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REVIEW

Huntingtin-Lowering Strategies in Huntington’s Disease: Antisense


Oligonucleotides, Small RNAs, and Gene Editing
Neil Aronin, MD1* and Marian DiFiglia, PhD2

1
Department of Medicine and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
2
Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, USA

ABSTRACT: The idea to lower mutant hunting- expressed in adeno-associated virus to provide long-
tin is especially appealing in Huntington’s disease (HD). term silencing of huntingtin mRNA and protein. We
It is autosomal dominant, so that expression of the expect that these approaches will be ready for clinical
mutant allele causes the disease. Advances in RNA and studies in the near future, once safety has been vali-
gene regulation provide foundations for the huntingtin dated. Our understanding of gene editing—changing
gene (both normal and mutant alleles) and possibly the the huntingtin gene itself—is rapidly progressing. Har-
mutant allele only. There is much preclinical animal nessing our knowledge of transcription and translation
work to support the concept of gene and RNA silenc- should push scientific creativity to new and exciting
ing, but, to date, no clinical studies have been advances that overcome the lethality of the mutant
attempted in HD. Preventing expression of mutant hun- gene in HD. VC 2014 International Parkinson and Move-

tingtin protein is at the cusp for a human trial. Antisense ment Disorder Society
oligonucleotides delivered to patients with amyotrophic
lateral sclerosis have been well tolerated; small RNAs K e y W o r d s : Huntington’s disease; huntingtin; gene
administered to rodent and nonhuman primate brain regulation; clinical trial
knocked down huntingtin messenger RNA (mRNA);
short-hairpin complementary DNA of microRNAs can be

The Basic Principle in Huntington’s movements. The correlation has much splay, consistent
with the idea that other genes or environmental factors
Disease Is Its Genetic Underpinning influence HD progression.4 A small number of patients
have de novo expansion of CAG repeats in series, with-
Huntington’s disease (HD) is foremost an autosomal-
out inheriting a mutant huntingtin gene,5 evidence for
dominant disease. The mutant gene is sufficient to con-
spontaneous generation of a new HD kindred. It is
vey the disease to offspring of an affected parent to
postulated that a high, but normal, CAG copy number
produce the disease. The mutation is an increase in a
expands into the disease range. For the vast majority of
series of CAG repeats near the start site of the hunting-
patients, the expanded CAG repeat explains the disease
tin gene.1 There are a few gaps in the genetic principle.
presentation.
The extent of CAG expansion does not exactly predict
Animal studies serve as good avenues to test
onset and progression of the clinical manifestations in
huntingtin-lowering strategies, but incorporate impor-
HD—cognitive impairment, depression, and abnormal
------------------------------------------------------------ tant caveats. The mode for the CAG repeat expansion
*Correspondence to: Dr. Neil Aronin, Department of Medicine, University in patients is 42, with some variance among reports.6
of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA
01655; Neil.Aronin@umassmed.edu
This number is important to bear in mind. Few animal
studies, including those emphasizing therapeutics,
Relevant conflicts of interest: Nothing to report.
Full financial disclosures and author roles may be found in the online ver- work with CAG repeat expansions at 42; most use
sion of this article. animals with over 70 CAG repeats, even over 100
Received: 1 August 2014; Revised: 12 August 2014; Accepted: 15 repeats, a rare repeat number in patients. The mutant
August 2014 huntingtin gene product has many properties of nor-
Published online 27 August 2014 in Wiley Online Library
mal huntingtin. Patients with mutation in both copies
(wileyonlinelibrary.com). DOI: 10.1002/mds.26020 of the gene do not have a more severe course of the

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disease than those with a single copy; the mutant gene effects (AEs) of the lumbar puncture, but not of the
with the highest number of repeats characterizes the drug itself. Treatment of SOD1 or HD patients would
clinical course of the disease.7 For practical reasons of probably require multiple administrations. Patients tol-
scientific study, animal models of HD need to develop erated retreatment. The pathology of SOD1 ALS cen-
signs of disease quickly (months), compared to ters in the spinal cord, adjacent to the delivery site of
patients in which changes in the brain occur over dec- the ASO. Whether lumbar infusion will reach the
ades before disease onset. At the time of diagnosis, striatum and cortex in patients with HD will need to
based on clinical symptoms and signs, we speculate be tested. The route of infusion (directly into the stria-
that many neurons have degenerated in the striatum tum or into the intracerebral ventricular system) might
and cortex. Therefore, the mutant gene in HD pro- be considered for therapy.
duces a protein (or messenger RNA [mRNA]) with RNAi uses a series of events in which a small RNA
small effects on normal physiology long before disease (siRNA) forms a complex with mRNA, bringing an
onset. Animal models lack the timing of onset of HD, assembly of proteins to the targeted mRNA (RNA
transforming it from a chronic- to a rapid-onset silencing complex, or RISC). The protein, Argonaute
disease. 2, has primacy in this complex and serves as a nucle-
ase to cleave the mRNA target. Destroying the mRNA
target prevents translation of the protein, in our case,
Targeting Huntingtin Transcripts huntingtin. RNAi requires a small starting RNA, usu-
Offers Promising Preclinical Results ally approximately 21 nucleotides for each strand of a
duplex (siRNA). Once in a cell, the siRNA associates
Two viable treatments reduce huntingtin mRNA with several proteins to form the RISC, so that a sin-
and thereby mutant huntingtin protein: antisense oli- gle strand (guide strand) binds to the target mRNA
gonucleotide (ASO) and RNA interference (RNAi). and protein in RISC cleave it. siRNAs have good, but
Each has a central, but not exclusive, enzymatic pro- imperfect, fidelity; other mRNA targets might be
cess inherent in the actual mRNA silencing.2,3,8-11 affected.14,15 siRNAs require a small sequence with
ASOs are DNA-based small molecules. Alterations complementarity to detect the mRNA target (seed
in oligonucleotide bonds extend their half-life in cells, sequence), but they can have single-nucleotide discrim-
improve duration of action, and lead to good pene- ination. siRNAs that are manufactured to make spe-
trance into cells.11 As with small interfering RNAs cific sequences can be designed to detect single-
(siRNAs), ASOs do not cross the blood–brain barrier nucleotide differences in mRNA alleles and can be
(BBB). They can be injected into the lumbar space and applied to single-nucleotide polymorphism (SNP) het-
traverse into brain cells.12 It appears, in nonhuman erozygosities. The molecular machinery that underpins
primates, that the neocortex and local spinal cord take RNAi through siRNAs is in place in mammalian cells
up ASO against huntingtin mRNA, but sufficient in and neurons.16 It is thought that the guide strand of
striatum to cause knockdown of huntingtin mRNA or siRNA and endogenous small RNAs, microRNAs
protein. Optimization of dose or delivery approach of (miRNA, or miR), use the same set of proteins in
ASO may improve therapeutic response.12 In mouse, RISC.
ASOs achieve good knockdown and appear to be safe A novel iteration of RNAi is the use of single-
(without detailed histology) for at least a few stranded RNA (ssRNA) for decreasing huntingtin pro-
months.12 ASOs use RNase H to cleave huntingtin tein.17 ssRNA are modified, stabilized small RNAs
mRNA.11 Rnase H recognizes DNA/RNA complexes that have good spread after intraparenchymal adminis-
and, presumably, act by this enzyme, although other tration in mouse brain. The ssRNAs are more potent
mechanisms are possible.11 Allele-specific knockdown than unmodified siRNAs (most designed for therapy
has been achieved with this molecular technology.13 will probably be modified to improve stability).
An advantage of ASOs over RNAi is that introns can Because ssRNAs reduce huntingtin protein, but not
be targeted, giving ASOs a wider range of site to tar- huntingtin mRNA, they might invoke RNA repression,
get. ASOs can enter the nucleus and target introns and rather than elimination, as the mechanism of action.
exons in unspliced RNA. Thus, DNA technologies The ssRNA knocked down mutant huntingtin in a
offer a valuable resource for oligonucleotide treat- human fibroblast from patients with HD. The mouse
ments in HD. knockdown worked when the CAG repeats were
ASO treatment in patients with HD has not yet greater than 100 in series. However, rare patients
been reported on. But, ASO has been used in another have CAG expansions of this size. It is conceivable
autosomal neurodegenerative disease: superoxide dis- that the high number of CAG repeats might make pos-
mutase 1 (SOD1) familial amyotrophic lateral sclerosis sible the ssRNA-based knockdown of the mutant hun-
(ALS).1 Infusion of ASO (ISIS 333611) into the intra- tingtin allele. A more relevant huntingtin allele-specific
thecal space of patients with SOD1 ALS was well tol- silencing would be testing ssRNA in mutant hunting-
erated overall. Many patients experienced adverse tin mRNA in a range of 40 to 50 CAG repeats,

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because this is the range typical for Huntington’s dis- delivery packages facilitating intercellular communica-
ease. The ssRNA modification demonstrates that crea- tion, including trans-synaptic.23,24 Current investiga-
tive modifications of siRNA can offer improvements tions address critical questions. What are exosomal
in therapy by knocking down mutant huntingtin contents? How many small molecules can be loaded?
protein. Can exosomes deliver sufficient amounts to transmit
miRNAs are naturally occurring small RNAs that molecular therapy? A wave of excitement emanated
populate cells in mammals, especially neurons.18 Clas- from the finding that exosomes expressing rabies virus
sically, whereas siRNAs are generally made with full glycoprotein (RVG) can cross from the circulation to
complementarity to the mRNA target, miRNAs fre- the neurons in brain, deposit siRNAs, and knock
quently have mismatches, except in the seed sequence. down a protein contributing to Alzheimer’s disease in
miRNAs affect the 30 untranslated region (UTR) rodents.24 It should be noted that naked siRNAs
mostly to reduce stability of mRNA and increase its (short-lived) were used, and more-stable siRNA can be
destruction.18 To place into context, the polyA tail of studied. The pharmacodynamics of RVG exosomes in
mRNA has a greater effect on mRNA stability than large animals is not established. Finding cells to pro-
do miRNAs, but miRNAs work in a cumulative, coop- duce exosomes for patient therapy will take careful
erative manner, with synergistic effects on mRNA selection. Exosomes constitute a delivery system in its
stability. infancy, but offer promise for small-nucleotide–based
siRNAs, ssRNAs, and miRNAs have therapeutic therapies.
value. siRNA can be introduced into the brain
directly, enter neurons and glia, and reduce huntingtin
mRNA and protein.19,20 The sequence of siRNA can Short-Term Delivery Turns Into
be formulated to distinguish between two polymorphic Long-Term Gain, With Caveats
alleles of huntingtin.21,22 Huntingtin alleles have
SNPs, some of which are frequent in the Western miRNAs have critical strengths for treatment of
European population.21 Five siRNAs can be used to HD. First, they can be sculpted to fit multiple targets.
distinguish between mutant and normal alleles in up A seed sequence can be made to detect both hunting-
to 80% of patients with HD.21 One of the SNP heter- tin mRNA alleles. Second, miRNAs fit into a short
ozygosities accesses 50% of patients with HD. The hairpin, a structure that has a loop at the apex, has
sites of the SNP heterozygosities are in the open read- similar strands of RNA at its base, and incorporates
ing frame and the 30 UTR. The practical use of SNP sites for cleavage in the nucleus (drosha enzyme) and
heterozygosities needs to be confirmed in vivo. A com- in the cytoplasm (dicer enzyme). The result is a tem-
pelling advantage of siRNA use is its limited duration porary two-stranded RNA. The guide sequence is gen-
of effect. Estimated influence is 2 to 4 weeks. If unto- erally selected to enter RISC. Targeted mRNA
ward effects are found, such as ASOs, siRNAs can be knockdown can ensue by rapid mRNA cleavage and
stopped. Furthermore, siRNAs can be modified. removal, destabilization of mRNA and slow removal,
Naked siRNAs are short-lived, but phosphorothiate or translational repression in which the mRNA does
modification extends survival. Possibly, other modifi- not proceed to protein production, but survives none-
cations can be tested to modify half-life and delivery theless. Third, the miRNA short hairpin can be
into cells. A caveat for siRNA base RNAi is that inserted into a virus. A commonly used virus type is
safety of siRNA against innate immunity will need to adeno-associated virus (AAV). Another is lentivirus.
be tested. AAV has multiple serotypes with different properties
A problem for siRNA-based therapy in HD is brain of cellular uptake. It is thought (based on limited
access. Direct administration would require bilateral information) that a particular AAV serotype varies
injection into the striatum and regions of the cortex. uptake based on mammalian species and cell type
The state of the art for siRNA delivery lags behind the (e.g., neuron and glia).25 AAV resides in the nucleus,
siRNA design and efficacy. As reported, pumps can but does not integrate into genomic DNA, unlike len-
inject siRNA into a single striatum, shown in nonhu- tivirus that integrates in the genome.
man primates.20 The disease, however, affects both AAV is used for gene therapy and, experimentally,
caudate and putamen in the striatum and many areas delivery of miRNA. Two promoters have been tested:
of the cortex, criteria that ought to be considered in Pol II and Pol III (U6). Both produce abundant miR-
the engineering for siRNA delivery. NAs from short hairpin complementary DNA inserted
Recent advances in vesicular trafficking might pro- into the AAV as cargo. Short hairpin (double-stranded
vide another avenue for delivery of small molecules: DNA with a DNA loop connecting the two DNA
siRNA, ssRNA, miRNA, and ASO. Exosomes are strands) is processed by DICER in the cytoplasm to
vesicles (50-120 nm) that originate in the lysosomal make siRNA, or drosha in the nucleus and DICER in
system, leave cells with their contents, and are taken the cytoplasm to make miRNA. AAV2 with U6 can
up by nearby cells. In essence, exosomes might be be toxic in mice, presumably because of excessive

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A R O N I N A N D D I F I G L I A

siRNA production.25,26 The cell type most affected in ribosomal translation rate. Slowing ribosomes along
HD, called striatal medium spiny neurons, degenerate. mRNA allows intercession by surveillance molecules
Exportin-5, which transports short hairpin RNA that can interrupt ribosomal progress and destroy the
(shRNA) and other RNAs from the nucleus to the cyto- mRNA. Reducing the amount of factors that aid
plasm, is sequestered by overproduction of siRNA. translation across lengthy CAG repeats (as in HD) can
Loss of exportin-5 function may be toxic.27 Safety of decrease production of mutant huntingtin.37 We spec-
AAV-delivered miRNA depends on the extent of ulate that processes that delay translation through the
miRNA expression and selectivity in targeting. CAG repeats in HD might have allele-specific silencing
AAV is generally delivered by direct brain injection, properties. For example, in animal models of HD in
because, in the current technology, few neurons will which the CAG is extraordinarily increased to greater
take up AAV from the circulation.28,29 AAV adminis- than 200 CAG repeats in series, two studies show that
tration is best achieved in the brain by convection the very high CAG expansion leads to increased lon-
enhanced delivery, under constant pressure.30 Entry gevity of the mice38,39 and reduction of huntingtin
into at least 40% of neurons and variable numbers of mRNA.39 Electrophysiological defects are corrected.40
glia is likely. Immune-neutralization antibodies (Abs) The puzzling result can be explained by destruction of
prevent cellular uptake of AAV. Presence of these Abs mutant huntingtin mRNA by no-go decay. The trans-
would be expected to limit repeated injections of lational slowing and surveillance system response
AAV. In theory, immune-neutralization Abs observed blocks further translation through the vastly expanded
in the circulation31 might be found in the brain, but CAG repeat and removes the mutant mRNA from
actual data are lacking. translational participation. What is especially interest-
AAV continues to deliver its cargo for many years in ing is that small molecules might detect slowed trans-
nonhuman primates and humans.32 The goal of the ther- lation and take up a position on the ribosome to
apy would be that single administration of AAV with a block further translation, thereby offering a kind of
short-hairpin–containing microRNA (shRNAmir) into allele selective silencing.
the striatum and areas of the cortex silences mutant
huntingtin for many years. The short hairpin is proc-
essed to produce the miRNA, which is approximately Attacking the Huntingtin Gene
20 nucleotides in length. Studies in large brain animals
(e.g., sheep, pigs, and nonhuman primates) should be There are currently three speculative approaches to
performed to test for safety, immune neutralization, edit genes in vivo: zinc finger nucleases (ZFNs); tran-
spread of AAV, and knockdown of human mutant hun- scription activator-like effectors nuclease (TALENS);
tingtin. AAV-shRNAmir has been used to ameliorate and Clustered Regularly Interspaced Short Palindromic
neurodegeneration of mutant huntingtin in mice,26,33,34 Repeats (CRISPR-Cas9).41-43 Each has a different mode
and short-term studies of safety in nonhuman primates of action in their ability to cut DNA to begin the edit-
look promising.35,36 An improvement in AAV-based ing process. ZFNs cut with two nucleases (requiring
therapy would be regulation of AAV-shRNAmir produc- zinc) to cut DNA at a certain length apart. The two
tion in vivo, so that miRNA production can be curtailed DNA parts can reassemble, insert another piece of
or shut off. In vitro tet-off promoters use a bacterial DNA, or add a piece of DNA. TALENS use designed
protein to respond to an antibiotic; how humans would proteins that bring nucleases to the target gene, thereby
respond to this protein is uncertain. “Tet” regulation in causing double-stranded breaks. Zinc finger and TAL-
animals is not fully controllable. ENS nucleases offer the possibility for in vivo correc-
In theory, AAV-based systems for delivery of hun- tion of mutations or corruption of mutant genes to
tingtin gene shRNAmirs incorporate long-term benefits: destroy production of the mutant protein in inheritable
a single injection; expression in neurons in affected disease genes. ZFNs can reduce mutant human hunting-
brain areas; evidence in mammals for huntingtin silenc- tin mRNA in a mouse model of HD.44 Administration
ing; and a plethora of AAV serotypes to be taken up in of ZFN overlapping CAG repeats into R6/2 mice
many brain cells. Eventual use will depend on spread in knocked down the human huntingtin mRNA, reduced
the brain and safety of shRNAmir. aggregates, and dampened aberrant behaviors. The
CAG expansion in these mice is large (over 100); use
of ZFNs in mice with 40 to 45 CAG repeats in a
human huntingtin gene will need to be established. Dis-
Can the Expanded CAG in crimination between two human huntingtin genes
Huntingtin mRNA Make It Vulnerable would make use of ZFN especially compelling. None-
to No-Go Decay? theless, this finding advances the idea that attacking the
gene is a useful strategy for therapy.
Translation is highly regulated. Molecular machin- CRISPR-Cas 9 causes cleavage through Cas 9.45-47
ery is geared to maintain an efficient, predictable poly- CRISPR has the role to bind to genes; binding sites

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can be designed in a similar way to RNAi. CRISPR tide therapy in humans will probably be given as an
brings Cas 9 to specific sites on the DNA, usually infusion, with the expectation that the salubrious
with a requisite spacer, and cuts open the targeted effects will last many weeks to several months. Single
gene. The exposed ends of the DNA can undergo injections of oligonucleotides into the brain would be
homologous recombination (with an inserted piece of minimally instructive, given that neither spread nor
DNA) to correct the gene mutation or disrupt the efficacy would be adequately tested in either the cor-
gene to inactivate it. CRISPR has an added benefit. It tex or striatum. Intraventricular delivery is an option,
can bring other molecules to the gene or multiple but not yet established in nonhuman primates, which
genes, favoring the addition of epigenetic factors. We have less than 10% of human brain size. Intraparen-
speculate (no data yet) that CRISPR, as with oligonu- chymal administration could improve targeted ther-
cleotides to RNA, might target DNA in genes in a apy; however, advances in engineering would need to
sequence manner, thereby allowing allele selective ensure sufficient bilateral infusion to the cortex and
silencing at the gene level. Elimination of the mutant striatum to evaluate effective therapeutics.
gene allele would reduce overall huntingtin expression ASO therapy has been applied to neurodegenerative
by one half; in contrast, changing both normal and disease. Under the conditions of the clinical experi-
mutant huntingtin genes in a single cell would reduce ment, infusion of ASO has AEs from the lumbar punc-
huntingtin expression fully. ture, but not the drug itself. This finding is a phase I,
short-term study, but the results are encouraging.
Soon, a phase I study to test ASO for huntingtin might
How Much Knockdown of be initiated. Huntingtin is less abundant than SOD1;
Huntingtin Is Safe? we do not know the threshold of safety for excessive
knockdown of both alleles in HD. This issue is appro-
Lowering huntingtin overall has important conse- priate to consider for safety evaluation. How to moni-
quences. The level of huntingtin to support neuronal tor the distribution of the oligonucleotide in the
functions is not established. Total loss of huntingtin in
human brain is not established; the ASO should reach
development is lethal and loss in later life is harmful
the striatum and cortex, a challenge for intrathecal
to neurons.48,49 In monocytes from HD patients, 50%
infusion. Intraventricular infusion might offer better
of total huntingtin knockdown (mutant plus normal)
distribution into cortical and subcortical structures.
by RNAi restores normal cytokine function in the
siRNA delivery would probably be direct into the
monocytes.50 Extension of this study in mammalian
striatum. As with ASO, bilateral spread to the stria-
brain is underway. How much total huntingtin is
tum and cortex presents a therapeutic hurdle. Once
needed for maintaining neurons is not established.
long-term safety is established (6 months) in large ani-
mals, a phase I trial seems practicable for safety and
Is Silencing the Huntingtin Gene or feasibility. To determine efficacy, short-term measure-
mRNA Practical? ments of the three categories of changes should be
apparent: cognition, mood, and motor. siRNA infu-
We are imbued with a wealth of opportunity to sion might depend on advances in engineering, given
silence mutant huntingtin. Abundant in vitro or in that siRNA modifications do not enter the brain from
vivo evidence supports mutant huntingtin knockdown the cerebral fluid space particularly well. ssRNA might
by ASO, siRNA, ssRNA, and viral (AAV) shRNAmir. be a feasible option for spread from the ventricles.
Treatment of mice is a first step in an in vivo model, The promise of long-standing therapy underlies
but enthusiasm of these data should be tempered AAV delivery of miRNA against huntingtin mRNA.
because access to neurons in a large brain to achieve The prospect is exciting. Nonetheless, its safety must
therapeutic benefit is a realistic hurdle. We become be clear. Unlike oligonucleotides, expression of
inured of the success of gene silencing in mouse mod- miRNA cargo from AAV cannot be stopped. The
els because of easy access to neurons. Still, HD is viruses are designed to express miRNA for years or
monogenic, has ready diagnosis through genotyping, decades. Might too much miRNA expression affect
and has an educated, motivated patient population to both huntingtin mRNA alleles to reduce levels below
study. Are we ready for a clinical trial? a safe threshold? Might excess miRNA production
It is a leap of faith to assume that results in the influence endogenous miRNA handling or affect off-
mouse, sheep, pig, and even nonhuman primate apply targets? These queries are currently unanswered. We
in all aspects to humans. We cannot assume that need to ensure safety of AAV and miRNA in a large
immune responses to AAV or neuronal uptake of brain, preferentially in an animal with the mutant
AAV serotypes are the same among mammals. Brain huntingtin mutation. Careful study necessitates a firm
sizes vary, presenting challenges to delivery of silenc- understanding of AAV serotype and promoters (pol II
ing agents. Whether RNA or DNA based, oligonucleo- vs. pol III), extent of miRNA production, as well as

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A R O N I N A N D D I F I G L I A

neuronal and glial spread. Use of AAV has the prom- 12. Kordasiewicz HB, Stanek LM, Wancewicz EV, et al: Sustained
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