ALDH1A3-regulated long non-coding RNA NRAD1 is a potential novel target for triple-negative breast tumors and cancer stem cells

Abstract

To discover novel therapeutic targets for triple-negative breast cancer (TNBC) and cancer stem cells (CSCs), we screened long non-coding RNAs (lncRNAs) most enriched in TNBCs for high expression in CSCs defined by high Aldefluor activity and associated with worse patient outcomes. This led to the identification of non-coding RNA in the aldehyde dehydrogenase 1 A pathway (NRAD1), also known as LINC00284. Targeting NRAD1 in TNBC tumors using antisense oligonucleotides reduced cell survival, tumor growth, and the number of cells with CSC characteristics. Expression of NRAD1 is regulated by an enzyme that causes Aldefluor activity in CSCs, aldehyde dehydrogenase 1A3 (ALDH1A3) and its product retinoic acid. Cellular fractionation revealed that NRAD1 is primarily nuclear localized, which suggested a potential function in gene regulation. This was confirmed by transcriptome profiling and chromatin isolation by RNA purification, followed by sequencing (ChIRP-seq), which demonstrated that NRAD1 has enriched chromatin interactions among the genes it regulates. Gene Ontology enrichment analysis revealed that NRAD1 regulates expression of genes involved in differentiation and catabolic processes. NRAD1 also contributes to gene expression changes induced by ALDH1A3; thereby, the induction of NRAD1 is a novel mechanism through which ALDH1A3 regulates gene expression. Together, these data identify lncRNA NRAD1 as a downstream effector of ALDH1A3, and a target for TNBCs and CSCs, with functions in cell survival and regulation of gene expression.

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

“…Oncogenic chromatin-binding lncRNA regulated by ALDH1A3 that contributes to ALDH1A3-mediated gene expression [70].…”

“…Functions as a ceRNA, sequestering miR-185-3p to upregulate NANOG via E2F1 [79]. Also, among several lncRNAs enriched in Aldefluor+ CSC populations in TNBCs [70].…”

“…Non-coding RNA in the aldehyde dehydrogenase 1A pathway (NRAD1), formerly referred to as LINC00284, is enriched in the ALDH high CSC populations of TNBCs [70]. Its expression is regulated by CSC marker ALDH1A3.…”

“…LINC00511 has been implicated in breast cancer tumorigenesis and stemness through modulation of the miR-185-3p/E2F1/NANOG axis [79]. LINC00511 was also among a shortlist of lncRNAs identified as enriched in ALDH high CSC populations of TNBCs [70]. Cytoplasmic LINC00511 functions as a ceRNA, sequestering miR-185-3p from gaining access to its target transcription factor E2F1.…”

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

“…Furthermore, MIR100HG negatively regulated p27 gene expression to control the cell cycle by forming RNA‐DNA triplex structures, impacting the progression of TNBC 94 . LncRNA NRAD1 was regulated by ALDH1A3 and was a therapeutic target for TNBC for its regulation of gene expression and effect on cancer cell survival 95 . LncRNA DANCR enhanced PI3K/AKT signals and TNBC proliferation by binding to RXRA and increasing its serine 49/78 phosphorylation to activate PIK3CA transcription 96 …”