Array CGH Analysis of Paired Blood and Tumor Samples from Patients with Sporadic Wilms Tumor

Submitted by sandra infurna ([email protected]) on 2016-03-01T16:49:50Z No. of bitstreams: 1 fernando2_vargas_etal_IOC_2015.pdf: 477665 bytes, checksum: 7b0ca95990e0ab5295b7e7bec530658b (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-03-01T17:11:58Z (GMT) No. of bitstreams: 1 fernando2_vargas_etal_IOC_2015.pdf: 477665 bytes, checksum: 7b0ca95990e0ab5295b7e7bec530658b (MD5)Made available in DSpace on 2016-03-01T17:11:58Z (GMT). No. of bitstreams: 1 fernando2_vargas_etal_IOC_2015.pdf: 477665 bytes, checksum: 7b0ca95990e0ab5295b7e7bec530658b (MD5) Previous issue date: 2015Instituto Nacional de Câncer. Divisão de Genética. Rio de Janeiro, RJ, Brasil.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain / CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain / CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain.Instituto Nacional de Câncer. Divisão de Patologia. Rio de Janeiro, RJ, Brasil.GT-CSGP Working Group.Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Hospital Universitario La Paz. Section of Clinical Genetics, . Madrid, Spain.CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain / Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Hospital Universitario La Paz. Section of Clinical Genetics, . Madrid, Spain.Universidade Federal do Rio de Janeiro. Departamento de Genética. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Epidemiologia de Malformações Congênitas. Rio de Janeiro, RJ, Brasil.Instituto Nacional de Câncer. Divisão de Genética. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Departamento de Genética. Rio de Janeiro, RJ, Brasil.Hospital Universitario La Paz. Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ. Section of Functional and Structural Genomics. Madrid, Spain / CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain.Wilms tumor (WT), the most common cancer of the kidney in infants and children, has a complex etiology that is still poorly understood. Identification of genomic copy number variants (CNV) in tumor genomes provides a better understanding of cancer development which may be useful for diagnosis and therapeutic targets. In paired blood and tumor DNA samples from 14 patients with sporadic WT, analyzed by aCGH, 22% of chromosome abnormalities were novel. All constitutional alterations identified in blood were segmental (in 28.6% of patients) and were also present in the paired tumor samples. Two segmental gains (2p21 and 20q13.3) and one loss (19q13.31) present in blood had not been previously described in WT. We also describe, for the first time, a small, constitutive partial gain of 3p22.1 comprising 2 exons of CTNNB1, a gene associated to WT. Among somatic alterations, novel structural chromosomal abnormalities were found, like gain of 19p13.3 and 20p12.3, and losses of 2p16.1-p15, 4q32.5-q35.1, 4q35.2-q28.1 and 19p13.3. Candidate genes included in these regions might be constitutively (SIX3, SALL4) or somatically (NEK1, PIAS4, BMP2) operational in the development and progression of WT. To our knowledge this is the first report of CNV in paired blood and tumor samples in sporadic WT

Variability in Phelan-McDermid Syndrome in a Cohort of 210 Individuals

Phelan-McDermid syndrome (PMS, OMIM# 606232) results from either different rearrangements at the distal region of the long arm of chromosome 22 (22q13.3) or pathogenic sequence variants in the SHANK3 gene. SHANK3 codes for a structural protein that plays a central role in the formation of the postsynaptic terminals and the maintenance of synaptic structures. Clinically, patients with PMS often present with global developmental delay, absent or severely delayed speech, neonatal hypotonia, minor dysmorphic features, and autism spectrum disorders (ASD), among other findings. Here, we describe a cohort of 210 patients with genetically confirmed PMS. We observed multiple variant types, including a significant number of small deletions

The clinical and molecular spectrum of QRICH1 associated neurodevelopmental disorder

International audienceDe novo variants in QRICH1 (Glutamine-rich protein 1) has recently been reported in 11 individuals with intellectual disability (ID). The function of QRICH1 is largely unknown but it is likely to play a key role in the unfolded response of endoplasmic reticulum stress through transcriptional control of proteostasis. In this study, we present 27 additional individuals and delineate the clinical and molecular spectrum of the individuals (n = 38) with QRICH1 variants. The main clinical features were mild to moderate developmental delay/ID (71%), nonspecific facial dysmorphism (92%) and hypotonia (39%). Additional findings included poor weight gain (29%), short stature (29%), autism spectrum disorder (29%), seizures (24%) and scoliosis (18%). Minor structural brain abnormalities were reported in 52% of the individuals with brain imaging. Truncating or splice variants were found in 28 individuals and 10 had missense variants. Four variants were inherited from mildly affected parents. This study confirms that heterozygous QRICH1 variants cause a neurodevelopmental disorder including short stature and expands the phenotypic spectrum to include poor weight gain, scoliosis, hypotonia, minor structural brain anomalies, and seizures. Inherited variants from mildly affected parents are reported for the first time, suggesting variable expressivity

FOXP1-related intellectual disability syndrome : a recognisable entity

Background: Mutations in forkhead box protein P1 (FOXP1) cause intellectual disability (ID) and specific language impairment (SLI), with or without autistic features (MIM: 613670). Despite multiple case reports no specific phenotype emerged so far. Methods: We correlate clinical and molecular data of 25 novel and 23 previously reported patients with FOXP1 defects. We evaluated FOXP1 activity by an in vitro luciferase model and assessed protein stability in vitro by western blotting. Results: Patients show ID, SLI, neuromotor delay (NMD) and recurrent facial features including a high broad forehead, bent downslanting palpebral fissures, ptosis and/or blepharophimosis and a bulbous nasal tip. Behavioural problems and autistic features are common. Brain, cardiac and urogenital malformations can be associated. More severe ID and NMD, sensorineural hearing loss and feeding difficulties are more common in patients with interstitial 3p deletions (14 patients) versus patients with monogenic FOXP1 defects (34 patients). Mutations result in impaired transcriptional repression and/or reduced protein stability. Conclusions: FOXP1-related ID syndrome is a recognisable entity with a wide clinical spectrum and frequent systemic involvement. Our data will be helpful to evaluate genotype-phenotype correlations when interpreting next-generation sequencing data obtained in patients with ID and/or SLI and will guide clinical management

Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder

In pleiotropic diseases, multiple organ systems are affected causing a variety of clinical manifestations. Here, we report a pleiotropic disorder with a unique constellation of neurological, endocrine, exocrine, and haematological findings that is caused by biallelic MADD variants. MADD, the mitogen-activated protein kinase (MAPK) activating death domain protein, regulates various cellular functions, such as vesicle trafficking, activity of the Rab3 and Rab27 small GTPases, tumour necrosis factor-α (TNF-α)-induced signalling and prevention of cell death. Through national collaboration and GeneMatcher, we collected 23 patients with 21 different pathogenic MADD variants identified by next-generation sequencing. We clinically evaluated the series of patients and categorized the phenotypes in two groups. Group 1 consists of 14 patients with severe developmental delay, endo- and exocrine dysfunction, impairment of the sensory and autonomic nervous system, and haematological anomalies. The clinical course during the first years of life can be potentially fatal. The nine patients in Group 2 have a predominant neurological phenotype comprising mild-to-severe developmental delay, hypotonia, speech impairment, and seizures. Analysis of mRNA revealed multiple aberrant MADD transcripts in two patient-derived fibroblast cell lines. Relative quantification of MADD mRNA and protein in fibroblasts of five affected individuals showed a drastic reduction or loss of MADD. We conducted functional tests to determine the impact of the variants on different pathways. Treatment of patient-derived fibroblasts with TNF-α resulted in reduced phosphorylation of the extracellular signal-regulated kinases 1 and 2, enhanced activation of the pro-apoptotic enzymes caspase-3 and -7 and increased apoptosis compared to control cells. We analysed internalization of epidermal growth factor in patient cells and identified a defect in endocytosis of epidermal growth factor. We conclude that MADD deficiency underlies multiple cellular defects that can be attributed to alterations of TNF-α-dependent signalling pathways and defects in vesicular trafficking. Our data highlight the multifaceted role of MADD as a signalling molecule in different organs and reveal its physiological role in regulating the function of the sensory and autonomic nervous system and endo- and exocrine glands

FOXP1-related intellectual disability syndrome: a recognisable entity

Mutations in forkhead box protein P1 (FOXP1) cause intellectual disability (ID) and specific language impairment (SLI), with or without autistic features (MIM: 613670). Despite multiple case reports no specific phenotype emerged so far.status: publishe

The neurodevelopmental and facial phenotype in individuals with a TRIP12 variant

Haploinsufficiency of TRIP12 causes a neurodevelopmental disorder characterized by intellectual disability associated with epilepsy, autism spectrum disorder and dysmorphic features, also named Clark-Baraitser syndrome. Only a limited number of cases have been reported to date. We aimed to further delineate the TRIP12-associated phenotype and objectify characteristic facial traits through GestaltMatcher image analysis based on deep-learning algorithms in order to establish a TRIP12 gestalt. 38 individuals between 3 and 66 years (F = 20, M = 18) - 1 previously published and 37 novel individuals - were recruited through an ERN ITHACA call for collaboration. 35 TRIP12 variants were identified, including frameshift (n = 15) and nonsense (n = 6) variants, as well as missense (n = 5) and splice (n = 3) variants, intragenic deletions (n = 4) and two multigene deletions disrupting TRIP12. Though variable in severity, global developmental delay was noted in all individuals, with language deficit most pronounced. About half showed autistic features and susceptibility to obesity seemed inherent to this disorder. A more severe expression was noted in individuals with a missense variant. Facial analysis showed a clear gestalt including deep-set eyes with narrow palpebral fissures and fullness of the upper eyelids, downturned corners of the mouth and large, often low-set ears with prominent earlobes. We report the largest cohort to date of individuals with TRIP12 variants, further delineating the associated phenotype and introducing a facial gestalt. These findings will improve future counseling and patient guidance