Integrated analysis of the prostate cancer small‐nucleolar transcriptome reveals SNORA55 as a driver of prostate cancer progression

Abstract

Metastasis is the primary cause of death in prostate cancer (PCa) patients. Small nucleolar RNAs (snoRNAs) have long been considered “housekeeping” genes with no relevance for cancer biology. Emerging evidence has challenged this assumption, suggesting that snoRNA expression is frequently modulated during cancer progression. Despite this, no study has systematically addressed the prognostic and functional significance of snoRNAs in PCa.

We performed RNA Sequencing on paired metastatic/non‐metastatic PCa xenografts derived from clinical specimens. The clinical significance of differentially expressed snoRNAs was further investigated in two independent primary PCa cohorts (131 and 43 patients, respectively). The snoRNA demonstrating the strongest association with clinical outcome was quantified in PCa patient‐derived serum samples and its functional relevance was investigated in PCa cells via gene expression profiling, pathway analysis and gene silencing.

Our comparison revealed 21 differentially expressed snoRNAs in the metastatic vs. non‐metastatic xenografts. Of those, 12 were represented in clinical databases and were further analyzed. SNORA55 emerged as a predictor of shorter relapse‐free survival (results confirmed in two independent databases). SNORA55 was reproducibly detectable in serum samples from PCa patients. SNORA55 silencing in PCa cell lines significantly inhibited cell proliferation and migration. Pathway analysis revealed that SNORA55 expression is significantly associated with growth factor signaling and pro‐inflammatory cytokine expression in PCa.

Our results demonstrate that SNORA55 up‐regulation predicts PCa progression and that silencing this non‐coding gene affects PCa cell proliferation and metastatic potential, thus positioning it as both a novel biomarker and therapeutic target.

Highlights

• The role of small nucleolar RNAs (SnoRNAs) in prostate cancer progression has been scarcely investigated.

• We analyzed the transcriptome of patient‐derived prostate cancer xenografts.

• Our analysis revealed that SNORA55 is up‐regulated in prostate cancer and associated with worse prognosis.

• SNORA55 inhibition impaired prostate cancer cell growth and metastatic potential.

• Pathway analysis revealed that SNORA55 interacts with pro‐oncogenic and inflammatory pathways.