RESUMEN
SHQ1 is essential for biogenesis of H/ACA ribonucleoproteins, a class of molecules important for processing ribosomal RNAs, modifying spliceosomal small nuclear RNAs and stabilizing telomerase. Components of the H/ACA ribonucleoprotein complex have been linked to neurological developmental defects. Here, we report two sibling pairs from unrelated families with compound heterozygous variants in SHQ1. Exome sequencing was used to detect disease causing variants, which were submitted to 'matching' platforms linked to MatchMaker Exchange. Phenotype comparisons supported these matches. The affected individuals present with early-onset dystonia, with individuals from one family displaying additional neurological phenotypes, including neurodegeneration. As a result of cerebrospinal fluid studies suggesting possible abnormal dopamine metabolism, a trial of levodopa replacement therapy was started but no clear response was noted. We show that fibroblasts from affected individuals have dramatic loss of SHQ1 protein. Variants from both families were expressed in Saccharomyces cerevisiae, resulting in a strong reduction in H/ACA snoRNA production and remarkable defects in rRNA processing and ribosome formation. Our study identifies SHQ1 as associated with neurological disease, including early-onset dystonia, and begins to delineate the molecular etiology of this novel condition.
Asunto(s)
Distonía , Trastornos Distónicos , Péptidos y Proteínas de Señalización Intracelular , Proteínas de Saccharomyces cerevisiae , Distonía/genética , Trastornos Distónicos/genética , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Proteínas Nucleares/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genéticaRESUMEN
ABHD16A (abhydrolase domain-containing protein 16A, phospholipase) encodes the major phosphatidylserine (PS) lipase in the brain. PS lipase synthesizes lysophosphatidylserine, an important signaling lipid that functions in the mammalian central nervous system. ABHD16A has not yet been associated with a human disease. In this report, we present a cohort of 11 affected individuals from six unrelated families with a complicated form of hereditary spastic paraplegia (HSP) who carry bi-allelic deleterious variants in ABHD16A. Affected individuals present with a similar phenotype consisting of global developmental delay/intellectual disability, progressive spasticity affecting the upper and lower limbs, and corpus callosum and white matter anomalies. Immunoblot analysis on extracts from fibroblasts from four affected individuals demonstrated little to no ABHD16A protein levels compared to controls. Our findings add ABHD16A to the growing list of lipid genes in which dysregulation can cause complicated forms of HSP and begin to describe the molecular etiology of this condition.
Asunto(s)
Parálisis Cerebral/patología , Discapacidad Intelectual/patología , Leucoencefalopatías/patología , Monoacilglicerol Lipasas/genética , Mutación , Paraplejía Espástica Hereditaria/patología , Adolescente , Adulto , Parálisis Cerebral/etiología , Parálisis Cerebral/metabolismo , Niño , Preescolar , Estudios de Cohortes , Femenino , Humanos , Discapacidad Intelectual/etiología , Discapacidad Intelectual/metabolismo , Leucoencefalopatías/etiología , Leucoencefalopatías/metabolismo , Masculino , Monoacilglicerol Lipasas/deficiencia , Linaje , Fenotipo , Paraplejía Espástica Hereditaria/etiología , Paraplejía Espástica Hereditaria/metabolismo , Adulto JovenRESUMEN
The DNA damage-binding protein 1 (DDB1) is part of the CUL4-DDB1 ubiquitin E3 ligase complex (CRL4), which is essential for DNA repair, chromatin remodeling, DNA replication, and signal transduction. Loss-of-function variants in genes encoding the complex components CUL4 and PHIP have been reported to cause syndromic intellectual disability with hypotonia and obesity, but no phenotype has been reported in association with DDB1 variants. Here, we report eight unrelated individuals, identified through Matchmaker Exchange, with de novo monoallelic variants in DDB1, including one recurrent variant in four individuals. The affected individuals have a consistent phenotype of hypotonia, mild to moderate intellectual disability, and similar facies, including horizontal or slightly bowed eyebrows, deep-set eyes, full cheeks, a short nose, and large, fleshy and forward-facing earlobes, demonstrated in the composite face generated from the cohort. Digital anomalies, including brachydactyly and syndactyly, were common. Three older individuals have obesity. We show that cells derived from affected individuals have altered DDB1 function resulting in abnormal DNA damage signatures and histone methylation following UV-induced DNA damage. Overall, our study adds to the growing family of neurodevelopmental phenotypes mediated by disruption of the CRL4 ubiquitin ligase pathway and begins to delineate the phenotypic and molecular effects of DDB1 misregulation.
Asunto(s)
Alelos , Reparación del ADN/genética , Proteínas de Unión al ADN/genética , Mutación , Trastornos del Neurodesarrollo/genética , Adolescente , Niño , Preescolar , Femenino , Humanos , Masculino , Fenotipo , SíndromeRESUMEN
Partial duplications of genes can be challenging to detect and interpret and, therefore, likely represent an underreported cause of human disease. X-linked dominant variants in ATRX are associated with Alpha-thalassemia/impaired intellectual development syndrome, X-linked (ATR-X syndrome), a clinically heterogeneous disease generally presenting with intellectual disability, hypotonia, characteristic facies, genital anomalies, and alpha-thalassemia. We describe an affected male with a de novo hemizygous intragenic duplication of ~43.6 kb in ATRX, detected by research genome sequencing following non-diagnostic clinical testing. RNA sequencing and DNA methylation episignature analyses were central in variant interpretation, and this duplication was subsequently interpreted as disease-causing. This represents the smallest reported tandem duplication within ATRX associated with disease. This case demonstrates the diagnostic utility of integrating multiple omics technologies, which can ultimately lead to a definitive diagnosis for rare disease patients.
Asunto(s)
Discapacidad Intelectual , Discapacidad Intelectual Ligada al Cromosoma X , Talasemia alfa , Humanos , Masculino , Talasemia alfa/diagnóstico , Talasemia alfa/genética , Proteína Nuclear Ligada al Cromosoma X/genética , Variaciones en el Número de Copia de ADN/genética , Discapacidad Intelectual Ligada al Cromosoma X/diagnóstico , Discapacidad Intelectual Ligada al Cromosoma X/genética , Discapacidad Intelectual/diagnóstico , Discapacidad Intelectual/genéticaRESUMEN
Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease-associated variants and understand the genetic basis of many rare diseases. Long-read genome sequencing provides improved sequencing in highly repetitive, homologous, and low-complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short-read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi-generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE-VNTR-Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss-of-function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss-of-expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long-read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short-read genomic testing.
Asunto(s)
Trastorno del Desarrollo Sexual 46,XY , Retroelementos , Humanos , Mutación , Intrones/genética , Retroelementos/genética , Trastorno del Desarrollo Sexual 46,XY/genética , Enfermedades Raras/genética , Desarrollo Sexual , Factor Esteroidogénico 1/genéticaRESUMEN
Repetitive genomic regions include tandem sequence repeats and interspersed repeats, such as endogenous retroviruses and LINE-1 elements. Repressive heterochromatin domains silence expression of these sequences through mechanisms that remain poorly understood. Here, we present evidence that the retinoblastoma protein (pRB) utilizes a cell-cycle-independent interaction with E2F1 to recruit enhancer of zeste homolog 2 (EZH2) to diverse repeat sequences. These include simple repeats, satellites, LINEs, and endogenous retroviruses as well as transposon fragments. We generated a mutant mouse strain carrying an F832A mutation in Rb1 that is defective for recruitment to repetitive sequences. Loss of pRB-EZH2 complexes from repeats disperses H3K27me3 from these genomic locations and permits repeat expression. Consistent with maintenance of H3K27me3 at the Hox clusters, these mice are developmentally normal. However, susceptibility to lymphoma suggests that pRB-EZH2 recruitment to repetitive elements may be cancer relevant.
Asunto(s)
Factor de Transcripción E2F1/genética , Proteína Potenciadora del Homólogo Zeste 2/genética , Silenciador del Gen , Linfoma/genética , Secuencias Repetitivas de Ácidos Nucleicos , Proteína de Retinoblastoma/genética , Animales , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/mortalidad , Carcinoma Hepatocelular/patología , Factor de Transcripción E2F1/metabolismo , Proteína Potenciadora del Homólogo Zeste 2/metabolismo , Fibroblastos/citología , Fibroblastos/metabolismo , Predisposición Genética a la Enfermedad , Histonas/genética , Histonas/metabolismo , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/mortalidad , Neoplasias Hepáticas/patología , Linfoma/metabolismo , Linfoma/mortalidad , Linfoma/patología , Mesenterio/metabolismo , Mesenterio/patología , Ratones , Mutación , Cultivo Primario de Células , Unión Proteica , Proteína de Retinoblastoma/metabolismo , Neoplasias del Bazo/genética , Neoplasias del Bazo/metabolismo , Neoplasias del Bazo/mortalidad , Neoplasias del Bazo/patología , Análisis de SupervivenciaRESUMEN
We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.
Asunto(s)
Pruebas Genéticas , Humanos , Pruebas Genéticas/métodos , Ontario/epidemiología , Secuenciación del ExomaRESUMEN
OBJECTIVE: Human genomics established that pathogenic variation in diverse genes can underlie a single disorder. For example, hereditary spastic paraplegia is associated with >80 genes, with frequently only few affected individuals described for each gene. Herein, we characterize a large cohort of individuals with biallelic variation in ENTPD1, a gene previously linked to spastic paraplegia 64 (Mendelian Inheritance in Man # 615683). METHODS: Individuals with biallelic ENTPD1 variants were recruited worldwide. Deep phenotyping and molecular characterization were performed. RESULTS: A total of 27 individuals from 17 unrelated families were studied; additional phenotypic information was collected from published cases. Twelve novel pathogenic ENTPD1 variants are described (NM 001776.6): c.398_399delinsAA; p.(Gly133Glu), c.540del; p.(Thr181Leufs*18), c.640del; p.(Gly216Glufs*75), c.185 T > G; p.(Leu62*), c.1531 T > C; p.(*511Glnext*100), c.967C > T; p.(Gln323*), c.414-2_414-1del, and c.146 A > G; p.(Tyr49Cys) including 4 recurrent variants c.1109 T > A; p.(Leu370*), c.574-6_574-3del, c.770_771del; p.(Gly257Glufs*18), and c.1041del; p.(Ile348Phefs*19). Shared disease traits include childhood onset, progressive spastic paraplegia, intellectual disability (ID), dysarthria, and white matter abnormalities. In vitro assays demonstrate that ENTPD1 expression and function are impaired and that c.574-6_574-3del causes exon skipping. Global metabolomics demonstrate ENTPD1 deficiency leads to impaired nucleotide, lipid, and energy metabolism. INTERPRETATION: The ENTPD1 locus trait consists of childhood disease onset, ID, progressive spastic paraparesis, dysarthria, dysmorphisms, and white matter abnormalities, with some individuals showing neurocognitive regression. Investigation of an allelic series of ENTPD1 (1) expands previously described features of ENTPD1-related neurological disease, (2) highlights the importance of genotype-driven deep phenotyping, (3) documents the need for global collaborative efforts to characterize rare autosomal recessive disease traits, and (4) provides insights into disease trait neurobiology. ANN NEUROL 2022;92:304-321.
Asunto(s)
Apirasa , Discapacidad Intelectual , Paraplejía Espástica Hereditaria , Sustancia Blanca , Apirasa/genética , Disartria , Humanos , Discapacidad Intelectual/genética , Mutación/genética , Paraplejía/genética , Linaje , Fenotipo , Paraplejía Espástica Hereditaria/genética , Sustancia Blanca/diagnóstico por imagen , Sustancia Blanca/patologíaAsunto(s)
Anomalías Múltiples , Cerebelo/anomalías , Anomalías del Ojo , Enfermedades Renales Quísticas , Retina/anomalías , Humanos , Anomalías Múltiples/diagnóstico , Anomalías Múltiples/genética , Anomalías del Ojo/diagnóstico , Anomalías del Ojo/genética , Enfermedades Renales Quísticas/diagnóstico , Enfermedades Renales Quísticas/genética , Hermanos , Mutación , Análisis de Secuencia de ARN , Intrones/genética , Proteínas de Ciclo Celular/genéticaAsunto(s)
Complejo I de Transporte de Electrón , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento , Enfermedades Mitocondriales , Humanos , Complejo I de Transporte de Electrón/genética , Complejo I de Transporte de Electrón/deficiencia , Enfermedades Mitocondriales/genética , Enfermedades Mitocondriales/patología , Enfermedades Mitocondriales/diagnóstico , Eliminación de Secuencia/genética , Masculino , Femenino , NiñoAsunto(s)
Anomalías Múltiples , Deformidades Congénitas de la Mano , Discapacidad Intelectual , Micrognatismo , Anomalías Múltiples/diagnóstico , Anomalías Múltiples/genética , Adulto , Proteínas de Unión al ADN/genética , Cara/anomalías , Deformidades Congénitas de la Mano/diagnóstico , Deformidades Congénitas de la Mano/genética , Humanos , Discapacidad Intelectual/diagnóstico , Discapacidad Intelectual/genética , Micrognatismo/diagnóstico , Micrognatismo/genética , Cuello/anomalías , Factores de Transcripción/genéticaAsunto(s)
Cerebelo/anomalías , Fosfolipasas A2 Grupo VI/genética , Mutación , Miopatías Estructurales Congénitas/genética , Adolescente , Alelos , Biopsia , Humanos , Masculino , Miopatías Estructurales Congénitas/enzimología , Miopatías Estructurales Congénitas/patología , Hermanos , Secuenciación Completa del GenomaRESUMEN
BACKGROUND: Intronic variants outside the canonical splice site are challenging to interpret and therefore likely represent an underreported cause of human disease. Autosomal recessive variants in DYNC2H1 are associated with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), a clinically heterogeneous disease generally presenting with short ribs, shortened tubular bones, narrow thorax and acetabular roof anomalies. We describe a case of SRTD3 with compound heterozygous frameshift and intronic variants and highlight the essential role of RNA sequencing (RNA-Seq) in variant interpretation. METHODS: Following inconclusive clinical genetic testing identifying a likely pathogenic frameshift variant and an intronic variant of uncertain significance (VUS) in DYNC2H1 in trans, the family enrolled in the Care4Rare Canada research program, where RNA-Seq studies were performed. RESULTS: The proband presented with post-axial polydactyly of all four limbs, a significantly small chest with a pectus excavatum and anterior flaring of the ribs. RNA-Seq investigations revealed a novel splice junction as a result of the intronic VUS and significantly decreased DYNC2H1 gene expression in the proband. CONCLUSION: This case demonstrates the diagnostic utility of RNA-Seq for variant interpretation following inconclusive clinical testing, which can ultimately lead to diagnosis for patients with rare disease.
RESUMEN
Interphase chromosomes are organized into topologically associated domains in order to establish and maintain integrity of transcriptional programs that remain poorly understood. Here, we show that condensin II and TFIIIC are recruited to bidirectionally transcribed promoters by a mechanism that is dependent on the retinoblastoma (RB) protein. Long-range chromosome contacts are disrupted by loss of condensin II loading, which leads to altered expression at bidirectional gene pairs. This study demonstrates that mammalian condensin II functions to organize long-range chromosome contacts and regulate transcription at specific genes. In addition, RB dependence of condensin II suggests that widespread misregulation of chromosome contacts and transcriptional alterations are a consequence of RB mutation.
Asunto(s)
Adenosina Trifosfatasas/metabolismo , Cromosomas/metabolismo , Proteínas de Unión al ADN/metabolismo , Complejos Multiproteicos/metabolismo , Proteína de Retinoblastoma/metabolismo , Factores de Transcripción TFIII/metabolismo , Animales , Células Cultivadas , Cromosomas/genética , Epigénesis Genética , Interfase , Ratones , Regiones Promotoras Genéticas , Activación TranscripcionalRESUMEN
Proliferative control in cancer cells is frequently disrupted by mutations in the retinoblastoma protein (RB) pathway. Intriguingly, RB1 mutations can arise late in tumorigenesis in cancer cells whose RB pathway is already compromised by another mutation. In this study, we present evidence for increased DNA damage and instability in cancer cells with RB pathway defects when RB1 mutations are induced. We generated isogenic RB1 mutant genotypes with CRISPR/Cas9 in a number of cell lines. Cells with even one mutant copy of RB1 have increased basal levels of DNA damage and increased mitotic errors. Elevated levels of reactive oxygen species as well as impaired homologous recombination repair underlie this DNA damage. When xenografted into immunocompromised mice, RB1 mutant cells exhibit an elevated propensity to seed new tumors in recipient lungs. This study offers evidence that late-arising RB1 mutations can facilitate genome instability and cancer progression that are beyond the preexisting proliferative control deficit.