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1.
Psychiatr Genet ; 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31568069

RESUMO

Studying the relationship between mental illnesses and their environmental and genetic risk factors in low-income countries holds excellent promises. These studies will improve our understanding of how risk factors identified predominantly in high-income countries also apply to other settings and will identify new, sometimes population-specific risk factors. Here we report the successful completion of two intertwined pilot studies on khat abuse, trauma, and psychosis at the Gilgel Gibe Field Research Center in Ethiopia. We found that the Gilgel Gibe Field Research Center offers a unique opportunity to collect well-characterized samples for mental health research and to perform genetic studies that, at this scale, have not been undertaken in Ethiopia yet. We also supported service development, education, and research for strengthening the professional profile of psychiatry at the site.

3.
Birth Defects Res ; 110(10): 871-882, 2018 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-29498243

RESUMO

BACKGROUND: Nonsyndromic cleft palate only (nsCPO) is a common and multifactorial form of orofacial clefting. In contrast to successes achieved for the other common form of orofacial clefting, that is, nonsyndromic cleft lip with/without cleft palate (nsCL/P), genome wide association studies (GWAS) of nsCPO have identified only one genome wide significant locus. Aim of the present study was to investigate whether common variants contribute to nsCPO and, if so, to identify novel risk loci. METHODS: We genotyped 33 SNPs at 27 candidate loci from 2 previously published nsCPO GWAS in an independent multiethnic sample. It included: (i) a family-based sample of European ancestry (n = 212); and (ii) two case/control samples of Central European (n = 94/339) and Arabian ancestry (n = 38/231), respectively. A separate association analysis was performed for each genotyped dataset, and meta-analyses were performed. RESULTS: After association analysis and meta-analyses, none of the 33 SNPs showed genome-wide significance. Two variants showed nominally significant association in the imputed GWAS dataset and exhibited a further decrease in p-value in a European and an overall meta-analysis including imputed GWAS data, respectively (rs395572: PMetaEU = 3.16 × 10-4 ; rs6809420: PMetaAll = 2.80 × 10-4 ). CONCLUSION: Our findings suggest that there is a limited contribution of common variants to nsCPO. However, the individual effect sizes might be too small for detection of further associations in the present sample sizes. Rare variants may play a more substantial role in nsCPO than in nsCL/P, for which GWAS of smaller sample sizes have identified genome-wide significant loci. Whole-exome/genome sequencing studies of nsCPO are now warranted.

4.
Nat Commun ; 8(1): 1511, 2017 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-29142228

RESUMO

Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs. Cis-acting SNPs of hippocampal meQTLs and eQTLs significantly overlap schizophrenia-associated SNPs. Correlations of CpG methylation and RNA expression are found for 34 genes. Our comprehensive maps of cis-acting hippocampal meQTLs and eQTLs provide a link between disease-associated SNPs and the regulatory genome that will improve the functional interpretation of non-coding genetic variants in the molecular genetic dissection of brain disorders.


Assuntos
Metilação de DNA , Epilepsia do Lobo Temporal/genética , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla/métodos , Hipocampo/metabolismo , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Adulto Jovem
5.
Nat Commun ; 8(1): 266, 2017 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-28814792

RESUMO

The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions. We characterize the dynamics of genetic regulation on early and late immune response and observe an enrichment of reQTLs in distal cis-regulatory elements. In addition, reQTLs are enriched for recent positive selection with an evolutionary trend towards enhanced immune response. Finally, we uncover reQTL effects in multiple GWAS loci and show a stronger enrichment for response than constant eQTLs in GWAS signals of several autoimmune diseases. This demonstrates the importance of infectious stimuli in modifying genetic predisposition to disease.Insight into the genetic influence on the immune response is important for the understanding of interindividual variability in human pathologies. Here, the authors generate transcriptome data from human blood monocytes stimulated with various immune stimuli and provide a time-resolved response eQTL map.


Assuntos
Acetilmuramil-Alanil-Isoglutamina/farmacologia , Adjuvantes Imunológicos/farmacologia , Doenças Autoimunes/genética , Expressão Gênica/efeitos dos fármacos , Lipopolissacarídeos/farmacologia , Monócitos/efeitos dos fármacos , RNA de Cadeia Dupla/farmacologia , RNA Mensageiro/efeitos dos fármacos , Adolescente , Adulto , Expressão Gênica/genética , Expressão Gênica/imunologia , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Predisposição Genética para Doença , Voluntários Saudáveis , Humanos , Indicadores e Reagentes , Lipídeos , Masculino , Monócitos/imunologia , Monócitos/metabolismo , Locos de Características Quantitativas , RNA Mensageiro/metabolismo , Sequências Reguladoras de Ácido Nucleico , Adulto Jovem
6.
BMC Dermatol ; 17(1): 3, 2017 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-28228108

RESUMO

BACKGROUND: Human hair follicle (HF) cycling is characterised by the tight orchestration and regulation of signalling cascades. Research shows that micro(mi)RNAs are potent regulators of these pathways. However, knowledge of the expression of miRNAs and their target genes and pathways in the human HF is limited. The objective of this study was to improve understanding of the role of miRNAs and their regulatory interactions in the human HF. METHODS: Expression levels of ten candidate miRNAs with reported functions in hair biology were assessed in HFs from 25 healthy male donors. MiRNA expression levels were correlated with mRNA-expression levels from the same samples. Identified target genes were tested for enrichment in biological pathways and accumulation in protein-protein interaction (PPI) networks. RESULTS: Expression in the human HF was confirmed for seven of the ten candidate miRNAs, and numerous target genes for miR-24, miR-31, and miR-106a were identified. While the latter include several genes with known functions in hair biology (e.g., ITGB1, SOX9), the majority have not been previously implicated (e.g., PHF1). Target genes were enriched in pathways of interest to hair biology, such as integrin and GnRH signalling, and the respective gene products showed accumulation in PPIs. CONCLUSIONS: Further investigation of miRNA expression in the human HF, and the identification of novel miRNA target genes and pathways via the systematic integration of miRNA and mRNA expression data, may facilitate the delineation of tissue-specific regulatory interactions, and improve our understanding of both normal hair growth and the pathobiology of hair loss disorders.


Assuntos
Folículo Piloso/metabolismo , MicroRNAs/metabolismo , Biologia Computacional , Regulação da Expressão Gênica , Cabelo/crescimento & desenvolvimento , Folículo Piloso/fisiologia , Humanos
7.
Acta Biomater ; 43: 369-382, 2016 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-27477848

RESUMO

UNLABELLED: Nickel-containing alloys are frequently used in the biomedical field, although, owing to corrosive processes metal ion leaching is inevitable. Due to nickel ion (Ni(2+)) leaching several adverse effects are described in the literature. However, only a few studies evaluated the genetic profile of Ni(2+) in human cells which is of great importance since nickel-induced effects differ between humans and mice as a result of species-specific receptor variability. Thus, we investigated gene expression induced by Ni(2+)in human monocytes using a transcriptome-wide approach determining new target genes implicated in nickel-induced pathologies. Monocytes were isolated from healthy volunteers of Central European origin using stringent inclusion criteria. Cells were challenged with different Ni(2+) concentrations. Array-based gene expression analysis was performed comprising more than 47,000 transcripts followed by pathway analyses. Transcriptional data were validated by protein and cell surface markers. Ni(2+) significantly influenced the expression of 1385 transcripts in a dose-dependent manner. Apart from known targets (CCL20↑, PTGS2↑, MTs↑, SLCs↑), we identified new candidates implicated in Ni(2+)-elicited processes (various microRNAs↑, INSIG1↑, NAMPT↑, MS4A6A↓, DHRS9↓). Several of these transcripts correspond to immunity, inflammation and were shown to be involved in cellular reactions related to hypersensitivity, cancer, colitis, and encephalitis. Moreover, 459 canonical pathways/signaling, 500 pathologies and 2687 upstream regulators were detected. Protein results validated our findings. To our knowledge, the present systematic transcriptome-wide expression study is the first which explored Ni(2+)-elicited cell responses in human primary monocytes identifying new target genes, pathways and upstream regulators of relevance to diagnostic and therapeutic strategies. STATEMENT OF SIGNIFICANCE: Nickel is widely applied in the biomedical field, although several adverse effects are documented in the literature due to nickel ion (Ni(2+)) leaching. In humans, allergic reactions like contact dermatitis are the most common adverse effect to Ni(2+), whereas serious concerns relate to possible systemic and carcinogenic activities. Using a systematic genome-wide transcriptional approach in human primary monocytes unveil new target genes, pathways and upstream regulators implicated in nickel-elicited immune response which are of significance to diagnostic and therapeutic strategies. This approach provides new information of how host-derived immune response contributes to the interaction with antigens and supports the interplay between metal ions and systemic diseases.


Assuntos
Genoma Humano , Monócitos/metabolismo , Níquel/farmacologia , Transcriptoma/genética , Adolescente , Adulto , Biomarcadores/metabolismo , Diferenciação Celular/efeitos dos fármacos , Diferenciação Celular/genética , Quimiocinas/metabolismo , Perfilação da Expressão Gênica , Humanos , Receptores de Lipopolissacarídeos/metabolismo , Masculino , Monócitos/efeitos dos fármacos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética , Transcriptoma/efeitos dos fármacos , Adulto Jovem
8.
Innate Immun ; 22(1): 72-84, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26608307

RESUMO

Chronic periodontitis (CP) is a prevalent pathogen-associated inflammatory disorder characterized by the destruction of tooth-supporting tissues, and linked to several systemic diseases. Both the periodontopathogen Porphyromonas gingivalis (Pg), and the genetically determined host immune response, are hypothesized to play a crucial role in this association. To identify new target genes for CP and its associated systemic diseases, we investigated the transcriptome induced by Pg in human monocytes using a genome-wide approach. Monocytes were isolated from healthy male volunteers of European origin and challenged with the Pg virulence factor LPS. Array-based gene expression analysis comprising >47,000 transcripts was performed followed by pathway analyses. Transcriptional data were validated by protein and cell surface markers. LPS Pg challenge led to the significant induction of 902 transcripts. Besides known periodontitis-associated targets, several new candidates were identified (CCL23↑, INDO↑, GBP 1/4↑, CFB↑, ISG20↑, MIR155HG↑, DHRS9↓). Moreover, various transcripts correspond to the host immune response, and have been linked to cancer, atherosclerosis and arthritis, thus highlighting the systemic impact of CP. Protein data of immunological markers validated our results. The present findings expand understanding of Pg elicited immune responses, and indicate new target genes and pathways of relevance to diagnostic and therapeutic strategies.


Assuntos
Infecções por Bacteroidaceae/imunologia , Periodontite Crônica/imunologia , Monócitos/imunologia , Porphyromonas gingivalis/imunologia , Adulto , Artrite/genética , Aterosclerose/genética , Infecções por Bacteroidaceae/genética , Carcinogênese/genética , Quimiocinas CC/genética , Quimiocinas CC/metabolismo , Genoma , Interações Hospedeiro-Patógeno , Humanos , Imunidade Inata/genética , Lipopolissacarídeos/metabolismo , Masculino , Transcriptoma , Adulto Jovem
9.
Am J Med Genet B Neuropsychiatr Genet ; 168B(5): 354-62, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26010163

RESUMO

Transcription factor 4 (TCF4) is one of the most robust of all reported schizophrenia risk loci and is supported by several genetic and functional lines of evidence. While numerous studies have implicated common genetic variation at TCF4 in schizophrenia risk, the role of rare, small-sized variants at this locus-such as single nucleotide variants and short indels which are below the resolution of chip-based arrays requires further exploration. The aim of the present study was to investigate the association between rare TCF4 sequence variants and schizophrenia. Exon-targeted resequencing was performed in 190 German schizophrenia patients. Six rare variants at the coding exons and flanking sequences of the TCF4 gene were identified, including two missense variants and one splice site variant. These six variants were then pooled with nine additional rare variants identified in 379 European participants of the 1000 Genomes Project, and all 15 variants were genotyped in an independent German sample (n = 1,808 patients; n = 2,261 controls). These data were then analyzed using six statistical methods developed for the association analysis of rare variants. No significant association (P < 0.05) was found. However, the results from our association and power analyses suggest that further research into the possible involvement of rare TCF4 sequence variants in schizophrenia risk is warranted by the assessment of larger cohorts with higher statistical power to identify rare variant associations.


Assuntos
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Predisposição Genética para Doença , Variação Genética , Esquizofrenia/genética , Fatores de Transcrição/genética , Grupo com Ancestrais do Continente Europeu/genética , Feminino , Genótipo , Humanos , Masculino , Fator de Transcrição 4
10.
Nat Commun ; 5: 5236, 2014 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-25327457

RESUMO

Toll-like receptors (TLRs) play a key role in innate immunity. Apart from their function in host defense, dysregulation in TLR signalling can confer risk to autoimmune diseases, septic shock or cancer. Here we report genetic variants and transcripts that are active only during TLR signalling and contribute to interindividual differences in immune response. Comparing unstimulated versus TLR4-stimulated monocytes reveals 1,471 expression quantitative trait loci (eQTLs) that are unique to TLR4 stimulation. Among these we find functional SNPs for the expression of NEU4, CCL14, CBX3 and IRF5 on TLR4 activation. Furthermore, we show that SNPs conferring risk to primary biliary cirrhosis (PBC), inflammatory bowel disease (IBD) and celiac disease are immune response eQTLs for PDGFB and IL18R1. Thus, PDGFB and IL18R1 represent plausible candidates for studying the pathophysiology of these disorders in the context of TLR4 activation. In summary, this study presents novel insights into the genetic basis of the innate immune response and exemplifies the value of eQTL studies in the context of exogenous cell stimulation.


Assuntos
Imunidade Inata , Monócitos/metabolismo , Receptor beta de Fator de Crescimento Derivado de Plaquetas/metabolismo , Receptores de Interleucina-18/metabolismo , Receptor 4 Toll-Like/metabolismo , Adolescente , Adulto , Alelos , Autoimunidade , Doença Celíaca/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Interação Gene-Ambiente , Estudo de Associação Genômica Ampla , Genótipo , Heterozigoto , Homozigoto , Humanos , Doenças Inflamatórias Intestinais/genética , Receptores de Lipopolissacarídeos/metabolismo , Masculino , Monócitos/citologia , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Transdução de Sinais , Adulto Jovem
11.
Birth Defects Res A Clin Mol Teratol ; 100(6): 493-8, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24706492

RESUMO

BACKGROUND: The genes Gremlin-1 (GREM1) and Noggin (NOG) are components of the bone morphogenetic protein 4 pathway, which has been implicated in craniofacial development. Both genes map to recently identified susceptibility loci (chromosomal region 15q13, 17q22) for nonsyndromic cleft lip with or without cleft palate (nsCL/P). The aim of the present study was to determine whether rare variants in either gene are implicated in nsCL/P etiology. METHODS: The complete coding regions, untranslated regions, and splice sites of GREM1 and NOG were sequenced in 96 nsCL/P patients and 96 controls of Central European ethnicity. Three burden and four nonburden tests were performed. Statistically significant results were followed up in a second case-control sample (n = 96, respectively). For rare variants observed in cases, segregation analyses were performed. RESULTS: In NOG, four rare sequence variants (minor allele frequency < 1%) were identified. Here, burden and nonburden analyses generated nonsignificant results. In GREM1, 33 variants were identified, 15 of which were rare. Of these, five were novel. Significant p-values were generated in three nonburden analyses. Segregation analyses revealed incomplete penetrance for all variants investigated. CONCLUSION: Our study did not provide support for NOG being the causal gene at 17q22. However, the observation of a significant excess of rare variants in GREM1 supports the hypothesis that this is the causal gene at chr. 15q13. Because no single causal variant was identified, future sequencing analyses of GREM1 should involve larger samples and the investigation of regulatory elements.


Assuntos
Proteínas de Transporte/genética , Fenda Labial/genética , Fissura Palatina/genética , Peptídeos e Proteínas de Sinalização Intercelular/genética , Alelos , Proteína Morfogenética Óssea 4/genética , Proteína Morfogenética Óssea 4/metabolismo , Proteínas de Transporte/metabolismo , Estudos de Casos e Controles , Cromossomos Humanos Par 15 , Cromossomos Humanos Par 17 , Fenda Labial/epidemiologia , Fenda Labial/metabolismo , Fissura Palatina/epidemiologia , Fissura Palatina/metabolismo , Análise Mutacional de DNA , Grupo com Ancestrais do Continente Europeu , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Frequência do Gene , Loci Gênicos , Estudo de Associação Genômica Ampla , Alemanha/epidemiologia , Humanos , Peptídeos e Proteínas de Sinalização Intercelular/metabolismo , Masculino , Fases de Leitura Aberta , Penetrância , Transdução de Sinais , Regiões não Traduzidas
12.
J Invest Dermatol ; 133(6): 1489-96, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23358095

RESUMO

The pathogenesis of androgenetic alopecia (AGA, male-pattern baldness) is driven by androgens, and genetic predisposition is the major prerequisite. Candidate gene and genome-wide association studies have reported that single-nucleotide polymorphisms (SNPs) at eight different genomic loci are associated with AGA development. However, a significant fraction of the overall heritable risk still awaits identification. Furthermore, the understanding of the pathophysiology of AGA is incomplete, and each newly associated locus may provide novel insights into contributing biological pathways. The aim of this study was to identify unknown AGA risk loci by replicating SNPs at the 12 genomic loci that showed suggestive association (5 × 10(-8)

Assuntos
Alopecia/epidemiologia , Alopecia/genética , Proteínas Wnt/genética , Via de Sinalização Wnt/fisiologia , Adulto , Alopecia/etiologia , Alopecia/metabolismo , Colestanotriol 26-Mono-Oxigenase/genética , Cromossomos Humanos Par 12 , Cromossomos Humanos Par 2 , Cromossomos Humanos Par 3 , Cromossomos Humanos Par 5 , Grupo com Ancestrais do Continente Europeu/genética , Grupo com Ancestrais do Continente Europeu/estatística & dados numéricos , Receptores Frizzled/genética , Predisposição Genética para Doença/epidemiologia , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco , Proteína Wnt3/genética
13.
Birth Defects Res A Clin Mol Teratol ; 94(11): 925-33, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23081944

RESUMO

BACKGROUND: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common of all congenital anomalies, and has a multifactorial etiology involving both environmental and genetic factors. Recent genome-wide association studies (GWAS) identified strong association between a locus on chromosome 10q25.3 and NSCL/P in European samples. One gene at 10q25.3, the ventral anterior homeobox 1 (VAX1) gene, is considered a strong candidate gene for craniofacial malformations. The purpose of the present study was to provide further evidence that VAX1 is the causal gene at the 10q25.3 locus through identification of an excess of rare mutations in patients with NSCL/P. METHODS: The 5'UTR, complete coding regions, and adjacent splice sites of the two known VAX1 isoforms were sequenced in 384 patients with NSCL/P and 384 controls of Central European descent. Observed variants were investigated with respect to familial cosegregation or de novo occurrence, and in silico analyses were performed to identify putative effects on the transcript or protein level. RESULTS: Eighteen single-base variants were found, 15 of them rare and previously unreported. In the long VAX1 isoform, predicted functionally relevant variants were observed more often in NSCL/P cases, although this difference was not significant (p = 0.17). Analysis of family members demonstrated incomplete cosegregation in most pedigrees. CONCLUSION: Our data do not support the hypothesis that highly penetrant rare variants in VAX1 are a cause of NSCL/P. To determine whether VAX1 is the causative gene at 10q25.3 further research, in particular into the biologic function of its long isoform, is warranted. Birth Defects Research (Part A), 2012.


Assuntos
Fenda Labial/genética , Fissura Palatina/genética , Grupo com Ancestrais do Continente Europeu , Proteínas de Homeodomínio/genética , Mutação , Polimorfismo de Nucleotídeo Único , Fatores de Transcrição/genética , Alelos , Sequência de Aminoácidos , Estudos de Casos e Controles , Cromossomos Humanos Par 10 , Fenda Labial/patologia , Fissura Palatina/patologia , Feminino , Loci Gênicos , Humanos , Masculino , Dados de Sequência Molecular , Linhagem , Isoformas de Proteínas/genética , Análise de Sequência de DNA
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