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

Abstract

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 4OHtamoxifen (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.

<p>Construction and Analysis of a Long Non-Coding RNA-Associated Competing Endogenous RNA Network Identified Potential Prognostic Biomarkers in Luminal Breast Cancer</p>

“…[6][7][8][10][11][12][13] Recent studies have revealed that lncRNAs played vital roles in the development of cancers. 21,22 Further, germline mutations can also predict tumor recurrence in breast cancer patients. 38 In the present study, we used ceRNA to detect and validate potential prognostic lncRNAs in the luminal BC.…”

“…21 In addition, prognostic roles and relationship with tamoxifen resistance were also mentioned. 13,22 Recently, competitive endogenous RNA (ceRNA), as a whole view of transcription, has gradually become a useful tool for identifying prognostic lncRNAs. The ceRNA hypothesis suggests that lncRNAs can competitively bind to miRNAs, thereby preventing their binding to mRNA, and consequently regulating mRNA expression.…”

BCL3 expression is strongly associated with the occurrence of breast cancer relapse under tamoxifen treatment in a retrospective cohort study

“…MCF-7 cells and a tamoxifen adapted MCF-7 cell line [24,25] were used for these studies. Cells were seeded onto glass slides (Sarstedt), fixed using ice cold methanol followed by acetone (− 20 °C) for 5 min each.…”

“…In addition to earlier studies on anti-estrogen resistance and the effect of cancer-associated fibroblasts, we initially investigated the BCL3 expression in our model for acquired tamoxifen resistance. In this model, the luminal A cell line MCF-7 was adapted to 4OH-tamoxifen for at least 12 weeks [23,24]. Here, we were particularly interested whether BCL3 localization and abundance has changed.…”

Regulation of ferroptosis by non‑coding RNAs in the development and treatment of cancer (Review)

“…Emerging evidence has indicated that lncRNAs Blnc1 ( 157 ), MALAT1 ( 158 – 162 ), Nrf2-lncRNA ( 163 ), AK094457 ( 164 ), Linc01213 ( 165 ), lncRNA74.1 ( 166 ), ODRUL ( 167 ), SNHG14 ( 168 ), UCA1 ( 126 ), LUCAT1 ( 169 ), TUG1 ( 170 – 172 ), Loc344887 ( 173 ), H19 ( 174 ), Mhrt ( 175 ), MIAT ( 176 ), MRAK052686 ( 177 ), AATBC ( 178 ), HOTAIR ( 179 ), NRAL ( 129 ), H19 ( 114 ), Sox2OT ( 180 ), MT1DP ( 125 ), MEG3 ( 127 , 128 , 181 ) and KRAL ( 117 ) may activate Nrf2 signaling by targeting Nrf2-related genes. Furthermore, circRNA-4099 may activate Nrf2 signaling by targeting miR-706, which augments H 2 O 2 -induced cell damage in the L0 2 cells ( 182 ).…”