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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

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Project description:As proteins represent cell function, proteomic analysis of prostate tissues may elucidate the mechanisms of prostate cancer (PCa) progression. To that end, formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources, but associated with large analytical difficulties due to protein cross-linking. Our aim is to characterize tissue protein changes associated with castration resistant PCa. This study focused at the development of a reliable protocol for the proteomic analysis of FFPE tissues which was followed by a pilot study using FFPE PCa clinical samples to investigate whether the optimized protocol can provide biologically relevant data in the context of PCa. Archival FFPE mouse tissues were processed using seven protein extraction protocols including combinations of homogenization means (beads, sonication, boiling) and buffers (Tris-HCl and Urea-Thiourea). The proteomics output was evaluated by SDS electrophoresis and high resolution LC-MS/MS analysis. FFPE tissues (3 sections, 15��m each per sample) from 10 patients with PCa corresponding to tumor (GS=6 or GS��8) and adjacent benign regions were processed with the optimized protocol. Extracted proteins were analyzed by GeLC-MS/MS followed by statistical and bioinformatics analysis using Cytsoscape and Open Targets tool. A combination of cell lysis by Tris-HCl, SDS and DTE with bead homogenization, sonication and boiling provided most efficient protein extraction from FFPE tissues based on protein identifications and reproducibility. Comparison between the FFPE and matched FF tissues showed a substantial overlap in protein identifications (502 common out of 1,216 IDs commonly identified in all FF samples and 530 IDs commonly identified in all FFPE samples) with a strong correlation in relative abundances (rs=0.846, p<.001). Proteins significantly deregulated between PCa GS��8 and PCa GS=6 represented extracellular matrix organisation, phosphorylation and gluconeogenesis pathways, while proteins deregulated between cancerous tissues and benign counterparts, reflected increased translation, peptide synthesis and protein metabolism in the former, as expected. Further disease association analysis using the Open Targets platform showed that 60% of the differentially expressed proteins in cancer versus normal adjacent were significantly associated with PCa. These results support the relevance of the proteomic findings in the context of PCa and the reliability of the optimized protocol for proteomics analysis of FFPE material. A large scale study including 160 clinical FFPE prostate cancer and benign tissues to define protein changes associated with aggressive PCa, is planned.

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

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