Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients

ABSTRACT: Background: Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patients’ outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive PCa subtypes. Methods: Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Through lentiviral transduction and CRISPR-Cas9 technology, we modulated the expression of NF-YA splice variants in prostate cancer cells. We investigated cellular and molecular effects on cancer programs through 2D/3D in vitro assays and RNA-seq profilings. The rank-rank hypergeometric overlap approach (RRHO) was used to identify concordant/discordant overlap between gene expression signatures of NF-YAs/NF-YAl cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. Results: NF-YA depletion affects the tumorigenic potential of prostate cancer cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive prostate cancer specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression in prostate cancer cells increases cell motility, while NF-YAs enhances both cell proliferation and invasive properties in 3D cultured spheroids and xenograft tumors. NF-YAs-transcriptome of multi-cellular spheroids has an extensive overlap with both localized and metastatic human PCa signatures. The ratio between NF-YAs and NF-YAl transcripts is higher in LumB PAM50 subtype, characterized by poor prognosis, and stratification of patients based on NF-YAs expression is predictive of clinical outcome. Conclusions: Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179990 | GEO | 2021/11/30

REPOSITORIES: GEO