NIPA1 Research Articles

LncRNA NIPA1-SO confers atherosclerotic protection by suppressing the transmembrane protein NIPA1

Long non-coding RNAs (lncRNAs) are emerging as important players in gene regulation and cardiovascular diseases. However, the roles of lncRNAs in atherosclerosis are poorly understood. In the present study, we found that the levels of NIPA1-SO were decreased while those of NIPA1 were increased in human atherosclerotic plaques. Furthermore, NIPA1-SO negatively regulated NIPA1 expression in human umbilical vein endothelial cells (HUVECs). Mechanistically, NIPA1-SO interacted with the transcription factor FUBP1 and the NIPA1 gene. The effect of NIPA1-SO on NIPA1 protein levels was reversed by the knockdown of FUBP1. NIPA1-SO overexpression increased, whilst NIPA1-SO knockdown decreased BMPR2 levels; these effects were enhanced by the knockdown of NIPA1. The overexpression of NIPA1-SO reduced while NIPA1-SO knockdown increased monocyte adhesion to HUVECs; these effects were diminished by the knockdown of BMPR2. The lentivirus-mediated-overexpression of NIPA1-SO or gene-targeted knockout of NIPA1 in low-density lipoprotein receptor-deficient mice reduced monocyte-endothelium adhesion and atherosclerotic lesion formation. Collectively, these findings revealed a novel anti-atherosclerotic role for the lncRNA NIPA1-SO and highlighted its inhibitory effects on vascular inflammation and intracellular cholesterol accumulation by binding to FUBP1 and consequently repressing NIPA1 expression.

Hereditary spastic paraplegia due to NIPA1 gene mutation: Case report

Introduction: Hereditary spastic paraplegia (HSP) is the term for a group of neurological disorders characterized by progressive spasticity and muscle weakness in the lower limbs. Its etiology is genetic and has been associated with mutations in more than 60 genes. HSP is rare and may be useful in the differential diagnosis of cerebral palsy. Case presentation: 16-year-old male with a diagnosis of HSP due to mutation of the NIPA1 gene:c.316G>A (p. Gly106arg), which corresponds to HSP type 6 (SPG6). The patient presented with clinical signs of progressive upper motor neuron syndrome in the lower limbs, such as spasticity, hyperreflexia and paraparesis, associated with focal onset seizures diagnosed at age 11 and successfully treated with valproic acid. Spasticity treatment was complex and included oral baclofen, intraoperative botulinum toxin, physical therapy, and multilevel orthopedic surgery for the management of musculoskeletal deformities. Conclusion: This is a rare case of complex HSP, associated with epilepsy, due to the mutation of the NIPA1 gene (SPG6), the most common pathogenic variant within this type of mutation. The present case demonstrates the importance of making an early diagnosis of GSP6 to perform timely interventions in these patients, prevent complications, and avoid a higher level of disability.

Clinical and Genetic Features of Chinese Patients With NIPA1-Related Hereditary Spastic Paraplegia Type 6.

Background: Mutations in the NIPA1 gene cause hereditary spastic paraplegia (HSP) type 6 (SPG6), which is a rare type of HSP with a frequency of less than 1% in Europe. To date, less than 30 SPG6 families and limited NIPA1 mutations have been reported in different ethnic regions. The clinical features are variable. Methods: We screened for NIPA1 mutations by whole exome sequencing or next generation sequencing in 35 unrelated Chinese families with HSP. The clinical manifestations were evaluated. Results: Two variants of NIPA1 were identified in three index patients (3/35, 8.6%), two of whom carried a previously reported common variant c.316G > A (p.G106R), and the third patient harbored a novel likely pathogenic variant c.126C > G (p.N42K). Both variants were de novo in the three index patients. The phenotype was pure HSP in two patients and complicated HSP with epilepsy in the third one. Conclusion: NIPA1-related HSP is more common in China than it in Europe. Both pure and complicated form of HSP can be found. The variant c.316G > A is a hotspot mutation, and the novel variant c.126C > G expands the mutational spectrum. The phenomenon of de novo mutations in NIPA1 emphasizes the need to consider autosomal dominant HSP-related genes in sporadic patients.

Is NIPA1-associated hereditary spastic paraplegia always ‘pure’? Further evidence of motor neurone disease and epilepsy as rare manifestations

Pathogenic variants in the nonimprinted in Prader-Willi/Angelman syndrome (NIPA1) gene typically present with pure hereditary spastic paraplegia (HSP) but complex cases are described. We present a patient with childhood idiopathic generalised epilepsy (IGE) who later developed HSP. She rapidly deteriorated 27years later with clinically definite amyotrophic lateral sclerosis (ALS). Her family history included HSP, IGE and motor neurone disease. Genetic testing identified a pathogenic variant in the NIPA1 gene associated with spastic paraplegia 6 (SPG6). This case provides the first description of NIPA1 in a family with epilepsy, ALS and thus complex HSP.

Comparative molecular approaches in Prader–Willi syndrome diagnosis

Prader–Willi and Angelman syndromes are two distinct neurogenetic disorders caused by chromosomal deletions, uniparental disomy or loss of the imprinted gene expression in the 15q11–q13 region. PWS results from the lack of the paternally expressed gene contribution in the region.The aim of our study was to compare a new molecular approach based on the quantification of the expression of non-imprinted bi-allelic gene (NIPA1 and OCA2) with in house MS-PCR and the MS-MLPA test. Blood samples were collected from 12 patients, clinical criteria positives for Prader–Willi syndrome. DNA and RNA samples were isolated from white blood cells. Epigenetic changes at SNRPN gene locus were evaluated by MS-PCR technique. The expression levels of two non-imprinted genes (NIPA1 and OCA2) were evaluated in qReal-Time PCR, in order to identify type 1 and type 2 deletions. SALSA MS-MLPA kit ME028 was used to detect copy number changes and to analyze CpG islands methylation of the 15q11 region.MS-MLPA test confirmed that 8/12 patients presented different types of deletion at the SNRPN gene level (promoter, introns, and exons) and 4/8 displayed type 1 or type 2 deletion. In children with 15q11–13 deletions, the decreased level of NIPA1and OCA2 gene expression is related to chromosomal abnormality in the investigated area. The deletions were confirmed by MS-MLPA analysis, thus recommending NIPA1 and OCA2 gene expression as an alternate method to investigate deletions.

Genetic and Morphological Features of Human iPSC-Derived Neurons with Chromosome 15q11.2 (BP1-BP2) Deletions

Background: Copy number variation on chromosome 15q11.2 (BP1-BP2) causes a deletion of CYFIP1, NIPA1, NIPA2 and TUBGCP5. Furthermore, it also affects brain structure and elevates the risk for several neurodevelopmental disorders that are associated with dendritic spine abnormalities. In rodents, altered cyfip1 expression changes dendritic spine morphology, motivating analyses of human neuronal cells derived from induced pluripotent stem cells (iPSCs; iPSC-neurons). Methods: iPSCs were generated from a mother and her offspring, both carrying the 15q11.2 (BP1-BP2) deletion, and a non-deletion control. Gene expression in the deletion region was estimated using quantitative real-time PCR assays. Neural progenitor cells (NPCs) and iPSC-neurons were characterized using immunocytochemistry. Results:CYFIP1, NIPA1, NIPA2 and TUBGCP5 gene expression was lower in iPSCs, NPCs and iPSC-neurons from the mother and her offspring in relation to control cells. CYFIP1 and PSD-95 protein levels were lower in iPSC-neurons derived from the copy number variant-bearing individuals using Western blot analysis. Ten weeks after differentiation, iPSC-neurons appeared to show dendritic spines, and qualitative analysis suggested that dendritic morphology was altered in 15q11.2-deletion subjects compared with control cells. Conclusions: The 15q11.2 (BP1-BP2) deletion is associated with a reduced expression of four genes in iPSC-derived neuronal cells; it may also be associated with altered iPSC-neuron dendritic morphology.

Low intracellular magnesium enhances the excitability of thalamocortical network and generates epileptic discharges

Objective To reveal the effects of low intracellular magnesium on the excitability of thalamocortical network. Methods Computational models and electrophysiological experiments were used to detect the effects of low intracellular magnesium on big-conductance potassium channels(BK channels), N-methyl-D-aspartate receptor(NMDAR) and thalamocortical network. Results 1.On BK channel model, low intracellular magnesium did not atte-nuate BK channel currents, and had no effect on neural excitability.2.On NMDAR model, low intracellular magnesium enhanced significantly excitatory postsynaptic potentials (EPSPs) by increasing NMDAR currents.3.In rat thalamocortical slice, increased EPSPs and epileptic discharges were observed, and they were attenuated by a specific NMDAR blocker. Conclusions Low intracellular magnesium may enhance the excitability of thalamocortical network and gene-rate epileptic discharges through NMDAR pathway.Our previous study had demonstrated that a magnesium transporter gene NIPA2 was highly associated with childhood absence epilepsy.Therefore, low intracellular magnesium causing epileptiform activity may provide a clue to reveal the pathogenesis of childhood absence epilepsy. Key words: Low intracellular magnesium; Big-conductance potassium channels; N-methyl-D-aspartate receptor; Thalamocortical network; Epileptic discharges

Does variation in NIPA2 contribute to genetic generalized epilepsy?

Does variation in NIPA2 contribute to genetic generalized epilepsy?

Familial 15q11.2 Micro deletions are not Fully Penetrant in Two Cases with Hereditary Spastic Paraplegia and Dysmorphic Features

Hereditary Spastic Paraplegias (HSP) is heterogenic neurodegenerative disorders with progressive spasticity of the lower limbs as a prominent feature. Spastic paraplegia type 6 (SPG6) is an autosomal dominant form of the disorder caused by point mutations in the NIPA1 gene on chromosome 15q11.2. The microdeletions within the region 15q11.2 and spanning the four genes TUBGCP5, CYFIP1, NIPA2, and NIPA1 were previously reported in several different syndromes, including mental retardation, and/or developmental delay with hypotonia. Furthermore, these genes were associated with several congenital abnormalities, including autism, developmental delay, motor, and language disturbances, behavioural problems, and Idiopathic General Epilepsies (IGE), suggesting the existence of a new microdeletion syndrome. Our index cases, in whom the microdeletion 15q11.2 was detected, suffer from spastic paraplegia, but neither cognitive impairment nor behavioural problems were observed in them and other tested relatives. We considered several interpretations of the 15q11.2 microdeletion’s phenotypic significance, including polymorphism, the pleiotropic effect of the microdeletion, and the influence of other modifiers. Specifying the exact range of the microdeletion 15q11.2 in patients with diverse clinical presentation is essential. Though the clinical implications of the microdeletion 15q11.2 remain unclear, our study contributes by extending the phenotypic variability of the subjects carrying this micro rearrangement.

Pure hereditary spastic paraplegia due to ade novomutation in theNIPA1gene

Hereditary spastic paraplegia (HSP) is a group of diseases with heterogeneous mode of inheritance and is characterized primarily by progressive spasticity of the lower limbs due to degeneration of long pyramidal tract. HSP type 6 (SPG6) is caused by mutations in the NIPA1 gene [1] (OMIM #600363) and accounts for less than 1% of autosomal dominant cases among Caucasians patients [2]. Traditionally, SPG6 was considered a pure (uncomplicated) form of HSP. Recent observations, however, expanded the phenotypic spectrum and linked NIPA1 mutations to some cases of more complex forms of HSP [3, 4]. We report here a family with a pure form of HSP due to a de novo transition mutation in the NIPA1 gene. The three affected members of the family were a 46 year-old parent and two children, aged 21 and 15 years of age. They all developed slowly progressive spastic gait that started during the first half of their second decade of life. Medical history was absent except for mild delayed speech development and attention deficit in the younger child and a single questionable generalized seizure in the older child that was not documented on electroencephalogram. This episode included a sudden loss of consciousness, lasted only few seconds and was associated with tongue biting and twitching of the left fingers but without clear postictal period. The proband, 36 years after symptom onset, had difficulty ambulating and was assisted by a walker. Both children had spastic gait but walked without assistance. Neurological examination of the affected family members was significant for marked spasticity, mild weakness of hip extensors, bilateral ankle clonus, globally hyperactive deep tendon reflexes that were more prominent in the lower extremities and extensor plantar responses. Cognition, ocular movements and cerebellar functions were all normal. Sequencing of the NIPA1 gene (Athena Diagnostics, Inc) revealed in all the affected family members a point mutation causing transition from adenine to guanine (G→A) at position 316. This mutation led to an amino acid change, from glycine to arginine, in codon 106. This specific mutation has been previously reported as pathogenic [3, 5] of a pure form of HSP, although cases of complicated HSP with epilepsy have been also documented [3]. Other ancillary tests included brain MRI studies, genetic testing for other autosomal dominant HSPs (SPG3A, SPG4 and SPG31) and extensive metabolic work-up were all normal. An MRI study of the proband’s thoracic spine showed spinal cord atrophy. Lack of symptoms or clinical signs in the parents of the proband led us to test them for a mutation in the NIPA1 gene (after they signed an informed consent for a research protocol approved by Columbia University IRB). The mutation was not present in the non-manifesting parents of the proband. True parenthood was confirmed using a panel of six highly informative unlinked microsatellite markers. To ensure specificity of this method, genetic polymorphism was also tested by three CEPH (1331-1, 1332-12, 1347-1) and showed perfect concordance. This finding supports the hypothesis that this was a de novo mutation. According to our knowledge, de novo mutations were never documented to cause SPG6 although such mutations were sparsely documented in other HSPs [6]. This finding strengths the assumption that this is a pathogenic mutation and emphasizes the need to consider autosomal dominant HSP even in the absence of family history.

Expansion of the phenotypic spectrum of SPG6 caused by mutation in NIPA1

BackgroundHereditary spastic paraplegia type 6 (SPG6) is caused by mutations in the NIPA1 gene, this is a rare cause of HSP, until now, all the affected individuals reported displayed “pure” spastic paraplegia. ObjectivesTo analyze the genotype/phenotype correlation of mutations so far described in NIPA1. MethodsEighty-six Chinese Han HSP patients were investigated for SPG6 mutations by direct sequencing of the NIPA1 gene. ResultsOne heterozygous missense mutation c.316G>C/p.G106R was identified in a complicated form of ADHSP family with peripheral nerves disease, and SPG6 mutation in our sample accounted for 3.6% (1/28) of ADHSP families and 1.1% (1/86) of non-ARHSP patients who were negative for SPG4, SPG3A and SPG31 mutations. ConclusionsWe report the first complicated case of SPG6 in the world by the presence of peripheral neuropathy, which extends the phenotype initially described.

NIPA1mutation in complex hereditary spastic paraplegia with epilepsy

Hereditary spastic paraplegia (HSP) is a group of clinically and genetically heterogeneous neurodegenerative disorders characterized in the 'pure' phenotype by progressive spasticity and weakness of the lower limbs. In the 'complex' phenotype, additional neurologic symptoms or signs are found. Mutations in the NIPA1 gene have been reported to cause spastic paraplegia type 6 (SPG6) in 10 families. SPG6 is a rare form of autosomal dominantly inherited HSP associated with a pure phenotype; however, in one complex SPG6 family, idiopathic generalized epilepsy (IGE) has been described and in addition, recurrent microdeletions at 15q11.2 including NIPA1 have been identified in patients with IGE. The purpose was to identify NIPA1 mutations in patients with pure and complex HSP. Fifty-two patients with HSP were screened for mutations in NIPA1. One previously reported missense mutation c.316G>A, p.Gly106Arg, was identified in a complex HSP patient with spastic dysarthria, facial dystonia, atrophy of the small hand muscles, upper limb spasticity, and presumably IGE. The epilepsy co-segregated with HSP in the family. NIPA1 mutations were rare in our population of patients with HSP, but can be found in patients with complex HSP. Epilepsy might be more common in SPG6 than in other forms of HSP because of a genetic risk factor closely linked to NIPA1.

Targeted Disruption of the Mouse Npal3 Gene Leads to Deficits in Behavior, Increased IgE Levels, and Impaired Lung Function

The non-imprinted in Prader-Willi/Angelman syndrome (NIPA) proteins are highly conserved receptors or transporters. Translocation of NIPA genes were found in patients with Prader-Willi syndrome, and loss-of-function of the NIPA1 gene was identified in hereditary spastic paraplegia. The family of NIPA-like domain containing (NPAL) proteins is closely related to the NIPA proteins, but to date nothing is known about their function. Here, we could demonstrate that both human NPAL3 and mouse Npal3 are ubiquitously expressed and encode highly conserved proteins. To further elucidate the function of the Npal3 gene, knockout (Npal3^–/–) mice were generated. Intensive phenotypic analyses revealed that disruption of the Npal3 gene results in a pleiotropic phenotype. The function of the nervous system was impaired in both mutant males and females which could be demonstrated in behavioral tests. In addition, in Npal3 mutants the number of NK cells was decreased and changes in IgM, IgG₂, and IgA were observed, indicating that the immune system is also affected. Interestingly, increased IgE levels as well as impaired lung functions were observed in mutant males but not in mutant females. It should be noted that the human NPAL3 gene is located at 1p36.12→p35.1, and atopic diseases were previously linked to this genomic region. Thus, the Npal3^–/– mice could serve as a valuable model system for studying atopic diseases.

Clinical and genetic study of SPG6 mutation in a Chinese family with hereditary spastic paraplegia

Mutations in the NIPA1 gene cause autosomal dominant hereditary spastic paraplegia (ADHSP). To date, little is known about the relationship between genotype–phenotype correlation. In order to examine the gene mutation associated with the genotype–phenotype of Chinese kindred with ADHSP, linkage analysis and mutation detection were performed. For affected family members, clinical analysis, electrophysiological examination and MRI of the brain and spinal cord were also performed. Every effected patient had a c316 (G106R) mutation in the NIPA1 gene. Neurophysiological examination revealed decreased amplitude of compound muscle action potentials (CMAP) from the tibial and peroneal motor nerves in most patients. Sensory nerve action potential (SNAP) from the tibialis nerve was not elicited in most patients. Central motor conduction time (CMCT) to the abductor pollicis brevis muscle (APB), first metatarsal interosseus muscle (FMI) and anterior tibial muscle (AT) were either absent or clearly prolonged in all patients. Spinal cord MRI showed different levels of atrophy in every affected individual. These lesions present an increased spot or patch signal on transverse axis T2WI and an intense signal of continual longitudinal strip on the anteroposterior axis. Our study supports that mutations in the NIPA1 gene cause ADHSP and further demonstrates genotype–phenotype correlations in SPG6.

NIPA1(SPG6), the Basis for Autosomal Dominant Form of Hereditary Spastic Paraplegia, Encodes a Functional Mg2+ Transporter

Mutations in the NIPA1(SPG6) gene, named for "nonimprinted in Prader-Willi/Angelman" has been implicated in one form of autosomal dominant hereditary spastic paraplegia (HSP), a neurodegenerative disorder characterized by progressive lower limb spasticity and weakness. However, the function of NIPA1 is unknown. Here, we show that reduced magnesium concentration enhances expression of NIPA1 suggesting a role in cellular magnesium metabolism. Indeed NIPA1 mediates Mg2+ uptake that is electrogenic, voltage-dependent, and saturable with a Michaelis constant of 0.69+/-0.21 mM when expressed in Xenopus oocytes. Subcellular localization with immunofluorescence showed that endogenous NIPA1 protein associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. As expected of a magnesium-responsive gene, we find that altered magnesium concentration leads to a redistribution between the endosomal compartment and the plasma membrane; high magnesium results in diminished cell surface NIPA1 whereas low magnesium leads to accumulation in early endosomes and recruitment to the plasma membrane. The mouse NIPA1 mutants, T39R and G100R, corresponding to the respective human mutants showed a loss-of-function when expressed in oocytes and altered trafficking in transfected COS7 cells. We conclude that NIPA1 normally encodes a Mg2+ transporter and the loss-of function of NIPA1(SPG6) due to abnormal trafficking of the mutated protein provides the basis of the HSP phenotype.

Childhood-Onset Spastic Paraplegia With NIPA1 Gene Mutation

Hereditary spastic paraplegia is a heterogeneous group of inherited neurodegenerative disorders in which the predominant clinical feature is gait disturbance owing to spasticity and weakness of the lower limbs. Autosomal dominant hereditary spastic paraplegia is the predominant form of the disorder. To date, 10 autosomal dominant hereditary spastic paraplegia gene loci and genes for 6 of them have been identified. Spastic paraplegia 6, with a typical teenage onset and considered to be one of the more severe forms of the disease, is due to mutations in the gene NIPA1. We report a childhood-onset, aggressive, spastic paraparesis in a North American family with a c.316G>A mutation of the NIPA1 gene, confirming c.316 as a mutational hot spot.

NIPA1 Gene Mutations Cause Autosomal Dominant Hereditary Spastic Paraplegia (SPG6)

The hereditary spastic paraplegias (HSPs) are genetically heterogeneous disorders characterized by progressive lower-extremity weakness and spasticity. The molecular pathogenesis is poorly understood. We report discovery of a dominant negative mutation in the NIPA1 gene in a kindred with autosomal dominant HSP (ADHSP), linked to chromosome 15q11-q13 (SPG6 locus); and precisely the same mutation in an unrelated kindred with ADHSP that was too small for meaningful linkage analysis. NIPA1 is highly expressed in neuronal tissues and encodes a putative membrane transporter or receptor. Identification of the NIPA1 function and ligand will aid an understanding of axonal neurodegeneration in HSP and may have important therapeutic implications.