Comprehensive genetic and epigenetic analysis of sporadic meningioma for macro-mutations on 22q and micro-mutations within the NF2 locus

BACKGROUND: Meningiomas are the most common intracranial neoplasias, representing a clinically and histopathologically heterogeneous group of tumors. The neurofibromatosis type 2 (NF2) tumor suppressor is the only gene known to be frequently involved in early development of meningiomas. The objective of this study was to identify genetic and/or epigenetic factors contributing to the development of these tumors. A large set of sporadic meningiomas were analyzed for presence of 22q macro-mutations using array-CGH in order to identify tumors carrying gene dosage aberrations not encompassing NF2. The NF2 locus was also comprehensively studied for point mutations within coding and conserved non-coding sequences. Furthermore, CpG methylation within the NF2 promoter region was thoroughly analyzed. RESULTS: Monosomy 22 was the predominant finding, detected in 47% of meningiomas. Thirteen percent of the tumors contained interstitial/terminal deletions and gains, present singly or in combinations. We defined at least two minimal overlapping regions outside the NF2 locus that are small enough (~550 kb and ~250 kb) to allow analysis of a limited number of candidate genes. Bialleinactivationo the NF2 gne was detected in 36% of meningiomas. Among the monosomy 22 cases, no additional NF2 mutations could be identified in 35% (17 out of 49) of tumors. Furthermore, the majority of tumors (9 out of 12) with interstitial/terminal deletions did not have any detectable NF2 mutations. Methylation within the NF2 promoter region was only identified at a single CpG site in one tumor sample. CONCLUSION: We confirmed previous findings of pronounced differences in mutation frequency between different histopathological subtypes. There is a higher frequency of biallelic NF2 inactivation in fibroblastic (52%) compared to meningothelial (18%) tumors. The presence of macro-mutations on 22q also shows marked differences between fibroblastic (86%) and meningothelial (39%) subtypes. Thus, inactivation of NF2, often combined with the presence of macro-mutation on 22q, is likely not as important for the development of the meningothelial subtype, as opposed to the fibroblastic form. Analysis of 40 CpG sites distributed within 750 bp of the promoter region suggests that NF2 promoter methylation does not play a major role in meningioma development

Clinical and genetic investigation of hypochondroplasia and dyschondrosteosis

Linear body growth is a multifactorial trait influenced by many environmental and intrinsic factors. Among the intrinsic determinants of body height, genetic and endocrine factors are considered to be the most important. Children with short stature are usually referred to paediatric endocrinology clinics and a significant proportion of these suffer from skeletal dysplasias. Hypochondroplasia and dyschondrosteosis (Léri-Weill syndrome) are characterised by disproportionate short stature. The phenotype in hypochondroplasia is mainly characterised by rhizomelic (proximal) shortening of the limbs, whereas dyschondrosteosis confers mesomelic short stature (shortening of the middle segment). An aberration of the forearm, called Madelung deformity, is a frequent feature of dyschondrosteosis. In both hypochondroplasia and dyschondrosteosis, the phenotype varies from moderate to severe short stature and body disproportion and it is usually mild in early childhood, which causes diagnostic difficulties. In these cases, molecular genetic analysis is an important diagnostic tool. Point mutations in the FGFR3 (fibroblast growth factor receptor 3) gene, causing the Asn54OLys substitution, have been described in 40-70% of hypochondroplasia cases. Haploinsufficiency of the SHOX (short stature homeobox-containing) gene due to deletions or point mutations has been found in dyschondrosteosis and in some cases of idiopathic short stature. In this study, the frequency of the Asn540Lys mutation was determined in 30 Swedish probands with clinically and radiologically confirmed hypochondroplasia. Nine unrelated individuals were found to be heterozygous for the Asn54OLys mutation, whereas one proband in a familial case with hypochondroplasia was found to have a novel mutation IIe538Val. Overall, FGFR3 mutations were found in only 33% of hypochondroplasia probands. In a single three-generation hypochondroplasia family, we excluded involvement of FGFR3, which supports the genetic heterogeneity in hypochondroplasia. The hypochondroplasia individuals without the Asn540Lys mutation were less disproportionate, suggesting that these cases might have a phenotype resembling idiopathic short stature or mild dyschondrosteosis. Considering the above-mentioned findings and clinical overlap between hypochondroplasia and dyschondrosteosis, we analysed 18 probands with hypochondroplasia (negative for the known FGFR3 mutations) and 32 probands with dyschondrosteosis, for mutations in the SHOX gene. In dyschondrosteosis group, 16 unrelated families (50%) had SHOX gene deletions, whereas 9 probands (28%) carried point mutations/minute deletions in the SHOX gene. In total 78% of the probands with dyschondrosteosis had mutations in the SHOX gene and seven mutations were previously not described. All novel mutations segregated with the dyschondrosteosis phenotype in familial cases and were not found in 90 unrelated, unaffected individuals, suggesting that these mutations are pathogenic. No SHOX mutations were found in hypochondroplasia individuals lacking known FGFR3 gene mutations, which suggests that SHOX gene defects are not involved in the pathogenesis of hypochondroplasia. Considering a high percentage of SHOX gene mutations in dyschondrosteosis and difficulties in differential diagnosis between hypochondroplasia and dyschondrosteosis, especially in children, molecular analysis of SHOX gene could be an important diagnostic tool. Seven sporadic cases with isolated Madelung deformity were also examined and no SHOX gene mutations that could be considered pathogenic were identified. Thus, it is less likely that mutations in the SHOX gene are involved in the development of isolated Madelung deformity

Deconvolution of seed and RNA-binding protein crosstalk in RNAi-based functional genomics

RNA interference (RNAi) is a major, powerful platform for gene perturbations, but is restricted by off-target mechanisms. Communication between RNAs, small RNAs, and RNA-binding proteins (RBPs) is a pervasive feature of cellular RNA networks. We present a crosstalk scenario, designated as crosstalk with endogenous RBPs' (ceRBP), in which small interfering RNAs or microRNAs with seed sequences that overlap RBP motifs have extended biological effects by perturbing endogenous RBP activity. Systematic analysis of small interfering RNA (siRNA) off-target data and genome-wide RNAi cancer lethality screens using 501 human cancer cell lines, a cancer dependency map, identified that seed-to-RBP crosstalk is widespread, contributes to off-target activity, and affects RNAi performance. Specifically, deconvolution of the interactions between gene knockdown and seed-mediated silencing effects in the cancer dependency map showed widespread contributions of seed-to-RBP crosstalk to growth-phenotype modulation. These findings suggest a novel aspect of microRNA biology and offer a basis for improvement of RNAi agents and RNAi-based functional genomics.National Institutes of Health (U.S.) (Grant R01-GM034277)National Institutes of Health (U.S.) (Grant R01-CA133404)National Cancer Institute (U.S.) (Grant P30-CA14051

Data from: Mutations in COL1A1 and COL1A2 and dental aberrations in children and adolescents with osteogenesis imperfecta - a retrospective cohort study

Osteogenesis imperfecta (OI) is a heterogeneous group of disorders of connective tissue, caused mainly by mutations in the collagen I genes (COL1A1 and COL1A2). Dentinogenesis imperfecta (DGI) and other dental aberrations are common features of OI. We investigated the association between collagen I mutations and DGI, taurodontism, and retention of permanent second molars in a retrospective cohort of 152 unrelated children and adolescents with OI. The clinical examination included radiographic evaluations. Teeth from 81 individuals were available for histopathological evaluation. COL1A1/2 mutations were found in 104 individuals by nucleotide sequencing. DGI was diagnosed clinically and radiographically in 29% of the individuals (44/152) and through isolated histological findings in another 19% (29/152). In the individuals with a COL1A1 mutation, 70% (7/10) of those with a glycine substitution located C-terminal of p.Gly305 exhibited DGI in both dentitions while no individual (0/7) with a mutation N-terminal of this point exhibited DGI in either dentition (p = 0.01). In the individuals with a COL1A2 mutation, 80% (8/10) of those with a glycine substitution located C terminal of p.Gly211 exhibited DGI in both dentitions while no individual (0/5) with a mutation N-terminal of this point (p = 0.007) exhibited DGI in either dentition. DGI was restricted to the deciduous dentition in 20 individuals. Seventeen had missense mutations where glycine to serine was the most prevalent substitution (53%). Taurodontism occurred in 18% and retention of permanent second molars in 31% of the adolescents. Dental aberrations are strongly associated with qualitatively changed collagen I. The varying expressivity of DGI is related to the location of the collagen I mutation. Genotype information may be helpful in identifying individuals with OI who have an increased risk of dental aberrations

Mutations in COL1A1 and COL1A2 and dental aberrations in children and adolescents with osteogenesis imperfecta - A retrospective cohort study

Osteogenesis imperfecta (OI) is a heterogeneous group of disorders of connective tissue, caused mainly by mutations in the collagen I genes (COL1A1 and COL1A2). Dentinogenesis imperfecta (DGI) and other dental aberrations are common features of OI. We investigated the association between collagen I mutations and DGI, taurodontism, and retention of permanent second molars in a retrospective cohort of 152 unrelated children and adolescents with OI. The clinical examination included radiographic evaluations. Teeth from 81 individuals were available for histopathological evaluation. COL1A1/2 mutations were found in 104 individuals by nucleotide sequencing. DGI was diagnosed clinically and radiographically in 29% of the individuals (44/152) and through isolated histological findings in another 19% (29/152). In the individuals with a COL1A1 mutation, 70% (7/10) of those with a glycine substitution located C-terminal of p. Gly305 exhibited DGI in both dentitions while no individual (0/7) with a mutation N-terminal of this point exhibited DGI in either dentition (p = 0.01). In the individuals with a COL1A2 mutation, 80% (8/10) of those with a glycine substitution located C terminal of p. Gly211 exhibited DGI in both dentitions while no individual (0/5) with a mutation N-terminal of this point (p = 0.007) exhibited DGI in either dentition. DGI was restricted to the deciduous dentition in 20 individuals. Seventeen had missense mutations where glycine to serine was the most prevalent substitution (53%). Taurodontism occurred in 18% and retention of permanent second molars in 31% of the adolescents. Dental aberrations are strongly associated with qualitatively changed collagen I. The varying expressivity of DGI is related to the location of the collagen I mutation. Genotype information may be helpful in identifying individuals with OI who have an increased risk of dental aberrations

A Case with Bladder Exstrophy and Unbalanced X Chromosome Rearrangement

Introduction Bladder exstrophy is a rare congenital malformation of the bladder and is believed to be a complex disorder with genetic and environmental background. We describe a young adult female with an isolated bladder exstrophy and with an X chromosome aberration. Patients and Methods Karyotyping identified an X chromosome rearrangement that was further characterized with array comparative genomic hybridization (CGH) and confirmed by multiplex ligation-dependent probe amplification and fluorescence in situ hybridization (FISH) analysis. Results The identified X chromosome rearrangement in our index patient consists of a gain of chromosomal material in region Xq26.3-> qter and loss in region Xp22.12->pter. This aberration was also carried by her mother and sister, none with bladder exstrophy. All three have a disproportionate short stature, as expected due to the deletion of one of the copies of the SHOX gene on Xp22.3. X-inactivation studies revealed a complete skewed inactivation pattern in carriers. Crossover events in the maternal germline furthermore resulted in different genetic material on the rearranged X chromosome between the index patient and her sister. Conclusion Our findings suggest an X-linked genetic risk factor for bladder exstrophy

Extending the phenotype of BMPER-related skeletal dysplasias to ischiospinal dysostosis

Ischiospinal dysostosis (ISD) is a polytopic dysostosis characterized by ischial hypoplasia, multiple segmental anomalies of the cervicothoracic spine, hypoplasia of the lumbrosacral spine and occasionally associated with nephroblastomatosis. ISD is similar to, but milder than the lethal/semilethal condition termed diaphanospondylodysostosis (DSD), which is associated with homozygous or compound heterozygous mutations of bone morphogenetic protein-binding endothelial regulator protein (BMPER) gene. Here we report for the first time biallelic BMPER mutations in two patients with ISD, neither of whom had renal abnormalities. Our data supports and further extends the phenotypic variability of BMPER-related skeletal disorders.Funding Agencies|Stockholm County Council; Karolinska Institutet; Kronprinsessan Lovisas; Axel Tiellmans Minnesfond Foundation; Samariten Foundation; Sallskapet Barnavard Foundation; Promobilia Foundations; Genome Technology to Business Translation Program of the National Research Foundation (NRF) - Ministry of Science, ICT &amp; Future Planning of the government of Republic of Korea [NRF-2014M3C9A2064684]</p

Extending the phenotype of BMPER-related skeletal dysplasias to ischiospinal dysostosis

Ischiospinal dysostosis (ISD) is a polytopic dysostosis characterized by ischial hypoplasia, multiple segmental anomalies of the cervicothoracic spine, hypoplasia of the lumbrosacral spine and occasionally associated with nephroblastomatosis. ISD is similar to, but milder than the lethal/semilethal condition termed diaphanospondylodysostosis (DSD), which is associated with homozygous or compound heterozygous mutations of bone morphogenetic protein-binding endothelial regulator protein (BMPER) gene. Here we report for the first time biallelic BMPER mutations in two patients with ISD, neither of whom had renal abnormalities. Our data supports and further extends the phenotypic variability of BMPER-related skeletal disorders.Funding Agencies|Stockholm County Council; Karolinska Institutet; Kronprinsessan Lovisas; Axel Tiellmans Minnesfond Foundation; Samariten Foundation; Sallskapet Barnavard Foundation; Promobilia Foundations; Genome Technology to Business Translation Program of the National Research Foundation (NRF) - Ministry of Science, ICT &amp; Future Planning of the government of Republic of Korea [NRF-2014M3C9A2064684]</p