Cancer-specific alternative polyadenylation shapes tumor phenotypes in vivo

Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although APA dysregulation is frequently associated with poor prognosis, the biological importance of most APA events remains unclear simply because few have been functionally studied. Here, we performed a CRISPR/Cas9-based screen to assess individual APA events' contributions to tumor growth in vivo. Forcing use of specific polyadenylation sites altered mRNA and protein levels to modify mouse melanoma growth in an immunocompetent host. Our screen highlighted APA events of potential clinical relevance. For example, forced Atg7 3' UTR lengthening in mouse melanoma reduced ATG7 protein levels and tumor immune infiltration; similarly, in human melanoma, a long ATG7 3' UTR and low mRNA levels were significantly associated with reduced anti-tumor T cell activity and failure of immune checkpoint blockade. Our data demonstrate that cancer-associated APA plays a causative role in tumorigenesis and motivate future studies of the therapeutic potential of modulating APA. Overall design: Comparative Poly(A) sequencing for B16-F10 melanoma and Melan-A cells (melanocyte cell line) completed 6x replicates. RNA-seq of 3x cells and 5x tumors of B16-F10 Cas9-expressing cells treated with a paired-guide RNA that force 3' UTR lengthening in the gene Atg7, relative to a control unexpressed gene (Crabp1).