Long non-coding RNA NEAT1 confers oncogenic role in triple-negative breast cancer through modulating chemoresistance and cancer stemness

Abstract

Triple-negative breast cancer (TNBC) is a malignant subtype of breast cancer with the absence of targeted therapy, resulting in poor prognosis in patients. Chemotherapy remains the mainstay of treatment for TNBC; however, development of drug resistance is the main obstacle for successful treatments. In recent years, long non-coding RNA (lncRNA) has been implicated in multiple biological functions in various diseases, particularly cancers. Accumulating evidence suggested that lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) expression is dysregulated in many human cancers and thus is a useful prognostic marker for cancer patients. Nevertheless, the mechanism of how NEAT1 confers drug resistance in TNBC is still largely unknown. We performed lncRNA profiling by the LncRNA Profiler qPCR Array Kit in normal control (NC) and breast cancers (BC) blood samples and further validated in a larger cohort of samples by qRT-PCR. Gene expression level and localization were investigated by qRT-PCR, western blotting, and immunofluorescence staining. Flow cytometric analysis was carried out to detect cancer stem cells. Functional studies were performed both in vitro and in vivo xenograft model. Among 90 lncRNAs, NEAT1 was highly expressed in the blood samples of breast cancer patients than in NC. In particular, the expression of NEAT1 was higher in TNBC tissues than other subgroups. Functional studies revealed that NEAT1 conferred oncogenic role by regulating apoptosis and cell cycle progression in TNBC cells. We identified that knockdown of NEAT1 sensitized cells to chemotherapy, indicating the involvement in chemoresistance. Importantly, shNEAT1 reduced stem cell populations such as CD44+/CD24−, ALDH+, and SOX2+, implicating that NEAT1 was closely related to cancer stemness in TNBC. Our data highlighted the roles of NEAT1 chemoresistance and cancer stemness, suggesting that it could be used as a new clinical therapeutic target for treating TNBC patients especially those with drug resistance.

Integrating multimodal data sets into a mathematical framework to describe and predict therapeutic resistance in cancer

“…Comparing these gene expression maps to the UMAP of resistant and sensitive cell classes ( Fig 4E) we can see that increased expression in NEAT1 is associated with resistance, while increased expression in UBE2S and TOP2A are associated with the sensitive state. Mechanistically, this corroborates previous findings, as NEAT1 has been shown to be associated with resistance in triple negative breast cancer (26). Although we do not perform detailed molecular analysis in this work, the framework presented here to distinguish sensitive and resistant cells over time can be used to perform a more detailed mechanistic investigation of molecular drivers of resistance, and that is an area of future work.…”

The Missing Lnc: The Potential of Targeting Triple-Negative Breast Cancer and Cancer Stem Cells by Inhibiting Long Non-Coding RNAs

“…We identified that NEAT1 expression is correlated with CD49f ( Table 2). While the relationship between NEAT1 and CD49f has not been studied previously, this correlation may provide insight into the mechanism underlying the chemoresistance found in NEAT1-enriched tumors [64].…”

“…In agreement with previous reports [122,123], our analysis also showed that NEAT1 and MALAT1 were enriched in ER+ breast cancers. This conflicts with other studies that have shown that these lncRNAs are TNBC-enriched [64,67]. For a comparison with potential protein-coding targets, we extended our analysis to include oncogene c-Myc, the hormone receptors, CSC markers, and key CSC-associated signaling pathway players ( Table 3).…”

“…The lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) has been identified in several human cancers and has been intimately linked to breast cancer progression by stimulating cell proliferation, EMT, and metastasis [89,90]. NEAT1 is reportedly elevated in TNBC and exerts an oncogenic function (regulation of apoptosis and cell cycle progression) in the subtype by promoting tumor growth, chemoresistance and the maintenance of breast CSCs [64]. NEAT1 knockdown in TNBC cells reduced CD44 high CD24 low , ALDH high , and SOX2 high CSC populations.…”

Systematic characterization of non‐coding RNAs in triple‐negative breast cancer

“…Studies have shown that lncRNA NEAT1 expression is upregulated in cisplatin‐ and taxol‐resistant cells compared with parental cells. By qRT‐PCR assay, it was demonstrated that when knocking down NEAT1 in sh‐NEAT1 cells, drug transporter genes, such as ATP7A and ATP7B, were downregulated, and functional analysis indicated that NEAT1 knockdown sensitized cells to chemotherapy through a synergistic effect 16 . BORG, an oncogenic lncRNA, was greatly responsive to cytotoxic drug treatment, particularly doxorubicin.…”