Identification of lncRNAs with a role in Melanoma progression and resistance to immunotherapy

• Grant number: 23/17737-8
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: December 01, 2024
• End date: January 31, 2028
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Miriam Galvonas Jasiulionis
• Grantee: Beatriz Cristina Biz Tonin
• Host Institution: Escola Paulista de Medicina (EPM). Universidade Federal de São Paulo (UNIFESP). Campus São Paulo. São Paulo , SP, Brazil
• Associated research grant: 22/00322-7 - Identification and characterization of ncRNAs playing a role in Melanoma phenotypic plasticity, AP.R
• Associated scholarship(s): 25/05877-5 - Exploring lncRNA-mediated immunotherapy resistance in melanoma through spatial analysis, BE.EP.DD

Abstract

Long non-coding RNAs (lncRNAs) are non-protein coding RNAs (ncRNAs) transcripts. It is estimated that 70 to 90% of the human genome is transcribed in ncRNAs. Studies have already demonstrated the importance of lncRNAs in modulating gene expression, making them a significant component of the epigenetic machinery. Melanomas are responsible for about 80% of all deaths related to skin cancers. This is due to its high potential of metastasizing and developing resistance to treatments. Our laboratory has developed a linear cellular model of melanoma progression using the murine non-tumorigenic melanocyte lineage, melan-a, which was subjected to several cycles of dedhesion and re-adhesion, resulting in malignant transformation and the generation of progressively more aggressive cell lines. With this model, we can study melanoma at various stages of its progression, from non-tumorigenic cells (melan-a) to cells with high metastatic potential (4C11+). For this work, we used four cell lines: melan-a, 4C, 4C11- and 4C11+, which were analyzed by RNA-seq for mRNA and lncRNA expression profiles and will undergo weighted co-expression network analysis (WGCNA). A preliminary in silico analysis, aimed at identifying lncRNAs near human genes with prognostic value, defined the lncRNA Slamon as the study target, which is upregulated in the 4C11+ lineage. After in vitro study, its relationship with the neighboring gene Slc25a13 was confirmed, with Slamon expression attenuating the effects caused by this gene, altering migration patterns, clonogenicity, proliferation, anoikis resistance, and drug sensitivity. Additionally, it was observed that both Slamon and Slc25a13 are targets of DNA methylation. These results provide a basis for studying the mechanism of action of this interaction network. The project aims to identify new lncRNAs relevant to melanoma progression using three distinct approaches. The first focuses on the regulatory mechanisms and actions of the Slamon and Slc25a13 genes. The second involves the analysis of lncRNAs by WGCNA, aiming to identify lncRNAs that act as nodes in regulatory networks of gene expression to understand their role in the expression and behavior of melanoma cells. In the third part, we will analyze lncRNAs associated with resistance to immunotherapies (anti-PD1) through spatial analysis of differentially expressed lncRNAs in anti-PD1-resistant and non-resistant melanoma samples, both in the tumor and in immune and stromal cells. These findings may reveal crucial lncRNAs in melanoma biology, indicating potential prognostic biomarkers and therapeutic targets. (AU)