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1.
Genome Res ; 23(7): 1130-41, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23570689

RESUMO

Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by meta-analyses of genome-wide association (GWA) studies are located at non-protein-coding regions. Here, we assessed the role of candidate regulatory variants associated with cell type-restricted, closely related hematological quantitative traits in biologically relevant hematopoietic cell types. We used formaldehyde-assisted isolation of regulatory elements followed by next-generation sequencing (FAIRE-seq) to map regions of open chromatin in three primary human blood cells of the myeloid lineage. In the precursors of platelets and erythrocytes, as well as in monocytes, we found that open chromatin signatures reflect the corresponding hematopoietic lineages of the studied cell types and associate with the cell type-specific gene expression patterns. Dependent on their signal strength, open chromatin regions showed correlation with promoter and enhancer histone marks, distance to the transcription start site, and ontology classes of nearby genes. Cell type-restricted regions of open chromatin were enriched in sequence variants associated with hematological indices. The majority (63.6%) of such candidate functional variants at platelet quantitative trait loci (QTLs) coincided with binding sites of five transcription factors key in regulating megakaryopoiesis. We experimentally tested 13 candidate regulatory variants at 10 platelet QTLs and found that 10 (76.9%) affected protein binding, suggesting that this is a frequent mechanism by which regulatory variants influence quantitative trait levels. Our findings demonstrate that combining large-scale GWA data with open chromatin profiles of relevant cell types can be a powerful means of dissecting the genetic architecture of closely related quantitative traits.


Assuntos
Montagem e Desmontagem da Cromatina , Cromatina/metabolismo , Variação Genética , Locos de Características Quantitativas , Característica Quantitativa Herdável , Sequências Reguladoras de Ácido Nucleico , Plaquetas/metabolismo , Linhagem da Célula/genética , Mapeamento Cromossômico , Análise por Conglomerados , Eritrócitos/metabolismo , Regulação da Expressão Gênica , Estudo de Associação Genômica Ampla , Histonas/metabolismo , Humanos , Células Mieloides/metabolismo , Nucleossomos/metabolismo , Especificidade de Órgãos/genética , Fenótipo , Polimorfismo de Nucleotídeo Único
2.
Nature ; 492(7429): 369-75, 2012 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-23222517

RESUMO

Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.


Assuntos
Eritrócitos/metabolismo , Loci Gênicos , Estudo de Associação Genômica Ampla , Fenótipo , Animais , Ciclo Celular/genética , Citocinas/metabolismo , Drosophila melanogaster/genética , Eritrócitos/citologia , Feminino , Regulação da Expressão Gênica/genética , Hematopoese/genética , Hemoglobinas/genética , Humanos , Masculino , Camundongos , Especificidade de Órgãos , Polimorfismo de Nucleotídeo Único/genética , Interferência de RNA , Transdução de Sinais/genética
3.
Blood ; 120(24): 4859-68, 2012 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-22972982

RESUMO

We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from hematopoietic stem cells by a process mainly controlled by transcription factors. The homeobox transcription factor MEIS1 is uniquely transcribed in megakaryocytes and not in the other lineage-committed blood cells. By ChIP-seq, we show that 5 of the 68 loci pinpoint a MEIS1 binding event within a group of 252 MK-overexpressed genes. In one such locus in DNM3, regulating platelet volume, the MEIS1 binding site falls within a region acting as an alternative promoter that is solely used in megakaryocytes, where allelic variation dictates different levels of a shorter transcript. The importance of dynamin activity to the latter stages of thrombopoiesis was confirmed by the observation that the inhibitor Dynasore reduced murine proplatelet for-mation in vitro.


Assuntos
Plaquetas/metabolismo , Dinamina III/genética , Genoma Humano/genética , Proteínas de Homeodomínio/genética , Megacariócitos/metabolismo , Proteínas de Neoplasias/genética , Regiões Promotoras Genéticas/genética , Animais , Sítios de Ligação/genética , Plaquetas/efeitos dos fármacos , Linhagem Celular Tumoral , Linhagem da Célula/genética , Células Cultivadas , Imunoprecipitação da Cromatina , Expressão Gênica , Variação Genética , Proteínas de Homeodomínio/metabolismo , Humanos , Hidrazonas/farmacologia , Camundongos , Proteína Meis1 , Proteínas de Neoplasias/metabolismo , Contagem de Plaquetas , Polimorfismo de Nucleotídeo Único , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de DNA , Sítio de Iniciação de Transcrição , Transcrição Gênica
4.
Nature ; 480(7376): 201-8, 2011 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-22139419

RESUMO

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.


Assuntos
Plaquetas/citologia , Hematopoese/genética , Megacariócitos/citologia , Animais , Plaquetas/metabolismo , Tamanho Celular , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Europa (Continente) , Perfilação da Expressão Gênica , Inativação Gênica , Genoma Humano/genética , Estudo de Associação Genômica Ampla , Humanos , Megacariócitos/metabolismo , Contagem de Plaquetas , Mapas de Interação de Proteínas , Transcrição Gênica/genética , Peixe-Zebra/genética , Proteínas de Peixe-Zebra/genética
5.
Nat Genet ; 43(8): 735-7, 2011 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-21765411

RESUMO

Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated individuals and identified NBEAL2 as the causative gene; it has no previously known function but is a member of a gene family that is involved in granule development. Silencing of nbeal2 in zebrafish abrogated thrombocyte formation.


Assuntos
Plaquetas/metabolismo , Grânulos Citoplasmáticos/metabolismo , Síndrome da Plaqueta Cinza/genética , Proteínas do Tecido Nervoso/genética , Vesículas Secretórias/metabolismo , Adulto , Idoso , Animais , Animais Geneticamente Modificados , Sequência de Bases , Plaquetas/patologia , Embrião não Mamífero/citologia , Embrião não Mamífero/metabolismo , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Proteínas do Tecido Nervoso/antagonistas & inibidores , Linhagem , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Adulto Jovem , Peixe-Zebra/crescimento & desenvolvimento , Peixe-Zebra/metabolismo
6.
Hum Mutat ; 30(6): 1003-11, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19370760

RESUMO

Cerebral cavernous malformations (CCMs) may cause recurrent headaches, seizures, and hemorrhagic stroke and have been associated with loss-of-function mutations in CCM1/KRIT1, CCM2, and CCM3/programmed cell death 10 (PDCD10). The CCM3/PDCD10 amino acid sequence does not reveal significant homologies to protein domains with known structure. With the help of the only published human in-frame deletion of the CCM3 gene (c.97-?_150+?del), CCM3:p.L33_K50del, we have identified the interaction domain of CCM3 with the oxidant stress response serine/threonine kinase 25 (STK25, YSK1, SOK1) and with the mammalian Ste20-like kinase 4 (MST4, MASK). Consistently, nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) analyses revealed two STK25 phosphorylation sites at serine 39 and threonine 43. The corresponding in-frame deletion of zebrafish ccm3a, dccm3:p.L31_K48del, also resulted in impaired interaction with STK25 and MST4. In agreement with the observed redundant biochemical functionality of zebrafish ccm3a and its duplicate ccm3b, simultaneous inactivation of both genes resulted in a progressive cardiovascular phenotype in zebrafish indistinguishable from ccm1 and ccm2 mutants. The pronounced cardiovascular dilatations could be recapitulated by morpholino-induced in-frame skipping of the exon encoding the STK25 and MST4 binding site of zebrafish Ccm3a if Ccm3b was repressed in parallel. Using a novel zebrafish model of CCM, we could thus demonstrate that the newly mapped STK25 and MST4 interaction domain within the CCM3 protein plays a crucial role for vascular development in zebrafish.


Assuntos
Aminoácidos/genética , Proteínas Reguladoras de Apoptose/genética , Mutação da Fase de Leitura/genética , Proteínas de Membrana/genética , Mapeamento de Interação de Proteínas , Proteínas Proto-Oncogênicas/genética , Deleção de Sequência , Proteínas de Peixe-Zebra/genética , Peixe-Zebra/genética , Animais , Proteínas Reguladoras de Apoptose/química , Proteínas Reguladoras de Apoptose/metabolismo , Anormalidades Cardiovasculares/embriologia , Anormalidades Cardiovasculares/metabolismo , Proteínas de Transporte/metabolismo , Linhagem Celular , Éxons/genética , Técnicas de Silenciamento de Genes , Coração/embriologia , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Proteína KRIT1 , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Fenótipo , Fosforilação , Fosfosserina/metabolismo , Fosfotreonina/metabolismo , Ligação Proteica , Proteínas Serina-Treonina Quinases/metabolismo , Estrutura Terciária de Proteína , Proteínas Proto-Oncogênicas/química , Proteínas Proto-Oncogênicas/metabolismo , Peixe-Zebra/embriologia , Proteínas de Peixe-Zebra/química
7.
Nat Genet ; 40(3): 329-34, 2008 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-18297070

RESUMO

Hypotrichosis simplex is a group of nonsyndromic human alopecias. We mapped an autosomal recessive form of this disorder to chromosome 13q14.11-13q21.33, and identified homozygous truncating mutations in P2RY5, which encodes an orphan G protein-coupled receptor. Furthermore, we identified oleoyl-L-alpha-lysophosphatidic acid (LPA), a bioactive lipid, as a ligand for P2Y5 in reporter gene and radioligand binding experiments. Homology and studies of signaling transduction pathways suggest that P2Y5 is a member of a subgroup of LPA receptors, which also includes LPA4 and LPA5. Our study is the first to implicate a G protein-coupled receptor as essential for and specific to the maintenance of human hair growth. This finding may provide opportunities for new therapeutic approaches to the treatment of hair loss in humans.


Assuntos
Cabelo/crescimento & desenvolvimento , Hipotricose/genética , Lisofosfolipídeos/fisiologia , Receptores Purinérgicos P2/fisiologia , Adulto , Animais , Sequência de Bases , Células COS , Chlorocebus aethiops , Mapeamento Cromossômico , Cromossomos Humanos Par 13 , Consanguinidade , Análise Mutacional de DNA , Família , Humanos , Lisofosfolipídeos/metabolismo , Modelos Biológicos , Linhagem , Filogenia , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Receptores Acoplados a Proteínas G/fisiologia , Receptores Purinérgicos P2/genética , Receptores Purinérgicos P2/metabolismo , Transfecção
8.
Hum Mutat ; 29(5): 709-17, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18300272

RESUMO

Cerebral cavernous malformations (CCM) are prevalent cerebrovascular lesions predisposing to chronic headaches, epilepsy, and hemorrhagic stroke. Using a combination of direct sequencing and MLPA analyses, we identified 15 novel and eight previously published CCM1 (KRIT1), CCM2, and CCM3 (PDCD10) mutations. The mutation detection rate was >90% for familial cases and >60% for isolated cases with multiple malformations. Splice site mutations constituted almost 20% of all CCM mutations identified. One of these proved to be a de novo mutation of the most 3' acceptor splice site of the CCM1 gene resulting in retention of intron 19. A further mutation affected the 3' splice site of CCM2 intron 2 leading to cryptic splice site utilization in both CCM2 and its transcript variant lacking exon 2. With the exception of one in-frame deletion of CCM2 exon 2, which corresponds to the naturally occurring splice variant of CCM2 on the RNA level and is predicted to result in the omission of 58 amino acids (CCM2:p.P11_K68del), all mutations lead to the introduction of premature stop codons. To gain insight into the likely mechanisms underlying the only known CCM2 in-frame deletion, we analyzed the functional consequences of loss of CCM2 exon 2. The CCM2:p.P11_K68del protein could be expressed in cell culture and complexed with CCM3. However, its ability to interact with CCM1 and to form a CCM1/CCM2/CCM3 complex was lost. These data are in agreement with a loss-of-function mechanism for CCM mutations, uncover an N-terminal CCM2 domain required for CCM1 binding, and demonstrate full-length CCM2 as the essential core protein in the CCM1/CCM2/CCM3 complex.


Assuntos
Proteínas Reguladoras de Apoptose/genética , Proteínas de Transporte/genética , Hemangioma Cavernoso do Sistema Nervoso Central/genética , Proteínas de Membrana/genética , Proteínas Associadas aos Microtúbulos/genética , Mutação , Proteínas Proto-Oncogênicas/genética , Deleção de Sequência , Proteínas Reguladoras de Apoptose/metabolismo , Sequência de Bases , Proteínas de Transporte/metabolismo , Linhagem Celular , Primers do DNA , Feminino , Humanos , Proteína KRIT1 , Masculino , Proteínas de Membrana/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Linhagem , Ligação Proteica , Proteínas Proto-Oncogênicas/metabolismo
9.
Neurogenetics ; 8(4): 249-56, 2007 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-17657516

RESUMO

Individuals carrying a mutation in one of the three cerebral cavernous malformation genes (CCM1/KRIT1, CCM2, CCM3) cannot be clinically distinguished, raising the possibility that they act within common molecular pathways. In this study, we demonstrate that CCM3 (PDCD10) coprecipitates and colocalizes with CCM2. We also show that CCM3 directly binds to serine/threonine kinase 25 (STK25, YSK1, SOK1) and the phosphatase domain of Fas-associated phosphatase-1 (FAP-1, PTPN13, PTP-Bas, PTP-BL). CCM3 is phosphorylated by STK25 but not by its other Yeast-Two hybrid interactor STK24, whereas the C-terminal catalytic domain of FAP-1 dephosphorylates CCM3. Finally, our experiments reveal that STK25 forms a protein complex with CCM2. Thus, our data link two proteins of unknown function, CCM3 and STK25, with CCM2, which is part of signaling pathways essential for vascular development and CCM pathogenesis.


Assuntos
Proteínas Reguladoras de Apoptose/genética , Proteínas de Transporte/genética , Hemangioma Cavernoso do Sistema Nervoso Central/genética , Proteínas de Membrana/genética , Proteínas Proto-Oncogênicas/genética , Sequência de Aminoácidos , Proteínas Reguladoras de Apoptose/química , Proteínas Reguladoras de Apoptose/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Linhagem Celular , Mutação em Linhagem Germinativa , Hemangioma Cavernoso do Sistema Nervoso Central/etiologia , Hemangioma Cavernoso do Sistema Nervoso Central/metabolismo , Humanos , Técnicas In Vitro , Peptídeos e Proteínas de Sinalização Intracelular , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Dados de Sequência Molecular , Fosforilação , Ligação Proteica , Mapeamento de Interação de Proteínas , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Estrutura Secundária de Proteína , Proteína Tirosina Fosfatase não Receptora Tipo 13/genética , Proteína Tirosina Fosfatase não Receptora Tipo 13/metabolismo , Proteínas Proto-Oncogênicas/química , Proteínas Proto-Oncogênicas/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Homologia de Sequência de Aminoácidos , Transdução de Sinais , Técnicas do Sistema de Duplo-Híbrido
10.
Eur J Immunol ; 34(5): 1405-13, 2004 May.
Artigo em Inglês | MEDLINE | ID: mdl-15114674

RESUMO

Notch receptors are involved in directing the choice between alternative cell fates in developmental scenarios such as thymopoiesis. By pharmacological interference in rat fetal thymus organ culture we show that inhibition of Notch signaling arrests T cell development at an early double-negative stage and is accompanied by a dramatic increase in the number of NK cells. These cells show an activated phenotype, lack recombination of the TCR beta gene locus and express perforin. Similarly, in thymic lobes reconstituted with fetal liver cells, progenitors predominantly develop into NK cells both after pharmacological interference of Notch and after treatment with a recombinant rat Notch1/Fc chimera. Collectively, this identifies the lineage decision of NK/T precursor cells as an important site of Notch action in rat thymocytes.


Assuntos
Diferenciação Celular/fisiologia , Células Matadoras Naturais/metabolismo , Proteínas de Membrana/metabolismo , Timo/metabolismo , Ácido gama-Aminobutírico/análogos & derivados , Secretases da Proteína Precursora do Amiloide , Animais , Antígenos de Superfície/metabolismo , Endopeptidases/efeitos dos fármacos , Lectinas Tipo C/metabolismo , Fígado/embriologia , Fígado/fisiologia , Proteínas de Membrana/efeitos dos fármacos , Subfamília B de Receptores Semelhantes a Lectina de Células NK , Ratos , Receptores Notch , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/fisiologia , Linfócitos T/efeitos dos fármacos , Linfócitos T/metabolismo , Triglicerídeos/farmacologia , Ácido gama-Aminobutírico/farmacologia
11.
J Exp Biol ; 207(Pt 3): 443-8, 2004 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-14691092

RESUMO

This study on common marmosets Callithrix jacchus is the first to examine noise-dependent mechanisms of vocal plasticity in a New World monkey. Since acoustic communication can be considerably impaired by environmental noise, some animals have evolved adaptations to counteract its masking effects. The studied marmosets increased the sound level of their spontaneous calls in response to increased levels of white noise broadcast to them. Possibly, such noise-dependent adjustment of vocal amplitude serves to maintain a specific signal-to-noise ratio that is favourable for signal production. Concurrently, the adjustment of vocal amplitude can maintain a given active space for communication. In contrast to some bird species, no noise-induced increase in the number of syllables per call series could be found, showing that an increased serial redundancy of vocal signals was not used to communicate under noisy conditions. Finally, we examined a possible noise-dependent prolongation of vocal signals. This approach was guided by the findings of perceptional studies, which suggest an increased detection probability of prolonged signals in noise by temporal summation. Marmosets indeed increased the duration of their call syllables along with increasing background noise levels. This is the first evidence of such mechanism of vocal plasticity in an animal communication system.


Assuntos
Adaptação Fisiológica , Callithrix/fisiologia , Ruído , Vocalização Animal/fisiologia , Animais , Espectrografia do Som , Fatores de Tempo
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