Global Changes in Processing of mRNA 3′ Untranslated Regions Characterize Clinically Distinct Cancer Subtypes

Abstract

Molecular cancer diagnostics are an important clinical advance in cancer management, but new methods are still needed. In this context, gene expression signatures obtained by microarray represent a useful molecular diagnostic. Here, we describe novel probe-level microarray analyses that reveal connections between mRNA processing and neoplasia in multiple tumor types, with diagnostic potential. We now show that characteristic differences in mRNA processing, primarily in the 3′-untranslated region, define molecular signatures that can distinguish similar tumor subtypes with different survival characteristics, with at least 74% accuracy. Using a mouse model of B-cell leukemia/lymphoma, we find that differences in transcript isoform abundance are likely due to both alternative polyadenylation (APA) and differential degradation. While truncation of the 3′-UTR is the most common observed pattern, genes with elongated transcripts were also observed, and distinct groups of affected genes are found in related but distinct tumor types. Genes with elongated transcripts are overrepresented in ontology categories related to cell-cell adhesion and morphology. Analysis of microarray data from human primary tumor samples revealed similar phenomena. Western blot analysis of selected proteins confirms that changes in the 3′-UTR can correlate with changes in protein expression. Our work suggests that alternative mRNA processing, particularly APA, can be a powerful molecular biomarker with prognostic potential. Finally, these findings provide insights into the molecular mechanisms of gene deregulation in tumorigenesis. [Cancer Res 2009;69(24):9422-30]

p53 inhibits mRNA 3′ processing through its interaction with the CstF/BARD1 complex

“…As DNA repair proceeds, the levels of p53 expression decrease allowing the recovery of total mRNA levels. Our results indicate that different cell lines exhibit different 3 0 processing profiles depending on p53 expression levels, consistent with the idea proposed by Singh et al (2009) that the interaction of the 3 0 processing machinery and factors involved in the DDR/ tumor suppression might result in cell-specific 3 0 processing profiles.…”

“…Other tumor suppressors, such as CSR1 and Cdc73, have also been shown to functionally associate with 3 0 processing factors, such as CPSF3 (Zhu et al, 2009) and CPSF/ CstF (Rozenblatt-Rosen et al, 2009). Recently, it has been shown that the use of alternative mRNA 3 0 cleavage and polyadenylation sites can control the expression of certain genes by eliminating or including several cis-acting elements, such as microRNA target sites and AU-rich elements, in cancer cells and during development (Sandberg et al, 2008;Zlotorynski and Agami, 2008;Ji et al, 2009;Mayr and Bartel, 2009;Singh et al, 2009). Although more work is necessary to determine the functional relevance of the CstF/BARD1/ p53 interaction in the regulation of expression of specific genes involved in DDR, it is possible that the p53-mediated inhibition of mRNA 3 0 processing might also play a role in the selection of different alternative mRNA 3 0 cleavage sites and, consequently, in the regulation of the mRNA levels of genes involved in DDR.…”

“…It has been shown that the regulation of mRNA 3 0 end formation can have significant roles in cancer (Kleiman and Manley, 2001;Topalian et al, 2001;Scorilas, 2002;Rozenblatt-Rosen et al, 2009). Most importantly, alternative mRNA cleavage and polyadenylation changes the length of the 3 0 -untranslated region and regulates gene expression of different mRNAs in cancer cells (Mayr and Bartel 2009;Singh et al, 2009) and during cell differentiation (Sandberg et al, 2008;Zlotorynski and Agami, 2008;Ji et al, 2009). Cleavagestimulation factor (CstF) is one of the essential 3 0 processing factors and is most likely active as a dimer of an heterotrimer, consisting of three protein factors called CstF3, CstF2 and CstF1.…”

To polyadenylate or to deadenylate

“…Cis-acting elements within the 3' untranslated region (3'UTR), such as APA signals, microRNA (miRNA) target sites and AU-rich elements (ARE), play also an important role regulating 3' processing. The relevance of these regulatory processes is highlighted by changes in the length of the 3'UTR of different mRNAs in cancer cells 10,11 and during cell differentiation. [12][13][14] For better understanding of basic aspects of 3' end formation and its regulation, we suggest the reading of a recent review by Mandel et al 5 As no mechanism has been described yet that regulates the length of the poly(A) tail during the nuclear cleavage/polyadenylation reaction, it is easy to view this modification as a default mRNA processing step.…”

“…Although a direct connection between APA and the polyadenylation/ deadenylation machinery has not been described, the selection between the distal or proximal alternative signals might cause the inclusion or exclusion of other cis-acting RNA elements involved in polyadenylation/deadenylation processes. The relevance of these regulatory processes is highlighted by the finding of changes in the length of the 3'UTRs of different mRNAs, which change the number of miRNA target sites and AREs, in cancer cells 10,11 and during cell differentiation. [12][13][14] miRNAs comprise a large family of small single-stranded non-coding RNAs (~21 nts in length), which are encoded within the genome of species ranging from protozoans to plants to mammals.…”