Staufen1, in melanoma progression and immune surveillance

Abstract

Cutaneous melanoma is the most aggressive and lethal form of skin cancer, characterized by its intrinsic metastatic potential and high mutational burden, contributing to a high neoantigen load and making melanoma more immunogenic. Therapeutic options are improving in this disease, particularly with the development of immune checkpoint blockers (ICBs). Nevertheless, melanoma presents a remarkable ability to escape from immune surveillance and a significant fraction of patients show minimal or no response to the ICBs. A main objective of this PhD thesis is to uncover mechanisms that make melanoma intrinsically immune tolerant. Melanomas are also characterized by a plethora of changes in the transcriptome. Still, one of the least understood aspects of this disease is the specific contribution of of RNA-binding proteins (RBPs) to melanoma progression and resistance to ICB. This is puzzling considering that deregulation of the RBPs can impinge on multiple transcriptional networks with major consequences in cancer development and response to therapy. Our group has recently identified new RBPs linked to lineage-specific oncogenes in melanoma (CEPB4, CELF1, IGF2BP1) and collaborated to identify translational modulators (UNR). Yet, our understanding of RBPs that bind dsRNA is still incomplete. Characterizing dsRBPs is relevant, as most mRNAs in eukaryotic cells are highly structured, representing recognition targets for multiple dsRBPs. Moreover, dsRBPs can also exert distinct roles on the stability and localization of their bound transcripts, but a precise analysis of the expression and specific requirement of these proteins in cancers such as melanoma is lacking. The main complication in the functional characterization of dsRBPs is their complexity, there are over nine dsRBP families and just one motif may have multiple functions. Computatinal analyses revealed the dsRNA Staufen1 (STAU1) as one of the most deregulated dsRBPs in the largest melanoma dataset (TCCGA). STAU1 was an attractive candidate for its multiple and context-dependent roles in mRNA metabolism. Importantly, STAU1 had not been associated with melanoma. This Ph.D. thesis was set to study the expression of Staufen1 at different stages of melanoma progression and determine its functional requirement. To this end, we used melanoma cell lines, genetically modified melanoma models, and clinical specimens. Next, we identified downstream effectors of STAU1, mapping the direct targets with a tri-pronged integration (proteomics, transcriptomics, and interactomics). Notably, this strategy revealed a novel impact of STAU1 in controlling dsRNA homeostasis, serving as an internal brake to an otherwise damaging interferon signalling cascade. Unexpected immunomodulatory signals linked to STAU1 included a variety of factors involved in antigen processing and presentation in melanoma. Moreover, we found STAU1 as a putative novel biomarker of ICB resistance. Together, these data identify new roles of STAU1 in melanoma with important translational potential