Spinal muscular atrophy due to double gene conversion event

Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by degeneration of the anterior horn cells of the spinal cord. The survival motor neuron (SMN) gene has been identified as an SMA-determining gene. SMN exists as two copies in 5q13, and deletions in exons 7 and 8 of the telomeric copy (SMN(T)) occur in 95% of patients, regardless of disease severity. In a minority of patients, exon 7 but not exon 8 of SMN(T) appears deleted. We now report a patient with typical features of SMA type II who carried homozygous deletions of SMN(T) exon 7 and centromeric SMN (SMN(C)) exon 8 but retained SMN(T) exon 8 and SMN(C) exon 7. Sequence analysis demonstrated that SMN(C) exon 7 was adjacent to SMN(T) exon 8 on both SMN copies, indicating a double conversion. We confirm that sequence conversion is a common event in SMA and is associated with the milder form of the disease. The severity, however, can be modified in either positive or negative direction by other factors.     

Spinal muscular atrophy due to an isolated deletion of exon 8 of the telomeric survival motor neuron gene

Patients with autosomal recessive spinal muscular atrophy (SMA) usually carry a homozygous deletion of exons 7 and 8 of the telomeric survival motor neuron (SMN^T) gene, although an isolated deletion of SMN ^T exon 8 has never been found. We now report on 2 patients with the typical fetures of SMA types II and III, who carried a homozygous deletion of SMN^T exon 8 but retained SMN^T 7. Importantly, to exclude a sequence conversion event of telomeric exon 8, we amplified a fragment that spanned exons 7 and 8 of the SMN gene. The resulting 1,010-base pair (bp) fragments were subjected to nested polymerase chain reaction (PCR) on exon 7. The subsequent restriction analysis failed to show any products of telomeric exon 7, as the site for primer 541 C1120 was lost in both alleles. These findings indicate a homozygous deletion of SMN^T exon 8. Direct sequencing of the cloned 1,010-bp fragment further confirmed that these 2 SMA patients did not possess telomeric exon 8. The present findings provide evidence that an isolated deletion of SMN^T exon 8 is associated with the milder subtypes of SMA. Our data also demonstrate that the additional deletion of the NAIP gene exacerbates the severity of the disease.     

Spinal muscular atrophy: SMN protein deficiency

Spinal muscular atrophy is a heterogeneous group of disorders characterised by the loss of alfa motor neurons in spinal cord. Autosomal recessive infantile and juvenile proximal spinal muscular atrophy is the most common form of the disease. The identification of the disease gene-Survival of Motor Neuron (SMN) was a major advance in understanding of the molecular basis of SMA. 98% of SMA patients show the homozygous absence of at least exon 7 telomeric copy of SMN, the rest carry small intragenic mutations, usually in exon 6. Two different mechanisms seem to be responsible for the absence of the telomeric copy: deletion in severe form and gene conversion associated with mild phenotype. Recently, biochemical studies resulted in identification of the 38kDa survival motor neuron (SMN) protein, probably involved in the biogenesis of spliceosomal snRNP. The SMN protein level was shown to be 100-fold reduced in spinal cord of SMA 1 patients.     

Correlation between deletion patterns of SMN and NAIP genes and the clinical features of spinal muscular atrophy in Indian patients

BACKGROUND: Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder involving degeneration of anterior horn cells of spinal cord resulting in progressive muscle weakness and atrophy. AIMS: The molecular analysis of two marker genes for spinal muscular atrophy (SMA) i.e, the survival motor neuron gene (SMN) and the neuronal apoptosis inhibitory protein gene (NAIP) was conducted in 39 Indian patients with clinical symptoms of SMA. Out of these, 28 showed homozygous deletions and the phenotypic features of these SMA patients were compared with the corresponding genotypes. SETTINGS: A tertiary care teaching Hospital. DESIGN: This is a prospective hospital based study. MATERIALS AND METHODS: Polymerase chain reaction (PCR) combined with restriction fragment length polymorphism (RFLP) was used to detect the deletion of exon 7 and exon 8 of SMN1 gene, as well as multiplex PCR for exon 5 and 13 of NAIP gene. RESULTS: Exons 7 and 8 of SMN and NAIP (exon 5) were homozygously deleted in 73% of SMA I and 27% of SMA II patients. SMN exon 7 and 8 deletions without NAIP deletions were seen in 27% of type I SMA and 46% of SMA type II patients. Two patients of type III SMA showed single deletion of SMN exon 7 along with 27% of SMA type II patients. CONCLUSION: With the advent of molecular biology techniques, SMN gene deletion studies have become the first line of investigation for confirmation of a clinical diagnosis of SMA. The findings of homozygous deletions of exons 7 and/or 8 of SMN1 gene confirms the diagnosis of SMA, even in patients with atypical clinical features. Deletions of NAIP gene were mainly seen in severely affected patients, hence is useful for predicting the prognosis.     

脊髓性肌萎缩症的快速基因诊断研究

目的研究我国近端型脊髓性肌萎缩症（ＳＭＡ）患者的运动神经元生存基因（ＳＭＮ）外显子的缺失情况,探讨其快速基因诊断的可行性和临床应用价值。方法应用ＰＣＲ－酶切法检测２６例确诊的ＳＭＡ患者及２０名正常对照ＳＭＮ基因的第７、８号外显子的缺失情况。结果在２６例及２５例患者中,分别发现缺失了端粒ＳＭＮ基因（ＳＭＮ１）的第７和８号外显子,缺失率达１００％（２６／２６）和９６％（２５／２６）,而正常对照及患者的家系成员均未发现外显子缺失。结论应用ＰＣＲ－酶切法检测ＳＭＮ１基因缺失从而进行ＳＭＡ患者的基因诊断,具有准确、简便和快速的优点。     

Gene conversion events in adult-onset spinal muscular atrophy

OBJECTIVE: To investigate the possible occurrence of a conversion event in three patients with adult-onset spinal muscular atrophy (SMA) type IV, which represents the mildest form within the spectrum of the SMA phenotype. MATERIAL AND METHODS: We observed three patients with adult onset SMA and apparent isolated deletion of telomeric survival motor neuron (SMN1) exon 7. To distinguish between a deletion and a sequence conversion event of exon 7, these patients were analyzed in greater detail by a simple PCR-based assay. RESULTS: Analysis by DdeI digestion showed products for both telomeric and centromeric copies of exon 8. These findings indicated a gene conversion event as the site for primer R111 was retained at least in one of two alleles. CONCLUSIONS: These results provide first evidence that a conversion event may be also associated with adult-onset SMA, and further support the notion that a gene conversion event is usually associated with a milder SMA phenotype and a later onset of disease.     

Clinical phenotypes of spinal muscular atrophy patients with hybrid SMN gene

BackgroundSpinal muscular atrophy (SMA) is a neuromuscular disease caused by homozygous deletion of SMN1 exons 7 and 8. However, exon 8 is retained in some cases, where SMN2 exon 7 recombines with SMN1 exon 8, forming a hybrid SMN gene. It remains unknown how the hybrid SMN gene contribute to the SMA phenotype.MethodWe analyzed 515 patients with clinical suspicion for SMA. SMN1 exons 7 and 8 deletion was detected by PCR followed by enzyme digestion. Hybrid SMN genes were further analyzed by nucleotide sequencing. SMN2 copy number was determined by real-time PCR.ResultsSMN1 exon 7 was deleted in 228 out of 515 patients, and SMN1 exon 8 was also deleted in 204 out of the 228 patients. The remaining 24 patients were judged to carry a hybrid SMN gene. In the patients with SMN1 exon 7 deletion, the frequency of the severe phenotype was significantly lower in the patients with hybrid SMN gene than in the patients without hybrid SMN gene. However, as for the distribution of SMN2 exon 7 copy number among the clinical phenotypes, there was no significant difference between both groups of SMA patients with or without hybrid SMN gene.ConclusionHybrid SMN genes are not rare in Japanese SMA patients, and it appears to be associated with a less severe phenotype. The phenotype of patients with hybrid SMN gene was determined by the copy number of SMN2 exon 7, as similarly for the patients without hybrid SMN gene.     

单链构象多态技术检测脊髓性肌萎缩症基因缺失

目的探讨中国人脊髓性肌萎缩症（ＳＭＡ）基因诊断的可行性。方法应用聚合酶链反应单链构象多态（ＰＣＲＳＳＣＰ）技术研究来自１６个家系的２０例ＳＭＡ患者及２０名正常对照的运动神经元生存（ＳＭＮ）基因的第７、８号外显子的缺失情况。结果２０例患者均缺失端粒ＳＭＮ（ＳＭＮＴ）基因的第７号外显子，１９例患者缺失第８号外显子，而正常对照均无外显子缺失。结论应用直接检测ＳＭＮＴ基因缺失的方法可准确快速地诊断中国人ＳＭＡ患者     

Extracellular pH change modulates the exon 7 splicing in SMN2 mRNA

Spinal muscular atrophy (SMA) is caused by homozygous deletions/mutations of SMN1 gene. All SMA patients carry a nearly identical SMN2 gene. A nucleotide change in SMN2 results in exon 7 exclusion in the majority of SMN2 mRNA, thus producing low level of SMN protein. Extracellular pH change has been shown to modulate alternative splicing of several pre-mRNAs. In this study, we showed that extracellular pH change can also modulate SMN2 exon 7 splicing in SMA cells. Low extracellular pH enhances SMN2 exon 7 skipping, whereas high extracellular pH promotes its inclusion. Low extracellular pH also reduces SMN protein expression but increases hnRNP A1 expression. In addition, we tested whether intracellular pH-modulating genes could be the modifier of SMA in a SMA discordant family and found that the mRNA levels of ATP6V1B2 gene are significantly higher in two affected siblings than the unaffected one. In conclusion, our results suggest that extracellular pH change modulates SMN2 exon 7 splicing through regulation of hnRNP A1 expression in SMA cells.     

Calpainopathy

Five affected siblings were referred with a probable diagnosis of proximal adult-type spinal muscular atrophy (SMA) based on lower motor neuron signs (muscle weakness and atrophy, hypotony, hypoactive or absent reflexes, and fasciculations), normal or borderline serum creatine kinase levels, and a neurogenic pattern on electromyography, compatible with motor neuron disease, in one patient. No exon 7-8 deletion in the survival motor neuron (SMN) gene was found. Linkage analysis excluded the SMN and all known autosomal recessive limb girdle muscular dystrophy loci, with the exception of LGMD-2A. A homozygous R769Q mutation in the calpain-3 gene and absence of muscle calpain-3 protein confirmed a calpainopathy. This family suggests that the clinical spectrum of calpainopathy might be broader and that this diagnosis might be considered in patients with an atypical motor neuron disease.     

Reduced TSC2 RNA and protein in sporadic astrocytomas and ependymomas

The spinal muscular atrophy—determining gene, survival motor neuron (SMN), is present in two copies, telSMN and cenSMN, which can be distinguished by base-pair changes in exons 7 and 8. The telSMN gene is often absent in spinal muscular atrophy patients, which could be due to deletion or sequence conversion (telSMN conversion to cenSMN giving rise to two cenSMN genes). To test for conversion events in spinal muscular atrophy, we amplified a 1-kb fragment that spanned exons 7 and 8 of SMN from 5 patients who retained telSMN exon 8 but lacked exon 7. In all patients, sequence analysis demonstrated that cenSMN exon 7 was adjacent to telSMN exon 8, indicating conversion. All 5 patients with this mutation had type II or III spinal muscular atrophy, strongly supporting an association with chronic spinal muscular atrophy. We also identified 3 families in which 2 siblings had no detectable telSMN but presented with markedly different phenotypes. We suggest that sequence conversion is a common event in spinal muscular atrophy and is associated with the milder form of the disease. The severity, however, can be modified in either a positive or negative direction by other factors that influence splicing or expression of the sequence converted SMN gene.     

Application of a rapid non-invasive technique in the molecular diagnosis of spinal muscular atrophy (SMA)

BACKGROUND AND PURPOSE: Proximal spinal muscular atrophy (SMA) is an autosomal recessive disorder caused by mutations of the SMN1 gene. The most frequent mutation is biallelic deletion of exon 7 of the SMN1 gene. A small percentage of SMA patients present compound heterozygosity with a point mutation on one allele and deletion on the other. In the remaining cases the disease is unlikely to be related to SMN1 defects. The aim of our study was to estimate the frequency of the common biallelic exon 7 SMN1 deletion in our Polish SMA cohort and implement a test for assessing a molecular defect at the SMN1 locus versus defects in the other genes. MATERIAL AND METHODS: The molecular analysis was performed in a group of 269 patients fulfilling diagnostic criteria of the International SMA Consortium. The common SMN1 exon 7 deletion was tested by a standard PCR analysis. Patients lacking the common mutation were subsequently analyzed for a number of SMN1 alleles with a quantitative test based on real-time PCR. RESULTS: The frequency of homozygous loss of exon 7 in the SMN1 gene was 96.6% (260/269) in our Polish SMA cohort. In 5 of 9 non-deleted patients the real-time PCR analysis showed a decreased number of SMN1 copies. We anticipate that the non-deleted allele carries a second mutation in SMN1 which may contribute to the pathogenesis of SMA. We have also identified 4 patients (1.5%) with SMA carrying two SMN1 alleles without the exon 7 deletion. CONCLUSIONS: The molecular analysis of the biallelic exon 7 of the SMN1 deletion is a standard and reliable test in cases of SMA. Introduction of a quantitative test based on "real-time PCR" further enhances the diagnostic potential by increasing the detection rate of cases likely to be caused by point mutation of the SMN1 gene.     

High incidence of SMN1 gene deletion in Moroccan adult-onset spinal muscular atrophy patients

Abstract. Spinal muscular atrophy (SMA) is an autosomal recessive motor neuropathy characterized by selective degeneration of anterior horn cells of the spinal cord. Childhood SMA is divided into three types (I–III) on the basis of age of onset and severity. These disorders have been linked to the 5q13 region, where mutations in the Survival Motor Neuron 1 (SMN1) gene have been found in affected individuals. In the case of adult-onset SMA (type IV), on the other hand, reports of homozygous absence of SMN1 gene have been rare. We conducted deletion analysis of SMN and a neighboring gene, NAIP (neuronal apoptosis inhibiting protein). Among 54SMA patients (types I–IV), all of Moroccan origin, Exon 7 of the SMN1 gene was homozygously absent in 100% of type I, 90% of type II, 74% of type III and 80% of type IV SMA patients. Deletion of SMN1 exon 8 was detected in 100% of type I, 53% of type II, 53% of type III and 80% of type IV patients. NAIP exon 5 was homozygously deleted in 67% of type I, 32% of type II, 5% of type III and 20% of type IV SMA patients. Thirty control individuals who were studied had normal SMN1 and NAIP genes. Our results show a high incidence of SMN1 gene deletion in adult-onset SMA patients indicating that SMN1 is the autosomal recessive adult SMA-causing gene. While NAIP is commonly deleted in SMA, this is unlikely to affect disease severity; it was deleted in two adult SMA patients with mild phenotypes.     

A new splice site mutation in the SMN1 gene causes discrepant results in SMN1 deletion screening approaches

In most patients with infantile spinal muscular atrophy (SMA) both exons 7 and 8 of the SMN1 gene are deleted, but the deletion may also be restricted to exon 7. We report on an SMA type I patient who was initially diagnosed to be homozygous for an exon 7 deletion only. However, multiplex ligation-dependent probe amplification (MLPA) analyses revealed a heterozygous deletion of exons 7 and 8 of the SMN1 gene. By sequencing a new subtle splice site mutation (IVS6-2A>G) was identified. This variant affects the target sequence of oligonucleotides of all applied tests in a way that it has contrary effects on the efficiencies of the different assays. The results have major impacts on genetic counselling and carrier detection of the patient's paternal relatives.     

Clinical and molecular genetic features of congenital spinal muscular atrophy

A neonate presented with the fetal hypokinesia sequence and signs of spinal muscular atorphy (SMA). Severe pathological changes including ballooned neurons and neuronophagia were found not only in themotor nerve nuclei but also in the thalamic, cerebellar, and brainstem nuclei as well as in the dorsal root ganglia. Direct DNA analysis showed the presence of chimeric SMN gene, with a rearrangment occurring between exon 7 of the centromeric SMN gene and exon 8 of the telomeric SMN gene. Circumstantial evidence suggests that only a single copy of this gene is present, with transciriptional characeristics of a centromeric SMN gene. In addition, a homozygous deletion in the NAIP genes was demonstrated. This observation demonstrates that at least some cases with fetal hypokinesia and SMA may represent the severe end of a spectrum of disorders caused by deletions in the SMA locus on chromosome 5q13. In addition, these findigns are compatible with a modifying role for the centromeric SMN genes and the NAIP genes in the severitiy of the SMA phenotype.     

Identification of bidirectional gene conversion between SMN1 and SMN2 by simultaneous analysis of SMN dosage and hybrid genes in a Chinese population

Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by programmed motoneuron death. The survival motor neuron 1 (SMN1) gene is an SMA-determining gene and SMN2 represents an SMA-modifying gene. Here, we applied capillary electrophoresis to quantify the SMN gene dosage in 163 normal individuals, 94 SMA patients and 138 of their parents. We further quantified exons 7 and 8 in SMN1 and SMN2. We found that the SMA patients carried the highest SMN2 copies, which was inversely correlated with disease severity among its three subtypes. Increased SMN1 was significantly associated with decreased SMN2 in the normal group. We also observed that parents of type I SMA patients had significantly fewer SMN2 copies than those of types II and III patients. The hybrid SMN genes were detected in two normal individuals and one patient and her mother. These results imply that increased SMN2 copies in SMA patient group might be derived from SMN1-to-SMN2 conversion, whereas the trend that normal individuals with higher SMN1 copies simultaneously carry fewer SMN2 copies suggested a reverse conversion, SMN2-to-SMN1. Together with the identification of hybrid SMN genes, our data provided additional evidence to support that SMN1 and SMN2 gene loci are interchangeable between population groups.