Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease causing the most frequent genetic childhood lethality. Recently, nusinersen, an antisense oligonucleotide (ASO) that corrects SMN2 splicing and thereby increases full-length SMN protein, has been approved by the FDA and EMA for SMA therapy. However, the administration of nusinersen in severe and/or post-symptomatic SMA-affected individuals is insufficient to counteract the disease. Therefore, additional SMN-independent therapies are needed to support the function of motoneurons and neuromuscular junctions. We recently identified asymptomatic SMN1-deleted individuals who were protected against SMA by reduced expression of neurocalcin delta (NCALD). NCALD reduction is proven to be a protective modifier of SMA across species, including worm, zebrafish, and mice. Here, we identified Ncald-ASO3—out of 450 developed Ncald ASOs—as the most efficient and non-toxic ASO for the CNS, by applying a stepwise screening strategy in cortical neurons and adult and neonatal mice. In a randomized-blinded preclinical study, a single subcutaneous low-dose SMN-ASO and a single intracerebroventricular Ncald-ASO3 or control-ASO injection were presymptomatically administered in a severe SMA mouse model. NCALD reduction of >70% persisted for about 1 month. While low-dose SMN-ASO rescues multiorgan impairment, additional NCALD reduction significantly ameliorated SMA pathology including electrophysiological and histological properties of neuromuscular junctions and muscle at P21 and motoric deficits at 3 months. The present study shows the additional benefit of a combinatorial SMN-dependent and SMN-independent ASO-based therapy for SMA. This work illustrates how a modifying gene, identified in some asymptomatic individuals, helps to develop a therapy for all SMA-affected individuals.
Keywords: spinal muscular atrophy, SMA, neuromuscular disorder, motor neuron disorder, neuromuscular junction, SMN1, SMN2, NCALD, modifier gene, ASO therapy
Main Text
Spinal muscular atrophy (SMA) is an autosomal-recessive neurodegenerative disease characterized by the loss of α-motoneurons in the anterior horns of the spinal cord causing symmetrical muscle weakness and atrophy of limb and trunk muscles. SMA affects 1 in 6,000—10,000 live births and is the leading genetic cause of infant mortality.1, 2 In the European population 1:35 and worldwide 1:51 individuals are SMA carriers.3, 4 SMA is caused by deletions or loss-of-function mutations of survival of motor neuron 1 (SMN1 [MIM: 600354]) and a variable number of mainly non-functional SMN2 copies resulting in low levels of the survival motor neuron (SMN) protein.5, 6 While SMN1 produces only full-length (FL)-SMN1 transcripts and protein, SMN2 (MIM: 601627) mainly produces alternatively spliced transcripts (SMN2Δ7), which generate a truncated and unstable SMNΔ7 protein. Only a small amount of SMN2 transcripts (∼10%) are correctly spliced and are of full length, generating an SMN protein identical to the one produced from SMN1 copies.7, 8 There is an inverse correlation between the number of SMN2 copies and the severity of the disease. It can range from type I (SMA1 [MIM: 253300]), which represents the severe end of the spectrum and accounts for approximately 60% of 5q-SMA-affected individuals, to type IV, the mildest and adult form.1, 2, 4, 9 SMN is crucial for all cells, but abnormal low levels of SMN mainly affect spinal motoneurons innervating proximal muscles.10
Recently, nusinersen, the first antisense oligonucleotide (ASO)-based therapy for SMA-affected individuals, has been approved by the US Food & Drug Administration (FDA) and the European Medicines Agency (EMA).11 Nusinersen is an SMN-ASO that increases SMN levels by blocking an intronic splice silencer in SMN2, thereby facilitating the exon 7 inclusion and generation of FL-SMN2 transcripts.12 Clinical studies in all types of SMA-affected individuals treated with nusinersen showed significant amelioration in motoric abilities in about half of them.13, 14 However, the therapeutic increment of SMN through the ASO approach seems to be insufficient to fully counteract the SMA pathology.13, 14 Despite encouraging on-going studies, it might be that even presymptomatic therapy with nusinersen is unable to provide sufficient SMN protein support for motoneuron function and thus stop disease progression over the patient’s life-time in individuals with only one or two SMN2 copies. Moreover, results from different animal models have shown a critical “therapeutic time window” in SMA, as increasing SMN postsymptomatically either fails or shows only a modest amelioration of symptoms in mice.15, 16, 17, 18, 19, 20 Similarly, in SMN1-deleted individuals, the highest effects were observed when early or presymptomatic therapeutic intervention was applied.13, 14 Since only few countries started to include SMN1 deletion testing into the neonatal screening, in most instances SMA is detected only after the first clinical signs appear, which means that a large number of motoneurons are already affected; this fact drastically reduces the beneficial effect of any therapy. Therefore, the development of SMN-independent therapies can be beneficial (1) as an additional support of motoneurons and neuromuscular junction (NMJ) function under conditions when SMN elevation via SMN-dependent therapy is insufficient (e.g., ASO therapy in SMA-affected individuals with SMA1, who possess only one or two SMN2 copies) and (2) after the disease onset in all SMA types, to support the function of motoneurons and NMJs in an SMN-independent manner.
The strongest support of a potential beneficial impact of SMN-independent therapeutic approaches originates from our knowledge gained on SMA-protective genetic modifiers in humans.21, 22 In asymptomatic SMN1-deleted individuals, we found two SMA-protective modifiers able to counteract the SMN deficiency and prevent the disease phenotype. In 2008, we identified the first human SMA genetic modifier, Plastin 3 (PLS3 [MIM: 300131]), and provided conclusive evidence that its overexpression exerts protective effects in in vitro and in vivo SMA models.21, 23, 24, 25 Further studies using AAV9-PLS3 in SMA mice strengthened our findings.26 In 2017, we reported a second SMA-protective modifier gene, Neurocalcin delta (NCALD [MIM: 606722]).22 We found that reduced levels of NCALD, which is a neuronal Ca2+ sensor protein, acts protective in a four-generation discordant family with five asymptomatic and two SMA1-affected individuals. Multiple in vitro and in vivo experiments have shown that reducing NCALD levels significantly ameliorate SMA pathology across SMA species.22 Most importantly, heterozygous Ncald knockout in a severely affected SMA mouse model (SMA-Ncaldko/wt) injected with a low dose SMN-ASO (30 μg) at P1 to rescue multiorgan dysfunction ameliorates the neuromuscular pathology including motor axon development, both NMJ size and maturation, muscle size, proprioceptive input on motoneuron soma, as well as endocytic uptake of FM1-43 dye at the NMJ and motoric abilities.22 Moreover, heterozygous in contrast to homozygous Ncald knockout has no effect on brain development and adult neurogenesis, but enhances spinal motor neuron development.27 Collectively, these results demonstrate that genetically mediated NCALD reduction acts beneficially on SMA pathology.
Based on these encouraging results, we (1) developed and analyzed specific Ncald-ASOs to efficiently downregulate NCALD in mouse spinal cord and (2) used them in a randomized and blinded preclinical study in the severely affected SMA mouse model in a combination with low-dose SMN splice switching ASOs. This is a proof of concept for a combinatorial SMN-dependent and SMN-independent ASO-based therapy in SMA mice.
To study in vivo the effect of NCALD downregulation and evaluate its effect on SMA pathology, we first had to develop a non-toxic and efficient ASO. Therefore, we designed 450 different 2′-O-methoxyethyl (MOE)-gapmer Ncald ASOs on mixed backbone, which were first tested in cultured embryonic mouse cortical neurons for downregulation of Ncald mRNA using a quantitative RT-PCR assay. A subset of 22 hits from the cell culture screen, mainly targeting the 3′ UTR of Ncald RNA, were further tested in adult mice for tolerability and efficiency (Figure 1A). Adult mice were treated by intracerebroventricular (i.c.v.) bolus injection with 500 μg of each ASO. Two weeks later, Ncald expression was verified in spinal cord and brain lysates by qRT-PCR (Figure 1B). None of the ASOs overlapped with the primer probe set (PPS) which were flanking exon 5–6 junction; therefore, amplicon effect of oligonucleotides was not a concern (Figure S1A). Since the Taiwanese SMA mice (who carry two human SMN2 copies per allele and no functional murine Smn gene) on C57BL6/N background survive around 2 weeks23, 28 and the best clinical outcome is expected in a presymptomatic therapy, the three most efficient Ncald-ASOs (Ionis #673672, #673663, #673756; further referred as Ncald-ASO1, -ASO2, or -ASO3, respectively) or a control ASO (Ionis #676626, Ctrl-ASO) were tested in neonatal mice (Figures S1B and S1C). To evaluate the tolerability and efficiency and to determine the optimal dose in these young animals, i.c.v. injections with different doses, ranging from 30 to 60 μg of Ncald-ASO1, -ASO2, -ASO3, and Ctrl-ASO were carried out at postnatal day 2 (P2). At P10 we examined NCALD downregulation in spinal cord and brain lysates of mice injected with Ncald-ASOs in comparison to Ctrl-ASO-injected mice. We found that i.c.v. delivery of Ncald-ASO1 and Ncald-ASO2 showed acute toxicity, since 30% and 50% of the injected animals died (data not shown); Ctrl-ASO and Ncald-ASO3 were well tolerated by all animals. Since mice treated with 30 to 60 μg of Ncald-ASO3 exhibited only a moderate downregulation of NCALD (Figure S2), we increased the dose to 100 μg and obtained an 80% and 75% NCALD downregulation in the spinal cord and the brain, respectively (Figure 1C). Therefore, 100 μg of Ncald-ASO3 was applied for the whole study.
All our experiments were carried out in the Taiwanese severe SMA mouse model on a mixed50 background (50% FVB/N: 50% C57BL6/N), which is slightly more robust than congenic FVB/N or C57BL6/N mice; SMA mice on mixed50 background die at 16.5 days.22, 23, 24 By applying our previously developed breeding scheme (Figure 2),29 50% of mice develop SMA (Smnko/ko;SMN2tg/0) and 50% are healthy SMA carriers (Smnko/wt;SMN2tg/0, defined as heterozygous [HET] and used as controls). Since our previous studies showed that none of the genetic modifiers (PLS3, NCALD, or CHP1) are able to rescue the severe SMA phenotype,22, 23, 24, 30 we pharmacologically elevated the SMN levels—mainly in the non-central nervous system organs—by applying subcutaneously a single low dose of the SMN splice switching ASO (SMN-ASO, nusinersen). Therefore, all animals were subcutaneously injected with 30 μg of SMN-ASO at P1 (Figure 2A). We confirmed our previous results, showing that systemic injection of low-dose SMN-ASO has a major impact on survival, while the mice still show all SMA typical deficits (reduced compound muscle action potential [CMAP] and motor unit estimation [MUNE], impaired NMJ and muscle structure, reduced motoric abilities). Note also, we avoided a high dose of SMN-ASO since this provides a full rescue of SMA in mice,31 making the analysis of the effect of the Ncald ASO impossible. Thus, the low-dose nusinersen-treated SMA model resembles a mild SMA phenotype, similar to an SMA-affected individual carrying 3–4 SMN2 copies or the genotype found in our asymptomatic individuals or an SMA1-affected individual treated with nusinersen.32, 33
To better evaluate the requirement of NCALD from birth to adult age and beyond, we first determined endogenous NCALD level in spinal cord and brain of HET and SMA mice (injected with 30 μg SMN-ASO at P1) at P4, P21, 6, and 10 months. Our data show that NCALD is particularly abundant in spinal cord at very early developmental stages and gradually decreases when NMJs starts to develop and mature and muscles became more and more active. This is in line with our former finding that NCALD suppresses clathrin-mediated endocytosis, a process highly required for synaptic vesicle recycling at the NMJ.22 In contrast, NCALD level in the brain increases at P21 and stays high throughout the adulthood, although it slightly decreases at 10 months (Figure S3); this is in line with its important role in adult neurogenesis.27
We next analyzed the efficiency of Ncald-ASO3 in spinal cord and brain. We obtained four different study groups originated from litters treated with Ncald-ASO3 (referred to as SMA Ncald-ASO3 and HET Ncald-ASO3 mice) and from litters injected with Ctrl-ASO (referred to as SMA Ctrl-ASO and HET Ctrl-ASO mice). Mice were sacrificed at P21 and 3 months to examine the efficiency of the Ncald-ASO3 in spinal cord and brain. At P21, the NCALD amount was significantly reduced in both SMA and HET mice treated with Ncald-ASO3 in comparison to Ctrl-injected mice (Figure 3A). However, no differences were observed at 3 months between Ncald- and Ctrl-ASO-treated mice (Figure 3B), suggesting that the Ncald-ASO3 effect persists for about 1 month and reaches Ctrl-ASO levels by 3 months. Importantly, the postnatal Ncald-ASO3 treatment has no effect on brain morphology, which is in line with our previous data from heterozygous Ncald knockout mice27 (Figure S4).
Since Ncald-ASO3 efficiently reduced NCALD levels in spinal cord at P21, we investigated the impact on main SMA-affected cell types, motoneurons and muscles, and studied neuromuscular circuitry and muscle strength by applying four independent approaches: (1) electrophysiological measurements, i.e., compound muscle action potential (CMAP) and motor unit estimation (MUNE), (2) immunostaining of histological sections to analyze neuromuscular junction (NMJ) size and maturity, (3) determination of muscle fiber size, and (4) examination of muscle force using the grip strength test.
First, we analyzed animals at P21, when NCALD was visibly reduced to >70%; moreover, this is a time point when NMJs are fully matured and functional in mice. Second, we analyzed the animals at 3 months. Although NCALD was no longer reduced upon a single injection, we speculated whether the effect on motoneuron development and function could be beneficial even at a later time point.
At P21, CMAP and MUNE, both known to be excellent predictors of muscle-nerve functionality at the NMJ, were performed. Both are well documented to be reduced in SMA mouse models and SMA individuals.19, 34, 35 CMAP represents the maximal response of a given muscle upon the stimulation of the efferent nerve, and MUNE gives information about the number of motor units that innervate a muscle or a group of muscles.36 The electrophysiological assays were performed in the gastrocnemius muscle. SMA Ctrl-ASO-treated mice exhibited highly decreased CMAP amplitude and MUNE in comparison with HET Ctrl-ASO-treated animals, which upon NCALD reduction was significantly ameliorated in SMA mice (Figure 4A).
To verify whether improved CMAP and MUNE are due to an increase in NMJ size and maturity, we next analyzed the NMJ architecture in the Transversus abdominis (TVA) muscle, which is a well-known vulnerable muscle in SMA.37 To discriminate NMJs individually, we stained the postsynaptic terminal with bungarotoxin, which reveals the distribution of the acetylcholine receptors (AChRs) and thus allows a determination of the size of the NMJ, and co-stained the presynaptic part with an antibody against neurofilament (Figure 4B). The area occupied by the AChRs in NMJs of SMA Ctrl-ASO-treated mice was reduced compared to HET Ctrl-ASO-treated mice. NCALD downregulation enhanced the amount of AChRs in SMA Ncald-ASO3-treated mice (Figure 4B). Moreover, NMJ maturity (defined as mature when ≥3 perforations and immature when <3 perforations are present19) was delayed in SMA Ctrl-ASO- compared to HET Ctrl-ASO-treated mice at P21, but rescued in SMA Ncald-ASO3-treated mice (Figure 4B).
Next, we assessed the effect of NCALD downregulation on muscle morphology by quantifying the diameter of gastrocnemius muscle fibers using transverse H&E-stained sections (Figure 4C). Muscle fibers were significantly smaller in SMA Ctrl-ASO mice compared to HET Ctrl-ASO-treated mice at P21. Upon NCALD downregulation, we observed that the mean size of the muscle fibers was rescued in SMA mice (Figure 4C). A detailed analysis of size-grouped fibers showed that the number of fibers with larger diameter, ranging from 200 to 400 μm, was significantly higher in SMA Ncald-ASO3 compared to SMA Ctrl-ASO mice (Figure 4C). These results suggest that NCALD downregulation in the nervous system of SMA mice ameliorates also muscle pathology.
Although the effect of a single injection of the Ncald-ASO3 at P2 was abolished at 3 months, we analyzed CMAP and MUNE at that age to ascertain whether the effect of early NCALD reduction that markedly restored motoneuron and muscle function to HET level could have a long-lasting effect and still improve the NMJ functionality and motor abilities. While SMA Ctrl-ASO-treated mice showed diminished CMAP amplitude and MUNE compared to HET Ctrl-ASO-treated mice, Ncald-ASO3 treatment had no positive effect on the electrophysiology biomarkers at 3 months (Figure S5A). While the area occupied by the AChRs in NMJs of SMA Ctrl-ASO-treated mice was reduced compared to HET Ctrl-ASO-treated mice, the early NCALD downregulation had no long-term effect on NMJ area (Figure S5B). Lastly, while the muscle fiber size was clearly decreased in SMA Ctrl-ASO-treated mice, it was not restored to HET Ctrl-ASO-treated level (Figure S5C). Strikingly, the number of fibers with larger diameter, ranging from 200 to 400 μm in SMA Ncald-ASO3-treated animals was similar to HET Ctrl-ASO-treated mice, suggesting a long-lasting effect of improved NMJs development and maturation under NCALD reduction on the muscle structure.
Lastly, to assess the motoric ability in these mice and to strengthen the electrophysiology and histological results, we performed a grip strength test with adult mice at 3 and 6 months.22 At both ages, SMA Ctrl-ASO-treated mice displayed reduced grip strength in comparison with HET Ctrl-ASO-treated mice. Interestingly, 3-month-old SMA Ncald-ASO3-treated animals performed significantly better in the grip strength test compared to SMA Ctrl-ASO mice (Figure 4D), but not at 6 months (Figure S5D). These data demonstrate a beneficial effect of neonatal NCALD downregulation on motor performance until 3 months in SMA mice, which might be driven by the early improvement in NMJ structure and innervation as well as by the increase in muscle fiber size.
In summary, we developed a Ncald-ASO that highly efficiently downregulates NCALD protein levels by about 70% for about 1 month and is non-toxic for CNS development and maturation. Previously, we and others have shown that endocytosis is strongly decreased in SMA. Through multiple in vitro and in vivo experiments, we have demonstrated that NCALD reduction restores impaired endocytosis in SMA.22 Thus, similar to the genetically induced NCALD reduction, a single i.c.v. injection of Ncald ASO3 reduces the NCALD amount especially during the most critical time of NMJ development and maturation and thus facilitates synaptic vesicles endocytosis and neurotransmission in SMA, which is severely affected.
Indeed, a single neonatal CNS injection of Ncald-ASO3 in a combinatorial therapy with a single low-dose SMN-ASO systemic injection improved all neuromuscular deficits in SMA mice including (1) electrophysiological properties (CMAP and MUNE) and thus NMJ neurotransmission, (2) NMJ area and maturity, and (3) muscle fiber size at P21. Furthermore, this beneficial effect of Ncald-ASO3 on the development and function of motoneurons and muscles has a long-lasting effect even 3 months later, when SMA Ncald-ASO3-treated mice show significantly increased motoric strength compared to SMA Ctrl-ASO-treated mice.
Since endogenous NCALD is gradually downregulated after P4 and reaches about 20%–25% at 10 months, it suggests that under physiological conditions, motoneurons downregulate NCALD levels postnatally to achieve the most efficient endocytic recycling of synaptic vesicles, required for proper NMJ function. Via Ncald ASO3 therapy, we achieve the facilitation of synaptic vesicle recycling earlier in the development, thus improving the neurotransmission and as a consequence the NMJ maturation and function in SMA.
While SMN-ASOs, small molecules, or SMN gene therapy show promising results in pre- or early-treated symptomatic SMA individuals, treatment in more advanced stages of the disease show only moderate or even no effect.1, 31, 33, 38, 39 For these SMA-affected individuals, amelioration or even stopping the disease progression is crucial and therefore requires further SMN-dependent and SMN-independent therapies.40, 41 Moreover, the capacity of SMN-ASOs or small molecules to restore endogenous SMN2 splicing is below 2-fold in spinal cord and brain, which is likely insufficient to counteract loss of SMN, especially in SMA1-affected individuals with only one or two SMN2 copies, even if treated presymtomatically.6, 33, 42, 43, 44 It has also been shown in SMA mice that SMN is mainly required before P17, corresponding to the period of NMJ development and maturation.18
Therefore, additional SMN-independent approaches allowing life-long maintenance of motoneurons and NMJ function are needed. The advantage of this system is that both genes (SMN and NCALD) will be targeted by the same system: an ASO approach. We accomplish NCALD downregulation (more than 70% of protein levels) in the targeted tissues by a specific Ncald-ASO administration in P2 mice via i.c.v. injection. However, the Ncald MOE gapmer ASOs used to downregulate the RNA in comparison to the SMN MOE ASOs (nusinersen) that restores SMN2 splicing were less metabolically stable. While the SMN-ASOs are very stable upon subcutaneous injection and have a positive effect in liver even after 6 months,31 the duration of the effect of the Ncald-ASO3 was highly efficient for about 1 month but disappeared after 3 months. This suggests that a monthly reinjection or further designs to optimize duration of action needs to be considered.
Our findings provide the proof of concept that NCALD-mediated ASO downregulation in CNS is possible and demonstrate that Ncald-ASO3 can ameliorate SMA pathology and motoric dysfunction upon a single presymptomatic injection in neonatal animals. Although NCALD protein and its repressor role is gradually downregulated in spinal cord from P4 to 10 months, it still could be that a repetitively monthly i.c.v. bolus injection of the Ncald-ASO3 in the first few months could further enhance the positive impact, resembling the effect of the genetically modified SMA-Ncaldko/wt mice.22 A future perspective of the present study is to design ASOs against human NCALD and analyze the effect in cultured motoneurons derived from human iPSC, which then might be used to treat SMA-affected individuals. Finally, this work illustrates how a modifying gene uncovered in some asymptomatic individuals contributes to development of a therapy for all SMA-affected individuals.
Declaration of interests
C.F.B., F.R., and K.K.L. are employees of IONIS Pharmaceuticals. B.W. holds US patent 9,988,626 B2 approved June 5, 2018, Neurocalcin Delta Inhibitors and Therapeutic and Non-Therapeutic Uses Thereof.
Acknowledgments
This study was support by DFG Wi945/17-1, RTG 1960, DFG Wi945/19-1, (B.W.), CMMC C16 (B.W.), DFG KO5091/2-1 (N.L.K.), SMA Europe (L.T.-B.), and Ottomar Päsel Stiftung (S.S.).
Published: June 20, 2019
Footnotes
Supplemental Data can be found online at https://doi.org/10.1016/j.ajhg.2019.05.008.
Supplemental Data
References
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