Refined physical map of the spinal muscular atrophy gene (SMA) region at 5q13 based on YAC and cosmid contiguous arrays

Spinal Muscular Atrophy: In the Challenge Lies a Solution

The path from gene discovery to therapy in spinal muscular atrophy (SMA) has been a highly challenging endeavor, but also led to one of the most successful stories in neurogenetics. In SMA, a neuromuscular disorder with an often fatal outcome until recently, with those affected never able to sit, stand, or walk, children now achieve these motoric abilities and almost age-based development when treated presymptomatically. This review summarizes the challenges along this 30-year journey. It is also meant to inspire early-career scientists not to give up when things become difficult but to try to uncover the biological underpinnings and transform the challenge into the next big discovery. Without doubt, the improvements seen with the three therapeutic strategies in SMA are impressive; many open questions remain and are discussed in this review.

Defective minor spliceosomes induce SMA-associated phenotypes through sensitive intron-containing neural genes in Drosophila

The minor spliceosome is evolutionarily conserved in higher eukaryotes, but its biological significance remains poorly understood. Here, by precise CRISPR/Cas9-mediated disruption of the U12 and U6atac snRNAs, we report that a defective minor spliceosome is responsible for spinal muscular atrophy (SMA) associated phenotypes in Drosophila. Using a newly developed bioinformatic approach, we identified a large set of minor spliceosome-sensitive splicing events and demonstrate that three sensitive intron-containing neural genes, Pcyt2, Zmynd10, and Fas3, directly contribute to disease development as evidenced by the ability of their cDNAs to rescue the SMA-associated phenotypes in muscle development, neuromuscular junctions, and locomotion. Interestingly, many splice sites in sensitive introns are recognizable by both minor and major spliceosomes, suggesting a new mechanism of splicing regulation through competition between minor and major spliceosomes. These findings reveal a vital contribution of the minor spliceosome to SMA and to regulated splicing in animals.

Genetic pattern of SMN1, SMN2, and NAIP genes in prognosis of SMA patients

Background

Spinal muscular atrophy (SMA) is the most common autosomal recessive disorder in humans after cystic fibrosis. It is classified into five clinical grades based on age of onset and severity of the disease. Although SMN1 was identified as the SMA disease-determining gene, modifier genes mapped to 5q13 were affirmed to play a crucial role in determination of disease severity and used as a target for SMA therapy. In this study, we determined SMN2 copy number and NAIP deletion status in SMA Egyptian patients with different clinical phenotypes and had homozygous deletion of SMN1. We aimed at finding a prognostic genetic pattern including SMN1, SMN2, and NAIP gene genotypes to determine the clinical SMA type of the patient to help in genetic counseling and prenatal diagnosis.

Results

Copy number variations (CNVs) of exon 7 of SMN2 gene were significantly decreased with the increase in disease severity. Homozygous deletion of exon 5 of NAIP was detected in 60% (12/20) of type I SMA and in 73% (8/11) of type III SMA cases. Combining the data of the SMN2 and NAIP genes showed 8 genotypes. Patients with D2 genotype (0 copies of NAIP and 2 copies of SMN2) were likely to have type I SMA. Type II SMA patients mostly had no homozygous deletion of NAIP and 2 copies of SMN2. However, patients with N3 genotype (> 1 copy of NAIP and 3 copies of SMN2) and patients with D3 genotype (0 copies of NAIP and > 3 copies of SMN2) had type III SMA.

Conclusion

SMN2 and NAIP are the most important modifier genes whose copy numbers can affect the severity of SMA. We concluded that the combination of modifier genes to provide prognostic genetic pattern for phenotype determination is preferable than using CNVs of exon 7 of SMN2 gene only. CNVs of exon 7 of SMN2 are of high importance to predict patients’ response to genetic therapy. On the other hand, deletion of exon5 of NAIP gene alone is not a sufficient predictor of SMA severity.

Development and validation of a haplotype-free technique for non-invasive prenatal diagnosis of spinal muscular atrophy

OBJECTIVE

To develop a technique for non-invasive prenatal diagnosis of spinal muscular atrophy and validate its performance.

STUDY DESIGN

Pregnant women with 1 copy of SMN1 and male fetuses were enrolled. Seventeen women were included in test set A, and 10 of them were selected into test set B randomly and blinded. The two sets were tested independently by two different researchers blinded to fetal genotypes. Fetal DNA fractions were calculated based on the relative proportion of mapped chromosome Y sequencing reads. An algorithm was developed to decide fetal SMN1 copy numbers.

RESULTS

The concordance rate with the results of MLPA testing of amniocyte DNA was 94.12% in test set A and 90% in set B. For all tests with a classifiable result, the percent of agreement with the results of MLPA testing of amniocyte DNA was up to 100% (25/25).

CONCLUSION

We have developed a direct, rapid, and low-cost technique, which has a potential to be utilized for first-trimester non-invasive prenatal diagnosis and screening for spinal muscular atrophy with considerable reliability and feasibility.

Identification and characterization of the porcine (Sus scrofa) survival motor neuron (SMN1) gene: an animal model for therapeutic studies

Spinal muscular atrophy (SMA) is an autosomal recessive disorder that is characterized by the degeneration of the motor neurons of the spinal cord leading to muscle atrophy. SMA is a result of a loss-of-function of the gene survival motor neuron-1 (SMN1). We have chosen to generate a transgenic swine model of SMA for the development and testing of therapeutics and evaluation of toxicology. To this end, we report the first cloning and identification of the swine SMN1 gene and show that there is significant sequence homology between swine and human SMN throughout the coding region. Reverse transcriptase-polymerase chain reaction results demonstrated slight changes in SMN RNA expression during development and in different tissues. In contrast, protein expression profiles were dramatically different based upon different tissues and developmental stages, consistent with human SMN expression. Porcine SMN localization is consistent with human SMN, localizing diffusely within the cytoplasm and in punctate nuclear structures characteristic of nuclear gems. Importantly, transient transfection of porcine SMN1 in 3813 SMA type 1 fibroblasts demonstrate that porcine SMN1 can rescue the deficiency of SMN protein and gem formation in these cells. These studies provide the first characterization of the porcine SMN1 gene and SMN protein and suggest that a transgenic swine SMA model is feasible.

Motor neuron degeneration in a 20-week male fetus: spinal muscular atrophy type 0

BACKGROUND

Neuropathological changes in degenerating motor neurons are well documented in the term neonate with spinal muscular atrophy, but not at midgestation.

METHODS

Postmortem neuropathological examination was performed in a 20-week male fetus with a hypoplastic left cardiac anomaly.

RESULTS

Selective degeneration of spinal and hypoglossal motor neurons was an incidental finding. Degenerating motor neurons were not immunoreactive with neuronal nuclear antigen (NeuN) or neuron-specific enolase (NSE), as were the normal motor neurons. Synaptophysin reactivity was reduced around the soma of degenerating normal motor neurons. Ubiquitin and tau were expressed in degenerating motor neurons. Gliosis, inflammation and microglial activation were lacking in the ventral horns of the spinal cord. Laryngeal striated muscle was unaltered for age. No cerebral malformations or hypoxic-ischaemic changes were found.

CONCLUSION

This case represents an early motor neuronal degeneration and corresponds to the recently described "type 0" spinal muscular atrophy. Lack of contractures is attributed to the early fetal age, since most muscular growth occurs in the second half of gestation.

Noninvasive Ventilation in Children with Spinal Muscular Atrophy Types 1 and 2

OBJECTIVE

Our aim was to assess the efficacy of noninvasive ventilation (NIV) for the treatment of thoracoabdominal asynchrony during sleep in children with spinal muscular atrophy (SMA) types 1 and 2.

DESIGN

Nine subjects underwent assessment for sleep apnea/hypopnea index (AHI), mean oxyhemoglobin saturation (SpO2), oxygen desaturation index, transcutaneous carbon dioxide tension (tcpCO2), and mean phase angle during sleep as a measure of thoracoabdominal coordination. A second sleep study was performed with use of NIV.

RESULTS

The nine patients (7 mos of age, range 2-33) had a baseline AHI of 2.1 events per hour (range 0.5-55.8), oxygen desaturation index of 3.7 events per hour (range 1.6-46.1), mean tcpCO2 of 46 mm Hg (range 37-60), and phase angle of 127 degrees (range 72.7-151.7). Comparing baseline and NIV sleep studies, we found significant improvement in oxygen desaturation index (P < 0.010), mean tcpCO2 (P < 0.001), and phase angle (P < 0.001). For five patients, phase-angle improvement became significant when using high-span bilevel positive airway pressure (PAP).

CONCLUSIONS

NIV improved sleep breathing parameters and thoracoabdominal coordination during sleep in SMA types 1 and 2. Phase-angle improvement correlated with bilevel PAP pressures. Phase angle may be useful for the evaluation and monitoring of therapeutic interventions such as NIV.

Spinal muscular atrophy and therapeutic prospects

The molecular genetic basis of spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disorder, is the loss of function of the survival motor neuron gene (SMN1). The SMN2 gene, a nearly identical copy of SMN1, has been detected as a promising target for SMA therapy. Both genes are ubiquitously expressed and encode identical proteins, but markedly differ in their splicing patterns: While SMN1 produces full-length (FL)-SMN transcripts only, the majority of SMN2 transcripts lacks exon 7. Transcriptional SMN2 activation or modulation of its splicing pattern to increase FL-SMN levels is believed to be clinically beneficial and therefore a crucial challenge in SMA research. Drugs such as valproic acid, phenylbutyrate, sodium butyrate, M344 and SAHA that mainly act as histone deacetylase inhibitors can mediate both: they stimulate the SMN2 gene transcription and/or restore the splicing pattern, thereby elevating the levels of FL-SMN2 protein. Preliminary phase II clinical trials and individual experimental curative approaches SMA patients show promising results. However, phase III double-blind placebo controlled clinical trials have to finally prove the efficacy of these drugs.

Sleep-Disordered Breathing in Spinal Muscular Atrophy Types 1 and 2

OBJECTIVE

Our aim was to assess the respiratory pattern during sleep in patients affected by spinal muscular atrophy types 1 and 2 and to compare their apnea-hypopnea indices with those of controls.

DESIGN

All consecutively referred patients underwent polysomnography. Sleep stages were defined as either wake, quiet sleep (QS), or active sleep (AS). As measures of thoracoabdominal coordination, we measured: phase angle during QS and AS (Ph Angle QS and AS), phase relation during inspiration and expiration during QS and AS: (Ph RIB QS, Ph RIB AS, Ph REB QS; Ph REB AS) and the apnea-hypopnea index.

RESULTS

The 14 consecutively referred infants and small children (age, 11.7 +/- 11.4 mos) showed a higher apnea-hypopnea index (P < 0.001), Ph Angle QS (P < 0.001), Ph Angle AS (P < 0.001), Ph RIB QS (P < 0.001), Ph RIB AS (P < 0.001), Ph REB QS (P < 0.001), and Ph REB AS (P < 0.001) compared with 28 healthy controls (age, 10.1 +/- 8.9 mos).

CONCLUSIONS

Patients affected by types 1 and 2 spinal muscular atrophy had significantly higher apnea-hypopnea indices than controls. Thoracoabdominal asynchrony was present during the inspiratory and expiratory phases in both quiet and active sleep. Measures of thoracoabdominal coordination may be useful for the evaluation and monitoring of therapeutic interventions for these patients.

Functional human NAIP promoter transcription regulatory elements for the NAIP and PsiNAIP genes

Neuronal apoptosis inhibitory protein (NAIP) has been shown to inhibit apoptosis in vitro and in vivo with an expression which is regulated in a variety of cells and tissues and may be modulated by a variety of external stimuli. To understand the molecular basis of the transcriptional regulation of the NAIP gene, we have analyzed the 5'-flanking region and transcription of the human NAIP gene. The functional promoter and silencer elements were identified by luciferase reporter constructs in transient transfection experiments using four different human cells. Although the location of the functional elements were shared among the different cells used, the activities for the NAIP promoter varied. Further, cell type-specific protein binding activities were observed by an electrophoretic mobility shift assay (EMSA). EMSA analysis with specific antibodies and DNA sequence analysis identified the POU domain transcription factor Brn-2 as a candidate transcriptional regulator of the NAIP gene. The DNA sequence of the promoter region of the PsiNAIP gene, a copy gene for NAIP, was nearly identical to that of the NAIP gene, indicating a common regulatory mechanism for transcription of the NAIP and PsiNAIP genes. Indeed, the transcript of the PsiNAIP gene was identified. These results provided the first evidence for the functional promoter and candidate transcriptional factor for the NAIP gene and transcription of the PsiNAIP gene.

Identification of a deletion hotspot on distal mouse chromosome 4 by YAC fingerprinting

Using repetitive elements as probes, genomic DNA fingerprints of four randomly selected yeast artificial chromosome (YAC) clones (two human and two mouse-derived YAC) were analyzed to determine the mutation level following X-ray exposure. Because the repetitive probes were derived from the mammalian host DNA, most of the fingerprint bands originated from the artificial chromosomes and not from the yeast genome. For none of the YAC clones was the mutation frequency elevated following X-ray exposure. However, for one mouse-derived YAC, the mutation level was unusually high (7%; 42 mutants of 607 clones analyzed), whereas for the other three YACs, the mutation level was nearly 0%. Surprisingly, 40 of the 42 mutations were deletions occurring only at three of the 20 mouse specific fingerprint bands. One of the frequently deleted fragments was cloned, sequenced and mapped to distal mouse chromosome 4, which has been repeatedly reported to be the most unstable region of the whole mouse genome, associated with various tumors. Deletion mapping of six YAC mutants revealed this fragment to be completely deleted in four YACs. In the other two mutants, recombination occurred within the fragment, in each case initiated at the same LINE-1 element. In conclusion, the presented YAC fingerprint is a useful tool for detecting and characterizing unstable regions in mammalian genomes.

Gene deletion patterns in spinal muscular atrophy patients with different clinical phenotypes

Spinal muscular atrophy (SMA) is an autosomal recessive disorder characterized by degeneration of lower motor neurons. We have assayed deletions in two candidate genes, the survival motor neuron (SMN) and neuronal apoptosis inhibitory protein (NAIP) genes, in 108 samples, of which 46 were from SMA patients, and 62 were from unaffected subjects. The SMA patients included 3 from Bahrain, 9 from South Africa, 2 from India, 5 from Oman, 1 from Saudi Arabia, and 26 from Kuwait. SMN gene exons 7 and 8 were deleted in all type I SMA patients. NAIP gene exons 5 and 6 were deleted in 22 of 23 type I SMA patients. SMN gene exon 7 was deleted in all type II SMA patients while exon 8 was deleted in 19 of 21 type II patients. In 1 type II SMA patient, both centromeric and telomeric copies of SMN exon 8 were deleted. NAIP gene exons 5 and 6 were deleted in only 1 type II SMA patient. In 1 of the 2 type III SMA patients, SMN gene exons 7 and 8 were deleted with no deletion in the NAIP gene, while in the second patient, deletions were detected in both SMN and NAIP genes. None of the 62 unaffected subjects had deletions in either the SMN or NAIP gene. The incidence of biallelic polymorphism in SMN gene exon 7 (BsmAI) was found to be similar (97%) to that (98%) reported in a Spanish population but was significantly different from that reported from Taiwan (0%). The incidence of a second polymorphism in SMN gene exon 8 (presence of the sequence ATGGCCT) was markedly different in our population (97%) and those reported from Spain (50%) and Taiwan (0%).

Cloning and characterization of the multiple murine homologues of NAIP (neuronal apoptosis inhibitory protein)

The spinal muscular atrophies (SMAs), characterized by degeneration of spinal cord motor neurons, are among the most common autosomal recessive disorders. We have previously reported the characterization of an SMA-associated gene designated NAIP (neuronal apoptosis inhibitory protein). This gene, which encodes a protein homologous to the baculoviral inhibitor of apoptosis proteins, is deleted in a significant proportion of individuals with type I SMA, is expressed in motor neurons, and inhibits apoptosis both in vitro and in vivo. Here we present the cloning and characterization of multiple copies of the mouse homologue of NAIP, Naip1-Naip6. Our analysis of the genomic organization of Naip indicated the existence of a minimum of six distinct Naip loci in the 129/SvJ mouse strain. However, Southern blot analysis revealed that only three of these loci contained the 5'UTR element essential for translation in the CNS. The coding region of one of these three potentially functional loci (Naip1) demonstrates 77% homology to NAIP at the nucleotide level and 68% identity at the amino acid level.

Sequence of a 131-kb region of 5q13.1 containing the spinal muscular atrophy candidate genes SMN and NAIP

The spinal muscular atrophies (SMA), which are characterized by motor neuron loss and progressive paralysis, are among the most common autosomal recessive disorders. The SMA region of chromosome 5q13.1 is distinguished by variable amplification of genomic sequence incorporating a number of genes and pseudogenes. Recently, two SMA candidate genes mapping to this area were identified: survival motor neuron (SMN) and neuronal apoptosis inhibitory protein (NAIP). The telomeric copy of SMN (SMNtel) is deleted in over 95% of cases of SMA, with NAIP deletions primarily seen in type I SMA. We present here 131 kb of genomic sequence from 5q13.1 incorporating both NAIP and SMNtel in addition to revisions of the original NAIP cDNA sequence. The Alu-rich NAIP-SMNtel interval contains the microsatellite polymorphisms that are deleted in as many as 80% of type I SMA chromosomes, focusing attention on this region in the pathogenesis of type I SMA.

The fight of viruses against apoptosis

The induction of apoptosis of virus-infected cells is an important host defense mechanism against invading pathogens. Some viruses express anti-apoptotic proteins that efficiently block apoptosis induced by death receptors or in response to stress signaled through mitochondria. Viral interference with host cell apoptosis leads to enhanced viral replication and may promote cancer.

Genomic variation and gene conversion in spinal muscular atrophy: implications for disease process and clinical phenotype

Autosomal recessive spinal muscular atrophy (SMA) is classified, on the basis of age at onset and severity, into three types: type I, severe; type II, intermediate; and type III, mild. The critical region in 5q13 contains an inverted repeat harboring several genes, including the survival motor neuron (SMN) gene, the neuronal apoptosis inhibitory protein (NAIP) gene, and the p44 gene, which encodes a transcription-factor subunit. Deletion of NAIP and p44 is observed more often in severe SMA, but there is no evidence that these genes play a role in the pathology of the disease. In > 90% of all SMA patients, exons 7 and 8 of the telomeric SMN gene (SMNtel) are not detectable, and this is also observed in some normal siblings and parents. Point mutations and gene conversions in SMNtel suggest that it plays a major role in the disease. To define a correlation between genotype and phenotype, we mapped deletions, using pulsed-field gel electrophoresis. Surprisingly, our data show that mutations in SMA types II and III, previously classed as deletions, are in fact due to gene-conversion events in which SMNtel is replaced by its centromeric counterpart, SMNcen. This results in a greater number of SMNcen copies in type II and type III patients compared with type I patients and enables a genotype/phenotype correlation to be made. We also demonstrate individual DNA-content variations of several hundred kilobases, even in a relatively isolated population from Finland. This explains why no consensus map of this region has been produced. This DNA variation may be due to a midisatellite repeat array, which would promote the observed high deletion and gene-conversion rate.

Cloning, characterization, and copy number of the murine survival motor neuron gene: homolog of the spinal muscular atrophy-determining gene

Because of a 500-kb inverted duplication, there are two copies of the survival motor neuron (SMN) gene in humans, cenSMN and telSMN. Both genes produce identical ubiquitously expressed transcripts; however, only mutations in telSMN are responsible for spinal muscular atrophy (SMA), the second most common autosomal recessive childhood disease. We have cloned the murine homolog Smn and mapped the gene to Chromosome 13 within the conserved syntenic region of human chromosome 5q13. We show that the Smn transcript (1.4 kb) is expressed as early as embryonic day 7. In contrast to humans, we found no evidence of alternative splicing. The predicted amino acid sequence between mouse and human SMN is 82% identical, and a putative nuclear localization signal is conserved. FISH data indicate that the duplication of the SMA region observed in humans is not present in the mouse. We also found no evidence of multiple Smn genes using Southern blot hybridization and single-strand conformation analysis. Using these methods, we detected at least four copies of Naip exon 5 clustering distal to Smn. Finally, three biallelic markers were identified within the Smn coding region; two are silent polymorphisms, whereas the third changes a cysteine residue to a tyrosine residue in exon 7. Overall, our results indicate that Smn is single copy within the mouse genome, which should facilitate gene disruption experiments to create an animal model of SMA.

Molecular analysis of the SMN and NAIP genes in Spanish spinal muscular atrophy (SMA) families and correlation between number of copies of cBCD541 and SMA phenotype

Spinal muscular atrophy is an autosomal recessive disorder which affects about 1 in 10,000 individuals. The three clinical forms of SMA were mapped to the 5q13 region. Three candidate genes have been isolated and shown to be deleted in SMA patients: the Survival Motor Neuron gene (SMN), the Neuronal Apoptosis Inhibitory Protein gene (NAIP) and the XS2G3 cDNA. In this report we present the molecular analysis of the SMN exons 7 and 8 and NAIP exon 5 in 65 Spanish SMA families. NAIP was mostly deleted in type I patients (67.9%) and SMN was deleted in 92.3% of patients with severe and milder forms. Most patients who lacked the NAIP gene also lacked the SMN gene, but we identified one type II patient deleted for NAIP exon 5 but not for SMN exons 7 and 8. Two other patients carried deletions of NAIP exon 5 and SMN exon 7 but retained the SMN exon 8. Three polymorphic variants from the SMN gene, showing changes on the sequence of the centromeric (cBCD541) and telomeric copies of the SMN gene, were found. In addition, we show several genetic rearrangements of the telomeric SMN gene, which include duplication of this gene in one normal chromosome, and putative gene conversion events in affected and normal chromosomes. Altogether these results corroborate the high genetic variability of the SMA region. Finally, we have determined the ratio between the number of centromeric and telomeric copies of the SMN gene in parents of SMA patients, showing that the majority of parents of types II and III patients carried three or more copies of the cBCD541 gene; we suggest a relationship between the number of copies of cBCD541 and the disease phenotype.

The gene for neuronal apoptosis inhibitory protein is partially deleted in individuals with spinal muscular atrophy

The spinal muscular atrophies (SMAs), characterized by spinal cord motor neuron depletion, are among the most common autosomal recessive disorders. One model of SMA pathogenesis invokes an inappropriate persistence of normally occurring motor neuron apoptosis. Consistent with this hypothesis, the novel gene for neuronal apoptosis inhibitory protein (NAIP) has been mapped to the SMA region of chromosome 5q13.1 and is homologous with baculoviral apoptosis inhibitor proteins. The two first coding exons of this gene are deleted in approximately 67% of type I SMA chromosomes compared with 2% of non-SMA chromosomes. Furthermore, RT-PCR analysis reveals internally deleted and mutated forms of the NAIP transcript in type I SMA individuals and not in unaffected individuals. These findings suggest that mutations in the NAIP locus may lead to a failure of a normally occurring inhibition of motor neuron apoptosis resulting in or contributing to the SMA phenotype.