Abstract
During pre-mRNA maturation 3′ end processing can occur at different polyadenylation sites in the 3′ untranslated region (3′ UTR) to give rise to transcript isoforms that differ in the length of their 3′ UTRs. Longer 3′ UTRs contain additional cis-regulatory elements that impact the fate of the transcript and/or of the resulting protein. Extensive alternative polyadenylation (APA) has been observed in cancers, but the mechanisms and roles remain elusive. In particular, it is unclear whether the APA occurs in the malignant cells or in other cell types that infiltrate the tumor. To resolve this, we developed a computational method, called SCUREL, that quantifies changes in 3′ UTR length between groups of cells, including cells of the same type originating from tumor and control tissue. We used this method to study APA in human lung adenocarcinoma (LUAD). SCUREL relies solely on annotated 3′ UTRs and on control systems such as T cell activation, and spermatogenesis gives qualitatively similar results at much greater sensitivity compared to the previously published scAPA method. In the LUAD samples, we find a general trend toward 3′ UTR shortening not only in cancer cells compared to the cell type of origin, but also when comparing other cell types from the tumor vs. the control tissue environment. However, we also find high variability in the individual targets between patients. The findings help in understanding the extent and impact of APA in LUAD, which may support improvements in diagnosis and treatment.
Highlights
The processing of most human pre-mRNAs involves 3′ end cleavage and addition of a polyadenosine [poly(A)] tail
While alternative polyadenylation (APA)-dependent 3′ untranslated region (3′ UTR) shortening has been observed in many cancers (Xia et al 2014; Schmidt et al 2018), it is presently unclear whether it is a manifestation of the change in cell composition of the tissue or of functional changes in all cell types within the tumor environment
Applying the method to single cell sequencing data from human lung adenocarcinoma (LUAD), we found that 3′ UTR shortening is not specific to a cell type but rather occurs in most cell types that compose the tumor
Summary
The processing of most human pre-mRNAs involves 3′ end cleavage and addition of a polyadenosine [poly(A)] tail. As single cell RNA sequencing (scRNA-seq) technologies capture mRNA 3′ ends, and data sets of tumor and matched control tissue samples have started to become available, this question can be addressed, provided a few challenges are overcome. To better understand the mechanism and function of APA in cancers, we identified two studies in which single cell sequencing of lung adenocarcinoma (LUAD) and matched control tissue from multiple patients was carried out on the same platform, 10x Genomics (Lambrechts et al 2018; Laughney et al 2020).
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