However, lncRNAs represent a steadily emerging “backstage” layer of epigenetic
regulation, in which they are responsible for directing the epigenetic machinery in
sculpting and moulding the epigenetic landscape in fine detail. As these “backstage”
workings of lncRNAs in health and disease become more clearly illuminated year on
year, so too does the potential of therapeutically targeting them in order to precisely
correct pathological epigenetic alterations. LncRNA-targeting approaches designed
to enact gene- and gene network-specific epigenetic change would in principle
minimise the occurrence of non-specific, undesired global perturbations of epigenetic traits that are inevitable with current epidrugs but that do nothing to alleviate
the diseases being treated. Therapeutically targeting lncRNAs could also expand
the repertoire of epidrug development by opening the previously untapped possibility of reactivating the expression of proteins that are silenced in diseased states.
Such an approach would not only be useful for reactivating silenced tumour
suppressors, such as KLF2 in certain types of cancer, but also for compensating
the inborn errors of the epigenetic machinery that characterise rare epigenetic
syndromes. For example, Angelman syndrome is caused by the dominant negative
mutational loss-of-function of the maternally expressed allele of the imprinted
Ube3a gene and the continued silencing of the paternal allele by its NAT Ube3aAS that prevents it from being able to compensate the loss of the maternal allele.
However, proof of concept for the effectiveness of reactivating the paternal Ube3a
allele by targeting the NAT of Ube3a with siRNA has been provided by results from
a mouse model of Angelman syndrome showing that anti-Ube3a-NAT siRNA
markedly reduced multiple symptoms of the disease [80]. Early in vitro success
has also been gained in applying ASOs to alleviate Friedreich’s ataxia (FRDA), the
most frequent genetic cause of ataxia that is provoked by expanded GAA motif
repeats in the first intron of the Frataxin (FXN)-coding mitochondrial gene FXN. It is
proposed that when mutated FXN is transcribed, the expanded repeat region binds
with the complementary genomic DNA sequence to form a transcription-disrupting
R-loop, which effectively causes the breakdown of its own transcription and in turn
depletes FXN protein expression [81]. Li et al. developed a strategy to recover FXN
transcription, showing that both duplex RNA and LNA against expanded FXN
repeats could increase FXN levels in fibroblasts derived from FDRA patients [82].
The potential usefulness of therapeutically targeting lncRNAs in non-cancer
diseases has also been demonstrated in the neuromuscular disease that is the
most common inherited cause of infant death, spinal muscular atrophy (SMA). It
is primarily caused by recessive inactivating mutations in the Survival Motor
Neuron 1 (SMN1) gene [83]. In addition, the homologous SMN2 gene is retained
in variable copy numbers and harbours a mutation that leads to reduced inclusion of
exon 7 during pre-mRNA splicing [84]. Most SMN2 mRNA transcripts thus
lack exon 7, and these transcripts in turn produce a truncated and unstable form of
SMN protein. The consequent lack of functional SMN protein in spinal motor
neurones severely impairs their survival [85]. Various studies have innovated
the use of splice switching oligonucleotides (SSOs) to correct this splicing defect
in SMN2 pre-mRNA to promote exon 7 inclusion and thereby increase the production of stable, full-length SMN protein [86, 87]. One such SMN2-targeting SSO,
418
D. Hanly et al.
regulation, in which they are responsible for directing the epigenetic machinery in
sculpting and moulding the epigenetic landscape in fine detail. As these “backstage”
workings of lncRNAs in health and disease become more clearly illuminated year on
year, so too does the potential of therapeutically targeting them in order to precisely
correct pathological epigenetic alterations. LncRNA-targeting approaches designed
to enact gene- and gene network-specific epigenetic change would in principle
minimise the occurrence of non-specific, undesired global perturbations of epigenetic traits that are inevitable with current epidrugs but that do nothing to alleviate
the diseases being treated. Therapeutically targeting lncRNAs could also expand
the repertoire of epidrug development by opening the previously untapped possibility of reactivating the expression of proteins that are silenced in diseased states.
Such an approach would not only be useful for reactivating silenced tumour
suppressors, such as KLF2 in certain types of cancer, but also for compensating
the inborn errors of the epigenetic machinery that characterise rare epigenetic
syndromes. For example, Angelman syndrome is caused by the dominant negative
mutational loss-of-function of the maternally expressed allele of the imprinted
Ube3a gene and the continued silencing of the paternal allele by its NAT Ube3aAS that prevents it from being able to compensate the loss of the maternal allele.
However, proof of concept for the effectiveness of reactivating the paternal Ube3a
allele by targeting the NAT of Ube3a with siRNA has been provided by results from
a mouse model of Angelman syndrome showing that anti-Ube3a-NAT siRNA
markedly reduced multiple symptoms of the disease [80]. Early in vitro success
has also been gained in applying ASOs to alleviate Friedreich’s ataxia (FRDA), the
most frequent genetic cause of ataxia that is provoked by expanded GAA motif
repeats in the first intron of the Frataxin (FXN)-coding mitochondrial gene FXN. It is
proposed that when mutated FXN is transcribed, the expanded repeat region binds
with the complementary genomic DNA sequence to form a transcription-disrupting
R-loop, which effectively causes the breakdown of its own transcription and in turn
depletes FXN protein expression [81]. Li et al. developed a strategy to recover FXN
transcription, showing that both duplex RNA and LNA against expanded FXN
repeats could increase FXN levels in fibroblasts derived from FDRA patients [82].
The potential usefulness of therapeutically targeting lncRNAs in non-cancer
diseases has also been demonstrated in the neuromuscular disease that is the
most common inherited cause of infant death, spinal muscular atrophy (SMA). It
is primarily caused by recessive inactivating mutations in the Survival Motor
Neuron 1 (SMN1) gene [83]. In addition, the homologous SMN2 gene is retained
in variable copy numbers and harbours a mutation that leads to reduced inclusion of
exon 7 during pre-mRNA splicing [84]. Most SMN2 mRNA transcripts thus
lack exon 7, and these transcripts in turn produce a truncated and unstable form of
SMN protein. The consequent lack of functional SMN protein in spinal motor
neurones severely impairs their survival [85]. Various studies have innovated
the use of splice switching oligonucleotides (SSOs) to correct this splicing defect
in SMN2 pre-mRNA to promote exon 7 inclusion and thereby increase the production of stable, full-length SMN protein [86, 87]. One such SMN2-targeting SSO,
418
D. Hanly et al.