Evaluating the Knockdown Activity of MALAT1 ENA Gapmers In Vitro

Iwashita, Shinzo; Shoji, Takao; Koizumi, Makoto

doi:10.1007/978-1-0716-0771-8_11

Cited by 3 publications

(4 citation statements)

References 14 publications

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“…Proteins interacting with MALAT1 in a whole-cell lysate of HEPG2 human HCC cells included proteins involved in RNA processing, splicing, and gene transcription [ 185 ]. MALAT1 is a therapeutic target using antisense oligonucleotides (ASO) and ‘gapmers’ with a central DNA flanked by modified oligonucleotides that interact with MALAT1 and degrade it via nuclear RNase H [ 186 , 187 ]. MALAT1 was identified in networks 1 and 3 ( Supplementary Table S4 , Figure 6 and Figure 7 ) and negatively regulates SMAD2 (SMAD family member 2) and miR-185-5p, discussed previously as being reduced in breast tumors (reviewed in [ 129 ].…”

Section: Resultsmentioning

confidence: 99%

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Muluhngwi

Klinge

2021

Cancers

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Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.

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Section: Resultsmentioning

confidence: 99%

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Muluhngwi

Klinge

2021

Cancers

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“…Although the MENβ triple helix is less studied than its counterpart in MALAT1, compounds like aurintricarboxylic acid, emodin, GW5074, mitoxantrone and rottlerin bind to the MENβ triple helix near the micromolar range, and the kinase inhibitor PIK-75 abolishes paraspeckles in the neuroblastoma cell line SH-SY5Y [30]. ASO therapeutics have been used to target and regulate the MALAT1 lncRNA in various cancer types [31][32][33][34][35][36][37][38][39][40][41][42][43][44][45]. A variety of ASOs, typically 16-20 nucleotides in length, have been designed, such as small interfering RNA (siRNA) [35][36][37]; gapmers with two to three locked nucleic acids (LNAs) [31,33,34,[38][39][40]; 2 ′ -O-methylethyl groups; 2 ′ -O,4 ′ -C-ethylene-bridged nucleic acid [41] or guanidine-bridged nucleic acid [42] at the end(s); PNA-DNA chimeras [43]; and the conjugation of ASO to single-wall carbon nanotubes [44], gold nanoparticles [32], TAT peptides [32], fatty acids [45] or membrane protein-binding aptamers [46] to improve delivery and biodistribution.…”

Section: Of 19mentioning

confidence: 99%

“…ASO therapeutics have been used to target and regulate the MALAT1 lncRNA in various cancer types [31][32][33][34][35][36][37][38][39][40][41][42][43][44][45]. A variety of ASOs, typically 16-20 nucleotides in length, have been designed, such as small interfering RNA (siRNA) [35][36][37]; gapmers with two to three locked nucleic acids (LNAs) [31,33,34,[38][39][40]; 2 ′ -O-methylethyl groups; 2 ′ -O,4 ′ -C-ethylene-bridged nucleic acid [41] or guanidine-bridged nucleic acid [42] at the end(s); PNA-DNA chimeras [43]; and the conjugation of ASO to single-wall carbon nanotubes [44], gold nanoparticles [32], TAT peptides [32], fatty acids [45] or membrane protein-binding aptamers [46] to improve delivery and biodistribution. Most ASO gapmers target unstructured regions of MALAT1, leading to RNase H-mediated knockdown from 2-50-fold [31,34,39,40].…”

Section: Of 19mentioning

confidence: 99%

Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels

Shivakumar,

Mahendran,

Brown

2024

IJMS

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Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5–13 °C more than the Watson–Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.

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“…It became more attractive when it was demonstrated that chimeric oligos (or gapmers) consisting of a central DNA-core of four deoxynucleotides flanked by stretches of 2′-O-methylated ribonucleotides, designed to base-pair with a target RNA of interest, could sufficiently elicit RNase-H mediated degradation of the RNA. While the design rules have been significantly improved over the years [ 79 , 80 , 81 ], the concept remains the same ( Figure 3 A). In a therapeutic setting, targeting a mutated mRNA could prevent the toxic effect associated with the expression of a gain-of-function or dominant-negative protein as a means of improving disease phenotypes.…”

Section: Antisense Mechanisms: Gapmers Sirnas and Splice-modulating Oligonucleotidesmentioning

confidence: 99%

From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies

Adachi

Hengesbach

et al. 2021

Biomedicines

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Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siRNAs). These antisense-based mechanisms can tackle several genetic disorders in a gene-specific manner, primarily by gene downregulation (gapmers and siRNAs) or splicing defects correction (exon-skipping oligos). Still, the challenge remains for the repair at the single-nucleotide level. The emerging field of epitranscriptomics and RNA modifications shows the enormous possibilities for recoding the transcriptome and repairing genetic mutations with high specificity while harnessing endogenously expressed RNA processing machinery. Some of these techniques have been proposed as alternatives to CRISPR-based technologies, where the exogenous gene-editing machinery needs to be delivered and expressed in the human cells to generate permanent (DNA) changes with unknown consequences. Here, we review the current FDA-approved antisense MoA (emphasizing some enabling technologies that contributed to their success) and three novel modalities based on post-transcriptional RNA modifications with therapeutic potential, including ADAR (Adenosine deaminases acting on RNA)-mediated RNA editing, targeted pseudouridylation, and 2′-O-methylation.

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Evaluating the Knockdown Activity of MALAT1 ENA Gapmers In Vitro

Cited by 3 publications

References 14 publications

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels

From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies

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