Dual masking of specific negative splicing regulatory elements resulted in maximal exon 7 inclusion of SMN2 gene.

Spinal muscular atrophy (SMA) is a fatal autosomal recessive disease caused by survival motor neuron (SMN) protein insufficiency due to SMN1 mutations. Boosting SMN2 expression is a potential therapy for SMA. SMN2 has identical coding sequence as SMN1 except for a silent C-to-T transition at the 6th nucleotide of exon 7, converting a splicing enhancer to a silencer motif. Consequently, most SMN2 transcripts lack exon 7. More than ten putative splicing regulatory elements (SREs) were reported to regulate exon 7 splicing. To investigate the relative strength of each negative SRE in inhibiting exon 7 inclusion, antisense oligonucleotides (AONs) were used to mask each element, and the fold increase of full-length SMN transcripts containing exon 7 were compared. The most potent negative SREs are at intron 7 (in descending order): ISS-N1, 3' splice site of exon 8 (ex8 3'ss) and ISS+100. Dual-targeting AONs were subsequently used to mask two nonadjacent SREs simultaneously. Notably, masking of both ISS-N1 and ex8 3'ss induced the highest fold increase of full-length SMN transcripts and proteins. Therefore, efforts should be directed towards the two elements simultaneously for the development of optimal AONs for SMA therapy.

A prospective study in the rational design of efficient antisense oligonucleotides for exon skipping in the DMD gene.

Antisense oligonucleotide (AON)-mediated exon skipping to restore dystrophin expression in Duchenne muscular dystrophy (DMD) therapy shown promise in a number of human clinical trials. Current AON design methods are semi-empirical, involving either trial-and-error and/or preliminary experimentations. Therefore, a rational approach to design efficient AONs to address the wide spectrum of patients' mutations is desirable. Retrospective studies have extracted many AON design variables, but they were not tested prospectively to design AONs for skipping DMD exons. Not only did the variables differ among the various studies, no numerical cutoff for each variable was inferred, which makes their use in AON design difficult. The challenge is to thus select a minimal set of key independent variables that can consistently design efficient AONs. In this prospective study, a novel set of design variables with respective cutoff values was used to design 23 novel AONs, each to skip one of nine DMD exons. Nineteen AONs were found to be efficacious in inducing specific exon skipping (83% of total), of which 14 were considered efficient (61% of total), i.e., they induced exon skipping in >25% of total transcripts. Notably, the satisfactory success rates were achieved by using only three design variables; namely, co-transcriptional binding accessibility of target site, presence of exonic splicing enhancers, and target length. Retrospective analyses revealed that the most efficient AON in every exon targeted has the lowest average cumulative position (ACP) score. Taking the prospective and retrospective studies together, we propose that design guidelines recommend using the ACP score to select the most efficient AON for each exon.

Identification and characterisation of human dysferlin transcript variants: implications for dysferlin mutational screening and isoforms.

In conducting dysferlin mutational screening using blood mRNA instead of genomic DNA, we identified the occurrence of alternative splicing involving novel dysferlin exons, i.e. exons 5a and 40a, in addition to previously reported alternative splicing of exon 17. Further study employing long range RT-PCR and subcloning revealed a total of fourteen dysferlin transcripts with maintained dysferlin reading frame. The study also characterised the differences in relative frequencies of the dysferlin transcripts in skeletal muscle and blood. The findings have potential implications for molecular diagnosis of dysferlinopathy and the identification of dysferlin isoforms.

Two eminently treatable genetic metabolic myopathies.

Treatment of the genetic metabolic myopathies remains generally unsatisfactory with the exception of a select few. Multiple Acyl Co-A Dehydrogenase Deficiency (Glutaric Aciduria type II), in particular, has been shown to respond well to riboflavin supplementation. Recently, studies have also confirmed the effectiveness of recombinant enzyme replacement therapy for Acid Maltase Deficiency (Pompe's Disease). Accurate and early diagnosis of these diseases is vital to prevent serious complications and impaired recovery following delayed treatment.

Fugu rubripes and human survival motor neuron genes: structural and functional similarities in comparative genome studies.

The compactness of the Fugu rubripes (Fugu) genome has supported its use in comparative genome analysis. Nevertheless, as Fugu is distinct evolution-wise from humans, it is essential to determine the similarity between a Fugu gene and its human counterpart to confirm its potential for comparative genome analysis. We cloned and analyzed the Fugu survival motor neuron gene (fsmn) for similarities with human SMN gene (huSMN). The Fugu genome has a single fsmn that is 13.4 times smaller than huSMN. fsmn and huSMN are highly similar in their genome organization and tissue expression patterns. The functional domains of the Fugu smn and human SMN molecules are also highly conserved. In human MCF-7 cells, expression of fsmn protein resulted in the formation of "gems" in the cytoplasm and nucleus, similar to observations reported for huSMN protein. In these cells, fsmn RNA was also processed correctly and produced alternatively spliced transcripts like huSMN2. These findings indicate close structural and functional similarities between fsmn and huSMN, suggesting that regulation of the two genes may also be similar and supporting the use of fsmn in comparative genome studies for the identification of functional regulatory elements of huSMN.

Dynamics of co-transcriptional pre-mRNA folding influences the induction of dystrophin exon skipping by antisense oligonucleotides.

Antisense oligonucleotides (AONs) mediated exon skipping offers potential therapy for Duchenne muscular dystrophy. However, the identification of effective AON target sites remains unsatisfactory for lack of a precise method to predict their binding accessibility. This study demonstrates the importance of co-transcriptional pre-mRNA folding in determining the accessibility of AON target sites for AON induction of selective exon skipping in DMD. Because transcription and splicing occur in tandem, AONs must bind to their target sites before splicing factors. Furthermore, co-transcriptional pre-mRNA folding forms transient secondary structures, which redistributes accessible binding sites. In our analysis, to approximate transcription elongation, a "window of analysis" that included the entire targeted exon was shifted one nucleotide at a time along the pre-mRNA. Possible co-transcriptional secondary structures were predicted using the sequence in each step of transcriptional analysis. A nucleotide was considered "engaged" if it formed a complementary base pairing in all predicted secondary structures of a particular step. Correlation of frequency and localisation of engaged nucleotides in AON target sites accounted for the performance (efficacy and efficiency) of 94% of 176 previously reported AONs. Four novel insights are inferred: (1) the lowest frequencies of engaged nucleotides are associated with the most efficient AONs; (2) engaged nucleotides at 3' or 5' ends of the target site attenuate AON performance more than at other sites; (3) the performance of longer AONs is less attenuated by engaged nucleotides at 3' or 5' ends of the target site compared to shorter AONs; (4) engaged nucleotides at 3' end of a short target site attenuates AON efficiency more than at 5' end.

Characterization of a novel S13F desmin mutation associated with desmin myopathy and heart block in a Chinese family.

Desmin myopathy was identified in a Chinese man with complete heart block and mild proximal and distal limb weakness. A novel heterozygous missense S13F mutation of the desmin gene was found to be associated with the myopathy. Family members carrying the mutation showed a similar or milder phenotype. The mutation is located at a protein kinase-C phosphorylation site within a highly conserved nonapeptide sequence in the head domain of the desmin protein. Expression of the mutant desmin cDNA in cell lines induced large desmin accumulations associated with preservation of a filamentous network.

Identification and characterization of a novel human dysferlin transcript: dysferlin_v1.

Mutations in the dysferlin (DYSF) gene are associated with limb girdle muscular dystrophy type 2B and Miyoshi myopathy. In this study, we report the identification and characterization of a novel dysferlin transcript that we named DYSF_v1 (GenBank accession: DQ267935). This transcript differs from the currently known dysferlin transcript (GenBank accession: AF075575) in the sequence of the entire first exon which spans 232 bases. This unique first exon is derived from intron 1 of DYSF, and has an immediate upstream 5' untranslated region containing CpG islands and sequences consistent with transcription factor binding sites. Exon 1 of DYSF_v1 shares 85% sequence homology and has similar genomic organization with the first exon of mouse dysferlin. Northern blot analysis showed that the DYSF_v1 transcript spans 7.5 kb and is expressed in human skeletal muscle, heart, placenta, brain, spleen, kidney, intestine, and lung tissues. DYSF_v1 retains phylogenic conservancy and shows similar expression pattern as the currently known human dysferlin.

Gene transfer to dorsal root ganglia by intrathecal injection: effects on regeneration of peripheral nerves.

Gene delivery to sensory neurons of the dorsal root ganglion (DRG) offers the prospect of developing new clinical interventions against peripheral nerve diseases and disorders. Here we show that genes can be transferred to rat DRG through lumbar intrathecal injection of delivery vectors into the cerebrospinal fluid. Genes could be transferred to DRG using polyethylenimine (PEI)/DNA complexes, Lipofectamine 2000/DNA complexes, adeno-associated virus vectors, or baculovirus vectors. We also show that nerve growth factor cDNA, delivered through lumbar intrathecal injection of PEI complexes, was able to improve regeneration of transected rat sciatic nerves. These data demonstrate the viability of using an intrathecal gene delivery approach for treating peripheral neuropathies.

Peripheral nerve regeneration with sustained release of poly(phosphoester) microencapsulated nerve growth factor within nerve guide conduits.

Prolonged delivery of neurotrophic proteins to the target tissue is valuable in the treatment of various disorders of the nervous system. We have tested in this study whether sustained release of nerve growth factor (NGF) within nerve guide conduits (NGCs), a device used to repair injured nerves, would augment peripheral nerve regeneration. NGF-containing polymeric microspheres fabricated from a biodegradable poly(phosphoester) (PPE) polymer were loaded into silicone or PPE conduits to provide for prolonged, site-specific delivery of NGF. The conduits were used to bridge a 10 mm gap in a rat sciatic nerve model. Three months after implantation, morphological analysis revealed higher values of fiber diameter, fiber population and fiber density and lower G-ratio at the distal end of regenerated nerve cables collected from NGF microsphere-loaded silicone conduits, as compared with those from control conduits loaded with either saline alone, BSA microspheres, or NGF protein without microencapsulation. Beneficial effects on fiber diameter, G-ratio and fiber density were also observed in the permeable PPE NGCs. Thus, the results confirm a long-term promoting effect of exogenous NGF on morphological regeneration of peripheral nerves. The tissue-engineering approach reported in this study of incorporation of a microsphere protein release system into NGCs holds potential for improved functional recovery in patients whose injured nerves are reconstructed by entubulation.

Serial diffusion-weighted magnetic resonance imaging in adult-onset citrullinaemia.

A 25-year-old Chinese man presented with a 2-year history of recurrent coma. His plasma ammonia level was extremely elevated, with raised citrulline level and absence of argininosuccinic acid. Adult-onset citrullinaemia, a condition rarely reported outside the Japanese population, was diagnosed. Serial magnetic resonance (MR) imaging, including diffusion-weighted (DW) studies, showed initial involvement of the insula cortex and cingulate gyrus, changing to a pattern of multiple small lesions in the depths of the cortical sulci. This changing pattern of lesions over time on DW MR imaging has not previously been described in adult-onset citrullinaemia.