Microenvironmental Influences on Splicesome Factor Expression Contribute to Melanoma Brain Metastasis Progression

With the advent of targeted therapies and the associated longer survival, brain metastasis is a complication with increasing incidence for melanoma patients. Due to melanoma’s high propensity to metastasize to the brain and the resulting poor prognosis, there is an urgent need to identify potential theranostic targets on melanomas and the metastatic niches. The dynamics and phenotypic plasticity of melanoma to thrive in diverse microenvironments are mainly governed by epigenetic mechanisms. Another epistasis mechanism that confers phenotypic plasticity is the alternative RNA splicing (AS). The AS is determined by the combination of ribonucleoproteins denominated spliceosome factors (SF). In this study, we evaluated the gene and isoform expression of melanoma cells in different tissue contexts, including primary melanoma (PRM), regional lymph node metastasis (LNM), and brain metastasis (MBM). We observed that CD44 variant 6-expressing (CD44v6⁺) PRMs favor homing to the brain. Functionally CD44v6⁺ cells exhibited increased migration in the presence of two particular molecules that are released during acute brain inflammation: hyaluronic acid (HA) and hepatocyte growth factor (HGF). To identify regulating factors in the expression of CD44v6 isoform, we evaluated the gene expression and DNA methylation of 190 SF in the progression to MBM. Importantly, our findings divulge that the AS of CD44 in PRM was regulated by ESRP1 and ESRP2 factors; however, ESRP1 was epigenetically silenced in MBM. Interestingly, within the brain’s microenvironment, we found CD44v6 being promoted by PTBP1 and U2AF2 factors. Consistently, PTBP1 knockdown resulted in significant reduction of CD44v6⁺ phenotype and migratory ability in brain’s microenvironment. Our results reveal a new avenue towards understanding melanoma cells’ high affinity for the brain, as well as the prospect of CD44v6 and SF as potential MBM-specific targets with theranostic utility.