Characterization of LncRNAs Associated with Metabolic Reprogramming During Melanoma Progression

• Grant number: 25/00242-1
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: September 01, 2025
• End date: July 31, 2028
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Eduardo Moraes Rego Reis
• Grantee: Pedro Henrique Fogaça Jordão
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Introduction: Melanoma is a neoplasm that arises from the malignant transformation of melanocytes and is characterized by its aggressiveness, high metastasis rate, and resistance to treatments. Melanocytes originate from neural crest (NC) stem cells, which, during early stages of embryonic development, undergo epithelial-mesenchymal transition (EMT), enabling them to migrate and differentiate into various cell types. Once specified, these precursors increase the expression of glycolytic enzymes in the presence of oxygen, where aerobic glycolysis becomes crucial for rapid ATP production, allowing them to acquire migratory properties. During the final differentiation into melanocytes, melanoblasts, the precursors to melanocytes, undergo another metabolic adaptation, activating oxidative phosphorylation (OXPHOS) for energy production. Interestingly, the transcriptional profiles of melanoma cells resemble those of differentiating NC cells, and as the tumor progresses, there is a shift in energy metabolism from OXPHOS to aerobic glycolysis, a phenomenon known as the Warburg effect. This metabolic reprogramming reflects the changes observed during the differentiation of melanocytes from NC precursors. In this context, lncRNAs (long non-coding RNAs) have been identified as potential regulators of cellular processes, including the migration and differentiation of melanocytes, as well as melanoma progression. Hypothesis: LncRNAs may regulate conserved epigenetic mechanisms that control the transition from OXPHOS metabolism to aerobic glycolysis, affecting melanocyte migration and differentiation, which are reactivated in melanoma, influencing cell motility and invasion, and contributing to tumor progression. Objectives: To identify and characterize lncRNAs with regulatory roles in energy metabolism reprogramming during melanocyte embryonic development and melanoma progression. Materials and Methods: Transcriptome data acquisition and analysis, including single-cell data, will be performed to identify lncRNA expression patterns in neural crest cells and during melanoma progression. Functional inference will be conducted using gene co-expression networks and evolutionary conservation analyses to assess the relevance of lncRNAs. Cell lines expressing Cas13d will be generated, and a custom sgRNA library will be constructed for lncRNA silencing using CRISPR-Cas13d, with silencing efficiency verified by RT-qPCR. Functional characterization of lncRNAs will include assays for glycolytic and oxidative phosphorylation activity, and the evaluation of EMT markers, proliferation, invasion, and migration. Additionally, the prognostic relevance of conserved lncRNAs will be analyzed in relation to clinical and pathological variables in melanoma patients. (AU)