Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact

• Published in: RNA biology Vol. 16; no. 5; pp. 661 - 674
• Main Authors: Porsch, Martin, Özdemir, Esra, Wisniewski, Martin, Graf, Sebastian, Bull, Fabian, Hoffmann, Katrin, Ignatov, Atanas, Haybaeck, Johannes, Grosse, Ivo, Kalinski, Thomas, Nass, Norbert
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 04.05.2019
• Subjects: biomarker; biomarkers; Breast cancer; breast neoplasms; Breast Neoplasms - drug therapy; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Cell Movement; Cell Proliferation; Drug Resistance, Neoplasm; estrogen receptors; estrogens; Female; gene expression; Gene Expression Profiling - methods; gene expression regulation; Gene Expression Regulation, Neoplastic; gene overexpression; Gene Regulatory Networks; genes; human cell lines; Humans; interferons; Internet; long-non coding RNAs; MCF-7 Cells; metabolism; non-coding RNA; nucleic acid hybridization; patients; premenopause; Prognosis; quantitative polymerase chain reaction; Receptors, Estrogen - metabolism; Research Paper; reverse transcriptase polymerase chain reaction; RNA, Long Noncoding - genetics; signal transduction; small interfering RNA; Tamoxifen; Time Factors; Breast cancer; biomarker; gene expression; tamoxifen; long-non coding RNAs
• ISSN: 1547-6286; 1555-8584; 1555-8584
• DOI: 10.1080/15476286.2019.1581597

Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique. Pathway enrichment analysis revealed that early responses concerned mainly amine synthesis and NRF2-related signaling and evolved into a stable gene expression pattern within 4 weeks characterized by changes in glucuronidation-, estrogen metabolism-, nuclear receptor- and interferon signaling pathways. As a large number of long non coding RNAs was subject to regulation, we investigated 5 of these (linc01213, linc00632 linc0992, LOC101929547 and XR_133213) in more detail. From these, only linc01213 was upregulated but all were less abundant in estrogen-receptor negative cell lines (MDA-MB 231, SKBR-3 and UACC3199). In a web-based survival analysis linc01213 and linc00632 turned out to have prognostic impact. Linc01213 was investigated further by plasmid-mediated over-expression as well as siRNA down-regulation in MCF-7 cells. Nevertheless, this had no effect on proliferation or expression of tamoxifen regulated genes, but migration was increased. In conclusion, the cellular model identified a set of lincRNAs with prognostic relevance for breast cancer. One of these, linc01213 although regulated by 4OH-tamoxifen, is not a central regulator of tamoxifen adaption, but interferes with the regulation of migration.