Whole-exome sequencing in a Japanese multiplex family identifies new susceptibility genes for intracranial aneurysms.

BACKGROUND: Intracranial aneurysms (IAs) cause subarachnoid hemorrhage, which has high rates of mortality and morbidity when ruptured. Recently, the role of rare variants in the genetic background of complex diseases has been increasingly recognized. The aim of this study was to identify rare variants for susceptibility to IA. METHODS: Whole-exome sequencing was performed on seven members of a Japanese pedigree with highly aggregated IA. Candidate genes harboring co-segregating rare variants with IA were re-sequenced and tested for association with IA using additional 500 probands and 323 non-IA controls. Functional analysis of rare variants detected in the pedigree was also conducted. RESULTS: We identified two gene variants shared among all four affected participants in the pedigree. One was the splicing donor c.1515+1G>A variant in NPNT (Nephronectin), which was confirmed to cause aberrant splicing by a minigene assay. The other was the missense p.P83T variant in CBY2 (Chibby family member 2). Overexpression of p.P83T CBY2 fused with red fluorescent protein tended to aggregate in the cytoplasm. Although Nephronectin has been previously reported to be involved in endothelial angiogenic functions, CBY2 is a novel molecule in terms of vascular pathophysiology. We confirmed that CBY2 was expressed in cerebrovascular smooth muscle cells in an isoform2-specific manner. Targeted CBY2 re-sequencing in additional case-control samples identified three deleterious rare variants (p.R46H, p.P83T, and p.L183R) in seven probands, showing a significant enrichment in the overall probands (8/501) compared to the controls (0/323) (p = 0.026, Fisher's extract test). CONCLUSIONS: NPNT and CBY2 were identified as novel susceptibility genes for IA. The highly heterogeneous and polygenic architecture of IA susceptibility can be uncovered by accumulating extensive analyses that focus on each pedigree with a high incidence of IA.

Identification of shared genomic aberrations between angiomatous and microcystic meningiomas.

BACKGROUND: Angiomatous and microcytic meningiomas are classified as rare subtypes of grade I meningiomas by World Health Organization (WHO). They typically exhibit distinct histopathological features as indicated by their WHO titles; however, these angiomatous and microcystic features are often intermixed. Recently, angiomatous meningiomas were reported to show characteristic chromosomal polysomies unlike the other WHO grade I meningiomas. In the present study, we hypothesize that microcystic meningiomas share similar cytogenetic abnormalities with angiomatous meningioma. METHODS: We performed copy number analysis using single nucleotide polymorphism (SNP) arrays for three angiomatous and eight microcystic meningiomas. Of these, three angiomatous and three microcystic meningiomas were also analyzed by whole exome sequencing and RNA sequencing. RESULTS: We first analyzed three angiomatous and three microcystic meningiomas for which both frozen tissues and peripheral blood were accessible. Copy number analysis confirmed previously reported multiple polysomies in angiomatous meningiomas, which were entirely replicated in microcystic meningiomas when analyzed on different analytical platforms with five additional samples prepared from formalin-fixed paraffin-embedded tumors. Polysomy of chromosome 5 was found in all cases, along with chromosome 6, 12, 17, 18, and 20 in more than half of the cases including both angiomatous and microcystic meningiomas. Furthermore, next generation sequencing did not reveal any distinctive somatic point mutations or differences in gene expression characterizing either angiomatous or microcystic meningiomas, indicating a common genetic mechanism underlying tumorigenesis. CONCLUSIONS: Angiomatous and microcystic meningiomas have substantially similar genetic profiles represented by the characteristic patterns of multiple polysomies originating from chromosome 5 amplification.

Novel and recurrent RNF213 variants in Japanese pediatric patients with moyamoya disease.

Moyamoya disease is a progressive steno-occlusive condition of the main intracranial arteries that results in the compensatory formation of fragile moyamoya vessels at the base of the brain. RNF213 is the most significant susceptibility gene and is often found with the p.Arg4810Lys founder variant in East Asian patients. We identified three putatively deleterious variants of this gene from three pediatric patients: two were novel, and one was a recurrent missense variant previously reported in other pediatric patients.

Exome Sequencing Identified CCER2 as a Novel Candidate Gene for Moyamoya Disease.

The etiology of Moyamoya disease (MMD) is still largely unclear, despite identification of RNF213 as the most significant susceptibility gene in East Asian patients. Following up our previous study confirming genetic heterogeneity in Japanese patients with MMD, we extensively surveyed novel candidate genes for a new perspective on the etiology of this disease. Two characteristic pedigrees without susceptibility variants in RNF213 were selected for whole-exome sequencing; 1 harbored 3 affected members, and the other included discordant monozygotic twins. In the former pedigree, 12 rare mutations in 12 genes were co-segregated with MMD. One of the most deleterious amino acid changes among these was p.T76_G80delinsPS in CCER2, which was also mutated in the latter pedigree (p.E242K), although the unaffected twin sister shared the same mutation reflecting reduced penetrance. These CCER2 mutations were predicted to promote aggregation or oligomerization of their protein product, using in silico functional analysis. Subsequent CCER2 re-sequencing in an additional 135 MMD probands identified 1 recurrent and an additional 2 in-frame insertion-deletion mutations, recurrent p.T76_G80delinsPS, p.H218_H220del, and p.E299del. Although CCER2 molecular function is not well characterized, it is a secretory protein expressed in the brain; therefore, it constitutes a potential biomarker of MMD.

KRIT1 mutations in three Japanese pedigrees with hereditary cavernous malformation.

Cerebral cavernous malformation is a neurovascular abnormality that can cause seizures, focal neurological deficits and intracerebral hemorrhage. Familial forms of this condition are characterized by de novo formation of multiple lesions and are autosomal-dominantly inherited via CCM1/KRIT1, CCM2/MGC4607 and CCM3/PDCD10 mutations. We identified three truncating mutations in KRIT1 from three Japanese families with CCMs: a novel frameshift mutation, a known frameshift mutation and a known splice-site mutation that had not been previously analyzed for aberrant splicing.

Association of Rare Nonsynonymous Variants in PKD1 and PKD2 with Familial Intracranial Aneurysms in a Japanese Population.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) caused by deleterious mutations in PKD1 (16p13.3) and PKD2 (4q21) often coexists with intracranial aneurysms (IAs). In this study, we investigated whether IAs without obvious renal diseases were also associated with these ADPKD genes. METHODS: We performed next-generation sequencing of the ADPKD genes in 150 Japanese familial IA patients and age- and sex-matched 150 non-IA controls without obvious renal diseases. Rare coding variants for the following association analysis were defined according to allelic frequencies of less than .5% either in our controls or in the 1000 genomes database. Association with IA was evaluated using burden and variance component methods: the weighted-sum statistic (WSS) and the sequence kernel association test (SKAT), respectively. RESULTS: A total of 44 rare candidate variants were confirmed by Sanger sequencing; 26 were identified from 33 patients, whereas 21 were identified from 20 controls. The candidate variants were all missense variants, except for 1 patient's nonsense variant (p.Q924X) in PKD2, and showed consistent association with IA in both burden and variance component tests (odds ratio [OR] = 1.80; WSS, P = .026; SKAT, P = .044). This association was largely derived from the variants found in the extracellular structural domains of PKD1 (OR = 2.06; WSS, P = .030; SKAT, P = .029). CONCLUSION: ADPKD genes are susceptibility genes for IA even in patients without ADPKD.

[Two Cases of Primary Intracranial Solitary Fibrous Tumor:Genetic Examination of NAB2-STAT6 Fusion and Its Association with Hemangiopericytoma].

Using whole exome and transcriptome sequencing, NAB2-STAT6 gene fusions have recently been identified in patients with solitary fibrous tumors (SFT). We report two cases of SFT in which NAB2-STAT6 fusions were identified. The patients were a 32-year-old man with a parasagittal tumor involving the superior sagittal sinus, and a 40-year-old man with a cerebellar convexity tumor partially involving the transverse sinus. Their tumors were gross totally resected and diagnosed to be SFT according to the following pathological findings:the tumors were composed of spindle cells with a patternless architecture, with prominent stromal collagen and staghorn vessels. An immunohistochemical study yielded positive results for CD34, CD99, and Bcl-2 and negative results for EMA, GFAP, and S100. The MIB-1 indexes were 13 and 7%, respectively. NAB2-STAT6 fusions were detected in both cases with a common fusion variant, NAB2ex6-STAT6ex16/17. We also identified NAB2-STAT6 fusions in two hemangiopericytomas diagnosed in the past with a common variant of NAB2ex6-STAT6ex16/17. These findings suggest that solitary fibrous tumor and hemangiopericytoma may be diagnosed based on the presence of NAB2-STAT6 fusion, and not classified separately because of the same genetic background.

Systematic Validation of RNF213 Coding Variants in Japanese Patients With Moyamoya Disease.

BACKGROUND: A founder variant of RNF213, p.R4810K (c.14429G>A, rs112735431), was recently identified as a major genetic risk factor for moyamoya disease (MMD) in Japan. Although the association of p.R4810K was reported to be highly significant and reproducible, the disease susceptibility of other RNF213 variants remains largely unknown. In the present study, we systematically evaluated the coding variants detected in Japanese patients and controls for associations with MMD. METHODS AND RESULTS: To detect variants of RNF213, all coding exons were sequenced in 27 Japanese MMD patients without p.R4810K. We also validated all previously reported variants in our case-control samples and tested for associations in combination with previous Japanese study cohorts, including the 1000 Genomes Project data set, as population-based controls. Forty-six missense variants other than p.R4810K were identified among 370 combined patients and 279 combined controls in Japan. Sixteen of 46 variants were polymorphisms with minor allele frequency >1%, and, after conditioning on the p.R4810K genotype, were not associated with MMD. We conducted a variable threshold test using Combined Annotation-Dependent Depletion on the remaining 30 rare variants (minor allele frequency <1%), and the results showed that the frequency of potentially functional variants was significantly higher in patients than in controls (permutation, minimum P=0.045). CONCLUSIONS: Not only p.4810K but also other functional missense variants of RNF213 conferred susceptibility to MMD. Our analysis also revealed that ≈20% of Japanese MMD patients did not harbor susceptibility variants of RNF213, indicating the presence of other susceptibility genes for MMD.

Spontaneous regression together with increased calcification of incidental meningioma.

BACKGROUND: Regression of meningioma has been reported after hemorrhage or hormonal withdrawal. However, meningioma regression is rarely observed spontaneously. CASE DESCRIPTION: A right falx meningioma was incidentally diagnosed and was followed at every one-year by magnetic resonance imaging (MRI) for over 7 years. The tumor, with a maximum diameter of 4 cm, showed a slightly high density and was enhanced on computed tomography (CT), and a high intensity with a low-intensity core on T2 MRI, with significant edema. The meningioma gradually shrank together with a decrease of edema and increase of calcification. The initial volume, 25.5 cm(3), regressed linearly to less than half, 9.9 cm(3). CONCLUSION: Here, we report a case of an incidentally diagnosed meningioma that regressed spontaneously. The pattern of the regression was similar to that following gamma knife radiosurgery.

Cerebral hypermetabolism demonstrated by FDG PET in familial Creutzfeldt-Jakob disease.

Right cerebral and contralateral cerebellar hypermetabolism were observed on FDG PET in a 68-year-old woman with familial Creutzfeldt-Jakob disease (CJD) at an early stage before seizures occurred. The disease progressed with frequent seizures, myoclonus, and a startle reaction. In all past reports, FDG PET studies demonstrated hypometabolism in the cerebrum, cerebellum, and thalamus in patients with CJD. Focal hypermetabolism corresponding with epileptic foci is a common finding in ictal epilepsy patients, and hypometabolism is common in patients with myoclonus or the startle reaction. This finding may reflect a prodromal pathophysiology of epilepsy. Attention should be paid to the diagnosis of CJD while using FDG PET.

[Genetic dissection of intracranial aneurysm].

Subarachnoid hemorrhage (SAH) due to rupture of an intracranial aneurysm (IA) is a devastating condition with high mortality and morbidity. Genetic as well as environment factors play important roles in the pathogenesis of SAH and IAs. We review the present knowledge on the genetic factors responsible for SAH or IAs. Linkage analysis and association study are used for genetic dissection. Genome-wide linkage analyses have specified several genetic loci for IAs and 6 loci (1p34-36, 7q11, 11q24-25, 14q22-31, 19q13, and Xp22) have been replicated in different populations. Numerous functional and/or positional candidate genes for IAs have been investigated by case-control association studies. The results of genetic association studies are modest because of small sample sizes. To date, no specific genes have been identified as responsible for IA development or rupture. Recent, large-scale genome-wide association (GWA) studies have revealed consistent and replicable genetic markers of several complex diseases such as coronary artery disease and type 2 diabetes. Although, thus far, no GWA studies have been performed for IAs, such a study may accomplish the breakthrough of genetic dissection of IAs. The identification of susceptible genes might lead to the understanding of the mechanism of IA formation or rupture and to novel therapeutic strategies.

Gene expression in a canine basilar artery vasospasm model: a genome-wide network-based analysis.

To investigate the changes of gene expression on the cerebral vasospasm after subarachnoid hemorrhage, we used genome-wide microarray for a canine double-hemorrhage model and analyzed the data by using a network-based analysis. Six dogs were assigned to two groups of three animals: control and hemorrhage. The effects were assessed by the changes in gene expressions in the artery 7 days after the first blood injection. Among 23,914 genes, 447 and 66 genes were up-regulated more than two- and fivefold, respectively, and 332 and 25 genes were down-regulated more than two- and fivefold, respectively. According to gene ontology, genes related to cell communication (P = 5.28E-10), host-pathogen interaction (7.65E-8), and defense-immunity protein activity (0.000183) were significantly overrepresented. The top high-level function for the merged network derived from the network-based analysis was cell signaling, revealing that the subgroup that regulates the quantity of Ca(2+) to have the strongest association significance (P = 4.75E-16). Canine microarray analysis followed by gene ontology profiling and connectivity analysis identified several functional groups and individual genes responding to cerebral vasospasm. Ca(2+) regulation may play a key role in these gene expression changes and may be involved in the pathogenesis of cerebral vasospasm.

Successful treatment of a blood blister-like aneurysm of the internal carotid artery by trapping with a high-flow bypass.

Treatment of blood blister-like aneurysms of the internal carotid artery (ICA) is difficult because the wall of the aneurysm is fragile and there is a high risk of rebleeding. There has been no consensus on the best way to treat these aneurysms. A 32-year-old woman presented with subarachnoid hemorrhage (SAH) caused by a ruptured blood blister-like aneurysm of the ICA. The site of the aneursym was clipped. Although angiography 1week after the operation showed that the aneurysm had been treated successfully, 3 weeks after the initial operation, the aneurysm was found to have recurred to the distal side. In a second operation, the aneurysm was successfully treated by trapping with a high-flow bypass. This case shows that clipping of the rupture site can be insufficient to treat blood blister-like aneurysm of the ICA causing SAH, even if the aneurysm seems to have resolved in follow-up angiographic studies. Trapping of the ICA with a bypass, if necessary a high-flow bypass, is recommended.

Nicardipine prolonged-release implants for preventing cerebral vasospasm after subarachnoid hemorrhage: effect and outcome in the first 100 patients.

Vasospasm following subarachnoid hemorrhage (SAH) remains difficult to prevent despite extensive investigative efforts. Nicardipine prolonged-release implants (NPRIs) have been used to prevent vasospasm in patients with SAH since October 1999. The present study analyzed the efficacy and safety of NPRIs in 100 patients with SAH and thick subarachnoid clot (mainly Fisher group 3) treated with NPRIs (diameter 2 mm, length 10 mm, containing 4 mg of nicardipine) during surgery after clipping of the aneurysm. The number and location of pellets depended on the amount and site of the subarachnoid clot on preoperative computed tomography and on the type of craniotomy. Two to 12 pellets were implanted in the cisterns of the internal carotid artery, middle cerebral artery, and/or anterior cerebral artery, where thick clots were present and vasospasm related to delayed ischemic neurological deficit (DIND) was highly likely. Only seven patients developed DIND and five patients suffered cerebral infarction. Angiography performed on days 7-12 revealed no vasospasm in any of the arteries close to the site of NPRI placement. NPRI placement can completely prevent vasospasm in arteries within the cisterns containing thick clots, but is less effective in remote locations.

Increased expression of ephrin A1 in brain arteriovenous malformation: DNA microarray analysis.

A number of previous studies have revealed the abnormal expression of various angiogenesis-related genes or products in brain arteriovenous malformation (AVM). To understand the molecular process of this disease, we analyzed gene expression profiles in brain AVM. Using a DNA microarray consisting of 17,086 genes, we identified differentially expressed genes in 5 brain AVMs from their draining veins, vessels retaining basic venous architecture. Not many genes were differentially expressed between the AVM nidus and the draining vein. When we applied an absolute cut-off value for normalized log2 (cy5/cy3 ratio) of 0.4, 19 genes were selected. Genes such as SOX8, TRIM2, FENA1 (ephrin A1), and AQP4 were upregulated, and genes such as I_1000105, KRT18, IGFBP7, EMILIN-2, and KRT14 were downregulated. Genes relating to angiogenesis, such as vascular endothelial growth factor and angiopoietin and other members of the ephrin family, were not differentiated. Among differentially expressed genes detected in this analysis, we focused on ephrin A1, a gene related to embryogenesis and angiogenesis. The expression of ephrin A1 was two and three to nine times higher than that of the draining vein and normal brain, respectively, using real-time reverse transcription-polymerase chain reaction. For the first time, here we report the increased expression of ephrin A1 in brain AVM, which may play an important role in the pathogenesis of AVM.

Using endothelial nitric oxide synthase gene polymorphisms to identify intracranial aneurysms more prone to rupture in Japanese patients.

OBJECT: Recent investigators found that the presence of three tandem polymorphisms of the endothelial nitric oxide synthase (eNOS) gene-promoter single nucleotide polymorphism (SNP) T-786C, intron-4 27-bp variable number of tandem repeats, and the G894T SNP in exon 7-was indicative of intracranial aneurysms more prone to rupture in a Caucasian patient sample. In the present study, the authors sought to determine whether the presence of these eNOS polymorphisms could indicate which Japanese patients with aneurysms were more endangered by a subarachnoid hemorrhage (SAH). METHODS: The three eNOS polymorphisms were genotyped in 297 patients with ruptured aneurysms (RAs), 108 patients with unruptured aneurysms (UAs), and 176 healthy volunteers by using polymerase chain reaction. The distribution of the variant alleles did not differ significantly (p > 0.05) between the RA group and the UA group. The frequency of the corresponding genotypes between the two groups and a haplotype analysis did not show any significant differences. Further comparisons of the RA and UA groups with the control group did not yield any significant allele or genotype frequency differences. Conclusions. These data show that the examined set of eNOS polymorphisms were not indicative of which Japanese patients with intracranial aneurysms would suffer an SAH. The presence of eNOS polymorphisms is not useful in identifying intracranial aneurysms that are more prone to rupture in a Japanese patient sample.

A haplotype spanning two genes, ELN and LIMK1, decreases their transcripts and confers susceptibility to intracranial aneurysms.

The rupture of an intracranial aneurysm (IA) results in subarachnoid hemorrhage, a catastrophic neurological condition with high morbidity and mortality. Following-up on our previous genome-wide linkage study in Japanese population, we extensively analyzed a 4.6 Mb linkage region around D7S2472 on 7q11 by genotyping 168 single nucleotide polymorphisms (SNPs). SNP association and window scan haplotype-based association studies revealed a susceptibility locus for IA on a single LD block covering the 3'-untranslated region (3'-UTR) of ELN and the entire region of LIMK1. An association study with 404 IA patients and 458 non-IA controls revealed that the ELN 3'-UTR G(+659)C SNP has the strongest association to IA (P=0.000002) and constitutes a tag-SNP for an at-risk haplotype, which contains two functional SNPs, the ELN 3'-UTR (+502) A insertion and the LIMK1 promoter C(-187)T SNP. These allelic and haplotype-based associations were confirmed in a Korean population. Ex vivo and in vitro analyses demonstrate that the functional impact of both SNPs is the decrease of transcript levels, either through accelerated ELN mRNA degradation or through decreased LIMK1 promoter activity. Elastin and LIMK1 protein are involved in the same actin depolymerization signaling pathway; therefore, these lines of evidence suggest a combined effect of the SNPs in the at-risk haplotype possibly by weakening the vascular wall and promoting the development of IA.