The circular RNome of primary breast cancer

• Published in: Genome research Vol. 29; no. 3; pp. 356 - 366
• Main Authors: Smid, Marcel, Wilting, Saskia M, Uhr, Katharina, Rodríguez-González, F Germán, de Weerd, Vanja, Prager-Van der Smissen, Wendy J C, van der Vlugt-Daane, Michelle, van Galen, Anne, Nik-Zainal, Serena, Butler, Adam, Martin, Sancha, Davies, Helen R, Staaf, Johan, van de Vijver, Marc J, Richardson, Andrea L, MacGrogan, Gaëten, Salgado, Roberto, van den Eynden, Gert G G M, Purdie, Colin A, Thompson, Alastair M, Caldas, Carlos, Span, Paul N, Sweep, Fred C G J, Simpson, Peter T, Lakhani, Sunil R, Van Laere, Steven, Desmedt, Christine, Paradiso, Angelo, Eyfjord, Jorunn, Broeks, Annegien, Vincent-Salomon, Anne, Futreal, Andrew P, Knappskog, Stian, King, Tari, Viari, Alain, Børresen-Dale, Anne-Lise, Stunnenberg, Hendrik G, Stratton, Mike, Foekens, John A, Sieuwerts, Anieta M, Martens, John W M
• Format: Journal Article
• Language: English; Norwegian
• Published: United States Cold Spring Harbor Laboratory Press 01.03.2019
• Subjects: Aromatase; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Breast cancer; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cancer and Oncology; Cancer och onkologi; Carrier Proteins - genetics; Carrier Proteins - metabolism; Clinical Medicine; CREB-Binding Protein - genetics; CREB-Binding Protein - metabolism; Female; Humans; Klinisk medicin; Life Sciences; Lymphatic Metastasis; MCF-7 Cells; Medical and Health Sciences; Medicin och hälsovetenskap; Repressor Proteins - genetics; Repressor Proteins - metabolism; RNA - genetics; RNA - metabolism; RNA, Circular; siRNA; Splice junctions; Splicing; Transcriptome; Tumor cell lines
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.238121.118

Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative ( < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of , , and in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.