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1.
Cell ; 146(6): 889-903, 2011 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-21925314

RESUMEN

Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.


Asunto(s)
Aberraciones Cromosómicas , Reparación del ADN , Discapacidades del Desarrollo/genética , Neoplasias/genética , Secuencia de Bases , Niño , Preescolar , Rotura Cromosómica , Hibridación Genómica Comparativa , Replicación del ADN , Femenino , Humanos , Hibridación Fluorescente in Situ , Lactante , Masculino , Datos de Secuencia Molecular
2.
Genome Res ; 23(1): 23-33, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23034409

RESUMEN

An unanticipated and tremendous amount of the noncoding sequence of the human genome is transcribed. Long noncoding RNAs (lncRNAs) constitute a significant fraction of non-protein-coding transcripts; however, their functions remain enigmatic. We demonstrate that deletions of a small noncoding differentially methylated region at 16q24.1, including lncRNA genes, cause a lethal lung developmental disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), with parent-of-origin effects. We identify overlapping deletions 250 kb upstream of FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete lung-specific lncRNA genes. These deletions define a distant cis-regulatory region that harbors, besides lncRNA genes, also a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter. We suggest that lung-transcribed 16q24.1 lncRNAs may contribute to long-range regulation of FOXF1 by GLI2 and other transcription factors. Perturbation of lncRNA-mediated chromatin interactions may, in general, be responsible for position effect phenomena and potentially cause many disorders of human development.


Asunto(s)
Variaciones en el Número de Copia de ADN , Metilación de ADN , Síndrome de Circulación Fetal Persistente/genética , ARN Largo no Codificante/genética , Cromatina/metabolismo , Cromosomas Humanos Par 16/genética , Islas de CpG , Elementos de Facilitación Genéticos , Resultado Fatal , Factores de Transcripción Forkhead/genética , Factores de Transcripción Forkhead/metabolismo , Regulación de la Expresión Génica , Impresión Genómica , Células HEK293 , Humanos , Recién Nacido , Factores de Transcripción de Tipo Kruppel/metabolismo , Proteínas Nucleares/metabolismo , Síndrome de Circulación Fetal Persistente/diagnóstico , Regiones Promotoras Genéticas , ARN Largo no Codificante/metabolismo , Eliminación de Secuencia , Transcripción Genética , Proteína Gli2 con Dedos de Zinc
3.
Hum Mutat ; 34(6): 801-11, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23505205

RESUMEN

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare and lethal developmental disorder of the lung defined by a constellation of characteristic histopathological features. Nonpulmonary anomalies involving organs of gastrointestinal, cardiovascular, and genitourinary systems have been identified in approximately 80% of patients with ACD/MPV. We have collected DNA and pathological samples from more than 90 infants with ACD/MPV and their family members. Since the publication of our initial report of four point mutations and 10 deletions, we have identified an additional 38 novel nonsynonymous mutations of FOXF1 (nine nonsense, seven frameshift, one inframe deletion, 20 missense, and one no stop). This report represents an up to date list of all known FOXF1 mutations to the best of our knowledge. Majority of the cases are sporadic. We report four familial cases of which three show maternal inheritance, consistent with paternal imprinting of the gene. Twenty five mutations (60%) are located within the putative DNA-binding domain, indicating its plausible role in FOXF1 function. Five mutations map to the second exon. We identified two additional genic and eight genomic deletions upstream to FOXF1. These results corroborate and extend our previous observations and further establish involvement of FOXF1 in ACD/MPV and lung organogenesis.


Asunto(s)
Factores de Transcripción Forkhead/genética , Factores de Transcripción Forkhead/metabolismo , Mutación , Síndrome de Circulación Fetal Persistente/genética , Síndrome de Circulación Fetal Persistente/metabolismo , Dominios y Motivos de Interacción de Proteínas/genética , Secuencia de Aminoácidos , Mapeo Cromosómico , Bases de Datos Genéticas , Femenino , Factores de Transcripción Forkhead/química , Dosificación de Gen , Orden Génico , Humanos , Lactante , Recién Nacido , Masculino , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , Síndrome de Circulación Fetal Persistente/mortalidad , Síndrome de Circulación Fetal Persistente/patología , Alineación de Secuencia
4.
Am J Hum Genet ; 87(6): 857-65, 2010 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-21109226

RESUMEN

We report 26 individuals from ten unrelated families who exhibit variable expression and/or incomplete penetrance of epilepsy, learning difficulties, intellectual disabilities, and/or neurobehavioral abnormalities as a result of a heterozygous microdeletion distally adjacent to the Williams-Beuren syndrome region on chromosome 7q11.23. In six families with a common recurrent ∼1.2 Mb deletion that includes the Huntingtin-interacting protein 1 (HIP1) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG) genes and that is flanked by large complex low-copy repeats, we identified sites for nonallelic homologous recombination in two patients. There were no cases of this ∼1.2 Mb distal 7q11.23 deletion copy number variant identified in over 20,000 control samples surveyed. Three individuals with smaller, nonrecurrent deletions (∼180-500 kb) that include HIP1 but not YWHAG suggest that deletion of HIP1 is sufficient to cause neurological disease. Mice with targeted mutation in the Hip1 gene (Hip1⁻(/)⁻) develop a neurological phenotype characterized by failure to thrive, tremor, and gait ataxia. Overall, our data characterize a neurodevelopmental and epilepsy syndrome that is likely caused by recurrent and nonrecurrent deletions, including HIP1. These data do not exclude the possibility that YWHAG loss of function is also sufficient to cause neurological phenotypes. Based on the current knowledge of Hip1 protein function and its proposed role in AMPA and NMDA ionotropic glutamate receptor trafficking, we believe that HIP1 haploinsufficiency in humans will be amenable to rational drug design for improved seizure control and cognitive and behavioral function.


Asunto(s)
Deleción Cromosómica , Cromosomas Humanos Par 7 , Proteínas de Unión al ADN/genética , Epilepsia/genética , Discapacidad Intelectual/genética , Trastornos Mentales/genética , Adolescente , Adulto , Animales , Niño , Preescolar , Variaciones en el Número de Copia de ADN , Femenino , Humanos , Lactante , Masculino , Ratones , Persona de Mediana Edad , Datos de Secuencia Molecular
5.
Proc Natl Acad Sci U S A ; 106(4): 1211-5, 2009 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-19139419

RESUMEN

Nitric Oxide (NO), produced by inducible nitric oxide synthase (iNOS), has been implicated in the pathogenesis of various biological and inflammatory disorders. Recent evidence suggests that aggresome formation is a physiologic stress response not limited to misfolded proteins. That stress response, termed "physiologic aggresome," is exemplified by aggresome formation of iNOS, an important host defense protein. The functional significance of cellular formation of the iNOS aggresome is hitherto unknown. In this study, we used live cell imaging, fluorescence microscopy, and intracellular fluorescence NO probes to map the subcellular location of iNOS and NO under various conditions. We found that NO production colocalized with cytosolic iNOS but aggresomes containing iNOS were distinctly devoid of NO production. Further, cells expressing iNOS aggresomes produced significantly less NO as compared with cells not expressing aggresomes. Importantly, primary normal human bronchial epithelial cells, stimulated by cytokines to express iNOS, progressively sequestered iNOS to the aggresome, a process that correlated with marked reduction of NO production. These results suggest that bronchial epithelial cells used the physiologic aggresome mechanism for iNOS inactivation. Our studies reveal a novel cellular strategy to terminate NO production via formation of the iNOS aggresome.


Asunto(s)
Cuerpos de Inclusión/enzimología , Óxido Nítrico Sintasa de Tipo II/metabolismo , Estrés Fisiológico , Bronquios/citología , Bronquios/enzimología , Supervivencia Celular/efectos de los fármacos , Células Cultivadas , Citocinas/farmacología , Activación Enzimática/efectos de los fármacos , Células Epiteliales/citología , Células Epiteliales/efectos de los fármacos , Células Epiteliales/enzimología , Humanos , Cuerpos de Inclusión/efectos de los fármacos , Óxido Nítrico/biosíntesis , Transporte de Proteínas/efectos de los fármacos , Rodaminas/metabolismo , Estrés Fisiológico/efectos de los fármacos , Fracciones Subcelulares/efectos de los fármacos , Fracciones Subcelulares/enzimología
6.
Genet Med ; 13(5): 447-52, 2011 May.
Artículo en Inglés | MEDLINE | ID: mdl-21293276

RESUMEN

PURPOSE: Mutations in the CDKL5 gene have been associated with an X-linked dominant early infantile epileptic encephalopathy-2. The clinical presentation is usually of severe encephalopathy with refractory seizures and Rett syndrome (RTT)-like phenotype. We attempted to assess the role of mosaic intragenic copy number variation in CDKL5. METHODS: We have used comparative genomic hybridization with a custom-designed clinical oligonucleotide array targeting exons of selected disease and candidate genes, including CDKL5. RESULTS: We have identified mosaic exonic deletions of CDKL5 in one male and two females with developmental delay and medically intractable seizures. These three mosaic changes represent 60% of all deletions detected in 12,000 patients analyzed by array comparative genomic hybridization and involving the exonic portion of CDKL5. CONCLUSION: We report the first case of an exonic deletion of CDKL5 in a male and emphasize the importance of underappreciated mosaic exonic copy number variation in patients with early-onset seizures and RTT-like features of both genders.


Asunto(s)
Exones/genética , Mosaicismo , Proteínas Serina-Treonina Quinasas/genética , Convulsiones/genética , Eliminación de Secuencia/genética , Edad de Inicio , Niño , Preescolar , Cromosomas Humanos X/genética , Femenino , Orden Génico , Humanos , Lactante , Masculino
7.
Am J Med Genet A ; 155A(6): 1442-7, 2011 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-21567932

RESUMEN

To date, over 70 mutations in the TGFBR2 gene have been reported in patients with Loeys-Dietz syndrome (LDS), Marfan syndrome type 2 (MFS2), or other hereditary thoracic aortic aneurysms and dissections. Whereas almost all of mutations analyzed thus far are predicted to disrupt the constitutively active C-terminal serine/threonine kinase domain of TGFBR2, mounting evidence suggests that the molecular mechanism underlying these diseases is more complex than simple haploinsufficiency. Using exon-targeted oligonucleotide array comparative genomic hybridization, we identified an ∼896 kb deletion of TGFBR2 in a 20-month-old female with microcephaly and global developmental delay, but no stigmata of LDS. FISH analysis showed no evidence of this deletion in the parental peripheral blood samples; however, somatic mosaicism was detected using PCR in the paternal DNA from peripheral blood lymphocytes and lymphoblasts. Our data suggest that TGFBR2 haploinsufficiency may cause a phenotype, which is distinct from LDS. Moreover, we propose that somatic mosaicism below the detection threshold of FISH analysis in asymptomatic parents of children with genomic disorders may be more common than previously recognized.


Asunto(s)
Discapacidades del Desarrollo/genética , Eliminación de Gen , Microcefalia/genética , Fenotipo , Proteínas Serina-Treonina Quinasas/genética , Receptores de Factores de Crecimiento Transformadores beta/genética , Hibridación Genómica Comparativa , Discapacidades del Desarrollo/patología , Femenino , Haploinsuficiencia , Humanos , Hibridación Fluorescente in Situ , Lactante , Microcefalia/patología , Mosaicismo , Receptor Tipo II de Factor de Crecimiento Transformador beta
8.
Eur J Hum Genet ; 22(9): 1071-6, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24424125

RESUMEN

Although deletions of CHRNA7 have been associated with intellectual disability (ID), seizures and neuropsychiatric phenotypes, the pathogenicity of CHRNA7 duplications has been uncertain. We present the first report of CHRNA7 triplication. Three generations of a family affected with various neuropsychiatric phenotypes, including anxiety, bipolar disorder, developmental delay and ID, were studied with array comparative genomic hybridization (aCGH). High-resolution aCGH revealed a 650-kb triplication at chromosome 15q13.3 encompassing the CHRNA7 gene, which encodes the alpha7 subunit of the neuronal nicotinic acetylcholine receptor. A small duplication precedes the triplication at the proximal breakpoint junction, and analysis of the breakpoint indicates that the triplicated segment is in an inverted orientation with respect to the duplication. CHRNA7 triplication appears to occur by a replication-based mechanism that produces inverted triplications embedded within duplications. Co-segregation of the CHRNA7 triplication with neuropsychiatric and cognitive phenotypes provides further evidence for dosage sensitivity of CHRNA7.


Asunto(s)
Variaciones en el Número de Copia de ADN , Discapacidades del Desarrollo/genética , Discapacidad Intelectual/genética , Linaje , Receptor Nicotínico de Acetilcolina alfa 7/genética , Adulto , Niño , Puntos de Rotura del Cromosoma , Cromosomas Humanos Par 15/genética , Discapacidades del Desarrollo/diagnóstico , Femenino , Humanos , Discapacidad Intelectual/diagnóstico , Masculino
9.
Immunity ; 27(1): 135-44, 2007 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-17658277

RESUMEN

Autophagy has recently been shown to be an important component of the innate immune response. The signaling pathways leading to activation of autophagy in innate immunity are not known. Here we showed that Toll-like receptor 4 (TLR4) served as a previously unrecognized environmental sensor for autophagy. Autophagy was induced by lipopolysaccharide (LPS) in primary human macrophages and in the murine macrophage RAW264.7 cell line. We defined a new molecular pathway in which LPS-induced autophagy was regulated through a Toll-interleukin-1 receptor domain-containing adaptor-inducing interferon-beta (TRIF)-dependent, myeloid differentiation factor 88 (MyD88)-independent TLR4 signaling pathway. Receptor-interacting protein (RIP1) and p38 mitogen-activated protein kinase were downstream components of this pathway. This signaling pathway did not affect cell viability, indicating that it is distinct from the autophagic death signaling pathway. We further showed that LPS-induced autophagy could enhance mycobacterial colocalization with the autophagosomes. This study links two ancient processes, autophagy and innate immunity, together through a shared signaling pathway.


Asunto(s)
Autofagia/inmunología , Inmunidad Innata , Receptor Toll-Like 4/fisiología , Animales , Línea Celular , Humanos , Lipopolisacáridos/inmunología , Macrófagos/inmunología , Macrófagos/metabolismo , Macrófagos/microbiología , Ratones , Mycobacterium tuberculosis/inmunología , Transducción de Señal/inmunología
10.
Proc Natl Acad Sci U S A ; 102(13): 4854-9, 2005 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-15781872

RESUMEN

Misfolding and aggregation of proteins play an important part in the pathogenesis of several genetic and degenerative diseases. Recent evidence suggests that cells have evolved a pathway that involves sequestration of aggregated proteins into specialized "holding stations" called aggresomes. Here we show that cells regulate inducible NO synthase (iNOS), an important host defense protein, through aggresome formation. iNOS aggresome formation depends on a functional dynein motor and the integrity of the microtubules. The iNOS aggresome represents a "physiologic aggresome" and thus defines a new paradigm for cellular regulation of protein processing. This study indicates that aggresome formation in response to misfolded proteins may merely represent an acceleration of an established physiologic regulatory process for specific proteins whose regulation by aggresome formation is deemed necessary by the cell.


Asunto(s)
Cuerpos de Inclusión/metabolismo , Óxido Nítrico Sintasa/metabolismo , Animales , Células Cultivadas , Dineínas/metabolismo , Recuperación de Fluorescencia tras Fotoblanqueo , Proteínas Fluorescentes Verdes , Humanos , Procesamiento de Imagen Asistido por Computador , Cuerpos de Inclusión/efectos de los fármacos , Indoles , Leupeptinas/farmacología , Ratones , Microscopía Electrónica , Centro Organizador de los Microtúbulos/efectos de los fármacos , Centro Organizador de los Microtúbulos/metabolismo , Óxido Nítrico Sintasa de Tipo II , Nocodazol/farmacología
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