The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells

Abstract

Aberrant microRNA expression contributes to breast cancer progression and endocrine resistance. We reported that although tamoxifen stimulated miR-29b-1/a transcription in tamoxifen (TAM)-resistant breast cancer cells, ectopic expression of miR-29b-1/a did not drive TAM-resistance in MCF-7 breast cancer cells. However, miR-29b-1/a overexpression significantly repressed TAM-resistant LCC9 cell proliferation, suggesting that miR-29b-1/a is not mediating TAM resistance but acts as a tumor suppressor in TAM-resistant cells. The target genes mediating this tumor suppressor activity were unknown. Here, we identify miR-29b-1 and miR-29a target transcripts in both MCF-7 and LCC9 cells. We find that miR-29b-1 and miR-29a regulate common and unique transcripts in each cell line. The cellspecific and common downregulated genes were characterized using the MetaCore Gene Ontology (GO) enrichment analysis algorithm. LCC9-sepecific miR-29b-1/a-regulated GO processes include oxidative phosphorylation, ATP metabolism, and apoptosis. Extracellular flux analysis of cells transfected with anti-or pre-miR-29a confirmed that miR-29a inhibits mitochondrial bioenergetics in LCC9 cells. qPCR,luciferase reporter assays, and western blot also verified the ATP synthase subunit genes ATP5G1 and ATPIF1 as bone fide miR29b-1/a targets. Our results suggest that miR-29 repression of TAMresistant breast cancer cell proliferation is mediated in part through repression of genes important in mitochondrial bioenergetics. microRNAs (miRNA, miRs) are 22 nt non-coding RNAs that recognize and bind complementary seed sequences in the 3′-UTR region of a target messenger RNA (mRNA) 1, 2 . This results in translational repression and/or transcriptional degradation of the target gene. By targeting several mRNAs, miRNAs regulate several cellular and biological processes including cell cycle, cell proliferation and cell differentiation, apoptosis, cellular respiration and glycolysis (reviewed in refs 3-6). Aberrant miRNA expression mediates disease initiation and progression in breast and other cancers 7 . Seventy percent of breast tumors express estrogen receptor alpha (ERα) implying eligibility for endocrine therapies including selective estrogen receptor modulators (SERMs), e.g., Tamoxifen (TAM), and aromatase inhibitors (AI), e.g., letrozole. The efficacy of endocrine therapy is limited by relapse in ~40% of patients 8,9 . Endocrine resistance is mediated by multiple mechanisms depending on the type of therapy used (reviewed in refs 10-14). Alterations in miRNA expression are also implicated in endocrine-resistance (reviewed in refs 15 and 16).Previously, we reported miR-29b-1 and miR-29a were downregulated by TAM in TAM-sensitive (TAM-S) MCF-7 BC cells and upregulated in TAM-resistant (TAM-R) LCC2, LCC9, and LY2 BC cells 17 . There are four miR-29 family members in the human genome: miR-29b-2 and miR-29c (chromosome 1q32.2) and miR-29b-1 and miR-29a (chromosome 7q32.3). miR-29b-1 and miR-29a are separated by ~652 bp on the same pri-miRNA transcript [18][1...

miRNAs and Long-term Breast Cancer Survival: Evidence from the WHEL Study

“…Concordant with our findings, miR-210 overexpression was associated with worse prognosis in multiple studies and systematic reviews (4, 5, 37-39) and likely characterizes an aggressive phenotype. The miR-29 family is reported to exhibit both tumor-suppressing and -promoting roles in breast cancer (40)(41)(42)(43). In our study, higher levels of miR-29c were associated with worse prognosis, in contrast to published findings in triple-negative breast cancer, where higher miR-29c levels were associated with better prognosis (44)(45)(46)(47).…”

Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication

“…Exosomes from TAM-resistant LCC2 cells, derived from MCF-7 cells, had higher levels of the lncRNA UCA1 than parental MCF-7 cells, and the incubation of MCF-7 cells with exosomes from LCC2 cells conferred TAM-resistance [336]. We reported that miR-29b-1/a directly targets ATP synthase subunit genes ATP5G1 and ATPIF1 and inhibit OCR and decrease ATP in MCF-7 and LCC9 breast cancer cells [337]. UCA1 activates AKT-mTOR signaling [338] and is a ceRNA for miR-18a, thus derepressing HIF-1α [137].…”

MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal-like breast cancer

“…This tumour suppressive role was mediated through targetting of SPIN1 effecting the downstream signaling of WNT/β-catenin and Akt. Furthermore the miR-29 family also acts as a tumour supressor in tamoxifen resistant breast cancer cells inhibiting cell proliferation through repressing genes involved in mitochondrial bioenergetics [ 30 , 31 ]. These data strengthen our finding that high expression of this miRNA is a biomarker for good prognosis.…”