Background: Messenger RNA (mRNA) is the target of a series of post-transcriptional modifications that can affect its structure and stability, one of the most relevant being RNA editing. The most common form of RNA editing in humans is of the A-to-I type and is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes. Currently, little is known about how RNA editing operates in cancer. The main objectives of this study were to investigate and characterize the extent of A-to-I RNA editing in breast cancer (BC) and to define the principles governing the editing process in this as well as other cancers.
Material and Methods: The exome and transcriptome of 58 BC samples representing the four main known subtypes, namely TN, HER2+, luminal A and luminal B, and 10 matched normal samples were sequenced using the Illumina platform. For the same series, gene expression and copy number profiles were obtained using the Affymetrix platform. RNA-DNA single nucleotide differences (RDDs) were called using a pipeline in line with the most updated bioinformatics tools and validated in an independent cohort of 15 BC samples and breast cell lines.
Results: Overall, we detected 16,027 RDDs present in one or more samples, with all possible base changes represented. Among these, 560 RDDs were located in Alu regions and were all of the A-to-I type consistent with the notion that A-to-I editing occurs predominantly in forward-facing Alu forming double stranded RNA duplexes processed by ADAR.
We found that the same sites were edited in normal and tumor breast tissues. However, the editing frequency was significantly higher in tumors compared to matched normal breast tissues. Moreover, high editing frequencies were observed in samples in which more editing sites were detectable and/or in which ADAR expression was high.
We identified two key factors that independently determine ADAR expression and therefore A-to-I RNA editing in breast and the majority of other human cancers: 1) the type-I interferon response in tumors and 2) gains in ADAR copy number. The mean editing frequency was found to be significantly correlated with the expression of STAT1 and other type I interferon target genes, both in our patient series, in a large pool of BC datasets and a panel of normal and breast cancer cell lines treated with interferon (IFN) α, β, or γ for 1, 2 and 5 days in vitro. Moreover, the association between editing and STAT1 expression or ADAR amplification was validated in 19 additional cancer types obtained from the TCGA dataset.
Conclusions: Our work, which represents the largest survey so far on RNA editing in BC, shows that A-to-I editing is a pervasive and well-controlled phenomenon in cancer that can drive aberrant transcriptome expression in breast and potentially the vast majority of cancers. Moreover, it suggests that the immune response can profoundly impact the transcriptome sequence in tumor cells and thereby influence the internal mechanisms governing their behavior.
Citation Format: Debora Fumagalli, David Gacquer, Françoise Rothé, Anne Lefort, Frederick Libert, David N Brown, Naima Kheddoumi, Adam Shlien, Tomasz Konopka, Roberto Salgado, Denis Larsimont, Kornelia Polyak, Karen Willard-Gallo, Christine Desmedt, Martine Piccart, Marc Abramowicz, Peter J Campbell, Vincent Detours, Christos Sotiriou. Principles governing A-to-I RNA editing in breast cancer transcriptome [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr S4-02.