Pre-mRNA Splicing Modulation by Antisense Oligonucleotides

Singh, Natalia N.; Luo, Diou; Singh, Ravindra

doi:10.1007/978-1-4939-8651-4_26

Cited by 36 publications

(18 citation statements)

References 51 publications

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“…The discovery of ISS-N1 was enabled in part by the employment of Anti-N1, a 20-mer ASO that substantially restored SMN2 exon 7 inclusion by masking ISS-N1 (Figure 1A) [37]. Thus far, dozens of ISS-N1-targeting ASOs have been independently tested for their efficacies in vitro and/or in vivo [6,[37][38][39][41][42][43][44][45][46][47][97][98][99][100][101][102][103][104][105][106]. Due to their tolerance for mismatches in base pairing, ASOs are expected to produce off-target effects, particularly when used at higher concentrations.…”

Section: Discussionmentioning

confidence: 99%

High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome

Ottesen

Luo

Singh

et al. 2021

IJMS

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Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.

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Section: Discussionmentioning

confidence: 99%

High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome

Ottesen

Luo

Singh

et al. 2021

IJMS

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“…105,106 Methods and mechanisms associated with the splicing correction by an ISS-N1-targeting ASO are reviewed elsewhere. [107][108][109] Collaborative studies conducted in the Krainer lab at Cold Spring Harbor Laboratories, New York and by Ionis Pharmaceuticals, Carlsbad, California played a pivotal role in the therapeutic development of nusinersen. 110 Several recent reports describe the efficacy of nusinersen in SMA patients.…”

Section: Context Of the Suboptimal 5′ss Of Smn2 Exonmentioning

confidence: 99%

The First Orally Deliverable Small Molecule for the Treatment of Spinal Muscular Atrophy

2020

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Spinal muscular atrophy (SMA) is 1 of the leading causes of infant mortality. SMA is mostly caused by low levels of Survival Motor Neuron (SMN) protein due to deletion of or mutation in the SMN1 gene. Its nearly identical copy, SMN2, fails to compensate for the loss of SMN1 due to predominant skipping of exon 7. Correction of SMN2 exon 7 splicing by an antisense oligonucleotide (ASO), nusinersen (Spinraza™), that targets the intronic splicing silencer N1 (ISS-N1) became the first approved therapy for SMA. Restoration of SMN levels using gene therapy was the next. Very recently, an orally deliverable small molecule, risdiplam (Evrysdi™), became the third approved therapy for SMA. Here we discuss how these therapies are positioned to meet the needs of the broad phenotypic spectrum of SMA patients.

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“…These include the non-sense-mediated decay (NMD) (Ward et al, 2014;Nomakuchi et al, 2016) and the no-go decay (NGD) (Liang et al, 2019a) which is triggered by ribosome stalling due to obstacles and collision of multiple ribosomes on the mRNA (Harigaya and Parker, 2010). Oligonucleotides targeted to either the 5 ′ or 3 ′ splice sites can interfere with splicing (Havens and Hastings, 2016;Singh et al, 2018). Interestingly, this can be used either to block mature protein expression or to correct aberrant splicing thereby restoring the protein function.…”

Section: Antisense Oligonucleotidesmentioning

confidence: 99%

Transcription and Translation Inhibitors in Cancer Treatment

et al. 2020

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Transcription and translation are fundamental cellular processes that govern the protein production of cells. These processes are generally up regulated in cancer cells, to maintain the enhanced metabolism and proliferative state of these cells. As such cancerous cells can be susceptible to transcription and translation inhibitors. There are numerous druggable proteins involved in transcription and translation which make lucrative targets for cancer drug development. In addition to proteins, recent years have shown that the "undruggable" transcription factors and RNA molecules can also be targeted to hamper the transcription or translation in cancer. In this review, we summarize the properties and function of the transcription and translation inhibitors that have been tested and developed, focusing on the advances of the last 5 years. To complement this, we also discuss some of the recent advances in targeting oncogenes tightly controlling transcription including transcription factors and KRAS. In addition to natural and synthetic compounds, we review DNA and RNA based approaches to develop cancer drugs. Finally, we conclude with the outlook to the future of the development of transcription and translation inhibitors.

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Pre-mRNA Splicing Modulation by Antisense Oligonucleotides

Cited by 36 publications

References 51 publications

High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome

High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome

The First Orally Deliverable Small Molecule for the Treatment of Spinal Muscular Atrophy

Transcription and Translation Inhibitors in Cancer Treatment

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