Androgen induces 3′UTR shortening of de novo lipogenesis genes by alternative polyadenylation in prostate cancer cells

Abstract Alternative polyadenylation (APA) is a pervasive mechanism that is emerging as a formidable player in post-transcriptional regulation. The transcriptional landscape can be altered via APA in response to various stimulating factors. Using the PacBio single-molecule long-read sequencing method, we present for the first time the 3′UTR landscape and reveal a global increase of APA events in prostate cancer (PCa) LNCaP cells in response to androgen dihydrotestosterone (DHT), a critical regulator of PCa progression. With evidence from differential gene expression analyses of Illumina RNA-sequencing data, we demonstrated that genes with DHT-induced changes in both expression and APA were enriched in lipid metabolism. These genes predominantly supported de novo fatty acid synthesis, such as FASN and ACSL3 . Furthermore, we showed that an isoform switch to the proximal poly(A) site of these genes depended on the androgen receptor, and the expression of cancer-associated genes was upregulated by the escape of miRNA-regulated repression machinery. To address the role of key gene shortening in PCa, we prepared 22RV1-FS cells missing the distal poly(A) signal of FASN in the AR + PCa cell line 22RV1 using CRISPR/Cas9 technology. As expected, the edited 22RV1-FS cells overexpressed FASN mRNA and protein and were inclined to cell proliferation in vitro and tumorigenesis in vivo . Interestingly, we found that FASN transcripts with a shortened 3′UTR were significantly increased in advanced PCa and castration-resistant prostate cancer compared with benign prostate hyperplasia, suggesting a possible association between usage of the proximal poly(A) site and disease progression. Therefore, our study highlights the importance of the APA mechanism in response to DHT stimulation in PCa cells and provides a novel regulatory mechanism through which DHT-induced APA causes altered expression of de novo lipogenesis genes, with a possible association with the progression of PCa.