Non-coding RNA profiling in BRAFV600E-mutant cutaneous melanoma models before and after Spry1 depletion
Background: Drugs directly targeting the BRAF protein and the constitutive activation of the mitogen-activated protein kinase (MAPK) pathway have provided remarkable response rates in BRAFV600-mutant metastatic cutaneous melanoma (CM) patients. However, the occurrence of resistance persists, requiring a better understanding of molecular mechanisms underlying the treatment's response to improve therapeutic strategies. Grown evidence has linked microRNAs (miRNAs) to the biology and drug sensitivity of CM, as several of them have been demonstrated to modulate pathways driving tumor pathogenesis and immune response. Yet, the connection between specific miRNA signatures and CM-developed resistance to BRAF inhibitors (BRAFi) has not been completely elucidated. We have already demonstrated that Spry1, an upstream regulator of the MAPK signaling pathway, may represent a novel putative target for BRAFV600-mutant CM since Spry1 depletion, both in vitro and in vivo, reduces cell proliferation inducing cell cycle arrest and apoptosis that improves response to BRAFi vemurafenib. Methods: Here we performed a small RNA  sequencing on three BRAFv600e-mutant metastatic CM cell lines stably engineered with Spry1 knock-down (Mel 593 Spry1KO clone 2, Mel 599 Spry1KO clone 9 and Mel 611 Spry1KO clone 4) to investigate the post-transcriptional gene regulation role of miRNAs in molecular and cellular functions modulation driven by loss of Spry1. Results: The classification of expressed sncRNA molecules revealed that, in all three clones, miRNAs were the most represented subclass, followed by small nuclear RNAs (snRNA), PIWI-interacting RNAs (piRNA), small nucleolar RNA (snoRNA) and RNA transfer (tRNA). We next compared miRNA profiles between Spry1KO clones and the parental cell lines to identify, among the clones, common and concordantly deregulated miRNAs which may have a role in the improved response to targeted therapy mediated by Spry1 depletion.