The circular RNome of primary breast cancer

Marcel Smid, Saskia M. Wilting, Katharina Uhr, F. Germán Rodríguez-González, Vanja De Weerd, Wendy J.C. Prager-Van Der Smissen, Michelle Van Der Vlugt-Daane, Anne Van Galen, Serena Nik-Zainal, Adam Butler, Sancha Martin, Helen R. Davies, Johan Staaf, Marc J. Van De Vijver, Andrea L. Richardson, Gaëten MacGrogan, Roberto Salgado, Gert G.G.M. Van Den Eynden, Colin A. Purdie, Alastair M. ThompsonCarlos Caldas, Paul N. Span, Fred C.G.J. Sweep, Peter T. Simpson, Sunil R. Lakhani, Steven Van Laere, Christine Desmedt, Angelo Paradiso, Jorunn Eyfjord, Annegien Broeks, Anne Vincent-Salomon, Andrew P. Futreal, Stian Knappskog, Tari King, Alain Viari, Anne Lise Børresen-Dale, Hendrik G. Stunnenberg, Mike Stratton, John A. Foekens, Anieta M. Sieuwerts, John W.M. Martens

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

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 ( R < 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 CNOT2, CREBBP, and RERE 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 circCNOT2 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, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 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.

Original languageEnglish
Pages (from-to)356-366
Number of pages11
JournalGenome Research
Volume29
Issue number3
Early online date28 Jan 2019
DOIs
Publication statusPublished - 1 Mar 2019

Fingerprint

Breast Neoplasms
RNA
circular RNA
Aromatase Inhibitors
Computer Simulation
Small Interfering RNA
Genes
Disease-Free Survival
Exons
Cell Line
Neoplasms

Keywords

  • Biomarkers, Tumor/genetics
  • Breast Neoplasms/genetics
  • CREB-Binding Protein/genetics
  • Carrier Proteins/genetics
  • Female
  • Humans
  • Lymphatic Metastasis
  • MCF-7 Cells
  • RNA/genetics
  • Repressor Proteins/genetics
  • Transcriptome

Cite this

Smid, M., Wilting, S. M., Uhr, K., Rodríguez-González, F. G., De Weerd, V., Prager-Van Der Smissen, W. J. C., ... Martens, J. W. M. (2019). The circular RNome of primary breast cancer. Genome Research, 29(3), 356-366. https://doi.org/10.1101/gr.238121.118
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. / The circular RNome of primary breast cancer. In: Genome Research. 2019 ; Vol. 29, No. 3. pp. 356-366.
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Smid, M, Wilting, SM, Uhr, K, Rodríguez-González, FG, De Weerd, V, Prager-Van Der Smissen, WJC, Van Der Vlugt-Daane, M, Van Galen, A, Nik-Zainal, S, Butler, A, Martin, S, Davies, HR, Staaf, J, Van De Vijver, MJ, Richardson, AL, MacGrogan, G, Salgado, R, Van Den Eynden, GGGM, Purdie, CA, Thompson, AM, Caldas, C, Span, PN, Sweep, FCGJ, Simpson, PT, Lakhani, SR, Van Laere, S, Desmedt, C, Paradiso, A, Eyfjord, J, Broeks, A, Vincent-Salomon, A, Futreal, AP, Knappskog, S, King, T, Viari, A, Børresen-Dale, AL, Stunnenberg, HG, Stratton, M, Foekens, JA, Sieuwerts, AM & Martens, JWM 2019, 'The circular RNome of primary breast cancer', Genome Research, vol. 29, no. 3, pp. 356-366. https://doi.org/10.1101/gr.238121.118

The circular RNome of primary breast cancer. / 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.

In: Genome Research, Vol. 29, No. 3, 01.03.2019, p. 356-366.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The circular RNome of primary breast cancer

AU - Smid, Marcel

AU - Wilting, Saskia M.

AU - Uhr, Katharina

AU - Rodríguez-González, F. Germán

AU - De Weerd, Vanja

AU - Prager-Van Der Smissen, Wendy J.C.

AU - Van Der Vlugt-Daane, Michelle

AU - Van Galen, Anne

AU - Nik-Zainal, Serena

AU - Butler, Adam

AU - Martin, Sancha

AU - Davies, Helen R.

AU - Staaf, Johan

AU - Van De Vijver, Marc J.

AU - Richardson, Andrea L.

AU - MacGrogan, Gaëten

AU - Salgado, Roberto

AU - Van Den Eynden, Gert G.G.M.

AU - Purdie, Colin A.

AU - Thompson, Alastair M.

AU - Caldas, Carlos

AU - Span, Paul N.

AU - Sweep, Fred C.G.J.

AU - Simpson, Peter T.

AU - Lakhani, Sunil R.

AU - Van Laere, Steven

AU - Desmedt, Christine

AU - Paradiso, Angelo

AU - Eyfjord, Jorunn

AU - Broeks, Annegien

AU - Vincent-Salomon, Anne

AU - Futreal, Andrew P.

AU - Knappskog, Stian

AU - King, Tari

AU - Viari, Alain

AU - Børresen-Dale, Anne Lise

AU - Stunnenberg, Hendrik G.

AU - Stratton, Mike

AU - Foekens, John A.

AU - Sieuwerts, Anieta M.

AU - Martens, John W.M.

PY - 2019/3/1

Y1 - 2019/3/1

N2 - 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 ( R < 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 CNOT2, CREBBP, and RERE 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 circCNOT2 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, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 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.

AB - 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 ( R < 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 CNOT2, CREBBP, and RERE 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 circCNOT2 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, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 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.

KW - Biomarkers, Tumor/genetics

KW - Breast Neoplasms/genetics

KW - CREB-Binding Protein/genetics

KW - Carrier Proteins/genetics

KW - Female

KW - Humans

KW - Lymphatic Metastasis

KW - MCF-7 Cells

KW - RNA/genetics

KW - Repressor Proteins/genetics

KW - Transcriptome

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DO - 10.1101/gr.238121.118

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VL - 29

SP - 356

EP - 366

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 3

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Smid M, Wilting SM, Uhr K, Rodríguez-González FG, De Weerd V, Prager-Van Der Smissen WJC et al. The circular RNome of primary breast cancer. Genome Research. 2019 Mar 1;29(3):356-366. https://doi.org/10.1101/gr.238121.118