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1.
Cell ; 135(4): 738-48, 2008 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-19013281

RESUMEN

The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations. Using bacterial artificial chromosome (BAC) transgenic mice that express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology for affinity purification of polysomal mRNAs from genetically defined cell populations in the brain. The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations. We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neurons display vastly different translational profiles and present examples of the physiological significance of such differences. This genetically targeted translating ribosome affinity purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.


Asunto(s)
Encéfalo/metabolismo , Técnicas Genéticas , Biosíntesis de Proteínas , Animales , Sistema Nervioso Central/metabolismo , Cromosomas Artificiales Bacterianos/metabolismo , Cocaína/farmacología , Inhibidores de Captación de Dopamina/farmacología , Proteínas Fluorescentes Verdes/metabolismo , Inmunohistoquímica/métodos , Ratones , Ratones Transgénicos , Modelos Biológicos , Neuronas/metabolismo , Ribosomas/metabolismo
2.
Int J Mol Sci ; 16(1): 1312-35, 2015 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-25574603

RESUMEN

Classical autism or autistic disorder belongs to a group of genetically heterogeneous conditions known as Autism Spectrum Disorders (ASD). Heritability is estimated as high as 90% for ASD with a recently reported compilation of 629 clinically relevant candidate and known genes. We chose to undertake a descriptive next generation whole exome sequencing case study of 30 well-characterized Caucasian females with autism (average age, 7.7 ± 2.6 years; age range, 5 to 16 years) from multiplex families. Genomic DNA was used for whole exome sequencing via paired-end next generation sequencing approach and X chromosome inactivation status. The list of putative disease causing genes was developed from primary selection criteria using machine learning-derived classification score and other predictive parameters (GERP2, PolyPhen2, and SIFT). We narrowed the variant list to 10 to 20 genes and screened for biological significance including neural development, function and known neurological disorders. Seventy-eight genes identified met selection criteria ranging from 1 to 9 filtered variants per female. Five females presented with functional variants of X-linked genes (IL1RAPL1, PIR, GABRQ, GPRASP2, SYTL4) with cadherin, protocadherin and ankyrin repeat gene families most commonly altered (e.g., CDH6, FAT2, PCDH8, CTNNA3, ANKRD11). Other genes related to neurogenesis and neuronal migration (e.g., SEMA3F, MIDN), were also identified.


Asunto(s)
Trastorno Autístico/genética , Adolescente , Ancirinas/genética , Cadherinas/genética , Niño , Preescolar , Femenino , Genoma Humano , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Neurogénesis/genética , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN
3.
Am J Hum Genet ; 88(2): 127-37, 2011 Feb 11.
Artículo en Inglés | MEDLINE | ID: mdl-21255762

RESUMEN

By using homozygosity mapping in a consanguineous Pakistani family, we detected linkage of nonsyndromic hearing loss to a 7.6 Mb region on chromosome 3q13.31-q21.1 within the previously reported DFNB42 locus. Subsequent candidate gene sequencing identified a homozygous nonsense mutation (c.1135G>T [p.Glu379X]) in ILDR1 as the cause of hearing impairment. By analyzing additional consanguineous families with homozygosity at this locus, we detected ILDR1 mutations in the affected individuals of 10 more families from Pakistan and Iran. The identified ILDR1 variants include missense, nonsense, frameshift, and splice-site mutations as well as a start codon mutation in the family that originally defined the DFNB42 locus. ILDR1 encodes the evolutionarily conserved immunoglobulin-like domain containing receptor 1, a putative transmembrane receptor of unknown function. In situ hybridization detected expression of Ildr1, the murine ortholog, early in development in the vestibule and in hair cells and supporting cells of the cochlea. Expression in hair cell- and supporting cell-containing neurosensory organs is conserved in the zebrafish, in which the ildr1 ortholog is prominently expressed in the developing ear and neuromasts of the lateral line. These data identify loss-of-function mutations of ILDR1, a gene with a conserved expression pattern pointing to a conserved function in hearing in vertebrates, as underlying nonsyndromic prelingual sensorineural hearing impairment.


Asunto(s)
Codón sin Sentido/genética , Genes Recesivos/genética , Predisposición Genética a la Enfermedad , Pérdida Auditiva/genética , Receptores de Superficie Celular/genética , Animales , Mapeo Cromosómico , Cromosomas Humanos Par 3/genética , Consanguinidad , Oído Interno , Femenino , Ligamiento Genético , Genotipo , Humanos , Hibridación in Situ , Escala de Lod , Masculino , Ratones , Linaje , Pez Cebra
4.
Proc Natl Acad Sci U S A ; 107(18): 8404-9, 2010 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-20404173

RESUMEN

A recently identified variant within the fat mass and obesity-associated (FTO) gene is carried by 46% of Western Europeans and is associated with an approximately 1.2 kg higher weight, on average, in adults and an approximately 1 cm greater waist circumference. With >1 billion overweight and 300 million obese persons worldwide, it is crucial to understand the implications of carrying this very common allele for the health of our aging population. FTO is highly expressed in the brain and elevated body mass index (BMI) is associated with brain atrophy, but it is unknown how the obesity-associated risk allele affects human brain structure. We therefore generated 3D maps of regional brain volume differences in 206 healthy elderly subjects scanned with MRI and genotyped as part of the Alzheimer's Disease Neuroimaging Initiative. We found a pattern of systematic brain volume deficits in carriers of the obesity-associated risk allele versus noncarriers. Relative to structure volumes in the mean template, FTO risk allele carriers versus noncarriers had an average brain volume difference of approximately 8% in the frontal lobes and 12% in the occipital lobes-these regions also showed significant volume deficits in subjects with higher BMI. These brain differences were not attributable to differences in cholesterol levels, hypertension, or the volume of white matter hyperintensities; which were not detectably higher in FTO risk allele carriers versus noncarriers. These brain maps reveal that a commonly carried susceptibility allele for obesity is associated with structural brain atrophy, with implications for the health of the elderly.


Asunto(s)
Alelos , Encéfalo/anatomía & histología , Obesidad/genética , Proteínas/genética , Anciano , Dioxigenasa FTO Dependiente de Alfa-Cetoglutarato , Encéfalo/metabolismo , Predisposición Genética a la Enfermedad , Humanos , Imagenología Tridimensional , Imagen por Resonancia Magnética , Tamaño de los Órganos , Factores de Riesgo
5.
Neuron ; 54(5): 713-20, 2007 Jun 07.
Artículo en Inglés | MEDLINE | ID: mdl-17553421

RESUMEN

The apolipoprotein E (APOE) epsilon4 allele is the best established genetic risk factor for late-onset Alzheimer's disease (LOAD). We conducted genome-wide surveys of 502,627 single-nucleotide polymorphisms (SNPs) to characterize and confirm other LOAD susceptibility genes. In epsilon4 carriers from neuropathologically verified discovery, neuropathologically verified replication, and clinically characterized replication cohorts of 1411 cases and controls, LOAD was associated with six SNPs from the GRB-associated binding protein 2 (GAB2) gene and a common haplotype encompassing the entire GAB2 gene. SNP rs2373115 (p = 9 x 10(-11)) was associated with an odds ratio of 4.06 (confidence interval 2.81-14.69), which interacts with APOE epsilon4 to further modify risk. GAB2 was overexpressed in pathologically vulnerable neurons; the Gab2 protein was detected in neurons, tangle-bearing neurons, and dystrophic neuritis; and interference with GAB2 gene expression increased tau phosphorylation. Our findings suggest that GAB2 modifies LOAD risk in APOE epsilon4 carriers and influences Alzheimer's neuropathology.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/genética , Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/metabolismo , Apolipoproteína E4/genética , Predisposición Genética a la Enfermedad/genética , Polimorfismo de Nucleótido Simple/genética , Encéfalo/metabolismo , Encéfalo/patología , Encéfalo/fisiopatología , Química Encefálica/genética , Línea Celular Tumoral , Análisis Mutacional de ADN , Regulación de la Expresión Génica/genética , Frecuencia de los Genes , Marcadores Genéticos/genética , Pruebas Genéticas , Haplotipos/genética , Humanos , Mutación , Ovillos Neurofibrilares/genética , Ovillos Neurofibrilares/metabolismo , Ovillos Neurofibrilares/patología , Fosforilación , Factores de Riesgo , Proteínas tau/metabolismo
6.
Hum Mol Genet ; 18(4): 785-96, 2009 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-19047183

RESUMEN

Age-related hearing impairment (ARHI), or presbycusis, is the most prevalent sensory impairment in the elderly. ARHI is a complex disease caused by an interaction between environmental and genetic factors. Here we describe the results of the first whole genome association study for ARHI. The study was performed using 846 cases and 846 controls selected from 3434 individuals collected by eight centers in six European countries. DNA pools for cases and controls were allelotyped on the Affymetrix 500K GeneChip for each center separately. The 252 top-ranked single nucleotide polymorphisms (SNPs) identified in a non-Finnish European sample group (1332 samples) and the 177 top-ranked SNPs from a Finnish sample group (360 samples) were confirmed using individual genotyping. Subsequently, the 23 most interesting SNPs were individually genotyped in an independent European replication group (138 samples). This resulted in the identification of a highly significant and replicated SNP located in GRM7, the gene encoding metabotropic glutamate receptor type 7. Also in the Finnish sample group, two GRM7 SNPs were significant, albeit in a different region of the gene. As the Finnish are genetically distinct from the rest of the European population, this may be due to allelic heterogeneity. We performed histochemical studies in human and mouse and showed that mGluR7 is expressed in hair cells and in spiral ganglion cells of the inner ear. Together these data indicate that common alleles of GRM7 contribute to an individual's risk of developing ARHI, possibly through a mechanism of altered susceptibility to glutamate excitotoxicity.


Asunto(s)
Predisposición Genética a la Enfermedad , Presbiacusia/genética , Receptores de Ácido Kaínico/genética , Factores de Edad , Anciano , Animales , Estudios de Casos y Controles , Oído Interno/metabolismo , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Ratones , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Presbiacusia/metabolismo , Receptores de Ácido Kaínico/metabolismo , Población Blanca/genética , Receptor Kainato GluK3
7.
Am J Hum Genet ; 82(1): 7-9, 2008 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-18179879

RESUMEN

In this issue of AJHG, Alarcón et al.,(1) Arking et al.,(2) and Bakkaloglu et al.(3) identify a series of functional variants in the CNTNAP2 gene that unequivocally implicate this gene as causing Type 1 autism in the general population.


Asunto(s)
Trastorno Autístico/genética , Predisposición Genética a la Enfermedad , Humanos , Proteínas de la Membrana/genética , Proteínas del Tejido Nervioso/genética , Estudios en Gemelos como Asunto
8.
Am J Hum Genet ; 82(2): 366-74, 2008 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-18252217

RESUMEN

Hypothalamic hamartomas (HH) are rare, benign congenital tumors associated with intractable epilepsy. Most cases are sporadic and nonsyndromic. Approximately 5% of HH cases are associated with Pallister-Hall syndrome (PHS), which is caused by haploinsufficiency of GLI3. We have investigated the possibility that HH pathogenesis in sporadic cases is due to a somatic (tumor-only) mutation in GLI3. We isolated genomic DNA from peripheral blood and surgically resected HH tissue in 55 patients with sporadic HH and intractable epilepsy. A genome-wide screen for loss of heterozygosity (LOH) and chromosomal abnormalities was performed with parallel analysis of blood and HH tissue with Affymetrix 10K SNP microarrays. Additionally, resequencing and fine mapping with SNP genotyping were completed for the GLI3 gene with comparisons between peripheral blood and HH tissue pairs. By analyzing chromosomal copy-number data for paired samples on the Affymetrix 10K array, we identified a somatic chromosomal abnormality on chromosome 7p in one HH tissue sample. Resequencing of GLI3 did not identify causative germline mutations but did identify LOH within the GLI3 gene in the HH tissue samples of three patients. Further genotyping of 28 SNPs within and surrounding GLI3 identified five additional patients exhibiting LOH. Together, these data provide evidence that the development of chromosomal abnormalities within GLI3 is associated with the pathogenesis of HH lesions in sporadic, nonsyndromic patients with HH and intractable epilepsy. Chromosomal abnormalities including the GLI3 locus were seen in 8 of 55 (15%) of the resected HH tissue samples. These somatic mutations appear to be highly variable.


Asunto(s)
Aberraciones Cromosómicas , Cromosomas Humanos Par 7/genética , Hamartoma/genética , Enfermedades Hipotalámicas/genética , Factores de Transcripción de Tipo Kruppel/genética , Proteínas del Tejido Nervioso/genética , Adolescente , Adulto , Secuencia de Bases , Niño , Preescolar , Cartilla de ADN/genética , Genotipo , Humanos , Lactante , Pérdida de Heterocigocidad/genética , Análisis por Micromatrices , Datos de Secuencia Molecular , Polimorfismo de Nucleótido Simple/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Proteína Gli3 con Dedos de Zinc
9.
Nat Methods ; 5(10): 887-93, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18794863

RESUMEN

We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8-90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.


Asunto(s)
Procesamiento Automatizado de Datos , Variación Genética , Genoma Humano , Humanos , Polimorfismo de Nucleótido Simple , Alineación de Secuencia
10.
PLoS Genet ; 4(8): e1000167, 2008 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-18769715

RESUMEN

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixture, then show, through simulations, the limits associated with our method, and finally demonstrate experimentally the identification of the presence of genomic DNA of specific individuals within a series of highly complex genomic mixtures, including mixtures where an individual contributes less than 0.1% of the total genomic DNA. These findings shift the perceived utility of SNPs for identifying individual trace contributors within a forensics mixture, and suggest future research efforts into assessing the viability of previously sub-optimal DNA sources due to sample contamination. These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed.


Asunto(s)
Genética Médica , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Polimorfismo de Nucleótido Simple , Simulación por Computador , Genoma Humano , Genotipo , Humanos
11.
Proc Natl Acad Sci U S A ; 105(11): 4441-6, 2008 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-18332434

RESUMEN

Alzheimer's disease (AD) is associated with regional reductions in fluorodeoxyglucose positron emission tomography (FDG PET) measurements of the cerebral metabolic rate for glucose, which may begin long before the onset of histopathological or clinical features, especially in carriers of a common AD susceptibility gene. Molecular evaluation of cells from metabolically affected brain regions could provide new information about the pathogenesis of AD and new targets at which to aim disease-slowing and prevention therapies. Data from a genome-wide transcriptomic study were used to compare the expression of 80 metabolically relevant nuclear genes from laser-capture microdissected non-tangle-bearing neurons from autopsy brains of AD cases and normal controls in posterior cingulate cortex, which is metabolically affected in the earliest stages; other brain regions metabolically affected in PET studies of AD or normal aging; and visual cortex, which is relatively spared. Compared with controls, AD cases had significantly lower expression of 70% of the nuclear genes encoding subunits of the mitochondrial electron transport chain in posterior cingulate cortex, 65% of those in the middle temporal gyrus, 61% of those in hippocampal CA1, 23% of those in entorhinal cortex, 16% of those in visual cortex, and 5% of those in the superior frontal gyrus. Western blots confirmed underexpression of those complex I-V subunits assessed at the protein level. Cerebral metabolic rate for glucose abnormalities in FDG PET studies of AD may be associated with reduced neuronal expression of nuclear genes encoding subunits of the mitochondrial electron transport chain.


Asunto(s)
Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/metabolismo , Metabolismo Energético , Regulación de la Expresión Génica/genética , Neuronas/metabolismo , Anciano , Encéfalo/metabolismo , Femenino , Humanos , Masculino
12.
J Biol Chem ; 284(31): 20927-35, 2009 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-19525223

RESUMEN

The tumor suppressor gene HIC1 (Hypermethylated in Cancer 1) that is epigenetically silenced in many human tumors and is essential for mammalian development encodes a sequence-specific transcriptional repressor. The few genes that have been reported to be directly regulated by HIC1 include ATOH1, FGFBP1, SIRT1, and E2F1. HIC1 is thus involved in the complex regulatory loops modulating p53-dependent and E2F1-dependent cell survival and stress responses. We performed genome-wide expression profiling analyses to identify new HIC1 target genes, using HIC1-deficient U2OS human osteosarcoma cells infected with adenoviruses expressing either HIC1 or GFP as a negative control. These studies identified several putative direct target genes, including CXCR7, a G-protein-coupled receptor recently identified as a scavenger receptor for the chemokine SDF-1/CXCL12. CXCR7 is highly expressed in human breast, lung, and prostate cancers. Using quantitative reverse transcription-PCR analyses, we demonstrated that CXCR7 was repressed in U2OS cells overexpressing HIC1. Inversely, inactivation of endogenous HIC1 by RNA interference in normal human WI38 fibroblasts results in up-regulation of CXCR7 and SIRT1. In silico analyses followed by deletion studies and luciferase reporter assays identified a functional and phylogenetically conserved HIC1-responsive element in the human CXCR7 promoter. Moreover, chromatin immunoprecipitation (ChIP) and ChIP upon ChIP experiments demonstrated that endogenous HIC1 proteins are bound together with the C-terminal binding protein corepressor to the CXCR7 and SIRT1 promoters in WI38 cells. Taken together, our results implicate the tumor suppressor HIC1 in the transcriptional regulation of the chemokine receptor CXCR7, a key player in the promotion of tumorigenesis in a wide variety of cell types.


Asunto(s)
Factores de Transcripción de Tipo Kruppel/metabolismo , Receptores CXCR/genética , Adenoviridae/genética , Oxidorreductasas de Alcohol/metabolismo , Secuencia de Bases , Línea Celular Tumoral , Proliferación Celular , Inmunoprecipitación de Cromatina , Secuencia Conservada , Proteínas de Unión al ADN/metabolismo , Regulación hacia Abajo/genética , Fibroblastos/metabolismo , Regulación Neoplásica de la Expresión Génica , Genes Relacionados con las Neoplasias , Vectores Genéticos/genética , Humanos , Factores de Transcripción de Tipo Kruppel/genética , Datos de Secuencia Molecular , Análisis de Secuencia por Matrices de Oligonucleótidos , Osteosarcoma/genética , Osteosarcoma/patología , Filogenia , Regiones Promotoras Genéticas/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores CXCR/metabolismo , Sirtuina 1 , Sirtuinas/genética , Sirtuinas/metabolismo
13.
BMC Genomics ; 11: 25, 2010 Jan 12.
Artículo en Inglés | MEDLINE | ID: mdl-20067632

RESUMEN

BACKGROUND: Neurofibrillary tangles (NFT), a cardinal neuropathological feature of Alzheimer's disease (AD) that is highly correlated with synaptic loss and dementia severity, appear to be partly attributable to increased phosphorylation of the microtubule stabilizing protein tau at certain AD-related residues. Identifying the kinases involved in the pathologic phosphorylation of tau may provide targets at which to aim new AD-modifying treatments. RESULTS: We report results from a screen of 572 kinases in the human genome for effects on tau hyperphosphorylation using a loss of function, high-throughput RNAi approach. We confirm effects of three kinases from this screen, the eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2), the dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and the A-kinase anchor protein 13 (AKAP13) on tau phosphorylation at the 12E8 epitope (serine 262/serine 356). We provide evidence that EIF2AK2 effects may result from effects on tau protein expression, whereas DYRK1A and AKAP13 are likely more specifically involved in tau phosphorylation pathways. CONCLUSIONS: These findings identify novel kinases that phosphorylate tau protein and provide a valuable reference data set describing the kinases involved in phosphorylating tau at an AD-relevant epitope.


Asunto(s)
Enfermedad de Alzheimer/enzimología , Proteínas Quinasas/análisis , ARN Interferente Pequeño/análisis , Proteínas tau/metabolismo , Enfermedad de Alzheimer/genética , Línea Celular Tumoral , Perfilación de la Expresión Génica , Pruebas Genéticas , Genoma Humano , Humanos , Fosforilación , Proteínas Quinasas/genética , ARN Interferente Pequeño/genética , Regulación hacia Arriba
14.
Neuroimage ; 51(2): 542-54, 2010 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-20197096

RESUMEN

In a genome-wide association study of structural brain degeneration, we mapped the 3D profile of temporal lobe volume differences in 742 brain MRI scans of Alzheimer's disease patients, mildly impaired, and healthy elderly subjects. After searching 546,314 genomic markers, 2 single nucleotide polymorphisms (SNPs) were associated with bilateral temporal lobe volume (P<5 x 10(-7)). One SNP, rs10845840, is located in the GRIN2B gene which encodes the N-methyl-d-aspartate (NMDA) glutamate receptor NR2B subunit. This protein - involved in learning and memory, and excitotoxic cell death - has age-dependent prevalence in the synapse and is already a therapeutic target in Alzheimer's disease. Risk alleles for lower temporal lobe volume at this SNP were significantly over-represented in AD and MCI subjects vs. controls (odds ratio=1.273; P=0.039) and were associated with mini-mental state exam scores (MMSE; t=-2.114; P=0.035) demonstrating a negative effect on global cognitive function. Voxelwise maps of genetic association of this SNP with regional brain volumes, revealed intense temporal lobe effects (FDR correction at q=0.05; critical P=0.0257). This study uses large-scale brain mapping for gene discovery with implications for Alzheimer's disease.


Asunto(s)
Enfermedad de Alzheimer/genética , Degeneración Nerviosa/genética , Receptores de N-Metil-D-Aspartato/genética , Lóbulo Temporal/patología , Anciano , Enfermedad de Alzheimer/patología , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Interpretación de Imagen Asistida por Computador , Imagen por Resonancia Magnética , Degeneración Nerviosa/patología , Polimorfismo de Nucleótido Simple
15.
N Engl J Med ; 357(8): 775-88, 2007 Aug 23.
Artículo en Inglés | MEDLINE | ID: mdl-17671248

RESUMEN

BACKGROUND: Approximately 90% of persons with amyotrophic lateral sclerosis (ALS) have the sporadic form, which may be caused by the interaction of multiple environmental factors and previously unknown genes. METHODS: We performed a genomewide association analysis using 766,955 single-nucleotide polymorphisms (SNPs) found in 386 white patients with sporadic ALS and 542 neurologically normal white controls (the discovery series). Associations of SNPs with sporadic ALS were confirmed in two independent replication populations: replication series 1, with 766 case patients with the disease and 750 neurologically normal controls, and replication series 2, with 135 case patients and 275 controls. RESULTS: We identified 10 genetic loci that are significantly associated (P<0.05) with sporadic ALS in three independent series of case patients and controls and an additional 41 loci that had significant associations in two of the three series. The most significant association with disease in white case patients as compared with controls was found for a SNP near an uncharacterized gene known as FLJ10986 (P=3.0x10(-4); odds ratio for having the genotype in patients vs. controls, 1.35; 95% confidence interval, 1.13 to 1.62). The FLJ10986 protein was found to be expressed in the spinal cord and cerebrospinal fluid of patients and of controls. Specific SNPs seem to be associated with sex, age at onset, and site of onset of sporadic ALS. CONCLUSIONS: Variants of FLJ10986 may confer susceptibility to sporadic ALS. FLJ10986 and 50 other candidate loci warrant further investigation for their potential role in conferring susceptibility to the disease.


Asunto(s)
Esclerosis Amiotrófica Lateral/genética , Proteínas del Líquido Cefalorraquídeo/genética , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple , Edad de Inicio , Estudios de Casos y Controles , Femenino , Genoma Humano , Genotipo , Humanos , Immunoblotting , Masculino , Mutación , Oportunidad Relativa , Factores de Riesgo , Análisis de Secuencia de ADN
16.
N Engl J Med ; 354(13): 1370-7, 2006 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-16571880

RESUMEN

Contactin-associated protein-like 2 (CASPR2) is encoded by CNTNAP2 and clusters voltage-gated potassium channels (K(v)1.1) at the nodes of Ranvier. We report a homozygous mutation of CNTNAP2 in Old Order Amish children with cortical dysplasia, focal epilepsy, relative macrocephaly, and diminished deep-tendon reflexes. Intractable focal seizures began in early childhood, after which language regression, hyperactivity, impulsive and aggressive behavior, and mental retardation developed in all children. Resective surgery did not prevent the recurrence of seizures. Temporal-lobe specimens showed evidence of abnormalities of neuronal migration and structure, widespread astrogliosis, and reduced expression of CASPR2.


Asunto(s)
Epilepsias Parciales/genética , Proteínas de la Membrana/genética , Proteínas del Tejido Nervioso/genética , Niño , Preescolar , Electroencefalografía , Epilepsias Parciales/patología , Epilepsias Parciales/fisiopatología , Epilepsias Parciales/cirugía , Expresión Génica , Homocigoto , Humanos , Angiografía por Resonancia Magnética , Proteínas de la Membrana/metabolismo , Mutación , Proteínas del Tejido Nervioso/metabolismo , Fenotipo , Reflejo de Estiramiento , Prevención Secundaria , Convulsiones/etiología , Lóbulo Temporal/metabolismo , Lóbulo Temporal/patología
17.
Bioinformatics ; 24(17): 1896-902, 2008 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-18617537

RESUMEN

For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling-based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations and increase genomic coverage. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r(2) provides a measure of linkage disequilibrium (LD) between pairs of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling-based GWA studies. We first give a theoretical framework and derivation of our multimarker method. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K and Affymetrix 5.0 platforms for a combined total of 1 333 631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling-based studies, allows for efficient integration of multiple microarray platforms and provides more accurate measures of significance than single marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in LD. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling.


Asunto(s)
Mapeo Cromosómico/métodos , Ligamiento Genético/genética , Marcadores Genéticos/genética , Haplotipos/genética , Desequilibrio de Ligamiento/genética , Polimorfismo de Nucleótido Simple/genética , Análisis de Secuencia de ADN/métodos , Secuencia de Bases , Análisis Mutacional de ADN/métodos , Datos de Secuencia Molecular
18.
Exp Eye Res ; 88(6): 1020-32, 2009 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-19450457

RESUMEN

A distinct structural change in the trabecular meshwork (TM) of patients with primary open-angle glaucoma (POAG) is the increase in fibrillar extracellular matrix (ECM) in the juxtacanalicular region of the TM. Transforming growth factor (TGF)-beta2 signaling may be involved, as TGF-beta2 is significantly increased in the aqueous humor of patients with POAG. In cultured human TM cells, TGF-beta2 causes an increase in ECM deposition, an effect that is blunted or prevented, if BMP7 is added in combination with TGF-beta2. In order to know more about the signaling network that is induced in HTM cells treated with BMP7, TGF-beta2 or the combination of both factors, we identified differentially regulated genes by microarray analysis, and confirmed selected genes by quantitative RT-PCR, Western blotting, or immunohistochemistry. We observed multiple effects of both TGF-beta2 and BMP7 on the expression of a considerable number of genes involved in growth factor signaling, ECM structure and turnover, and modification of the cytoskeleton. Among the genes that were found to be regulated were CAPZA1, CDC42BPB, EFEMP1, FGF5, FSTL3, HBEGF, LTBP1, LTBP2, MATN2, NRP1, SERPINE1, SH3MD1, SMTN, SMAD7, TFPI2, TNFAIP6, and VEGF. Since SMAD7 encodes for Smad7, an inhibitory Smad that acts in a negative-feedback loop to inhibit TGF-beta activity, we silenced Smad7 mRNA in cultured human TM cells by a specific small interfering RNA. Silencing of its mRNA caused a substantial knock down of Smad7 in TM cells. Following combined BMP7/TGF-beta2 treatment, the antagonizing effect of BMP7 on TGF-beta2-induced CTGF expression was abolished. We conclude that Smad7 is the key molecular switch that inhibits TGF-beta2 signaling, and mediates the blunting effects of BMP7 on TGF-beta2 in TM cells. A therapeutic modulation of Smad7 might be a promising approach to influence ECM turnover in the TM and to treat POAG.


Asunto(s)
Proteína Morfogenética Ósea 7/farmacología , Proteína smad7/fisiología , Malla Trabecular/efectos de los fármacos , Factor de Crecimiento Transformador beta2/farmacología , Células Cultivadas , Citocinas/biosíntesis , Citocinas/genética , Proteínas del Citoesqueleto/biosíntesis , Proteínas del Citoesqueleto/genética , Matriz Extracelular/metabolismo , Proteínas de la Matriz Extracelular/biosíntesis , Proteínas de la Matriz Extracelular/genética , Proteínas del Ojo/biosíntesis , Proteínas del Ojo/genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/efectos de los fármacos , Técnicas de Silenciamiento del Gen/métodos , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Receptores de Citocinas/biosíntesis , Receptores de Citocinas/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Transducción de Señal/efectos de los fármacos , Transducción de Señal/fisiología , Proteína smad7/genética , Malla Trabecular/metabolismo
19.
Behav Neurosci ; 123(1): 218-23, 2009 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-19170447

RESUMEN

Previously, utilizing a series of genome-wide association, brain imaging, and gene expression studies we implicated the KIBRA gene and the RhoA/ROCK pathway in hippocampal-mediated human memory. Here we show that peripheral administration of the ROCK inhibitor hydroxyfasudil improves spatial learning and working memory in the rodent model. This study supports the action of ROCK on learning and memory, suggests the potential value of ROCK inhibition for the promotion of cognition in humans, and highlights the powerful potential of unbiased genome-wide association studies to inform potential novel uses for existing pharmaceuticals.


Asunto(s)
1-(5-Isoquinolinesulfonil)-2-Metilpiperazina/análogos & derivados , Aprendizaje por Laberinto/efectos de los fármacos , Memoria a Corto Plazo/efectos de los fármacos , Proteína de Unión al GTP rhoA/antagonistas & inhibidores , 1-(5-Isoquinolinesulfonil)-2-Metilpiperazina/farmacología , Envejecimiento , Animales , Relación Dosis-Respuesta a Droga , Masculino , Ratas , Ratas Endogámicas F344
20.
Physiol Genomics ; 33(2): 240-56, 2008 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-18270320

RESUMEN

Alzheimer's Disease (AD) is the most widespread form of dementia during the later stages of life. If improved therapeutics are not developed, the prevalence of AD will drastically increase in the coming years as the world's population ages. By identifying differences in neuronal gene expression profiles between healthy elderly persons and individuals diagnosed with AD, we may be able to better understand the molecular mechanisms that drive AD pathogenesis, including the formation of amyloid plaques and neurofibrillary tangles. In this study, we expression profiled histopathologically normal cortical neurons collected with laser capture microdissection (LCM) from six anatomically and functionally discrete postmortem brain regions in 34 AD-afflicted individuals, using Affymetrix Human Genome U133 Plus 2.0 microarrays. These regions include the entorhinal cortex, hippocampus, middle temporal gyrus, posterior cingulate cortex, superior frontal gyrus, and primary visual cortex. This study is predicated on previous parallel research on the postmortem brains of the same six regions in 14 healthy elderly individuals, for which LCM neurons were similarly processed for expression analysis. We identified significant regional differential expression in AD brains compared with control brains including expression changes of genes previously implicated in AD pathogenesis, particularly with regard to tangle and plaque formation. Pinpointing the expression of factors that may play a role in AD pathogenesis provides a foundation for future identification of new targets for improved AD therapeutics. We provide this carefully phenotyped, laser capture microdissected intraindividual brain region expression data set to the community as a public resource.


Asunto(s)
Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/patología , Encéfalo/metabolismo , Encéfalo/patología , Bases de Datos Genéticas , Regulación de la Expresión Génica , Neuronas/metabolismo , Anciano , Enfermedad de Alzheimer/enzimología , Precursor de Proteína beta-Amiloide/metabolismo , Encéfalo/enzimología , Perfilación de la Expresión Génica , Humanos , Chaperonas Moleculares/metabolismo , Ovillos Neurofibrilares/genética , Ovillos Neurofibrilares/patología , Neuronas/patología , Especificidad de Órganos , Placa Amiloide/genética , Placa Amiloide/patología , Proteínas Quinasas/metabolismo , Reproducibilidad de los Resultados , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
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