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1.
Genome Res ; 32(7): 1242-1253, 2022 07.
Article in English | MEDLINE | ID: mdl-35710300

ABSTRACT

Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within the HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or CTCF site (CTCF-5Δ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior/posterior limb expression patterns of SHH pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a CTCF site, and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9 INV/+) in mice that does not disrupt Hdac9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidates essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence. It suggests that SVs encompassing protein-coding sequences could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.


Subject(s)
Craniosynostoses , Histone Deacetylases , Nuclear Proteins , Polydactyly , Repressor Proteins , Twist-Related Protein 1 , Animals , Craniosynostoses/genetics , Gene Expression Regulation , Histone Deacetylases/genetics , Humans , Mice , Nuclear Proteins/genetics , Phenotype , Polydactyly/genetics , Repressor Proteins/genetics , Twist-Related Protein 1/genetics
2.
Am J Hum Genet ; 108(7): 1330-1341, 2021 07 01.
Article in English | MEDLINE | ID: mdl-34102099

ABSTRACT

Adaptor protein (AP) complexes mediate selective intracellular vesicular trafficking and polarized localization of somatodendritic proteins in neurons. Disease-causing alleles of various subunits of AP complexes have been implicated in several heritable human disorders, including intellectual disabilities (IDs). Here, we report two bi-allelic (c.737C>A [p.Pro246His] and c.1105A>G [p.Met369Val]) and eight de novo heterozygous variants (c.44G>A [p.Arg15Gln], c.103C>T [p.Arg35Trp], c.104G>A [p.Arg35Gln], c.229delC [p.Gln77Lys∗11], c.399_400del [p.Glu133Aspfs∗37], c.747G>T [p.Gln249His], c.928-2A>C [p.?], and c.2459C>G [p.Pro820Arg]) in AP1G1, encoding gamma-1 subunit of adaptor-related protein complex 1 (AP1γ1), associated with a neurodevelopmental disorder (NDD) characterized by mild to severe ID, epilepsy, and developmental delay in eleven families from different ethnicities. The AP1γ1-mediated adaptor complex is essential for the formation of clathrin-coated intracellular vesicles. In silico analysis and 3D protein modeling simulation predicted alteration of AP1γ1 protein folding for missense variants, which was consistent with the observed altered AP1γ1 levels in heterologous cells. Functional studies of the recessively inherited missense variants revealed no apparent impact on the interaction of AP1γ1 with other subunits of the AP-1 complex but rather showed to affect the endosome recycling pathway. Knocking out ap1g1 in zebrafish leads to severe morphological defect and lethality, which was significantly rescued by injection of wild-type AP1G1 mRNA and not by transcripts encoding the missense variants. Furthermore, microinjection of mRNAs with de novo missense variants in wild-type zebrafish resulted in severe developmental abnormalities and increased lethality. We conclude that de novo and bi-allelic variants in AP1G1 are associated with neurodevelopmental disorder in diverse populations.


Subject(s)
Adaptor Protein Complex 1/genetics , Developmental Disabilities/genetics , Epilepsy/genetics , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Alleles , Animals , DNA Mutational Analysis , Female , HEK293 Cells , Humans , Male , Pedigree , Rats , Zebrafish/genetics
3.
Haematologica ; 108(7): 1909-1919, 2023 Jul 01.
Article in English | MEDLINE | ID: mdl-36519321

ABSTRACT

Inherited thrombocytopenias (IT) are genetic diseases characterized by low platelet count, sometimes associated with congenital defects or a predisposition to develop additional conditions. Next-generation sequencing has substantially improved our knowledge of IT, with more than 40 genes identified so far, but obtaining a molecular diagnosis remains a challenge especially for patients with non-syndromic forms, having no clinical or functional phenotypes that raise suspicion about specific genes. We performed exome sequencing (ES) in a cohort of 116 IT patients (89 families), still undiagnosed after a previously validated phenotype-driven diagnostic algorithm including a targeted analysis of suspected genes. ES achieved a diagnostic yield of 36%, with a gain of 16% over the diagnostic algorithm. This can be explained by genetic heterogeneity and unspecific genotype-phenotype relationships that make the simultaneous analysis of all the genes, enabled by ES, the most reasonable strategy. Furthermore, ES disentangled situations that had been puzzling because of atypical inheritance, sex-related effects or false negative laboratory results. Finally, ES-based copy number variant analysis disclosed an unexpectedly high prevalence of RUNX1 deletions, predisposing to hematologic malignancies. Our findings demonstrate that ES, including copy number variant analysis, can substantially contribute to the diagnosis of IT and can solve diagnostic problems that would otherwise remain a challenge.


Subject(s)
Genetic Testing , Thrombocytopenia , Humans , Exome Sequencing , Phenotype , Genetic Testing/methods , Genotype , Thrombocytopenia/diagnosis , Thrombocytopenia/genetics
4.
Brain ; 145(7): 2313-2331, 2022 07 29.
Article in English | MEDLINE | ID: mdl-35786744

ABSTRACT

Epilepsy is one of the most frequent neurological diseases, with focal epilepsy accounting for the largest number of cases. The genetic alterations involved in focal epilepsy are far from being fully elucidated. Here, we show that defective lipid signalling caused by heterozygous ultra-rare variants in PIK3C2B, encoding for the class II phosphatidylinositol 3-kinase PI3K-C2ß, underlie focal epilepsy in humans. We demonstrate that patients' variants act as loss-of-function alleles, leading to impaired synthesis of the rare signalling lipid phosphatidylinositol 3,4-bisphosphate, resulting in mTORC1 hyperactivation. In vivo, mutant Pik3c2b alleles caused dose-dependent neuronal hyperexcitability and increased seizure susceptibility, indicating haploinsufficiency as a key driver of disease. Moreover, acute mTORC1 inhibition in mutant mice prevented experimentally induced seizures, providing a potential therapeutic option for a selective group of patients with focal epilepsy. Our findings reveal an unexpected role for class II PI3K-mediated lipid signalling in regulating mTORC1-dependent neuronal excitability in mice and humans.


Subject(s)
Class II Phosphatidylinositol 3-Kinases , Epilepsies, Partial , Animals , Class II Phosphatidylinositol 3-Kinases/genetics , Epilepsies, Partial/genetics , Humans , Lipids , Mechanistic Target of Rapamycin Complex 1 , Mice , Mutation/genetics , Phosphatidylinositol 3-Kinases/genetics , Seizures
5.
Am J Hum Genet ; 105(4): 689-705, 2019 10 03.
Article in English | MEDLINE | ID: mdl-31495489

ABSTRACT

Sphingomyelinases generate ceramide from sphingomyelin as a second messenger in intracellular signaling pathways involved in cell proliferation, differentiation, or apoptosis. Children from 12 unrelated families presented with microcephaly, simplified gyral pattern of the cortex, hypomyelination, cerebellar hypoplasia, congenital arthrogryposis, and early fetal/postnatal demise. Genomic analysis revealed bi-allelic loss-of-function variants in SMPD4, coding for the neutral sphingomyelinase-3 (nSMase-3/SMPD4). Overexpression of human Myc-tagged SMPD4 showed localization both to the outer nuclear envelope and the ER and additionally revealed interactions with several nuclear pore complex proteins by proteomics analysis. Fibroblasts from affected individuals showed ER cisternae abnormalities, suspected for increased autophagy, and were more susceptible to apoptosis under stress conditions, while treatment with siSMPD4 caused delayed cell cycle progression. Our data show that SMPD4 links homeostasis of membrane sphingolipids to cell fate by regulating the cross-talk between the ER and the outer nuclear envelope, while its loss reveals a pathogenic mechanism in microcephaly.


Subject(s)
Arthrogryposis/genetics , Microcephaly/genetics , Neurodevelopmental Disorders/genetics , Sphingomyelin Phosphodiesterase/genetics , Arthrogryposis/pathology , Cell Lineage , Child , Endoplasmic Reticulum/metabolism , Female , Gene Expression Profiling , HEK293 Cells , Humans , Male , Microcephaly/pathology , Mitosis , Neurodevelopmental Disorders/pathology , Pedigree , RNA Splicing
6.
J Cell Mol Med ; 25(5): 2459-2470, 2021 03.
Article in English | MEDLINE | ID: mdl-33476483

ABSTRACT

Autism spectrum disorder (ASD) is characterized by a complex polygenic background, but with the unique feature of a subset of cases (~15%-30%) presenting a rare large-effect variant. However, clinical interpretation in these cases is often complicated by incomplete penetrance, variable expressivity and different neurodevelopmental trajectories. NRXN1 intragenic deletions represent the prototype of such ASD-associated susceptibility variants. From chromosomal microarrays analysis of 104 ASD individuals, we identified an inherited NRXN1 deletion in a trio family. We carried out whole-exome sequencing and deep sequencing of mitochondrial DNA (mtDNA) in this family, to evaluate the burden of rare variants which may contribute to the phenotypic outcome in NRXN1 deletion carriers. We identified an increased burden of exonic rare variants in the ASD child compared to the unaffected NRXN1 deletion-transmitting mother, which remains significant if we restrict the analysis to potentially deleterious rare variants only (P = 6.07 × 10-5 ). We also detected significant interaction enrichment among genes with damaging variants in the proband, suggesting that additional rare variants in interacting genes collectively contribute to cross the liability threshold for ASD. Finally, the proband's mtDNA presented five low-level heteroplasmic mtDNA variants that were absent in the mother, and two maternally inherited variants with increased heteroplasmic load. This study underlines the importance of a comprehensive assessment of the genomic background in carriers of large-effect variants, as penetrance modulation by additional interacting rare variants to might represent a widespread mechanism in neurodevelopmental disorders.


Subject(s)
Autism Spectrum Disorder/etiology , Calcium-Binding Proteins/genetics , Genetic Predisposition to Disease , Heterozygote , Neural Cell Adhesion Molecules/genetics , Penetrance , Sequence Deletion , Adult , Autism Spectrum Disorder/diagnosis , Autism Spectrum Disorder/psychology , Comparative Genomic Hybridization , Computational Biology/methods , DNA Copy Number Variations , Exons , Female , Gene Expression Profiling , Gene Regulatory Networks , Genetic Association Studies , Genetic Variation , Genome, Mitochondrial , Genomics/methods , Humans , Infant , Male , Phenotype , Exome Sequencing
7.
Hum Genet ; 139(11): 1429-1441, 2020 Nov.
Article in English | MEDLINE | ID: mdl-32488467

ABSTRACT

Autozygosity-driven exome analysis has been shown effective for identification of genes underlying recessive diseases especially in countries of the so-called Greater Middle East (GME), where high consanguinity unravels the phenotypic effects of recessive alleles and large family sizes facilitate homozygosity mapping. In Italy, as in most European countries, consanguinity is estimated low. Nonetheless, consanguineous Italian families are not uncommon in publications of genetic findings and are often key to new associations of genes with rare diseases. We collected 52 patients from 47 consanguineous families with suspected recessive diseases, 29 originated in GME countries and 18 of Italian descent. We performed autozygosity-driven exome analysis by detecting long runs of homozygosity (ROHs > 1.5 Mb) and by prioritizing candidate clinical variants within. We identified a pathogenic synonymous variant that had been previously missed in NARS2 and we increased an initial high diagnostic rate (47%) to 55% by matchmaking our candidate genes and including in the analysis shorter ROHs that may also happen to be autozygous. GME and Italian families contributed to diagnostic yield comparably. We found no significant difference either in the extension of the autozygous genome, or in the distribution of candidate clinical variants between GME and Italian families, while we showed that the average autozygous genome was larger and the mean number of candidate clinical variants was significantly higher (p = 0.003) in mutation-positive than in mutation-negative individuals, suggesting that these features influence the likelihood that the disease is autozygosity-related. We highlight the utility of autozygosity-driven genomic analysis also in countries and/or communities, where consanguinity is not widespread cultural tradition.


Subject(s)
Genetic Testing/methods , Genome, Human/genetics , Chromosome Mapping/methods , Consanguinity , Exome/genetics , Family , Female , Genes, Recessive/genetics , Humans , Italy , Male , Middle East , Mutation/genetics , Pedigree
8.
Int J Mol Sci ; 21(22)2020 Nov 15.
Article in English | MEDLINE | ID: mdl-33203071

ABSTRACT

Schimke immuno-osseous dysplasia (SIOD) is a rare multisystemic disorder with a variable clinical expressivity caused by biallelic variants in SMARCAL1. A phenotype-genotype correlation has been attempted and variable expressivity of biallelic SMARCAL1 variants may be associated with environmental and genetic disturbances of gene expression. We describe two siblings born from consanguineous parents with a diagnosis of SIOD revealed by whole exome sequencing (WES). Results: A homozygous missense variant in the SMARCAL1 gene (c.1682G>A; p.Arg561His) was identified in both patients. Despite carrying the same variant, the two patients showed substantial renal and immunological phenotypic differences. We describe features not previously associated with SIOD-both patients had congenital anomalies of the kidneys and of the urinary tract and one of them succumbed to a classical type congenital mesoblastic nephroma. We performed an extensive characterization of the immunophenotype showing combined immunodeficiency characterized by a profound lymphopenia, lack of thymic output, defective IL-7Rα expression, and disturbed B plasma cells differentiation and immunoglobulin production in addition to an altered NK-cell phenotype and function. Conclusions: Overall, our results contribute to extending the phenotypic spectrum of features associated with SMARCAL1 mutations and to better characterizing the underlying immunologic disorder with critical implications for therapeutic and management strategies.


Subject(s)
Arteriosclerosis , DNA Helicases , Kidney , Killer Cells, Natural/immunology , Mutation, Missense , Nephroma, Mesoblastic , Nephrotic Syndrome , Osteochondrodysplasias , Phenotype , Primary Immunodeficiency Diseases , Pulmonary Embolism , Urinary Tract , Amino Acid Substitution , Arteriosclerosis/diagnostic imaging , Arteriosclerosis/genetics , Arteriosclerosis/immunology , DNA Helicases/genetics , DNA Helicases/immunology , Female , Humans , Interleukin-7 Receptor alpha Subunit/genetics , Interleukin-7 Receptor alpha Subunit/immunology , Kidney/abnormalities , Kidney/diagnostic imaging , Kidney/immunology , Male , Nephroma, Mesoblastic/diagnostic imaging , Nephroma, Mesoblastic/genetics , Nephroma, Mesoblastic/immunology , Nephrotic Syndrome/diagnostic imaging , Nephrotic Syndrome/genetics , Nephrotic Syndrome/immunology , Osteochondrodysplasias/diagnostic imaging , Osteochondrodysplasias/genetics , Osteochondrodysplasias/immunology , Primary Immunodeficiency Diseases/diagnostic imaging , Primary Immunodeficiency Diseases/genetics , Primary Immunodeficiency Diseases/immunology , Pulmonary Embolism/diagnostic imaging , Pulmonary Embolism/genetics , Pulmonary Embolism/immunology , Urinary Tract/abnormalities , Urinary Tract/diagnostic imaging , Urinary Tract/immunology , Whole Genome Sequencing
9.
Hum Genet ; 138(3): 257-269, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30806792

ABSTRACT

Rubinstein-Taybi syndrome (RSTS) is an autosomal-dominant neurodevelopmental disease affecting 1:125,000 newborns characterized by intellectual disability, growth retardation, facial dysmorphisms and skeletal abnormalities. RSTS is caused by mutations in genes encoding for writers of the epigenetic machinery: CREBBP (~ 60%) or its homologous EP300 (~ 10%). No causative mutation is identified in up to 30% of patients. We performed whole-exome sequencing (WES) on eight RSTS-like individuals who had normal high-resolution array CGH testing and were CREBBP- and EP300-mutation -negative, to identify the molecular cause. In four cases, we identified putatively causal variants in three genes (ASXL1, KMT2D and KMT2A) encoding members of the epigenetic machinery known to be associated with the Bohring-Opitz, Kabuki and Wiedemann-Steiner syndromes. Each variant is novel, de novo, fulfills the ACMG criteria and is predicted to result in loss-of-function leading to haploinsufficiency of the epi-gene. In two of the remaining cases, homozygous/compound heterozygous variants in XYLT2 and PLCB4 genes, respectively, associated with spondyloocular and auriculocondylar 2 syndromes and in the latter an additional candidate variant in XRN2, a gene yet unrelated to any disease, were detected, but their pathogenicity remains uncertain. These results underscore the broad clinical spectrum of Mendelian disorders of the epigenetic apparatus and the high rate of WES disclosure of the genetic basis in cases which may pose a challenge for phenotype encompassing distinct syndromes. The overlapping features of distinct intellectual disability syndromes reflect common pathogenic molecular mechanisms affecting the complex regulation of balance between open and closed chromatin.


Subject(s)
Exome Sequencing , Genetic Association Studies , Rubinstein-Taybi Syndrome/diagnosis , Rubinstein-Taybi Syndrome/genetics , CREB-Binding Protein/genetics , Child , Child, Preschool , Comparative Genomic Hybridization , E1A-Associated p300 Protein/genetics , Epigenesis, Genetic , Facies , Female , Humans , Infant , Infant, Newborn , Male , Mutation , Phenotype
10.
Am J Hum Genet ; 99(4): 831-845, 2016 Oct 06.
Article in English | MEDLINE | ID: mdl-27640307

ABSTRACT

ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane protein implicated in mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. We identified a recurrent de novo ATAD3A c.1582C>T (p.Arg528Trp) variant by whole-exome sequencing (WES) in five unrelated individuals with a core phenotype of global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. We also describe two families with biallelic variants in ATAD3A, including a homozygous variant in two siblings, and biallelic ATAD3A deletions mediated by nonallelic homologous recombination (NAHR) between ATAD3A and gene family members ATAD3B and ATAD3C. Tissue-specific overexpression of borR534W, the Drosophila mutation homologous to the human c.1582C>T (p.Arg528Trp) variant, resulted in a dramatic decrease in mitochondrial content, aberrant mitochondrial morphology, and increased autophagy. Homozygous null bor larvae showed a significant decrease of mitochondria, while overexpression of borWT resulted in larger, elongated mitochondria. Finally, fibroblasts of an affected individual exhibited increased mitophagy. We conclude that the p.Arg528Trp variant functions through a dominant-negative mechanism that results in small mitochondria that trigger mitophagy, resulting in a reduction in mitochondrial content. ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations.


Subject(s)
Adenosine Triphosphatases/genetics , Alleles , Membrane Proteins/genetics , Mitochondria/metabolism , Mitochondria/pathology , Mitochondrial Proteins/genetics , Mutation , Nervous System Diseases/genetics , ATPases Associated with Diverse Cellular Activities , Adult , Animals , Axons/pathology , Cardiomyopathies/genetics , Child , Child, Preschool , DNA Copy Number Variations/genetics , Developmental Disabilities/genetics , Drosophila melanogaster/genetics , Female , Fibroblasts , Homozygote , Humans , Infant , Infant, Newborn , Male , Muscle Hypotonia/genetics , Muscles/pathology , Nervous System Diseases/metabolism , Nervous System Diseases/pathology , Neurons/pathology , Optic Atrophy/genetics , Phenotype , Polymorphism, Single Nucleotide/genetics , Syndrome , Young Adult
11.
Am J Med Genet A ; 176(11): 2395-2403, 2018 11.
Article in English | MEDLINE | ID: mdl-30244536

ABSTRACT

The application of array-based comparative genomic hybridization and next-generation sequencing has identified many chromosomal microdeletions and microduplications in patients with different pathological phenotypes. Different copy number variations are described within the short arm of chromosome 18 in patients with skin diseases. In particular, full or partial monosomy 18p has also been associated with keratosis pilaris. Here, for the first time, we report a young male patient with intellectual disability, diabetes mellitus (type I), and keratosis pilaris, who exhibited a de novo 45-kb microduplication of exons 4-22 of LAMA1, located at 18p11.31, and a 432-kb 18p11.32 microduplication of paternal origin containing the genes METTL4, NDC80, and CBX3P2 and exons 1-15 of the SMCHD1 gene. The microduplication of LAMA1 was identified in skin fibroblasts but not in lymphocytes, whereas the larger microduplication was present in both tissues. We propose LAMA1 as a novel candidate gene for keratosis pilaris. Although inherited from a healthy father, the 18p11.32 microduplication, which included relevant genes, could also contribute to phenotype manifestation.


Subject(s)
Abnormalities, Multiple/genetics , Chromosome Duplication/genetics , Darier Disease/complications , Darier Disease/genetics , Eyebrows/abnormalities , Intellectual Disability/complications , Intellectual Disability/genetics , Laminin/genetics , Mosaicism , Adolescent , Child , Child, Preschool , Comparative Genomic Hybridization , Fibroblasts/metabolism , Gene Expression Regulation , Humans , Infant , Infant, Newborn , Male , Skin/pathology
12.
Hum Mol Genet ; 24(10): 2746-56, 2015 May 15.
Article in English | MEDLINE | ID: mdl-25637521

ABSTRACT

Adult-onset autosomal dominant leukodystrophy (ADLD) is a slowly progressive neurological disorder characterized by autonomic dysfunction, followed by cerebellar and pyramidal features. ADLD is caused by duplication of the lamin B1 gene (LMNB1), which leads to its increased expression. The molecular pathways involved in the disease are still poorly understood. Hence, we analyzed global gene expression in fibroblasts and whole blood of LMNB1 duplication carriers and used Gene Set Enrichment Analysis to explore their gene signatures. We found that LMNB1 duplication is associated with dysregulation of genes involved in the immune system, neuronal and skeletal development. Genes with an altered transcriptional profile clustered in specific genomic regions. Among the dysregulated genes, we further studied the role of RAVER2, which we found to be overexpressed at mRNA and protein level. RAVER2 encodes a putative trans regulator of the splicing repressor polypyrimidine tract binding protein (PTB) and is likely implicated in alternative splicing regulation. Functional studies demonstrated an abnormal splicing pattern of several PTB-target genes and of the myelin protein gene PLP1, previously demonstrated to be involved in ADLD. Mutant mice with different lamin B1 expression levels confirmed that Raver2 expression is dependent on lamin B1 in neural tissue and determines an altered splicing pattern of PTB-target genes and Plp1. Overall our results demonstrate that deregulation of lamin B1 expression induces modified splicing of several genes, likely driven by raver-2 overexpression, and suggest that an alteration of mRNA processing could be a pathogenic mechanism in ADLD.


Subject(s)
Alternative Splicing , Heterogeneous-Nuclear Ribonucleoproteins/genetics , Lamin Type B/genetics , Pelizaeus-Merzbacher Disease/genetics , Animals , Fibroblasts/metabolism , Gene Duplication , Gene Expression Profiling , Humans , Leukocytes/metabolism , Mice , Mice, Knockout , Pelizaeus-Merzbacher Disease/metabolism , Up-Regulation
13.
Hum Mutat ; 37(2): 175-83, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26486927

ABSTRACT

Rubinstein-Taybi syndrome (RSTS) is a rare congenital neurodevelopmental disorder characterized by growth deficiency, skeletal abnormalities, dysmorphic features, and intellectual disability. Causative mutations in CREBBP and EP300 genes have been identified in ∼55% and ∼8% of affected individuals. To date, only 28 EP300 alterations in 29 RSTS clinically described patients have been reported. EP300 analysis of 22 CREBBP-negative RSTS patients from our cohort led us to identify six novel mutations: a 376-kb deletion depleting EP300 gene; an exons 17-19 deletion (c.(3141+1_3142-1)_(3590+1_3591-1)del/p.(Ile1047Serfs*30)); two stop mutations, (c.3829A>T/p.(Lys1277*) and c.4585C>T/p.(Arg1529*)); a splicing mutation (c.1878-12A>G/p.(Ala627Glnfs*11)), and a duplication (c.4640dupA/p.(Asn1547Lysfs*3)). All EP300-mutated individuals show a mild RSTS phenotype and peculiar findings including maternal gestosis, skin manifestation, especially nevi or keloids, back malformations, and a behavior predisposing to anxiety. Furthermore, the patient carrying the complete EP300 deletion does not show a markedly severe clinical picture, even if a more composite phenotype was noticed. By characterizing six novel EP300-mutated patients, this study provides further insights into the EP300-specific clinical presentation and expands the mutational repertoire including the first case of a whole gene deletion. These new data will enhance EP300-mutated cases identification highlighting distinctive features and will improve the clinical practice allowing a better genotype-phenotype correlation.


Subject(s)
E1A-Associated p300 Protein/genetics , Genome, Human , Mutation , Rubinstein-Taybi Syndrome/genetics , Adolescent , CREB-Binding Protein/genetics , Child , Female , Gene Expression , Genetic Association Studies , Genetic Variation , Humans , In Situ Hybridization, Fluorescence , Male , Phenotype , Rubinstein-Taybi Syndrome/pathology , Sequence Analysis, DNA , Young Adult
14.
Hum Mol Genet ; 23(13): 3607-17, 2014 Jul 01.
Article in English | MEDLINE | ID: mdl-24556213

ABSTRACT

Loss-of-function mutations in PAK3 contribute to non-syndromic X-linked intellectual disability (NS-XLID) by affecting dendritic spine density and morphology. Linkage analysis in a three-generation family with affected males showing ID, agenesis of corpus callosum, cerebellar hypoplasia, microcephaly and ichthyosis, revealed a candidate disease locus in Xq21.33q24 encompassing over 280 genes. Subsequent to sequencing all coding exons of the X chromosome, we identified a single novel variant within the linkage region, affecting a conserved codon of PAK3. Biochemical studies showed that, similar to previous NS-XLID-associated lesions, the predicted amino acid substitution (Lys389Asn) abolished the kinase activity of PAK3. In addition, the introduced residue conferred a dominant-negative function to the protein that drives the syndromic phenotype. Using a combination of in vitro and in vivo studies in zebrafish embryos, we show that PAK3(N389) escapes its physiologic degradation and is able to perturb MAPK signaling via an uncontrolled kinase-independent function, which in turn leads to alterations of cerebral and craniofacial structures in vivo. Our data expand the spectrum of phenotypes associated with PAK3 mutations, characterize a novel mechanism resulting in a dual molecular effect of the same mutation with a complex PAK3 functional deregulation and provide evidence for a direct functional impact of aberrant PAK3 function on MAPK signaling.


Subject(s)
Mitogen-Activated Protein Kinases/metabolism , p21-Activated Kinases/genetics , ras Proteins/metabolism , Animals , Exons/genetics , Humans , Karyotyping , Mitogen-Activated Protein Kinases/genetics , Mutation , Signal Transduction/genetics , Signal Transduction/physiology , ras Proteins/genetics
16.
Am J Med Genet A ; 170(12): 3258-3264, 2016 12.
Article in English | MEDLINE | ID: mdl-27612164

ABSTRACT

Simpson-Golabi-Behmel syndrome (SGBS) is an overgrowth syndrome and it is usually diagnosed postnatally, on the basis of phenotype. Prenatal ultrasonography may show fetal alterations, but they are not pathognomonic and most of them are frequently detectable only from the 20th week of gestation. Nevertheless, early diagnosis is important to avoid neonatal complications and make timely and informed decisions about the pregnancy. We report on four fetuses from two unrelated families, in whom the application of whole exome sequencing and array-CGH allowed the identification of GPC3 alterations causing SGBS. The careful follow up of pregnancies and more sophisticated analysis of ultrasound findings led to the identification of early prenatal alterations, which will improve the antenatal diagnosis of SGBS. © 2016 Wiley Periodicals, Inc.


Subject(s)
Arrhythmias, Cardiac/diagnosis , Genetic Diseases, X-Linked/diagnosis , Gigantism/diagnosis , Heart Defects, Congenital/diagnosis , Intellectual Disability/diagnosis , Phenotype , Abortion, Induced , Adult , Arrhythmias, Cardiac/genetics , Autopsy , Comparative Genomic Hybridization , Exome , Female , Fetus , Genes, X-Linked , Genetic Diseases, X-Linked/genetics , Gigantism/genetics , Heart Defects, Congenital/genetics , High-Throughput Nucleotide Sequencing , Humans , Intellectual Disability/genetics , Male , Mutation , Pedigree , Prenatal Diagnosis , Ultrasonography, Prenatal
17.
Am J Med Genet A ; 170A(1): 162-9, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26333654

ABSTRACT

Temple syndrome (TS) is caused by abnormal expression of genes at the imprinted locus 14q32. A subset of TS patients carry 14q32 deletions of paternal origin. We aimed to define possible genotype-phenotype correlations and to highlight the prevalence of thyroid dysfunction, which is a previously unreported feature of TS. We described four new patients who carry deletions of paternal origin at 14q32 detected by array-CGH and reviewed nine patients reported in the medical literature. We compared clinical features with respect to deletion size and position. Expression of DLK1 is altered in all the patients with TS, but intellectual disability (ID) is present only in patients with larger deletions extending proximally to the imprinted locus. This study led to the identification of an ID "critical region" containing four annotated genes including YY1 as the strongest candidate. Furthermore, we described three patients with thyroid dysfunction, which progressed to papillary carcinoma at a very young age in two of them. We conclude that DLK1 loss of function is likely to be responsible for the core features of TS, while haploinsufficiency of a gene outside the imprinted region causes ID. Thyroid cancer may be an unrecognized feature and monitoring for thyroid dysfunction should thus be considered in TS patients.


Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 14/genetics , Hallux/abnormalities , Intellectual Disability/genetics , Nails, Malformed/genetics , Thumb/abnormalities , Thyroid Neoplasms/etiology , Adolescent , Adult , Comparative Genomic Hybridization , Female , Genotype , Hallux/pathology , Humans , Intellectual Disability/complications , Intellectual Disability/pathology , Male , Nails, Malformed/complications , Nails, Malformed/pathology , Phenotype , Risk Factors , Thumb/pathology , Thyroid Neoplasms/pathology , Young Adult
19.
Am J Hum Genet ; 88(1): 115-20, 2011 Jan 07.
Article in English | MEDLINE | ID: mdl-21211618

ABSTRACT

THC2, an autosomal-dominant thrombocytopenia described so far in only two families, has been ascribed to mutations in MASTL or ACBD5. Here, we show that ANKRD26, another gene within the THC2 locus, and neither MASTL nor ACBD5, is mutated in eight unrelated families. ANKRD26 was also found to be mutated in the family previously reported to have an ACBD5 mutation. We identified six different ANKRD26 mutations, which were clustered in a highly conserved 19 bp sequence located in the 5' untranslated region. Mutations were not detected in 500 controls and are absent from the 1000 Genomes database. Available data from an animal model and Dr. Watson's genome give evidence against haploinsufficiency as the pathogenetic mechanism for ANKRD26-mediated thrombocytopenia. The luciferase reporter assay suggests that these 5' UTR mutations might enhance ANKRD26 expression. ANKRD26 is the ancestor of a family of primate-specific genes termed POTE, which have been recently identified as a family of proapoptotic proteins. Dysregulation of apoptosis might therefore be the pathogenetic mechanism, as demonstrated for another thrombocytopenia, THC4. Further investigation is needed to provide evidence supporting this hypothesis.


Subject(s)
Ankyrin Repeat/genetics , Genes, Dominant , Mutation , Base Sequence , Chromosome Breakage , Chromosome Disorders/genetics , Conserved Sequence/genetics , Female , Genetic Loci , Haploinsufficiency , Humans , Male , Molecular Sequence Data , Pedigree , Thrombocytopenia/congenital , Thrombocytopenia/genetics
20.
Haematologica ; 99(8): 1387-94, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24763399

ABSTRACT

Pregnancy in women with inherited thrombocytopenias is a major matter of concern as both the mothers and the newborns are potentially at risk of bleeding. However, medical management of this condition cannot be based on evidence because of the lack of consistent information in the literature. To advance knowledge on this matter, we performed a multicentric, retrospective study evaluating 339 pregnancies in 181 women with 13 different forms of inherited thrombocytopenia. Neither the degree of thrombocytopenia nor the severity of bleeding tendency worsened during pregnancy and the course of pregnancy did not differ from that of healthy subjects in terms of miscarriages, fetal bleeding and pre-term births. The degree of thrombocytopenia in the babies was similar to that in the mother. Only 7 of 156 affected newborns had delivery-related bleeding, but 2 of them died of cerebral hemorrhage. The frequency of delivery-related maternal bleeding ranged from 6.8% to 14.2% depending on the definition of abnormal blood loss, suggesting that the risk of abnormal blood loss was increased with respect to the general population. However, no mother died or had to undergo hysterectomy to arrest bleeding. The search for parameters predicting delivery-related bleeding in the mother suggested that hemorrhages requiring blood transfusion were more frequent in women with history of severe bleedings before pregnancy and with platelet count at delivery below 50 × 10(9)/L.


Subject(s)
Pregnancy Complications, Hematologic/diagnosis , Pregnancy Complications, Hematologic/epidemiology , Thrombocytopenia/diagnosis , Thrombocytopenia/epidemiology , Adult , Female , Humans , Infant, Newborn , Pregnancy , Pregnancy Complications, Hematologic/genetics , Retrospective Studies , Thrombocytopenia/genetics , Young Adult
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