What question did this study set out to answer?

To determine how alternative polyadenylation of the NFYA transcription factor regulatory subunit contributes to prostate cancer progression and whether it can be therapeutically targeted.

August 26, 2026Journal of Experimental & Clinical Cancer Research0 citationsOpen Access

Mapping the NFYA 3′UTR landscape identifies alternative polyadenylation as a targetable vulnerability in prostate cancer

GPGiulia Pagani CCChiara Casirati CPCecilia Pandini

Key Points

To determine how alternative polyadenylation of the NFYA transcription factor regulatory subunit contributes to prostate cancer progression and whether it can be therapeutically targeted.
Interrogated bulk, single-cell, and 3′-end RNA sequencing from prostate cancer cell lines and patient samples to quantify NFYA 3′UTR isoform dynamics.
Investigated regulatory mechanisms via reporter assays and reprogrammed NFYA 3′UTR length using CRISPR/Cas9 signal deletion and antisense oligonucleotide (ASO)-mediated masking in vitro and in vivo.
Identified four NFYA 3′UTR isoforms, showing that widespread 3′UTR shortening in prostate cancer correlates with higher tumor grade, elevated NF-YA protein levels, and increased cell proliferation.
Demonstrated that 3′UTR lengthening diminishes NF-YA protein expression by reducing mRNA stability, impairing translation, and promoting nuclear retention rather than miRNA repression.
Enforced 3′UTR lengthening via CRISPR/Cas9 or ASOs reduced NF-YA protein abundance and suppressed aggressive tumor phenotypes across in vitro and in vivo prostate cancer models.

Abstract

Abstract Background Alternative polyadenylation (APA) is increasingly recognized as a pervasive oncogenic mechanism that reshapes post-transcriptional gene regulation and promotes tumor aggressiveness. Whether APA contributes to the dysregulation of NFYA —encoding the regulatory subunit of the oncogenic transcription factor NF-Y—in prostate cancer (PCa) remains largely uncharacterized. Methods We interrogated bulk, single cell and 3’-end RNA-sequencing data from PCa cell lines and patient samples to re-annotate and quantify the usage of NFYA 3′UTRs. The functional consequences of APA were assessed using reporter assays. NFYA APA was experimentally reprogrammed using CRISPR/Cas9-mediated deletion and antisense oligonucleotide (ASO)-based masking of polyadenylation signals, followed by in vitro and in vivo phenotypic analyses. Results Four functional NFYA 3′UTR isoforms were identified, with one predominantly used across cell lines and tissues. PCa displayed pervasive NFYA 3′UTR shortening, which correlated with tumor grade, increased NF-YA protein abundance, and enhanced proliferation, whereas 3′UTR lengthening was associated with cellular quiescence. Mechanistically, 3′UTR lengthening reduced NF-YA protein expression through decreased mRNA stability, impaired translation, and enhanced nuclear retention, rather than increased miRNA-mediated repression. Enforced NFYA 3′UTR lengthening in PCa cells via CRISPR/Cas9 or ASOs diminished NF-YA protein levels and suppressed aggressive tumor traits both in vitro and in vivo . Conclusions These findings establish NFYA APA as a critical determinant of NF-YA oncogenic output and downstream tumor-promoting programs, and as a previously unrecognized driver of PCa progression. Importantly, they provide proof-of-concept for gene-specific, APA-directed therapeutic strategies. ASO-mediated modulation of polyadenylation indeed emerges as a clinically translatable approach to fine-tune oncogene expression, thus opening new avenues for RNA-based precision interventions in aggressive PCa.

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