in biological processes, such as proliferation, differentiation and cellular migration. Changes in their expression have been associated to several diseases, including cancer. Melanoma is one of the most aggressive types of cancer, with high probability of metastasis and showing an unfavorable response to therapies. Our lab has developed a melanoma progression model, which was established by exposing nontumorigenic melanocytes to sustained stressed conditions (cycles of adhesion blockage), sequentially generating 4 cell lines (melan-a, nontumorigenic melanocytes; 4C, premalignant melanocytes; 4C11-, non-metastatic melanoma cells; 4C11+, metastatic melanoma cells) in which different cell lines represent distinct stages of the progression. Previous data comparing the RNA sequencing results from all 4 cell lines identified a total of 3662 genes, coding and non-coding, which displayed differentiated expression (DE) levels when comparing two or more cell lines. Out of them, 492 were DE lncRNAs. We categorized them into three distinct signatures: malignancy, epithelial mesenchymal transition (EMT), or metastasis, according to their expression profile. We analyzed the neighboring genes from those lncRNAs, as it is well described that lncRNA might regulate the gene expression of its neighbors in cis. We identified the lncRNA Dlx4os, with 6 neighbor genes correlated to EMT signature and overall survival of melanoma patients using two different melanoma cohorts (TCGA and Leeds). Among them, the Dlx4 gene, which expression correlates to poor prognosis, shares the same promoter site on opposite strands in chromosome 11 with Dlx4os. We also identified HOTAIR, a well described lncRNA, altered in the EMT signature. We silenced HOTAIR, Dlx4os and Dlx4 on 4C and 4C11- cell lines through RNA interference. We studied their impact on EMT-related genes and observed a change in RNA and protein expression levels, indicating that they might play a role on EMT. Dlx4os also altered cell migration in vitro and tumorigenesis in vivo. We aim to identify lncRNAs that have specific roles in melanoma progression and understand their mode of action. The results could be used as the basis for new prognostics techniques, diagnostic and melanoma therapy, as it may contribute to a better understanding of the role of lncRNAs on the melanoma genesis and progression. Citation Format: Ana L. Ayub, Diogo Pessoa, Lenial A. Sejour, Ioannis Vlachos, Jeremie Nsengimana, Julia Newton-Bishop, Eduardo M. Reis, Frank J. Slack, Miriam G. Jasiulionis. Transcriptome analysis from a linear melanoma progression model reveals lncRNAs involved with malignancy, EMT and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2392.