Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer

Tejal Joshi, Daniel Elias, Jan Stenvang, Carla L. Alves, Fei Teng, Maria B. Lyng, Anne E. Lykkesfeldt, Nils Brünner, Jun Wang, Ramneek Gupta, Christopher Workman, Henrik J. Ditzel

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    Abstract

    Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer, however, tamoxifen resistance is frequently observed. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies. Although the target genes affected by the altered miRNA in the three TamRs differed, good agreement in terms of affected molecular pathways was observed. Moreover, we found evidence of miRNA-mediated regulation of ESR1, PGR1, FOXM1 and 14-3-3 family genes. Integrating the inferred miRNA-target relationships, we investigated the functional importance of 2 central genes, SNAI2 and FYN, which showed increased expression in TamR cells, while their corresponding regulatory miRNA were downregulated. Using specific chemical inhibitors and siRNAmediated gene knockdown, we showed that both SNAI2 and FYN significantly affect the growth of TamR cell lines. Finally, we show that a combination of 2 miRNAs (miR-190b and miR-516a-5p) exhibiting altered expression in TamR cell lines were predictive of treatment outcome in a cohort of ER+ breast cancer patients receiving adjuvant tamoxifen mono-therapy. Our results provide new insight into the molecular mechanisms of tamoxifen resistance and may form the basis for future medical intervention for the large number of women with tamoxifen-resistant ER+ breast cancer.
    Original languageEnglish
    JournalOncoTarget
    Volume7
    Issue number35
    Pages (from-to)57239-57253
    Number of pages15
    ISSN1949-2553
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    Licensed under a Creative Commons Attribution 3.0 License.

    Keywords

    • Antihormonal therapy
    • Breast cancer
    • Endocrine resistance
    • MiRNA-mediated gene regulation
    • miRNAs

    Cite this

    Joshi, T., Elias, D., Stenvang, J., Alves, C. L., Teng, F., Lyng, M. B., ... Ditzel, H. J. (2016). Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer. OncoTarget, 7(35), 57239-57253. https://doi.org/10.18632/oncotarget.11136
    Joshi, Tejal ; Elias, Daniel ; Stenvang, Jan ; Alves, Carla L. ; Teng, Fei ; Lyng, Maria B. ; Lykkesfeldt, Anne E. ; Brünner, Nils ; Wang, Jun ; Gupta, Ramneek ; Workman, Christopher ; Ditzel, Henrik J. / Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer. In: OncoTarget. 2016 ; Vol. 7, No. 35. pp. 57239-57253.
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    title = "Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer",
    abstract = "Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer, however, tamoxifen resistance is frequently observed. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies. Although the target genes affected by the altered miRNA in the three TamRs differed, good agreement in terms of affected molecular pathways was observed. Moreover, we found evidence of miRNA-mediated regulation of ESR1, PGR1, FOXM1 and 14-3-3 family genes. Integrating the inferred miRNA-target relationships, we investigated the functional importance of 2 central genes, SNAI2 and FYN, which showed increased expression in TamR cells, while their corresponding regulatory miRNA were downregulated. Using specific chemical inhibitors and siRNAmediated gene knockdown, we showed that both SNAI2 and FYN significantly affect the growth of TamR cell lines. Finally, we show that a combination of 2 miRNAs (miR-190b and miR-516a-5p) exhibiting altered expression in TamR cell lines were predictive of treatment outcome in a cohort of ER+ breast cancer patients receiving adjuvant tamoxifen mono-therapy. Our results provide new insight into the molecular mechanisms of tamoxifen resistance and may form the basis for future medical intervention for the large number of women with tamoxifen-resistant ER+ breast cancer.",
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    author = "Tejal Joshi and Daniel Elias and Jan Stenvang and Alves, {Carla L.} and Fei Teng and Lyng, {Maria B.} and Lykkesfeldt, {Anne E.} and Nils Br{\"u}nner and Jun Wang and Ramneek Gupta and Christopher Workman and Ditzel, {Henrik J.}",
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    Joshi, T, Elias, D, Stenvang, J, Alves, CL, Teng, F, Lyng, MB, Lykkesfeldt, AE, Brünner, N, Wang, J, Gupta, R, Workman, C & Ditzel, HJ 2016, 'Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer', OncoTarget, vol. 7, no. 35, pp. 57239-57253. https://doi.org/10.18632/oncotarget.11136

    Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer. / Joshi, Tejal; Elias, Daniel; Stenvang, Jan; Alves, Carla L.; Teng, Fei; Lyng, Maria B.; Lykkesfeldt, Anne E.; Brünner, Nils; Wang, Jun; Gupta, Ramneek; Workman, Christopher; Ditzel, Henrik J.

    In: OncoTarget, Vol. 7, No. 35, 2016, p. 57239-57253.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer

    AU - Joshi, Tejal

    AU - Elias, Daniel

    AU - Stenvang, Jan

    AU - Alves, Carla L.

    AU - Teng, Fei

    AU - Lyng, Maria B.

    AU - Lykkesfeldt, Anne E.

    AU - Brünner, Nils

    AU - Wang, Jun

    AU - Gupta, Ramneek

    AU - Workman, Christopher

    AU - Ditzel, Henrik J.

    N1 - Licensed under a Creative Commons Attribution 3.0 License.

    PY - 2016

    Y1 - 2016

    N2 - Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer, however, tamoxifen resistance is frequently observed. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies. Although the target genes affected by the altered miRNA in the three TamRs differed, good agreement in terms of affected molecular pathways was observed. Moreover, we found evidence of miRNA-mediated regulation of ESR1, PGR1, FOXM1 and 14-3-3 family genes. Integrating the inferred miRNA-target relationships, we investigated the functional importance of 2 central genes, SNAI2 and FYN, which showed increased expression in TamR cells, while their corresponding regulatory miRNA were downregulated. Using specific chemical inhibitors and siRNAmediated gene knockdown, we showed that both SNAI2 and FYN significantly affect the growth of TamR cell lines. Finally, we show that a combination of 2 miRNAs (miR-190b and miR-516a-5p) exhibiting altered expression in TamR cell lines were predictive of treatment outcome in a cohort of ER+ breast cancer patients receiving adjuvant tamoxifen mono-therapy. Our results provide new insight into the molecular mechanisms of tamoxifen resistance and may form the basis for future medical intervention for the large number of women with tamoxifen-resistant ER+ breast cancer.

    AB - Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer, however, tamoxifen resistance is frequently observed. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies. Although the target genes affected by the altered miRNA in the three TamRs differed, good agreement in terms of affected molecular pathways was observed. Moreover, we found evidence of miRNA-mediated regulation of ESR1, PGR1, FOXM1 and 14-3-3 family genes. Integrating the inferred miRNA-target relationships, we investigated the functional importance of 2 central genes, SNAI2 and FYN, which showed increased expression in TamR cells, while their corresponding regulatory miRNA were downregulated. Using specific chemical inhibitors and siRNAmediated gene knockdown, we showed that both SNAI2 and FYN significantly affect the growth of TamR cell lines. Finally, we show that a combination of 2 miRNAs (miR-190b and miR-516a-5p) exhibiting altered expression in TamR cell lines were predictive of treatment outcome in a cohort of ER+ breast cancer patients receiving adjuvant tamoxifen mono-therapy. Our results provide new insight into the molecular mechanisms of tamoxifen resistance and may form the basis for future medical intervention for the large number of women with tamoxifen-resistant ER+ breast cancer.

    KW - Antihormonal therapy

    KW - Breast cancer

    KW - Endocrine resistance

    KW - MiRNA-mediated gene regulation

    KW - miRNAs

    U2 - 10.18632/oncotarget.11136

    DO - 10.18632/oncotarget.11136

    M3 - Journal article

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    JF - OncoTarget

    SN - 1949-2553

    IS - 35

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