Selection and functional analysis of lncRNAs under the effect of DNA methylation involved in tumor progression in an immune-mediated dormancy model

Abstract

Cutaneous melanoma is a typically aggressive malignant neoplasm due to its high metastatic capacity. The causal process is multifaceted, with potential contributions from genetic, phenotypic, and environmental factors. Exposure to ultraviolet light is the primary risk factor for disease development due to its high mutagenic potential in cellular genetic material. In addition to permanent genome mutations, there are epigenetic changes also associated with the development and progression of tumors in multiple types of malignancies.One form of epigenetic modulation arises from long non-coding RNA sequences (lncRNAs), which are especially important for their ability to form secondary structures and interact with the genome, regulating gene expression before, during, and after transcription. Another important epigenetic mark is DNA methylation, directly linked to the phenotype adopted by the cell. In the context of cancer, these marks mostly involve the activation of oncogenes or the repression of tumor suppressor genes.Regarding tumor maintenance and progression, the role of the microenvironment is crucial, primarily due to its capacity to corrupt and orchestrate physiological processes, aiming for a more migratory and flexible cellular phenotype. As the immune system often facilitates and frequently contributes to tumor spread, it is understood that when there is a "stalemate" between the immune response and neoplastic cells, it can remain in a state of tumor dormancy (immunomediated). Any disturbance tending toward either side can trigger the resumption of the tumorigenic process or its annulment.Our laboratory has a well-established cellular model of tumor progression consisting of melanocytes (melan-a), non-metastatic melanoma cells, and metastatic melanoma cells (referred to as 4C11- and 4C11+, respectively). Additionally, there is a model of immunomediated tumor dormancy achieved by injecting a sub-tumorigenic dose (103 cells) of melanoma cells along with a large number of apoptotic cells. Thus, two groups of mice were subjected to the injection of a tumorigenic dose (2.105 cells) or the co-injection by the dormancy model (103 melanoma cells + 106 apoptotic cells), with half of the animals in each group left untreated and half treated with a demethylating agent (5azaCdR).Tumors collected from these groups underwent DNA and RNA extraction for analysis of the methylome and transcriptome, respectively. The data obtained will be evaluated for lncRNAs whose expression and methylation have been altered by treatment with the demethylating agent, aiming to select lncRNAs related to tumor promotion under the action of DNA methylation for in vitro and in vivo functional studies. This study may reveal epigenetically regulated lncRNAs with a role in tumor progression and the awakening of dormant melanoma cells, which could be future therapeutic targets.