Niemann-Pick type C disease: subcellular location and functional characterization of NPC2 proteins with naturally occurring missense mutations

Niemann-Pick disease type C (NPC), a severe neurovisceral lysosomal disorder, is due to mutations on the NPC1 gene or, in a minority of families, the NPC2 gene. Few investigations have been devoted to the NPC2 protein, for which only 13 different disease-causing mutations (including three novel ones in this report) have been described. Among the currently known NPC2 mutant alleles, six resulted in a premature stop codon. Only five missense mutations, c.115G>A (p.V39M), c.140G>T (p.C47F), c.199T>C (p.S67P), c.278G>T (p.C93F), and (this report) c.295T>C (p.C99R) were identified. In the present study, we generated cDNA constructs harboring each of these missense mutations and, upon overexpression in human fibroblasts with a nonsense NPC2 mutation, characterized the mutated proteins by immunoblotting, immunocytofluorescence microscopy, and complementation. Mutation p.V39M, described in the homozygous state in two patients with an adult-onset neurological disease, resulted in the synthesis of apparently functional recombinant proteins correctly targeted to lysosomes. Although a mild functional impact could possibly be overlooked in our overexpression system, comparative studies with NPC1 mutants indicated that mild mutations might not necessarily affect localization of the protein or its quantity in the native state. Conversely, mutations p.C47F, p.C93R, p.C99R but also, less predictably, p.S67P, led to the synthesis of misfolded recombinant proteins that colocalized with an endoplasmic reticulum marker. The four latter proteins were normally secreted but were unable to correct cholesterol storage in NPC2(-/-) cells. Functional characterization of the mutant proteins showed an excellent genotype-phenotype correlation in the three cases for whom a clinical history was available.     

NPC1: Complete genomic sequence,mutation analysis,and characterization of haplotypes

Niemann‐Pick type C disease (NP‐C) is a rare, autosomal recessive lipid storage disorder. At least 96% of all NP‐C patients link to NPC1 which encodes for a lysosomally‐targeted protein. We describe the complete genomic sequence of 57,052 kb corresponding to the transcribed region of human NPC1 including several exonic and intronic single nucleotide polymorphisms (SNPs). Sequencing of all exons, splice sites, and the promoter region of NPC1 in 12 unrelated Caucasian NP‐C patients revealed nine novel and four known most likely disease‐causing mutations. Ten unique mutations found only once in 24 disease alleles were observed in patients being compound heterozygous for two different mutations. Two of the three missense mutations identified more than once were observed in a total of four patients homozygous for the respective mutation along with homozygosity for the underlying haplotype. The patients were offspring of most likely nonconsanguineous couples. Based upon genotyping exonic SNPs c.2572A>G (I858V; g.45020A>G) and c.2793C>T (N931N; g.45686C>T) and segregation analysis we characterized the haplotype of all 24 NPC1 alleles and of 138 alleles of healthy Caucasian control subjects. All four permutations between the two SNPs were identified in the control alleles: 2572A‐2793C (50%), 2572G‐2793T (41%), 2572G‐2793C (5%), and 2572A‐2793T (4%). These data are suggestive for an ancestral intragenic recombination within a genomic fragment of <666 bp. While 17 of 24 NP‐C alleles (71%) shared haplotype 2572G‐2793T, this haplotype accounted for only 41% in the controls (p=0.007; 2‐sided Fisher exact test) suggesting the possibility of an influence of the haplotypic background on expression of missense mutations in NPC1. Hum Mutat 19:30–38, 2002. © 2001 Wiley‐Liss, Inc.     

New BZLF1 sequence variations in EBV-associated undifferentiated nasopharyngeal carcinoma in southern China

The viral lytic gene BZLF1 triggers replication of the Epstein–Barr virus (EBV), which is commonly found in nasopharyngeal carcinoma (NPC). Here, RT-PCR revealed five new BZLF1 variants in 8 of 12 NPC and 4 of 12 non-NPC nasopharyngeal biopsies from an NPC-endemic area in southern China. The deduced peptide sequence of the dominant BZLF1 variant differed by 11 amino acids from that of the prototypical strain B95.8 (V01555). Anti-ZEBRA antibody levels were higher in NPC than that in non-NPC patients (P < 0.001). These findings demonstrated a dominant BZLF1 variant in southern Chinese EBV-associated NPC and non-NPC patients.     

Niemann-Pick C disease: use of denaturing high performance liquid chromatography for the detection of NPC1 and NPC2 genetic variations and impact on management of patients and families

Niemann-Pick disease type C (NPC), a neurovisceral disorder characterized by accumulation of unesterified cholesterol and glycolipids in the lysosomal/late endosomal system, is due to mutations on either the NPC1 or the NPC2 genes. While the corresponding proteins appear essential for proper cellular cholesterol trafficking, their precise function and relationship are still unclear. Mutational analysis of patients, useful for the study of structure/function relationships, is especially valuable for proper management of affected families. Correlations have been found between genotypes and the severity of the neurological outcome of the patients, and molecular genetics constitutes the optimal approach for prenatal diagnosis. However, mutation detection in NPC disease is a challenge. The NPC1 gene, affected in >95% of the families, is large in size (approximately 50 kb), and the already known disease-causing mutations and numerous polymorphisms are scattered over 25 exons. Furthermore, detection of NPC2 patients by complex genetic complementation tests is unpractical. In the present study, we describe a rapid and reliable strategy for detecting NPC genetic variations using DHPLC analysis. Conditions of analysis were optimized for all the NPC1 and NPC2 30 exons and validated using 38 previously genotyped patients. These conditions were then applied to screen a panel of 35 genetically uncharacterized, unrelated NPC patients. Pathogenic mutations were identified in 68/70 alleles. Among the mutations identified, 29 were novel, including two of the NPC2 gene. We conclude that DHPLC is a rapid, low-cost, highly accurate, and efficient technique for the detection of NPC genetic variants.     

中国广东人CYP2F1基因遗传多态性研究

目的检测广东地区正常人群和鼻咽癌患者中细胞色素P450酶系CYP2F1基因的多态性，并分析该基因遗传多态性与鼻咽癌易感性的关联。方法采用直接测序法检测40例鼻咽癌患者全血标本中CYP2F1基因全部10个外显子的多态性变化。对于等位基因频率较高的多态性位点，进一步采用错配聚合酶链反应．限制性片段长度多态性检测368例鼻咽癌患者和344名正常对照人群中该位点的等位基因频率。结果在40例鼻咽癌样本中，共检测到CYP2F1基因的35个单核苷酸多态性。其中，10个单核甘酸引起编码的氨基酸改变，1个移码突变，15～16bp之间插入C引起移码突变（15-16ins C），该等位基因频率为25％。但病例-对照分析却未能显示该位点突变与鼻咽癌易感的相关性（P〉0．05）。结论中国广东人的CYP2F1基因遗传多态性位点较多，但暂未发现与鼻咽癌的易感性关联的单一多态位点，多个多态性位点或不同基因多态性位点的协同互补作用可能才是鼻咽癌发生发展的关键影响因素。     

Germline mutations of the LKB1 (STK11) gene in Peutz-Jeghers patients

Germline mutations of the LKB1 (STK11) serine/threonine kinase gene (chromosome 19p13.3) cause Peutz-Jeghers syndrome, which is characterised by hamartomas of the gastrointestinal tract and typical pigmentation. Peutz-Jeghers syndrome carries an overall risk of cancer that may be up to 20 times that of the general population. Here, we report the results of a screen for germline LKB1 mutations by DNA sequencing in 12 Peutz-Jeghers patients (three sporadic and nine familial cases). Mutations were found in seven (58%) cases, in exons 1, 2, 4, 6, and 9. Five of these mutations, two of which are identical, are predicted to lead to a truncated protein (three frameshifts, two nonsense changes). A further mutation is an in frame deletion of 6 bp, resulting in a deletion of lysine and asparagine; the second of these amino acids is conserved between species. The seventh mutation is a missense change in exon 2, converting lysine to arginine, affecting non-conserved amino acids and of uncertain functional significance. Despite the fact that Peutz-Jeghers syndrome is usually an early onset disease with characteristic clinical features, predictive and diagnostic testing for LKB1 mutations will be useful for selected patients in both familial and non-familial contexts.     

Defective endocytic trafficking of NPC1 and NPC2 underlying infantile Niemann-Pick type C disease

Niemann-Pick type C (NPC) disease is a fatal recessively inherited lysosomal cholesterol-sphingolipidosis. Mutations in the NPC1 gene cause approximately 95% of the cases, the rest being caused by NPC2 mutations. Here the molecular basis of a severe infantile form of the disease was dissected. The level of NPC1 protein in the patient fibroblasts was similar to that in control cells. However, the protein was partially mislocalized from late endocytic organelles diffusely to the cell periphery. In contrast, NPC2 was upregulated and accumulated in cholesterol storing late endocytic organelles. Two point mutations and a four-nucleotide deletion were identified in the NPC1 gene, leading to the amino acid substitutions C113R, P237S and deletion of 37 C-terminal amino acids (delC). Overexpression of individual NPC1 mutations revealed that delC produced an unstable protein, wild-type and NPC1-P237S colocalized with Rab7-positive late endosomes whereas NPC1-C113R localized to the ER, Rab7-negative endosomes and the cell surface. Expression of wild-type or NPC1-P237S cleared the lysosomal cholesterol accumulation in NPC1-deficient cells whereas C113R or delC did not. In the Finnish and Swedish population samples, alleles carrying C113R or delC were not identified, whereas approximately 5% of the alleles carried P237S. Our studies identify P237S as a prevalent NPC1 polymorphism and delC and C113R as deleterious NPC1 mutations. Moreover, they show that delC leads to rapid degradation of NPC1 and C113R to endocytic missorting of the protein. These changes are accompanied by lysosomal accumulation of NPC2, suggesting that NPC1 governs the endocytic transport of NPC2.     

Comprehensive scanning of the ATM gene with DOVAM-S

Mutation detection at the ATM locus has been difficult because of the large size of the gene (66 exons), the fact that mutations are located throughout the entire gene with no hotspots, and the difficulty of distinguishing mutations from polymorphisms. In this study, the entire coding region (exons 4-65) was scanned, as well as the adjacent intronic regions, using DOVAM-S (Detection Of Virtually All Mutations-SSCP), a robotically-enhanced, multiplexed scanning method that is a highly sensitive modification of SSCP. Forty-three unrelated patients and four obligate carriers were studied. Of the 90 expected mutant alleles, 71 were identified (79%). The mutations included 17 nonsense (24%), 20 frameshift (28%), 20 splice (28%), 10 missense (14%), one in-frame deletion (1%), and three that alter the initiation codon (4%). Among the ataxia-telangiectasia patients, two potentially causative mutations were identified in 30 individuals: 22 had two truncating mutations, four had one truncating and one missense mutation, three had two missense mutations, and one had a truncating mutation and an in-frame deletion of three amino acids. For seven A-T patients and all four obligate carriers, only one truncating mutation was detected. Six of the 43 A-T patients had no detected mutations (14%). Twelve novel mutations and six novel polymorphisms were detected. The results of this complete scan of the ATM coding region showed that 86% of causative ATM mutations were truncating and 14% were missense. DOVAM-S is a rapid, efficient method of performing A-T diagnosis and carrier testing on a clinical time scale.     

Neurofilament light chain in cerebrospinal fluid as a novel biomarker in evaluating both clinical severity and therapeutic response in Niemann-Pick disease type C1

PurposeNiemann-Pick disease type C1 (NPC1) is a neurodegenerative lysosomal disorder caused by pathogenic variants in NPC1. Disease progression is monitored using the NPC Neurological Severity Scale, but there are currently no established validated or qualified biomarkers. Neurofilament light chain (NfL) is being investigated as a biomarker in multiple neurodegenerative diseases.MethodsCross-sectional and longitudinal cerebrospinal fluid (CSF) samples were obtained from 116 individuals with NPC1. NfL levels were measured using a solid-phase sandwich enzyme-linked immunosorbent assay and compared with age-appropriate non-NPC1 comparison samples.ResultsMedian levels of NfL were elevated at baseline (1152 [680-1840] pg/mL) in NPC1 compared with controls (167 [82-372] pg/mL; P < .001). Elevated NfL levels were associated with more severe disease as assessed by both the 17-domain and 5-domain NPC Neurological Severity Score. Associations were also observed with ambulation, fine motor, speech, and swallowing scores. Although treatment with the investigational drug 2-hydroxypropyl-β-cyclodextrin (adrabetadex) did not decrease CSF NfL levels, miglustat therapy over time was associated with a decrease (odds ratio = 0.77, 95% CI = 0.62-0.96).ConclusionCSF NfL levels are increased in individuals with NPC1, associated with clinical disease severity, and decreased with miglustat therapy. These data suggest that NfL is a biomarker that may have utility in future therapeutic trials.     

Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria

The methylmalonic acidurias are metabolic disorders resulting from deficient methylmalonyl-CoA mutase activity, a vitamin B(12)-dependent enzyme. We have cloned the gene for the cblB complementation group caused by deficient activity of a cob(I)alamin adenosyltransferase. This was accomplished by searching bacterial genomes for genes in close proximity to the methylmalonyl-CoA mutase gene that might encode a protein with the properties of an adenosyltransferase. A candidate was identified in the Archaeoglobus fulgidus genome and was used to probe the human genome database. It yielded a gene on chromosome 12q24 that encodes a predicted protein of 250 amino acids with 45% similarity to PduO in Salmonella enterica, a characterized cob(I)alamin adenosyltransferase. A northern blot revealed an RNA species of 1.1 kb predominating in liver and skeletal muscle. The gene was evaluated for deleterious mutations in cblB patient cell lines. Several mutations were identified including a 5 bp deletion (5del572gggcc576), two splice site mutations (IVS2-1G>T, IVS3-1G>A), andt several point mutations (A135T, R186W, R191W and E193K). Two additional amino acid substitutions (R19Q and M239K) were found in several patient cell lines but were found to be common polymorphisms (36% and 46%) in control alleles. The R186W mutation, which we suggest is disease-linked, is present in four of the six patient cell lines examined (homoallelic in two) and in 4 of 240 alleles in control samples. These data confirm that the identified gene, MMAB, corresponds to the cblB complementation group and has the appearance of a cob(I)alamin adenosyltransferase, as predicted from biochemical data.     

Recurrent mutations of BRCA1 and BRCA2 in Poland: an update

Three founder alleles of BRCA1 (C61G, 4153delA, 5382insC) were reported in Poland in 2000, and these three mutations have comprised the standard testing panel used throughout the country. However, since 2000, other recurrent mutations of BRCA1 and BRCA2 have been reported. To establish if the inclusion of one or more of these mutations will increase the sensitivity of the standard test panel, we studied 1164 Polish women with unselected breast cancer diagnosed at age of 50 or below. All women were genotyped for 12 recurrent mutations of BRCA1 and BRCA2. We identified a mutation in 83 of 1164 patients (7.1%) including 61 women with one of the original three mutations (C61G, 4153delA, 5382insC) and 22 women with a different mutation (1.9%). Three new mutations (3819del5, 185delAG and 5370C>T) were seen in multiple families. By including these three mutations in the extended panel, the mutant frequency increased from 5.2 to 6.7%. Polish women with breast cancer diagnosed at age of 50 or below should be screened with a panel of six founder mutations of BRCA1 (C61G, 4153delA, 5382insC, 3819del5, 185delAG and 5370C>T).     

Specific IgA antibody to Epstein-Barr viral capsid antigen: a better marker for screening nasopharyngeal carcinoma than EBV-DNA detection by polymerase chain reaction

Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. To assess whether EBV DNA detection by polymerase chain reaction (PCR) or presence of specific serum antibody to viral capsid antigen (VCA) was a better marker for screening NPC, nasopharyngeal tissues and blood samples from 58 NPC patients and 24 non-NPC patients (23 with laryngotracheal stenosis and 1 with chronic tonsillitis) were tested for the presence of EBV DNA and serum specific VCA antibodies, respectively. EBV DNA was detected in 56 (96.5%) of NPC patients and 15 (62.5%) of non-NPC controls, with predominantly EBV type A in both groups. On the other hand, specific VCA IgA antibody was detected in the majority of NPC patients: 52 (89.7%) while only 4 (16.7%) were detected in non-NPC controls. Therefore, specific VCA IgA antibody may serve as a better marker for screening NPC than EBV DNA detected by PCR.     

Identification of a common PEX1 mutation in Zellweger syndrome

The Zellweger spectrum of disease, encompassing Zellweger syndrome and the progressively milder phenotypes of neonatal adrenoleukodystrophy and infantile Refsum disease, is due to a failure to form functional peroxisomes. Cell fusion complementation studies demonstrated that these diseases are genetically heterogeneous, with two‐thirds of all patients lying within a single complementation group, CG1. Molecular genetic and cell biology studies have shown that PEX1 is deficient in many CG1 patients. However, previous studies have focused on mildly affected patients and there is still no report of two mutant PEX1 alleles in any Zellweger syndrome patient. Furthermore, mutations in the PMP70 gene have also been identified in two Zellweger syndrome patients from CG1, raising the possibility that CG1 patients may represent a mixture of PEX1‐deficient and PMP70‐deficient individuals. To address the molecular basis of disease in Zellweger syndrome patients from CG1, we examined all 24 PEX1 exons in four patients, including both patients that have mutations in PMP70. PEX1 mutations were detected in all four patients, including a 1‐bp insertion (c.2097insT) in exon 13 that was present in three of the four patients. Subsequent studies demonstrated that this mutation is present in one‐half of all CG1 patients and correlates with the Zellweger syndrome phenotype. As this mutation leads to a loss of protein function its frequency makes it the most common cause of Zellweger syndrome, helping to explain the high percentage of patients that belong to CG1. Hum Mutat 14:45–53, 1999. © 1999 Wiley‐Liss, Inc.     

中国上海家族性乳腺癌BRCA1和BRCA2基因的突变

目的研究上海地区家族性乳腺癌中BRCA1／BRCA2基因的突变位点及携带情况。方法研究对象来自35个汉族家族性乳腺癌家系，家系中至少有一个一级亲属乳腺癌患病史。共35例患者，其中13例发病年龄≤加岁。由静脉血提取基因组DNA，对BRCA1／BRCA2基因的全部编码序列进行扩增。扩增产物突变分析先由变性高效液相色谱分析进行筛查，之后进行DNA直接测序证实。结果在BRCA1基因中发现有4个突变位点，其中2个为新发现位点——拼接点突变（IVS17-1G〉T；IVS21＋1G〉C）；另两个为已报道的致病突变位点——移码突变（1100delAT；5640delA）。BRCA2基因的1个致病突变位点位于11号外显子上，为移码突变（5802delAATT）。另外，共发现有12个新的单核苷重复多态位点，都未引起氨基酸编码改变；其中，8个在BRCA1基因上，4个在BRCA2基因上。在家族性乳腺癌中，BRCA1突变频率（11．4％）高于BRCA2基因（2．9％）。结论新发现的2个BRCA1基因的拼接点突变可能是中国上海人群家族性乳腺癌的特有突变位点；在我国上海地区人群中，BRCA1基因突变起着比BRCA2基因更大的作用；该研究丰富了中国人群中BRCA基因的突变谱，并为未来的临床基因检测提供了筛查模式。     

Molecular Genetic Analysis of SLC3A1 and SLC7A9 Genes in Czech and Slovak Cystinuric Patients

Cystinuria is a frequently inherited metabolic disorder in the Czech population (frequency 1/5,600) caused by a defect in the renal transport of cystine and dibasic amino acids (arginine, lysine and ornithine). The disease is characterized by increased urinary excretion of the amino acids and often leads to recurrent nephrolithiasis. Cystinuria is classified into two subtypes (type I and type non‐I). Type I is caused predominantly by mutations in the SLC3A1 gene (2p16.3), encoding heavy subunit (rBAT) of the heterodimeric transporter. Cystinuria non‐I type is caused by mutations in the SLC7A9 gene (19q13.1). In this study, we present results of molecular genetic analysis of the SLC3A1 and the SLC7A9 genes in 24 unrelated cystinuria families. Individual exons of the SLC3A1 and SLC7A9 genes were analyzed by direct sequencing. We found ten different mutations in the SLC3A1 gene including six novel ones: three missense mutations (G140R), D179Y and R365P), one splice site mutation (1137‐2A>G), one deletion (1515_1516delAA), and one nonsense mutation (Q119X). The most frequent mutation, M467T; was detected in 36% of all type I classified alleles. In the SLC7A9 gene we found six mutations including three new ones: one missense mutation (G319R), one insertion (611_612insA) and one deletion (205_206delTG). One patient was compound heterozygote for one SLC3A1 and one SLC7A9 mutation. Our results confirm that cystinuria is a heterogeneous disorder at the molecular level, and contribute to the understanding of the distribution and frequency of mutations causing cystinuria in the Caucasian population.     

Identification of two novel mutations in the murine Nsdhl sterol dehydrogenase gene and development of a functional complementation assay in yeast

Nsdhl is a 3beta-hydroxysterol dehydrogenase that is involved in the removal of C-4 methyl groups in the cholesterol biosynthetic pathway. Mutations in this gene are associated with the X-linked male lethal mouse mutations bare patches (Bpa) and striated (Str) and human CHILD syndrome. We have now detected the missense mutations V53D and A94T in conserved amino acids in two additional Bpa alleles. The latter alters the same amino acid as a missense mutation found in two unrelated CHILD patients, strongly suggesting that differences in the phenotype between Bpa mice and females with CHILD syndrome are unlikely to be explained by different types or sites of mutations. We have also demonstrated that the mouse NSDHL protein can rescue the lethality of erg26 deficient cells of Saccharomyces cerevisiae that lack the yeast ortholog, substantiating the role of NSDHL as a C-3 sterol dehydrogenase. Using this in vivo assay, we have demonstrated that two Str alleles function as hypomorphs, while three Bpa and one Str allele provide no complementation or rescue.